From 58dd967d8fa61276b09d2ec21570d3e2cec9e58c Mon Sep 17 00:00:00 2001
From: Lewin Probst <info@emirror.de>
Date: Fri, 1 May 2020 16:48:38 +0200
Subject: [PATCH] Introduced profile2rfb converter.
The nemo2profile library has been integrated to enable this feature.
---
VERSION | 2 +-
.../+controller/+file/+profile2rfb/close.m | 27 +
.../+controller/+file/+profile2rfb/open.m | 18 +
lib/+artoa/+controller/+main/open.m | 1 +
lib/+artoa/+gui/+file/convertProfilesToRfb.m | 202 ++++
lib/+artoa/+gui/main.m | 15 +
.../+nemo/+analysis/create_csv_table.m | 127 +++
.../+nemo/+analysis/create_html_summaries.m | 197 ++++
.../+convert/combined_float2nemostruct.m | 970 ++++++++++++++++++
.../nemo2profilelib/+nemo/+convert/float.m | 969 +++++++++++++++++
.../+nemo/+convert/optimare2nemostruct.m | 48 +
.../nemo2profilelib/+nemo/+float/collect.m | 192 ++++
.../+nemo/+float/extract_startup_message.m | 60 ++
.../+nemo/+float/fetch_process_mails.m | 202 ++++
.../nemo2profilelib/+nemo/+float/find.m | 49 +
.../+nemo/+float/get_changed_profiles.m | 57 +
.../+nemo/+float/process_mission_parameter.m | 127 +++
.../+nemo/+float/save_startup_message.m | 107 ++
.../+nemo/+float/sort_by_profile_number.m | 34 +
.../+nemo/+float/sort_profile_data.m | 26 +
.../nemo2profilelib/+nemo/+ftp/upload.m | 137 +++
.../+nemo/+load/additional_content.m | 29 +
.../nemo2profilelib/+nemo/+load/config.m | 110 ++
lib/vendor/nemo2profilelib/+nemo/+load/data.m | 87 ++
.../+nemo/+load/float_metadata.m | 34 +
.../+nemo/+load/float_transmission_info.m | 48 +
.../+nemo/+load/floats2nemostruct.m | 56 +
.../+nemo/+load/latest_profile.m | 46 +
.../nemo2profilelib/+nemo/+load/moorings.m | 103 ++
.../nemo2profilelib/+nemo/+load/rfb_config.m | 101 ++
.../+nemo/+load/single_float.m | 40 +
.../nemo2profilelib/+nemo/+load/xml_file.m | 61 ++
.../nemo2profilelib/+nemo/+mail/connect.m | 62 ++
.../+nemo/+mail/export_attachment.m | 50 +
.../nemo2profilelib/+nemo/+mail/extract.m | 63 ++
.../+nemo/+mail/fetch_messages.m | 69 ++
.../+nemo/+mail/fetch_unread.m | 60 ++
.../+nemo/+mail/process_inline.m | 84 ++
.../+nemo/+optimare/+cnv/devicedata.m | 65 ++
.../+nemo/+optimare/+cnv/phext_t2.m | 285 +++++
.../+nemo/+optimare/+cnv/press.m | 30 +
.../+nemo/+optimare/+cnv/salt.m | 19 +
.../+nemo/+optimare/+cnv/temp.m | 31 +
.../+nemo/+optimare/decode_nemo.m | 316 ++++++
.../+nemo/+optimare/process_moms.m | 340 ++++++
.../+nemo/+optimare/readSBDmsg.m | 55 +
.../+nemo/+optimare/read_sensors.m | 75 ++
.../+nemo/+optimare/stat2str.m | 70 ++
.../+nemo/+plot/+templates/create_south.m | 157 +++
.../+nemo/+plot/arrival_of_profiles.m | 261 +++++
.../+plot/arrival_of_profiles_overview.m | 232 +++++
.../nemo2profilelib/+nemo/+plot/ascent.m | 207 ++++
.../+nemo/+plot/categorized_timings.m | 327 ++++++
.../+nemo/+plot/float_to_template_south.m | 137 +++
.../nemo2profilelib/+nemo/+plot/floats.m | 128 +++
.../nemo2profilelib/+nemo/+plot/rafos.m | 186 ++++
.../nemo2profilelib/+nemo/+plot/temp_sal.m | 191 ++++
.../+nemo/+plot/temp_sal_ptemp.m | 211 ++++
.../+nemo/+plot/timing_information.m | 507 +++++++++
.../add_software_profile_times2rtc.m | 100 ++
.../+datetime/create_best_guess.m | 148 +++
.../+position/create_best_guess.m | 53 +
.../+position/estimate_best_guess.m | 142 +++
.../+position/estimate_unknowns.m | 185 ++++
.../+nemo/+postprocessing/delete_profile.m | 68 ++
.../+nemo/+postprocessing/quality_check.m | 105 ++
.../+nemo/+postprocessing/sort_profile_data.m | 27 +
.../+profile/calc_rtc_software_difference.m | 40 +
.../nemo2profilelib/+nemo/+profile/compare.m | 79 ++
.../nemo2profilelib/+nemo/+profile/find.m | 19 +
.../nemo2profilelib/+nemo/+profile/get_gps.m | 32 +
.../+nemo/+profile/get_iridium.m | 32 +
.../+profile/get_rtc_datevec_of_ctd_sample.m | 84 ++
.../+nemo/+profile/get_status.m | 13 +
.../+nemo/+profile/has_best_guess.m | 36 +
.../nemo2profilelib/+nemo/+profile/has_gps.m | 31 +
.../+nemo/+profile/has_iridium.m | 31 +
.../+nemo/+profile/has_no_gps_but_iridium.m | 52 +
.../+nemo/+profile/has_no_iridium_but_gps.m | 31 +
.../+nemo/+profile/has_status.m | 36 +
.../+profile/has_status_and_coordinates.m | 56 +
.../+nemo/+profile/has_status_and_gps.m | 42 +
.../nemo2profilelib/+nemo/+profile/load.m | 165 +++
.../nemo2profilelib/+nemo/+profile/map_to.m | 75 ++
.../+nemo/+profile/positions_differ_by.m | 38 +
.../nemo2profilelib/+nemo/+profile/save.m | 179 ++++
.../+nemo/+profile/sort_profile_data.m | 27 +
.../+nemo/+profile/verify_iridium.m | 38 +
.../nemo2profilelib/+nemo/+rfb/create.m | 239 +++++
.../+nemo/+rfb/create_and_save_collection.m | 49 +
lib/vendor/nemo2profilelib/+nemo/+rfb/save.m | 174 ++++
.../nemo2profilelib/+nemo/+sbd/decode_float.m | 41 +
.../+nemo/+test/best_guess_nan.m | 23 +
.../+nemo/+test/compare_nemo_data.m | 16 +
.../+nemo/+test/mail_development.m | 24 +
.../+nemo/+test/process_nemo.m | 82 ++
.../+nemo/+test/sbd2nemostruct.m | 7 +
.../+nemo/find_float_in_metadata.m | 50 +
.../+nemo/get_data_with_setting.m | 35 +
.../+nemo/get_profiles_in_polygon.m | 88 ++
.../+nemo/get_profiles_in_timerange.m | 87 ++
lib/vendor/nemo2profilelib/+nemo/save_data.m | 101 ++
.../+nemo/save_startup_messages.m | 29 +
.../+nemo/sort_data_by_float_serial.m | 36 +
.../+nemo/sync_metadata_to_nemodata.m | 16 +
.../+nemo/update_nemo_data_mat.m | 44 +
lib/vendor/nemo2profilelib/+utils/suplabel.m | 101 ++
lib/vendor/nemo2profilelib/+utils/xml_read.m | 550 ++++++++++
lib/vendor/nemo2profilelib/+utils/xml_write.m | 447 ++++++++
lib/vendor/nemo2profilelib/exclude_elements.m | 38 +
lib/vendor/nemo2profilelib/exclude_files.m | 30 +
111 files changed, 12770 insertions(+), 1 deletion(-)
create mode 100644 lib/+artoa/+controller/+file/+profile2rfb/close.m
create mode 100644 lib/+artoa/+controller/+file/+profile2rfb/open.m
create mode 100644 lib/+artoa/+gui/+file/convertProfilesToRfb.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+analysis/create_csv_table.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+analysis/create_html_summaries.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+convert/combined_float2nemostruct.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+convert/float.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+convert/optimare2nemostruct.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+float/collect.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+float/extract_startup_message.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+float/fetch_process_mails.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+float/find.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+float/get_changed_profiles.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+float/process_mission_parameter.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+float/save_startup_message.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+float/sort_by_profile_number.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+float/sort_profile_data.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+ftp/upload.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+load/additional_content.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+load/config.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+load/data.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+load/float_metadata.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+load/float_transmission_info.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+load/floats2nemostruct.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+load/latest_profile.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+load/moorings.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+load/rfb_config.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+load/single_float.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+load/xml_file.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+mail/connect.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+mail/export_attachment.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+mail/extract.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+mail/fetch_messages.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+mail/fetch_unread.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+mail/process_inline.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/devicedata.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/phext_t2.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/press.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/salt.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/temp.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+optimare/decode_nemo.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+optimare/process_moms.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+optimare/readSBDmsg.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+optimare/read_sensors.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+optimare/stat2str.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+plot/+templates/create_south.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+plot/arrival_of_profiles.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+plot/arrival_of_profiles_overview.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+plot/ascent.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+plot/categorized_timings.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+plot/float_to_template_south.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+plot/floats.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+plot/rafos.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+plot/temp_sal.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+plot/temp_sal_ptemp.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+plot/timing_information.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+postprocessing/+datetime/add_software_profile_times2rtc.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+postprocessing/+datetime/create_best_guess.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+postprocessing/+position/create_best_guess.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+postprocessing/+position/estimate_best_guess.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+postprocessing/+position/estimate_unknowns.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+postprocessing/delete_profile.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+postprocessing/quality_check.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+postprocessing/sort_profile_data.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/calc_rtc_software_difference.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/compare.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/find.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/get_gps.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/get_iridium.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/get_rtc_datevec_of_ctd_sample.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/get_status.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/has_best_guess.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/has_gps.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/has_iridium.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/has_no_gps_but_iridium.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/has_no_iridium_but_gps.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/has_status.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/has_status_and_coordinates.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/has_status_and_gps.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/load.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/map_to.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/positions_differ_by.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/save.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/sort_profile_data.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+profile/verify_iridium.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+rfb/create.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+rfb/create_and_save_collection.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+rfb/save.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+sbd/decode_float.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+test/best_guess_nan.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+test/compare_nemo_data.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+test/mail_development.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+test/process_nemo.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/+test/sbd2nemostruct.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/find_float_in_metadata.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/get_data_with_setting.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/get_profiles_in_polygon.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/get_profiles_in_timerange.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/save_data.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/save_startup_messages.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/sort_data_by_float_serial.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/sync_metadata_to_nemodata.m
create mode 100644 lib/vendor/nemo2profilelib/+nemo/update_nemo_data_mat.m
create mode 100644 lib/vendor/nemo2profilelib/+utils/suplabel.m
create mode 100644 lib/vendor/nemo2profilelib/+utils/xml_read.m
create mode 100644 lib/vendor/nemo2profilelib/+utils/xml_write.m
create mode 100644 lib/vendor/nemo2profilelib/exclude_elements.m
create mode 100644 lib/vendor/nemo2profilelib/exclude_files.m
diff --git a/VERSION b/VERSION
index 0947c33..66321c0 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-188
\ No newline at end of file
+189
\ No newline at end of file
diff --git a/lib/+artoa/+controller/+file/+profile2rfb/close.m b/lib/+artoa/+controller/+file/+profile2rfb/close.m
new file mode 100644
index 0000000..945ffe8
--- /dev/null
+++ b/lib/+artoa/+controller/+file/+profile2rfb/close.m
@@ -0,0 +1,27 @@
+function [ ] = close(pSource, ~)
+%CLOSE Cleans up all variables that are used by the pSource GUI.
+% Changes to the data is not being modified.
+
+global artoaGui;
+
+%% Setup variables
+figureName = 'convertProfilesToRfb';
+
+%% Close the figure
+if nargin > 1 && isvalid(pSource)
+ delete(pSource);
+elseif isfield(artoaGui.figures, figureName) && isvalid(artoaGui.figures.(figureName))
+ delete(artoaGui.figures.(figureName));
+end
+
+%% Clean up variables
+
+if artoa.data.hasMember(artoaGui, {figureName})
+ artoaGui = rmfield(artoaGui, figureName);
+end
+
+if artoa.data.hasMember(artoaGui, {'figures', figureName})
+ artoaGui.figures = rmfield(artoaGui.figures, figureName);
+end
+
+end
\ No newline at end of file
diff --git a/lib/+artoa/+controller/+file/+profile2rfb/open.m b/lib/+artoa/+controller/+file/+profile2rfb/open.m
new file mode 100644
index 0000000..77a59bc
--- /dev/null
+++ b/lib/+artoa/+controller/+file/+profile2rfb/open.m
@@ -0,0 +1,18 @@
+function [] = open(~, ~)
+%OPEN Summary of this function goes here
+% Detailed explanation goes here
+
+global artoaGui;
+
+%% Check if the gui is already opened
+
+if isfield(artoaGui.figures, 'convertProfilesToRfb')
+ figure(artoaGui.figures.convertProfilesToRfb);
+ return
+end
+
+%% Open the gui
+artoa.gui.file.convertProfilesToRfb();
+
+end
+
diff --git a/lib/+artoa/+controller/+main/open.m b/lib/+artoa/+controller/+main/open.m
index 3410aa5..881d1d0 100644
--- a/lib/+artoa/+controller/+main/open.m
+++ b/lib/+artoa/+controller/+main/open.m
@@ -30,6 +30,7 @@ callbacks.openEditOffsets = @artoa.controller.edit.offsets.open;
callbacks.openTrackParameter = @artoa.controller.track.parameter.open;
callbacks.openTrackTrajectoryOutput = @artoa.controller.track.trajectoryOutput.open;
callbacks.switchHideDeletedDataPoints = @artoa.controller.switchHideDeletedPoints;
+callbacks.convertProfilesToRfb = @artoa.controller.file.profile2rfb.open;
%% Prepare callbacks for track parameter
callbacks.checkboxDopplerCorrection = @artoa.controller.track.parameter.checkboxDopplerCorrection;
diff --git a/lib/+artoa/+gui/+file/convertProfilesToRfb.m b/lib/+artoa/+gui/+file/convertProfilesToRfb.m
new file mode 100644
index 0000000..2783704
--- /dev/null
+++ b/lib/+artoa/+gui/+file/convertProfilesToRfb.m
@@ -0,0 +1,202 @@
+function [] = convertProfilesToRfb()
+%CONVERTPROFILESTORFB Defines the profile to rfb conversion tool.
+
+global artoaGui;
+
+%% Initialize required variables
+
+windowTitle = 'ARTOA4 - Profile to RFB converter';
+
+
+%% Initialize gui
+
+artoaGui.figures.convertProfilesToRfb = figure( ...
+ 'Name', windowTitle, ...
+ 'NumberTitle', 'off' ...
+);
+
+
+artoaGui.convertProfilesToRfb = struct();
+
+set( ...
+ artoaGui.figures.convertProfilesToRfb, ...
+ 'CloseRequestFcn', ...
+ @artoa.controller.file.profile2rfb.close, ...
+ 'Units', 'normalized' ...
+);
+
+%% Generate Controls
+
+left = .05;
+width = .9;
+
+%% Source frame
+artoaGui.convertProfilesToRfb.frameSource = uipanel( ...
+ 'Parent', artoaGui.figures.convertProfilesToRfb, ...
+ 'Title', 'Source folder (*.profiles)', ...
+ 'Units', 'normalized', ...
+ 'BackgroundColor', 'white', ...
+ 'Position', [left .65 width .3] ...
+);
+
+artoaGui.convertProfilesToRfb.buttonSelectFolder = uicontrol( ...
+ 'Parent', artoaGui.convertProfilesToRfb.frameSource, ...
+ 'String', 'Pick a folder', ...
+ 'Style', 'PushButton', ...
+ 'FontSize', 8, ...
+ 'Units', 'normalized', ...
+ 'Position', [.7 .5 .25 .3], ...
+ 'Callback', @selectSourceFolder ...
+);
+
+artoaGui.convertProfilesToRfb.textSourceFolder = uicontrol( ...
+ 'Parent', artoaGui.convertProfilesToRfb.frameSource, ...
+ 'Style', 'edit', ...
+ 'FontSize', 8, ...
+ 'Units', 'normalized', ...
+ 'Enable', 'off', ...
+ 'Position', [.05 .5 .6 .3] ...
+);
+
+artoaGui.convertProfilesToRfb.buttonSelectMetadata = uicontrol( ...
+ 'Parent', artoaGui.convertProfilesToRfb.frameSource, ...
+ 'String', 'Pick metadata file', ...
+ 'Style', 'PushButton', ...
+ 'FontSize', 8, ...
+ 'Units', 'normalized', ...
+ 'Position', [.7 .1 .25 .3], ...
+ 'Callback', @selectSourceMetadata ...
+);
+
+artoaGui.convertProfilesToRfb.textSourceMetadata = uicontrol( ...
+ 'Parent', artoaGui.convertProfilesToRfb.frameSource, ...
+ 'Style', 'edit', ...
+ 'FontSize', 8, ...
+ 'Units', 'normalized', ...
+ 'Enable', 'off', ...
+ 'Position', [.05 .1 .6 .3] ...
+);
+
+%% Target frame
+artoaGui.convertProfilesToRfb.frameTarget = uipanel( ...
+ 'Parent', artoaGui.figures.convertProfilesToRfb, ...
+ 'Title', 'Target file (*.rfb)', ...
+ 'Units', 'normalized', ...
+ 'BackgroundColor', 'white', ...
+ 'Position', [left .4 width .2] ...
+);
+
+artoaGui.convertProfilesToRfb.buttonSelectTargetFile = uicontrol( ...
+ 'Parent', artoaGui.convertProfilesToRfb.frameTarget, ...
+ 'String', 'Select a file', ...
+ 'Style', 'PushButton', ...
+ 'FontSize', 8, ...
+ 'Units', 'normalized', ...
+ 'Position', [.7 .4 .25 .4], ...
+ 'Callback', @selectTargetFile ...
+);
+
+artoaGui.convertProfilesToRfb.textTargetFile = uicontrol( ...
+ 'Parent', artoaGui.convertProfilesToRfb.frameTarget, ...
+ 'Style', 'edit', ...
+ 'FontSize', 8, ...
+ 'Units', 'normalized', ...
+ 'Enable', 'off', ...
+ 'Position', [.05 .4 .6 .4] ...
+);
+
+%% Execute frame
+artoaGui.convertProfilesToRfb.frameExecute = uipanel( ...
+ 'Parent', artoaGui.figures.convertProfilesToRfb, ...
+ 'Title', 'Convert', ...
+ 'Units', 'normalized', ...
+ 'BackgroundColor', 'white', ...
+ 'Position', [left .1 width .2] ...
+);
+
+artoaGui.convertProfilesToRfb.textStatus = uicontrol( ...
+ 'Parent', artoaGui.convertProfilesToRfb.frameExecute, ...
+ 'String', 'Please input source and target...', ...
+ 'Style', 'Text', ...
+ 'FontSize', 8, ...
+ 'Units', 'normalized', ...
+ 'Position', [.1 .4 .35 .4] ...
+);
+
+artoaGui.convertProfilesToRfb.buttonExecuteConversion = uicontrol( ...
+ 'Parent', artoaGui.convertProfilesToRfb.frameExecute, ...
+ 'String', 'Start conversion', ...
+ 'Style', 'PushButton', ...
+ 'FontSize', 8, ...
+ 'Units', 'normalized', ...
+ 'Enable', 'off', ...
+ 'Position', [.5 .4 .3 .4], ...
+ 'Callback', @convert ...
+);
+
+%% Helper functions
+
+ function selectSourceFolder(~, ~)
+ dirname = uigetdir(pwd, 'Select source folder');
+ if (dirname == 0)
+ return
+ end
+ artoaGui.convertProfilesToRfb.textSourceFolder.String = dirname;
+ checkInputs();
+ end
+
+ function selectSourceMetadata(~, ~)
+ [filename, path] = uigetfile('*.xml', 'Select metadata file');
+ if (filename == 0)
+ return
+ end
+ artoaGui.convertProfilesToRfb.textSourceMetadata.String = ...
+ fullfile(path, filename);
+ checkInputs();
+ end
+
+ function selectTargetFile(~, ~)
+ [filename, path] = uiputfile('*.rfb', 'Select target file');
+ if (filename == 0)
+ return
+ end
+ artoaGui.convertProfilesToRfb.textTargetFile.String = ...
+ fullfile(path, filename);
+ checkInputs();
+ end
+
+ function checkInputs(~, ~)
+ if all(strcmp({ ...
+ artoaGui.convertProfilesToRfb.textSourceFolder.String, ...
+ artoaGui.convertProfilesToRfb.textTargetFile.String, ...
+ artoaGui.convertProfilesToRfb.textSourceMetadata.String ...
+ }, '') == 0)
+ artoaGui.convertProfilesToRfb.buttonExecuteConversion.Enable = 'on';
+ setStatus('Ready for conversion!');
+ else
+ artoaGui.convertProfilesToRfb.buttonExecuteConversion.Enable = 'off';
+ setStatus('Please input source and target...');
+ end
+ end
+
+ function setStatus(pStatusMessage)
+ artoaGui.convertProfilesToRfb.textStatus.String = pStatusMessage;
+ end
+
+ function convert(~, ~)
+ setStatus('Loading files...');
+ metadata = artoaGui.convertProfilesToRfb.textSourceMetadata.String;
+ inputFolder = artoaGui.convertProfilesToRfb.textSourceFolder.String;
+ target = artoaGui.convertProfilesToRfb.textTargetFile.String;
+ float = nemo.load.single_float(inputFolder, filesep);
+ setStatus('Creating rfb structure...');
+ [rfb, ~] = nemo.rfb.create(float, nemo.load.float_metadata(metadata));
+ setStatus('Save to target...');
+ if ~nemo.rfb.save(rfb, target, true)
+ setStatus('Something failed during conversion!');
+ end
+ setStatus('...success!');
+ end
+
+end
+
diff --git a/lib/+artoa/+gui/main.m b/lib/+artoa/+gui/main.m
index 2a3c4d9..3168510 100644
--- a/lib/+artoa/+gui/main.m
+++ b/lib/+artoa/+gui/main.m
@@ -15,6 +15,7 @@ availableCallbacks = { ...
'saveInterim', ...
'saveOptimumTables', ...
'loadArtoaIni', ...
+ 'convertProfilesToRfb', ...
'quit', ...
'openEditTemperature', ...
'openEditPressure', ...
@@ -135,6 +136,20 @@ uimenu( ...
'Callback', pCallbacks.saveOptimumTables ...
);
+% CONVERT
+artoaGui.main.menus.fileConvert = uimenu( ...
+ artoaGui.main.menus.file, ...
+ 'Label', 'Convert', ...
+ 'Enable', 'on' ...
+);
+
+uimenu( ...
+ artoaGui.main.menus.fileConvert, ...
+ 'Label', '*.profile to .rfb', ...
+ 'Callback', pCallbacks.convertProfilesToRfb ...
+);
+
+% RELOAD ARTOA INI
artoaGui.main.menus.fileReloadArtoaIni = uimenu( ...
artoaGui.main.menus.file, ...
'Label', 'Reload artoa.ini', ...
diff --git a/lib/vendor/nemo2profilelib/+nemo/+analysis/create_csv_table.m b/lib/vendor/nemo2profilelib/+nemo/+analysis/create_csv_table.m
new file mode 100644
index 0000000..4bb30a8
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+analysis/create_csv_table.m
@@ -0,0 +1,127 @@
+function [ boolean ] = create_csv_table( p_metadata, p_config )
+%CREATE_CSV_TABLE Creates a csv file containing table with information of all floats.
+%
+% Parameters:
+% p_metadata: Struct containing all floats (load with nemo.load.data)
+% p_config: Struct containing global configuration file (load with
+% nemo.load.config()).
+%
+% Returns:
+% boolean: False if something went wrong during the creation of the table.
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check
+
+if (~iscell(p_metadata) || ~isstruct(p_config))
+ disp([mfilename ': Wrong parameter. Please check your input!']);
+ return
+end
+
+%% Collect all required information
+
+serial = [];
+imei = [];
+wmoid = [];
+deployment_datetime = [];
+deployment_lat = [];
+deployment_lon = [];
+profile_count = [];
+latest_transmission = [];
+
+float_count = length(p_metadata);
+
+for o_float = 1:float_count % collect all required information of every float
+ % load the latest float
+ [current_profile, current_profile_count] = nemo.load.latest_profile( ...
+ p_config, ...
+ p_metadata{o_float}.GENERAL_INFO.SERIAL ...
+ );
+
+ % get all numbers of nemo floats
+ serial(end+1, 1) = p_metadata{o_float}.GENERAL_INFO.SERIAL;
+ imei(end+1, 1) = p_metadata{o_float}.GENERAL_INFO.IMEI;
+ wmoid(end+1, 1) = p_metadata{o_float}.GENERAL_INFO.WMO_ID;
+ % deploment info
+ deployment_datetime(end+1, :) = datevec( ...
+ [ ...
+ p_metadata{o_float}.DEPLOYMENT_INFO.DEPLOYMENT_DATE ...
+ p_metadata{o_float}.DEPLOYMENT_INFO.DEPLOYMENT_TIME ...
+ ], 'dd.mm.yyyyHH:MM');
+
+
+%
+% [ ...
+% p_metadata{o_float}.DEPLOYMENT_INFO.deployment_date(3), ...
+% current_profile.DEPLOYMENT_INFO.deployment_date(2), ...
+% current_profile.DEPLOYMENT_INFO.deployment_date(1), ...
+% current_profile.DEPLOYMENT_INFO.deployment_time, ...
+% 0];
+ deployment_lat(end+1, 1) = p_metadata{o_float}.DEPLOYMENT_INFO.DEPLOYMENT_LAT;
+ deployment_lon(end+1, 1) = p_metadata{o_float}.DEPLOYMENT_INFO.DEPLOYMENT_LON;
+ % number of received profiles
+ profile_count(end+1, 1) = current_profile_count;
+ % last float transmittion
+ if ~isempty(current_profile) && ~isempty(current_profile.IRIDIUM_DATA)
+ latest_transmission(end+1, :) = current_profile.IRIDIUM_DATA(4:9);
+ else
+ latest_transmission(end+1, :) = nan(1, 6);
+ end
+
+end
+
+% create filename
+filename = fullfile( ...
+ p_config.ANALYSIS_RESULTS.output_path, ...
+ p_config.ANALYSIS_RESULTS.compact_info_filename ...
+ );
+
+% create folder if necessary
+if ~exist(p_config.ANALYSIS_RESULTS.output_path, 'dir')
+ mkdir(p_config.ANALYSIS_RESULTS.output_path);
+end
+
+% create header of table
+table_header = { ...
+ 'serial', 'imei', 'wmo_id', 'deployment_time', 'deployment_lat', 'deployment_lon', ...
+ 'latest_transmission', 'profile_count' ...
+};
+
+% create matlab table with the collected information
+compact_info = table(serial, imei, wmoid, datetime(deployment_datetime, 'Format', 'yyyy-MM-dd HH:m'), deployment_lat, deployment_lon, ...
+ datetime(latest_transmission, 'Format', 'yyyy-MM-dd HH:mm'), profile_count, 'VariableNames', table_header);
+
+% write data to file
+writetable(compact_info, filename, 'Delimiter', ',');
+try
+% copy template file to csv folder
+copyfile(p_config.ANALYSIS_RESULTS.compact_info_html_template, [ ...
+ p_config.ANALYSIS_RESULTS.output_path ...
+ 'index.html' ...
+]);
+% update its timestamp via java
+import java.io.File java.text.SimpleDateFormat
+f = File([ p_config.ANALYSIS_RESULTS.output_path 'index.html' ]);
+sdf = SimpleDateFormat('HH:mm dd/MM/yyyy');
+today = datetime('now');
+newDate = sdf.parse([ ...
+ int2str(today.Hour) ':' int2str(today.Minute) ' ' ...
+ int2str(today.Day) '/' int2str(today.Month) '/' int2str(today.Year) ...
+]);
+f.setLastModified(newDate.getTime);
+clear f;
+% copy javascript folder
+copyfile(p_config.ANALYSIS_RESULTS.input_javascript_folder, ...
+ [p_config.ANALYSIS_RESULTS.output_path 'js' p_config.GENERAL.folder_separator] ...
+);
+catch ex
+warning('Could not copy templates or JavaScript folder. If you experience Problems try deleting those files/folders and rerun!');
+boolean = false;
+return;
+end
+
+% everything went fine! :)
+boolean = true;
+
+end
diff --git a/lib/vendor/nemo2profilelib/+nemo/+analysis/create_html_summaries.m b/lib/vendor/nemo2profilelib/+nemo/+analysis/create_html_summaries.m
new file mode 100644
index 0000000..af40e37
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+analysis/create_html_summaries.m
@@ -0,0 +1,197 @@
+function [ boolean ] = create_html_summaries( p_nemo_data, p_config )
+%CREATE_HTML_SUMMARY Generates a summary of every float given in the nemo data.
+% Uses the nemo configuration for linking the html summaries to the
+% overview table generated by create_csv_table
+%
+% Parameters:
+% p_nemo_data: The nemo data where the summaries will be
+% generated from.
+% p_config: The nemo configuration
+%
+% Returns:
+% boolean: Always true.
+
+path = fullfile(p_config.ANALYSIS_RESULTS.output_path, 'html');
+
+if (~exist(path, 'dir'))
+ mkdir(path);
+end
+
+for i = 1:length(p_nemo_data)
+
+ f = p_nemo_data{i};
+ float_number = f{1}.FLOAT_IDENTIFICATION.float_serial_number;
+ html = ['<!DOCTYPE html><head><title>Summary of Float ' ...
+ num2str(float_number) ...
+ '</title><style>' ...
+ 'body, a{font-family: Arial;color: #4B4B4D;}' ...
+ 'th{line-height: 60px;background: #00ACE5;color: #003E6E;font-size: 30px;}' ...
+ 'td{line-height: 40px;border: thin solid black; padding-left: 5px;}' ...
+ '.value{width: 70%;}' ...
+ '.name{width: 30%;background: #BCBDBF;font-weight: bold;}' ...
+ 'table{border-collapse: collapse;border: thin solid black;width: 100%;}' ...
+ 'img{width: 100%;font-weight: bold;font-size: 30px;}' ...
+ '.overlay{z-index: 2;}' ...
+ '#show-floattable{padding:20px;background: #00ACE5;color: #003E6E;font-size: 18px;position: fixed;right: 20px;top: 10px;cursor: pointer;}' ...
+ '</style>' ...
+ '</head><body>' ...
+ '<a id="show-floattable" class="overlay" onclick="(function(){history.back();})()">Show all floats</a>' ...
+ '<table>'];
+
+
+ %% Add latest update time
+ html = [ html '<tr><td class="name">Updated on:</td><td class="value">' datestr(datetime('now', 'TimeZone', 'Europe/London')) '</td></tr>'];
+
+
+ %% Add float identification table
+ html = [ html '<th colspan="2">FLOAT_IDENTIFICATION</th>' ];
+
+ fnames = fieldnames(f{1}.FLOAT_IDENTIFICATION);
+ for j = 1:length(fnames)
+
+ fieldvalue = f{1}.FLOAT_IDENTIFICATION.(fnames{j});
+
+ switch(class(fieldvalue))
+ case {'double', 'logical'}
+ fieldvalue = num2str(fieldvalue);
+ end
+ html = [ html ...
+ '<tr><td class="name">' fnames{j} ...
+ '</td><td class="value">' fieldvalue ...
+ '</td></tr>' ...
+ ];
+ end
+
+ %% Add float deployment table
+ html = [ html '<th colspan="2">DEPLOYMENT_INFO</th>' ];
+
+ fnames = fieldnames(f{1}.DEPLOYMENT_INFO);
+ for j = 1:length(fnames)
+
+ fieldvalue = f{1}.DEPLOYMENT_INFO.(fnames{j});
+
+ switch(class(fieldvalue))
+ case {'double', 'logical'}
+ fieldvalue = num2str(fieldvalue);
+ end
+ html = [ html ...
+ '<tr><td class="name">' fnames{j} ...
+ '</td><td class="value">' fieldvalue ...
+ '</td></tr>' ...
+ ];
+ end
+
+ %% Add float deployment table
+ html = [ html '<th colspan="2">OVERALL_MISSION_INFORMATION</th>' ];
+
+ fnames = fieldnames(f{1}.OVERALL_MISSION_INFORMATION);
+ for j = 1:length(fnames)
+
+ fieldvalue = f{1}.OVERALL_MISSION_INFORMATION.(fnames{j});
+
+ switch(class(fieldvalue))
+ case {'double', 'logical'}
+ fieldvalue = num2str(fieldvalue);
+ end
+ html = [ html ...
+ '<tr><td class="name">' fnames{j} ...
+ '</td><td class="value">' fieldvalue ...
+ '</td></tr>' ...
+ ];
+ end
+
+ %% Add plots
+
+ html = [ html '<th colspan="2">PLOTS</th>' ];
+
+ html = [ html '<tr><td class="name">Arrival of profiles</td>' ...
+ '<td class="value"><a href="../../plots/' ...
+ p_config.PLOT_ARRIVAL_OF_PROFILES.storage_directory_fig ...
+ p_config.PLOT_ARRIVAL_OF_PROFILES.figure_filename ...
+ num2str(float_number) '.fig">' ...
+ '<img alt="No image available!" src="../../plots/' ...
+ p_config.PLOT_ARRIVAL_OF_PROFILES.storage_directory_image ...
+ p_config.PLOT_ARRIVAL_OF_PROFILES.image_filename ...
+ num2str(float_number) '.png"></a>' ...
+ '</td></tr>'];
+ html = [ html '<tr><td class="name">Ascent</td>' ...
+ '<td class="value"><a href="../../plots/' ...
+ p_config.PLOT_ASCENT.storage_directory_fig ...
+ p_config.PLOT_ASCENT.figure_filename ...
+ num2str(float_number) '.fig">' ...
+ '<img alt="No image available!" src="../../plots/' ...
+ p_config.PLOT_ASCENT.storage_directory_image ...
+ p_config.PLOT_ASCENT.image_filename ...
+ num2str(float_number) '.png"></a>' ...
+ '</td></tr>'];
+ html = [ html '<tr><td class="name">Categorized timings</td>' ...
+ '<td class="value"><a href="../../plots/' ...
+ p_config.PLOT_CATEGORIZED_TIMINGS.storage_directory_fig ...
+ p_config.PLOT_CATEGORIZED_TIMINGS.figure_filename ...
+ num2str(float_number) '.fig">' ...
+ '<img alt="No image available!" src="../../plots/' ...
+ p_config.PLOT_CATEGORIZED_TIMINGS.storage_directory_image ...
+ p_config.PLOT_CATEGORIZED_TIMINGS.image_filename ...
+ num2str(float_number) '.png"></a>' ...
+ '</td></tr>'];
+ html = [ html '<tr><td class="name">Timing information</td>' ...
+ '<td class="value"><a href="../../plots/' ...
+ p_config.PLOT_TIMING_INFORMATION.storage_directory_fig ...
+ p_config.PLOT_TIMING_INFORMATION.figure_filename ...
+ num2str(float_number) '.fig">' ...
+ '<img alt="No image available!" src="../../plots/' ...
+ p_config.PLOT_TIMING_INFORMATION.storage_directory_image ...
+ p_config.PLOT_TIMING_INFORMATION.image_filename ...
+ num2str(float_number) '.png"></a>' ...
+ '</td></tr>'];
+ html = [ html '<tr><td class="name">RAFOS</td>' ...
+ '<td class="value"><a href="../../plots/' ...
+ p_config.PLOT_RAFOS.storage_directory_fig ...
+ p_config.PLOT_RAFOS.figure_filename ...
+ num2str(float_number) '.fig">' ...
+ '<img alt="No image available!" src="../../plots/' ...
+ p_config.PLOT_RAFOS.storage_directory_image ...
+ p_config.PLOT_RAFOS.image_filename ...
+ num2str(float_number) '.png"></a>' ...
+ '</td></tr>'];
+ html = [ html '<tr><td class="name">Single floats map</td>' ...
+ '<td class="value"><a href="../../plots/' ...
+ p_config.PLOT_SINGLE_FLOAT_SOUTH.storage_directory_fig ...
+ num2str(float_number) '.fig">' ...
+ '<img alt="No image available!" src="../../plots/' ...
+ p_config.PLOT_SINGLE_FLOAT_SOUTH.storage_directory_image ...
+ num2str(float_number) '.png"></a>' ...
+ '</td></tr>'];
+ html = [ html '<tr><td class="name">Temperature, Salinity</td>' ...
+ '<td class="value"><a href="../../plots/' ...
+ p_config.PLOT_TEMP_SAL.storage_directory_fig ...
+ p_config.PLOT_TEMP_SAL.figure_filename ...
+ num2str(float_number) '.fig">' ...
+ '<img alt="No image available!" src="../../plots/' ...
+ p_config.PLOT_TEMP_SAL.storage_directory_image ...
+ p_config.PLOT_TEMP_SAL.image_filename ...
+ num2str(float_number) '.png"></a>' ...
+ '</td></tr>'];
+ html = [ html '<tr><td class="name">Temperature, Salinity, Potential Temperature</td>' ...
+ '<td class="value"><a href="../../plots/' ...
+ p_config.PLOT_TEMP_SAL_PTEMP.storage_directory_fig ...
+ p_config.PLOT_TEMP_SAL_PTEMP.figure_filename ...
+ num2str(float_number) '.fig">' ...
+ '<img alt="No image available!" src="../../plots/' ...
+ p_config.PLOT_TEMP_SAL_PTEMP.storage_directory_image ...
+ p_config.PLOT_TEMP_SAL_PTEMP.image_filename ...
+ num2str(float_number) '.png"></a>' ...
+ '</td></tr>'];
+
+ html = [ html '</table></body></html>' ];
+
+ %% Write html file
+
+ fid = fopen(fullfile(path, [num2str(float_number) '.html']), 'w');
+ fwrite(fid, html);
+ fclose(fid);
+
+end
+
+boolean = true;
+end
diff --git a/lib/vendor/nemo2profilelib/+nemo/+convert/combined_float2nemostruct.m b/lib/vendor/nemo2profilelib/+nemo/+convert/combined_float2nemostruct.m
new file mode 100644
index 0000000..408bf57
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+convert/combined_float2nemostruct.m
@@ -0,0 +1,970 @@
+function [ nemo_float ] = combined_float2nemostruct( p_combined_float )
+%FLOAT Converts the given float in optimare structure to the structre of AWI.
+% This is only a temporary function and will be deprecated as soon as the
+% decoding process has been rewritten. During the decoding, optimare created a
+% variable structure that differs from the one AWI is using. This function
+% transfers all variables into the AWI format. In addition to that, it also
+% checks for incomplete profiles and always saves the profile with the biggest
+% size of CTD data.
+%
+% Parameters:
+% p_float: Structure that was created during the decoding process.
+%
+% Returns:
+% nemo_float: Structure that is being used by AWI. False
+% if there is no data, no profiles or if something went wrong
+% during conversion.
+
+%% Initialize return variables
+nemo_float = {};
+
+%% Convert information to AWI structure
+
+if ~isfield(p_combined_float, 'DECODED_SBD')
+ % no data available
+ nemo_float = false;
+ return
+end
+% get fieldnames of every decoded profile
+profile_fieldnames = fieldnames(p_combined_float.DECODED_SBD);
+
+% sort iridium messages by profile number
+[profile_numbers_sorted, sorted_indices] = sort_iridium_messages(profile_fieldnames);
+
+if ~sorted_indices
+ % something went wrong, for example only incomplete iridium messages available
+ nemo_float = false;
+ return
+end
+
+% get profiles with most CTD data if multiple ones have been transmitted
+best_ctd_indices = filter_multiple_profiles(sorted_indices);
+
+% count valid profiles
+valid_profile_count = length(best_ctd_indices);
+
+
+%% Get format data that is always the same
+deployment_info_struct = deployment_info();
+rafos_values_format_struct = rafos_values_format();
+profile_header_struct = profile_header();
+quality_control_header_struct = qualtiy_control_header();
+profile_data_header_struct = profile_data_header();
+surface_gps_data_format_struct = surface_gps_data_format();
+iridium_positions_format_struct = iridium_positions_format();
+iridium_data_format_struct = iridium_data_format();
+
+% create variable, counting available valid profiles
+% differs to valid_profile_count because only "Profile Message" is being accepted
+valid_profiles = 0;
+
+for o_profile = 1:valid_profile_count
+ % get index of current profile, may not be same as o_profile because optimare
+ % structure is not sorted by profile numbers
+ current_index = best_ctd_indices(o_profile);
+
+ if ~strcmp( ...
+ p_combined_float.DECODED_SBD.(profile_fieldnames{current_index}).DATATYPE, ...
+ 'Profile Message' ...
+ )
+ % everything that is not a profile or a test message is being ignored
+ continue
+ else
+ % increase number of valid profiles
+ valid_profiles = valid_profiles + 1;
+ end
+ try % converting the input structure
+
+ %% FLOAT_IDENTIFICATION
+ nemo_float{1, valid_profiles}.FLOAT_IDENTIFICATION = ...
+ float_identification(profile_fieldnames{current_index});
+ %% OVERALL_MISSION_INFORMATION
+ nemo_float{1, valid_profiles}.OVERALL_MISSION_INFORMATION = ...
+ overall_mission_information(profile_fieldnames{current_index});
+ %% DEPLOYMENT_INFO
+ nemo_float{1, valid_profiles}.DEPLOYMENT_INFO = ...
+ deployment_info_struct;
+ %% PROFILE_TECHNICAL_DATA
+ nemo_float{1, valid_profiles}.PROFILE_TECHNICAL_DATA = ...
+ profile_technical_data(profile_fieldnames{current_index});
+ %% BOTTOM_VALUES_DURING_DRIFT
+ nemo_float{1, valid_profiles}.BOTTOM_VALUES_DURING_DRIFT = ...
+ bottom_values_during_drift(profile_fieldnames{current_index});
+ %% RAFOS_VALUES_FORMAT
+ nemo_float{1, valid_profiles}.RAFOS_VALUES_FORMAT = ...
+ rafos_values_format_struct;
+ %% RAFOS_VALUES
+ nemo_float{1, valid_profiles}.RAFOS_VALUES = ...
+ rafos_values(profile_fieldnames{current_index});
+ %% PROFILE_HEADER
+ nemo_float{1, valid_profiles}.PROFILE_HEADER = ...
+ profile_header_struct;
+ %% QUALITY_CONTROL_HEADER
+ nemo_float{1, valid_profiles}.QUALITY_CONTROL_HEADER = ...
+ quality_control_header_struct;
+ %% PROFILE_DATA_HEADER
+ nemo_float{1, valid_profiles}.PROFILE_DATA_HEADER = ...
+ profile_data_header_struct;
+ %% PROFILE_DATA
+ nemo_float{1, valid_profiles}.PROFILE_DATA = ...
+ profile_data(profile_fieldnames{current_index});
+
+ % if there is no profile data, clean up and go to next profile
+ if isempty(nemo_float{1, valid_profiles}.PROFILE_DATA)
+ % skip profiles without data
+ nemo_float{1, valid_profiles} = [];
+ valid_profiles = valid_profiles - 1;
+ continue
+ end
+
+ %% SURFACE_GPS_DATA_FORMAT
+ nemo_float{1, valid_profiles}.SURFACE_GPS_DATA_FORMAT = ...
+ surface_gps_data_format_struct;
+ %% SURFACE_GPS_DATA
+ nemo_float{1, valid_profiles}.SURFACE_GPS_DATA = ...
+ surface_gps_data(profile_fieldnames{current_index});
+ %% IRIDIUM_POSITIONS_FORMAT
+ nemo_float{1, valid_profiles}.IRIDIUM_POSITIONS_FORMAT = ...
+ iridium_positions_format_struct;
+ %% IRIDIUM_POSITIONS & IRIDIUM_DATA
+ [ iridium_positions, iridium_best ] = ...
+ iridium_positions_and_data(profile_fieldnames{current_index});
+ nemo_float{1, valid_profiles}.IRIDIUM_POSITIONS = iridium_positions;
+ clear iridium_positions
+ %% IRIDIUM_DATA_FORMAT
+ nemo_float{1, valid_profiles}.IRIDIUM_DATA_FORMAT = ...
+ iridium_data_format_struct;
+ nemo_float{1, valid_profiles}.IRIDIUM_DATA = iridium_best;
+ clear iridium_best
+
+
+ catch exception
+ % something went wrong, so complain and return false
+ warning([mfilename ': ' exception.message]);
+ nemo_float = false;
+ return;
+ end
+
+
+end
+
+% if there is no profile data at all, return false
+if valid_profiles == 0
+ nemo_float = false;
+ return;
+end
+
+%% Sort float
+nemo_float = nemo.float.sort_profile_data(nemo_float);
+nemo_float = nemo.float.sort_by_profile_number(nemo_float);
+
+%% Exit this function
+
+return; % end of combined_float2nemostruct
+
+%% Helper functions
+
+ function [ value ] = store_if_available(p_search, p_needle)
+ % if the given needle is a member of search, return the containing value.
+ if isfield(p_search, p_needle)
+ value = p_search.(p_needle);
+ switch class(value)
+ case 'char'
+ value = strtrim(value);
+ end
+ return
+ else
+ value = NaN;
+ return
+ end
+ end
+
+
+%% FLOAT_IDENTIFICATION
+
+ function [ awi_struct ] = float_identification(p_profile_fieldname)
+
+ awi_struct = {};
+
+
+ if isfield( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname),'DEVICE') ...
+ && strcmp(strtrim( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname).DEVICE),'NEMO Standard' ...
+ )
+ awi_struct.transmission_type = 'IRIDIUM SBD';
+ else
+ awi_struct.transmission_type = NaN;
+ end
+
+ if isfield(p_combined_float.GENERAL_INFO, 'IMEI')
+ awi_struct.transmission_id_number_dec = ...
+ p_combined_float.GENERAL_INFO.IMEI;
+ else
+ awi_struct.transmission_id_number_dec = NaN;
+ end
+
+ awi_struct.transmission_id_number_hex = NaN;
+
+ awi_struct.wmo_id_number = store_if_available( ...
+ p_combined_float.GENERAL_INFO, 'WMO_ID');
+
+ awi_struct.wmo_instrument_type = store_if_available( ...
+ p_combined_float.GENERAL_INFO, 'WMO_INSTRUMENT_TYPE');
+
+
+
+ awi_struct.wmo_recorder_type = store_if_available( ...
+ p_combined_float.GENERAL_INFO, 'WMO_RECORD_TYPE');
+
+ awi_struct.instrument_type = store_if_available( ...
+ p_combined_float.GENERAL_INFO, 'INSTRUMENT_TYPE');
+
+ awi_struct.float_manufacturer = store_if_available( ...
+ p_combined_float.GENERAL_INFO, 'FLOAT_MANUFACTURER');
+
+ awi_struct.float_serial_number = store_if_available( ...
+ p_combined_float.GENERAL_INFO, 'SERIAL');
+
+ awi_struct.ice_detection_software = store_if_available( ...
+ p_combined_float.SENSOR_INFO, 'ICE_DETECTION');
+
+
+ awi_struct.float_provider = store_if_available( ...
+ p_combined_float.PROVIDER_DEPLOYER_INFO, 'PROVIDER_NAME');
+
+
+ awi_struct.float_provider_institution = store_if_available( ...
+ p_combined_float.PROVIDER_DEPLOYER_INFO, 'PROVIDER_INSTITUTE');
+
+ awi_struct.originating_country = store_if_available( ...
+ p_combined_float.PROVIDER_DEPLOYER_INFO, 'PROVIDER_COUNTRY');
+
+
+ end
+
+%% OVERALL_MISSION_INFORMATION
+
+ function [ awi_struct ] = overall_mission_information(p_profile_fieldname)
+
+ awi_struct = {};
+
+ if isfield(p_combined_float.DECODED_SBD.(p_profile_fieldname), 'TIME_CYCLE')
+ awi_struct.total_cycle = [ ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname).TIME_CYCLE/(60*24) ...
+ 0 0];
+ else
+ awi_struct.total_cycle = NaN;
+ end
+
+ awi_struct.down_time = NaN;
+ awi_struct.up_time = NaN;
+ awi_struct.transmission_repetition_rate = NaN;
+ awi_struct.clock_drift = NaN;
+ awi_struct.nominal_drift_depth = NaN;
+ awi_struct.max_departure_from_drift_depth = NaN;
+
+ awi_struct.nominal_profile_depth = store_if_available( ...
+ p_combined_float.MISSION_PARAMETERS, 'PROFILE_PRESSURE');
+
+ if isfield(p_combined_float.DEPLOYMENT_INFO, 'START_DATE')
+ tmp_mat = strsplit(p_combined_float.DEPLOYMENT_INFO.START_DATE, '.');
+ awi_struct.start_date = [ ...
+ str2double(tmp_mat{1}) ...
+ str2double(tmp_mat{2}) ...
+ str2double(tmp_mat{3})];
+ clear tmp_mat
+ else
+ awi_struct.start_date = NaN;
+ end
+
+ if isfield(p_combined_float.DEPLOYMENT_INFO, 'START_TIME')
+ tmp_mat = strsplit(p_combined_float.DEPLOYMENT_INFO.START_TIME, ':');
+ awi_struct.start_time = [ ...
+ str2double(tmp_mat{1}) ...
+ str2double(tmp_mat{2})];
+ clear tmp_mat
+ else
+ awi_struct.start_time = NaN;
+ end
+
+ awi_struct.RAFOS_clock_offset_at_start = NaN;
+ awi_struct.start_surface_pressure = NaN;
+
+ awi_struct.ice_detection_temperature_threshold = store_if_available( ...
+ p_combined_float.MISSION_PARAMETERS, 'ICE_TEMPERATURE');
+
+
+ end
+
+%% DEPLOYMENT_INFO
+ function [ awi_struct ] = deployment_info()
+
+ awi_struct.float_deployer = store_if_available( ...
+ p_combined_float.PROVIDER_DEPLOYER_INFO, 'DEPLOYER_NAME');
+
+ awi_struct.float_deployer_institution = store_if_available( ...
+ p_combined_float.PROVIDER_DEPLOYER_INFO, 'DEPLOYER_INSTITUTE');
+
+ awi_struct.deployment_platform_type = store_if_available( ...
+ p_combined_float.DEPLOYMENT_INFO, 'DEPLOYMENT_PLATFORM');
+
+ awi_struct.deployment_platform_code = store_if_available( ...
+ p_combined_float.DEPLOYMENT_INFO, 'DEPLOYMENT_PLATFORM_SIGN');
+
+ if isfield(p_combined_float.DEPLOYMENT_INFO, 'DEPLOYMENT_PLATFORM_EXPEDITION')
+ tmp_string = strsplit( ...
+ p_combined_float.DEPLOYMENT_INFO.DEPLOYMENT_PLATFORM_EXPEDITION, ...
+ '/');
+ if length(tmp_string) == 2
+ awi_struct.deployment_platform_cruise_name = tmp_string{1};
+ try
+ awi_struct.deployment_platform_leg = str2double(tmp_string{2});
+ catch
+ awi_struct.deployment_platform_leg = tmp_string{2};
+ end
+ else
+ awi_struct.deployment_platform_cruise_name = ...
+ p_combined_float.DEPLOYMENT_INFO.DEPLOYMENT_PLATFORM_EXPEDITION;
+ awi_struct.deployment_platform_leg = 'none';
+ end
+ clear tmp_string
+ else
+ awi_struct.deployment_platform_cruise_name = NaN;
+ awi_struct.deployment_platform_leg = 'none';
+ end
+
+ awi_struct.deployment_ctd_station = NaN;
+
+ if isfield(p_combined_float.DEPLOYMENT_INFO, 'DEPLOYMENT_DATE')
+ tmp_string = strsplit( ...
+ p_combined_float.DEPLOYMENT_INFO.DEPLOYMENT_DATE, ...
+ '.');
+ awi_struct.deployment_date = [ str2double(tmp_string{1}) ...
+ str2double(tmp_string{2}) ...
+ str2double(tmp_string{3}) ];
+ clear tmp_string
+ else
+ awi_struct.deployment_date = NaN;
+ end
+
+ if isfield(p_combined_float.DEPLOYMENT_INFO, 'DEPLOYMENT_TIME')
+ tmp_string = strsplit( ...
+ p_combined_float.DEPLOYMENT_INFO.DEPLOYMENT_TIME, ...
+ ':');
+ awi_struct.deployment_time = [ str2double(tmp_string{1}) ...
+ str2double(tmp_string{2}) ];
+ clear tmp_string
+ else
+ awi_struct.deployment_time = NaN;
+ end
+
+ if isfield(p_combined_float.DEPLOYMENT_INFO, 'DEPLOYMENT_LAT') ...
+ && isfield(p_combined_float.DEPLOYMENT_INFO, 'DEPLOYMENT_LON')
+ awi_struct.deployment_position = [ ...
+ p_combined_float.DEPLOYMENT_INFO.DEPLOYMENT_LAT ...
+ p_combined_float.DEPLOYMENT_INFO.DEPLOYMENT_LON];
+ else
+ awi_struct.deployment_position = NaN;
+ end
+
+ awi_struct.deployment_speed = NaN;
+
+ awi_struct.deployment_sea_state = store_if_available( ...
+ p_combined_float.DEPLOYMENT_INFO, 'DEPLOYMENT_SEA_STATE');
+
+ awi_struct.deployment_wave_height = NaN;
+
+ awi_struct.deployment_ice_coverage = store_if_available( ...
+ p_combined_float.DEPLOYMENT_INFO, 'DEPLOYMENT_SEA_ICE');
+
+ awi_struct.delay_of_first_down_time = NaN;
+
+ end
+
+%% PROFILE_TECHNICAL_DATA
+
+ function [ awi_struct ] = profile_technical_data(p_profile_fieldname)
+
+ awi_struct = {};
+
+ awi_struct.xmit_profile_number = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PROFILE_NUMBER');
+
+ awi_struct.xmit_serial_number = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'SERIAL');
+
+ awi_struct.xmit_upcast_status = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'STATUS_UPCAST');
+
+ awi_struct.xmit_older_profiles_not_send = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PROFILE_OLDER');
+
+ awi_struct.xmit_motor_errors_count = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ERROR_MOTOR');
+
+ awi_struct.xmit_sbe42_ctd_errors = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ERROR_CTD');
+
+ awi_struct.xmit_o2_optode_errors = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ERROR_OPTODE');
+
+ awi_struct.xmit_rafos_errors = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ERROR_RAFOS');
+
+ awi_struct.xmit_cpu_battery_voltage = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'BATT_CPU');
+
+ awi_struct.xmit_pump_battery_voltage = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'BATT_PMP');
+
+ awi_struct.xmit_motor_current = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'CURR_MOTOR');
+
+ awi_struct.xmit_motor_current_mean = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'CURR_MOTOR_MEAN');
+
+ awi_struct.xmit_internal_pressure_surface = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PRES_TUBE_SURFACE');
+
+ awi_struct.xmit_internal_pressure_depth = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PRES_TUBE_DEPTH');
+
+ awi_struct.xmit_pressure_offset = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PRES_OFFSET');
+
+ awi_struct.xmit_surface_pressure = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PRES_SURFACE');
+
+ awi_struct.xmit_parking_pressure_median = median(store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'DS2_PRES'));
+
+ awi_struct.xmit_depth_pressure = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PRES_DEPTH');
+
+ awi_struct.xmit_depth_pressure_max = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PRES_MAX');
+
+ awi_struct.xmit_profile_recovery = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'RECOVERY_START');
+
+ awi_struct.xmit_piston_counts_surface = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PIST_SURFACE');
+
+ awi_struct.xmit_piston_counts_parking = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PIST_PARKING');
+
+ awi_struct.xmit_piston_counts_calc = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PIST_CALC');
+
+ awi_struct.xmit_piston_counts_eop = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PIST_EOP');
+
+ awi_struct.xmit_descent_start_time = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'MCNT_DESCENT');
+
+ awi_struct.xmit_parking_start_time = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'MCNT_PARKING');
+
+ awi_struct.xmit_upcast_start_time = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'MCNT_SAG');
+
+ awi_struct.xmit_ascent_start_time = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'MCNT_ASCENT');
+
+ awi_struct.xmit_ascent_end_time = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'MCNT_ASCENT_END');
+
+ awi_struct.xmit_surface_start_time = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'MCNT_SURFACE');
+
+ if isfield(p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'DATA_RECORDS2') ...
+ && length(p_combined_float.DECODED_SBD.(p_profile_fieldname).DATA_RECORDS2) == 5
+ awi_struct.xmit_profile_length_1 = ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname).DATA_RECORDS2(1);
+ awi_struct.xmit_profile_length_2 = ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname).DATA_RECORDS2(2);
+ awi_struct.xmit_profile_length_3 = ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname).DATA_RECORDS2(3);
+ awi_struct.xmit_profile_length_4 = ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname).DATA_RECORDS2(4);
+ awi_struct.xmit_profile_length_5 = ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname).DATA_RECORDS2(5);
+ else
+ awi_struct.xmit_profile_length_1 = NaN;
+ awi_struct.xmit_profile_length_2 = NaN;
+ awi_struct.xmit_profile_length_3 = NaN;
+ awi_struct.xmit_profile_length_4 = NaN;
+ awi_struct.xmit_profile_length_5 = NaN;
+ end
+
+ awi_struct.xmit_surface_detection_GPS = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ICEGPS_TIME');
+
+ awi_struct.xmit_surface_detection_Iridium = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ICEIRDM_TIME');
+
+ awi_struct.xmit_airpump_runtime = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'AIRPUMP_RUNTIME');
+
+ awi_struct.xmit_ice_detection_temp_median = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ICE_TEMPMEDIAN');
+
+ end
+
+%% BOTTOM_VALUES_DURING_DRIFT
+ function [ awi_struct ] = bottom_values_during_drift(p_profile_fieldname)
+
+ awi_struct = {};
+
+ awi_struct.xmit_bottom_pressure = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), 'DS2_PRES');
+
+ awi_struct.xmit_bottom_salt = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), 'DS2_SAL');
+
+ awi_struct.xmit_bottom_temperature = store_if_available( ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldname), 'DS2_TEMP');
+
+ end
+
+%% RAFOS_VALUES_FORMAT
+
+ function [ awi_struct ] = rafos_values_format()
+
+ awi_struct = { ...
+ 'status'; 'rtc_year'; 'rtc_month'; 'rtc_day'; 'rtc_hour'; ...
+ 'rtc_minute'; 'rtc_second'; '1STCORHEIGHT'; '1STTRAVELTIME'; ...
+ '2NDCORHEIGHT'; '2NDTRAVELTIME'; '3RDCORHEIGHT'; '3RDTRAVELTIME'; ...
+ '4THCORHEIGHT'; '4THTRAVELTIME'; '5THCORHEIGHT'; '5THTRAVELTIME'; ...
+ '6THCORHEIGHT'; '6THTRAVELTIME'; 'pressure'; 'salinity'; 'temp' ...
+ }';
+
+ end
+
+%% RAFOS_VALUES
+
+ function [ awi_struct ] = rafos_values(p_profile_fieldname)
+
+ p = p_combined_float.DECODED_SBD.(p_profile_fieldname);
+ if isfield(p, 'DS3_DATE_year') && isfield(p, 'DS3_DATE_month') ...
+ && isfield(p, 'DS3_DATE_day') && isfield(p, 'DS3_TIME') ...
+ && isfield(p, 'DS3_STATUS') && isfield(p, 'DS3_RAFOSAMP') ...
+ && isfield(p, 'DS3_RAFOSRANK') && isfield(p, 'DS3_PRES') ...
+ && isfield(p, 'DS3_SAL') && isfield(p, 'DS3_TEMP')
+
+ y = (1/(4836-4464) .* p.DS3_DATE_year) + 2000;
+ mon = p.DS3_DATE_month;
+ d = p.DS3_DATE_day;
+
+ h = floor(p.DS3_TIME./3600);
+ m = floor((p.DS3_TIME - (h*3600))/60);
+ s = uint8(mod(p.DS3_TIME,60));
+
+ prefix = [p.DS3_STATUS', y', mon', d', h', m', double(s')];
+
+ awi_struct = [ ...
+ prefix, ...
+ p.DS3_RAFOSAMP(:, 1), p.DS3_RAFOSRANK(:, 1), ...
+ p.DS3_RAFOSAMP(:, 2), p.DS3_RAFOSRANK(:, 2), ...
+ p.DS3_RAFOSAMP(:, 3), p.DS3_RAFOSRANK(:, 3), ...
+ p.DS3_RAFOSAMP(:, 4), p.DS3_RAFOSRANK(:, 4), ...
+ p.DS3_RAFOSAMP(:, 5), p.DS3_RAFOSRANK(:, 5), ...
+ p.DS3_RAFOSAMP(:, 6), p.DS3_RAFOSRANK(:, 6), ...
+ p.DS3_PRES', p.DS3_SAL', p.DS3_TEMP' ...
+ ];
+ else
+ awi_struct = [];
+ end
+
+
+ end
+
+%% PROFILE_HEADER
+
+ function [ awi_struct ] = profile_header()
+
+ awi_struct = {};
+
+ awi_struct.number_of_columns = 13;
+ awi_struct.column_1 = 'line_number';
+ awi_struct.column_2 = 'hour';
+ awi_struct.column_3 = 'minute';
+ awi_struct.column_4 = 'second';
+ awi_struct.column_5 = 'temperature [deg C]';
+ awi_struct.column_6 = 'temperature flag';
+ awi_struct.column_7 = 'pressure [dbar]';
+ awi_struct.column_8 = 'pressure flag';
+ awi_struct.column_9 = 'salinity [psu]';
+ awi_struct.column_10 = 'salinity flag';
+ awi_struct.column_11 = 'temperature raw';
+ awi_struct.column_12 = 'pressure raw';
+ awi_struct.column_13 = 'salinity raw';
+ awi_struct.temperature_conversion_equation = 'T=cnts/1000, if(cnts>62535),cnts=cnts-65536';
+ awi_struct.pressure_conversion_equation = 'P=cnts/10';
+ awi_struct.salinity_conversion_equation = 'S=cnts/1000';
+
+ end
+
+%% QUALITY_CONTROL_HEADER
+
+ function [ awi_struct ] = qualtiy_control_header()
+
+ awi_struct = {};
+
+ awi_struct.overall_flag_for_T = 0;
+ awi_struct.overall_flag_for_P = 0;
+ awi_struct.overall_flag_for_S = 0;
+ awi_struct.maximum_speed_check_flag = 0;
+ awi_struct.maximum_analysis_check_T_flag = 0;
+ awi_struct.maximum_climatology_T_flag = 0;
+ awi_struct.maximum_gross_check_T_flag = 0;
+ awi_struct.maximum_vertical_gradient_T_flag = 0;
+ awi_struct.maximum_spike_check_T_flag = 0;
+ awi_struct.maximum_analysis_check_S_flag = 0;
+ awi_struct.maximum_climatology_S_flag = 0;
+ awi_struct.maximum_gross_check_S_flag = 0;
+ awi_struct.maximum_vertical_gradient_S_flag = 0;
+ awi_struct.maximum_spike_check_S_flag = 0;
+ awi_struct.sigma_used_for_T_climatology = 10;
+ awi_struct.sigma_used_for_T_analysis = 10;
+ awi_struct.sigma_used_for_S_climatology = 10;
+ awi_struct.sigma_used_for_S_analysis = 10;
+
+ end
+
+%% PROFILE_DATA_HEADER
+
+ function [ awi_struct ] = profile_data_header()
+
+ awi_struct = { ...
+ '#'; 'hour'; 'minute'; 'second'; 'temp'; 'temp_flag'; 'pressure'; ...
+ 'pres_flag'; 'salinity'; 'sal_flag'; 'temp_raw'; 'pres_raw'; ...
+ 'sal_raw'; 'light_442_nm'; 'light_550_nm'; 'light_676_nm' ...
+ }';
+
+ end
+
+%% PROFILE_DATA
+
+ function [ awi_struct ] = profile_data(p_profile_fieldname)
+
+ p = p_combined_float.DECODED_SBD.(p_profile_fieldname);
+ if isfield(p, 'DS4_TIME') && isfield(p, 'DS4_TEMP') ...
+ && isfield(p, 'DS4_PRES') && isfield(p, 'DS4_SAL')
+
+ h = floor(p.DS4_TIME./3600);
+ m = floor((p.DS4_TIME - (h*3600))/60);
+ s = uint8(mod(p.DS4_TIME, 60));
+ profile_numbers = 1:length(h);
+ flags = zeros(1, length(h));
+
+ prefix = [profile_numbers', h', m', double(s')];
+
+ % somtimes LICH1-3 has different length than TEMP, PRES & SAL
+ if ~isfield(p, 'DS4_LICH1') || ~isfield(p, 'DS4_LICH2') ...
+ || ~isfield(p, 'DS4_LICH3') || (length(p.DS4_LICH1) ~= length(p.DS4_TEMP))
+ LICH1 = flags;
+ LICH2 = flags;
+ LICH3 = flags;
+ else
+ LICH1 = p.DS4_LICH1;
+ LICH2 = p.DS4_LICH2;
+ LICH3 = p.DS4_LICH3;
+ end
+
+ awi_struct = [ ...
+ prefix, ...
+ p.DS4_TEMP', flags', ...
+ p.DS4_PRES', flags', ...
+ p.DS4_SAL', flags', ...
+ p.DS4_TEMP', p.DS4_PRES', p.DS4_SAL', ...
+ LICH1', LICH2', LICH3' ...
+ ];
+ else
+ awi_struct = [];
+ end
+
+
+ end
+
+%% SURFACE_GPS_DATA_FORMAT
+
+ function [ awi_struct ] = surface_gps_data_format()
+
+ awi_struct = { ...
+ '#'; 'rtc_year'; 'rtc_month'; 'rtc_day'; 'rtc_hour'; 'rtc_minute'; ...
+ 'rtc_second'; 'GPS_year'; 'GPS_month'; 'GPS_day'; 'GPS_hour'; ...
+ 'GPS_minute'; 'GPS_second'; 'lat'; 'lon' ...
+ }';
+
+ end
+
+%% SURFACE_GPS_DATA
+
+ function [ awi_struct ] = surface_gps_data(p_profile_fieldname)
+
+ p = p_combined_float.DECODED_SBD.(p_profile_fieldname);
+ if isfield(p, 'DS5_GPS') && isfield(p, 'DS5_RTC') ...
+ && isfield(p, 'DS5_LAT') && isfield(p, 'DS5_LON')
+
+ gps_datevec = datevec(p.DS5_GPS);
+ % check if gps date is correct
+ if gps_datevec(1) == 1999 && gps_datevec(2) == 12 ...
+ && gps_datevec(3) == 31
+ gps_datevec = [NaN, NaN, NaN, NaN, NaN, NaN];
+ end
+
+ awi_struct = [ ...
+ 1, ...
+ datevec(p.DS5_RTC), ...
+ gps_datevec, ...
+ p.DS5_LAT, ...
+ p.DS5_LON ...
+ ];
+ else
+ awi_struct = [];
+ end
+
+
+ end
+
+%% IRIDIUM_POSITIONS_FORMAT
+
+ function [ awi_struct ] = iridium_positions_format()
+
+ awi_struct = { ...
+ 'sbd_lat'; 'sbd_lon'; 'sbd_cep'; ...
+ 'yyyy'; 'mm'; 'dd'; ...
+ 'hh'; 'mm'; 'ss'
+ }';
+
+ end
+
+%% IRIDIUM_POSITIONS
+
+ function [ iridium_positions, iridium_best ] = ...
+ iridium_positions_and_data(p_profile_fieldname)
+
+ iridium_positions = [];
+ iridium_best = [];
+
+ p = p_combined_float.DECODED_SBD.(p_profile_fieldname);
+ sbd_info = p_combined_float.SBD_MESSAGES_INFO;
+
+ if (isa(p_combined_float.TRANSMISSION_INFO, 'struct'))
+ p_combined_float.TRANSMISSION_INFO = struct2table(p_combined_float.TRANSMISSION_INFO);
+ end
+
+ % BUGFIX, delete all rows with empty profilenumber_lsb values
+ sbd_info = sbd_info(~cellfun('isempty', {sbd_info.profilenumber_lsb}));
+ % get all profile numbers of the transmitted iridium messsages
+ sbd_info = struct2table(sbd_info);
+ % be sure that it is sorted!
+ sbd_info = sortrows(sbd_info,'momsn','ascend');
+ % get all corresponding messages
+ iridium_messages = sbd_info(sbd_info.profilenumber_lsb == p.PROFILE_NUMBER, :);
+ iridium_messages = sortrows(iridium_messages, 'momsn', 'ascend');
+ iridium_messages_count = size(iridium_messages, 1);
+
+ % filter incomplete transmissions
+ first_sbd_index = 1;
+ tmp_index = 0;
+ sbd_total_num = iridium_messages.total_num(first_sbd_index);
+ for i = 1:iridium_messages_count
+ current_elementary = iridium_messages.elementary_num(i);
+ if (current_elementary ~= iridium_messages.elementary_num(first_sbd_index) + tmp_index)
+ first_sbd_index = i;
+ sbd_total_num = iridium_messages.total_num(first_sbd_index);
+ tmp_index = 1;
+ else
+ tmp_index = tmp_index + 1;
+ end
+ if (tmp_index == sbd_total_num)
+ %tmp_index = tmp_index - 1;
+ break;
+ end
+ end
+
+ iridium_messages = iridium_messages(first_sbd_index:first_sbd_index + tmp_index - 1, :);
+
+ clear iridium_messages_count;
+
+ xmit_info = table();
+
+ iridium_messages_count = size(iridium_messages, 1);
+ for o_iridium = 1:iridium_messages_count
+ current_momsn = iridium_messages(o_iridium, :).momsn;
+ current_xmit_info = p_combined_float.TRANSMISSION_INFO( ...
+ p_combined_float.TRANSMISSION_INFO.MOMSN == current_momsn ...
+ , :);
+
+ index = 1;
+ if size(current_xmit_info, 1) > 1
+ warning([mfilename ': More than one SBD Message with MOMSN ' current_momsn ' has been found!']);
+ %[~, index] = min(current_xmit_info.CEPRAD);
+ end
+
+ xmit_info = [xmit_info; current_xmit_info(index, :)];
+ end
+
+ if (isempty(xmit_info))
+ iridium_positions = [];
+ iridium_best = [];
+ return
+ end
+
+ % create return structure for all positions
+ iridium_positions = [ ...
+ xmit_info.IRIDIUM_LAT, ...
+ xmit_info.IRIDIUM_LON, ...
+ xmit_info.CEPRAD, ...
+ xmit_info.TIMEOFSESSION ...
+ ];
+
+ % get best position & time
+ iridium_best = iridium_positions(iridium_positions(:, 3) == min(iridium_positions(:, 3)), :);
+ iridium_best = iridium_best(end, :);
+ % get closest time to the surface time
+ iridium_best(4:9) = iridium_positions(1, 4:9);
+
+
+ end
+
+%% IRIDIUM_DATA_FORMAT
+
+ function [ awi_struct ] = iridium_data_format()
+
+ awi_struct = { ...
+ 'mean_lat'; 'mean_lon'; 'mean_cep'; ...
+ 'yyyy'; 'mm'; 'dd'; ...
+ 'hh'; 'mm'; 'ss'
+ }';
+
+ end
+
+%% SORT IRIDIUM MESSAGES
+
+ function [ profile_numbers_sorted, indices ] = sort_iridium_messages(p_profile_fieldnames)
+ profile_numbers_unsorted = [];
+ tmp_valid_profile_count = 0;
+ % collect all profile numbers
+ for o_fields = 1:length(p_profile_fieldnames)
+ current_profile = ...
+ p_combined_float.DECODED_SBD.(p_profile_fieldnames{o_fields});
+ if ~strcmp(p_combined_float.DECODED_SBD.(p_profile_fieldnames{o_fields}).DATATYPE, 'Profile Message') ...
+ || ~isfield(p_combined_float.DECODED_SBD.(p_profile_fieldnames{o_fields}), 'PROFILE_NUMBER') ...
+ || isnan(p_combined_float.DECODED_SBD.(p_profile_fieldnames{o_fields}).PROFILE_NUMBER)
+ continue;
+ end
+ tmp_valid_profile_count = tmp_valid_profile_count + 1;
+ profile_numbers_unsorted(tmp_valid_profile_count, :) = ...
+ [p_combined_float.DECODED_SBD.(p_profile_fieldnames{o_fields}).PROFILE_NUMBER, ...
+ o_fields];
+ end
+ % sort them
+ if ~isempty(profile_numbers_unsorted)
+ [profile_numbers_sorted, indices] = sortrows(profile_numbers_unsorted, 1);
+ indices = profile_numbers_sorted(:, 2);
+ else
+ indices = false;
+ profile_numbers_sorted = false;
+ end
+ end
+
+ function [best_ctd_indices] = filter_multiple_profiles(sorted_indices)
+ % initialize return variable
+ best_ctd_indices = [];
+ best_indices_count = 0;
+ % get profile number of the first element
+ if isfield(p_combined_float.DECODED_SBD.(profile_fieldnames{sorted_indices(1)}), 'DATA_RECORDS2') ...
+ && p_combined_float.DECODED_SBD.(profile_fieldnames{sorted_indices(1)}).DATA_RECORDS2(4) > 0
+ % if it is < 0, there is no possibility to compare CTD data
+ best_indices_count = best_indices_count + 1;
+ last_profile_number = p_combined_float.DECODED_SBD.(profile_fieldnames{sorted_indices(1)}).PROFILE_NUMBER;
+ best_ctd_indices(best_indices_count) = sorted_indices(1);
+ end
+
+ for o_index = 2:length(sorted_indices)
+ if ~isfield(p_combined_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}), 'DATA_RECORDS2') ...
+ || p_combined_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DATA_RECORDS2(4) == 0
+ continue
+ end
+ % get current profile number
+ current_profile_number = p_combined_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).PROFILE_NUMBER;
+ if best_indices_count > 0 && current_profile_number == last_profile_number
+ % check which ctd data is better
+ current_ctd_length = p_combined_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DATA_RECORDS2(4);
+ last_ctd_length = p_combined_float.DECODED_SBD.(profile_fieldnames{best_ctd_indices(best_indices_count)}).DATA_RECORDS2(4);
+ if current_ctd_length > last_ctd_length
+ best_ctd_indices(best_indices_count) = sorted_indices(o_index);
+ elseif current_ctd_length == last_ctd_length
+ % take the one without or less NaN's
+ tmp_current = [ ...
+ p_combined_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DS4_TIME; ...
+ p_combined_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DS4_FORMAT; ...
+ p_combined_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DS4_PRES; ...
+ p_combined_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DS4_TEMP; ...
+ p_combined_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DS4_SAL ...
+ ];
+ tmp_last = [ ...
+ p_combined_float.DECODED_SBD.(profile_fieldnames{best_ctd_indices(best_indices_count)}).DS4_TIME; ...
+ p_combined_float.DECODED_SBD.(profile_fieldnames{best_ctd_indices(best_indices_count)}).DS4_FORMAT; ...
+ p_combined_float.DECODED_SBD.(profile_fieldnames{best_ctd_indices(best_indices_count)}).DS4_PRES; ...
+ p_combined_float.DECODED_SBD.(profile_fieldnames{best_ctd_indices(best_indices_count)}).DS4_TEMP; ...
+ p_combined_float.DECODED_SBD.(profile_fieldnames{best_ctd_indices(best_indices_count)}).DS4_SAL ...
+ ];
+ sum_current = sum(sum(isnan(tmp_current)));
+ sum_last = sum(sum(isnan(tmp_last)));
+ if sum_last > sum_current
+ best_ctd_indices(best_indices_count) = sorted_indices(o_index);
+ end
+ clear tmp_current tmp_last sum_current sum_last
+
+ end
+ else
+ best_indices_count = best_indices_count + 1;
+ best_ctd_indices(best_indices_count) = sorted_indices(o_index);
+ end
+
+ last_profile_number = current_profile_number;
+ end
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+convert/float.m b/lib/vendor/nemo2profilelib/+nemo/+convert/float.m
new file mode 100644
index 0000000..b1a2515
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+convert/float.m
@@ -0,0 +1,969 @@
+function [ awi_float ] = float( p_optimare_float )
+%FLOAT Converts the given float in optimare structure to the structre of AWI.
+% This is only a temporary function and will be deprecated as soon as the
+% decoding process has been rewritten. During the decoding, optimare created a
+% variable structre that differs from the one AWI is using. This function
+% transfers all variables into the AWI format. In addition to that, it also
+% checks for incomplete profiles and always saves the profile with the biggest
+% size of CTD data.
+%
+% Parameters:
+% p_optimare_float: Structure that was created during the decoding process.
+%
+% Returns:
+% awi_float: Structure with the structure that is being used by AWI. False
+% if there is no data, no profiles or if something went wrong
+% during conversion.
+
+%% Initialize return variables
+awi_float = {};
+
+%% Convert information to AWI structure
+
+if ~isfield(p_optimare_float, 'DECODED_SBD')
+ % no data available
+ awi_float = false;
+ return
+end
+% get fieldnames of every decoded profile
+profile_fieldnames = fieldnames(p_optimare_float.DECODED_SBD);
+
+% sort iridium messages by profile number
+[profile_numbers_sorted, sorted_indices] = sort_iridium_messages(profile_fieldnames);
+
+if ~sorted_indices
+ % something went wrong, for example only incomplete iridium messages available
+ awi_float = false;
+ return
+end
+
+% get profiles with most CTD data if multiple ones have been transmitted
+best_ctd_indices = filter_multiple_profiles(sorted_indices);
+
+% count valid profiles
+valid_profile_count = length(best_ctd_indices);
+
+
+%% Get format data that is always the same
+deployment_info_struct = deployment_info();
+rafos_values_format_struct = rafos_values_format();
+profile_header_struct = profile_header();
+quality_control_header_struct = qualtiy_control_header();
+profile_data_header_struct = profile_data_header();
+surface_gps_data_format_struct = surface_gps_data_format();
+iridium_positions_format_struct = iridium_positions_format();
+iridium_data_format_struct = iridium_data_format();
+
+% create variable, counting available valid profiles
+valid_profiles = 0;
+
+for o_profile = 1:valid_profile_count
+ % get index of current profile, may not be same as o_profile because optimare
+ % structure is not sorted by profile numbers
+ current_index = best_ctd_indices(o_profile);
+
+ if ~strcmp(p_optimare_float.DECODED_SBD.(profile_fieldnames{current_index}).DATATYPE, ...
+ 'Profile Message')
+ % everything that is not a profile message is being ignored
+ continue
+ else
+ % increase number of valid profiles
+ valid_profiles = valid_profiles + 1;
+ end
+ try % converting the input structure
+
+ %% FLOAT_IDENTIFICATION
+ awi_float{1, valid_profiles}.FLOAT_IDENTIFICATION = ...
+ float_identification(profile_fieldnames{current_index});
+ %% OVERALL_MISSION_INFORMATION
+ awi_float{1, valid_profiles}.OVERALL_MISSION_INFORMATION = ...
+ overall_mission_information(profile_fieldnames{current_index});
+ %% DEPLOYMENT_INFO
+ awi_float{1, valid_profiles}.DEPLOYMENT_INFO = ...
+ deployment_info_struct;
+ %% PROFILE_TECHNICAL_DATA
+ awi_float{1, valid_profiles}.PROFILE_TECHNICAL_DATA = ...
+ profile_technical_data(profile_fieldnames{current_index});
+ %% BOTTOM_VALUES_DURING_DRIFT
+ awi_float{1, valid_profiles}.BOTTOM_VALUES_DURING_DRIFT = ...
+ bottom_values_during_drift(profile_fieldnames{current_index});
+ %% RAFOS_VALUES_FORMAT
+ awi_float{1, valid_profiles}.RAFOS_VALUES_FORMAT = ...
+ rafos_values_format_struct;
+ %% RAFOS_VALUES
+ awi_float{1, valid_profiles}.RAFOS_VALUES = ...
+ rafos_values(profile_fieldnames{current_index});
+ %% PROFILE_HEADER
+ awi_float{1, valid_profiles}.PROFILE_HEADER = ...
+ profile_header_struct;
+ %% QUALITY_CONTROL_HEADER
+ awi_float{1, valid_profiles}.QUALITY_CONTROL_HEADER = ...
+ quality_control_header_struct;
+ %% PROFILE_DATA_HEADER
+ awi_float{1, valid_profiles}.PROFILE_DATA_HEADER = ...
+ profile_data_header_struct;
+ %% PROFILE_DATA
+ awi_float{1, valid_profiles}.PROFILE_DATA = ...
+ profile_data(profile_fieldnames{current_index});
+
+ % if there is no profile data, clean up and go to next profile
+ if isempty(awi_float{1, valid_profiles}.PROFILE_DATA)
+ % skip profiles without data
+ awi_float{1, valid_profiles} = [];
+ valid_profiles = valid_profiles - 1;
+ continue
+ end
+
+ %% SURFACE_GPS_DATA_FORMAT
+ awi_float{1, valid_profiles}.SURFACE_GPS_DATA_FORMAT = ...
+ surface_gps_data_format_struct;
+ %% SURFACE_GPS_DATA
+ awi_float{1, valid_profiles}.SURFACE_GPS_DATA = ...
+ surface_gps_data(profile_fieldnames{current_index});
+ %% IRIDIUM_POSITIONS_FORMAT
+ awi_float{1, valid_profiles}.IRIDIUM_POSITIONS_FORMAT = ...
+ iridium_positions_format_struct;
+ %% IRIDIUM_POSITIONS & IRIDIUM_DATA
+ [ iridium_positions, iridium_best ] = ...
+ iridium_positions_and_data(profile_fieldnames{current_index});
+ awi_float{1, valid_profiles}.IRIDIUM_POSITIONS = iridium_positions;
+ clear iridium_positions
+ %% IRIDIUM_DATA_FORMAT
+ awi_float{1, valid_profiles}.IRIDIUM_DATA_FORMAT = ...
+ iridium_data_format_struct;
+ awi_float{1, valid_profiles}.IRIDIUM_DATA = iridium_best;
+ clear iridium_best
+
+
+ catch exception
+ % something went wrong, so complain by returning false
+ awi_float = false;
+ return;
+ end
+
+
+end
+
+% if there is no profile data at all, return false
+if valid_profiles == 0
+ awi_float = false;
+ return;
+end
+
+ function [ value ] = store_if_available(p_search, p_needle)
+ % if the given needle is a member of search, return the containing value.
+ if isfield(p_search, p_needle)
+ value = p_search.(p_needle);
+ switch class(value)
+ case 'char'
+ value = strtrim(value);
+ end
+ return
+ else
+ value = NaN;
+ return
+ end
+ end
+
+
+%% FLOAT_IDENTIFICATION
+
+ function [ awi_struct ] = float_identification(p_profile_fieldname)
+
+ % abbreveations usually not allowed, this time used for better overview
+ awi_struct = {};
+
+ awi_struct.internal_ID_number = store_if_available( ...
+ p_optimare_float.DECODED_SBD, 'internal_ID_number');
+
+ if isfield( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname),'DEVICE') ...
+ && strcmp(strtrim( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname).DEVICE),'NEMO Standard' ...
+ )
+ awi_struct.transmission_type = 'IRIDIUM SBD';
+ else
+ awi_struct.transmission_type = NaN;
+ end
+
+ if isfield(p_optimare_float.GENERAL_INFO, 'IMEI')
+ awi_struct.transmission_id_number_dec = ...
+ p_optimare_float.GENERAL_INFO.IMEI;
+ awi_struct.transmission_id_number_hex = NaN;
+ else
+ awi_struct.transmission_id_number_dec = NaN;
+ awi_struct.transmission_id_number_hex = NaN;
+ end
+
+ awi_struct.wmo_id_number = store_if_available( ...
+ p_optimare_float.GENERAL_INFO, 'WMO_ID');
+
+ awi_struct.wmo_instrument_type = store_if_available( ...
+ p_optimare_float.GENERAL_INFO, 'WMO_INSTRUMENT_TYPE');
+
+
+
+ awi_struct.wmo_recorder_type = store_if_available( ...
+ p_optimare_float.GENERAL_INFO, 'WMO_RECORD_TYPE');
+
+ awi_struct.instrument_type = store_if_available( ...
+ p_optimare_float.GENERAL_INFO, 'INSTRUMENT_TYPE');
+
+ awi_struct.float_manufacturer = store_if_available( ...
+ p_optimare_float.GENERAL_INFO, 'FLOAT_MANUFACTURER');
+
+ awi_struct.float_serial_number = store_if_available( ...
+ p_optimare_float.GENERAL_INFO, 'SERIAL');
+
+ awi_struct.ice_detection_software = store_if_available( ...
+ p_optimare_float.SENSOR_INFO, 'ICE_DETECTION');
+
+
+ awi_struct.float_provider = store_if_available( ...
+ p_optimare_float.PROVIDER_DEPLOYER_INFO, 'PROVIDER_NAME');
+
+
+ awi_struct.float_provider_institution = store_if_available( ...
+ p_optimare_float.PROVIDER_DEPLOYER_INFO, 'PROVIDER_INSTITUTE');
+
+ awi_struct.originating_country = store_if_available( ...
+ p_optimare_float.PROVIDER_DEPLOYER_INFO, 'PROVIDER_COUNTRY');
+
+
+ end
+
+%% OVERALL_MISSION_INFORMATION
+
+ function [ awi_struct ] = overall_mission_information(p_profile_fieldname)
+
+ awi_struct = {};
+
+ if isfield(p_optimare_float.DECODED_SBD.(p_profile_fieldname), 'TIME_CYCLE')
+ awi_struct.total_cycle = [ ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname).TIME_CYCLE/(60*24) ...
+ 0 0];
+ else
+ awi_struct.total_cycle = NaN;
+ end
+
+ awi_struct.down_time = NaN;
+ awi_struct.up_time = NaN;
+ awi_struct.transmission_repetition_rate = NaN;
+ awi_struct.clock_drift = NaN;
+ awi_struct.nominal_drift_depth = NaN;
+ awi_struct.max_departure_from_drift_depth = NaN;
+
+ awi_struct.nominal_profile_depth = store_if_available( ...
+ p_optimare_float.MISSION_PARAMETERS, 'PROFILE_PRESSURE');
+
+ if isfield(p_optimare_float.DEPLOYMENT_INFO, 'START_DATE')
+ tmp_mat = strsplit(p_optimare_float.DEPLOYMENT_INFO.START_DATE, '.');
+ awi_struct.start_date = [ ...
+ str2double(tmp_mat{1}) ...
+ str2double(tmp_mat{2}) ...
+ str2double(tmp_mat{3})];
+ clear tmp_mat
+ else
+ awi_struct.start_date = NaN;
+ end
+
+ if isfield(p_optimare_float.DEPLOYMENT_INFO, 'START_TIME')
+ tmp_mat = strsplit(p_optimare_float.DEPLOYMENT_INFO.START_TIME, ':');
+ awi_struct.start_time = [ ...
+ str2double(tmp_mat{1}) ...
+ str2double(tmp_mat{2})];
+ clear tmp_mat
+ else
+ awi_struct.start_time = NaN;
+ end
+
+ awi_struct.RAFOS_clock_offset_at_start = NaN;
+ awi_struct.start_surface_pressure = NaN;
+
+ awi_struct.ice_detection_temperature_threshold = store_if_available( ...
+ p_optimare_float.MISSION_PARAMETERS, 'ICE_TEMPERATURE');
+
+
+ end
+
+%% DEPLOYMENT_INFO
+ function [ awi_struct ] = deployment_info()
+
+ awi_struct.float_deployer = store_if_available( ...
+ p_optimare_float.PROVIDER_DEPLOYER_INFO, 'DEPLOYER_NAME');
+
+ awi_struct.float_deployer_institution = store_if_available( ...
+ p_optimare_float.PROVIDER_DEPLOYER_INFO, 'DEPLOYER_INSTITUTE');
+
+ awi_struct.deployment_platform_type = store_if_available( ...
+ p_optimare_float.DEPLOYMENT_INFO, 'DEPLOYMENT_PLATFORM');
+
+ awi_struct.deployment_platform_code = store_if_available( ...
+ p_optimare_float.DEPLOYMENT_INFO, 'DEPLOYMENT_PLATFORM_SIGN');
+
+ if isfield(p_optimare_float.DEPLOYMENT_INFO, 'DEPLOYMENT_PLATFORM_EXPEDITION')
+ tmp_string = strsplit( ...
+ p_optimare_float.DEPLOYMENT_INFO.DEPLOYMENT_PLATFORM_EXPEDITION, ...
+ '/');
+ if length(tmp_string) == 2
+ awi_struct.deployment_platform_cruise_name = tmp_string{1};
+ awi_struct.deployment_platform_leg = tmp_string{2};
+ else
+ awi_struct.deployment_platform_cruise_name = ...
+ p_optimare_float.DEPLOYMENT_INFO.DEPLOYMENT_PLATFORM_EXPEDITION;
+ awi_struct.deployment_platform_leg = 'none';
+ end
+ clear tmp_string
+ else
+ awi_struct.deployment_platform_cruise_name = NaN;
+ awi_struct.deployment_platform_leg = 'none';
+ end
+
+ awi_struct.deployment_ctd_station = NaN;
+
+ if isfield(p_optimare_float.DEPLOYMENT_INFO, 'DEPLOYMENT_DATE')
+ tmp_string = strsplit( ...
+ p_optimare_float.DEPLOYMENT_INFO.DEPLOYMENT_DATE, ...
+ '.');
+ awi_struct.deployment_date = [ str2double(tmp_string{1}) ...
+ str2double(tmp_string{2}) ...
+ str2double(tmp_string{3}) ];
+ clear tmp_string
+ else
+ awi_struct.deployment_date = NaN;
+ end
+
+ if isfield(p_optimare_float.DEPLOYMENT_INFO, 'DEPLOYMENT_TIME')
+ tmp_string = strsplit( ...
+ p_optimare_float.DEPLOYMENT_INFO.DEPLOYMENT_TIME, ...
+ ':');
+ awi_struct.deployment_time = [ str2double(tmp_string{1}) ...
+ str2double(tmp_string{2}) ];
+ clear tmp_string
+ else
+ awi_struct.deployment_time = NaN;
+ end
+
+ if isfield(p_optimare_float.DEPLOYMENT_INFO, 'DEPLOYMENT_LAT') ...
+ && isfield(p_optimare_float.DEPLOYMENT_INFO, 'DEPLOYMENT_LON')
+ awi_struct.deployment_position = [ ...
+ p_optimare_float.DEPLOYMENT_INFO.DEPLOYMENT_LAT ...
+ p_optimare_float.DEPLOYMENT_INFO.DEPLOYMENT_LON];
+ else
+ awi_struct.deployment_position = NaN;
+ end
+
+ awi_struct.deployment_speed = NaN;
+
+ awi_struct.deployment_sea_state = store_if_available( ...
+ p_optimare_float.DEPLOYMENT_INFO, 'DEPLOYMENT_SEA_STATE');
+
+ awi_struct.deployment_wave_height = NaN;
+
+ awi_struct.deployment_ice_coverage = store_if_available( ...
+ p_optimare_float.DEPLOYMENT_INFO, 'DEPLOYMENT_SEA_ICE');
+
+ awi_struct.delay_of_first_down_time = NaN;
+
+ end
+
+%% PROFILE_TECHNICAL_DATA
+
+ function [ awi_struct ] = profile_technical_data(p_profile_fieldname)
+
+ awi_struct = {};
+
+ awi_struct.xmit_profile_number = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PROFILE_NUMBER');
+
+ awi_struct.xmit_serial_number = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'SERIAL');
+
+ awi_struct.xmit_upcast_status = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'STATUS_UPCAST');
+
+ awi_struct.xmit_older_profiles_not_send = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PROFILE_OLDER');
+
+ awi_struct.xmit_motor_errors_count = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ERROR_MOTOR');
+
+ awi_struct.xmit_sbe42_ctd_errors = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ERROR_CTD');
+
+ awi_struct.xmit_o2_optode_errors = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ERROR_OPTODE');
+
+ awi_struct.xmit_rafos_errors = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ERROR_RAFOS');
+
+ awi_struct.xmit_cpu_battery_voltage = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'BATT_CPU');
+
+ awi_struct.xmit_pump_battery_voltage = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'BATT_PMP');
+
+ awi_struct.xmit_motor_current = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'CURR_MOTOR');
+
+ awi_struct.xmit_motor_current_mean = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'CURR_MOTOR_MEAN');
+
+ awi_struct.xmit_internal_pressure_surface = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PRES_TUBE_SURFACE');
+
+ awi_struct.xmit_internal_pressure_depth = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PRES_TUBE_DEPTH');
+
+ awi_struct.xmit_pressure_offset = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PRES_OFFSET');
+
+ awi_struct.xmit_surface_pressure = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PRES_SURFACE');
+
+ awi_struct.xmit_parking_pressure_median = median(store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'DS2_PRES'));
+
+ awi_struct.xmit_depth_pressure = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PRES_DEPTH');
+
+ awi_struct.xmit_depth_pressure_max = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PRES_MAX');
+
+ awi_struct.xmit_profile_recovery = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'RECOVERY_START');
+
+ awi_struct.xmit_piston_counts_surface = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PIST_SURFACE');
+
+ awi_struct.xmit_piston_counts_parking = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PIST_PARKING');
+
+ awi_struct.xmit_piston_counts_calc = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PIST_CALC');
+
+ awi_struct.xmit_piston_counts_eop = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'PIST_EOP');
+
+ awi_struct.xmit_descent_start_time = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'MCNT_DESCENT');
+
+ awi_struct.xmit_parking_start_time = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'MCNT_PARKING');
+
+ awi_struct.xmit_upcast_start_time = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'MCNT_SAG');
+
+ awi_struct.xmit_ascent_start_time = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'MCNT_ASCENT');
+
+ awi_struct.xmit_ascent_end_time = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'MCNT_ASCENT_END');
+
+ awi_struct.xmit_surface_start_time = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'MCNT_SURFACE');
+
+ if isfield(p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'DATA_RECORDS2') ...
+ && length(p_optimare_float.DECODED_SBD.(p_profile_fieldname).DATA_RECORDS2) == 5
+ awi_struct.xmit_profile_length_1 = ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname).DATA_RECORDS2(1);
+ awi_struct.xmit_profile_length_2 = ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname).DATA_RECORDS2(2);
+ awi_struct.xmit_profile_length_3 = ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname).DATA_RECORDS2(3);
+ awi_struct.xmit_profile_length_4 = ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname).DATA_RECORDS2(4);
+ awi_struct.xmit_profile_length_5 = ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname).DATA_RECORDS2(5);
+ else
+ awi_struct.xmit_profile_length_1 = NaN;
+ awi_struct.xmit_profile_length_2 = NaN;
+ awi_struct.xmit_profile_length_3 = NaN;
+ awi_struct.xmit_profile_length_4 = NaN;
+ awi_struct.xmit_profile_length_5 = NaN;
+ end
+
+ awi_struct.xmit_surface_detection_GPS = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ICEGPS_TIME');
+
+ awi_struct.xmit_surface_detection_Iridium = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ICEIRDM_TIME');
+
+ awi_struct.xmit_airpump_runtime = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'AIRPUMP_RUNTIME');
+
+ awi_struct.xmit_ice_detection_temp_median = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), ...
+ 'ICE_TEMPMEDIAN');
+
+ end
+
+%% BOTTOM_VALUES_DURING_DRIFT
+ function [ awi_struct ] = bottom_values_during_drift(p_profile_fieldname)
+
+ awi_struct = {};
+
+ awi_struct.xmit_bottom_pressure = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), 'DS2_PRES');
+
+ awi_struct.xmit_bottom_salt = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), 'DS2_SAL');
+
+ awi_struct.xmit_bottom_temperature = store_if_available( ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldname), 'DS2_TEMP');
+
+ end
+
+%% RAFOS_VALUES_FORMAT
+
+ function [ awi_struct ] = rafos_values_format()
+
+ awi_struct = { ...
+ 'status'; 'rtc_year '; 'rtc_month'; 'rtc_day'; 'rtc_hour'; ...
+ 'rtc_minute'; 'rtc_second'; '1STCORHEIGHT'; '1STTRAVELTIME'; ...
+ '2NDCORHEIGHT'; '2NDTRAVELTIME'; '3RDCORHEIGHT'; '3RDTRAVELTIME'; ...
+ '4THCORHEIGHT'; '4THTRAVELTIME'; '5THCORHEIGHT'; '5THTRAVELTIME'; ...
+ '6THCORHEIGHT'; '6THTRAVELTIME'; 'pressure'; 'salinity'; 'temp' ...
+ }';
+
+ end
+
+%% RAFOS_VALUES
+
+ function [ awi_struct ] = rafos_values(p_profile_fieldname)
+
+ p = p_optimare_float.DECODED_SBD.(p_profile_fieldname);
+ if isfield(p, 'DS3_DATE_year') && isfield(p, 'DS3_DATE_month') ...
+ && isfield(p, 'DS3_DATE_day') && isfield(p, 'DS3_TIME') ...
+ && isfield(p, 'DS3_STATUS') && isfield(p, 'DS3_RAFOSAMP') ...
+ && isfield(p, 'DS3_RAFOSRANK') && isfield(p, 'DS3_PRES') ...
+ && isfield(p, 'DS3_SAL') && isfield(p, 'DS3_TEMP')
+
+ y = (1/(4836-4464) .* p.DS3_DATE_year) + 2000;
+ mon = p.DS3_DATE_month;
+ d = p.DS3_DATE_day;
+
+ h = floor(p.DS3_TIME./3600);
+ m = floor((p.DS3_TIME - (h*3600))/60);
+ s = uint8(mod(p.DS3_TIME,60));
+
+ prefix = [p.DS3_STATUS', y', mon', d', h', m', double(s')];
+
+ awi_struct = [ ...
+ prefix, ...
+ p.DS3_RAFOSAMP(:, 1), p.DS3_RAFOSRANK(:, 1), ...
+ p.DS3_RAFOSAMP(:, 2), p.DS3_RAFOSRANK(:, 2), ...
+ p.DS3_RAFOSAMP(:, 3), p.DS3_RAFOSRANK(:, 3), ...
+ p.DS3_RAFOSAMP(:, 4), p.DS3_RAFOSRANK(:, 4), ...
+ p.DS3_RAFOSAMP(:, 5), p.DS3_RAFOSRANK(:, 5), ...
+ p.DS3_RAFOSAMP(:, 6), p.DS3_RAFOSRANK(:, 6), ...
+ p.DS3_PRES', p.DS3_SAL', p.DS3_TEMP' ...
+ ];
+ else
+ awi_struct = [];
+ end
+
+
+ end
+
+%% PROFILE_HEADER
+
+ function [ awi_struct ] = profile_header()
+
+ awi_struct = {};
+
+ awi_struct.number_of_columns = 13;
+ awi_struct.column_1 = 'line_number';
+ awi_struct.column_2 = 'hour';
+ awi_struct.column_3 = 'minute';
+ awi_struct.column_4 = 'second';
+ awi_struct.column_5 = 'temperature [deg C]';
+ awi_struct.column_6 = 'temperature flag';
+ awi_struct.column_7 = 'pressure [dbar]';
+ awi_struct.column_8 = 'pressure flag';
+ awi_struct.column_9 = 'salinity [psu]';
+ awi_struct.column_10 = 'salinity flag';
+ awi_struct.column_11 = 'temperature raw';
+ awi_struct.column_12 = 'pressure raw';
+ awi_struct.column_13 = 'salinity raw';
+ awi_struct.temperature_conversion_equation = 'T=cnts/1000, if(cnts>62535),cnts=cnts-65536';
+ awi_struct.pressure_conversion_equation = 'P=cnts/10';
+ awi_struct.salinity_conversion_equation = 'S=cnts/1000';
+
+ end
+
+%% QUALITY_CONTROL_HEADER
+
+ function [ awi_struct ] = qualtiy_control_header()
+
+ awi_struct = {};
+
+ awi_struct.overall_flag_for_T = 0;
+ awi_struct.overall_flag_for_P = 0;
+ awi_struct.overall_flag_for_S = 0;
+ awi_struct.maximum_speed_check_flag = 0;
+ awi_struct.maximum_analysis_check_T_flag = 0;
+ awi_struct.maximum_climatology_T_flag = 0;
+ awi_struct.maximum_gross_check_T_flag = 0;
+ awi_struct.maximum_vertical_gradient_T_flag = 0;
+ awi_struct.maximum_spike_check_T_flag = 0;
+ awi_struct.maximum_analysis_check_S_flag = 0;
+ awi_struct.maximum_climatology_S_flag = 0;
+ awi_struct.maximum_gross_check_S_flag = 0;
+ awi_struct.maximum_vertical_gradient_S_flag = 0;
+ awi_struct.maximum_spike_check_S_flag = 0;
+ awi_struct.sigma_used_for_T_climatology = 10;
+ awi_struct.sigma_used_for_T_analysis = 10;
+ awi_struct.sigma_used_for_S_climatology = 10;
+ awi_struct.sigma_used_for_S_analysis = 10;
+
+ end
+
+%% PROFILE_DATA_HEADER
+
+ function [ awi_struct ] = profile_data_header()
+
+ awi_struct = { ...
+ '#'; 'hour'; 'minute'; 'second'; 'temp'; 'temp_flag'; 'pressure'; ...
+ 'pres_flag'; 'salinity'; 'sal_flag'; 'temp_raw'; 'pres_raw'; ...
+ 'sal_raw'; 'light_442_nm'; 'light_550_nm'; 'light_676_nm' ...
+ }';
+
+ end
+
+%% PROFILE_DATA
+
+ function [ awi_struct ] = profile_data(p_profile_fieldname)
+
+ p = p_optimare_float.DECODED_SBD.(p_profile_fieldname);
+ if isfield(p, 'DS4_TIME') && isfield(p, 'DS4_TEMP') ...
+ && isfield(p, 'DS4_PRES') && isfield(p, 'DS4_SAL')
+
+ h = floor(p.DS4_TIME./3600);
+ m = floor((p.DS4_TIME - (h*3600))/60);
+ s = uint8(mod(p.DS4_TIME, 60));
+ profile_numbers = 1:length(h);
+ flags = zeros(1, length(h));
+
+ prefix = [profile_numbers', h', m', double(s')];
+
+ % somtimes LICH1-3 has different length than TEMP, PRES & SAL
+ if ~isfield(p, 'DS4_LICH1') || ~isfield(p, 'DS4_LICH2') ...
+ || ~isfield(p, 'DS4_LICH3') || (length(p.DS4_LICH1) ~= length(p.DS4_TEMP))
+ LICH1 = flags;
+ LICH2 = flags;
+ LICH3 = flags;
+ else
+ LICH1 = p.DS4_LICH1;
+ LICH2 = p.DS4_LICH2;
+ LICH3 = p.DS4_LICH3;
+ end
+
+ awi_struct = [ ...
+ prefix, ...
+ p.DS4_TEMP', flags', ...
+ p.DS4_PRES', flags', ...
+ p.DS4_SAL', flags', ...
+ p.DS4_TEMP', p.DS4_PRES', p.DS4_SAL', ...
+ LICH1', LICH2', LICH3' ...
+ ];
+ else
+ awi_struct = [];
+ end
+
+
+ end
+
+%% SURFACE_GPS_DATA_FORMAT
+
+ function [ awi_struct ] = surface_gps_data_format()
+
+ awi_struct = { ...
+ '#'; 'rtc_year'; 'rtc_month'; 'rtc_day'; 'rtc_hour'; 'rtc_minute'; ...
+ 'rtc_second'; 'GPS_year'; 'GPS_month'; 'GPS_day'; 'GPS_hour'; ...
+ 'GPS_minute'; 'GPS_second'; 'lat'; 'lon' ...
+ }';
+
+ end
+
+%% SURFACE_GPS_DATA
+
+ function [ awi_struct ] = surface_gps_data(p_profile_fieldname)
+
+ p = p_optimare_float.DECODED_SBD.(p_profile_fieldname);
+ if isfield(p, 'DS5_GPS') && isfield(p, 'DS5_RTC') ...
+ && isfield(p, 'DS5_LAT') && isfield(p, 'DS5_LON')
+
+ gps_datevec = datevec(p.DS5_GPS);
+ % check if gps date is correct
+ if gps_datevec(1) == 1999 && gps_datevec(2) == 12 ...
+ && gps_datevec(3) == 31
+ gps_datevec = [NaN, NaN, NaN, NaN, NaN, NaN];
+ end
+
+ awi_struct = [ ...
+ 1, ...
+ datevec(p.DS5_RTC), ...
+ gps_datevec, ...
+ p.DS5_LAT, ...
+ p.DS5_LON ...
+ ];
+ else
+ awi_struct = [];
+ end
+
+
+ end
+
+%% IRIDIUM_POSITIONS_FORMAT
+
+ function [ awi_struct ] = iridium_positions_format()
+
+ awi_struct = { ...
+ 'sbd_lat'; 'sbd_lon'; 'sbd_cep'; ...
+ 'yyyy'; 'mm'; 'dd'; ...
+ 'hh'; 'mm'; 'ss'
+ }';
+
+ end
+
+%% IRIDIUM_POSITIONS
+
+ function [ iridium_positions, iridium_best ] = ...
+ iridium_positions_and_data(p_profile_fieldname)
+
+ p = p_optimare_float.DECODED_SBD.(p_profile_fieldname);
+ sbd_info = p_optimare_float.SBD_MESSAGES_INFO;
+
+ if ~isfield(p_optimare_float.TRANSMISSION_INFO, 'MOMSN') ...
+ || ~isfield(p_optimare_float.TRANSMISSION_INFO, 'TIMEOFSESSION') ...
+ || ~isfield(p_optimare_float.TRANSMISSION_INFO, 'IRIDIUM_LAT') ...
+ || ~isfield(p_optimare_float.TRANSMISSION_INFO, 'IRIDIUM_LON') ...
+ || ~isfield(p_optimare_float.TRANSMISSION_INFO, 'CEPRAD')
+ return; % one of the fields is not available
+ end
+
+ % get transmission info
+ momsn = p_optimare_float.TRANSMISSION_INFO.MOMSN;
+ time_of_session = p_optimare_float.TRANSMISSION_INFO.TIMEOFSESSION;
+ lat = p_optimare_float.TRANSMISSION_INFO.IRIDIUM_LAT;
+ lon = p_optimare_float.TRANSMISSION_INFO.IRIDIUM_LON;
+ cep = p_optimare_float.TRANSMISSION_INFO.CEPRAD;
+
+ sbd_info_count = length(sbd_info);
+
+ ir_lat = [];
+ ir_lon = [];
+ ir_cep = [];
+ ir_time = [];
+ ir_time_datevec = [];
+
+ % get all profile numbers of the transmitted iridium messsages
+ table_sbd_info = struct2table(sbd_info);
+ profile_number_lsb = table_sbd_info(:, {'profilenumber_lsb'});
+ % transform them to be able to use it as comparison
+ profile_number_lsb = table2array(profile_number_lsb);
+ % compare them to the current one
+ tmp_logical_array = (profile_number_lsb(:) == p.PROFILE_NUMBER);
+ % get all corresponding messages
+ iridium_messages = table_sbd_info(tmp_logical_array, :);
+ iridium_messages_count = size(iridium_messages, 1);
+
+ for o_iridium = 1:iridium_messages_count
+ tmp_logical_array = (momsn == iridium_messages(o_iridium, :).momsn);
+ % get current lat
+ current_lat = lat(tmp_logical_array);
+ current_lon = lon(tmp_logical_array);
+ current_cep = cep(tmp_logical_array);
+ current_time = time_of_session(tmp_logical_array);
+ current_time_datevec = datevec(current_time);
+ if length(current_lat) > 1
+ % get line with best cep
+ [~, index] = min(current_cep);
+ current_lat = nanmean(current_lat(index));
+ current_lon = nanmean(current_lon(index));
+ current_cep = nanmean(current_cep(index));
+ current_time = nanmean(current_time(index));
+ current_time_datevec = datevec(current_time);
+ end
+ ir_lat = [ir_lat; current_lat];
+ ir_lon = [ir_lon; current_lon];
+ ir_cep = [ir_cep; current_cep];
+ ir_time = [ir_time; current_time];
+ ir_time_datevec = [ir_time_datevec; current_time_datevec];
+ end
+
+
+ if isempty(ir_lat) || isempty(ir_lon) || isempty(ir_cep) ...
+ || isempty(ir_time)
+ iridium_positions = [];
+ iridium_best = [];
+ return
+% else
+% % delete all cep > 10, if there is nothing left store all to prevent
+% % NaN's
+% tmp_logical_array = (ir_cep < 10);
+% if sum(tmp_logical_array) > 0
+% ir_lat = ir_lat(tmp_logical_array);
+% ir_lon = ir_lon(tmp_logical_array);
+% ir_cep = ir_cep(tmp_logical_array);
+% ir_time = ir_time(tmp_logical_array);
+% ir_time_datevec = datevec(ir_time);
+% end
+ end
+
+ % create return structure for all positions
+ iridium_positions = [ ...
+ ir_lat, ir_lon, ir_cep, ir_time_datevec ...
+ ];
+
+ % get best position
+ best_ceps = unique(ir_cep);
+ ix_best = (ir_cep == min(best_ceps));
+ ir_lat_mean = nanmean(ir_lat(ix_best));
+ ir_lon_mean = nanmean(ir_lon(ix_best));
+ ir_cep_mean = nanmean(ir_cep(ix_best));
+ %ir_time_mean = nanmean(ir_time(ix_best));
+
+ iridium_best = [ ...
+ ir_lat_mean, ir_lon_mean, ir_cep_mean, ir_time_datevec(end, :)
+ ];
+
+ end
+
+%% IRIDIUM_DATA_FORMAT
+
+ function [ awi_struct ] = iridium_data_format()
+
+ awi_struct = { ...
+ 'mean_lat'; 'mean_lon'; 'mean_cep'; ...
+ 'yyyy'; 'mm'; 'dd'; ...
+ 'hh'; 'mm'; 'ss'
+ }';
+
+ end
+
+%% SORT IRIDIUM MESSAGES
+
+ function [ profile_numbers_sorted, indices ] = sort_iridium_messages(p_profile_fieldnames)
+ profile_numbers_unsorted = [];
+ tmp_valid_profile_count = 0;
+ % collect all profile numbers
+ for o_fields = 1:length(p_profile_fieldnames)
+ current_profile = ...
+ p_optimare_float.DECODED_SBD.(p_profile_fieldnames{o_fields});
+ if ~strcmp(p_optimare_float.DECODED_SBD.(p_profile_fieldnames{o_fields}).DATATYPE, 'Profile Message') ...
+ || ~isfield(p_optimare_float.DECODED_SBD.(p_profile_fieldnames{o_fields}), 'PROFILE_NUMBER') ...
+ || isnan(p_optimare_float.DECODED_SBD.(p_profile_fieldnames{o_fields}).PROFILE_NUMBER)
+ continue;
+ end
+ tmp_valid_profile_count = tmp_valid_profile_count + 1;
+ profile_numbers_unsorted(tmp_valid_profile_count, :) = ...
+ [p_optimare_float.DECODED_SBD.(p_profile_fieldnames{o_fields}).PROFILE_NUMBER, ...
+ o_fields];
+ end
+ % sort them
+ if ~isempty(profile_numbers_unsorted)
+ [profile_numbers_sorted, indices] = sortrows(profile_numbers_unsorted, 1);
+ indices = profile_numbers_sorted(:, 2);
+ else
+ indices = false;
+ profile_numbers_sorted = false;
+ end
+ end
+
+ function [best_ctd_indices] = filter_multiple_profiles(sorted_indices)
+ % initialize return variable
+ best_ctd_indices = [];
+ best_indices_count = 0;
+ % get profile number of the first element
+ if isfield(p_optimare_float.DECODED_SBD.(profile_fieldnames{sorted_indices(1)}), 'DATA_RECORDS2') ...
+ && p_optimare_float.DECODED_SBD.(profile_fieldnames{sorted_indices(1)}).DATA_RECORDS2(4) > 0
+ % if it is < 0, there is no possibility to compare CTD data
+ best_indices_count = best_indices_count + 1;
+ last_profile_number = p_optimare_float.DECODED_SBD.(profile_fieldnames{sorted_indices(1)}).PROFILE_NUMBER;
+ best_ctd_indices(best_indices_count) = sorted_indices(1);
+ end
+
+ for o_index = 2:length(sorted_indices)
+ if ~isfield(p_optimare_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}), 'DATA_RECORDS2') ...
+ || p_optimare_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DATA_RECORDS2(4) == 0
+ continue
+ end
+ % get current profile number
+ current_profile_number = p_optimare_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).PROFILE_NUMBER;
+ if best_indices_count > 0 && current_profile_number == last_profile_number
+ % check which ctd data is better
+ current_ctd_length = p_optimare_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DATA_RECORDS2(4);
+ last_ctd_length = p_optimare_float.DECODED_SBD.(profile_fieldnames{best_ctd_indices(best_indices_count)}).DATA_RECORDS2(4);
+ if current_ctd_length > last_ctd_length
+ best_ctd_indices(best_indices_count) = sorted_indices(o_index);
+ elseif current_ctd_length == last_ctd_length
+ % take the one without or less NaN's
+ tmp_current = [ ...
+ p_optimare_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DS4_TIME; ...
+ p_optimare_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DS4_FORMAT; ...
+ p_optimare_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DS4_PRES; ...
+ p_optimare_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DS4_TEMP; ...
+ p_optimare_float.DECODED_SBD.(profile_fieldnames{sorted_indices(o_index)}).DS4_SAL ...
+ ];
+ tmp_last = [ ...
+ p_optimare_float.DECODED_SBD.(profile_fieldnames{best_ctd_indices(best_indices_count)}).DS4_TIME; ...
+ p_optimare_float.DECODED_SBD.(profile_fieldnames{best_ctd_indices(best_indices_count)}).DS4_FORMAT; ...
+ p_optimare_float.DECODED_SBD.(profile_fieldnames{best_ctd_indices(best_indices_count)}).DS4_PRES; ...
+ p_optimare_float.DECODED_SBD.(profile_fieldnames{best_ctd_indices(best_indices_count)}).DS4_TEMP; ...
+ p_optimare_float.DECODED_SBD.(profile_fieldnames{best_ctd_indices(best_indices_count)}).DS4_SAL ...
+ ];
+ sum_current = sum(sum(isnan(tmp_current)));
+ sum_last = sum(sum(isnan(tmp_last)));
+ if sum_last > sum_current
+ best_ctd_indices(best_indices_count) = sorted_indices(o_index);
+ end
+ clear tmp_current tmp_last sum_current sum_last
+
+ end
+ else
+ best_indices_count = best_indices_count + 1;
+ best_ctd_indices(best_indices_count) = sorted_indices(o_index);
+ end
+
+ last_profile_number = current_profile_number;
+ end
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+convert/optimare2nemostruct.m b/lib/vendor/nemo2profilelib/+nemo/+convert/optimare2nemostruct.m
new file mode 100644
index 0000000..ff7c052
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+convert/optimare2nemostruct.m
@@ -0,0 +1,48 @@
+function [ boolean, nemo_data ] = optimare2nemostruct( p_optimare_data )
+%OPTIMARE2NEMOSTRUCT Converts the optimare data structure to nemo format.
+% Converts the given optimare data structure to the nemo data format that
+% is used by this library.
+%
+% Parameters:
+% p_optimare_float: Data structure created by the decoding process
+% written by optimare. In case of the source
+% nemo2profile, this should be
+% handles.all_floats.(float_name)
+%
+% Returns:
+% boolean: False if the conversion failed.
+% nemo_data: The converted float data.
+%
+
+%% Initialize return variables
+boolean = false;
+nemo_data = {};
+
+%% Parameter check (not implemented yet)
+
+floatnames = fieldnames(p_optimare_data);
+converted_floatcount = 0;
+
+for o_float = 1:length(floatnames)
+
+ % get current float data
+ current_float = p_optimare_data.(floatnames{o_float});
+
+ converted_float = nemo.convert.float(current_float);
+
+ if ~iscell(converted_float)
+ warning(['Error converting ' floatnames{o_float} '!']);
+ else
+ % store it to nemo data
+ converted_floatcount = converted_floatcount + 1;
+ nemo_data{converted_floatcount} = converted_float;
+ clear converted_float
+ end
+
+end
+
+boolean = true;
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+float/collect.m b/lib/vendor/nemo2profilelib/+nemo/+float/collect.m
new file mode 100644
index 0000000..9e8bd64
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+float/collect.m
@@ -0,0 +1,192 @@
+function [ data ] = collect( p_nemo_float, p_section, p_member, p_options )
+%COLLECT Collects given section and/or member of float for every profile.
+% Iterates through every profile in the given nemo float and stores the
+% selected data either into a cell or a matrix depending on the class
+% that is being collected. This function is helpful if you require one
+% parameter of the float of all profiles in one variable.
+%
+% Parameters:
+% p_nemo_float: Float from which the data is being collected.
+% p_section: String, Section identifier of the data that should
+% be stored.
+% p_member: String, member of the section that should be
+% stored. If this equals an empty string, the
+% complete section is being stored.
+% p_options: Currently the following options can be passed to
+% the function:
+%
+% 'col2mat, {COLUMN_INTEGER}'
+% -> collects the given column and combines it to a
+% matrix (used for collecting pressure data of all
+% profiles for example)
+%
+% 'combine'
+% -> collects the given section/member and combines
+% it as a matrix
+%
+% Returns:
+% data: Collected data for every profile of the given
+% float.
+
+%% Initialize return variable
+data = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~iscell(p_nemo_float) || ~ischar(p_section))
+ parameter_error = true;
+end
+
+if (exist('p_options', 'var') && ~ischar(p_options))
+ parameter_error = true;
+elseif (~exist('p_options', 'var'))
+ p_options = '';
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% Collect data
+
+profile_count = length(p_nemo_float);
+
+if (profile_count == 0)
+ return;
+end
+
+% Calculate internal clock if option is given
+if (strcmp(p_section, 'xmitDatevec'))
+ data = collect_and_calculate_xmit_datevec(p_member);
+ return
+end
+
+if ~exist('p_member', 'var') || strcmp(p_member, '') % the whole section is being collected
+
+ switch class(p_nemo_float{1}.(p_section))
+
+ case 'double' % it may be possible to store it as matrix
+ % be sure that data is always one line
+ one_line_double = true;
+ column_count = 0;
+ for o_profiles = 1:profile_count
+ if ~isempty(p_nemo_float{o_profiles}.(p_section)) ...
+ && size(p_nemo_float{o_profiles}.(p_section), 1) ~= 1
+ one_line_double = false;
+ break;
+ end
+ if column_count == 0 && ~isempty(p_nemo_float{o_profiles}.(p_section))
+ column_count = size(p_nemo_float{o_profiles}.(p_section), 2);
+ end
+ end
+
+ if one_line_double
+ % only one line per profile, so create a matrix
+ data = [];
+ for o_profiles = 1:profile_count
+ if ~isempty(p_nemo_float{o_profiles}.(p_section))
+ data(o_profiles, :) = p_nemo_float{o_profiles}.(p_section);
+ else
+ data(o_profiles, 1:column_count) = NaN;
+ end
+ end
+ elseif (is_option_set('col2mat'))
+ % the given column will be collected from all profiles and
+ % combined into a column-wise matrix
+ all_options = get_options(p_options);
+ [column_number, status] = str2int(all_options{2});
+ if (~status)
+ disp([mfilename ': Cannot convert option number 2 to integer!']);
+ return
+ end
+ data = [];
+ for o_profiles = 1:profile_count
+ if isfield(p_nemo_float{o_profiles}, p_section)
+ data = [data, p_nemo_float{o_profiles}.(p_section)(:, column_number)];
+ end
+ end
+ elseif (is_option_set('combine'))
+ % user selected to get a matrix containing all values
+ % instead of seperated cells
+ data = [];
+ for o_profiles = 1:profile_count
+ if isfield(p_nemo_float{o_profiles}, p_section)
+ data = [data; p_nemo_float{o_profiles}.(p_section)];
+ end
+ end
+ else
+ % create a struct because there are more lines in every profile
+ data = {};
+ for o_profiles = 1:profile_count
+ if ~isfield(p_nemo_float{o_profiles}, p_section)
+ data{o_profiles} = NaN;
+ else
+ data{o_profiles} = p_nemo_float{o_profiles}.(p_section);
+ end
+ end
+ end
+
+ otherwise
+ data = {};
+ for o_profiles = 1:profile_count
+ data{o_profiles} = p_nemo_float{o_profiles}.(p_section);
+ end
+
+ end
+else
+ % exact the same passage as above, but in this one there is a member given
+ switch class(p_nemo_float{1}.(p_section).(p_member))
+
+ case 'double'
+ if size(p_nemo_float{1}.(p_section).(p_member), 1) == 1
+ % only one line, so create a matrix
+ data = [];
+ for o_profiles = 1:profile_count
+ data(o_profiles, :) = p_nemo_float{o_profiles}.(p_section).(p_member);
+ end
+ else
+ data = {};
+ for o_profiles = 1:profile_count
+ data{o_profiles} = p_nemo_float{o_profiles}.(p_section).(p_member);
+ end
+ end
+
+ otherwise
+ data = {};
+ for o_profiles = 1:profile_count
+ data{o_profiles} = p_nemo_float{o_profiles}.(p_section).(p_member);
+ end
+ end
+
+end
+
+ function boolean = is_option_set(option_string)
+ options = strsplit(p_options, ',');
+ boolean = any(cellfun(@(x) strcmp(x, option_string), options));
+ end
+
+ function options = get_options(option_string)
+ options = strtrim(strsplit(p_options, ','));
+ end
+
+ function data = collect_and_calculate_xmit_datevec(p_xmit_parameter_name)
+ data = NaN(profile_count, 6);
+ for i = 1:profile_count
+ data(i, :) = ...
+ datevec( ...
+ datetime([ ...
+ fliplr(p_nemo_float{i}.OVERALL_MISSION_INFORMATION.start_date), ...
+ p_nemo_float{i}.OVERALL_MISSION_INFORMATION.start_time 0 ...
+ ]) ...
+ + seconds(p_nemo_float{i}.PROFILE_TECHNICAL_DATA.(p_xmit_parameter_name)) ...
+ );
+ end
+ end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+float/extract_startup_message.m b/lib/vendor/nemo2profilelib/+nemo/+float/extract_startup_message.m
new file mode 100644
index 0000000..adcef52
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+float/extract_startup_message.m
@@ -0,0 +1,60 @@
+function [ startup_messages ] = extract_startup_message( p_combined_float )
+%DECODE_STARTUP_MESSAGE Extracts the startup messages of the given float
+% Detailed explanation goes here
+
+%% Initialize return variable
+startup_messages = false;
+
+%% Check if float is not empty
+if ~isfield(p_combined_float, 'DECODED_SBD')
+ % no data available
+ return
+end
+
+%% Search startup messages and get them into the awi structure
+
+startup_messages = {};
+
+% get fieldnames of every profile
+profile_fieldnames = fieldnames(p_combined_float.DECODED_SBD);
+
+for i = 1:length(profile_fieldnames)
+
+ if ~strcmp( ...
+ p_combined_float.DECODED_SBD.(profile_fieldnames{i}).DATATYPE, ...
+ 'Startup Test Message' ...
+ )
+ % everything that is not a profile or a test message is being ignored
+ continue
+ else
+ % extract the message
+ current_message = p_combined_float.DECODED_SBD.(profile_fieldnames{i});
+ startup_messages{end + 1} = struct();
+ startup_messages{end}.float_serial_number = current_message.SERIAL;
+ startup_messages{end}.software_version = current_message.SOFTWARE;
+ startup_messages{end}.real_time_clock = current_message.RTC;
+ startup_messages{end}.piston_max_count = current_message.PISTON_MAX;
+ startup_messages{end}.piston_min_count = current_message.PISTON_MIN;
+ startup_messages{end}.cpu_battery_voltage = current_message.BATT_CPU;
+ startup_messages{end}.pump_battery_voltage = current_message.BATT_PMP;
+ startup_messages{end}.ext_battery_voltage = current_message.BATT_EXT;
+ startup_messages{end}.pressure_tube_surface = current_message.PRES_TUBE_SURFACE;
+ startup_messages{end}.pressure_profile_depth = current_message.PRES_PROFILE;
+ startup_messages{end}.transmission_time = current_message.TIME_TX;
+ startup_messages{end}.parking_sample_time = current_message.TIME_PARKSAMPLE;
+ startup_messages{end}.cycle_time = current_message.TIME_CYCLE;
+ startup_messages{end}.descent_mode = current_message.DESCENT_MODE;
+ startup_messages{end}.start_recovery = current_message.RECOVERY_START;
+ startup_messages{end}.descent_speed = current_message.DESCENT_SPEED;
+ startup_messages{end}.ice_detection_temperature = current_message.TEMP_ICEDETECT;
+ startup_messages{end}.recovery_transmission = current_message.RECOVERY_TX;
+ startup_messages{end}.recovery_no_transmission = current_message.RECOVERY_NOTX;
+ startup_messages{end}.gps_datetime = current_message.GPS_DATETIME;
+ startup_messages{end}.gps_lat = current_message.GPS_LAT;
+ startup_messages{end}.gps_lon = current_message.GPS_LON;
+ end
+
+end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+float/fetch_process_mails.m b/lib/vendor/nemo2profilelib/+nemo/+float/fetch_process_mails.m
new file mode 100644
index 0000000..3c7d0f3
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+float/fetch_process_mails.m
@@ -0,0 +1,202 @@
+function [ boolean, float_imeis ] = fetch_process_mails( p_config, p_metadata )
+%FETCH_MAILS Fetches the mails of the floats in p_metadata
+% Fetches mails of the given floats in p_metadata. For this, javax.mail
+% package is being used.
+%
+% Parameters:
+% p_config: Configuration structure, must contain the
+% following values:
+% -username {string}
+% -password {string}
+% -port {integer}
+% -ssl {0 or 1}
+% -server {string}
+% -imap_timeout {integer}
+% -imaps_connection_timeout {integer}
+% -storage_directory {string}
+% -folder_to_fetch {string}
+% -sort_by_imei {0 or 1}
+% -separate_sbd_and_txt {0 or 1}
+% -mark_read_after_fetch {0 or 1}
+% -fetch_unread_only {0 or 1}
+% -sender_address {string}
+% -use_sender_address {0 or 1}
+%
+% Returns:
+% boolean: True, if successful.
+% float_imeis List with length of p_metadata. Contains either 0
+% or the IMEI number of the float if there are new
+% mails that have been fetched.
+
+%% Initialize return variables
+boolean = false;
+
+%% Parameter check
+if (~isstruct(p_config) || (~isstruct(p_metadata) && ~iscell(p_metadata)))
+ warning([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+end
+
+%% Setup some alias
+fetch_unread_only = p_config.MAIL.fetch_unread_only;
+mark_read_after_fetch = p_config.MAIL.mark_read_after_fetch;
+sort_by_imei = p_config.MAIL.sort_by_imei;
+storage_directory = p_config.MAIL.storage_directory;
+separate_sbd_and_txt = p_config.MAIL.separate_sbd_and_txt;
+
+%% Setup folder
+if (~isdir(storage_directory))
+ mkdir(storage_directory);
+end
+
+%% Connect to mail server
+imapstore = nemo.mail.connect(p_config);
+if (~imapstore.isConnected()) % warning is already given in connect()
+ return;
+end
+
+%% Create search and flag term
+% there are difficulties accessing static class members of an inner java
+% class. This solution has been found at:
+% http://undocumentedmatlab.com/blog/accessing-internal-java-class-members
+if (fetch_unread_only)
+ search_flag = javax.mail.Flags(); % create search flag
+ tmp = search_flag.getClass.getDeclaredClasses;
+ seen_flag = tmp(1).getField('SEEN').get(1);
+ clear tmp;
+ search_flag.add(seen_flag);
+ flag_term = javax.mail.search.FlagTerm(search_flag, false);
+else
+ flag_term = false;
+end
+
+if (~isfield(p_config.MAIL, 'sender_address') || ~isfield(p_config.MAIL, 'use_sender_address'))
+ warning([mfilename ': Config does not include a MAIL.sender_address or MAIL.use_sender_address field!']);
+ return;
+elseif (p_config.MAIL.use_sender_address)
+ java_sender_address = java.lang.String(p_config.MAIL.sender_address);
+ sender_term = javax.mail.search.FromStringTerm(java_sender_address);
+else
+ sender_term = false;
+end
+
+
+
+%% Fetch all mails and save them to disk
+
+switch class(p_metadata)
+ case 'struct'
+ % only one float has to be processed
+ [boolean, float_imeis] = process_float(p_metadata);
+ case 'cell'
+ [booleans, float_imeis] = cellfun(@process_float, p_metadata);
+ if (~all(booleans))
+ warning([mfilname ': Something went wrong during message download! Please contact developer or system administrator!']);
+ else
+ boolean = true;
+ end
+end
+
+clear imapstore;
+
+
+ function [boolean, float_imei] = process_float(p_float_metadata)
+ imei_int = p_float_metadata.GENERAL_INFO.IMEI;
+ imei_str = int2str(imei_int);
+ float_imei = 0; % will be overridden if there are messages to process
+ %% Check for directories
+ if (sort_by_imei)
+ float_storage_directory = [storage_directory imei_str p_config.GENERAL.folder_separator];
+ else
+ float_storage_directory = storage_directory;
+ end
+ % check if folders exists
+ if (~isdir(float_storage_directory))
+ mkdir(float_storage_directory);
+ end
+ if (separate_sbd_and_txt)
+ float_txt_directory = [float_storage_directory 'txt' p_config.GENERAL.folder_separator];
+ float_sbd_directory = [float_storage_directory 'sbd' p_config.GENERAL.folder_separator];
+ float_incomplete_directory = [float_storage_directory 'incomplete' p_config.GENERAL.folder_separator];
+ if (~isdir(float_sbd_directory))
+ mkdir(float_sbd_directory);
+ end
+ if (~isdir(float_txt_directory))
+ mkdir(float_txt_directory);
+ end
+ if (~isdir(float_incomplete_directory))
+ mkdir(float_incomplete_directory);
+ end
+ else
+ float_sbd_directory = float_storage_directory;
+ float_txt_directory = float_sbd_directory;
+ end
+
+ %% Create term for message filtering
+ subject_term = javax.mail.search.SubjectTerm(imei_str);
+ if isa(flag_term, 'javax.mail.search.FlagTerm') ...
+ && isa(sender_term, 'javax.mail.search.FromStringTerm')
+ tmp_comb = javax.mail.search.AndTerm(subject_term, flag_term);
+ combined_terms = javax.mail.search.AndTerm(tmp_comb, sender_term);
+ elseif isa(flag_term, 'javax.mail.search.FlagTerm')
+ combined_terms = javax.mail.search.AndTerm(flag_term, subject_term);
+ elseif isa(sender_term, 'javax.mail.search.FromStringTerm')
+ combined_terms = javax.mail.search.AndTerm(sender_term, subject_term);
+ else
+ combined_terms = subject_term;
+ end
+
+ %% Get mail that fit the terms
+ [messages, folder] = nemo.mail.fetch_messages(imapstore, ...
+ p_config.MAIL.folder_to_fetch, ...
+ combined_terms, ...
+ ~mark_read_after_fetch ...
+ );
+
+ %% Process all messages
+ for i = 1:messages.length
+ [from, ~, inline, attachments] = nemo.mail.extract(messages(i));
+ if (p_config.MAIL.use_sender_address && ~strcmp(from, p_config.MAIL.sender_address))
+ disp([mfilename ': Filter fetched the wrong address: ' from{1} '! Skipping message...']);
+ continue;
+ end
+
+ if (~isempty(attachments))
+ % store the float serial
+ float_imei = imei_int;
+ filename = char(attachments{1});
+ [~, file, ~] = fileparts(filename);
+ % export inline as well as attachment
+ nemo.mail.export_attachment(attachments{2}, [float_sbd_directory filename]);
+ % save inline
+ fid = fopen([float_txt_directory file '.txt'], 'wt');
+ fprintf(fid, inline);
+ fclose(fid);
+ else % mail has been received but no attachment
+ % export only inline to incomplete folder
+ processed_inline = nemo.mail.process_inline(inline);
+ fid = fopen([float_incomplete_directory int2str(processed_inline.MOMSN) '.txt'], 'wt');
+ fprintf(fid, inline);
+ fclose(fid);
+ end
+ clear from subject inline attachments filename;
+ end
+
+ if (mark_read_after_fetch && messages.length > 0)
+ % mark processed as read
+ flag = javax.mail.Flags(); % create search flag
+ tmp_class = flag.getClass.getDeclaredClasses;
+ flag_seen = tmp_class(1).getField('SEEN').get(1);
+ clear tmp_class;
+ flag.add(flag_seen);
+ folder.setFlags(messages, flag, true);
+ clear flag
+ end
+ clear messages combined_terms subject_term messages folder;
+
+ boolean = true;
+
+ end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+float/find.m b/lib/vendor/nemo2profilelib/+nemo/+float/find.m
new file mode 100644
index 0000000..3725dfa
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+float/find.m
@@ -0,0 +1,49 @@
+function [ floats, indices ] = find( p_nemo_data, p_float_number )
+%FIND Returns the float with the given p_float_number.
+% Searches for the given float in p_nemo_struct.
+%
+% Parameters:
+% p_nemo_data: The nemo data to be searched.
+% p_float_number: The float number that is being searched for.
+% It can also be a 1D vector of float numbers.
+%
+% Returns:
+% float: Copy from p_nemo_data of the float with the given
+% float number.
+% index: The index of the float in p_nemo_data.
+
+%index = cellfun(@(x) x{1}.FLOAT_IDENTIFICATION.float_serial_number == p_float_number, p_nemo_data);
+
+indices = [];
+floats = {};
+
+float_number_length = length(p_float_number);
+for current_float_number = 1:float_number_length
+ index = cellfun(@(x) find_float(x), p_nemo_data);
+ if (~any(index))
+ continue;
+ elseif (sum(index) > 1)
+ disp(['Multiple floats found: ' index]);
+ return
+ end
+
+ indices = [indices find(index)];
+ floats{end + 1} = p_nemo_data{index};
+
+
+end
+
+if (length(p_float_number) == 1)
+ floats = floats{1};
+end
+
+ function [ is_float ] = find_float(p_float)
+ if isfield(p_float, 'GENERAL_INFO')
+ is_float = p_float.GENERAL_INFO.SERIAL == p_float_number(current_float_number);
+ else
+ is_float = p_float{1}.FLOAT_IDENTIFICATION.float_serial_number == p_float_number(current_float_number);
+ end
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+float/get_changed_profiles.m b/lib/vendor/nemo2profilelib/+nemo/+float/get_changed_profiles.m
new file mode 100644
index 0000000..8e506d8
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+float/get_changed_profiles.m
@@ -0,0 +1,57 @@
+function [ changed_profiles ] = get_changed_profiles( p_config, p_float )
+%GET_CHANGED_PROFILES Loads the old profiles from the harddisk and compares them to the structure given in p_float.
+% Compares the old profiles that are saved on the harddisk with the given
+% float in p_float. Compares the profiles by using the
+% nemo.profile.compare function.
+%
+% Parameters:
+% p_config: The nemo configuration file.
+% p_float: The nemo data where the old profiles will be
+% compared with.
+%
+% Returns:
+% changed_profiles: Cell array containing the profiles that have
+% changed.
+
+%% Initialize return variables
+changed_profiles = false;
+
+%% Parameter check
+if (~isstruct(p_config) || ~iscell(p_float))
+ disp([ mfilename ': Please check your parameter!']);
+ return;
+end
+
+%% Save the float to a temporary folder and load it afterwards
+% this is because the comparison does not work with a float loaded from HDD
+% and directly converted from SBD messages in RAM
+
+
+%% Load old profiles
+
+old_profiles = nemo.load.data( ...
+ [ ...
+ p_config.OUTPUT_FILES.output_path ...
+ sprintf('%04d', p_float{1}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ ] ...
+);
+
+%% Compare them to the current ones
+
+old_profiles = nemo.float.sort_by_profile_number(old_profiles);
+p_float = nemo.float.sort_by_profile_number(p_float);
+changed_profiles = {};
+
+for i = 1:length(p_float)
+ current_profile = p_float{i};
+ old_profile = nemo.profile.find(old_profiles, current_profile.PROFILE_TECHNICAL_DATA.xmit_profile_number);
+ if (isa(old_profile, 'logical') && ~old_profile) ...
+ || ~nemo.profile.compare(old_profile, current_profile)
+ changed_profiles{end + 1} = current_profile;
+ continue;
+ end
+end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+float/process_mission_parameter.m b/lib/vendor/nemo2profilelib/+nemo/+float/process_mission_parameter.m
new file mode 100644
index 0000000..b9f6909
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+float/process_mission_parameter.m
@@ -0,0 +1,127 @@
+function [ mission_parameters ] = process_mission_parameter( p_mission_parameter_string )
+%PROCESS_MISSION_PARAMETER Summary of this function goes here
+% Detailed explanation goes here
+
+
+ try
+ ix = regexp(p_mission_parameter_string,'Serial number ','end');
+ mission_parameters.SERIAL=str2num(p_mission_parameter_string(ix:ix+3));
+ catch
+ mission_parameters.SERIAL=NaN;
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'Firmware version ','end');
+ mission_parameters.FIRMWARE_VERSION=str2num(p_mission_parameter_string(ix:ix+6));
+ catch
+ mission_parameters.FIRMWARE_VERSION=NaN;
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'Startup time: ','end');
+ mission_parameters.STARTUP_TIME=str2num(p_mission_parameter_string(ix:ix+4));
+ catch
+ mission_parameters.STARTUP_TIME=NaN;
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'Cycle time: ','end');
+ mission_parameters.START_CYCLETIME=str2num(p_mission_parameter_string(ix:ix+5));
+ catch
+ mission_parameters.START_CYCLETIME=NaN;
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'Change cycletime to ','end');
+ mission_parameters.CYCLETIME=str2num(p_mission_parameter_string(ix:ix+6));
+ catch
+ mission_parameters.CYCLETIME=NaN;
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'minutes in profile ','end');
+ mission_parameters.CYCLE_CHANGE=str2num(p_mission_parameter_string(ix:ix+3));
+ catch
+ mission_parameters.CYCLE_CHANGE=NaN;
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'Startup delay: ','end');
+ mission_parameters.STARTUP_DELAY=(p_mission_parameter_string(ix:ix+3));
+ catch
+ mission_parameters.STARTUP_DELAY='NaN';
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'Startprofiles: ','end');
+ mission_parameters.STARTPROFILES=str2num(p_mission_parameter_string(ix:ix+3));
+ catch
+ mission_parameters.STARTPROFILES=NaN;
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'Profile pressure: ','end');
+ mission_parameters.PROFILE_PRESSURE=str2num(p_mission_parameter_string(ix:ix+5));
+ catch
+ mission_parameters.PROFILE_PRESSURE=NaN;
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'Maximum pressure: ','end');
+ mission_parameters.MAX_PRESSURE=str2num(p_mission_parameter_string(ix:ix+5));
+ catch
+ mission_parameters.MAX_PRESSURE=NaN;
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'PistonOut @ alert = ','end');
+ mission_parameters.PISTON_OUT_ALERT=str2num(p_mission_parameter_string(ix:ix+4));
+ catch
+ mission_parameters.PISTON_OUT_ALERT=NaN;
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'Last min/max piston counts: ','end');
+ mission_parameters.LAST_PISTON_MIN_MAX=(p_mission_parameter_string(ix:ix+9));
+ catch
+ mission_parameters.LAST_PISTON_MIN_MAX='NaN';
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'RAFOS Start time ','end');
+ mission_parameters.RAFOS_STARTTIME=(p_mission_parameter_string(ix:ix+6));
+ catch
+ mission_parameters.RAFOS_STARTTIME='NaN';
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'Duration ','end');
+ mission_parameters.RAFOS_DURATION=str2num(p_mission_parameter_string(ix:ix+4));
+ catch
+ mission_parameters.RAFOS_DURATION=NaN;
+ end
+ clear ix
+
+ try
+ ix = regexp(p_mission_parameter_string,'temperature = ','end');
+ mission_parameters.ICE_TEMPERATURE=str2num(p_mission_parameter_string(ix:ix+5));
+ catch
+ mission_parameters.ICE_TEMPERATURE=NaN;
+ end
+ clear ix
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+float/save_startup_message.m b/lib/vendor/nemo2profilelib/+nemo/+float/save_startup_message.m
new file mode 100644
index 0000000..e6cdac4
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+float/save_startup_message.m
@@ -0,0 +1,107 @@
+function [ boolean ] = save_startup_message( p_startup_messages, p_filepath, p_overwrite )
+%SAVE_STARTUP_MESSAGES Summary of this function goes here
+% Detailed explanation goes here
+
+%% Initialize variables
+boolean = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~iscell(p_startup_messages) || ~ischar(p_filepath))
+ parameter_error = true;
+end
+
+if (~exist('p_overwrite', 'var') || isempty(p_overwrite))
+ p_overwrite = 1; % default setting is to overwrite existing profile files
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% File existence checks
+
+if ~exist(p_filepath, 'dir')
+ mkdir(p_filepath);
+end
+
+%% Configuration parameters
+double_format = '%.15g';
+help_tabs = ['\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t'];
+desired_tab_count = 12;
+
+
+%% Write message to file
+
+%for outer = 1:length(p_startup_messages) % required if there are multiple messages
+current_message = p_startup_messages{end};
+filename = [ ...
+ p_filepath ...
+ sprintf('%04d', current_message.float_serial_number) ...
+ '.startup_message' ...
+ ];
+
+if exist(filename, 'file') == 2 && ~p_overwrite
+ % file will not be overwritten
+ boolean = true;
+ return
+end
+
+of_id = fopen(filename, 'w'); % open file for writing
+fprintf(of_id, '[STARTUP_MESSAGE]\n');
+write_struct(current_message);
+fclose(of_id);
+
+boolean = true;
+%end
+
+ function [ tabs ] = get_tabs_to_insert(p_member_name)
+ % this function computes the required tabs to insert, making the
+ % textfile easier to read.
+ tablength = 4;
+ tab_count = desired_tab_count - floor((length(p_member_name)+1)/tablength);
+ tabs = help_tabs(1:(tab_count*2));
+ end
+
+ function write_struct(p_input_struct)
+ % get all fieldnames and write them to the file
+ member_names = fieldnames(p_input_struct);
+ member_count = length(member_names);
+ for o_member = 1:member_count % run through all members
+ % calculate how many tabs have to be inserted to have a
+ % good table layout
+ tabstring = get_tabs_to_insert(member_names{o_member});
+ fprintf(of_id, ['-' member_names{o_member} tabstring]);
+ current_member = p_input_struct.(member_names{o_member});
+ current_member_class = class(current_member);
+ switch current_member_class
+ case {'double', 'logical'}
+ write_double(current_member);
+ case 'char'
+ fprintf(of_id, [current_member '\n']);
+ otherwise
+ disp(['Unknown class in file: ' class(current_member)]);
+ end
+
+ end
+ clear o_member
+ end
+
+ function write_double(p_input_double)
+
+ for o_double = 1:size(p_input_double, 1)
+ if length(p_input_double(o_double, :)) > 1
+ fprintf(of_id, sprintf([double_format '\t'], p_input_double(o_double, 1:end-1)));
+ end
+ fprintf(of_id, [double_format '\n'], p_input_double(o_double, end));
+ end
+ clear o_double
+
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+float/sort_by_profile_number.m b/lib/vendor/nemo2profilelib/+nemo/+float/sort_by_profile_number.m
new file mode 100644
index 0000000..d9ece54
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+float/sort_by_profile_number.m
@@ -0,0 +1,34 @@
+function [ sorted_float ] = sort_by_profile_number( p_float )
+%SORT_BY_PROFILE_NUMBER Gets the input float and sorts its profile by their numbers
+%
+% Parameters:
+% p_float: Float that will be sorted.
+%
+% Returns:
+% sorted_float: Sorted float by profile number.
+
+% get all profile numbers
+profile_numbers = nemo.float.collect(p_float, 'PROFILE_TECHNICAL_DATA', 'xmit_profile_number');
+
+% sort them and get the indices
+[~, indices] = sort(profile_numbers);
+
+% create helping variable to check if the float is already sorted
+sorted = [1:length(profile_numbers)]';
+if indices == sorted
+ % indeed it is, so save work and just return the input one :)
+ sorted_float = p_float;
+ return
+end
+
+% sorting required
+sorted_float = {};
+
+% indices have already been taken so just run through them
+for i = 1:length(p_float)
+ sorted_float{i} = p_float{indices(i)};
+end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+float/sort_profile_data.m b/lib/vendor/nemo2profilelib/+nemo/+float/sort_profile_data.m
new file mode 100644
index 0000000..4747285
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+float/sort_profile_data.m
@@ -0,0 +1,26 @@
+function [ sorted_float ] = sort_profile_data( p_float )
+%SORT_PROFILE_DATA Sorts the profile data of the given float ascending by pressure.
+% Sorts every CTD profile ascending by pressure of the given float.
+%
+% Parameters:
+% p_float: The float containing the CTD data to be sorted.
+%
+% Returns:
+% sorted_float: Copy of the float with sorted CTD data.
+
+
+%% Initialize return variable
+sorted_float = false;
+
+%% Parameter check
+if (~iscell(p_float))
+ disp([mfilename ': Unknown input type! Please check your input parameter!']);
+ return
+end
+
+%% Sort profile data by time
+sorted_float = cellfun(@nemo.profile.sort_profile_data, p_float, 'UniformOutput', false);
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+ftp/upload.m b/lib/vendor/nemo2profilelib/+nemo/+ftp/upload.m
new file mode 100644
index 0000000..0dea90a
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+ftp/upload.m
@@ -0,0 +1,137 @@
+function [ is_successful ] = upload( p_config, p_nemo_data )
+%ftp_server_upload Uploads profiles to the ftp.awi.de server as user argo.
+% If p_nemo_data is given, only the given profiles will be uploaded.
+% Otherwise all profiles on the harddisk will be uploaded to the server
+% as defined in p_config.
+% Some default names are being ignored.
+% Existing files on the server will be overwritten. Files
+% existing ONLY on the server will not be touched.
+%
+% Parameters:
+% p_config: The nemo configuration.
+% p_nemo_data: Optional, the nemo data that will be uploaded to
+% the server.
+
+
+%% Initialize return variables
+is_successful = false;
+
+%% Check input parameter
+if (~isstruct(p_config) || ~isfield(p_config, 'FTP')) % display a warning
+ disp([ mfilename ': Please provide valid nemo configuration!']);
+ return;
+end
+
+if (exist('p_files_to_upload', 'var') && ~iscell(p_nemo_data))
+ disp([ mfilename ': Please provide a cell of strings in p_files_to_upload!']);
+ return;
+end
+
+%% Set up server connection
+
+try % connecting to ftp server
+ ftp_server = ftp( ...
+ p_config.FTP.server, ...
+ p_config.FTP.username, ...
+ p_config.FTP.password ...
+ );
+catch error
+ disp([mfilename sprintf(': Failed to connect to server!\n') error]);
+ return;
+end
+
+% change to correct folder if necessary
+if (~strcmp(cd(ftp_server), p_config.FTP.remote_folder))
+ cd(ftp_server, p_config.FTP.remote_folder);
+end
+
+%% Start upload process
+
+if exist('p_nemo_data', 'var') % upload files that have been given
+ for i = 1:length(p_nemo_data)
+ for k = 1:length(p_nemo_data{i})
+ profile_filename = [ ...
+ sprintf('%04d', p_nemo_data{i}{k}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ '_' ...
+ sprintf('%04d', p_nemo_data{i}{k}.PROFILE_TECHNICAL_DATA.xmit_profile_number) ...
+ '.profile'
+ ];
+ mkdir( ...
+ ftp_server, ...
+ [ ...
+ p_config.FTP.remote_folder ...
+ p_config.FTP.folder_separator ...
+ sprintf('%04d', p_nemo_data{i}{k}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ ] ...
+ );
+ cd( ...
+ ftp_server, ...
+ [ ...
+ p_config.FTP.remote_folder ...
+ p_config.FTP.folder_separator ...
+ sprintf('%04d', p_nemo_data{i}{k}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ ] ...
+ );
+ mput(ftp_server, ...
+ [ ...
+ p_config.OUTPUT_FILES.output_path ...
+ sprintf('%04d', p_nemo_data{i}{k}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ p_config.GENERAL.folder_separator ...
+ profile_filename ...
+ ] ...
+ );
+ end
+ end
+
+else
+
+ directory_content = dir(p_config.OUTPUT_FILES.output_path); % should contain all float directories
+
+ % run through every content of the folder
+ for current = 1:size(directory_content, 1)
+ if (directory_content(current).isdir)
+ % create directory
+ mkdir(ftp_server, ...
+ [ ...
+ p_config.FTP.remote_folder ...
+ p_config.FTP.folder_separator ...
+ directory_content(current).name ...
+ ] ...
+ );
+ % switch to it on the server side
+ cd(ftp_server, [p_config.FTP.remote_folder p_config.FTP.folder_separator directory_content(current).name]);
+ % upload all .profile files
+ current_profiles = dir([p_config.OUTPUT_FILES.output_path directory_content(current).name p_config.GENERAL.folder_separator '*.profile']);
+ for i = 1:size(current_profiles, 1)
+ if (strcmp(current_profiles(i).name, 'Startup_Test_Message.profile') ...
+ || strcmp(current_profiles(i).name, 'MTM_Report_Message.profile') ...
+ || strcmp(current_profiles(i).name, 'nemo_0NaN_NaN.profile'))
+ continue % skip some default names
+ end
+ % upload the file
+ mput(ftp_server, [p_config.OUTPUT_FILES.output_path ...
+ directory_content(current).name p_config.GENERAL.folder_separator current_profiles(i).name]);
+ end
+ end
+ end
+
+end
+
+
+
+
+%% Close server connection
+
+try % closing the connection
+ close(ftp_server);
+catch error
+ disp([mfilename sprintf(': Closing connection to server failed:\n') getReport(error)]);
+end
+
+is_successful = true;
+
+return
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+load/additional_content.m b/lib/vendor/nemo2profilelib/+nemo/+load/additional_content.m
new file mode 100644
index 0000000..e6e1cd8
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+load/additional_content.m
@@ -0,0 +1,29 @@
+function [ additional_content ] = additional_content( p_config )
+%LOAD_ADDITIONAL_CONTENT Loads content that is defined in [ADDITIONAL_CONTENT] section of the global configuration file.
+
+
+%% Initialize return variable
+additional_content = {};
+
+%% Load all additional content
+
+ice_cover_location = p_config.ADDITIONAL_CONTENT.antarctic_sea_ice_coverage_file;
+grid_location = p_config.ADDITIONAL_CONTENT.antarctic_grid_file;
+
+additional_content.antarctic_latitudes = ...
+ hdfread(grid_location, '/Latitudes', 'Index', {[1 1],[1 1],[1328 1264]});
+additional_content.antarctic_longitudes = ...
+ hdfread(grid_location, '/Longitudes', 'Index', {[1 1],[1 1],[1328 1264]});
+additional_content.antarctic_ice_concentration = ...
+ hdfread(ice_cover_location, '/ASI Ice Concentration', 'Index', {[1 1],[1 1],[1328 1264]});
+% get etopo
+[additional_content.etopo_z, additional_content.etopo_refvec] = ...
+ etopo(p_config.ADDITIONAL_CONTENT.etopo_file, 1, ...
+ p_config.PLOT_OVERVIEW_SOUTH.latitude_limit, ...
+ p_config.PLOT_OVERVIEW_SOUTH.longitude_limit);
+% load moorings
+additional_content.moorings = ...
+ nemo.load.moorings(p_config.ADDITIONAL_CONTENT.moorings_file);
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+load/config.m b/lib/vendor/nemo2profilelib/+nemo/+load/config.m
new file mode 100644
index 0000000..2a27547
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+load/config.m
@@ -0,0 +1,110 @@
+function [ config ] = config( p_filename, p_force_load )
+%LOAD_CONFIG Loads the given config file.
+%
+% Parameters:
+% p_filename: String, absolute or relative filepath to the target file.
+% It is recommended to give the absolute filepath.
+%
+% Returns: Struct, containing the sections and member of the
+% configuration file.
+%
+
+%% Initialize input parameter
+config = false;
+
+if ~exist('p_force_load', 'var')
+ p_force_load = false;
+end
+
+%% Parameter check
+parameter_error = false;
+
+if (~ischar(p_filename))
+ warning([mfilename ': Please check input parameter. p_filename is not a string!']);
+ parameter_error = true;
+elseif ~p_force_load
+ % get filename details
+ [pathstr, name, ext] = fileparts(p_filename);
+ if (~strcmp(ext, '.conf'))
+ warning([mfilename ': Please check input parameter. Wrong file extension! Should be .conf!']);
+ parameter_error = true;
+ end
+end
+
+if parameter_error
+ return; % return if parameter check has not been passed successfully
+else
+ clear parameter_error;
+end
+
+%% Check if file exists
+if exist(p_filename, 'file') ~= 2
+ return;
+end
+
+%% Load configuration into variable
+
+% initialize all required variables
+config = {};
+current_section = '';
+comment_char = '%'; % character to indicate comments
+section_char = '[';
+
+% open file
+file_id = fopen(p_filename);
+fseek(file_id, 0, 'bof');
+
+
+% read file line by line
+current_line = fgetl(file_id);
+while (ischar(current_line))
+ if length(current_line) == 0 || strcmp(current_line(1), comment_char)
+ current_line = fgetl(file_id);
+ continue
+ end
+
+ switch current_line(1)
+ case section_char % this indicates a new section
+ current_line = strtrim(current_line);
+ current_section = current_line(2:end-1);
+ read_section
+ end
+ %current_line = fgetl(file_id);
+end
+
+fclose(file_id);
+
+ function read_section
+ % read complete section
+ current_line = fgetl(file_id);
+ while ischar(current_line) && ~isempty(current_line) ...
+ && ~strcmp(current_line(1), section_char)
+ if strcmp(current_line(1), comment_char) % it is a comment line
+ current_line = fgetl(file_id);
+ continue
+ end
+
+ % if it contains a comment char anywhere, just take the string
+ % before it
+ found_comment = strfind(current_line, comment_char);
+ if ~isempty(found_comment)
+ current_line = current_line(1:found_comment(1)-1);
+ end
+
+ % get variable name and value
+ [token, remain] = strtok(current_line);
+ % try to convert remain to a number
+ remain_as_num = str2num(strtrim(remain));
+ if (~isempty(remain_as_num))
+ config.(current_section).(token(2:end)) = remain_as_num;
+ else
+ config.(current_section).(token(2:end)) = strtrim(remain);
+ end
+
+ current_line = fgetl(file_id);
+ end
+ end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+load/data.m b/lib/vendor/nemo2profilelib/+nemo/+load/data.m
new file mode 100644
index 0000000..033be95
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+load/data.m
@@ -0,0 +1,87 @@
+function [ nemo_data ] = data(p_path)
+%LOAD_DATA Loads nemo data from the file structure into memory.
+%
+% Parameters:
+% p_path: Absolute or relative filepath to the file structure
+% containing the nemo data.
+%
+% Returns: Struct, containing loaded nemo data from the text files.
+
+%% Initialize input parameter
+nemo_data = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~ischar(p_path))
+ warning([mfilename ': Please check input parameter. p_path is not a string!']);
+ parameter_error = true;
+end
+
+if parameter_error
+ return; % return if parameter check has not been passed successfully
+else
+ clear parameter_error;
+end
+
+if (~exist('p_folder_separator', 'var'))
+ p_folder_separator = '\';
+end
+
+% check if last character is a \
+if (~strcmp(p_path(end), p_folder_separator))
+ p_path = [p_path p_folder_separator];
+end
+
+%% Read profiles
+
+nemo_folder_names = dir(p_path); % get all elements in given directory
+folders_to_exclude = {'.', '..'}; % these folders will be excluded from the list
+nemo_folder_names = exclude_files(nemo_folder_names);
+nemo_folder_names = exclude_elements(nemo_folder_names, folders_to_exclude, 'dir');
+
+%% Loop through every float
+
+files_to_exclude = { ...
+ 'Startup_Test_Message.profile', ...
+ 'MTM_Report_Message.profile', ...
+ 'nemo_0NaN_NaN.profile' ...
+ };
+
+if (isempty(nemo_folder_names))
+ nemo_data = nemo.load.single_float(p_path, p_folder_separator, files_to_exclude);
+ return;
+end
+
+nemo_data = {}; % initialize return variable as struct
+nemo_data_count = 0;
+
+for o_float_index = 1:length(nemo_folder_names) % every float directory
+ % getting the absolute path to the current directory
+ current_dir = [p_path nemo_folder_names(o_float_index).name];
+ % get all files in it
+ current_files = dir(fullfile([current_dir p_folder_separator], '*.profile'));
+ current_files = exclude_elements(current_files, files_to_exclude, 'dir');
+
+ profile_count = length(current_files);
+
+ if (profile_count > 0)
+ current_profiles = {};
+
+ for o_profile_index = 1:profile_count
+ % read current profile
+ profile = nemo.profile.load(fullfile([current_dir p_folder_separator], current_files(o_profile_index).name));
+ current_profiles{o_profile_index} = profile;
+ clear profile;
+ end
+
+ nemo_data_count = nemo_data_count + 1;
+ nemo_data{nemo_data_count} = current_profiles;
+ clear current_profiles;
+ end
+
+end
+
+return
+
+end
diff --git a/lib/vendor/nemo2profilelib/+nemo/+load/float_metadata.m b/lib/vendor/nemo2profilelib/+nemo/+load/float_metadata.m
new file mode 100644
index 0000000..2e6f6bc
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+load/float_metadata.m
@@ -0,0 +1,34 @@
+function [ float_metadata ] = float_metadata( p_filename )
+%FLOAT_METADATA Loads the given metadata file.
+% If p_filename is a directory, all files with the .xml extension are
+% being selected and loaded.
+%
+% Parameters:
+% p_filename: The file or folder to be loaded.
+%
+% Returns:
+% float_metadata: The loaded metadata files in a cell.
+
+%% Initialize return value
+float_metadata = false;
+
+%% Parameter is already being checked in nemo.load.xml_file
+float_metadata = nemo.load.xml_file(p_filename);
+
+switch (class(float_metadata))
+ case 'struct'
+ float_metadata.MISSION_PARAMETERS = ...
+ nemo.float.process_mission_parameter(float_metadata.MISSION_PARAMETER_STRING);
+ case 'cell'
+ for i = 1:length(float_metadata)
+ float_metadata{i}.MISSION_PARAMETERS = ...
+ nemo.float.process_mission_parameter(float_metadata{i}.MISSION_PARAMETER_STRING);
+ end
+ otherwise
+ warning([mfilename ': Something went wrong while loading the xml file(s)!']);
+ return;
+end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+load/float_transmission_info.m b/lib/vendor/nemo2profilelib/+nemo/+load/float_transmission_info.m
new file mode 100644
index 0000000..e03e46b
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+load/float_transmission_info.m
@@ -0,0 +1,48 @@
+function [ processed_inline ] = float_transmission_info( p_config, p_imei )
+%FLOAT_TRANSMITTION_INFO Reads the transmittion information stored in the mail body.
+% Loads all mail bodies of the given IMEI and stores the processed text
+% in a cell.
+%
+% Parameters:
+% p_config: The nemo configuration.
+% p_imei: The IMEI to load the information.
+%
+% Returns:
+% processed_inline: A cell containing the processed information.
+
+%% Initialize return variables
+processed_inline = false;
+
+%% TODO: Parameter check
+
+
+%% Load inline file(s)
+txt = ['txt' p_config.GENERAL.folder_separator];
+if (~ischar(p_imei))
+ imei = int2str(p_imei);
+else
+ imei = p_imei;
+end
+
+% create full filepath
+filepath = p_config.MAIL.storage_directory;
+
+if (p_config.MAIL.sort_by_imei)
+ filepath = [filepath imei p_config.GENERAL.folder_separator];
+end
+if (p_config.MAIL.separate_sbd_and_txt)
+ filepath = [filepath txt];
+end
+filenames = struct2table(dir([filepath '*.txt']));
+if (isempty(filenames.name))
+ return;
+end
+absolute_filenames = cellfun(@(name) [filepath p_config.GENERAL.folder_separator name], filenames.name, 'UniformOutput', false);
+processed_inline = cellfun(@read_file, absolute_filenames);
+
+ function inline = read_file(filename)
+ inline = nemo.mail.process_inline(fileread(filename));
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+load/floats2nemostruct.m b/lib/vendor/nemo2profilelib/+nemo/+load/floats2nemostruct.m
new file mode 100644
index 0000000..35142a5
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+load/floats2nemostruct.m
@@ -0,0 +1,56 @@
+function [ nemo_struct, startup_messages ] = floats2nemostruct( p_config, p_metadata )
+%SBD2OPTIMARE Converts and combines the float .sbd data into the nemo structure.
+% Uses nemo.sbd.decode_float function to decode the profiles and
+% nemo.convert.combined_float2nemostruct to convert the combined profiles
+% to the nemo structure.
+%
+% Parameters:
+% p_config: The nemo configuration.
+% p_metadata: The metadata information about the floats to process.
+%
+% Returns:
+% nemo_struct: The resulting nemo struct.
+
+%% Run through metadata and process every float
+nemo_struct = cell(length(p_metadata), 1);
+startup_messages = cell(length(p_metadata), 1);
+
+if (isa(p_metadata, 'struct'))
+ tmp = p_metadata;
+ p_metadata = {};
+ p_metadata{1} = tmp;
+ clear tmp;
+end
+
+for i = 1:length(p_metadata)
+ % copy all metadata to new struct
+ current_float = p_metadata{i};
+ imei_int = p_metadata{i}.GENERAL_INFO.IMEI;
+ %serial_str = sprintf('%04d', p_metadata{i}.GENERAL_INFO.SERIAL);
+
+ % collect all information from harddisk
+ [decoded_sbd, sbd_messages_info] = nemo.sbd.decode_float(p_config, imei_int);
+ current_float.DECODED_SBD = decoded_sbd;
+ current_float.SBD_MESSAGES_INFO = sbd_messages_info;
+ transmission_info = nemo.load.float_transmission_info(p_config, imei_int);
+ current_float.TRANSMISSION_INFO = transmission_info;
+
+ % convert startup messages
+ startup_messages{i} = nemo.float.extract_startup_message(current_float);
+ % convert this information to the nemo structure
+ nemo_struct{i} = nemo.convert.combined_float2nemostruct(current_float);
+ % add startup message
+ if ~isempty(startup_messages{i}) ...
+ && ~isempty(startup_messages{i}{end}) ...
+ && ~isa(nemo_struct{i}, 'logical')
+ nemo_struct{i} = cellfun(@add_startup_message, nemo_struct{i}, 'UniformOutput', false);
+ end
+
+end
+
+ function [ p_float ] = add_startup_message(p_float)
+ p_float.STARTUP_MESSAGE = startup_messages{i}{end};
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+load/latest_profile.m b/lib/vendor/nemo2profilelib/+nemo/+load/latest_profile.m
new file mode 100644
index 0000000..1aaba6c
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+load/latest_profile.m
@@ -0,0 +1,46 @@
+function [ nemo_profile, profile_count ] = latest_profile( p_config, p_float_number )
+%LATEST_PROFILE Loads the latest profile of the given float.
+%
+
+%% Initialize return variable
+nemo_profile = {};
+
+%% Parameter check
+if ~isstruct(p_config) || ~isa(p_float_number, 'double')
+ disp([mfilename ': Wrong parameters, please check your input!']);
+ return;
+end
+
+%% Determine the latest profile file
+profile_files = dir( ...
+ [ ...
+ p_config.OUTPUT_FILES.output_path ...
+ sprintf('%04d', p_float_number) ...
+ p_config.GENERAL.folder_separator ...
+ '*.profile' ...
+ ] ...
+);
+
+profile_files = {profile_files.name};
+profile_files = sort(profile_files);
+
+if isempty(profile_files)
+ profile_count = 0;
+ return
+end
+filename = profile_files{end};
+profile_count = length(profile_files);
+
+%% Now load the profile if available
+nemo_profile = nemo.profile.load( ...
+ [ ...
+ p_config.OUTPUT_FILES.output_path ...
+ sprintf('%04d', p_float_number) ...
+ p_config.GENERAL.folder_separator ...
+ filename ...
+ ] ...
+);
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+load/moorings.m b/lib/vendor/nemo2profilelib/+nemo/+load/moorings.m
new file mode 100644
index 0000000..537232c
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+load/moorings.m
@@ -0,0 +1,103 @@
+function [ moorings ] = moorings( p_filename )
+%LOAD_MOORINGS Loads all moorings from a file into memory
+% Almost the same procedure as nemo.load.config(). It has some changes
+% to make it useful for loading moorings configuration file.
+
+%% Initialize input parameter
+moorings = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~ischar(p_filename))
+ warning([mfilename ': Please check input parameter. p_filename is not a string!']);
+ parameter_error = true;
+else
+ % get filename details
+ if ~exist(p_filename, 'file')
+ warning([mfilename ': Please check input parameter, given file does not exist!']);
+ parameter_error = true;
+ end
+end
+
+if parameter_error
+ return; % return if parameter check has not been passed successfully
+else
+ clear parameter_error;
+end
+
+%% Load profile into variable
+
+% initialize all required variables
+moorings = {};
+current_section = '';
+comment_char = '%'; % character to indicate comments
+section_char = '['; % character indicating new section
+mooring_count = 1;
+
+% open file
+file_id = fopen(p_filename);
+fseek(file_id, 0, 'bof');
+
+
+% read file line by line
+current_line = fgetl(file_id);
+while (ischar(current_line))
+ if length(current_line) == 0 || strcmp(current_line(1), comment_char)
+ current_line = fgetl(file_id);
+ continue
+ end
+
+ switch current_line(1)
+ case section_char % this indicates a new section
+ current_line = strtrim(current_line);
+ current_section = current_line(2:end-1);
+ moorings{mooring_count}.name = current_section;
+ read_section
+ mooring_count = mooring_count + 1;
+ end
+ %current_line = fgetl(file_id);
+end
+
+fclose(file_id);
+
+ function read_section
+ % read complete section
+ current_line = fgetl(file_id);
+ while ischar(current_line) && ~isempty(current_line) ...
+ && ~strcmp(current_line(1), section_char)
+
+ % ignore comment char
+ if strcmp(current_line(1), comment_char)
+ current_line = fgetl(file_id);
+ continue
+ end
+
+ % if it contains a comment char anywhere, just take the string
+ % before it
+ found_comment = strfind(current_line, comment_char);
+ if ~isempty(found_comment)
+ current_line = current_line(1:found_comment(1)-1);
+ end
+
+ % get variable name and value
+ [token, remain] = strtok(current_line);
+ if (strcmp(token(2:end), 'pong_time'))
+ moorings{mooring_count}.(token(2:end)) = strtrim(remain);
+ else
+ % try to convert remain to a number
+ remain_as_num = str2num(strtrim(remain));
+ if (~isempty(remain_as_num))
+ moorings{mooring_count}.(token(2:end)) = remain_as_num;
+ else
+ moorings{mooring_count}.(token(2:end)) = strtrim(remain);
+ end
+ end
+
+ current_line = fgetl(file_id);
+ end
+ end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+load/rfb_config.m b/lib/vendor/nemo2profilelib/+nemo/+load/rfb_config.m
new file mode 100644
index 0000000..2baafb2
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+load/rfb_config.m
@@ -0,0 +1,101 @@
+function [ config ] = rfb_config( p_filename )
+%RFB_CONFIG Loads the given config file.
+%
+% Parameters:
+% p_filename: String, absolute or relative filepath to the target file.
+% It is recommended to give the absolute filepath.
+%
+% Returns: Struct, containing the sections and member of the
+% configuration file.
+%
+
+%% Initialize input parameter
+config = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~ischar(p_filename))
+ warning([mfilename ': Please check input parameter. p_filename is not a string!']);
+ parameter_error = true;
+else
+ % get filename details
+ [pathstr, name, ext] = fileparts(p_filename);
+ if (~strcmp(ext, '.conf'))
+ warning([mfilename ': Please check input parameter. Wrong file extension! Should be .conf!']);
+ parameter_error = true;
+ end
+end
+
+if parameter_error
+ return; % return if parameter check has not been passed successfully
+else
+ clear parameter_error;
+end
+
+%% Load profile into variable
+
+% initialize all required variables
+config = {};
+current_section = '';
+comment_char = '%'; % character to indicate comments
+section_char = '[';
+
+% open file
+file_id = fopen(p_filename);
+fseek(file_id, 0, 'bof');
+
+
+% read file line by line
+current_line = fgetl(file_id);
+while (ischar(current_line))
+ if length(current_line) == 0 || strcmp(current_line(1), comment_char)
+ current_line = fgetl(file_id);
+ continue
+ end
+
+ switch current_line(1)
+ case section_char % this indicates a new section
+ current_line = strtrim(current_line);
+ current_section = current_line(2:end-1);
+ read_section
+ end
+ %current_line = fgetl(file_id);
+end
+
+fclose(file_id);
+
+ function read_section
+ % read complete section
+ current_line = fgetl(file_id);
+ while ischar(current_line) && ~isempty(current_line) ...
+ && ~strcmp(current_line(1), section_char)
+ if strcmp(current_line(1), comment_char) % it is a comment line
+ current_line = fgetl(file_id);
+ continue
+ end
+
+ % if it contains a comment char anywhere, just take the string
+ % before it
+ found_comment = strfind(current_line, comment_char);
+ if ~isempty(found_comment)
+ current_line = current_line(1:found_comment(1)-1);
+ end
+
+ % get variable name and value
+ [token, remain] = strtok(current_line);
+ % try to convert remain to a number
+ remain_as_num = str2num(strtrim(remain));
+ if (~isempty(remain_as_num))
+ config.(current_section).(token(2:end)) = remain_as_num;
+ else
+ config.(current_section).(token(2:end)) = strtrim(remain);
+ end
+
+ current_line = fgetl(file_id);
+ end
+ end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+load/single_float.m b/lib/vendor/nemo2profilelib/+nemo/+load/single_float.m
new file mode 100644
index 0000000..319ed14
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+load/single_float.m
@@ -0,0 +1,40 @@
+function [ float_data ] = single_float( p_path, p_folder_separator, p_files_to_exclude )
+%SINGLE_FLOAT Loads a float from the harddisk.
+% Loads all profiles of a float in the given path.
+%
+% Parameters:
+% p_path: The filepath where the .profile files are stored.
+% p_folder_separator: The folder separator character.
+% p_files_to_exclude: List of files that will be ignored.
+%
+% Returns:
+% float_data: The loaded profiles.
+
+%% Initialize return variable
+float_data = {};
+
+%% Get all files in the folder and load profiles
+if (~exist('p_folder_separator', 'var'))
+ p_folder_separator = '\';
+end
+current_files = dir(fullfile([p_path p_folder_separator], '*.profile'));
+if (exist('p_files_to_exclude', 'var'))
+ current_files = exclude_elements(current_files, p_files_to_exclude, 'dir');
+end
+
+profile_count = length(current_files);
+
+if (profile_count > 0)
+ float_data = {};
+
+ for o_profile_index = 1:profile_count
+ % read current profile
+ profile = nemo.profile.load(fullfile([p_path p_folder_separator], current_files(o_profile_index).name));
+ float_data{o_profile_index} = profile;
+ clear profile;
+ end
+
+end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+load/xml_file.m b/lib/vendor/nemo2profilelib/+nemo/+load/xml_file.m
new file mode 100644
index 0000000..06e4062
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+load/xml_file.m
@@ -0,0 +1,61 @@
+function [ xml_file ] = xml_file( p_filename, p_filemask )
+%FLOAT_METADATA Loads xml files into a matlab cell.
+% Loads either one xml file or all xml files from the given directory.
+%
+% Parameter:
+% p_filename: string, if empty the complete directory is being loaded.
+% p_filemask: string, the filemask of the files to be selected, for
+% example: *float_*
+%
+% Returns:
+% xml_file: cell, containing all files that have been read.
+
+%% Initialize return variables
+xml_file = false;
+
+%% Parameter check
+parameter_error = false;
+file_only = false;
+
+if (~ischar(p_filename) || (exist('p_filemask', 'var') && ~ischar(p_filemask)))
+ parameter_error = true;
+end
+
+if (~isdir(p_filename))
+ file_only = true;
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% Check operating system
+if (ismac || isunix)
+ folder_separator = '/';
+elseif (ispc)
+ folder_separator = '\';
+end
+
+%% Load metadata files
+if (file_only)
+ if ~exist(p_filename, 'file') % warn user
+ warning([mfilename ': Float metadata file ' p_filename ' does not exist!']);
+ return
+ end
+ xml_file = utils.xml_read(p_filename);
+else
+ if (exist('p_filemask', 'var'))
+ filenames = struct2table(dir([p_filename folder_separator p_filemask '.xml']));
+ else
+ filenames = struct2table(dir([p_filename folder_separator '*.xml']));
+ end
+
+ absolute_filenames = cellfun(@(name) [p_filename folder_separator name], filenames.name, 'UniformOutput', false);
+ xml_file = cellfun(@(name) utils.xml_read(name), absolute_filenames, 'UniformOutput', false);
+end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+mail/connect.m b/lib/vendor/nemo2profilelib/+nemo/+mail/connect.m
new file mode 100644
index 0000000..eeb352e
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+mail/connect.m
@@ -0,0 +1,62 @@
+function [ imapstore ] = connect( p_config )
+%CONNECT Connects with the specified server details where nemo emails are stored.
+% This functions connects to the mail server given in the config
+% parameter. Therefore the java library javax.mail.jar (javaMail) and
+% activation.jar (JavaBeans Activation Framework) is required. There is no
+% disconnect function, use 'clear imapstore' instead.
+% javaMail Documentation: https://javamail.java.net/nonav/docs/api/
+%
+% Parameter:
+% p_config: struct, containing the content of the nemo config file.
+%
+% Returns:
+% imapstore: IMAPSSLSTORE/IMAPSTORE java object, false on fail.
+
+%% Initialize return variable
+imapstore = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~isstruct(p_config))
+ parameter_error = true;
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+if (~isfield(p_config, 'MAIL'))
+ disp('No MAIL section found in p_config.');
+ return;
+end
+
+%% Prepare connection
+try
+ props = java.util.Properties; % default imap properties
+ props.put('mail.imap.port', p_config.MAIL.port);
+ props.put('mail.imap.timeout', p_config.MAIL.imap_timeout);
+ props.put('mail.imaps.connectiontimeout', p_config.MAIL.imaps_connection_timeout);
+ session = javax.mail.Session.getInstance(props); % create a session
+ if (p_config.MAIL.ssl) % get the ssl store object
+ imapstore = session.getStore('imaps');
+ else % get the store object
+ imapstore = session.getStore('imap');
+ end
+ imapstore.connect( ...
+ p_config.MAIL.server, ...
+ p_config.MAIL.port, ...
+ p_config.MAIL.username, ...
+ p_config.MAIL.password ...
+ );
+catch
+ warning('Something failed during the establishment of the imap connection!');
+ imapstore = false;
+ return;
+end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+mail/export_attachment.m b/lib/vendor/nemo2profilelib/+nemo/+mail/export_attachment.m
new file mode 100644
index 0000000..41f96bf
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+mail/export_attachment.m
@@ -0,0 +1,50 @@
+function [ Boolean ] = export_attachment( Attachment, AbsoluteFilename )
+%EXPORT_ATTACHMENT Exports the given attachment to the given filename.
+% Exports the attachment (type of com.sun.mail.util.BASE64DecoderStream)
+% to the given filename.
+%
+% Parameters:
+% Attachment: The attachment to be saved.
+% AbsoluteFilename: The filename where the attachment is being
+% exported to.
+%
+% Returns:
+% Boolean: True if successful.
+
+%% Initialize return variable
+Boolean = false;
+
+%% Check parameter
+
+if (~isa(Attachment, 'com.sun.mail.util.BASE64DecoderStream') ...
+ || ~ischar(AbsoluteFilename))
+ warning([mfilename ': Input parameter check failed!']);
+ return
+end
+
+%% Create file and export attachment to it
+
+[Path, ~, ~] = fileparts(AbsoluteFilename);
+
+if (~isdir(Path)) % create it
+ mkdir(Path);
+end
+
+% save every byte in attachment to file
+File = java.io.File(AbsoluteFilename);
+OutputStream = java.io.FileOutputStream(File);
+
+Byte = Attachment.read();
+while (Byte ~= -1)
+ OutputStream.write(Byte);
+ Byte = Attachment.read();
+end
+
+OutputStream.flush(); % prevent loosing bytes in write process
+OutputStream.close();
+Attachment.close();
+
+Boolean = true;
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+mail/extract.m b/lib/vendor/nemo2profilelib/+nemo/+mail/extract.m
new file mode 100644
index 0000000..0262492
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+mail/extract.m
@@ -0,0 +1,63 @@
+function [ FromArray, Subject, Inline, AttachmentArray ] = extract( Message )
+%EXTRACT Extracts basic information from the given message.
+% Extracts the message created by the javax.mail library.
+%
+% Parameters:
+% Message: The message to be extracted from.
+%
+% Returns:
+% FromArray: All senders addresses (usually just one)
+% Subject: Subject of the message.
+% Inline: The message body.
+% AttachmentArray: All attachments of the message.
+
+%% Initialize return variables
+FromArray = false;
+Subject = false;
+Inline = '';
+AttachmentArray = false;
+
+%% Get from address
+FromArray = Message.getFrom();
+nFrom = FromArray.length;
+% convert to matlab char
+tmp = {};
+for i = 1:nFrom
+ tmp{i} = char(FromArray(i));
+end
+FromArray = tmp;
+clear tmp;
+
+%% Get subject
+Subject = char(Message.getSubject());
+
+%% Get inline text and attachments
+MessageContent = Message.getContent();
+if (~isempty(strfind(Message.getContentType, 'text/plain')))
+ Inline = MessageContent;
+ AttachmentArray = {};
+ return
+end
+nBodies = MessageContent.getCount();
+if (nBodies > 0)
+ AttachmentArray = {};
+end
+
+for iBody = 0:nBodies - 1
+ BodyPart = MessageContent.getBodyPart(iBody);
+ if (BodyPart.isMimeType('text/plain') ...
+ || BodyPart.isMimeType('text/html'))
+ Inline = char(BodyPart.getContent());
+ elseif (BodyPart.isMimeType('attachment') ...
+ || BodyPart.isMimeType('application/x-zip-compressed'))
+ AttachmentArray{iBody, 1} = BodyPart.getDataHandler.getName();
+ AttachmentArray{iBody, 2} = BodyPart.getDataHandler.getInputStream();
+ else
+ disp([mfilename ': MimeType ' char(BodyPart.getContentType()) ' not supported!']);
+ end
+
+end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+mail/fetch_messages.m b/lib/vendor/nemo2profilelib/+nemo/+mail/fetch_messages.m
new file mode 100644
index 0000000..f39ef0b
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+mail/fetch_messages.m
@@ -0,0 +1,69 @@
+function [ messages, folder ] = fetch_messages( p_imapstore, p_foldername, p_searchterm, p_read_only )
+%FETCH_UNREAD Fetches all messages in the given folder.
+% Fetches all messages that match the given searchterm from the given
+% folder.
+%
+% Parameters:
+% p_imapstore: The imapstore object of javax.mail library.
+% p_foldername: The foldername where the messages will be
+% fetched from.
+% p_searchterm: The searchterm created with javax.mail library.
+% p_read_only: If true, the folder will be opened as read
+% only.
+%
+% Returns:
+% messages: The messages that match the searchterm.
+% folder: The folder object.
+
+%% Initialize return variables
+messages = false;
+
+if (~exist('p_read_only', 'var'))
+ p_read_only = true;
+end
+
+%% Parameter check
+parameter_error = false;
+
+if (~ischar(p_foldername))
+ parameter_error = true;
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% Check connection
+
+if (~p_imapstore.isConnected())
+ disp('IMAPStore not connected, trying to reconnect...');
+ p_imapstore.connect();
+ if (~p_imapstore.isConnected())
+ warning('IMAPStore reconnect failed. Please check your configuration!');
+ return;
+ else
+ disp('... success!');
+ end
+end
+
+%% Get and open folder
+folder = p_imapstore.getFolder(p_foldername);
+if (~p_read_only)
+ folder.open(folder.READ_WRITE);
+else
+ folder.open(folder.READ_ONLY);
+end
+
+%% Fetch messages
+if (isa(p_searchterm, 'logical') || strcmp(p_searchterm, ''))
+ messages = folder.getMessages();
+else
+ messages = folder.search(p_searchterm);
+end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+mail/fetch_unread.m b/lib/vendor/nemo2profilelib/+nemo/+mail/fetch_unread.m
new file mode 100644
index 0000000..0e02e12
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+mail/fetch_unread.m
@@ -0,0 +1,60 @@
+function [ unread_messages, folder ] = fetch_unread( p_imapstore, p_foldername )
+%FETCH_UNREAD Fetches all messages that are flagged as unread on the server.
+% Fetches all messages that are flagged as unread in the given folder.
+%
+% Parameters:
+% p_imapstore: The imapstore object.
+% p_foldername: The folder name where the messages are stored.
+%
+% Returns:
+% unread_messages: The messages that have been fetched.
+% folder: The folder object.
+
+%% Initialize return variables
+unread_messages = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~ischar(p_foldername))
+ parameter_error = true;
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% Check connection
+
+if (~p_imapstore.isConnected())
+ disp('IMAPStore not connected, trying to reconnect...');
+ p_imapstore.connect();
+ if (~p_imapstore.isConnected())
+ warning('IMAPStore reconnect failed. Please check your configuration!');
+ return;
+ end
+end
+
+%% Get and open folder
+folder = p_imapstore.getFolder(p_foldername);
+folder.open(folder.READ_ONLY);
+
+%% Fetch all unread messages
+
+% there are difficulties accessing static class members of an inner java
+% class. This solution has been found at:
+% http://undocumentedmatlab.com/blog/accessing-internal-java-class-members
+search_flag = javax.mail.Flags(); % create search flag
+tmp = search_flag.getClass.getDeclaredClasses;
+seen_flag = tmp(1).getField('SEEN').get(1);
+clear tmp;
+search_flag.add(seen_flag);
+flagterm = javax.mail.search.FlagTerm(search_flag, false);
+unread_messages = folder.search(flagterm);
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+mail/process_inline.m b/lib/vendor/nemo2profilelib/+nemo/+mail/process_inline.m
new file mode 100644
index 0000000..9c46a96
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+mail/process_inline.m
@@ -0,0 +1,84 @@
+function [ processed_inline ] = process_inline( p_inline )
+%PROCESS_INLINE Searches the given inline text by the Iridium information and extracts them.
+% Processes the given inline text and extracts the iridium information.
+%
+% Parameters:
+% p_inline: The inline text to be processed.
+%
+% Returns:
+% processed_inline: Struct, containing the found information. Contains
+% false on fail.
+
+%% Initialize return variable
+processed_inline = false;
+
+%% Parameter check
+if (~ischar(p_inline))
+ warning([mfilename ': Wrong parameter given. Please check them carefully!']);
+ return;
+end
+
+%% Initialize values to extract
+utc = 'Time of Session (UTC): ';
+momsn = 'MOMSN: ';
+mtmsn = 'MTMSN: ';
+session_status = 'Session Status: ';
+message_size_in_bytes = 'Message Size (bytes): ';
+unit_location = 'Unit Location: ';
+cep_radius = 'CEPradius = ';
+
+%% Split message by lines
+lines = strsplit(p_inline, '\n');
+
+% find values and store them
+
+location = process_if_available(unit_location);
+if (~isa(location, 'logical'))
+ location = strsplit(strtrim(location));
+ iridium_lat = str2double(location{3});
+ iridium_lon = str2double(location{6});
+else
+ iridium_lat = false;
+ iridium_lon = false;
+end
+
+processed_inline = struct( ...
+ 'TIMEOFSESSION', process_if_available(utc), ...
+ 'MOMSN', process_if_available(momsn), ...
+ 'MTMSN', process_if_available(mtmsn), ...
+ 'SESSIONSTATUS', process_if_available(session_status), ...
+ 'MESSAGESIZE', process_if_available(message_size_in_bytes), ...
+ 'IRIDIUM_LAT', iridium_lat, ...
+ 'IRIDIUM_LON', iridium_lon, ...
+ 'CEPRAD', process_if_available(cep_radius) ...
+);
+
+
+%% Convert to usable matlab values
+if (~isa(processed_inline.TIMEOFSESSION, 'logical'))
+ processed_inline.TIMEOFSESSION = datevec(processed_inline.TIMEOFSESSION, 'ddd mmm dd HH:MM:SS yyyy');
+end
+if (~isa(processed_inline.MOMSN, 'logical'))
+ processed_inline.MOMSN = str2double(processed_inline.MOMSN);
+end
+if (~isa(processed_inline.MTMSN, 'logical'))
+ processed_inline.MTMSN = str2double(processed_inline.MTMSN);
+end
+if (~isa(processed_inline.MESSAGESIZE, 'logical'))
+ processed_inline.MESSAGESIZE = str2double(processed_inline.MESSAGESIZE);
+end
+if (~isa(processed_inline.CEPRAD, 'logical'))
+ processed_inline.CEPRAD = str2double(processed_inline.CEPRAD);
+end
+
+ function value = process_if_available(p_variable)
+ value = false;
+ try
+ value = lines{find(~cellfun(@isempty, strfind(lines, p_variable)))}(length(p_variable):end);
+ catch ex
+ return
+ end
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/devicedata.m b/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/devicedata.m
new file mode 100644
index 0000000..ca0be17
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/devicedata.m
@@ -0,0 +1,65 @@
+function [device,data,status]=devicedata(devicedata)
+
+ % Decode types
+ dd = dec2bin(devicedata,8);
+ data = bin2dec(dd(5:8));
+ device = bin2dec(dd(1:4));
+ status = 1;
+
+ % Set device and data type
+ switch (device)
+ case 1
+ % NEMO float
+ device = 'NEMO Standard ';
+ switch (data)
+ case 0
+ % Test/Startup data
+ data = 'Startup Test Message';
+ case 1
+ % Profile data
+ data = 'Profile Message';
+ case 2
+ % Report data
+ data = 'MTM Report Message';
+ case 3
+ % Recovery data
+ data = 'Recovery Message';
+ case 4
+ % File data
+ data = 'File transmission Message';
+ case 5
+ % Reserved profile data
+ data = 'Reserved profile Message';
+ case 6
+ % Filtered continous profile data
+ data = 'Filtered CTD data Message';
+
+ otherwise
+ % Unknown data
+ data = 'Unknown Message';
+ %disp(['Unknown data type ('+num2str(dd)+')']);
+ status = 0;
+ end
+
+ case 2
+ % CTD Profiler
+ device = 'CTD Profiler/Logger';
+ switch (data)
+ case 1
+ % Profile data
+ data = 'Profile Message';
+
+ otherwise
+ % Unknown data
+ data = 'Unknown Message';
+ %disp(['Unknown data type ('+num2str(dd)+')']);
+ status = 0;
+ end
+
+ otherwise
+ % Unknown device type
+ device = 'Unknown';
+ status = 0;
+ end
+
+end
\ No newline at end of file
diff --git a/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/phext_t2.m b/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/phext_t2.m
new file mode 100644
index 0000000..91f67c3
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/phext_t2.m
@@ -0,0 +1,285 @@
+function [S,offset] = phext_t2(S,offset,k)
+
+% Decode different NEMO profile header extensions type 2 (mission
+% configuration)
+%
+%
+
+% Optimare Sensorsysteme, 24.05.2012 M.Busack
+
+switch (S.DS1_FORMAT(k))
+
+ case 1
+ % Format 1 vom 8-Mar-2012
+ S.SERIAL = S.uD(offset+1)*256 + S.uD(offset);
+ S.AIRPUMPTIME = S.uD(offset+3)*256 + S.uD(offset+2);
+ S.STARTUPTIME = (S.uD(offset+5)*256 + S.uD(offset+4))/60;
+ S.TIME_CYCLE = S.uD(offset+7)*256 + S.uD(offset+6);
+ S.PRES_PROFILE = NaN; %orginal double
+ S.PISTON_MIN = S.uD(offset+13)*256 + S.uD(offset+12);
+ S.PISTON_MAX = S.uD(offset+15)*256 + S.uD(offset+14);
+ S.STARTUPDELAY = S.uD(offset+17)*256 + S.uD(offset+16);
+ S.DESCENT_MODE = S.uD(offset+18);
+ % Byte 19 not used
+ S.SPEED_DESCENT = NaN; %orginal double
+ S.DESCENT_TIMEOUTFACTOR = NaN; %orginal double
+ S.DESCENT_PISTONINTERVAL_MIN = S.uD(offset+28);
+ S.DESCENT_DEPTH_CONTROL = S.uD(offset+29);
+ S.DESCENT_PISTONINTERVAL = S.uD(offset+31)*256 + S.uD(offset+30);
+ S.DESCENT_PISTON_ONTIME = S.uD(offset+32);
+ % Byte 33 not used
+ S.PRES_DESCENT_MARGIN = NaN; %orginal double
+ S.PRES_PARKING = NaN; %orginal double
+ S.PRES_PARKING_HYSTERESE = S.uD(offset+42);
+ % Byte 43 not used
+ S.ATTENUATION_FACTOR = NaN; %orginal double
+ S.TIME_PARKSAMPLE = (S.uD(offset+51)*16777216 + S.uD(offset+50)*65536 + S.uD(offset+49)*256 + S.uD(offset+48))/60;
+ S.PARKING_SAMPLES = S.uD(offset+52);
+ S.PARKING_DELAY = S.uD(offset+53);
+ S.PRES_PARKINGHIGH = S.uD(offset+55)*256 + S.uD(offset+54);
+ S.SAFETYZONE_MARGIN = S.uD(offset+57)*256 + S.uD(offset+56);
+ S.SAFETYZONE_COUNTCHANGE = S.uD(offset+59)*256 + S.uD(offset+58);
+ S.SAFETYZONE_INCREMENT = S.uD(offset+61)*256 + S.uD(offset+60);
+ S.INITIAL_PARKCOUNT = S.uD(offset+63)*256 + S.uD(offset+62);
+ S.SPEED_SAG = NaN; %orginal double
+ S.SAG_TIMEOUTFACTOR = NaN; %orginal double
+ S.ASCENT_MODE = S.uD(offset+72);
+ % Byte 73 not used
+ S.SPEED_ASCENT = NaN; %orginal double
+ S.ASCENT_TIMEOUTFACTOR = NaN; %orginal double
+ S.ASCENT_PISTONINTERVAL_MIN = S.uD(offset+82);
+ S.ASCENT_DEPTH_CONTROL = S.uD(offset+83);
+ S.ASCENT_PISTONINTERVAL = S.uD(offset+85)*256 + S.uD(offset+84);
+ S.ASCENT_PISTON_ONTIME = S.uD(offset+86);
+ % Byte 87 not used
+ S.TEMP_ICEDETECT = NaN; %orginal double
+ S.PRES_ICEUP = S.uD(offset+93)*256 + S.uD(offset+92); %until here verified with sbd 1
+ S.PRES_ICEDOWN = S.uD(offset+95)*256 + S.uD(offset+94);
+ S.PRES_ICEINTERVAL = S.uD(offset+96);
+ S.SUCCESSFUL_ASCENTS = S.uD(offset+97);
+ S.POST_UPCAST_SAMPLES = S.uD(offset+98);
+ S.POST_UPCAST_DELAY = S.uD(offset+99);
+ S.TIME_SURFACE_ATTEMP = S.uD(offset+100);
+ % Byte 101 not used
+ S.TIME_TX = (S.uD(offset+105)*16777216 + S.uD(offset+104)*65536 + S.uD(offset+103)*256 + S.uD(offset+102))/60;
+ S.MULTIMSG = [S.uD(offset+106) S.uD(offset+107) S.uD(offset+108) S.uD(offset+109)];
+ S.ARGOSID = S.uD(offset+110);
+ S.RAFOS_MODULEADR = S.uD(offset+111);
+ S.RECOVERY_START = S.uD(offset+113)*256 + S.uD(offset+112);
+ S.RECOVERY_TX = S.uD(offset+114);
+ % Byte 115 not used
+ S.RECOVERY_NOTX = S.uD(offset+117)*256 + S.uD(offset+116);
+ S.LOGMODE = S.uD(offset+118);
+ S.TESTMODE = S.uD(offset+119);
+ S.TIME_CO2WARMUP = (S.uD(offset+121)*256 + S.uD(offset+120))/60;
+ S.TIME_GPSFIX = (S.uD(offset+123)*256 + S.uD(offset+122))/60;
+ S.PRES_MAXALARM = S.uD(offset+125)*256 + S.uD(offset+124);
+ S.COUNT_MAXALARM = S.uD(offset+127)*256 + S.uD(offset+126);
+ S.CTDCP_FILTER = S.uD(offset+129)*256 + S.uD(offset+128);
+ S.PRES_CTDOFF_MAX = (S.sD(offset+131)*256 + S.uD(offset+130))/10;
+ S.PRES_CTDOFF_MIN = (S.sD(offset+133)*256 + S.uD(offset+132))/10;
+ S.PRES_CTDOFF_CHN = (S.uD(offset+135)*256 + S.uD(offset+134))/10;
+ S.PRES_PCUTOFF = (S.uD(offset+137)*256 + S.uD(offset+136))/10;
+ S.PRES_SAFETY = NaN; %orginal double
+ S.STARTPROFILE = S.uD(offset+143)*256 + S.uD(offset+142);
+ S.ICEGPS_TIMEOUT = S.uD(offset+144);
+ S.ICEIRDM_TIMEOUT = S.uD(offset+145);
+ S.CONFIGTX = S.uD(offset+146);
+ S.RAFOS_ACTIVE = [S.uD(offset+147) S.uD(offset+148) S.uD(offset+149) S.uD(offset+150) S.uD(offset+151)];
+ S.RAFOS_STARTHH = [S.uD(offset+152) S.uD(offset+153) S.uD(offset+154) S.uD(offset+155) S.uD(offset+156)];
+ S.RAFOS_STARTMM = [S.uD(offset+157) S.uD(offset+158) S.uD(offset+159) S.uD(offset+160) S.uD(offset+161)];
+ S.RAFOS_ONMM = [S.uD(offset+163)*256+S.uD(offset+162) S.uD(offset+165)*256+S.uD(offset+164) ...
+ S.uD(offset+167)*256+S.uD(offset+166) S.uD(offset+169)*256+S.uD(offset+168) ...
+ S.uD(offset+171)*256+S.uD(offset+170)];
+ offset = offset + 172;
+
+ case 2
+ % Format 2 vom 23-May-2012
+ S.SERIAL = S.uD(offset+1)*256 + S.uD(offset);
+ S.AIRPUMPTIME = S.uD(offset+3)*256 + S.uD(offset+2);
+ S.STARTUPTIME = (S.uD(offset+5)*256 + S.uD(offset+4))/60;
+ S.TIME_CYCLE = S.uD(offset+7)*256 + S.uD(offset+6);
+ S.PRES_PROFILE = NaN; %orginal double
+ S.PISTON_MIN = S.uD(offset+13)*256 + S.uD(offset+12);
+ S.PISTON_MAX = S.uD(offset+15)*256 + S.uD(offset+14);
+ S.STARTUPDELAY = S.uD(offset+17)*256 + S.uD(offset+16);
+ S.DESCENT_MODE = S.uD(offset+18);
+ % Byte 19 not used
+ S.SPEED_DESCENT = NaN; %orginal double
+ S.DESCENT_TIMEOUTFACTOR = NaN; %orginal double
+ S.DESCENT_PISTONINTERVAL_MIN = S.uD(offset+28);
+ S.DESCENT_DEPTH_CONTROL = S.uD(offset+29);
+ S.DESCENT_PISTONINTERVAL = S.uD(offset+31)*256 + S.uD(offset+30);
+ S.DESCENT_PISTON_ONTIME = S.uD(offset+32);
+ % Byte 33 not used
+ S.PRES_DESCENT_MARGIN = NaN; %orginal double
+ S.PRES_PARKING = NaN; %orginal double
+ S.PRES_PARKING_HYSTERESE = S.uD(offset+42);
+ % Byte 43 not used
+ S.ATTENUATION_FACTOR = NaN; %orginal double
+ S.TIME_PARKSAMPLE = (S.uD(offset+51)*16777216 + S.uD(offset+50)*65536 + S.uD(offset+49)*256 + S.uD(offset+48))/60;
+ S.PARKING_SAMPLES = S.uD(offset+52);
+ S.PARKING_DELAY = S.uD(offset+53);
+ S.PRES_PARKINGHIGH = S.uD(offset+55)*256 + S.uD(offset+54);
+ S.SAFETYZONE_MARGIN = S.uD(offset+57)*256 + S.uD(offset+56);
+ S.SAFETYZONE_COUNTCHANGE = S.uD(offset+59)*256 + S.uD(offset+58);
+ S.SAFETYZONE_INCREMENT = S.uD(offset+61)*256 + S.uD(offset+60);
+ S.INITIAL_PARKCOUNT = S.uD(offset+63)*256 + S.uD(offset+62);
+ S.SPEED_SAG = NaN; %orginal double
+ S.SAG_TIMEOUTFACTOR = NaN; %orginal double
+ S.ASCENT_MODE = S.uD(offset+72);
+ % Byte 73 not used
+ S.SPEED_ASCENT = NaN; %orginal double
+ S.ASCENT_TIMEOUTFACTOR = NaN; %orginal double
+ S.ASCENT_PISTONINTERVAL_MIN = S.uD(offset+82);
+ S.ASCENT_DEPTH_CONTROL = S.uD(offset+83);
+ S.ASCENT_PISTONINTERVAL = S.uD(offset+85)*256 + S.uD(offset+84);
+ S.ASCENT_PISTON_ONTIME = S.uD(offset+86);
+ % Byte 87 not used
+ S.TEMP_ICEDETECT = NaN; %orginal double
+ S.PRES_ICEUP = S.uD(offset+93)*256 + S.uD(offset+92); %until here verified with sbd 1
+ S.PRES_ICEDOWN = S.uD(offset+95)*256 + S.uD(offset+94);
+ S.PRES_ICEINTERVAL = S.uD(offset+96);
+ S.SUCCESSFUL_ASCENTS = S.uD(offset+97);
+ S.POST_UPCAST_SAMPLES = S.uD(offset+98);
+ S.POST_UPCAST_DELAY = S.uD(offset+99);
+ S.TIME_SURFACE_ATTEMP = S.uD(offset+100);
+ % Byte 101 not used
+ S.TIME_TX = (S.uD(offset+105)*16777216 + S.uD(offset+104)*65536 + S.uD(offset+103)*256 + S.uD(offset+102))/60;
+ S.MULTIMSG = [S.uD(offset+106) S.uD(offset+107) S.uD(offset+108) S.uD(offset+109)];
+ S.ARGOSID = S.uD(offset+110);
+ S.RAFOS_MODULEADR = S.uD(offset+111);
+ S.RECOVERY_START = S.uD(offset+113)*256 + S.uD(offset+112);
+ S.RECOVERY_TX = S.uD(offset+114);
+ % Byte 115 not used
+ S.RECOVERY_NOTX = S.uD(offset+117)*256 + S.uD(offset+116);
+ S.LOGMODE = S.uD(offset+118);
+ S.TESTMODE = S.uD(offset+119);
+ S.TIME_CO2WARMUP = (S.uD(offset+121)*256 + S.uD(offset+120))/60;
+ S.TIME_GPSFIX = (S.uD(offset+123)*256 + S.uD(offset+122))/60;
+ S.PRES_MAXALARM = S.uD(offset+125)*256 + S.uD(offset+124);
+ S.COUNT_MAXALARM = S.uD(offset+127)*256 + S.uD(offset+126);
+ S.CTDCP_FILTER = S.uD(offset+129)*256 + S.uD(offset+128);
+ S.PRES_CTDOFF_MAX = (S.sD(offset+131)*256 + S.uD(offset+130))/10;
+ S.PRES_CTDOFF_MIN = (S.sD(offset+133)*256 + S.uD(offset+132))/10;
+ S.PRES_CTDOFF_CHN = (S.uD(offset+135)*256 + S.uD(offset+134))/10;
+ S.PRES_PCUTOFF = (S.uD(offset+137)*256 + S.uD(offset+136))/10;
+ S.PRES_SAFETY = NaN; %orginal double
+ S.STARTPROFILE = S.uD(offset+143)*256 + S.uD(offset+142);
+ S.ICEGPS_TIMEOUT = S.uD(offset+144);
+ S.ICEIRDM_TIMEOUT = S.uD(offset+145);
+ S.CONFIGTX = S.uD(offset+146);
+ % New
+ S.AIRPUMP_MODE = S.uD(offset+147);
+ S.AIRPUMP_PRESSDIFF = S.uD(offset+149)*256 + S.uD(offset+148);
+ S.AIRPUMP_TIMEOUT = S.uD(offset+151)*256 + S.uD(offset+150);
+ S.MISSION_MOD = S.uD(offset+153)*256 + S.uD(offset+152);
+ S.TIME_CYCLE2 = S.uD(offset+155)*256 + S.uD(offset+154);
+ % Changed
+ S.RAFOS_ACTIVE = [S.uD(offset+156) S.uD(offset+157) S.uD(offset+158) S.uD(offset+159) S.uD(offset+160)];
+ S.RAFOS_STARTHH = [S.uD(offset+161) S.uD(offset+162) S.uD(offset+163) S.uD(offset+164) S.uD(offset+165)];
+ S.RAFOS_STARTMM = [S.uD(offset+166) S.uD(offset+167) S.uD(offset+168) S.uD(offset+169) S.uD(offset+170)];
+ % Byte 171 not used
+ S.RAFOS_ONMM = [S.uD(offset+173)*256+S.uD(offset+172) S.uD(offset+175)*256+S.uD(offset+174) ...
+ S.uD(offset+177)*256+S.uD(offset+176) S.uD(offset+179)*256+S.uD(offset+178) ...
+ S.uD(offset+181)*256+S.uD(offset+180)];
+ offset = offset + 182;
+
+ case 3
+ % Format 3 vom 12-June-2012 (Ice detection temperature A01 change)
+ S.SERIAL = S.uD(offset+1)*256 + S.uD(offset);
+ S.AIRPUMPTIME = S.uD(offset+3)*256 + S.uD(offset+2);
+ S.STARTUPTIME = (S.uD(offset+5)*256 + S.uD(offset+4))/60;
+ S.TIME_CYCLE = S.uD(offset+7)*256 + S.uD(offset+6);
+ S.PRES_PROFILE = NaN; %orginal double
+ S.PISTON_MIN = S.uD(offset+13)*256 + S.uD(offset+12);
+ S.PISTON_MAX = S.uD(offset+15)*256 + S.uD(offset+14);
+ S.STARTUPDELAY = S.uD(offset+17)*256 + S.uD(offset+16);
+ S.DESCENT_MODE = S.uD(offset+18);
+ % Byte 19 not used
+ S.SPEED_DESCENT = NaN; %orginal double
+ S.DESCENT_TIMEOUTFACTOR = NaN; %orginal double
+ S.DESCENT_PISTONINTERVAL_MIN = S.uD(offset+28);
+ S.DESCENT_DEPTH_CONTROL = S.uD(offset+29);
+ S.DESCENT_PISTONINTERVAL = S.uD(offset+31)*256 + S.uD(offset+30);
+ S.DESCENT_PISTON_ONTIME = S.uD(offset+32);
+ % Byte 33 not used
+ S.PRES_DESCENT_MARGIN = NaN; %orginal double
+ S.PRES_PARKING = NaN; %orginal double
+ S.PRES_PARKING_HYSTERESE = S.uD(offset+42);
+ % Byte 43 not used
+ S.ATTENUATION_FACTOR = NaN; %orginal double
+ S.TIME_PARKSAMPLE = (S.uD(offset+51)*16777216 + S.uD(offset+50)*65536 + S.uD(offset+49)*256 + S.uD(offset+48))/60;
+ S.PARKING_SAMPLES = S.uD(offset+52);
+ S.PARKING_DELAY = S.uD(offset+53);
+ S.PRES_PARKINGHIGH = S.uD(offset+55)*256 + S.uD(offset+54);
+ S.SAFETYZONE_MARGIN = S.uD(offset+57)*256 + S.uD(offset+56);
+ S.SAFETYZONE_COUNTCHANGE = S.uD(offset+59)*256 + S.uD(offset+58);
+ S.SAFETYZONE_INCREMENT = S.uD(offset+61)*256 + S.uD(offset+60);
+ S.INITIAL_PARKCOUNT = S.uD(offset+63)*256 + S.uD(offset+62);
+ S.SPEED_SAG = NaN; %orginal double
+ S.SAG_TIMEOUTFACTOR = NaN; %orginal double
+ S.ASCENT_MODE = S.uD(offset+72);
+ % Byte 73 not used
+ S.SPEED_ASCENT = NaN; %orginal double
+ S.ASCENT_TIMEOUTFACTOR = NaN; %orginal double
+ S.ASCENT_PISTONINTERVAL_MIN = S.uD(offset+82);
+ S.ASCENT_DEPTH_CONTROL = S.uD(offset+83);
+ S.ASCENT_PISTONINTERVAL = S.uD(offset+85)*256 + S.uD(offset+84);
+ S.ASCENT_PISTON_ONTIME = S.uD(offset+86);
+ % Byte 87 not used
+ S.TEMP_ICEDETECT = NaN; %orginal double
+ S.ICE_DTMEDIAN = S.uD(offset+92);
+ S.ICE_DTENTRY = S.uD(offset+93);
+ S.SUCCESSFUL_ASCENTS = S.uD(offset+94);
+ S.POST_UPCAST_SAMPLES = S.uD(offset+95);
+ S.POST_UPCAST_DELAY = S.uD(offset+96);
+ S.TIME_SURFACE_ATTEMP = S.uD(offset+97);
+ S.TIME_TX = (S.uD(offset+101)*16777216 + S.uD(offset+100)*65536 + S.uD(offset+99)*256 + S.uD(offset+98))/60;
+ S.MULTIMSG = [S.uD(offset+102) S.uD(offset+103) S.uD(offset+104) S.uD(offset+105)];
+ S.ARGOSID = S.uD(offset+106);
+ S.RAFOS_MODULEADR = S.uD(offset+107);
+ S.RECOVERY_START = S.uD(offset+109)*256 + S.uD(offset+108);
+ S.RECOVERY_TX = S.uD(offset+110);
+ % Byte 111 not used
+ S.RECOVERY_NOTX = S.uD(offset+113)*256 + S.uD(offset+112);
+ S.LOGMODE = S.uD(offset+114);
+ S.TESTMODE = S.uD(offset+115);
+ S.TIME_CO2WARMUP = (S.uD(offset+117)*256 + S.uD(offset+116))/60;
+ S.TIME_GPSFIX = (S.uD(offset+119)*256 + S.uD(offset+118))/60;
+ S.PRES_MAXALARM = S.uD(offset+121)*256 + S.uD(offset+120);
+ S.COUNT_MAXALARM = S.uD(offset+123)*256 + S.uD(offset+122);
+ S.CTDCP_FILTER = S.uD(offset+125)*256 + S.uD(offset+124);
+ S.PRES_CTDOFF_MAX = (S.sD(offset+127)*256 + S.uD(offset+126))/10;
+ S.PRES_CTDOFF_MIN = (S.sD(offset+129)*256 + S.uD(offset+128))/10;
+ S.PRES_CTDOFF_CHN = (S.uD(offset+131)*256 + S.uD(offset+130))/10;
+ S.PRES_PCUTOFF = (S.uD(offset+133)*256 + S.uD(offset+132))/10;
+ S.PRES_SAFETY = NaN; %orginal double
+ S.STARTPROFILE = S.uD(offset+139)*256 + S.uD(offset+138);
+ S.ICEGPS_TIMEOUT = S.uD(offset+140);
+ S.ICEIRDM_TIMEOUT = S.uD(offset+141);
+ S.CONFIGTX = S.uD(offset+142);
+ S.AIRPUMP_MODE = S.uD(offset+143);
+ S.AIRPUMP_PRESSDIFF = S.uD(offset+145)*256 + S.uD(offset+144);
+ S.AIRPUMP_TIMEOUT = S.uD(offset+147)*256 + S.uD(offset+146);
+ S.MISSION_MOD = S.uD(offset+149)*256 + S.uD(offset+148);
+ S.TIME_CYCLE2 = S.uD(offset+151)*256 + S.uD(offset+150);
+ % Changed
+ S.RAFOS_ACTIVE = [S.uD(offset+152) S.uD(offset+153) S.uD(offset+154) S.uD(offset+155) S.uD(offset+156)];
+ S.RAFOS_STARTHH = [S.uD(offset+157) S.uD(offset+158) S.uD(offset+159) S.uD(offset+160) S.uD(offset+161)];
+ S.RAFOS_STARTMM = [S.uD(offset+162) S.uD(offset+163) S.uD(offset+164) S.uD(offset+165) S.uD(offset+166)];
+ % Byte 167 not used
+ S.RAFOS_ONMM = [S.uD(offset+169)*256+S.uD(offset+168) S.uD(offset+171)*256+S.uD(offset+170) ...
+ S.uD(offset+173)*256+S.uD(offset+172) S.uD(offset+175)*256+S.uD(offset+174) ...
+ S.uD(offset+177)*256+S.uD(offset+176)];
+ offset = offset + 178;
+ otherwise
+ % Do nothing
+
+end
+
+% function end
+end
+
+
+
\ No newline at end of file
diff --git a/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/press.m b/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/press.m
new file mode 100644
index 0000000..85885b5
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/press.m
@@ -0,0 +1,30 @@
+function p=press(DATA, off, cnt)
+
+ if cnt == 2
+ % Low resulution mode
+ p = DATA(off+1)*256 + DATA(off);
+ if p <= 32767
+ p = p/10;
+ else
+ p= (65535-p+1)/10*-1;
+ end
+ end
+
+ if cnt == 4
+ % High resulution mode
+ p = DATA(off+3)*16777216 + DATA(off+2)*65536 + DATA(off+1)*256 + DATA(off);
+ if p <= 2147483647
+ p = p / 100;
+ else
+ p = (4294967295-p+1)/100*-1;
+ end
+ end
+
+
+% function p=cnv_press(cnt)
+%
+% if cnt <= 32767
+% p=cnt/10;
+% else
+% p=(65535-cnt+1)/10*-1;
+% end
diff --git a/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/salt.m b/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/salt.m
new file mode 100644
index 0000000..e382cfc
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/salt.m
@@ -0,0 +1,19 @@
+function S=salt(DATA, off, cnt)
+
+ if cnt == 2
+ % Low resulution mode
+ S = DATA(off+1)*256 + DATA(off);
+ S = S / 1000;
+ end
+
+ if cnt == 4
+ % High resulution mode
+ S = DATA(off+3)*16777216 + DATA(off+2)*65536 + DATA(off+1)*256 + DATA(off);
+ S = S / 10000;
+ end
+
+
+% function S=cnv_salt(cnt)
+%
+% S=cnt/1000;
+%
diff --git a/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/temp.m b/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/temp.m
new file mode 100644
index 0000000..74fb89e
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+optimare/+cnv/temp.m
@@ -0,0 +1,31 @@
+function T=temp(DATA, off, cnt)
+
+ if cnt == 2
+ % Low resulution mode
+ T = DATA(off+1)*256 + DATA(off);
+ if T <= 62535
+ T = T/1000;
+ else
+ T= (65535-T+1)/1000*-1;
+ end
+ end
+
+ if cnt == 4
+ % High resulution mode
+ T = DATA(off+3)*16777216 + DATA(off+2)*65536 + DATA(off+1)*256 + DATA(off);
+ if T <= 2147483647
+ T = T / 10000;
+ else
+ T = (4294967295-T+1)/10000*-1;
+ end
+ end
+
+
+
+% function T=cnv_temp(cnt)
+%
+% if cnt <= 62535
+% T=cnt/1000;
+% else
+% T=(65535-cnt+1)/1000*-1;
+% end
diff --git a/lib/vendor/nemo2profilelib/+nemo/+optimare/decode_nemo.m b/lib/vendor/nemo2profilelib/+nemo/+optimare/decode_nemo.m
new file mode 100644
index 0000000..f0aee1e
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+optimare/decode_nemo.m
@@ -0,0 +1,316 @@
+function S = decode_nemo(S)
+
+% Decode different NEMO message types
+%
+%
+
+% Optimare Sensorsysteme, 22.10.2010 M.Busack
+
+
+% Enable(1)/Disable(0) 3830 Optode sensor
+funco2 = 1;
+
+switch S.DEVICE
+
+ case 'CTD Profiler/Logger'
+ % Device type = CTD-Profiler/Logger
+ switch S.DATATYPE
+
+ case 'Profile Message'
+ % Read profile header
+ S.SERIAL = S.uD(4)*256 + S.uD(3);
+ S.PROFILE_NUMBER = S.uD(2)*256 + S.uD(1);
+ S.STATUS_UPCAST = nemo.optimare.stat2str(S.uD(5),'C');
+ % Startdate bytes 6,7,8 not used now
+ S.DS4_START = S.uD(9)*3600 + S.uD(10)*60 + S.uD(11);
+ S.BATT_CPU = S.uD(12) / 10;
+ S.BATT_PMP = S.uD(13) / 10;
+ S.PRES_TUBE_DEPTH = ( S.uD(14) / 10 ) * 68.9475;
+ % Enddate bytes 15,16,17 not used now
+ S.DS4_STOP = S.uD(18)*3600 + S.uD(19)*60 + S.uD(20);
+ S.BATT_CPU2 = S.uD(21) / 10;
+ S.BATT_PMP2 = S.uD(22) / 10;
+ S.PRES_TUBE_SURFACE = ( S.uD(23) / 10 ) * 69.9475;
+ %S.DATA_RECORDS_COMPLETE = S.uD(25)*256 + S.uD(24);
+ S.DATA_RECORDS1 = [0, 0, 0, S.uD(25)*256+S.uD(24), 0];
+ S.DATA_RECORDS2 = S.DATA_RECORDS1;
+ offset = 26;
+ % Read sample data
+ if S.DATA_RECORDS1(4) > 0
+ for k=1:S.DATA_RECORDS1(4)
+ S.DS4_PRES(k) = nemo.optimare.cnv.press(S.uD, offset, 2);
+ S.DS4_TEMP(k) = nemo.optimare.cnv.temp(S.uD, offset+2, 2);
+ S.DS4_SAL(k) = nemo.optimare.cnv.salt(S.uD, offset+4, 2);
+ offset = offset + 6;
+ end
+ end
+
+ end
+
+
+ case 'NEMO Standard '
+ % Device type = NEMO float
+
+ switch S.DATATYPE
+
+ case 'Startup Test Message'
+ S.SERIAL = S.uD(2)*256 + S.uD(1);
+ dt = [S.uD(3)+2000,S.uD(4),S.uD(5),0,0,0];
+ S.SOFTWARE = datestr(dt);
+ dt = [S.uD(6)+2000,S.uD(7),S.uD(8),S.uD(9),S.uD(10),0];
+ S.RTC = datestr(dt);
+ S.PISTON_MAX = S.uD(12)*256 + S.uD(11);
+ S.PISTON_MIN = S.uD(14)*256 + S.uD(13);
+ S.BATT_CPU = S.uD(15) / 10;
+ S.BATT_PMP = S.uD(16) / 10;
+ S.BATT_EXT = S.uD(17) / 10;
+ S.PRES_TUBE_SURFACE = (S.uD(18) / 10) * 68.94757;
+ S.PRES_PROFILE = nemo.optimare.cnv.press(S.uD, 19, 2);
+ S.PRES_PARKING = nemo.optimare.cnv.press(S.uD, 21, 2);
+ S.TIME_TX = S.uD(24)*256 + S.uD(23);
+ S.TIME_PARKSAMPLE = S.uD(26)*256 + S.uD(25);
+ S.TIME_CYCLE = S.uD(28)*256 + S.uD(27);
+ S.DESCENT_MODE = S.uD(29);
+ S.RECOVERY_START = S.uD(32)*256 + S.uD(31);
+ S.DESCENT_SPEED = (S.uD(34)*256 + S.uD(33))/1000;
+ S.TEMP_ICEDETECT = (S.sD(36)*256 + S.uD(35))/1000;
+ S.RECOVERY_TX = S.uD(37);
+ S.RECOVERY_NOTX = S.uD(40)*256 + S.uD(39);
+ dt = [S.uD(41)+2000,S.uD(42),S.uD(43),S.uD(44),S.uD(45),0];
+ S.GPS_DATETIME = datestr(dt);
+ S.GPS_LAT = (S.sD(48)*256 + S.uD(47)) / 100;
+ S.GPS_LON = (S.sD(50)*256 + S.uD(49)) / 100;
+
+ case 'Profile Message'
+ % Read profile header (ab rev.224)
+ S.SERIAL = S.uD(4)*256 + S.uD(3);
+ S.PROFILE_NUMBER = S.uD(2)*256 + S.uD(1);
+ S.STATUS_UPCAST = nemo.optimare.stat2str(S.uD(5),'P');
+ % Byte 6 nicht benutzt
+ S.PROFILE_OLDER = S.uD(8)*256 + S.uD(7);
+ S.ERROR_MOTOR = S.uD(9);
+ S.ERROR_CTD = S.uD(10);
+ S.ERROR_OPTODE = S.uD(11);
+ S.ERROR_RAFOS = S.uD(12);
+ S.BATT_CPU = S.uD(13) / 10;
+ S.BATT_PMP = S.uD(14) / 10;
+ S.BATT_EXT = S.uD(15) / 10;
+ S.CURR_MOTOR = S.uD(16) / 100;
+ S.CURR_MOTOR_MEAN = S.uD(17) / 100;
+ if isnan(S.uD(18))
+ S.CTD_MODE = NaN;
+ S.CTD_RES = NaN;
+ else
+ S.CTD_MODE = bitget(S.uD(18),1);
+ S.CTD_RES = bitget(S.uD(18),2);
+ end
+ S.PRES_TUBE_SURFACE = S.uD(20)*256 + S.uD(19);
+ S.TEMP_TUBE_SURFACE = (S.sD(22)*256 + S.uD(21))/10;
+ S.PRES_TUBE_SURFACE2 = S.uD(24)*256 + S.uD(23);
+ S.TEMP_TUBE_SURFACE2 = (S.sD(26)*256 + S.uD(25))/10;
+ S.PRES_TUBE_DEPTH = S.uD(28)*256 + S.uD(27);
+ S.TEMP_TUBE_DEPTH = (S.sD(30)*256 + S.uD(29))/10;
+ S.TEMP_SHT = (S.sD(32)*256 + S.uD(31)) / 10;
+ S.HUM_SHT = (S.uD(34)*256 + S.uD(33)) / 10;
+ S.PRES_OFFSET = nemo.optimare.cnv.press(S.uD, 35, 2);
+ S.PRES_SURFACE = nemo.optimare.cnv.press(S.uD, 37, 2);
+ S.PRES_PARKING = nemo.optimare.cnv.press(S.uD, 39, 2);
+ S.PRES_DEPTH = nemo.optimare.cnv.press(S.uD, 41, 2);
+ S.PRES_MAX = nemo.optimare.cnv.press(S.uD, 43, 2);
+ S.RECOVERY_START = S.uD(46)*256 + S.uD(45);
+ S.DATA_RECORDS1 = [S.uD(48)*256+S.uD(47), S.uD(50)*256+S.uD(49),...
+ S.uD(52)*256+S.uD(51), S.uD(54)*256+S.uD(53), S.uD(56)*256+S.uD(55)];
+ S.PIST_SURFACE = S.uD(58)*256 + S.uD(57);
+ S.PIST_PARKING = S.uD(60)*256 + S.uD(59);
+ S.PIST_CALC = S.uD(62)*256 + S.uD(61);
+ S.PIST_DEPTH = S.uD(64)*256 + S.uD(63);
+ S.PIST_EOP = S.uD(66)*256 + S.uD(65);
+ S.MCNT_DESCENT = S.uD(70)*16777216 + S.uD(69)*65536 + S.uD(68)*256 + S.uD(67);
+ S.MCNT_PARKING = S.uD(74)*16777216 + S.uD(73)*65536 + S.uD(72)*256 + S.uD(71);
+ S.MCNT_SAG = S.uD(78)*16777216 + S.uD(77)*65536 + S.uD(76)*256 + S.uD(75);
+ S.MCNT_ASCENT = S.uD(82)*16777216 + S.uD(81)*65536 + S.uD(80)*256 + S.uD(79);
+ S.MCNT_ASCENT_END = S.uD(86)*16777216 + S.uD(85)*65536 + S.uD(84)*256 + S.uD(83);
+ S.MCNT_SURFACE = S.uD(90)*16777216 + S.uD(89)*65536 + S.uD(88)*256 + S.uD(87);
+ S.DATA_RECORDS2 = [S.uD(92)*256+S.uD(91), S.uD(94)*256+S.uD(93),...
+ S.uD(96)*256+S.uD(95), S.uD(98)*256+S.uD(97), S.uD(100)*256+S.uD(99)];
+ % Verify data record quantity
+ for k = 1:5
+ if ( (S.DATA_RECORDS1(k) == 0) && (S.DATA_RECORDS2(k) > 0) )
+ q(k) = S.DATA_RECORDS2(k);
+ else
+ q(k) = S.DATA_RECORDS1(k);
+ end
+ end
+ % Set offset in array and resulution increment
+ offset = 101;
+ if S.CTD_RES == 0
+ ctda = 2;
+ else
+ ctda = 4;
+ end
+ % Read profile data sets (ab Rev.224)
+ % Dataset 1 (profile header extensions)
+ if q(1) > 0
+ for k=1:q(1)
+ % This record header is always there
+ S.DS1_TYPE(k) = S.uD(offset);
+ S.DS1_FORMAT(k) = S.uD(offset+1);
+ offset = offset + 2;
+ switch(S.DS1_TYPE(k))
+ case 1 % Surface detect data only
+ if S.DS1_FORMAT(k) == 1 % Default format
+ S.ICEGPS_TIME = S.uD(offset);
+ S.ICEIRDM_TIME = S.uD(offset+1);
+ offset = offset + 2;
+ end
+ % Paste additional formats for type 1 here
+
+ case 2 % Mission configuration data
+ [S,offset] = nemo.optimare.cnv.phext_t2(S,offset,k);
+ % Paste additional formats for type 2 here
+
+ case 3 % Airpump control data
+ if S.DS1_FORMAT(k) == 1 % Default format
+ S.AIRPUMP_RUNTIME = S.uD(offset+1)*256 + S.uD(offset);
+ offset = offset + 2;
+ end
+ % Paste additional formats for type 3 here
+
+ case 4 % Ice detection temperature data
+ if S.DS1_FORMAT(k) == 1 % Default format
+ S.ICE_TEMPMEDIAN = ( S.sD(offset+3)*16777216 + S.uD(offset+2)*65536 +...
+ S.uD(offset+1)*256 + S.uD(offset) ) / 10000;
+% S.ICE_TEMPMEDIAN = ( S.uD(offset+3)*16777216 + S.uD(offset+2)*65536 +...
+% S.uD(offset+1)*256 + S.uD(offset) ) / 10000;
+ offset = offset + 4;
+ end
+ % Paste additional formats for type 4 here
+
+ % Paste additional types here
+
+ otherwise
+ % Do nothing
+
+ end
+ end
+ end
+ % Dataset 2 (Parking data)
+ if q(2) > 0
+ for k=1:q(2)
+ S.DS2_PRES(k) = nemo.optimare.cnv.press(S.uD, offset, ctda);
+ S.DS2_TEMP(k) = nemo.optimare.cnv.temp(S.uD, offset+ctda, ctda);
+ S.DS2_SAL(k) = nemo.optimare.cnv.salt(S.uD, offset+2*ctda, ctda);
+ offset = offset + 3*ctda;
+ end
+ end
+ % Dataset 3 (Rafos data)
+ if q(3) > 0
+ for k=1:q(3)
+ S.DS3_STATUS(k) = S.uD(offset);
+ S.DS3_DATE(k) = S.uD(offset+1)*372 + S.uD(offset+2)*31 + S.uD(offset+3);
+ S.DS3_DATE_year(k) = S.uD(offset+1)*372 ;
+ S.DS3_DATE_month(k) = S.uD(offset+2);
+ S.DS3_DATE_day(k) = S.uD(offset+3);
+
+ S.DS3_TIME(k) = S.uD(offset+4)*3600 + S.uD(offset+5)*60 + S.uD(offset+6);
+ for i=1:6
+ S.DS3_RAFOSAMP(k,i) = S.uD(offset+6+i);
+ S.DS3_RAFOSRANK(k,i) = (S.uD(offset+15+(i-1)*2)*256 + S.uD(offset+14+(i-1)*2))*0.3075;
+ end
+ % Evtl muss hier noch ein dummy byte eingefügt werden
+ % (ist im 160 0 00 00 502 schon drin)
+ % todo testen und in Firmware auch diesen datensatz
+ % evtl. mit high resulution !
+ S.DS3_PRES(k) = nemo.optimare.cnv.press(S.uD, offset+26, 2);
+ S.DS3_TEMP(k) = nemo.optimare.cnv.temp(S.uD, offset+28, 2);
+ S.DS3_SAL(k) = nemo.optimare.cnv.salt(S.uD, offset+30, 2);
+ offset = offset + 32;
+ end
+ end
+ % Dataset 4 (Upcast profile data)
+ if q(4) > 0
+ for k=1:q(4)
+ S.DS4_TIME(k) = S.uD(offset)*3600 + S.uD(offset+1)*60 + S.uD(offset+2);
+ S.DS4_FORMAT(k) = S.uD(offset+3);
+ S.DS4_PRES(k) = nemo.optimare.cnv.press(S.uD, offset+4, ctda);
+ offset = offset + 4 + ctda;
+ if S.CTD_MODE == 0
+ % Discrete profile with full ctd data
+ S.DS4_TEMP(k) = nemo.optimare.cnv.temp(S.uD, offset, ctda);
+ S.DS4_SAL(k) = nemo.optimare.cnv.salt(S.uD, offset+ctda, ctda);
+ offset = offset + ctda*2;
+ else
+ % Cont. profile or NaN
+ S.DS4_TEMP(k) = NaN;
+ S.DS4_SAL(k) = NaN;
+ end
+ if ((funco2 > 0) || (S.DS4_FORMAT(k) > 0) )
+ % Read additionaly sensor data
+ [S,offset] = nemo.optimare.read_sensors(S, k, offset);
+ end
+ end
+ end
+ % Dataset 5 (Extended surface data)
+ if q(5) > 0
+ for k=1:q(5)
+ dt = [S.uD(offset)+2000,S.uD(offset+1),S.uD(offset+2),S.uD(offset+3),S.uD(offset+4),S.uD(offset+5)];
+ %S.DS5_RTC(k) = datestr(dt);
+ S.DS5_RTC(k) = datenum(dt);
+ dt = [S.uD(offset+6)+2000,S.uD(offset+7),S.uD(offset+8),S.uD(offset+9),S.uD(offset+10),S.uD(offset+11)];
+ %S.DS5_GPS(k) = datestr(dt);
+ S.DS5_GPS(k) = datenum(dt);
+ S.DS5_LAT(k) = (S.sD(offset+15)*16777216 + S.uD(offset+14)*65536 + S.uD(offset+13)*256 + S.uD(offset+12)) / 10000000;
+ S.DS5_LON(k) = (S.sD(offset+19)*16777216 + S.uD(offset+18)*65536 + S.uD(offset+17)*256 + S.uD(offset+16)) / 10000000;
+ offset = offset + 20;
+ end
+ end
+
+ case 'MTM Report Message'
+
+
+
+ case 'Recovery Message'
+
+
+
+ case 'File transmission message'
+
+
+ case 'Filtered CTD data Message'
+ % Read continous profile data header (filtered)
+ S.SERIAL = S.uD(2)*256 + S.uD(1);
+ S.PROFILE_NUMBER = S.uD(4)*256 + S.uD(3);
+ S.DS4_START = S.uD(5)*3600 + S.uD(6)*60 + S.uD(7);
+ S.DS4_STOP = S.uD(8)*3600 + S.uD(9)*60 + S.uD(10);
+ S.DATA_RECORDS_COMPLETE = S.uD(12)*256 + S.uD(11);
+ S.DATA_RECORDS1 = [0, 0, 0, S.uD(14)*256+S.uD(13), 0];
+ S.DATA_RECORDS2 = S.DATA_RECORDS1;
+ S.CTD_RES = bitget(S.uD(15),2);
+ offset = 16;
+ if S.CTD_RES == 0
+ ctda = 2;
+ else
+ ctda = 4;
+ end
+ % Read sample data
+ if S.DATA_RECORDS1(4) > 0
+ for k=1:S.DATA_RECORDS1(4)
+ S.DS4_PRES(k) = nemo.optimare.cnv.press(S.uD, offset, ctda);
+ S.DS4_TEMP(k) = nemo.optimare.cnv.temp(S.uD, offset+ctda, ctda);
+ S.DS4_SAL(k) = nemo.optimare.cnv.salt(S.uD, offset+2*ctda, ctda);
+ offset = offset + 3*ctda;
+ end
+ end
+
+ end
+
+ otherwise
+ % Unknown device type
+
+end
+
+% function end
+end
+
+
+
\ No newline at end of file
diff --git a/lib/vendor/nemo2profilelib/+nemo/+optimare/process_moms.m b/lib/vendor/nemo2profilelib/+nemo/+optimare/process_moms.m
new file mode 100644
index 0000000..3f4688a
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+optimare/process_moms.m
@@ -0,0 +1,340 @@
+function [S_all,S,SBD] = process_moms(filepath, imei)
+
+% Find and indentify mobile originated messages (mom) from Iridium SBD
+% Transmitter.
+%
+%
+% ATTENTION: Include path to repository /oze/functions !
+
+% Optimare Sensorsysteme, 21.10.2010 M.Busack
+
+% compatibility fix, LP, 26.04.17:
+S_all = struct();
+
+% Get version from SVN
+S.VERSION = '$Id: SBD2PROF.m 999 2012-06-18 10:00:00Z michael $';
+%S_all.empty=[];
+%clear all;
+
+% % Set filepath or get path via file dialog
+% filepath='/home/michael/src/matlab/sbd2prof/sbd';
+% filepath=uigetdir;
+
+% Added support for searching specific imei
+% Get all files from directory with .sbd extension
+if (~exist('imei', 'var'))
+ D = dir(fullfile(filepath,'*.sbd'));
+else
+ D = dir(fullfile(filepath, ['*' char(imei) '*.sbd']));
+end
+
+filelist=char(D.name);
+
+% Create figure
+%figure;
+%hold on;
+
+% bugfix: Output argument "SBD" (and maybe others) not assigned during
+% call to "nemo.optimare.process_moms".
+% LP, 27.04.17
+if (length(D) == 0)
+ SBD = [];
+end
+
+% Read files
+for i=1:length(D)
+ % Open file
+ infile=fullfile(filepath,filelist(i,:));
+ % Read Message
+ SBD(i) = nemo.optimare.readSBDmsg(infile);
+end
+
+
+% Init processing variables
+state = 'Readpart';
+findex = 0; % File index
+grpflag = 0; % Message group flag, set to 1 if startmsg was found. Set to 0 at end of group.
+msgcnt = 1; % Message counter
+ofid = 0; % No output file
+exit = 0;
+
+% Init overall energy variables
+pnr = 0;
+E.ENERGYCOMPLETE = 0;
+
+% Process messages
+while exit == 0
+
+ %state
+ switch state
+
+ case 'Readpart'
+ % Increment file counter index
+ findex = findex + 1;
+ if findex <= length(D)
+ % We have at least one file to read.
+ % Read SBD message
+ filename = fullfile(filepath,filelist(findex,:));
+ %SBD(findex) = nemo.optimare.readSBDmsg(filename);
+ % Check if we have a valid message type
+ if SBD(findex).status == 1
+ % Yes, this is a known device/data message
+ state = 'Getpart';
+ else
+ % No, try again with next message
+ disp('Error: File has unknown device/data type');
+ state = 'Readpart';
+ end
+ else
+ % We reached the end of filelist.
+ % Before end, check if there is a group pending.
+ if grpflag == 1
+ % A message group is pending, finish this first.
+ state = 'Endgroup';
+ else
+ % Everything if finished, end function.
+ exit = 1;
+ end
+ end
+
+ case 'Getpart'
+ % Decodable message was found
+ if SBD(findex).elementary_num == 1
+ % This is the first message of a group
+ if grpflag == 0
+ % Last group was finished successfully.
+ % => Everything is ok.
+ state = 'Startgroup';
+ else
+ % We have an incomplete group pending.
+ % => Finish this group before starting the next one.
+ % Because findex in incremented after process,
+ % decrement here to prevent skipping of a file.
+ findex = findex - 1;
+ state = 'Endgroup';
+ end
+ else
+ % This is not the first message of a group
+ if grpflag == 0
+ % Group was not started before.
+ % => This can happen if the first message is missing
+ state = 'Startgroup';
+ else
+ % Start of group was received before.
+ % => Everything is ok.
+ % Exception: Last message of group before is missing
+ % AND first message of next group is missing also !
+ % TBD!!
+ state = 'Checkpart';
+ end
+ end
+
+ case 'Startgroup'
+ % Start of message group found.
+ % First, clear data from group before.
+ clear S;
+ grpflag = 1;
+ % Init device/data type
+ S.DEVICE = SBD(findex).device;
+ S.DATATYPE = SBD(findex).data;
+ % Set message counter
+ msgcnt = SBD(findex).elementary_num;
+ % Init buffer
+ l = SBD(findex).total_num * SBD(findex).ldata + 10;
+ l = l * 1.3;
+ l = ceil(l); % OB: added ceil, as ones requires interger parameter
+ S.uD=ones(1,l)*NaN;
+ S.sD=S.uD;
+ % Offset for uD/sD Array. All messages must have the same
+ % datasize here (expect the last one).
+ S.DATAPAYLOAD = SBD(findex).ldata;
+ % Create output file name with .out extension
+ filename = filelist(findex,:);
+ l = length(filename);
+ filename(l) = 't';
+ filename(l-1) = 'u';
+ filename(l-2) = 'o';
+ % Open file for output
+ outfile = fullfile(filepath,filename);
+ %ofid = fopen(outfile,'w');
+ % Next state
+ state = 'Checkpart';
+
+ case 'Checkpart'
+ % Check for message consitence
+ if SBD(findex).elementary_num == msgcnt
+ % Expected message number is ok
+ state = 'Writepart';
+ else
+ % Message number read is not the expected one
+ % This can happen if one message/file is missing
+ %fprintf(ofid,'\r\nFilename: %s Device: %s Data type: %s Message: %3d of %3d, not found',...
+ % filelist(findex,:), SBD(findex).device, SBD(findex).data, msgcnt, SBD(findex).total_num);
+ % What to do ?
+ if msgcnt < SBD(findex).elementary_num
+ % Expected message number is smaller than received one.
+ % This can happen if a group file in the middle is missing.
+ % Try again expecting next message.
+ msgcnt = msgcnt + 1;
+ else
+ % Expected message number is larger than received one.
+ state = 'Endgroup';
+
+ % Ist das richtig ? :
+ % This can happen if this is the next group, already.
+ % Maybe the last message from the group before and the
+ % first message of the next group are missing.
+ end
+ end
+
+ case 'Writepart'
+ % Write header information to file
+ %fprintf(ofid,'\r\nFilename: %s Device: %s Data type: %s Message: %3d of %3d, %3d bytes of data',...
+ % filelist(findex,:), SBD(findex).device, SBD(findex).data, SBD(findex).elementary_num,...
+ % SBD(findex).total_num, SBD(findex).ldata);
+ % Copy data to buffer
+ offset = (SBD(findex).elementary_num-1)*S.DATAPAYLOAD;
+ i = offset+1:offset+SBD(findex).ldata;
+ S.uD(i) = SBD(findex).udata;
+ S.sD(i) = SBD(findex).sdata;
+ % Check if message is last in set
+ if SBD(findex).elementary_num == SBD(findex).total_num
+ % Message is last one in set, end of group reached.
+ state = 'Endgroup';
+ else
+ % Not the last message, read next one.
+ msgcnt = msgcnt + 1;
+ state = 'Readpart';
+ end
+
+ case 'Endgroup'
+ % Finish group
+ % Wir auch aufgerufen, wenn die leltzte msg fehlt !
+ % Close file.
+ %fprintf(ofid,'\r\nNo more messages to read.');
+ %fclose(ofid);
+ % Set flag to 'group closed successfully'
+ grpflag = 0;
+ state = 'Process';
+
+ case 'Process'
+ try
+ % Process the received group
+ % First, decode data
+ S = nemo.optimare.decode_nemo(S);
+ % Write data to output file
+ %write_NEMO(S,outfile);
+ catch ex
+ end
+ if findex > length(D)
+ exit = 1;
+ else
+ %state = 'Energycalculation'; % with energy calculation
+ state = 'Readpart'; % without any calculations
+ end
+ expr=['S_all.S_' num2str(findex) '=S;'];
+ eval(expr);
+
+ case 'Energycalculation'
+ % Perform energy calculation from mission runtime and piston
+ % movements
+ if isfield(S,'DATA_RECORDS1'),
+ if S.DATA_RECORDS1(4) > 0
+ %plot(S.DS4_PRES+findex); % Datset 4 pressure
+ %plot(S.PROFILE_NUMBER, S.DS4_LICH1+S.DS4_LICH2+S.DS4_LICH3, '.-b');
+ %plot(S.PROFILE_NUMBER,S.DS4_LICH1,'.-r',...
+ % S.PROFILE_NUMBER,S.DS4_LICH2,'.-g',...
+ % S.PROFILE_NUMBER,S.DS4_LICH3,'.-b');
+
+ end
+ end
+ % Calculate overall energy (works only if all data from same float)
+ if isfield(S,'PROFILE_NUMBER'),
+ pnr = pnr + 1;
+ E.VALID(pnr) = 1;
+ E.PROFNR(pnr) = S.PROFILE_NUMBER;
+
+ if ( (isfield(S,'PIST_SURFACE')) & (isfield(S,'PIST_PARKING')) )
+ E.PISTON_DESCENT(pnr) = S.PIST_PARKING - S.PIST_SURFACE;
+ else
+ E.VALID(pnr) = 0;
+ end
+ if ( (isfield(S,'PIST_DEPTH')) & (isfield(S,'PIST_EOP')) & (E.VALID(pnr) == 1) )
+ E.PISTON_ASCENT(pnr) = S.PIST_DEPTH - S.PIST_EOP;
+ else
+ E.VALID(pnr) = 0;
+ end
+ if ( (isfield(S,'CURR_MOTOR_MEAN')) & (E.VALID(pnr) == 1) )
+ E.MOTORCURRENT(pnr) = S.CURR_MOTOR_MEAN;
+ else
+ E.VALID(pnr) = 0;
+ end
+ if E.VALID(pnr) == 1
+ E.ENERGY(pnr) = (E.PISTON_DESCENT(pnr) + E.PISTON_ASCENT(pnr)) * E.MOTORCURRENT(pnr);
+ E.ENERGYCOMPLETE = E.ENERGYCOMPLETE + E.ENERGY(pnr);
+ end
+ end
+ % Start again
+ state = 'Readpart';
+
+ otherwise
+ % End loop
+ disp('State machine error');
+ exit = 1;
+ end
+end
+
+%hold off;
+
+%whos;
+
+%
+%
+% % This is the first message of a set.
+% if ( (findex > 1) & (msgcnt < SBD(findex-1).total_num) )
+% % Only if this is NOT the first file from the list
+% % and the expected elementray number (msgcnt) is
+% % smaller than the total number of this set.
+% % This can happen if the last set was not received
+% % completly (one or more messages missing at the
+% % end)
+% % Todo: Search for any of the missing files.
+% state = 'Checkpart';
+%
+% % Note: msgcnt is equal to total number if last
+% % set was completly received. So, we have a set with
+% % at least the last file missing.
+% % Use header informations from last message.
+% %SBD(findex).device = SBD(findex-1).device;
+% %SBD(findex).data = SBD(findex-1).data;
+% %SBD(findex).total_num = SBD(findex-1).total_num;
+% %msgcnt = msgcnt + 1;
+% %state = 'Checkpart';
+%
+% else
+% % Start of message set (i.e. a profile) found
+% if ofid > 0
+% % Close open output file
+% % This can happen, if last file of message set is
+% % missing
+% fclose(ofid);
+% end
+% % Start of new message set
+% state = 'Startpart';
+% end
+% else
+% % Message is not the first one
+% if ofid == 0
+% % No output file was created before.
+% % This can happen, if first message of set is missing
+% state = 'Startpart';
+% msgcnt = SBD(findex).elementary_num;
+% else
+% % Output file present, regular writing of data
+% state = 'Checkpart';
+% end
+% end
+
+
+
+%end
\ No newline at end of file
diff --git a/lib/vendor/nemo2profilelib/+nemo/+optimare/readSBDmsg.m b/lib/vendor/nemo2profilelib/+nemo/+optimare/readSBDmsg.m
new file mode 100644
index 0000000..f5d6bae
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+optimare/readSBDmsg.m
@@ -0,0 +1,55 @@
+function sbdmsg = readSBDmsg(infi)
+
+% Read data from SBD file
+%
+
+% Optimare Sensorsysteme, 21.10.2010 M.Busack
+
+% VERSION = '$Id: CTD2awi.m 701 2010-10-21 10:00:00Z michael $';
+
+
+
+% Open file for reading
+fid=fopen(infi,'r');
+
+% Read first header byte : crc_status
+sbdmsg.crc_status = fread(fid,1,'uchar');
+
+% Read next : checksum
+sbdmsg.checksum = fread(fid,1,'uint16');
+
+% Read next : mtmsn
+sbdmsg.mtmsn = fread(fid,1,'uchar');
+
+% Read next : elementry message number
+sbdmsg.elementary_num = fread(fid,1,'uchar');
+
+% Read next : total message number
+sbdmsg.total_num = fread(fid,1,'uchar');
+
+% Read next : device/data type
+device_data = fread(fid,1,'uchar');
+[sbdmsg.device,sbdmsg.data,sbdmsg.status] = nemo.optimare.cnv.devicedata(device_data);
+
+% Read next : profile number LSB
+sbdmsg.profilenumber_lsb = fread(fid,1,'uchar');
+
+% Read rest of file and store to 'udata' and 'sdata' array
+offset = ftell(fid);
+sbdmsg.udata = fread(fid,inf,'uchar');
+fseek(fid,offset,'bof'); % OB what is this good for?
+sbdmsg.sdata = fread(fid,inf,'schar');
+sbdmsg.ldata = ftell(fid) - offset;
+
+sbdmsg.sbdfilename=infi;
+[~, filename, ~] = fileparts(infi);
+splitted_file = strsplit(filename, '_');
+sbdmsg.imei = str2num(splitted_file{1});
+sbdmsg.momsn = str2num(splitted_file{2});
+
+
+% Close file
+fclose(fid);
+
+
+end
diff --git a/lib/vendor/nemo2profilelib/+nemo/+optimare/read_sensors.m b/lib/vendor/nemo2profilelib/+nemo/+optimare/read_sensors.m
new file mode 100644
index 0000000..3e31b39
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+optimare/read_sensors.m
@@ -0,0 +1,75 @@
+function [S,off] = read_sensors(S, i, off)
+
+% Read optinal data from additional sensors
+%
+%
+
+% Optimare Sensorsysteme, 26.10.2010 M.Busack
+
+o2type = 3830;
+%o2type = 4330;
+
+% Format
+%sen = uint8(S.uD(off));
+%off = off + 2;
+sen = uint8(S.DS4_FORMAT(i));
+
+% O2 Optode data
+if bitget(sen,2) == 1
+ if o2type == 4330
+ % 4330 Optode
+ S.DS4_O2CONC(i) = (S.uD(off+3)*16777216 + S.uD(off+2)*65536 + S.uD(off+1)*256 + S.uD(off)) / 1000;
+ S.DS4_O2SATU(i) = (S.uD(off+7)*16777216 + S.uD(off+6)*65536 + S.uD(off+5)*256 + S.uD(off+4)) / 1000;
+ S.DS4_O2TEMP(i) = (S.uD(off+11)*16777216 + S.uD(off+10)*65536 + S.uD(off+9)*256 + S.uD(off+8)) / 1000;
+ S.DS4_O2CALP(i) = (S.uD(off+15)*16777216 + S.uD(off+14)*65536 + S.uD(off+13)*256 + S.uD(off+12)) / 1000;
+ S.DS4_O2TCP(i) = (S.uD(off+19)*16777216 + S.uD(off+18)*65536 + S.uD(off+17)*256 + S.uD(off+16)) / 1000;
+ off = off + 20;
+ %disp(['Read_sensors offset ',num2str(off)]);
+ end
+ if o2type == 3830
+ % 3830 Optode
+ S.DS4_O2CONC(i) = ( (S.uD(off+1)*256 + S.uD(off)) / 100 ) - 10;
+ S.DS4_O2SATU(i) = ( (S.uD(off+3)*256 + S.uD(off+2)) / 100 ) - 10;
+ S.DS4_O2TEMP(i) = ( (S.uD(off+5)*256 + S.uD(off+4)) / 100 ) - 10;
+ off = off + 6;
+ if bitget(sen,1) == 1
+ % Raw data format
+ S.DS4_O2DPHASE(i) = (S.uD(off+1)*256 + S.uD(off)) / 100;
+ S.DS4_O2BPHASE(i) = (S.uD(off+3)*256 + S.uD(off+2)) / 100;
+ S.DS4_O2RPHASE(i) = (S.uD(off+5)*256 + S.uD(off+4)) / 100;
+ S.DS4_O2BAMP(i) = (S.uD(off+9)*16777216 + S.uD(off+8)*65536 + S.uD(off+7)*256 + S.uD(off+6)) / 10;
+ S.DS4_O2BPOT(i) = (S.uD(off+11)*256 + S.uD(off+10)) / 100;
+ S.DS4_O2RAMP(i) = (S.uD(off+15)*16777216 + S.uD(off+14)*65536 + S.uD(off+13)*256 + S.uD(off+12)) / 10;
+ S.DS4_O2RAWTEMP(i) = (S.sD(off+19)*16777216 + S.uD(off+18)*65536 + S.uD(off+17)*256 + S.uD(off+16)) / 100;
+ off = off + 20;
+ end
+ end
+end
+
+
+% CO2 sensor data
+if bitget(sen,3) == 1
+ dt = [S.uD(off)+2000,S.uD(off+1),S.uD(off+2),S.uD(off+3),S.uD(off+4),S.uD(off+5)];
+ %S.DS4_CO2DATETIME(i) = datestr(dt);
+ S.DS4_CO2DATETIME(i) = datenum(dt);
+ S.DS4_CO2PNDIR(i) = S.uD(off+9)*16777216 + S.uD(off+8)*65536 + S.uD(off+7)*256 + S.uD(off+6);
+ S.DS4_CO2PIN(i) = S.uD(off+13)*16777216 + S.uD(off+12)*65536 + S.uD(off+11)*256 + S.uD(off+10);
+ S.DS4_CO2SRAW(i) = S.uD(off+15)*256 + S.uD(off+14);
+ S.DS4_CO2SREF(i) = S.uD(off+17)*256 + S.uD(off+16);
+ S.DS4_CO2TSEN(i) = S.uD(off+19)*256 + S.uD(off+18);
+ S.DS4_CO2PCO2(i) = S.sD(off+23)*16777216 + S.uD(off+22)*65536 + S.uD(off+21)*256 + S.uD(off+20);
+ S.DS4_CO2TCTRL(i) = S.uD(off+25)*256 + S.uD(off+24);
+ S.DS4_CO2TGAS(i) = S.uD(off+27)*256 + S.uD(off+26);
+ S.DS4_CO2RHGAS(i) = S.uD(off+31)*16777216 + S.uD(off+30)*65536 + S.uD(off+29)*256 + S.uD(off+28);
+ off = off + 32;
+end
+
+
+% Lightsensor data
+if bitget(sen,4) == 1
+ S.DS4_LICH1(i) = S.uD(off+1)*256 + S.uD(off);
+ S.DS4_LICH2(i) = S.uD(off+3)*256 + S.uD(off+2);
+ S.DS4_LICH3(i) = S.uD(off+5)*256 + S.uD(off+4);
+ off = off + 6;
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+optimare/stat2str.m b/lib/vendor/nemo2profilelib/+nemo/+optimare/stat2str.m
new file mode 100644
index 0000000..674c102
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+optimare/stat2str.m
@@ -0,0 +1,70 @@
+function txt = stat2str(status, type)
+
+% Convert number of status to string
+%
+%
+
+% Optimare Sensorsysteme, 22.10.2010 M.Busack
+
+if type == 'R'
+ switch (status)
+
+ case 0
+ txt = sprintf('OFF ');
+
+ case 1
+ txt = sprintf('ON ');
+
+ case 2
+ txt = sprintf('DONE ');
+
+ case 3
+ txt = sprintf('OVERLAP ERROR');
+
+ case 4
+ txt = sprintf('ENDON ERROR ');
+
+ case 5
+ txt = sprintf('COM ERROR ');
+
+ otherwise
+ txt = sprintf('UNKNOWN ');
+ end
+
+end
+
+if type == 'P'
+ switch (status)
+
+ case 0
+ txt = sprintf('BUSY ');
+
+ case 1
+ txt = sprintf('DONE ');
+
+ case 2
+ txt = sprintf('TIMEOUT ');
+
+ case 3
+ txt = sprintf('ICE DETECTION');
+
+ otherwise
+ txt = sprintf('UNKNOWN ');
+ end
+
+end
+
+if type == 'C'
+ switch (status)
+
+ case 0
+ txt = sprintf('DONE ');
+
+ case 1
+ txt = sprintf('CTD FAILURE ');
+
+ otherwise
+ txt = sprintf('UNKNOWN ');
+ end
+
+end
diff --git a/lib/vendor/nemo2profilelib/+nemo/+plot/+templates/create_south.m b/lib/vendor/nemo2profilelib/+nemo/+plot/+templates/create_south.m
new file mode 100644
index 0000000..30697ef
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+plot/+templates/create_south.m
@@ -0,0 +1,157 @@
+function [ figure_id ] = create_south( p_config )
+%CREATE_SOUTH Creates a template plot that can be used for a variety of plots that require Weddell Sea as location.
+%
+% Returns:
+% figure_id: Figure handle of the template.
+%
+% Parameters:
+% p_config: Global configuration file, load it using nemo.load.config().
+
+
+%% Initialize return variable
+figure_id = false;
+
+%% Create template
+
+% load additional files from disk
+additional_content = nemo.load.additional_content(p_config);
+
+% store loaded data (should be changed on long term thought)
+Latitudes = additional_content.antarctic_latitudes;
+Longitudes = additional_content.antarctic_longitudes;
+ASI_Ice_Concentration = additional_content.antarctic_ice_concentration;
+Z = additional_content.etopo_z;
+refvec = additional_content.etopo_refvec;
+moorings = additional_content.moorings;
+
+clear additional_content
+
+% initialize figure
+figure_tmp = figure('Visible', 'off');
+% prepare contour variables
+[C1000,~] = contourm(Z,refvec,[-1000, -1000]);
+[C2000,~] = contourm(Z,refvec,[-2000, -2000]);
+[C3000,~] = contourm(Z,refvec,[-3000, -3000]);
+%[C3500,~] = contourm(Z,refvec,[-3500 -3500]);
+%[C4000,~] = contourm(Z,refvec,[-4000 -4000]);
+close(figure_tmp);
+clear figure_tmp Z refvec
+
+%figure_id = figure();
+figure_id = figure('Visible', 'Off');
+
+%set(figure_id,'color',[1 1 1],'Position',get(0,'ScreenSize'));
+%set(figure_id,'color',[1 1 1],'Position',[0, 0, 4000, 2250]);
+worldmap(p_config.PLOT_OVERVIEW_SOUTH.latitude_limit, ...
+ p_config.PLOT_OVERVIEW_SOUTH.longitude_limit);
+load coast
+plotm(lat,long,'k');
+
+geoshow(Latitudes, Longitudes, ASI_Ice_Concentration, 'DisplayType','surface');
+contourcmap('gray',10,'colorbar','off','location','horizontal', 'Visible', 'off');
+nValues = 128; %# The number of unique values in the colormap
+%map = [linspace(0.5,1,nValues)' linspace(0.7,1,nValues)' ones(nValues,1)]; %'# 128-by-3 colormap
+%colormap(map);
+cmocean('ice', 'pivot', '-1');
+
+ax_1000=plotm(C1000(2,:),C1000(1,:),'color',[0.2 0.6 .8]);
+ax_2000=plotm(C2000(2,:),C2000(1,:),'color',[0 0 1]);
+ax_3000= plotm(C3000(2,:),C3000(1,:),'color',[0.2 .4 0.8]);
+
+%ax_3500= plotm(C3500(2,:),C3500(1,:),'color',[0.2 .2 0.8]);
+%ax_4000= plotm(C4000(2,:),C4000(1,:),'color',[0.2 .0 0.8]);
+
+%% make legend
+%opengl hardware; % can only be used on pc with dedicated graphics
+
+ax_deploy=plot3m(0,0,-1,'marker',p_config.PLOT_STYLE_SOUTH.deploy_marker,'markersize',p_config.PLOT_STYLE_SOUTH.deploy_markersize,'color', p_config.PLOT_STYLE_SOUTH.deploy_color,'linestyle','none');
+ax_gps=plot3m(0,0,-1,'marker',p_config.PLOT_STYLE_SOUTH.gps_marker,'markersize',p_config.PLOT_STYLE_SOUTH.gps_markersize,'color',p_config.PLOT_STYLE_SOUTH.gps_color,'MarkerFaceColor', p_config.PLOT_STYLE_SOUTH.gps_color,'linestyle','none');
+ax_gps_interpolated=plot3m(0,0,-1,'marker',p_config.PLOT_STYLE_SOUTH.gps_marker,'markersize',p_config.PLOT_STYLE_SOUTH.gps_markersize,'color',p_config.PLOT_STYLE_SOUTH.gps_color_interpolated,'MarkerFaceColor', p_config.PLOT_STYLE_SOUTH.gps_color_interpolated,'linestyle','none');
+ax_last_transmittion=plot3m(0,0,-1,'marker',p_config.PLOT_STYLE_SOUTH.last_transmittion_marker,'markersize',p_config.PLOT_STYLE_SOUTH.last_transmittion_markersize,'color',p_config.PLOT_STYLE_SOUTH.last_transmittion_color,'MarkerFaceColor',p_config.PLOT_STYLE_SOUTH.last_transmittion_color,'linestyle','none');
+
+
+legend([ax_deploy,ax_gps,ax_gps_interpolated,ax_last_transmittion,ax_1000,ax_2000,ax_3000],'Deployment positions','Best guess positions', 'Best guess positions (interpolated)', 'Last known position','-1000m','-2000m','-3000m');
+%legend([ax_deploy,ax_gps,ax_gps_interpolated,ax_last_transmittion,ax_3000,ax_3500,ax_4000],'Deployment positions','Best guess positions', 'Best guess positions (interpolated)', 'Last known position','-3000m','-3500m','-4000m');
+
+% cb=colorbar('southoutside');
+% ylabel(cb, 'Sea ice concentration in %');
+
+%% create title
+text_figure_title = title('', 'position', [4.367541205137968 -5154159.006427274 99.99999999999999]);
+set(text_figure_title,'interpreter','none','fontsize',14);
+
+%% plot soso
+
+earthradius = 3.4401e+003; % nm
+
+
+if p_config.PLOT_OVERVIEW_SOUTH.show_moorings == 1
+
+ if ~iscell(moorings)
+ warning([mfilename ': Error loading moorings, skipping...']);
+ else
+ for o_moorings = 1:length(moorings)
+ lat = moorings{o_moorings}.lat;
+ lon = moorings{o_moorings}.lon;
+ detection_radius = moorings{o_moorings}.detection_radius;
+ if (~moorings{o_moorings}.hide_mooring)
+ switch (p_config.PLOT_STYLE_SOUTH.moorings_display_format)
+ case 1
+ plot3m(lat,lon,140,'.c','markersize',24);
+ [latc,longc,] = scircle1(lat, lon, detection_radius,[],earthradius);
+ height=ones(numel(latc),1)*200;
+ plot3m(latc,longc,height,'color','k');
+ case 2
+ plot3m(lat, lon, 140, 'pg','markersize',8,'MarkerFaceColor','k');
+ case 3
+ plotm(lat, lon,'.c','markersize',24);
+ [latc,longc] = scircle1(lat, lon, detection_radius,[],earthradius);
+ height=ones(numel(latc),1)*200;
+ plot3m(latc,longc,height,'color','k');
+ case 4
+ plot3m(lat, lon, 140,'dr','markersize',6,'LineWidth',3);
+ [latc,longc] = scircle1(lat, lon, detection_radius,[],earthradius);
+ height=ones(numel(latc),1)*200;
+ plot3m(latc,longc,height,'color','k');
+ case 5
+ plot3m(lat, lon,140,'.','markersize',30,'color',[.8 .8 .8]);
+ [latc,longc] = scircle1(lat, lon, detection_radius,[],earthradius);
+ height=ones(numel(latc),1)*200;
+ plot3m(latc,longc,height,'color',[.8 .8 .8]);
+ case 6
+ plot3m(lat, lon,140,'ok','markersize',6,'linewidth',2.5);
+ [latc,longc] = scircle1(lat, lon, detection_radius,[],earthradius);
+ height=ones(numel(latc),1)*200;
+ plot3m(latc,longc,height,'color','k');
+ case 7
+ plot3m(lat, lon,140,'og','markersize',6,'linewidth',2.5);
+ [latc,longc] = scircle1(lat, lon, detection_radius,[],earthradius);
+ geoshow(latc,longc,'color','k');
+ case 8
+ plot3m(lat, lon,140,'k*','markersize',8);
+ case 9
+ plot3m(lat, lon,140,'.','markersize',30,'color',[.8 .8 .8]);
+ [latc,longc] = scircle1(lat, lon, detection_radius,[],earthradius);
+ height=ones(numel(latc),1)*200;
+ plot3m(latc,longc,height,'color',[0 0 0]);
+ otherwise
+ plot3m(lat, lon,140,'.','markersize',30,'color',[.8 .8 .8]);
+ [latc,longc] = scircle1(lat, lon, detection_radius,[],earthradius);
+ height=ones(numel(latc),1)*200;
+ plot3m(latc,longc,height,'color',[0 0 0]);
+ end
+
+ if moorings{o_moorings}.show_name
+ h2=textm(lat, lon,140, moorings{o_moorings}.name);
+ set(h2,'Color','k', 'FontSize',6,'FontWeight','bold','HorizontalAlignment','center');
+ end
+
+ end
+ end
+ clear lat lon detection_radius
+ end
+
+end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+plot/arrival_of_profiles.m b/lib/vendor/nemo2profilelib/+nemo/+plot/arrival_of_profiles.m
new file mode 100644
index 0000000..5091df5
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+plot/arrival_of_profiles.m
@@ -0,0 +1,261 @@
+function [ boolean ] = arrival_of_profiles( p_nemo_data, p_config )
+%ARRIVAL_OF_PROFILES Plots details about iridium data.
+%
+% Returns:
+% boolean: False if something went wrong during the plotting process.
+%
+% Parameters:
+% p_nemo_data: Struct, containing all float data (load with nemo.load.data()).
+% p_config: Global configuration file. Load using nemo.load.config().
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~iscell(p_nemo_data) || ~isstruct(p_config))
+ parameter_error = true;
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% Setup directories
+directory = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_ARRIVAL_OF_PROFILES.storage_directory_image);
+directory_fig = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_ARRIVAL_OF_PROFILES.storage_directory_fig);
+image_type = p_config.PLOT_ARRIVAL_OF_PROFILES.image_type;
+if ~exist(directory, 'dir')
+ system(['mkdir ' directory]);
+end
+if ~exist(directory_fig, 'dir')
+ mkdir(directory_fig);
+end
+
+%% Process every float
+
+float_count = length(p_nemo_data);
+
+for o_float = 1:float_count
+
+ % collect required data
+
+ % count of profiles that have not been send earlier
+ unsent_profiles_count = nemo.float.collect( ...
+ p_nemo_data{o_float}, ...
+ 'PROFILE_TECHNICAL_DATA', ...
+ 'xmit_older_profiles_not_send' ...
+ );
+
+ % average time when the profile has been transmitted
+ iridium_mean_times = nemo.float.collect( ...
+ p_nemo_data{o_float}, ...
+ 'IRIDIUM_DATA', ...
+ '' ...
+ );
+ % extract only datevec from it
+ iridium_mean_times = datetime(iridium_mean_times(:, 4:9));
+
+ % data about every iridium message that has been transmitted for this profile
+ iridium_data = nemo.float.collect( ...
+ p_nemo_data{o_float}, ...
+ 'IRIDIUM_POSITIONS', ...
+ '' ...
+ );
+ iridium_message_count = zeros(1, length(iridium_data));
+ % time will be stored in seconds using etime
+ iridium_transmittion_time = zeros(1, length(iridium_data));
+ for o_tmp = 1:length(iridium_data)
+ iridium_message_count(o_tmp) = size(iridium_data{o_tmp}, 1);
+ % get iridium transmittion time if available
+ if iridium_message_count(o_tmp) > 1
+ tmp_min = iridium_data{o_tmp}(1, 4:9);
+ tmp_max = iridium_data{o_tmp}(end, 4:9);
+ iridium_transmittion_time(o_tmp) = etime(tmp_max, tmp_min);
+ else
+ iridium_transmittion_time(o_tmp) = NaN;
+ end
+ end
+
+ clear o_tmp iridium_data
+
+ % get numbers of the profiles that have been received
+ transmitted_profiles = nemo.float.collect(p_nemo_data{o_float}, ...
+ 'PROFILE_TECHNICAL_DATA', ...
+ 'xmit_profile_number' ...
+ );
+
+ % get gps data
+ gps_datetime = nemo.float.collect(p_nemo_data{o_float}, ...
+ 'SURFACE_GPS_DATA', ...
+ '' ...
+ );
+
+ best_guess_datevec = nemo.float.collect(p_nemo_data{o_float}, ...
+ 'SECOND_ORDER_INFORMATION', ...
+ 'best_guess_datevec' ...
+ );
+ best_guess_datenum = datenum(best_guess_datevec);
+
+ if isempty(gps_datetime)
+ disp(['No arrival of profiles generated for nemo ' ...
+ num2str(p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ '. No GPS information available!']);
+ continue;
+ end
+
+
+ % get plot details
+ width = p_config.PLOT_ARRIVAL_OF_PROFILES.image_width;
+ height = p_config.PLOT_ARRIVAL_OF_PROFILES.image_height;
+ paperunit = p_config.PLOT_ARRIVAL_OF_PROFILES.image_paperunit;
+
+ % plot collected data
+
+ figure_id = figure('Visible', 'off'); % create figure
+ % initialize figure
+ set(figure_id,'InvertHardcopy','on');
+ set(figure_id,'PaperUnits', paperunit);
+ papersize = get(figure_id, 'PaperSize');
+ left = (papersize(1)- width)/2;
+ bottom = (papersize(2)- height)/2;
+ myfiguresize = [left, bottom, width, height];
+ set(figure_id,'PaperPosition', myfiguresize);
+
+ clear height width left bottom papersize myfiguresize
+
+ %set(gcf, 'Position', get(0,'ScreenSize'), 'color', [1 1 1]);
+ sub = {};
+
+ sub{1} = subplot(4,1,1);
+ hold on
+ set(gca, 'YLimMode', 'manual', 'YLim', [1, length(transmitted_profiles)+1]);
+% set(gca, 'XLimMode', 'manual', 'XLim', [min_datenum, max_datenum]);
+% set_x_axis();
+
+ disp([' Processing arrival information of float number ',num2str(p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number)]) % OB
+
+ plot(best_guess_datenum, transmitted_profiles,'marker','.','color',[0.5 0.5 0.5],'linestyle','none','linewidth',1,'markersize',20);
+
+ % OB START: for float 173 iridium_mean_times is of type datetime, which does not
+ % comply with plot command
+ % Old Code:
+ % plot(iridium_mean_times, transmitted_profiles,'marker','.','color',[0 0 0],'linestyle','none','linewidth',1,'markersize',20);
+
+ % New Code
+ if isa(iridium_mean_times,'double')
+ plot(iridium_mean_times, transmitted_profiles,'marker','.','color',[0 0 0],'linestyle','none','linewidth',1,'markersize',20);
+ elseif isa(iridium_mean_times,'datetime')
+ plot(datenum(iridium_mean_times), transmitted_profiles,'marker','.','color',[0 0 0],'linestyle','none','linewidth',1,'markersize',20);
+ end
+ % OB END
+
+ t = title([ 'Float ' ...
+ num2str(p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ ' @ ' ...
+ datestr(datetime('now', 'Format', 'dd-MMM-yyyy HH:mm:SS')) ...
+ ]);
+ set(t, 'FontSize', 18);
+ clear t
+ ylabel('Profile number');
+ grid on
+ box on
+ hold off
+
+ % unsent profiles_count
+ sub{2} = subplot(4,1,2);
+ hold on
+% set(gca, 'XLimMode', 'manual', 'XLim', [min_datenum, max_datenum]);
+% set_x_axis();
+ plot(best_guess_datenum, unsent_profiles_count, 'marker','s','color',[0 0 0],'markerfacecolor',[0 0 0],'linestyle','none','markersize',4);
+
+
+ ylabel('Unsent profile count');
+ grid on
+ box on
+ hold off
+
+ sub{3} = subplot(4,1,3);
+ hold on
+ plot(best_guess_datenum, iridium_transmittion_time./60, '.-','Markersize',15 );
+ ylabel('Transmission time [min]');
+
+ grid on
+ box on
+ hold off
+
+ sub{4} = subplot(4,1,4);
+ hold on
+ plot(best_guess_datenum, iridium_message_count, '.-', 'linestyle', 'none','Markersize',15 );
+
+ ylabel('Message count');
+ grid on
+ box on
+
+ hold off
+
+ sub = cellfun(@set_x_axis, sub, 'UniformOutput', false);
+
+ % store plot
+
+ image_filename = [p_config.PLOT_ARRIVAL_OF_PROFILES.image_filename ...
+ num2str(p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number)];
+ figure_filename = [p_config.PLOT_ARRIVAL_OF_PROFILES.figure_filename ...
+ num2str(p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number)];
+
+ print(figure_id, [directory image_filename], image_type);
+
+ if (p_config.PLOT_ARRIVAL_OF_PROFILES.save_figure)
+ set(gcf,'CreateFcn','set(gcf,''Visible'',''on'')');
+ saveas(figure_id, ...
+ [directory_fig figure_filename]);
+ end
+
+ close(figure_id);
+
+end
+
+boolean = true;
+
+
+ function current_plot = set_x_axis(current_plot)
+
+ % get min and max datevec
+ min_datenum = min(datenum(best_guess_datevec));
+ max_datenum = max(datenum(best_guess_datevec));
+ if (min_datenum == max_datenum)
+ max_datenum = max_datenum + 1;
+ end
+ diff_datenum = max_datenum - min_datenum;
+ if (diff_datenum > 365)
+ x_tick = [min_datenum:365:max_datenum];
+ elseif (diff_datenum > 30)
+ x_tick = [min_datenum:30:max_datenum];
+ elseif (diff_datenum > 5)
+ x_tick = [min_datenum:5:max_datenum];
+ else
+ x_tick = [min_datenum:1:max_datenum];
+ end
+ if (x_tick(end) < max_datenum)
+ x_tick = [ x_tick max_datenum ];
+ end
+ x_tick_labels = cellstr(datestr(x_tick, 'yyyy-mm-dd'));
+ x_tick_labels_top = cellstr(datestr(x_tick, 'yyyy-mm-dd'));
+
+ if (~isempty(x_tick_labels))
+ x_tick_labels{end} = '';
+ end
+
+ set(current_plot, 'XLimMode', 'manual', ...
+ 'XLim', [min_datenum, max_datenum], ...
+ 'XTick', x_tick, ...
+ 'XTickLabel', x_tick_labels);
+
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+plot/arrival_of_profiles_overview.m b/lib/vendor/nemo2profilelib/+nemo/+plot/arrival_of_profiles_overview.m
new file mode 100644
index 0000000..54f6cf9
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+plot/arrival_of_profiles_overview.m
@@ -0,0 +1,232 @@
+function [ boolean ] = arrival_of_profiles_overview( p_nemo_data, p_config )
+%ARRIVAL_OF_PROFILES Plots details about iridium data.
+%
+% Returns:
+% boolean: False if something went wrong during the plotting process.
+%
+% Parameters:
+% p_nemo_data: Struct, containing all float data (load with nemo.load.data()).
+% p_config: Global configuration file. Load using nemo.load.config().
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~iscell(p_nemo_data) || ~isstruct(p_config))
+ parameter_error = true;
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% Setup directories
+directory = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_ARRIVAL_OF_PROFILES_OVERVIEW.storage_directory_image);
+directory_fig = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_ARRIVAL_OF_PROFILES_OVERVIEW.storage_directory_fig);
+image_type = p_config.PLOT_ARRIVAL_OF_PROFILES_OVERVIEW.image_type;
+if ~exist(directory, 'dir')
+ system(['mkdir ' directory]);
+end
+if ~exist(directory_fig, 'dir')
+ mkdir(directory_fig);
+end
+
+
+%% Collect required data
+
+first_deployment_datenum = NaN; % contains the earliest deployment date of all floats
+latest_profile_datenum = NaN; % contains the latest profile that has been transmitted
+
+best_guess_datenum = {};
+transmitted_profiles = {};
+iridium_mean_times = {};
+float_serials = [];
+
+float_count = length(p_nemo_data);
+
+for o_float = 1:float_count
+
+ % get serial number
+ float_serials = [float_serials; p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number];
+
+ % get the deployment dates
+ current_deployment_datenum = datenum( ...
+ [ ...
+ p_nemo_data{o_float}{1}.DEPLOYMENT_INFO.deployment_date ...
+ p_nemo_data{o_float}{1}.DEPLOYMENT_INFO.deployment_time ...
+ 0 ...
+ ] ...
+ );
+ if isnan(first_deployment_datenum) || (current_deployment_datenum < first_deployment_datenum)
+ first_deployment_datenum = current_deployment_datenum;
+ end
+ current_latest_profile_datenum = datenum(p_nemo_data{o_float}{end}.SECOND_ORDER_INFORMATION.best_guess_datevec);
+ % get latest profile date
+ if ~all(isnan(current_latest_profile_datenum)) && (isnan(latest_profile_datenum) || (current_latest_profile_datenum > latest_profile_datenum))
+ latest_profile_datenum = current_latest_profile_datenum;
+ end
+
+ % check if gps data available
+ gps_datetime = nemo.float.collect(p_nemo_data{o_float}, ...
+ 'SURFACE_GPS_DATA', ...
+ '' ...
+ );
+ if isempty(gps_datetime)
+ continue;
+ end
+
+
+ % collect required data
+
+ best_guess_datevec = nemo.float.collect(p_nemo_data{o_float}, ...
+ 'SECOND_ORDER_INFORMATION', ...
+ 'best_guess_datevec' ...
+ );
+ best_guess_datenum{o_float} = datenum(best_guess_datevec);
+
+ % get numbers of the profiles that have been received
+ transmitted_profiles{o_float} = nemo.float.collect(p_nemo_data{o_float}, ...
+ 'PROFILE_TECHNICAL_DATA', ...
+ 'xmit_profile_number' ...
+ );
+
+ % average time when the profile has been transmitted
+ iridium_mean_times{o_float} = nemo.float.collect( ...
+ p_nemo_data{o_float}, ...
+ 'IRIDIUM_DATA', ...
+ '' ...
+ );
+ % extract only datevec from it
+ iridium_mean_times{o_float} = datetime(iridium_mean_times{o_float}(:, 4:9));
+
+
+end
+
+% get min and max datevec
+if (first_deployment_datenum == latest_profile_datenum)
+ latest_profile_datenum = latest_profile_datenum + 1;
+end
+diff_datenum = latest_profile_datenum - first_deployment_datenum;
+if (diff_datenum > 365)
+ x_tick = [first_deployment_datenum:365:latest_profile_datenum];
+elseif (diff_datenum > 30)
+ x_tick = [first_deployment_datenum:30:latest_profile_datenum];
+elseif (diff_datenum > 5)
+ x_tick = [first_deployment_datenum:5:latest_profile_datenum];
+else
+ x_tick = [first_deployment_datenum:1:latest_profile_datenum];
+end
+x_tick = [ x_tick(1:end-1) latest_profile_datenum ];
+
+% get plot details
+width = p_config.PLOT_ARRIVAL_OF_PROFILES_OVERVIEW.image_width;
+height = p_config.PLOT_ARRIVAL_OF_PROFILES_OVERVIEW.image_height;
+paperunit = p_config.PLOT_ARRIVAL_OF_PROFILES_OVERVIEW.image_paperunit;
+
+% plot collected data
+
+figure_id = figure('Visible', 'off'); % create figure
+% initialize figure
+set(figure_id,'InvertHardcopy','on');
+set(figure_id,'PaperUnits', paperunit);
+papersize = get(figure_id, 'PaperSize');
+left = (papersize(1)- width)/2;
+bottom = (papersize(2)- height)/2;
+myfiguresize = [left, bottom, width, height];
+set(figure_id,'PaperPosition', myfiguresize);
+clear height width left bottom papersize myfiguresize
+
+%set(gcf, 'Position', get(0,'ScreenSize'), 'color', [1 1 1]);
+sub = {};
+
+sub{1} = subplot(2,1,1);
+hold on
+% set(gca, 'XLimMode', 'manual', 'XLim', [min_datenum, max_datenum]);
+% set_x_axis();
+for o_float = 1:float_count
+ y = repmat(float_serials(o_float), length(transmitted_profiles{o_float}), 1);
+ plot(transmitted_profiles{o_float}, y,'marker','.','color',[0 0 0],'linestyle','none','linewidth',1,'markersize',20);
+ clear y
+end
+
+t = title([ 'Arrival of profiles overview @ ' ...
+ datestr(datetime('now', 'Format', 'dd-MMM-yyyy HH:mm:SS')) ...
+ ]);
+set(t, 'FontSize', 18);
+clear t
+ylabel('Float serial number');
+xlabel('Profile number');
+grid on
+box on
+hold off
+
+
+
+sub{2} = subplot(2,1,2);
+hold on
+% set(gca, 'XLimMode', 'manual', 'XLim', [min_datenum, max_datenum]);
+% set_x_axis();
+for o_float = 1:float_count
+
+ disp([' Processing arrival overview information of float number ',num2str(p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number)]) % OB
+
+ y = repmat(float_serials(o_float), length(best_guess_datenum{o_float}), 1);
+ plot(best_guess_datenum{o_float}, y,'marker','.','color',[0.5 0.5 0.5],'linestyle','none','linewidth',1,'markersize',20);
+ y = repmat(float_serials(o_float), length(transmitted_profiles{o_float}), 1);
+
+ % OB START: for float 173 iridium_mean_times is of type datetime, which does not
+ % comply with plot command
+ % Old Code:
+ % plot(iridium_mean_times{o_float}, y,'marker','.','color',[0 0 0],'linestyle','none','linewidth',1,'markersize',20);
+ % New Code
+ if isa(iridium_mean_times{o_float},'double')
+ plot(iridium_mean_times{o_float}, y,'marker','.','color',[0 0 0],'linestyle','none','linewidth',1,'markersize',20);
+ elseif isa(iridium_mean_times{o_float},'datetime')
+ plot(datenum(iridium_mean_times{o_float}), y,'marker','.','color',[0 0 0],'linestyle','none','linewidth',1,'markersize',20);
+ end
+ % OB END
+
+ clear y
+end
+
+ylabel('Float serial number');
+xlabel('Iridium timestamp');
+grid on
+box on
+hold off
+
+% set_x_axis(sub{2});
+
+
+% store plot
+
+image_filename = p_config.PLOT_ARRIVAL_OF_PROFILES_OVERVIEW.image_filename;
+figure_filename = p_config.PLOT_ARRIVAL_OF_PROFILES_OVERVIEW.figure_filename;
+
+print(figure_id, [directory image_filename], image_type);
+
+ if (p_config.PLOT_ARRIVAL_OF_PROFILES_OVERVIEW.save_figure)
+ saveas(figure_id, ...
+ [directory_fig figure_filename]);
+ end
+
+close(figure_id);
+
+boolean = true;
+
+
+ function current_plot = set_x_axis(current_plot)
+ set(current_plot, 'XLimMode', 'manual', ...
+ 'XLim', [first_deployment_datenum, latest_profile_datenum], ...
+ 'XTick', x_tick);
+ datetick(current_plot, 'x', 'yyyy-mm-dd', 'keepticks');
+
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+plot/ascent.m b/lib/vendor/nemo2profilelib/+nemo/+plot/ascent.m
new file mode 100644
index 0000000..21cdcbc
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+plot/ascent.m
@@ -0,0 +1,207 @@
+function [ boolean ] = ascent( p_nemo_data, p_config )
+%ASCENT Generates plots showing the ascent data of the float.
+% Generates a plot for every float in p_nemo_data containing the depth on
+% recorded time of day, profile recording time on profile number as well
+% as 0 to 50m depth on profile number.
+%
+% Parameters:
+% p_nemo_data: The float data.
+% p_config: The nemo configuration.
+%
+% Returns:
+% boolean: True if successful.
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check %TODO
+
+%% Get config parameter
+% get plot details
+width = p_config.PLOT_ASCENT.image_width;
+height = p_config.PLOT_ASCENT.image_height;
+paperunit = p_config.PLOT_ASCENT.image_paperunit;
+image_type = p_config.PLOT_ASCENT.image_type;
+directory = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_ASCENT.storage_directory_image);
+directory_fig = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_ASCENT.storage_directory_fig);
+ylabel_fontsize = p_config.PLOT_ASCENT.ylabel_fontsize;
+xlabel_fontsize = p_config.PLOT_ASCENT.ylabel_fontsize;
+axis_fontsize = p_config.PLOT_ASCENT.axis_fontsize;
+title_fontsize = p_config.PLOT_ASCENT.title_fontsize;
+
+if (~isdir(directory))
+ mkdir(directory);
+end
+if ~exist(directory_fig, 'dir')
+ mkdir(directory_fig);
+end
+
+%% Collect required data
+
+switch (class(p_nemo_data{1}))
+ case 'struct' % only one float is to be processed
+ boolean = plot_float(p_nemo_data);
+ case 'cell' % more than one float has to be processed
+ boolean = all(cellfun(@plot_float, p_nemo_data));
+ otherwise
+ disp([mfilename ': Class ' class(p_nemo_data{1}) ' not supported for plotting!']);
+end
+
+ function boolean = plot_float(p_float)
+ boolean = false;
+ profile_data = nemo.float.collect(p_float, 'PROFILE_DATA', '');
+ profile_best_guess_datevec = nemo.float.collect(p_float, ...
+ 'SECOND_ORDER_INFORMATION', ...
+ 'best_guess_datevec');
+% profiles_best_guess_datenum = datenum([1970, 1, 1, profiles_best_guess_datevec(:, 4:6)]);
+ if (isempty(profile_data))
+ boolean = true;
+ return
+ end
+
+ % initialize figure
+ figure_id = figure('Visible', 'Off');
+ set(figure_id,'InvertHardcopy','on');
+ set(figure_id,'PaperUnits', paperunit, 'Position', [ 0 0 width height]);
+ papersize = get(figure_id, 'PaperSize');
+ left = (papersize(1) - width)/2;
+ bottom = (papersize(2) - height)/2;
+ myfiguresize = [left, bottom, width, height];
+ set(figure_id,'PaperPosition', myfiguresize);
+
+ % Depth on time plot
+ sub(1) = subplot(2, 2, 1);
+ hold on
+ set(gca, 'YLimMode', 'manual', 'YLim', [0 2000], ...
+ 'YTick', [0:200:2000], 'YDir', 'reverse');
+ xlimits = [datenum(0, 0, 0, 0, 0, 0) datenum(0, 0, 0, 24, 0, 0)];
+ set(gca, 'XLim', xlimits, 'XTick', linspace(xlimits(1), xlimits(2), 7));
+ for i = 1:length(profile_data)
+ plot_x = mod(datenum([ ...
+ repmat(1970, length(profile_data{i}), 1) ...
+ , ones(length(profile_data{i}), 1) ...
+ , ones(length(profile_data{i}), 1) ...
+ , profile_data{i}(:, 2:4)]), 1);
+ plot_y = profile_data{i}(:, 7);
+ plot_c = [0 0 1] * i/length(profile_data);
+ scatter(plot_x, plot_y, 30, plot_c, 'filled');
+ end
+ datetick('x','HH:MM', 'keepticks', 'keeplimits');
+ a = get(gca, 'YTickLabel');
+ set(gca, 'YTickLabel', a, 'fontsize', axis_fontsize)
+ a = get(gca, 'XTickLabel');
+ set(gca, 'XTickLabel', a, 'fontsize', axis_fontsize)
+ ylabel('Depth [m]', 'FontSize', ylabel_fontsize);
+ xlabel('Time of day', 'FontSize', xlabel_fontsize);
+ box on
+ grid on
+ hold off
+
+ % Profile data time on profile number
+ sub(2) = subplot(2, 2, 3);
+ hold on
+ ylimits = [datenum(0, 0, 0, 0, 0, 0) datenum(0, 0, 0, 24, 0, 0)];
+ set(gca, 'YLimMode', 'manual', 'YLim', ylimits, 'YTick', linspace(ylimits(1), ylimits(2), 7));
+ % get required information about x-axis limits and ticks
+ profile_best_guess_datenum = datenum(profile_best_guess_datevec);
+% start_datenum = min(profile_best_guess_datenum);
+% end_datenum = max(profile_best_guess_datenum);
+% x_diff = max(profile_best_guess_datenum) ...
+% - min(profile_best_guess_datenum);
+% if (start_datenum ~= end_datenum)
+% set(gca, ...
+% 'XLimMode', 'manual', ...
+% 'XLim', [start_datenum, end_datenum]);
+% end
+% if (x_diff < 30)
+% set(gca, 'XTick', [start_datenum:5:end_datenum]);
+% elseif (x_diff < 365)
+% set(gca, 'XTick', [start_datenum:30:end_datenum]);
+% else
+% set(gca, 'XTick', [start_datenum:365:end_datenum]);
+% end
+ for i = 1:length(profile_data)
+ plot_x = ones(1, length(profile_data{i}(:, 1))) * i;
+ plot_y = datenum([zeros(length(profile_data{i}(:, 1)), 1), ...
+ zeros(length(profile_data{i}(:, 1)), 1), ...
+ zeros(length(profile_data{i}(:, 1)), 1), ...
+ profile_data{i}(:,2:4)]);
+ scatter(plot_x, plot_y, 30, [0 0 0], 'filled');
+ end
+ datetick('y','HH:MM', 'keepticks', 'keeplimits');
+% datetick('x','yyyy-mm-dd', 'keepticks', 'keeplimits');
+ set(gca, 'fontsize', axis_fontsize)
+ ylabel('Profile recording time [HH:MM]', 'FontSize', ylabel_fontsize);
+ xlabel('Profile number', 'FontSize', xlabel_fontsize);
+ box on
+ grid on
+ hold off
+
+ % Zoom on upper 50m water column
+ sub(3) = subplot(1, 2, 2);
+ hold on
+ set(gca, 'YLimMode', 'manual', 'YDir', 'reverse', 'YLim', [0 50], ...
+ 'XLimMode', 'auto');
+ set(gca, 'fontsize', axis_fontsize)
+ ylabel('Depth [m]', 'FontSize', ylabel_fontsize);
+ xlabel('Profile number', 'FontSize', xlabel_fontsize);
+ % get required information about x-axis limits and ticks
+ for i = 1:length(profile_data)
+ temperature = profile_data{i}(:, 5);
+ pressure = profile_data{i}(:, 7);
+ % erase all invalid values
+ valid_points = (pressure >= 0) & (pressure <= 50);
+ temperature = temperature(valid_points);
+ pressure = pressure(valid_points);
+ x_axis = ones(size(pressure, 1), 1) * i;
+ scatter(x_axis, pressure, 45, temperature, 'filled');
+ end
+ c = colorbar;
+ cmocean('thermal');
+ %colormap(gca, 'jet');
+ %caxis([-5, 15]);
+ c.Label.String = 'Temperature [°C]';
+ clear c
+
+
+ % create main title
+ if (p_float{1}.SECOND_ORDER_INFORMATION.best_guess_position_lat > 0)
+ deployment_string = ' (Arctic)';
+ else
+ deployment_string = ' (Antarctica)';
+ end
+ t = title([ 'Float ' ...
+ num2str(p_float{1}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ ' @ ' ...
+ datestr(datetime('now', 'Format', 'dd-MMM-yyyy HH:mm:SS')) ...
+ deployment_string ...
+ ]);
+ set(t, 'FontSize', title_fontsize);
+ clear t
+
+ box on
+ grid on
+ hold off
+
+ set(gcf, 'Renderer', 'painters');
+ print(figure_id, ...
+ [directory p_config.PLOT_ASCENT.image_filename ...
+ num2str(p_float{1}.FLOAT_IDENTIFICATION.float_serial_number)] ...
+ , image_type);
+
+ if (p_config.PLOT_ASCENT.save_figure)
+ set(gcf,'CreateFcn','set(gcf,''Visible'',''on'')');
+ saveas(figure_id, ...
+ [directory_fig ...
+ p_config.PLOT_ASCENT.figure_filename ...
+ num2str(p_float{1}.FLOAT_IDENTIFICATION.float_serial_number)]);
+ end
+
+ close(figure_id);
+ clear figure_id f
+ boolean = true;
+
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+plot/categorized_timings.m b/lib/vendor/nemo2profilelib/+nemo/+plot/categorized_timings.m
new file mode 100644
index 0000000..bef2ee2
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+plot/categorized_timings.m
@@ -0,0 +1,327 @@
+function [ boolean ] = categorized_timings( p_nemo_data, p_config )
+%TIMING_INFORMATION Plots clock details.
+%
+% Returns:
+% boolean: False if something went wrong during the plotting process.
+%
+% Parameters:
+% p_nemo_data: Struct, containing all float data (load with nemo.load.data()).
+% p_config: Global configuration file. Load using nemo.load.config().
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~iscell(p_nemo_data) || ~isstruct(p_config))
+ parameter_error = true;
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% Setup directories
+directory = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_CATEGORIZED_TIMINGS.storage_directory_image);
+directory_fig = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_CATEGORIZED_TIMINGS.storage_directory_fig);
+image_type = p_config.PLOT_CATEGORIZED_TIMINGS.image_type;
+if ~exist(directory, 'dir')
+ system(['mkdir ' directory]);
+end
+if ~exist(directory_fig, 'dir')
+ mkdir(directory_fig);
+end
+
+%% Process every float
+
+float_count = length(p_nemo_data);
+
+for o_float = 1:float_count
+
+ current_float = p_nemo_data{o_float};
+
+ start_date = current_float{end}.OVERALL_MISSION_INFORMATION.start_date;
+ start_time = current_float{end}.OVERALL_MISSION_INFORMATION.start_time;
+ xmit_ascent_start_time = nemo.float.collect(current_float, 'PROFILE_TECHNICAL_DATA', 'xmit_ascent_start_time');
+ xmit_ascent_end_time = nemo.float.collect(current_float, 'PROFILE_TECHNICAL_DATA', 'xmit_ascent_end_time');
+ xmit_descent_start_time = nemo.float.collect(current_float, 'PROFILE_TECHNICAL_DATA', 'xmit_descent_start_time');
+ xmit_parking_start_time = nemo.float.collect(current_float, 'PROFILE_TECHNICAL_DATA', 'xmit_parking_start_time');
+ xmit_upcast_start_time = nemo.float.collect(current_float, 'PROFILE_TECHNICAL_DATA', 'xmit_upcast_start_time');
+ xmit_surface_start_time = nemo.float.collect(current_float, 'PROFILE_TECHNICAL_DATA', 'xmit_surface_start_time');
+ xmit_profile_number = nemo.float.collect(current_float, 'PROFILE_TECHNICAL_DATA', 'xmit_profile_number');
+
+ combined_xmit_times = [ ...
+ xmit_descent_start_time, ...
+ xmit_parking_start_time, ...
+ xmit_upcast_start_time, ...
+ xmit_ascent_start_time, ...
+ xmit_ascent_end_time, ...
+ xmit_surface_start_time ...
+ ];
+
+ combined_diff_times = [ ...
+% NaN(length(xmit_descent_start_time), 1), ...
+ (xmit_descent_start_time - xmit_parking_start_time), ...
+ (xmit_parking_start_time - xmit_upcast_start_time), ...
+ (xmit_upcast_start_time - xmit_ascent_start_time), ...
+ (xmit_ascent_start_time - xmit_ascent_end_time), ...
+ (xmit_ascent_end_time - xmit_surface_start_time), ...
+ [NaN; (xmit_surface_start_time(1:end -1) - xmit_descent_start_time(2:end))]
+ ];
+
+ [p_row, ~] = size(combined_xmit_times);
+ tmp_xmit_times = [];
+ tmp_diff_times = [];
+ for o_row = 1:p_row
+ tmp_xmit_times = [ tmp_xmit_times; combined_xmit_times(o_row, :)'];
+ tmp_diff_times = [ tmp_diff_times; combined_diff_times(o_row, :)'];
+ end
+ % categorize them
+ combined_xmit_times = [repmat([3:6, 2, 1]', length(tmp_xmit_times)/6, 1), tmp_xmit_times];
+ combined_diff_times = [repmat([3:6, 2, 1]', length(tmp_diff_times)/6, 1), tmp_diff_times];
+ clear tmp_xmit_times tmp_diff_times
+
+
+ % get plot details
+ width = p_config.PLOT_CATEGORIZED_TIMINGS.image_width;
+ height = p_config.PLOT_CATEGORIZED_TIMINGS.image_height;
+ paperunit = p_config.PLOT_CATEGORIZED_TIMINGS.image_paperunit;
+
+ % plot collected data
+
+ figure_id = figure('Visible', 'off'); % create figure
+ % initialize figure
+ set(figure_id,'InvertHardcopy','on');
+ set(figure_id,'PaperUnits', paperunit);
+ papersize = get(figure_id, 'PaperSize');
+ left = (papersize(1)- width)/2;
+ bottom = (papersize(2)- height)/2;
+ myfiguresize = [left, bottom, width, height];
+ set(figure_id,'PaperPosition', myfiguresize);
+
+ clear height width left bottom papersize myfiguresize
+
+ %set(gcf, 'Position', get(0,'ScreenSize'), 'color', [1 1 1]);
+ sub = {};
+
+ sub{1} = subplot(2,1,1);
+ hold on
+
+
+ plot(combined_xmit_times(:, 2), combined_xmit_times(:, 1), ...
+ 'color', [0 0 0], ...
+ 'linestyle', '-', ...
+ 'linewidth', 1 ...
+ );
+ scatter(combined_xmit_times(combined_xmit_times(:, 1) == 3, 2), combined_xmit_times(combined_xmit_times(:, 1) == 3, 1), ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', [1 0 0], ...
+ 'MarkerEdgeColor', [1 0 0] ...
+ );
+ scatter(combined_xmit_times(combined_xmit_times(:, 1) == 4, 2), combined_xmit_times(combined_xmit_times(:, 1) == 4, 1), ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', [0 1 0], ...
+ 'MarkerEdgeColor', [0 1 0] ...
+ );
+ scatter(combined_xmit_times(combined_xmit_times(:, 1) == 5, 2), combined_xmit_times(combined_xmit_times(:, 1) == 5, 1), ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', [0 0 1], ...
+ 'MarkerEdgeColor', [0 0 1] ...
+ );
+ scatter(combined_xmit_times(combined_xmit_times(:, 1) == 6, 2), combined_xmit_times(combined_xmit_times(:, 1) == 6, 1), ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', [1 1 0], ...
+ 'MarkerEdgeColor', [1 1 0] ...
+ );
+ scatter(combined_xmit_times(combined_xmit_times(:, 1) == 2, 2), combined_xmit_times(combined_xmit_times(:, 1) == 2, 1), ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', [0 1 1], ...
+ 'MarkerEdgeColor', [0 1 1] ...
+ );
+ scatter(combined_xmit_times(combined_xmit_times(:, 1) == 1, 2), combined_xmit_times(combined_xmit_times(:, 1) == 1, 1), ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', [1 0 1], ...
+ 'MarkerEdgeColor', [1 0 1] ...
+ );
+
+ ylabel('Category');
+ xlabel('Seconds since start');
+ axis ij;
+% legend('SurfaceStart-GPS', 'SurfaceStart-IRIDIUM', 'AscentStart-RTC2000');
+ leg1 = legend('TimesConnected', 'DescentStart', 'ParkingStart', 'UpcastStart', 'AscentStart', 'AscentEnd', 'SurfaceStart');
+ set(leg1, 'Location', 'eastoutside', 'Orientation', 'vertical');
+ clear leg1
+ t = title(...
+ [ 'Float ' ...
+ num2str(p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ ' @ ' ...
+ datestr(datetime('now', 'Format', 'dd-MMM-yyyy HH:mm:SS')) ...
+ ]);
+ set(t, 'FontSize', 18);
+ clear t
+ grid on
+ box on
+ hold off
+
+ sub{2} = subplot(2,1,2);
+ hold on
+
+
+ plot(combined_xmit_times(:, 2), combined_diff_times(:, 2), ...
+ 'color', [0 0 0], ...
+ 'linestyle', '-', ...
+ 'linewidth', 1 ...
+ );
+ scatter(combined_xmit_times(combined_xmit_times(:, 1) == 3, 2), combined_diff_times(combined_diff_times(:, 1) == 3, 2), ...
+ 'marker', 'o', ...
+ 'MarkerEdgeColor', [1 0 0] ...
+ );
+ scatter(combined_xmit_times(combined_xmit_times(:, 1) == 4, 2), combined_diff_times(combined_diff_times(:, 1) == 4, 2), ...
+ 'marker', 'o', ...
+ 'MarkerEdgeColor', [0 1 0] ...
+ );
+ scatter(combined_xmit_times(combined_xmit_times(:, 1) == 5, 2), combined_diff_times(combined_diff_times(:, 1) == 5, 2), ...
+ 'marker', 'o', ...
+ 'MarkerEdgeColor', [0 0 1] ...
+ );
+ scatter(combined_xmit_times(combined_xmit_times(:, 1) == 6, 2), combined_diff_times(combined_diff_times(:, 1) == 6, 2), ...
+ 'marker', 'o', ...
+ 'MarkerEdgeColor', [1 1 0] ...
+ );
+ scatter(combined_xmit_times(combined_xmit_times(:, 1) == 2, 2), combined_diff_times(combined_diff_times(:, 1) == 2, 2), ...
+ 'marker', 'o', ...
+ 'MarkerEdgeColor', [0 1 1] ...
+ );
+ scatter(combined_xmit_times(combined_xmit_times(:, 1) == 1, 2), combined_diff_times(combined_diff_times(:, 1) == 1, 2), ...
+ 'marker', 'o', ...
+ 'MarkerEdgeColor', [1 0 1] ...
+ );
+
+
+ % plot all times > 0 and hide them from legend
+ selector = combined_diff_times(:, 1) == 3 & combined_diff_times(:, 2) > 0;
+ scat1 = scatter(combined_xmit_times(selector, 2), combined_diff_times(selector, 2), ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', [1 0 0], ...
+ 'MarkerEdgeColor', [1 0 0] ...
+ );
+ hasbehavior(scat1, 'legend', false);
+ selector = combined_diff_times(:, 1) == 4 & combined_diff_times(:, 2) > 0;
+ scat1 = scatter(combined_xmit_times(selector, 2), combined_diff_times(selector, 2), ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', [0 1 0], ...
+ 'MarkerEdgeColor', [0 1 0] ...
+ );
+ hasbehavior(scat1, 'legend', false);
+ selector = combined_diff_times(:, 1) == 5 & combined_diff_times(:, 2) > 0;
+ scat1 = scatter(combined_xmit_times(selector, 2), combined_diff_times(selector, 2), ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', [0 0 1], ...
+ 'MarkerEdgeColor', [0 0 1] ...
+ );
+ hasbehavior(scat1, 'legend', false);
+ selector = combined_diff_times(:, 1) == 6 & combined_diff_times(:, 2) > 0;
+ scat1 = scatter(combined_xmit_times(selector, 2), combined_diff_times(selector, 2), ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', [1 1 0], ...
+ 'MarkerEdgeColor', [1 1 0] ...
+ );
+ hasbehavior(scat1, 'legend', false);
+ selector = combined_diff_times(:, 1) == 2 & combined_diff_times(:, 2) > 0;
+ scat1 = scatter(combined_xmit_times(selector, 2), combined_diff_times(selector, 2), ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', [0 1 1], ...
+ 'MarkerEdgeColor', [0 1 1] ...
+ );
+ hasbehavior(scat1, 'legend', false);
+ selector = combined_diff_times(:, 1) == 1 & combined_diff_times(:, 2) > 0;
+ scat1 = scatter(combined_xmit_times(selector, 2), combined_diff_times(selector, 2), ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', [1 0 1], ...
+ 'MarkerEdgeColor', [1 0 1] ...
+ );
+ hasbehavior(scat1, 'legend', false);
+ clear scat1
+
+
+ ylabel('Time difference [sec]');
+ xlabel('Seconds since start');
+% axis ij;
+% legend('SurfaceStart-GPS', 'SurfaceStart-IRIDIUM', 'AscentStart-RTC2000');
+ leg1 = legend('DiffsConnected', 'DescentStart-ParkingStart', 'ParkingStart-UpcastStart', 'UpcastStart-AscentStart', 'AscentStart-AscentEnd', 'AscentEnd-SurfaceStart', 'SurfaceStart-DescentStart');
+ set(leg1, 'Location', 'eastoutside', 'Orientation', 'vertical');
+ clear leg1
+ grid on
+ box on
+ hold off
+
+ sub1_pos = get(sub{1}, 'Position');
+ sub2_pos = get(sub{2}, 'Position');
+% leg1_pos = get(leg1, 'Position');
+ set(sub{1}, 'Position', [sub1_pos(1:2) 0.6652 sub1_pos(4)]);
+ set(sub{2}, 'Position', [sub2_pos(1:2) 0.6652 sub2_pos(4)]);
+
+ % store plot
+
+ image_filename = [p_config.PLOT_CATEGORIZED_TIMINGS.image_filename ...
+ num2str(p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number)];
+ figure_filename = [p_config.PLOT_CATEGORIZED_TIMINGS.figure_filename ...
+ num2str(p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number)];
+
+ if (p_config.PLOT_CATEGORIZED_TIMINGS.save_figure)
+ set(gcf,'CreateFcn','set(gcf,''Visible'',''on'')');
+ saveas(figure_id, ...
+ [directory_fig figure_filename]);
+ end
+
+
+ print(figure_id, [directory image_filename], image_type);
+
+ close(figure_id);
+
+end
+
+boolean = true;
+
+
+ function current_plot = set_x_axis(current_plot)
+
+ best_guess_datevec = nemo.float.collect(current_float, 'SECOND_ORDER_INFORMATION', 'best_guess_datevec');
+ % get min and max datevec
+ min_datenum = min(datenum(best_guess_datevec));
+ max_datenum = max(datenum(best_guess_datevec));
+ if (min_datenum == max_datenum)
+ max_datenum = max_datenum + 1;
+ end
+ diff_datenum = max_datenum - min_datenum;
+ if (diff_datenum > 365)
+ x_tick = [min_datenum:365:max_datenum];
+ elseif (diff_datenum > 30)
+ x_tick = [min_datenum:30:max_datenum];
+ elseif (diff_datenum > 5)
+ x_tick = [min_datenum:5:max_datenum];
+ else
+ x_tick = [min_datenum:1:max_datenum];
+ end
+ if (x_tick(end) < max_datenum)
+ x_tick = [ x_tick max_datenum ];
+ end
+ x_tick_labels = cellstr(datestr(x_tick, 'yyyy-mm-dd'));
+
+ if (~isempty(x_tick_labels))
+ x_tick_labels{end} = '';
+ end
+
+ set(current_plot, 'XLimMode', 'manual', ...
+ 'XLim', [min_datenum, max_datenum], ...
+ 'XTick', x_tick, ...
+ 'XTickLabel', x_tick_labels);
+
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+plot/float_to_template_south.m b/lib/vendor/nemo2profilelib/+nemo/+plot/float_to_template_south.m
new file mode 100644
index 0000000..dc66496
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+plot/float_to_template_south.m
@@ -0,0 +1,137 @@
+function [ modification_history ] = float_to_template_south( p_nemo_float, p_template, p_config, p_single_float )
+%FLOAT_TO_TEMPLATE_SOUTH Plots the float positions to the given template.
+%
+% Parameters:
+% p_nemo_float: The float data, can be more than one.
+% p_template: The template generated by
+% nemo.plots.templates.create_south function
+% p_config: The nemo configuration.
+% p_single_float: If true, just one float is being plotted to the
+% template at a time. If false, all floats will
+% be plotted into the plot.
+%
+% Returns:
+% modification_history: The modifications made by this function to the
+% template.
+
+% make template the current figure
+set(0, 'currentfigure', p_template);
+
+% get style of plot
+plot_style = p_config.PLOT_STYLE_SOUTH;
+
+if p_single_float
+ show_profile_numbers = p_config.PLOT_SINGLE_FLOAT_SOUTH.show_profile_numbers;
+else
+ show_profile_numbers = p_config.PLOT_OVERVIEW_SOUTH.show_profile_numbers;
+end
+
+modification_history = [];
+
+profile_count = length(p_nemo_float);
+bgp_lat = nan(profile_count, 1);
+bgp_lon = nan(profile_count, 1);
+
+% store the first position manually, because then its possible to save
+% the source of the previous index
+% best guess positions (abbr. bgp)
+bgp_lat(1) = p_nemo_float{1}.SECOND_ORDER_INFORMATION.best_guess_position_lat;
+bgp_lon(1) = p_nemo_float{1}.SECOND_ORDER_INFORMATION.best_guess_position_lon;
+bgp_src{1} = p_nemo_float{1}.SECOND_ORDER_INFORMATION.best_guess_position_src;
+profile_numbers(1, 1) = p_nemo_float{1}.PROFILE_TECHNICAL_DATA.xmit_profile_number;
+measured_ranges = []; % ranges of measured positions will be stored in here
+
+if (strcmp(bgp_src{1}, 'gps') || strcmp(bgp_src{1}, 'iridium'))
+ % it is a measured position, so save the index!
+ measured_start_index = 1;
+else
+ measured_start_index = 0; % because zero is not a valid index
+end
+
+for ii=2:profile_count
+
+ % best guess positions (abbr. bgp)
+ bgp_lat(ii) = p_nemo_float{ii}.SECOND_ORDER_INFORMATION.best_guess_position_lat;
+ bgp_lon(ii) = p_nemo_float{ii}.SECOND_ORDER_INFORMATION.best_guess_position_lon;
+ bgp_src{ii} = p_nemo_float{ii}.SECOND_ORDER_INFORMATION.best_guess_position_src;
+ profile_numbers(ii, 1) = p_nemo_float{ii}.PROFILE_TECHNICAL_DATA.xmit_profile_number;
+
+ % get all pairs of measured positions
+ if (measured_start_index == 0) && (strcmp(bgp_src{ii}, 'gps') || strcmp(bgp_src{ii}, 'iridium'))
+ % no starting index is set, but a measured position has been
+ % found
+ measured_start_index = ii;
+ elseif (measured_start_index > 0) && ((~strcmp(bgp_src{ii}, 'gps') && ~strcmp(bgp_src{ii}, 'iridium')))
+ % starting index valid, but a not measured position has been
+ % found, so store endpoint
+ measured_ranges = [measured_ranges; [measured_start_index ii-1]];
+ measured_start_index = 0; % set invalid start index
+ elseif ((measured_start_index > 0) && (ii == profile_count))
+ % the last position is also valid
+ measured_ranges = [measured_ranges; [measured_start_index ii]];
+ measured_start_index = 0; % set invalid start index
+ end
+
+end
+
+% draw all bgp positions first
+modification_history(end+1) = plotm(bgp_lat,bgp_lon,'marker',plot_style.gps_marker,'markersize',plot_style.gps_markersize,'color',plot_style.gps_color_interpolated, 'linestyle', '-'); % GPS positions
+
+% get deployment position
+dep_lat = p_nemo_float{1}.DEPLOYMENT_INFO.deployment_position(1);
+dep_lon = p_nemo_float{1}.DEPLOYMENT_INFO.deployment_position(2);
+
+if (~isempty(measured_ranges)) && (measured_ranges(1, 1) == 1) % first position is a measured position
+ % plot a black line from deployment position to first profile
+ % position
+ modification_history(end+1) = plotm([dep_lat; bgp_lat(1)], [dep_lon; bgp_lon(1)],'marker',plot_style.gps_marker,'markersize',plot_style.gps_markersize,'color',plot_style.gps_color, 'linestyle', '-'); % GPS positions
+else
+ % plot a interpolated line
+ modification_history(end+1) = plotm([dep_lat; bgp_lat(1)], [dep_lon; bgp_lon(1)],'marker',plot_style.gps_marker,'markersize',plot_style.gps_markersize,'color',plot_style.gps_color_interpolated, 'linestyle', '-');
+end
+
+% draw all measured (iridium or gps) positions above it
+measured_length = size(measured_ranges, 1);
+for o_measured_index = 1:measured_length
+ modification_history(end+1) = ...
+ plotm(bgp_lat(measured_ranges(o_measured_index, 1):measured_ranges(o_measured_index, 2)), ...
+ bgp_lon(measured_ranges(o_measured_index, 1):measured_ranges(o_measured_index, 2)), ...
+ 'marker',plot_style.gps_marker,...
+ 'markersize',plot_style.gps_markersize, ...
+ 'color', plot_style.gps_color, 'linestyle', '-'); % GPS positions
+end
+
+% plot deployment position
+modification_history(end+1) = plotm(dep_lat,dep_lon,150,'marker',plot_style.deploy_marker,'markersize',plot_style.deploy_markersize,'color',plot_style.deploy_color,'linestyle','none'); % plot deplyoment position as crossed square
+
+% plot last transmittion
+modification_history(end+1) = plotm(bgp_lat(end),bgp_lon(end),150,'marker',plot_style.gps_marker,'markersize',plot_style.gps_markersize,'color',plot_style.last_transmittion_color,'linestyle','none'); % plot final gps position
+% plot serial number of float to the last transmitted profile
+text_serial_number = textm(bgp_lat(end)+0.2,bgp_lon(end)+0.2,num2str(p_nemo_float{end}.FLOAT_IDENTIFICATION.float_serial_number));
+set(text_serial_number,'interpreter','none', 'FontSize', 6,'FontWeight','bold');
+modification_history(end+1) = text_serial_number;
+clear measured_ranges measured_length measured_start_index profile_count text_serial_number
+
+% change figure title
+if p_single_float
+ set(get(gca, 'title'), 'String', ['Float ' num2str(p_nemo_float{end}.FLOAT_IDENTIFICATION.float_serial_number) ', ' datestr(now) ]);
+else
+ set(get(gca, 'title'), 'String', datestr(now));
+end
+
+
+if show_profile_numbers == 1
+ % plot profile numbers
+ text_profile_numbers = textm(bgp_lat(10:10:end)+0.2,bgp_lon(10:10:end)+0.2,num2str(profile_numbers(10:10:end)));
+ set(text_profile_numbers,'interpreter','none', 'FontSize', 6,'FontWeight','bold');
+ if length(text_profile_numbers) > 1
+ modification_history = [modification_history, text_profile_numbers'];
+ elseif length(text_profile_numbers) == 1
+ modification_history(end+1) = text_profile_numbers;
+ end
+end
+
+clear bgp_lat bgp_lon dep_lat dep_lon bgp_src profile_numbers text_profile_numbers
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+plot/floats.m b/lib/vendor/nemo2profilelib/+nemo/+plot/floats.m
new file mode 100644
index 0000000..d991185
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+plot/floats.m
@@ -0,0 +1,128 @@
+function [ boolean ] = floats(p_nemo_data, p_config, p_hemisphere, p_single_float)
+%FLOATS Creates a template figure and plots the given floats on it.
+%
+% Returns:
+% boolean: True if everything went successful.
+%
+% Parameters:
+% p_nemo_data: Struct containing float data, load with nemo.load.data().
+% p_config: Struct containing the global configuration file. Load
+% using nemo.load.config().
+% p_hemisphere: String, either 'south' or 'north'. If it is given an
+% empty string, both hemispheres are being plotted.
+% WARNING: North is not implemented yet.
+% p_single_float: If true, every float will be plotted in a separate plot.
+
+
+%% Initialize return variable
+boolean = false;
+
+%% Update sea ice coverage
+if p_config.GENERAL.update_sea_ice_coverage
+ try
+ websave(p_config.ADDITIONAL_CONTENT.antarctic_sea_ice_coverage_file, ...
+ p_config.REMOTE_CONTENT.antarctic_sea_ice_coverage);
+ catch ex
+ warning([mfilename ': Updating sea ice coverage failed with error: ' ...
+ getReport(ex)]);
+ end
+end
+
+% run through every float and generate an overview plot
+float_count = length(p_nemo_data);
+
+switch p_hemisphere
+ case 'south'
+ % prepare directory and parameters
+ if p_single_float
+ directory = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_SINGLE_FLOAT_SOUTH.storage_directory_image);
+ directory_fig = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_SINGLE_FLOAT_SOUTH.storage_directory_fig);
+ image_type = p_config.PLOT_SINGLE_FLOAT_SOUTH.image_type;
+ width = p_config.PLOT_SINGLE_FLOAT_SOUTH.image_width;
+ height = p_config.PLOT_SINGLE_FLOAT_SOUTH.image_height;
+ paperunit = p_config.PLOT_SINGLE_FLOAT_SOUTH.image_paperunit;
+ else
+ directory = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_OVERVIEW_SOUTH.storage_directory_image);
+ directory_fig = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_OVERVIEW_SOUTH.storage_directory_fig);
+ image_type = p_config.PLOT_OVERVIEW_SOUTH.image_type;
+ image_filename = p_config.PLOT_OVERVIEW_SOUTH.image_filename;
+ figure_filename = p_config.PLOT_OVERVIEW_SOUTH.figure_filename;
+ width = p_config.PLOT_OVERVIEW_SOUTH.image_width;
+ height = p_config.PLOT_OVERVIEW_SOUTH.image_height;
+ paperunit = p_config.PLOT_OVERVIEW_SOUTH.image_paperunit;
+ end
+ if ~exist(directory,'dir')
+ mkdir(directory);
+ end
+ if ~exist(directory_fig,'dir')
+ mkdir(directory_fig);
+ end
+
+ template_id_south = nemo.plot.templates.create_south(p_config);
+ for o_float = 1:float_count
+ if p_nemo_data{o_float}{1}.DEPLOYMENT_INFO.deployment_position(1) > 0
+ continue
+ end
+ float_serial_number = ...
+ p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number;
+ modification_history = ...
+ nemo.plot.float_to_template_south(p_nemo_data{o_float}, ...
+ template_id_south, p_config, p_single_float);
+
+ if p_single_float
+ %saveas(template_id_south,[directory num2str(float_serial_number) '.' image_type], image_type);
+ set(template_id_south,'InvertHardcopy','on');
+ set(template_id_south,'PaperUnits', paperunit);
+ papersize = get(template_id_south, 'PaperSize');
+ left = (papersize(1)- width)/2;
+ bottom = (papersize(2)- height)/2;
+ myfiguresize = [left, bottom, width, height];
+ set(template_id_south,'PaperPosition', myfiguresize);
+
+ print(template_id_south, ...
+ [directory num2str(float_serial_number)], image_type);
+
+ if (p_config.PLOT_SINGLE_FLOAT_SOUTH.save_figure)
+ set(gcf,'CreateFcn','set(gcf,''Visible'',''on'')');
+ saveas(template_id_south,[directory_fig num2str(float_serial_number)]);
+ end
+ delete(modification_history);
+ end
+ clear modification_history
+ end
+
+ if ~p_single_float
+
+ set(template_id_south,'InvertHardcopy','on');
+ set(template_id_south,'PaperUnits', paperunit);
+ papersize = get(template_id_south, 'PaperSize');
+ left = (papersize(1)- width)/2;
+ bottom = (papersize(2)- height)/2;
+ myfiguresize = [left, bottom, width, height];
+ set(template_id_south,'PaperPosition', myfiguresize);
+
+ print(template_id_south, [directory image_filename], image_type);
+
+ if (p_config.PLOT_OVERVIEW_SOUTH.save_figure)
+ set(gcf,'CreateFcn','set(gcf,''Visible'',''on'')');
+ saveas(template_id_south, ...
+ [directory_fig ...
+ figure_filename]);
+ end
+ end
+
+ close(template_id_south);
+ case 'north'
+ warning('Northern overview plot is not implemented yet...');
+ otherwise
+ % if anything else is given, just plot both hemispheres
+ nemo.plot.floats(p_nemo_data, p_config, 'south', p_single_float);
+ nemo.plot.floats(p_nemo_data, p_config, 'north', p_single_float);
+end
+
+boolean = true;
+
+return
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+plot/rafos.m b/lib/vendor/nemo2profilelib/+nemo/+plot/rafos.m
new file mode 100644
index 0000000..b07b39d
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+plot/rafos.m
@@ -0,0 +1,186 @@
+function [ boolean ] = rafos( p_nemo_data, p_config )
+%RAFOS Plots the RAFOS data. of the given nemo floats.
+%
+% Parameters:
+% p_nemo_data: The nemo data which will be plotted.
+% p_config: The nemo configuration.
+%
+% Returns:
+% boolean: True if successful.
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check %TODO
+
+%% Get config parameter
+% get plot details
+width = p_config.PLOT_RAFOS.image_width;
+height = p_config.PLOT_RAFOS.image_height;
+paperunit = p_config.PLOT_RAFOS.image_paperunit;
+image_type = p_config.PLOT_RAFOS.image_type;
+directory = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_RAFOS.storage_directory_image);
+directory_fig = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_RAFOS.storage_directory_fig);
+ylabel_fontsize = p_config.PLOT_RAFOS.ylabel_fontsize;
+xlabel_fontsize = p_config.PLOT_RAFOS.xlabel_fontsize;
+axis_fontsize = p_config.PLOT_RAFOS.axis_fontsize;
+title_fontsize = p_config.PLOT_RAFOS.title_fontsize;
+
+if (~isdir(directory))
+ mkdir(directory);
+end
+if ~exist(directory_fig, 'dir')
+ mkdir(directory_fig);
+end
+
+%% Collect required data
+
+switch (class(p_nemo_data{1}))
+ case 'struct' % only one float is to be processed
+ rafos_names = p_nemo_data{1}.RAFOS_VALUES_FORMAT;
+ boolean = plot_float(p_nemo_data);
+ case 'cell' % more than one float has to be processed
+ rafos_names = p_nemo_data{1}{1}.RAFOS_VALUES_FORMAT;
+ boolean = all(cellfun(@plot_float, p_nemo_data));
+ otherwise
+ disp([mfilename ': Class ' class(p_nemo_data{1}) ' not supported for plotting!']);
+end
+
+ function boolean = plot_float(p_float)
+ boolean = false;
+ rafos_data = nemo.float.collect(p_float, 'RAFOS_VALUES', '', 'combine');
+
+ if (isempty(rafos_data))
+ boolean = true;
+ return
+ end
+
+
+ plot_c = [];
+ plot_y = [];
+ plot_x = [];
+ plot_status = [];
+ for i = 8:2:18
+ rafos_correlation = rafos_data(:, i);
+
+ plot_c = [plot_c; rafos_correlation];
+ plot_y = [plot_y; rafos_data(:, i + 1)];
+ plot_x = [plot_x; datenum(rafos_data(:, 2:7))];
+ plot_status = [plot_status; rafos_data(:, 1)];
+ end
+
+ % sort rows by color
+ sorted_plot = [plot_x, plot_y, plot_c];
+ sorted_plot = flipud(sortrows(sorted_plot, 3));
+ plot_x = sorted_plot(:, 1);
+ plot_y = sorted_plot(:, 2);
+ plot_c = sorted_plot(:, 3);
+ clear sorted_plot;
+
+
+ % initialize figure
+ figure_id = figure('Visible', 'off'); % create figure
+ %figure_id = figure(); % create figure
+ set(figure_id,'InvertHardcopy','on');
+ set(figure_id,'PaperUnits', paperunit);
+ papersize = get(figure_id, 'PaperSize');
+ left = (papersize(1)- width)/2;
+ bottom = (papersize(2)- height)/2;
+ myfiguresize = [left, bottom, width, height];
+ set(figure_id,'PaperPosition', myfiguresize);
+
+ % plot data
+ sub(1) = subplot(5, 1, 1:4); % travel time
+ hold on
+ box on
+ grid on
+ % get required information about x-axis limits and ticks
+ x_diff = max(plot_x) - min(plot_x);
+ set(gca, 'XLimMode', 'manual', 'XLim', [min(plot_x), max(plot_x)]);
+ if (x_diff < 30)
+ set(gca, 'XTick', [min(plot_x):5:max(plot_x)]);
+ elseif (x_diff < 365)
+ set(gca, 'XTick', [min(plot_x):30:max(plot_x)]);
+ else
+ set(gca, 'XTick', [min(plot_x):365:max(plot_x)]);
+ end
+
+ s = scatter3(plot_x, plot_y, plot_c, 12, plot_c, 'filled');
+ view(0, 90);
+ c = colorbar;
+ caxis([0 255]);
+ colormap(flipud(colormap));
+ c.Label.String = 'Correlation Height (ch)';
+
+ ylim(p_config.PLOT_RAFOS.ylim);
+ ylabel('RAFOS Time of Arrival [s]', 'FontSize', ylabel_fontsize);
+% xlabel('Date of profile', 'FontSize', xlabel_fontsize);
+ if (p_float{1}.SECOND_ORDER_INFORMATION.best_guess_position_lat > 0)
+ deployment_string = ' (Arctic)';
+ else
+ deployment_string = ' (Antarctica)';
+ end
+ title(sub(1), [ 'Float ' ...
+ num2str(p_float{1}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ ' @ ' ...
+ datestr(datetime('now', 'Format', 'dd-MMM-yyyy HH:mm:SS')) ...
+ deployment_string ...
+ ], 'FontSize', title_fontsize);
+ datetick('x','yyyy-mm-dd', 'keepticks', 'keeplimits');
+ set(gca, 'fontsize', axis_fontsize)
+ clear s
+ hold off
+
+
+ sub(2) = subplot(5, 1, 5); % rafos status
+ hold on
+ box on
+ grid on
+ % get required information about x-axis limits and ticks
+ x_diff = max(plot_x) - min(plot_x);
+ set(gca, 'XLimMode', 'manual', 'XLim', [min(plot_x), max(plot_x)]);
+ if (x_diff < 30)
+ set(gca, 'XTick', [min(plot_x):5:max(plot_x)]);
+ elseif (x_diff < 365)
+ set(gca, 'XTick', [min(plot_x):30:max(plot_x)]);
+ else
+ set(gca, 'XTick', [min(plot_x):365:max(plot_x)]);
+ end
+ set(gca, 'YTickMode', 'manual', 'YLimMode', 'manual', ...
+ 'YTick', [0:2:10], 'YLim', [0, 10]);
+
+ s = stairs(datenum(rafos_data(:, 2:7)), rafos_data(:, 1), ...
+ 'Marker', 'o');
+ s.DisplayName = rafos_names{1};
+
+ clear s
+% title(sub(2), 'RAFOS status', 'FontSize', p_config.PLOT_RAFOS.title_fontsize);
+ datetick('x','yyyy-mm-dd', 'keepticks', 'keeplimits');
+ ylim([0 8]);
+ ylabel('Status', 'FontSize', ylabel_fontsize);
+ xlabel('Date of profile', 'FontSize', xlabel_fontsize);
+ set(gca, 'fontsize', axis_fontsize)
+ clear a
+ hold off
+
+ print(figure_id, ...
+ [directory p_config.PLOT_RAFOS.image_filename ...
+ num2str(p_float{1}.FLOAT_IDENTIFICATION.float_serial_number)] ...
+ , image_type);
+
+ if (p_config.PLOT_RAFOS.save_figure)
+ set(gcf,'CreateFcn','set(gcf,''Visible'',''on'')');
+ saveas(figure_id, ...
+ [directory_fig ...
+ p_config.PLOT_RAFOS.figure_filename ...
+ num2str(p_float{1}.FLOAT_IDENTIFICATION.float_serial_number)]);
+ end
+
+ close(figure_id);
+ boolean = true;
+ end
+
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+plot/temp_sal.m b/lib/vendor/nemo2profilelib/+nemo/+plot/temp_sal.m
new file mode 100644
index 0000000..e7426bf
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+plot/temp_sal.m
@@ -0,0 +1,191 @@
+function [ boolean ] = temp_sal( p_nemo_data, p_config )
+%TEMP_SAL Generates a temperature/salinity plot for every float given.
+% Generates a plot with two subplots, depth on time.
+% The colors of the first plot are given by the temperature, the second
+% one shows the salinity.
+%
+% Parameters:
+% p_nemo_data: The nemo data.
+% p_config: The nemo configuration.
+%
+% Returns:
+% boolean: False on fail.
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check %TODO
+
+%% Get config parameter
+% get plot details
+width = p_config.PLOT_TEMP_SAL.image_width;
+height = p_config.PLOT_TEMP_SAL.image_height;
+paperunit = p_config.PLOT_TEMP_SAL.image_paperunit;
+image_type = p_config.PLOT_TEMP_SAL.image_type;
+directory = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_TEMP_SAL.storage_directory_image);
+directory_fig = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_TEMP_SAL.storage_directory_fig);
+ylabel_fontsize = p_config.PLOT_TEMP_SAL.ylabel_fontsize;
+xlabel_fontsize = p_config.PLOT_TEMP_SAL.ylabel_fontsize;
+axis_fontsize = p_config.PLOT_TEMP_SAL.axis_fontsize;
+title_fontsize = p_config.PLOT_TEMP_SAL.title_fontsize;
+
+if (~isdir(directory))
+ mkdir(directory);
+end
+if ~exist(directory_fig, 'dir')
+ mkdir(directory_fig);
+end
+
+%% Collect required data
+
+switch (class(p_nemo_data{1}))
+ case 'struct' % only one float is to be processed
+ boolean = plot_float(p_nemo_data);
+ case 'cell' % more than one float has to be processed
+ boolean = all(cellfun(@plot_float, p_nemo_data));
+ otherwise
+ disp([mfilename ': Class ' class(p_nemo_data{1}) ' not supported for plotting!']);
+end
+
+ function boolean = plot_float(p_float)
+ boolean = false;
+ profiles_data = nemo.float.collect(p_float, 'PROFILE_DATA', '');
+ profiles_data_combined = nemo.float.collect(p_float, 'PROFILE_DATA', '', 'combine');
+ max_pressure = max(profiles_data_combined(:, 7));
+ profiles_datetime = nemo.float.collect(p_float, ...
+ 'SECOND_ORDER_INFORMATION', ...
+ 'best_guess_datevec');
+ profiles_datetime = datenum(profiles_datetime(:, 1:6));
+ if (isempty(profiles_data))
+ boolean = true;
+ return
+ end
+
+ % initialize figure
+ figure_id = figure('Visible', 'Off');
+ set(figure_id,'InvertHardcopy','on');
+ set(figure_id,'PaperUnits', paperunit, 'Position', [ 0 0 width height]);
+ papersize = get(figure_id, 'PaperSize');
+ left = (papersize(1) - width)/2;
+ bottom = (papersize(2) - height)/2;
+ myfiguresize = [left, bottom, width, height];
+ set(figure_id,'PaperPosition', myfiguresize);
+
+ % Temperature plot
+ sub(1) = subplot(2, 1, 1);
+ hold on
+ box on
+ grid on
+ set(gca, 'YLimMode', 'manual', 'YDir', 'reverse', 'YLim', [0 max_pressure]);
+ set(gca, 'fontsize', axis_fontsize)
+ ylabel('Depth [m]', 'FontSize', ylabel_fontsize);
+ % get required information about x-axis limits and ticks
+ x_diff = max(profiles_datetime) - min(profiles_datetime);
+ set(gca, 'XLimMode', 'auto');
+ if (x_diff < 30)
+ set(gca, 'XTick', [min(profiles_datetime):5:max(profiles_datetime)]);
+ elseif (x_diff < 365)
+ set(gca, 'XTick', [min(profiles_datetime):30:max(profiles_datetime)]);
+ else
+ set(gca, 'XTick', [min(profiles_datetime):365:max(profiles_datetime)]);
+ end
+ time_combined = [];
+ for i = 1:size(profiles_datetime, 1)
+ temperature = profiles_data{i}(:, 5);
+ pressure = profiles_data{i}(:, 7);
+ % erase all invalid values
+ valid_points = (pressure >= 0) & (pressure <= 2000) & (temperature < 10);
+ temperature = temperature(valid_points);
+ pressure = pressure(valid_points);
+ time = repmat(profiles_datetime(i, :), size(pressure, 1), 1);
+ time_combined = [time_combined; time];
+ scatter(time, pressure, 45, temperature, 'filled');
+ end
+ datetick('x','yyyy-mm-dd', 'keepticks', 'keeplimits');
+% xlabel('Date of profile', 'FontSize', xlabel_fontsize);
+
+
+ c = colorbar;
+ cmocean('thermal');
+ %colormap(gca, 'jet');
+ %caxis([-5, 15]);
+ c.Label.String = ['Temperature [' char(176) 'C]'];
+ clear c
+ % create main title
+ if (p_float{1}.SECOND_ORDER_INFORMATION.best_guess_position_lat > 0)
+ deployment_string = ' (Arctic)';
+ else
+ deployment_string = ' (Antarctica)';
+ end
+ t = title(...
+ [ 'Float ' ...
+ num2str(p_float{1}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ ' @ ' ...
+ datestr(datetime('now', 'Format', 'dd-MMM-yyyy HH:mm:SS')) ...
+ deployment_string ...
+ ]);
+ set(t, 'FontSize', title_fontsize);
+ clear t
+ hold off
+
+ % Salinity plot
+ sub(2) = subplot(2, 1, 2);
+ hold on
+ box on
+ grid on
+ set(gca, 'YLimMode', 'manual', 'YDir', 'reverse', 'YLim', [0 max_pressure]);
+ set(gca, 'fontsize', axis_fontsize)
+ ylabel('Depth [m]', 'FontSize', ylabel_fontsize);
+ xlabel('Date of profile', 'FontSize', xlabel_fontsize);
+
+ % get required information about x-axis limits and ticks
+ x_diff = max(profiles_datetime) - min(profiles_datetime);
+ set(gca, 'XLimMode', 'auto');
+ if (x_diff < 30)
+ set(gca, 'XTick', [min(profiles_datetime):5:max(profiles_datetime)]);
+ elseif (x_diff < 365)
+ set(gca, 'XTick', [min(profiles_datetime):30:max(profiles_datetime)]);
+ else
+ set(gca, 'XTick', [min(profiles_datetime):365:max(profiles_datetime)]);
+ end
+ for i = 1:size(profiles_datetime, 1)
+ salinity = profiles_data{i}(:, 9);
+ pressure = profiles_data{i}(:, 7);
+ % erase all invalid values
+ valid_points = (pressure >= 0) & (pressure <= 2000) & (salinity > 10);
+ time = repmat(profiles_datetime(i, :), size(pressure(valid_points), 1), 1);
+ scatter(time, ...
+ pressure(valid_points), 45, salinity(valid_points), 'filled');
+ end
+ datetick('x','yyyy-mm-dd', 'keepticks', 'keeplimits');
+ c = colorbar;
+ cmocean('haline');
+ %colormap(gca, [0:0.001:1; repmat(0, 1, 1001); fliplr(0:0.001:1)]');
+ %caxis([33, 36]);
+ c.Label.String = 'Salinity';
+ hold off
+
+
+ set(gcf, 'Renderer', 'painters');
+ print(figure_id, ...
+ [directory p_config.PLOT_TEMP_SAL.image_filename ...
+ num2str(p_float{1}.FLOAT_IDENTIFICATION.float_serial_number)] ...
+ , image_type);
+
+ if (p_config.PLOT_TEMP_SAL.save_figure)
+ set(gcf,'CreateFcn','set(gcf,''Visible'',''on'')');
+ saveas(figure_id, ...
+ [directory_fig ...
+ p_config.PLOT_TEMP_SAL.figure_filename ...
+ num2str(p_float{1}.FLOAT_IDENTIFICATION.float_serial_number)]);
+ end
+
+ close(figure_id);
+
+ clear figure_id f
+ boolean = true;
+
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+plot/temp_sal_ptemp.m b/lib/vendor/nemo2profilelib/+nemo/+plot/temp_sal_ptemp.m
new file mode 100644
index 0000000..c278403
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+plot/temp_sal_ptemp.m
@@ -0,0 +1,211 @@
+function [ boolean ] = temp_sal_ptemp( p_nemo_data, p_config )
+%TEMP_SAL_PTEMP Plots the temperature, salinity and the potential temperature.
+%
+% Parameters:
+% p_nemo_data: The nemo data to be plotted.
+% p_config: The nemo configuration.
+%
+% Returns:
+% boolean: True if successful.
+
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check %TODO
+
+%% Get config parameter
+% get plot details
+width = p_config.PLOT_TEMP_SAL_PTEMP.image_width;
+height = p_config.PLOT_TEMP_SAL_PTEMP.image_height;
+paperunit = p_config.PLOT_TEMP_SAL_PTEMP.image_paperunit;
+image_type = p_config.PLOT_TEMP_SAL_PTEMP.image_type;
+directory = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_TEMP_SAL_PTEMP.storage_directory_image);
+directory_fig = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_TEMP_SAL_PTEMP.storage_directory_fig);
+ylabel_fontsize = p_config.PLOT_TEMP_SAL_PTEMP.ylabel_fontsize;
+xlabel_fontsize = p_config.PLOT_TEMP_SAL_PTEMP.xlabel_fontsize;
+axis_fontsize = p_config.PLOT_TEMP_SAL_PTEMP.axis_fontsize;
+
+if (~isdir(directory))
+ mkdir(directory);
+end
+if ~exist(directory_fig, 'dir')
+ mkdir(directory_fig);
+end
+
+%% Collect required data
+
+switch (class(p_nemo_data{1}))
+ case 'struct' % only one float is to be processed
+ boolean = plot_float(p_nemo_data);
+ case 'cell' % more than one float has to be processed
+ boolean = all(cellfun(@plot_float, p_nemo_data));
+ otherwise
+ disp([mfilename ': Class ' class(p_nemo_data{1}) ' not supported for plotting!']);
+end
+
+ function boolean = plot_float(p_float)
+ boolean = false;
+ profile_data = nemo.float.collect(p_float, 'PROFILE_DATA', '');
+ combined_profile_data = nemo.float.collect(p_float, 'PROFILE_DATA', '', 'combine');
+ best_guess_lat = nemo.float.collect(p_float, 'SECOND_ORDER_INFORMATION', 'best_guess_position_lat');
+ best_guess_lon = nemo.float.collect(p_float, 'SECOND_ORDER_INFORMATION', 'best_guess_position_lon');
+
+ max_pressure = max(combined_profile_data(:, 7));
+ max_salinity = max(combined_profile_data(:, 9));
+ max_temperature = max(combined_profile_data(:, 5));
+ min_pressure = min(combined_profile_data(:, 7));
+ min_salinity = min(combined_profile_data(:, 9));
+ min_temperature = min(combined_profile_data(:, 5));
+
+ if (isempty(profile_data))
+ boolean = true;
+ return
+ end
+
+ % initialize figure
+ figure_id = figure('Visible', 'Off');
+ set(figure_id,'InvertHardcopy','on');
+ set(figure_id,'PaperUnits', paperunit, 'Position', [ 0 0 width height]);
+ papersize = get(figure_id, 'PaperSize');
+ left = (papersize(1) - width)/2;
+ bottom = (papersize(2) - height)/2;
+ myfiguresize = [left, bottom, width, height];
+ set(figure_id,'PaperPosition', myfiguresize);
+
+ % Salinity plot
+ sub(1) = subplot(1, 3, 1);
+ hold on
+ set(gca, 'YLimMode', 'manual', ...
+ 'YLim', [min_pressure max_pressure], ...
+ 'YTick', [min_pressure:200:max_pressure], ...
+ 'YDir', 'reverse', ...
+ 'XLimMode', 'manual', ...
+ 'XLim', [min_salinity max_salinity], ...
+ 'XTickMode', 'auto');
+ for i = 1:length(profile_data)
+ pressure = profile_data{i}(:, 7);
+ salinity = profile_data{i}(:, 9);
+ plot(salinity, pressure, ...
+ 'color', [0 0 1] * i/length(profile_data));
+ end
+ box on
+ grid on
+ hold off
+
+ % create main title
+ t = title(...
+ [ 'Float ' ...
+ num2str(p_float{1}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ ' @ ' ...
+ datestr(datetime('now', 'Format', 'dd-MMM-yyyy HH:mm:SS')) ...
+ ]);
+ set(t, 'FontSize', 18);
+ clear t
+ xlabel('Salinity [PSU]', 'FontSize', xlabel_fontsize);
+ ylabel('Depth [m]', 'FontSize', ylabel_fontsize);
+ set(gca, 'fontsize', axis_fontsize);
+% set(gca, 'YDir', 'reverse', 'YTick', [0:2000]);
+% ylim([-2000 0]);
+
+% set(gca, 'YLimMode', 'manual', 'YLim', [-2000 0], 'YTick', [-2000:200:0]);
+
+ clear salinity pressure a
+
+ % Temperature plot
+ sub(2) = subplot(1, 3, 2);
+ hold on
+ set(gca, 'YLimMode', 'manual', ...
+ 'YLim', [min_pressure max_pressure], ...
+ 'YTick', [min_pressure:200:max_pressure], ...
+ 'YDir', 'reverse', ...
+ 'XLimMode', 'manual', ...
+ 'XLim', [min_temperature, max_temperature], ...
+ 'XTickMode', 'auto');
+ for i = 1:length(profile_data)
+ pressure = profile_data{i}(:, 7);
+ temperature = profile_data{i}(:, 5);
+ plot(temperature, pressure, ...
+ 'color', [1 0 0] * i/length(profile_data));
+ end
+ xlabel('Temperature [°C]', 'FontSize', xlabel_fontsize);
+ ylabel('Depth [m]', 'FontSize', ylabel_fontsize);
+ set(gca, 'fontsize', axis_fontsize);
+ box on
+ grid on
+ hold off
+ clear pressure temperature a
+
+ % Potential temperature plot
+ sub(3) = subplot(2, 3, 3);
+ hold on
+ set(gca, 'XLimMode', 'manual', ...
+ 'XLim', [min_salinity max_salinity], ...
+ 'XTick', [min_salinity:max_salinity], ...
+ 'XTickMode', 'auto', ...
+ 'YLimMode', 'manual', ...
+ 'YTickMode', 'auto', ...
+ 'YLim', [min_temperature, max_temperature]);
+ for i = 1:length(profile_data)
+ pressure = profile_data{i}(:, 7);
+ temperature = profile_data{i}(:, 5);
+ salinity = profile_data{i}(:, 9);
+ plot(salinity, sw_ptmp(salinity, temperature, pressure, 0), ...
+ 'Linestyle', 'none', ...
+ 'color', [0 1 0] * i/length(profile_data), ...
+ 'marker','.' ...
+ );
+ end
+ ylabel('\theta (Potential temperature) [°C]', 'FontSize', xlabel_fontsize);
+ xlabel('Salinity [PSU]', 'FontSize', ylabel_fontsize);
+ set(gca, 'fontsize', axis_fontsize);
+ box on
+ grid on
+ hold off
+ clear a
+
+ sub(4) = subplot(2, 3, 6);
+ hold on
+ latlim = [-80 80];
+ lonlim = [-90 70];
+ worldmap(latlim,lonlim);
+ setm(gca, 'MLabelParallel', 'south')
+ if (~exist('map', 'var'))
+ map = load('coast');
+ end
+ plotm(map.lat,map.long,'k');
+ plot3m(best_guess_lat,best_guess_lon,150,'marker','.','markersize',8,'color',[0 1 0],'linestyle','none');
+ xlabel('Longitude', 'FontSize', xlabel_fontsize);
+ ylabel('Latitude', 'FontSize', ylabel_fontsize);
+ set(gca, 'fontsize', axis_fontsize);
+ box on
+ grid on
+ hold off
+ clear a
+
+
+ set(gcf, 'Renderer', 'painters');
+ print(figure_id, ...
+ [directory p_config.PLOT_TEMP_SAL_PTEMP.image_filename ...
+ num2str(p_float{1}.FLOAT_IDENTIFICATION.float_serial_number)] ...
+ , image_type);
+
+ if (p_config.PLOT_TEMP_SAL_PTEMP.save_figure)
+ set(gcf,'CreateFcn','set(gcf,''Visible'',''on'')');
+ saveas(figure_id, ...
+ [directory_fig ...
+ p_config.PLOT_TEMP_SAL_PTEMP.figure_filename ...
+ num2str(p_float{1}.FLOAT_IDENTIFICATION.float_serial_number)]);
+ end
+
+ close(figure_id);
+ clear figure_id f
+ boolean = true;
+
+ end
+
+
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+plot/timing_information.m b/lib/vendor/nemo2profilelib/+nemo/+plot/timing_information.m
new file mode 100644
index 0000000..3c53bbd
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+plot/timing_information.m
@@ -0,0 +1,507 @@
+function [ boolean ] = timing_information( p_nemo_data, p_config )
+%TIMING_INFORMATION Plots clock details.
+%
+% Returns:
+% boolean: False if something went wrong during the plotting process.
+%
+% Parameters:
+% p_nemo_data: Struct, containing all float data (load with nemo.load.data()).
+% p_config: Global configuration file. Load using nemo.load.config().
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~iscell(p_nemo_data) || ~isstruct(p_config))
+ parameter_error = true;
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% Setup directories
+directory = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_TIMING_INFORMATION.storage_directory_image);
+directory_fig = fullfile(p_config.GENERAL.storage_directory_plots, p_config.PLOT_TIMING_INFORMATION.storage_directory_fig);
+image_type = p_config.PLOT_TIMING_INFORMATION.image_type;
+if ~exist(directory, 'dir')
+ system(['mkdir ' directory]);
+end
+if ~exist(directory_fig, 'dir')
+ mkdir(directory_fig);
+end
+
+%% Process every float
+
+% create dummy legend item to make the boxes be all of the same size
+
+float_count = length(p_nemo_data);
+
+for o_float = 1:float_count
+
+
+ gps_profile_data = struct();
+ all_profile_data = struct();
+ all_profile_data.profiles = p_nemo_data{o_float};
+ all_profile_data.best_guess_position_src = nemo.float.collect(p_nemo_data{o_float}, 'SECOND_ORDER_INFORMATION', 'best_guess_position_src');
+ all_profile_data.best_guess_datevec = nemo.float.collect(p_nemo_data{o_float}, 'SECOND_ORDER_INFORMATION', 'best_guess_datevec');
+
+ gps_profile_data.profiles = {};
+ for i = 1:length(all_profile_data.best_guess_position_src)
+ if (strcmp(all_profile_data.best_guess_position_src{i}, 'gps'))
+ gps_profile_data.profiles{end + 1} = p_nemo_data{o_float}{i};
+ end
+ end
+%
+% if isempty(gps_profile_data.profiles)
+% continue
+% end
+
+ gps_profile_data.best_guess_datevec = nemo.float.collect(gps_profile_data.profiles, 'SECOND_ORDER_INFORMATION', 'best_guess_datevec');
+
+ all_profile_data.start_date = p_nemo_data{o_float}{end}.OVERALL_MISSION_INFORMATION.start_date;
+ all_profile_data.start_time = p_nemo_data{o_float}{end}.OVERALL_MISSION_INFORMATION.start_time;
+ gps_profile_data.surface_gps_data = nemo.float.collect(gps_profile_data.profiles, 'SURFACE_GPS_DATA');
+
+ plot_data = struct();
+ % required data for plot 1
+
+ % SURFACESTART - GPSFix
+ if ~isempty(gps_profile_data.profiles)
+ plot_data.surfaceStart_GPS = struct();
+ gps_profile_data.xmit_surface_start_datevec = nemo.float.collect(gps_profile_data.profiles, 'xmitDatevec', 'xmit_surface_start_time');
+ plot_data.surfaceStart_GPS.y = ( ...
+ datenum(gps_profile_data.xmit_surface_start_datevec) - ...
+ datenum(gps_profile_data.surface_gps_data(:, 8:13)) ...
+ ) * 86400;
+ plot_data.surfaceStart_GPS.x = datenum(gps_profile_data.best_guess_datevec);
+ end
+
+ % RTC0015 - GPSFix
+ if ~(isempty(gps_profile_data.profiles))
+ gps_profile_data.profile_data = nemo.float.collect(gps_profile_data.profiles, 'PROFILE_DATA');
+ plot_data.RTC0015_GPSFix = struct();
+ % get values near to 15m depth
+ [~, indices] = cellfun(@(x) find_nearest_value_to(x(:, 7), 15), gps_profile_data.profile_data, 'UniformOutput', false);
+ time_15m = cellfun(@(x,y) x(y, 2:4), gps_profile_data.profile_data, indices, 'UniformOutput', false);
+ time_15m = cell2mat(time_15m');
+ gps_profile_data.RTC0015_datevec = gps_profile_data.surface_gps_data(:, 8:13);
+ gps_profile_data.RTC0015_datevec(:, 4:6) = time_15m;
+ tmp_subtract_one_day = (gps_profile_data.surface_gps_data(:, 11) >= 21 & gps_profile_data.surface_gps_data(:, 11) <= 23) ...
+ & (time_15m(:, 1) >= 0 & time_15m(:, 1) <= 3);
+ tmp_add_one_day = (gps_profile_data.surface_gps_data(:, 11) >= 0 & gps_profile_data.surface_gps_data(:, 11) <= 3) ...
+ & (time_15m(:, 1) >= 21 & time_15m(:, 1) <= 23);
+
+ if (any(tmp_subtract_one_day))
+ % GPS is more trustworthy, so reduce the RTC date by 1
+ tmp_indices = find(tmp_subtract_one_day);
+ for i = 1:length(tmp_indices)
+ gps_profile_data.RTC0015_datevec(tmp_indices(i), :) = datevec(addtodate(datenum([gps_profile_data.RTC0015_datevec(tmp_indices(i), 1:3), time_15m(tmp_indices(i), :)]), -1, 'day'));
+ end
+ end
+ if (any(tmp_add_one_day))
+ % same here, but now add 1 day
+ tmp_indices = find(tmp_add_one_day);
+ for i = 1:length(tmp_indices)
+ gps_profile_data.RTC0015_datevec(tmp_indices(i), :) = datevec(addtodate(datenum([gps_profile_data.RTC0015_datevec(tmp_indices(i), 1:3), time_15m(tmp_indices(i), :)]), +1, 'day'));
+ end
+ end
+ clear tmp_indices tmp_subtract_one_day tmp_add_one_day
+
+ plot_data.RTC0015_GPSFix.y = ( ...
+ datenum(gps_profile_data.RTC0015_datevec) - ...
+ datenum(gps_profile_data.surface_gps_data(:, 8:13)) ...
+ ) * 86400;
+ plot_data.RTC0015_GPSFix.x = datenum(gps_profile_data.best_guess_datevec);
+ end
+
+
+ % SURFACESTART - IRIDIUM
+ if ~isempty(gps_profile_data.profiles)
+ plot_data.surfaceStart_Iridium = struct();
+ gps_profile_data.iridium_data = nemo.float.collect(gps_profile_data.profiles, 'IRIDIUM_DATA');
+ plot_data.surfaceStart_Iridium.y = ( ...
+ datenum(gps_profile_data.xmit_surface_start_datevec) - ...
+ datenum(gps_profile_data.iridium_data(:, 4:9)) ...
+ ) * 86400;
+ plot_data.surfaceStart_Iridium.x = datenum(gps_profile_data.best_guess_datevec);
+ end
+
+ % ASCENTSTART - RTC2000
+ plot_data.ascentStart_RTC2000 = struct();
+ all_profile_data.xmit_ascent_start_datevec = nemo.float.collect(all_profile_data.profiles, 'xmitDatevec', 'xmit_ascent_start_time');
+ all_profile_data.profile_data = nemo.float.collect(all_profile_data.profiles, 'PROFILE_DATA');
+ all_profile_data.profile_data_2000 = cellfun(@(x) x(end, 2:4), all_profile_data.profile_data, 'UniformOutput', false);
+ all_profile_data.profile_data_2000 = cell2mat(all_profile_data.profile_data_2000');
+ all_profile_data.profile_data_2000_datevec = datevec(datetime([all_profile_data.xmit_ascent_start_datevec(:, 1:3), all_profile_data.profile_data_2000]));
+
+ tmp_subtract_one_day = (all_profile_data.profile_data_2000(:, 1) >= 21 & all_profile_data.profile_data_2000(:, 1) <= 23) ...
+ & (all_profile_data.xmit_ascent_start_datevec(:, 4) >= 0 & all_profile_data.xmit_ascent_start_datevec(:, 4) <= 3);
+ tmp_add_one_day = (all_profile_data.profile_data_2000(:, 1) >= 0 & all_profile_data.profile_data_2000(:, 1) <= 3) ...
+ & (all_profile_data.xmit_ascent_start_datevec(:, 4) >= 21 & all_profile_data.xmit_ascent_start_datevec(:, 4) <= 23);
+
+ if (any(tmp_subtract_one_day))
+ % RTC is more trustworthy, so reduce the software date by 1
+ tmp_indices = find(tmp_subtract_one_day);
+ for i = 1:length(tmp_indices)
+ all_profile_data.profile_data_2000_datevec(tmp_indices(i), :) = datevec(addtodate(datenum([all_profile_data.xmit_ascent_start_datevec(tmp_indices(i), 1:3), all_profile_data.profile_data_2000(tmp_indices(i), :)]), -1, 'day'));
+ end
+ end
+ if (any(tmp_add_one_day))
+ % same here, but now add 1 day
+ tmp_indices = find(tmp_add_one_day);
+ for i = 1:length(tmp_indices)
+ all_profile_data.profile_data_2000_datevec(tmp_indices(i), :) = datevec(addtodate(datenum([all_profile_data.xmit_ascent_start_datevec(tmp_indices(i), 1:3), all_profile_data.profile_data_2000(tmp_indices(i), :)]), +1, 'day'));
+ end
+ end
+ clear tmp_indices tmp_subtract_one_day tmp_add_one_day
+ plot_data.ascentStart_RTC2000.y = ( ...
+ datenum(all_profile_data.xmit_ascent_start_datevec) - ...
+ datenum(all_profile_data.profile_data_2000_datevec) ...
+ ) * 86400;
+ plot_data.ascentStart_RTC2000.x = datenum(all_profile_data.best_guess_datevec);
+
+ % SURFACESTART - RTC0000
+ plot_data.surfaceStart_RTC0000 = struct();
+ all_profile_data.xmit_surface_start_datevec = nemo.float.collect(all_profile_data.profiles, 'xmitDatevec', 'xmit_surface_start_time');
+ all_profile_data.profile_data_0000 = cellfun(@(x) x(1, 2:4), all_profile_data.profile_data, 'UniformOutput', false);
+ all_profile_data.profile_data_0000 = cell2mat(all_profile_data.profile_data_0000');
+ all_profile_data.profile_data_0000_datevec = datevec(datetime([all_profile_data.xmit_surface_start_datevec(:, 1:3), all_profile_data.profile_data_0000]));
+
+ tmp_subtract_one_day = (all_profile_data.profile_data_0000(:, 1) >= 21 & all_profile_data.profile_data_0000(:, 1) <= 23) ...
+ & (all_profile_data.xmit_surface_start_datevec(:, 4) >= 0 & all_profile_data.xmit_surface_start_datevec(:, 4) <= 3);
+ tmp_add_one_day = (all_profile_data.profile_data_0000(:, 1) >= 0 & all_profile_data.profile_data_0000(:, 1) <= 3) ...
+ & (all_profile_data.xmit_surface_start_datevec(:, 4) >= 21 & all_profile_data.xmit_surface_start_datevec(:, 4) <= 23);
+
+ if (any(tmp_subtract_one_day))
+ % RTC is more trustworthy, so reduce the software date by 1
+ tmp_indices = find(tmp_subtract_one_day);
+ for i = 1:length(tmp_indices)
+ all_profile_data.profile_data_0000_datevec(tmp_indices(i), :) = datevec(addtodate(datenum([all_profile_data.xmit_surface_start_datevec(tmp_indices(i), 1:3), all_profile_data.profile_data_0000(tmp_indices(i), :)]), -1, 'day'));
+ end
+ end
+ if (any(tmp_add_one_day))
+ % same here, but now add 1 day
+ tmp_indices = find(tmp_add_one_day);
+ for i = 1:length(tmp_indices)
+ all_profile_data.profile_data_0000_datevec(tmp_indices(i), :) = datevec(addtodate(datenum([all_profile_data.xmit_surface_start_datevec(tmp_indices(i), 1:3), all_profile_data.profile_data_0000(tmp_indices(i), :)]), +1, 'day'));
+ end
+ end
+ clear tmp_indices tmp_subtract_one_day tmp_add_one_day
+ plot_data.surfaceStart_RTC0000.y = ( ...
+ datenum(all_profile_data.xmit_surface_start_datevec) - ...
+ datenum(all_profile_data.profile_data_0000_datevec) ...
+ ) * 86400;
+ plot_data.surfaceStart_RTC0000.x = datenum(all_profile_data.best_guess_datevec);
+
+
+ % required data for plot 2
+ % get values near to 15m depth
+ clear indices
+ [~, indices] = cellfun(@(x) find_nearest_value_to(x(:, 7), 15), all_profile_data.profile_data, 'UniformOutput', false);
+ all_time_15m = cellfun(@(x,y) x(y, 2:4), all_profile_data.profile_data, indices, 'UniformOutput', false);
+ all_time_15m = cell2mat(all_time_15m');
+
+ % required data for plot 3
+ % GPS - IRIDIUM
+ if ~isempty(gps_profile_data.profiles)
+ plot_data.GPS_Iridium = struct();
+ plot_data.GPS_Iridium.y = ( ...
+ datenum(gps_profile_data.surface_gps_data(:, 8:13)) - ...
+ datenum(gps_profile_data.iridium_data(:, 4:9)) ...
+ ) * 86400;
+ plot_data.GPS_Iridium.x = datenum(gps_profile_data.best_guess_datevec);
+
+ % GPS - GPSRTC
+ plot_data.GPS_GPSRTC = struct();
+ plot_data.GPS_GPSRTC.y = ( ...
+ datenum(gps_profile_data.surface_gps_data(:, 8:13)) - ...
+ datenum(gps_profile_data.surface_gps_data(:, 2:7)) ...
+ ) * 86400;
+ plot_data.GPS_GPSRTC.x = datenum(gps_profile_data.best_guess_datevec);
+ end
+
+ % get plot details
+ width = p_config.PLOT_TIMING_INFORMATION.image_width;
+ height = p_config.PLOT_TIMING_INFORMATION.image_height;
+ paperunit = p_config.PLOT_TIMING_INFORMATION.image_paperunit;
+
+ % plot collected data
+
+ figure_id = figure('Visible', 'off'); % create figure
+ % initialize figure
+ set(figure_id,'InvertHardcopy','on');
+ set(figure_id,'PaperUnits', paperunit);
+ papersize = get(figure_id, 'PaperSize');
+ left = (papersize(1)- width)/2;
+ bottom = (papersize(2)- height)/2;
+ myfiguresize = [left, bottom, width, height];
+ set(figure_id,'PaperPosition', myfiguresize);
+
+ clear height width left bottom papersize myfiguresize
+
+ %set(gcf, 'Position', get(0,'ScreenSize'), 'color', [1 1 1]);
+ sub = {};
+ figure_count = 3;
+
+ sub{1} = subplot(figure_count,1,1);
+ hold on
+
+ %yyaxis left
+ if ~isempty(gps_profile_data.profiles)
+ plot(plot_data.surfaceStart_GPS.x, plot_data.surfaceStart_GPS.y, ...
+ 'color', [1 0 0], ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', [1 0 0], ...
+ 'MarkerEdgeColor', [1 0 0], ...
+ 'linestyle', '-', ...
+ 'linewidth', 1,...
+ 'markersize', 5);
+ plot(plot_data.surfaceStart_Iridium.x, plot_data.surfaceStart_Iridium.y, ...
+ 'color', [0 0.5 0], ...
+ 'marker', 'x', ...
+ 'MarkerEdgeColor', [0 0.5 0], ...
+ 'linestyle', '-', ...
+ 'linewidth', 1, ...
+ 'markersize', 10);
+ plot(plot_data.RTC0015_GPSFix.x, plot_data.RTC0015_GPSFix.y, ...
+ 'color', [0 0.5 1], ...
+ 'marker', 'd', ...
+ 'MarkerEdgeColor', [0 0.5 1], ...
+ 'linestyle', '-', ...
+ 'linewidth', 1, ...
+ 'markersize', 10);
+ end
+ plot(plot_data.ascentStart_RTC2000.x, plot_data.ascentStart_RTC2000.y, ...
+ 'color', [1 0 1], ...
+ 'marker', '+', ...
+ 'MarkerEdgeColor', [1 0 1], ...
+ 'linestyle', '-', ...
+ 'linewidth', 1, ...
+ 'markersize', 10);
+ plot(plot_data.surfaceStart_RTC0000.x, plot_data.surfaceStart_RTC0000.y, ...
+ 'color', [0 0 1], ...
+ 'marker', 's', ...
+ 'MarkerEdgeColor', [0 0 1], ...
+ 'linestyle', '-', ...
+ 'linewidth', 1, ...
+ 'markersize', 10);
+
+
+ t = title([ 'Float ' ...
+ num2str(p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ ' @ ' ...
+ datestr(datetime('now', 'Format', 'dd-MMM-yyyy HH:mm:SS')) ...
+ ]);
+ set(t, 'FontSize', 18);
+ ylabel('Time differences [sec]');
+ if ~isempty(gps_profile_data.profiles)
+ leg1 = legend('SurfaceStart-GPSFix', 'SurfaceStart-IRIDIUM', 'RTC0015 - GPSFix', 'AscentStart-RTC2000', 'SurfaceStart-RTC0000');
+ else
+ leg1 = legend('AscentStart-RTC2000', 'SurfaceStart-RTC0000');
+ end
+ set(leg1, 'Location', 'eastoutside', 'Orientation', 'vertical');
+ grid on
+ box on
+ hold off
+
+ sub{2} = subplot(figure_count,1,2);
+ hold on
+ ylabel('Time of day [HH:MM]');
+
+ if ~isempty(gps_profile_data.profiles)
+ scatter(datenum(gps_profile_data.surface_gps_data(:, 8:13)), mod(datenum(gps_profile_data.surface_gps_data(:, 8:13)), 1), 20, ...
+ 'marker', 'o', ...
+ 'MarkerFaceColor', '1 0 0', ...
+ 'MarkerEdgeColor', '1 0 0');
+ scatter(datenum(gps_profile_data.best_guess_datevec), mod(datenum(gps_profile_data.iridium_data(:, 4:9)), 1), 50, ...
+ 'marker', 's', ...
+ 'MarkerEdgeColor', '0 0.5 0');
+
+ end
+
+ scatter(datenum(all_profile_data.best_guess_datevec), mod(datenum([repmat([1 1 1970], size(all_time_15m, 1), 1), all_time_15m]), 1), 50, ...
+ 'marker', '^', ...
+ 'MarkerEdgeColor', '0 0.5 1');
+ scatter(datenum(all_profile_data.best_guess_datevec), mod(datenum(all_profile_data.xmit_surface_start_datevec), 1), 50, ...
+ 'marker', '+', ...
+ 'MarkerEdgeColor', '0 0 1');
+
+ set(gca, 'YLimMode', 'manual',...
+ 'YLim', [0, 1], ...
+ 'YTick', [0:6:24]./24);
+ datetick('y','HH:mm', 'keepticks');
+
+
+ if ~isempty(gps_profile_data.profiles)
+ legend('GPSFix', 'IRIDIUM', 'RTC0015', 'SurfaceStart');
+ else
+ legend('RTC0015', 'SurfaceStart');
+ end
+ legend('Location', 'eastoutside', 'Orientation', 'vertical');
+ box on
+ grid on
+ hold off
+
+ sub{3} = subplot(figure_count,1,3);
+ hold on
+ if ~isempty(gps_profile_data.profiles)
+ plot(plot_data.GPS_Iridium.x, plot_data.GPS_Iridium.y, ...
+ 'color', [0 0 1], ...
+ 'marker', '+', ...
+ 'MarkerEdgeColor', [0 0 1], ...
+ 'linestyle', '-', ...
+ 'linewidth', 1, ...
+ 'markersize', 10);
+
+ plot(plot_data.GPS_GPSRTC.x, plot_data.GPS_GPSRTC.y, ...
+ 'color', [0 1 1], ...
+ 'marker', '.', ...
+ 'MarkerEdgeColor', [0 1 1], ...
+ 'linestyle', '-', ...
+ 'linewidth', 1, ...
+ 'markersize', 10);
+
+ else
+ dim = [0.5 0 .3 .3];
+ str = 'No data!';
+ a = annotation('textbox', dim, 'String', str, 'FitBoxToText', 'on');
+ a.FontSize = 16;
+ clear dim str a
+ end
+
+ ylabel('Time differences [sec]');
+ legend('GPSFix-IRIDIUM', 'GPSFix-GPSRTC');
+ legend('Location', 'eastoutside', 'Orientation', 'vertical');
+ grid on
+ box on
+ hold off
+
+ sub1_pos = get(sub{1}, 'Position');
+ sub2_pos = get(sub{2}, 'Position');
+ sub3_pos = get(sub{3}, 'Position');
+% leg1_pos = get(leg1, 'Position');
+ set(sub{1}, 'Position', [sub1_pos(1:2) 0.6652 sub1_pos(4)]);
+ set(sub{2}, 'Position', [sub2_pos(1:2) 0.6652 sub2_pos(4)]);
+ set(sub{3}, 'Position', [sub3_pos(1:2) 0.6652 sub3_pos(4)]);
+
+% % align all legends
+% leg1_pos = get(hleg1, 'position');
+% leg2_pos = get(hleg2, 'position');
+% leg3_pos = get(hleg3, 'position');
+% legend_positions = sortrows([ leg1_pos; leg2_pos; leg3_pos ], 1);
+% leg_width = max(legend_positions(:, 3));
+% max_height = max(legend_positions(:, 4));
+%
+% set(hleg1, 'units', 'normalized', 'position', [ legend_positions(1, 1) leg1_pos(2) leg_width max_height ]);
+% set(hleg2, 'units', 'normalized', 'position', [ legend_positions(1, 1) leg2_pos(2) leg_width max_height ]);
+% set(hleg3, 'units', 'normalized', 'position', [ legend_positions(1, 1) leg3_pos(2) leg_width max_height ]);
+%
+% % set width of all plots to the same
+% sub1_pos = get(sub{1}, 'position');
+% sub2_pos = get(sub{2}, 'position');
+% sub3_pos = get(sub{3}, 'position');
+% sub_positions = sortrows([ sub1_pos; sub2_pos; sub3_pos ], 3);
+% max_width = max(sub_positions(:, 3));
+% set(sub{1}, 'units', 'normalized', 'position', [ sub1_pos(1:2) legend_positions(1, 1) sub1_pos(4) ]);
+% set(sub{2}, 'units', 'normalized', 'position', [ sub2_pos(1:2) legend_positions(1, 1) sub2_pos(4) ]);
+% set(sub{3}, 'units', 'normalized', 'position', [ sub3_pos(1:2) legend_positions(1, 1) sub3_pos(4) ]);
+
+ sub = cellfun(@set_x_axis, sub, 'UniformOutput', false);
+
+% sub{3} = subplot(4, 1, 4);
+% hold on
+% %plot(combined_xmit_times);
+% plot(xmit_profile_number, xmit_ascent_start_time_ori, 'marker', '+');
+% plot(xmit_profile_number, xmit_ascent_end_time, 'marker', 'o');
+% plot(xmit_profile_number, xmit_descent_start_time, 'marker', 'x');
+% plot(xmit_profile_number, xmit_parking_start_time, 'marker', '*');
+% plot(xmit_profile_number, xmit_upcast_start_time, 'marker', '+');
+% plot(xmit_profile_number, xmit_surface_start_time, 'marker', '+');
+% legend('ascentstart', 'ascentend', 'descentstart', 'parkingstart', 'upcaststart', 'surfacestart');
+% box on
+% grid on
+% hold off
+
+
+
+ % create main title
+% heading = utils.suplabel(...
+% [ 'Float ' ...
+% num2str(p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number) ...
+% ' @ ' ...
+% datestr(datetime('now', 'Format', 'dd-MMM-yyyy HH:mm:SS')) ...
+% ], 't');
+% set(heading, 'FontSize', 18);
+
+ % store plot
+
+ image_filename = [p_config.PLOT_TIMING_INFORMATION.image_filename ...
+ num2str(p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number)];
+ figure_filename = [p_config.PLOT_TIMING_INFORMATION.figure_filename ...
+ num2str(p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number)];
+
+ if (p_config.PLOT_TIMING_INFORMATION.save_figure)
+ set(gcf,'CreateFcn','set(gcf,''Visible'',''on'')');
+ saveas(figure_id, ...
+ [directory_fig figure_filename]);
+ end
+
+
+ print(figure_id, [directory image_filename], image_type);
+
+ close(figure_id);
+
+end
+
+boolean = true;
+
+ function current_plot = set_x_axis(current_plot)
+
+ % get min and max datevec
+ min_datenum = min(datenum(all_profile_data.best_guess_datevec));
+ max_datenum = max(datenum(all_profile_data.best_guess_datevec));
+ if (min_datenum == max_datenum)
+ max_datenum = max_datenum + 1;
+ end
+ diff_datenum = max_datenum - min_datenum;
+ if (diff_datenum > 365)
+ x_tick = [min_datenum:365:max_datenum];
+ elseif (diff_datenum > 30)
+ x_tick = [min_datenum:30:max_datenum];
+ elseif (diff_datenum > 5)
+ x_tick = [min_datenum:5:max_datenum];
+ else
+ x_tick = [min_datenum:1:max_datenum];
+ end
+ if (x_tick(end) < max_datenum)
+ x_tick = [ x_tick max_datenum ];
+ end
+ x_tick_labels = cellstr(datestr(x_tick, 'yyyy-mm-dd'));
+
+ if (~isempty(x_tick_labels))
+ x_tick_labels{end} = '';
+ end
+
+ set(current_plot, 'XLimMode', 'manual', ...
+ 'XLim', [min_datenum, max_datenum], ...
+ 'XTick', x_tick, ...
+ 'XTickLabel', x_tick_labels);
+
+ end
+
+ function [value, index] = find_nearest_value_to(p_matrix, p_value)
+ [value, index] = min(abs(p_matrix - p_value));
+ if (length(value) > 1)
+ index = min(index);
+ value = p_matrix(index);
+ end
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+datetime/add_software_profile_times2rtc.m b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+datetime/add_software_profile_times2rtc.m
new file mode 100644
index 0000000..2209e7b
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+datetime/add_software_profile_times2rtc.m
@@ -0,0 +1,100 @@
+function [ extended_nemo_data ] = add_software_profile_times2rtc( p_nemo_data )
+%ADD_SOFTWARE_PROFILE_TIMES_IN_RTC Summary of this function goes here
+% Detailed explanation goes here
+
+%% Parameter check
+if ~iscell(p_nemo_data)
+ disp([mfilename ': Please check your input parameter!']);
+end
+
+%% Variables to convert
+variable_names_to_convert = { ...
+ 'xmit_descent_start_time', ...
+ 'xmit_parking_start_time', ...
+ 'xmit_upcast_start_time', ...
+ 'xmit_ascent_end_time', ...
+ 'xmit_surface_start_time' ...
+};
+
+%% Calculate datevec
+
+extended_nemo_data = cellfun(@(x) extend_float(x), p_nemo_data, 'UniformOutput', false);
+
+ function [ extended_float ] = extend_float(p_float)
+ extended_float = cellfun(@(x) extend_profile(x), p_float, 'UniformOutput', false);
+ end
+
+ function [ extended_profile ] = extend_profile(p_profile)
+
+ extended_profile = p_profile;
+ if isempty(p_profile)
+ return
+ end
+ if ~isfield(extended_profile, 'SECOND_ORDER_INFORMATION')
+ extended_profile.SECOND_ORDER_INFORMATION = struct();
+ end
+
+ % initialize variables
+ for i = 1:length(variable_names_to_convert)
+ extended_profile.SECOND_ORDER_INFORMATION.(variable_names_to_convert{i}) = NaN(1, 6);
+ end
+ extended_profile.SECOND_ORDER_INFORMATION.xmit_ascent_start_time = NaN(1, 6);
+
+ % calculate software <-> rtc correction
+ % xmit_ascent_start_time + 10s = RTC @ 2000m
+ [rtc_datevec, software_datevec] = find_rtc_datevec(p_profile);
+ extended_profile.SECOND_ORDER_INFORMATION.xmit_ascent_start_time = datevec(datetime(rtc_datevec) - seconds(10));
+
+ drift_rtc_software = etime(rtc_datevec, software_datevec) + 10;
+ for i = 1:length(variable_names_to_convert)
+ extended_profile.SECOND_ORDER_INFORMATION.(variable_names_to_convert{i}) = ...
+ datevec(datetime([ ...
+ fliplr(extended_profile.OVERALL_MISSION_INFORMATION.start_date), ...
+ extended_profile.OVERALL_MISSION_INFORMATION.start_time 0 ...
+ ]) ...
+ + seconds(extended_profile.PROFILE_TECHNICAL_DATA.(variable_names_to_convert{i})) ...
+ + seconds(drift_rtc_software));
+
+ end
+ extended_profile.SECOND_ORDER_INFORMATION.difference_rtc_software = drift_rtc_software;
+
+
+ end
+
+ function [ rtc_datevec, software_datevec ] = find_rtc_datevec(profile)
+ software_datevec = ...
+ datevec( ...
+ datetime([ ...
+ fliplr(profile.OVERALL_MISSION_INFORMATION.start_date), ...
+ profile.OVERALL_MISSION_INFORMATION.start_time 0 ...
+ ]) ...
+ + seconds(profile.PROFILE_TECHNICAL_DATA.xmit_ascent_start_time) ...
+ );
+ software_time = software_datevec(4:6);
+ % get internal clock (RTC) @ 2000m
+ rtc_time = profile.PROFILE_DATA( ...
+ profile.PROFILE_DATA(:, 7) == max(profile.PROFILE_DATA(:, 7)), ...
+ 2:4);
+ % if there are multiple pressure levels get the one with the
+ % earliest time
+ rtc_time = sortrows(rtc_time, [1:3]);
+ if isempty(rtc_time) || isempty(software_datevec) % prevent errors if empty
+ rtc_datevec = NaN(1, 6);
+ software_datevec = NaN(1, 6);
+ return;
+ end
+ rtc_time = rtc_time(end, :);
+
+ rtc_datevec = datevec(datetime([software_datevec(1:3), rtc_time]));
+
+ if (any(rtc_time(1) == 21:23) && any(software_time(1) == 0:3))
+ % RTC is more trustworthy, so reduce the software date by 1
+ rtc_datevec = datevec(datetime([software_datevec(1:3), rtc_time]) - days(1));
+ elseif (any(rtc_time(1) == 0:3) && any(software_time(1) == 21:23))
+ % same here, but now add 1 day
+ rtc_datevec = datevec(datetime([software_datevec(1:3), rtc_time]) + days(1));
+ end
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+datetime/create_best_guess.m b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+datetime/create_best_guess.m
new file mode 100644
index 0000000..eb6fa3d
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+datetime/create_best_guess.m
@@ -0,0 +1,148 @@
+function [ nemo_data ] = create_best_guess( p_nemo_data )
+%CREATE_BEST_GUESS Estimates and writes the best guess datetime to the given structure.
+% The Iridium time is only being taken if no GPS time is available, and it is
+% not the first profile after a series with xmit_upcast_status="ICE DETECTION".
+%
+% Priority that is being used:
+% 1) GPS time
+% 2) Iridium time
+% 3) Internal float clock time
+%
+%
+% Returns: p_nemo_data with an additional struct containing the best
+% guess datetime.
+%
+% Parameters:
+% p_nemo_data: Struct, containing all floats that should be edited.
+
+%% Initialize return variables
+nemo_data = false;
+
+%% Parameter check
+parameter_error = false; % indicates if a parameter error was raised
+
+if (ischar(p_nemo_data)) % read profiles using read_profiles.m
+ if (~isdir(p_nemo_data)) % parameter is not a directory
+ parameter_error = true;
+ else % read profiles
+ nemo_data = nemo.load.data(p_nemo_data);
+ end
+else if (~iscell(p_nemo_data)) % raise error
+ parameter_error = true;
+ else
+ nemo_data = p_nemo_data; % store nemo data in return variable
+ end
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please provide either a ' ...
+ 'directory path or a struct created by nemo.load.data!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% Estimate best datetime
+
+% run through every float/profile
+nemo_data = p_nemo_data;
+float_count = length(p_nemo_data);
+for o_float = 1:float_count
+
+ current_float = p_nemo_data{o_float};
+ profile_count = length(current_float);
+
+ for o_profile_index = 1:profile_count
+ % get internal clock (software)
+ software_datevec = ...
+ datevec( ...
+ datetime([ ...
+ fliplr(current_float{o_profile_index}.OVERALL_MISSION_INFORMATION.start_date), ...
+ current_float{o_profile_index}.OVERALL_MISSION_INFORMATION.start_time 0 ...
+ ]) ...
+ + seconds(current_float{o_profile_index}.PROFILE_TECHNICAL_DATA.xmit_surface_start_time) ...
+ );
+ software_time = software_datevec(4:6);
+ % get internal clock (RTC)
+ rtc_time = current_float{o_profile_index}.PROFILE_DATA( ...
+ current_float{o_profile_index}.PROFILE_DATA(:, 7) == min(current_float{o_profile_index}.PROFILE_DATA(:, 7)), ...
+ 2:4);
+ % if there are multiple pressure levels get the one with the latest
+ % time
+ rtc_time = sortrows(rtc_time, [1:3]);
+
+ if isempty(rtc_time) || isempty(software_datevec) % prevent errors if empty
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.best_guess_datevec = NaN(1, 6);
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.best_guess_datevec_src = 'none';
+ continue;
+ end
+
+ rtc_time = rtc_time(1, :);
+
+ current_datevec = datevec(datetime([software_datevec(1:3), rtc_time]));
+
+ if (any(rtc_time(1) == 21:23) && any(software_time(1) == 0:3))
+ % RTC is more trustworthy, so reduce the software date by 1
+ current_datevec = datevec(datetime([software_datevec(1:3), rtc_time]) - days(1));
+ elseif (any(rtc_time(1) == 0:3) && any(software_time(1) == 21:23))
+ % same here, but now add 1 day
+ current_datevec = datevec(datetime([software_datevec(1:3), rtc_time]) + days(1));
+ end
+
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.best_guess_datevec = current_datevec;
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.best_guess_datevec_src = 'internal_rtc';
+% current_datevec = [];
+% if o_profile_index ~= 1
+% previous_profile = current_float{o_profile_index - 1};
+% else
+% previous_profile = {};
+% end
+%
+% if o_profile_index < profile_count
+% next_profile = current_float{o_profile_index + 1};
+% else
+% next_profile = {};
+% end
+%
+% % decide which time should be taken
+%
+% if nemo.profile.has_gps(current_float{o_profile_index}) ...
+% && nemo.profile.has_status(current_float{o_profile_index}, 'DONE')
+% % get gps datetime
+% current_datevec = nemo.profile.get_gps(current_float{o_profile_index});
+% current_datevec = current_datevec(8:13);
+% current_source = 'gps';
+% elseif nemo.profile.has_iridium(current_float{o_profile_index}) ...
+% && nemo.profile.has_status(current_float{o_profile_index}, 'DONE') ...
+% && nemo.profile.has_status(previous_profile, 'DONE') ...
+% && (isempty(next_profile) || nemo.profile.verify_iridium(current_float{o_profile_index}, next_profile))
+% % get iridium datetime
+% current_datevec = nemo.profile.get_iridium(current_float{o_profile_index});
+% current_datevec = current_datevec(4:9);
+% current_source = 'iridium';
+% else
+% % get internal clock
+% current_datevec = ...
+% datevec( ...
+% datetime([ ...
+% %fliplr(current_float{o_profile_index}.DEPLOYMENT_INFO.deployment_date), ...
+% %current_float{o_profile_index}.DEPLOYMENT_INFO.deployment_time 0 ...
+% fliplr(current_float{o_profile_index}.OVERALL_MISSION_INFORMATION.start_date), ...
+% current_float{o_profile_index}.OVERALL_MISSION_INFORMATION.start_time 0 ...
+% ]) ...
+% + seconds(current_float{o_profile_index}.PROFILE_TECHNICAL_DATA.xmit_surface_start_time) ...
+% );
+% current_source = 'internal';
+% end
+% % store datetime
+% if (~isfield(current_float{o_profile_index}, 'SECOND_ORDER_INFORMATION'))
+% current_float{o_profile_index}.SECOND_ORDER_INFORMATION = {};
+% end
+% current_float{o_profile_index}.SECOND_ORDER_INFORMATION.best_guess_datevec = current_datevec;
+% current_float{o_profile_index}.SECOND_ORDER_INFORMATION.best_guess_datevec_src = current_source;
+ end
+ nemo_data{o_float} = current_float;
+end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+position/create_best_guess.m b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+position/create_best_guess.m
new file mode 100644
index 0000000..40fb8de
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+position/create_best_guess.m
@@ -0,0 +1,53 @@
+function [ nemo_data ] = create_best_guess( p_nemo_data, p_estimation_method )
+%CREATE_BEST_GUESS_POSITION Creates a struct "best_guess_position" in every profile.
+% Calls the following functions to estimate the best position that is
+% available from the given profile data:
+% 1) nemo.estimate_best_guess_position
+% 2) nemo.estimate_unknown_positions
+% WARNING: Please take care that this is the only possible calling procedure if
+% you want to have consistent position data!
+%
+% Returns: p_nemo_data with an additional struct containing the best
+% position that could be estimated.
+%
+% Requirements:
+% - nemo library (this function is part of the library, so you should have it)
+% - Mapping Toolbox
+%
+
+%% Initialize return variables
+nemo_data = false;
+
+%% Parameter check
+parameter_error = false; % indicates if a parameter error was raised
+
+if (ischar(p_nemo_data)) % read profiles using read_profiles.m
+ if (~isdir(p_nemo_data)) % parameter is not a directory
+ parameter_error = true;
+ else % read profiles
+ nemo_data = nemo.load.data(p_nemo_data);
+ end
+else if (~iscell(p_nemo_data)) % raise error
+ parameter_error = true;
+ else
+ nemo_data = p_nemo_data; % store nemo data in return variable
+ end
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please provide either a ' ...
+ 'directory path or a struct created by nemo.load.data!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% create struct and fill with data
+
+% create best_guess_position struct
+nemo_data = nemo.postprocessing.position.estimate_best_guess(p_nemo_data);
+% estimate all positions that have no gps coordinate
+nemo_data = nemo.postprocessing.position.estimate_unknowns(nemo_data, p_estimation_method);
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+position/estimate_best_guess.m b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+position/estimate_best_guess.m
new file mode 100644
index 0000000..76e347a
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+position/estimate_best_guess.m
@@ -0,0 +1,142 @@
+function [ estimated_nemo_data ] = estimate_best_guess( p_nemo_data )
+%ESTIMATE_BEST_GUESS_POSITION Gets the most trusted position and stores it into SECOND_ORDER_INFORMATION struct.
+% WARNING: Do not use this function alone! If you want to have consistent
+% position data, please use
+% nemo.postprocessing.create_best_guess_position().
+%
+% Creates a struct called best_guess_position in every profile and copies
+% either gps or iridium coordinates to it. If the status of the profile
+% is "ICE DETECTION", NaN will be placed into the member of the struct.
+% Same is being done, when there is neither gps nor iridium available.
+%
+% Returns: Input struct, extended by best_guess_position member in SECOND_ORDER_INFORMATION.
+%
+% Parameters:
+% p_nemo_data: Either has to be a multidimensional struct (created by
+% nemo.load.data()) or a string, where the nemo float data
+% is stored.
+
+%% Initialize return variables
+estimated_nemo_data = false;
+
+%% Parameter check
+parameter_error = false; % default value if function fails
+
+if (ischar(p_nemo_data)) % load profile data from file
+ if (~isdir(p_nemo_data)) % parameter is not a directory
+ parameter_error = true;
+ else % load data
+ estimated_nemo_data = nemo.load.data(p_nemo_data);
+ end
+else if (~iscell(p_nemo_data)) % raise error
+ parameter_error = true;
+ else
+ estimated_nemo_data = p_nemo_data; % store nemo data in return variable
+ end
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please provide either a ' ...
+ 'directory path or a struct created by nemo.load.data.m!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% Estimate best position
+% Priority:
+% 1) GPS
+% 2) Iridium
+
+% setup format structure
+section_name = 'SECOND_ORDER_INFORMATION';
+gps_section_name = 'SURFACE_GPS_DATA';
+gps_section_format_name = 'SURFACE_GPS_DATA_FORMAT';
+iridium_section_name = 'IRIDIUM_DATA';
+iridium_section_format_name = 'IRIDIUM_DATA_FORMAT';
+
+% process every single float
+for o_float_index = 1:length(estimated_nemo_data)
+ % get profile count of current float
+ profile_count = length(estimated_nemo_data{o_float_index});
+
+ % run through every profile
+ for o_profile_index = 1:profile_count
+ % get current profile
+ current_profile = ...
+ estimated_nemo_data{o_float_index}{o_profile_index};
+ if o_profile_index ~= 1
+ % get previous profile
+ previous_profile = ...
+ estimated_nemo_data{o_float_index}{o_profile_index - 1};
+ else
+ previous_profile = {};
+ end
+
+ if o_profile_index < profile_count
+ % get previous profile
+ next_profile = ...
+ estimated_nemo_data{o_float_index}{o_profile_index + 1};
+ else
+ next_profile = {};
+ end
+
+ % check status first
+ if (nemo.profile.has_status(current_profile, 'ICE DETECTION') ...
+ || (~isempty(previous_profile) && nemo.profile.has_status(previous_profile, 'ICE DETECTION')))
+ % no position is available
+ current_profile.(section_name).best_guess_position_lat = NaN;
+ current_profile.(section_name).best_guess_position_lon = NaN;
+ current_profile.(section_name).best_guess_position_src = NaN;
+ elseif (nemo.profile.has_gps(current_profile))
+ % gps available so take it
+ % get indices of lat and lon
+ index_lat = find(not(cellfun('isempty', ...
+ strfind(current_profile.(gps_section_format_name), 'lat') ...
+ )));
+ index_lon = find(not(cellfun('isempty', ...
+ strfind(current_profile.(gps_section_format_name), 'lon') ...
+ )));
+ current_profile.(section_name).best_guess_position_lat = ...
+ current_profile.(gps_section_name)(index_lat);
+ current_profile.(section_name).best_guess_position_lon = ...
+ current_profile.(gps_section_name)(index_lon);
+ current_profile.(section_name).best_guess_position_src = ...
+ 'gps';
+
+ clear index_lon index_lat;
+ elseif (nemo.profile.has_no_gps_but_iridium(current_profile) ...
+ && (isempty(next_profile) || nemo.profile.verify_iridium(current_profile, next_profile)) ...
+ )
+ % iridium available
+ % get indices of lat and lon
+ index_lat = find(not(cellfun('isempty', ...
+ strfind(current_profile.(iridium_section_format_name), 'mean_lat') ...
+ )));
+ index_lon = find(not(cellfun('isempty', ...
+ strfind(current_profile.(iridium_section_format_name), 'mean_lon') ...
+ )));
+ current_profile.(section_name).best_guess_position_lat = ...
+ current_profile.(iridium_section_name)(index_lat);
+ current_profile.(section_name).best_guess_position_lon = ...
+ current_profile.(iridium_section_name)(index_lon);
+ current_profile.(section_name).best_guess_position_src = ...
+ 'iridium';
+ clear index_lon index_lat;
+ else
+ current_profile.(section_name).best_guess_position_lat = NaN;
+ current_profile.(section_name).best_guess_position_lon = NaN;
+ current_profile.(section_name).best_guess_position_src = NaN;
+ end
+
+ % store updated profile
+ estimated_nemo_data{o_float_index}{o_profile_index} = current_profile;
+
+ end
+
+
+end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+position/estimate_unknowns.m b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+position/estimate_unknowns.m
new file mode 100644
index 0000000..aee1e44
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/+position/estimate_unknowns.m
@@ -0,0 +1,185 @@
+function [ fixed_nemo_data ] = estimate_unknowns( p_nemo_data, p_estimation_method )
+%ESTIMATE_UNKNOWN_POSITIONS Calculates the "best guess" profile positions.
+% WARNING: Do not use this function alone! If you want to have consistent
+% position data, please use
+% nemo.postprocessing.position.create_best_guess.
+%
+% This function iterates over all nemo floats, given in the parameter
+% p_nemo_data, determining the missing GPS information of profiles where
+% the float did not come to the water surface. This is done via gcwaypts
+% (Mapping Toolbox) between the known GPS/Iridium positions. They have been
+% stored in the SECOND_ORDER_INFORMATION struct by
+% nemo.postprocessing.position.estimate_best_guess().
+% If p_nemo_data is a string, it reads the profiles with the
+% read_profiles function. So be sure that you added read_profiles.m to
+% your search path!
+%
+% Returns: p_nemo_data with interpolated positions, false on fail.
+%
+% Parameters:
+% p_nemo_data: Either has to be a multidimensional struct (created by
+% nemo.load.data()) or a string, where the nemo float data
+% is stored.
+
+
+%% Initialize return variables
+fixed_nemo_data = false; % default value if function fails
+
+%% Check passed parameter and read profiles if necessary
+parameter_error = false; % indicates if a parameter error was raised
+
+if (ischar(p_nemo_data)) % read profiles using read_profiles.m
+ if (~isdir(p_nemo_data)) % parameter is not a directory
+ parameter_error = true;
+ else % read profiles
+ fixed_nemo_data = nemo.load.data(p_nemo_data);
+ end
+else if (~iscell(p_nemo_data)) % raise error
+ parameter_error = true;
+ else
+ fixed_nemo_data = p_nemo_data; % store nemo data in return variable
+ end
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please provide either a ' ...
+ 'directory path or a struct created by read_profiles.m!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+% If estimation method nan is chosen, do nothing because there is already
+% NaN given in the unknown positions by
+% nemo.postprocessing.position.estimate_best_guess().
+if (strcmp(p_estimation_method, 'nan'))
+ return
+end
+
+%% Position estimation
+
+for o_float_index = 1:length(fixed_nemo_data)
+
+ current_float = fixed_nemo_data{o_float_index}; % stores current float in tmp var
+ profile_count = length(current_float);
+
+
+ % find all pairs that have incomplete positions in between
+
+ o_profile_index = 1;
+
+ while (o_profile_index <= profile_count) % process every profile
+ if (~isfield(current_float{o_profile_index}, 'SECOND_ORDER_INFORMATION') ...
+ || ~isfield(current_float{o_profile_index}.SECOND_ORDER_INFORMATION, 'best_guess_position_lat') ...
+ || ~isfield(current_float{o_profile_index}.SECOND_ORDER_INFORMATION, 'best_guess_position_lon') ...
+ || ~isfield(current_float{o_profile_index}.SECOND_ORDER_INFORMATION, 'best_guess_position_src')) % security check
+ disp([mfilename ': No best guess position available in float ' num2str(current_float{o_profile_index}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ ' profile ' num2str(current_float{o_profile_index}.PROFILE_TECHNICAL_DATA.xmit_profile_number) '! Skipping...']);
+ o_profile_index = o_profile_index + 1;
+ continue
+ end
+
+ % check for NaN, if it is the first index, the deployment position
+ % will be the first position for the interpolation
+ index_last_position = o_profile_index;
+ while (o_profile_index <= profile_count) ...
+ && isnan(current_float{o_profile_index}.SECOND_ORDER_INFORMATION.best_guess_position_lat)
+ o_profile_index = o_profile_index + 1;
+ end
+ index_next_position = o_profile_index;
+
+ if (index_last_position == index_next_position) % no gap has been found
+ % increase iteration var and continue
+ o_profile_index = o_profile_index + 1;
+ continue;
+ else
+ % a gap has been found, so the last position index is wrong!
+ index_last_position = index_last_position - 1;
+ end
+
+ % a gap has been found
+ if (index_last_position == 0) % use deployment position as last position
+ last_position.lat = current_float{1}.DEPLOYMENT_INFO.deployment_position(1);
+ last_position.lon = current_float{1}.DEPLOYMENT_INFO.deployment_position(2);
+ last_position.src = 'deployment';
+ last_position.datetime = 0;
+ else
+ last_position.lat = current_float{index_last_position}.SECOND_ORDER_INFORMATION.best_guess_position_lat;
+ last_position.lon = current_float{index_last_position}.SECOND_ORDER_INFORMATION.best_guess_position_lon;
+ last_position.src = current_float{index_last_position}.SECOND_ORDER_INFORMATION.best_guess_position_src;
+ last_position.datetime = current_float{index_last_position}.PROFILE_TECHNICAL_DATA.xmit_surface_start_time;
+ end
+
+ % if there is no position at all of the float, do not create best
+ % guess for it
+ if index_next_position > profile_count
+ break;
+ end
+ next_position.lat = current_float{index_next_position}.SECOND_ORDER_INFORMATION.best_guess_position_lat;
+ next_position.lon = current_float{index_next_position}.SECOND_ORDER_INFORMATION.best_guess_position_lon;
+ next_position.src = current_float{index_next_position}.SECOND_ORDER_INFORMATION.best_guess_position_src;
+ next_position.datetime = current_float{index_next_position}.PROFILE_TECHNICAL_DATA.xmit_surface_start_time;
+
+ intermediate_profile_count = index_next_position - index_last_position;
+
+ switch p_estimation_method
+ case 'position based'
+ position_based_estimation
+ case 'time based'
+ time_based_estimation
+ otherwise
+ warning([mfilename ': Estimation method not available. Using position based instead...']);
+ position_based_estimation
+ end
+
+
+
+ end
+
+ % store the corrected profiles into struct that will be returned
+ fixed_nemo_data{o_float_index} = current_float;
+
+
+end
+
+ function position_based_estimation
+ % calculate intermediate points
+ [intermediate_points_lat, intermediate_points_lon] = gcwaypts( ...
+ last_position.lat, ...
+ last_position.lon, ...
+ next_position.lat, ...
+ next_position.lon, ...
+ intermediate_profile_count ... % function requires legs, not points
+ );
+
+ % store all positions in best guess variable
+ for i = 1:intermediate_profile_count
+ current_float{index_last_position + i}.SECOND_ORDER_INFORMATION.best_guess_position_lat = intermediate_points_lat(i + 1);
+ current_float{index_last_position + i}.SECOND_ORDER_INFORMATION.best_guess_position_lon = intermediate_points_lon(i + 1);
+ current_float{index_last_position + i}.SECOND_ORDER_INFORMATION.best_guess_position_src = [ last_position.src '_gcwaypts_' next_position.src ];
+ end
+ end
+
+ function time_based_estimation
+ difference_in_seconds = next_position.datetime - last_position.datetime;
+
+ [intermediate_points_lat, intermediate_points_lon] = gcwaypts( ...
+ last_position.lat, ...
+ last_position.lon, ...
+ next_position.lat, ...
+ next_position.lon, ...
+ difference_in_seconds + 1 ... % function requires legs, not points
+ );
+
+ for i = 1:intermediate_profile_count-1
+ profile_datetime = current_float{index_last_position + i}.PROFILE_TECHNICAL_DATA.xmit_surface_start_time;
+ profile_to_last_position = profile_datetime - last_position.datetime;
+ current_float{index_last_position + i}.SECOND_ORDER_INFORMATION.best_guess_position_lat = intermediate_points_lat(profile_to_last_position);
+ current_float{index_last_position + i}.SECOND_ORDER_INFORMATION.best_guess_position_lon = intermediate_points_lon(profile_to_last_position);
+ current_float{index_last_position + i}.SECOND_ORDER_INFORMATION.best_guess_position_src = [ last_position.src '_gcwaypts_' next_position.src ];
+ end
+
+ end
+
+end % estimate_unknowns
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+postprocessing/delete_profile.m b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/delete_profile.m
new file mode 100644
index 0000000..2b772cd
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/delete_profile.m
@@ -0,0 +1,68 @@
+function [ filtered_nemo_data ] = delete_profile( p_nemo_data, p_float_serial, p_profile_number )
+%DELETE_PROFILE Deletes the given profile from the given float.
+%
+% Parameters:
+% p_nemo_data Nemo data, loaded by nemo.load.data().
+% p_float_number Input float serial number.
+% p_profile_number Profile to be deleted.
+%
+% Returns:
+% filtered_nemo_data Nemo data with deleted profile.
+%
+%
+% TODO: SECURITY CHECKS MISSING
+
+% search float
+float_count = length(p_nemo_data);
+current_float = 1;
+while current_float <= float_count
+ current_serial = ...
+ p_nemo_data{current_float}{1}.FLOAT_IDENTIFICATION.float_serial_number;
+ if current_serial == p_float_serial
+ break
+ else
+ current_float = current_float + 1;
+ end
+end
+
+if current_float > float_count
+ filtered_nemo_data = p_nemo_data;
+ disp([mfilename ': Float could not be found in data, skipping...']);
+ return
+end
+
+% found the right float, now find the profile
+profile_count = length(p_nemo_data{current_float});
+current_profile = 1;
+while current_profile <= profile_count
+ current_profile_number = ...
+ p_nemo_data{current_float}{current_profile}.PROFILE_TECHNICAL_DATA.xmit_profile_number;
+ if current_profile_number == p_profile_number
+ break
+ else
+ current_profile = current_profile + 1;
+ end
+end
+
+if current_profile > profile_count
+ filtered_nemo_data = p_nemo_data;
+ disp([mfilename ': Profile could not be found in data, skipping...']);
+ return
+end
+
+filtered_nemo_data = p_nemo_data;
+if current_profile == profile_count
+ filtered_float = p_nemo_data{current_float}(1:end-1);
+elseif current_profile == 1
+ filtered_float = p_nemo_data{current_float}(2:end);
+else
+ filtered_float = {};
+ filtered_float{1:current_profile-1} = ...
+ p_nemo_data{current_float}(1:current_profile-1);
+ filtered_float{current_profile+1:end} = ...
+ p_nemo_data{current_float}(current_profile+1:end);
+end
+filtered_nemo_data{current_float} = filtered_float;
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+postprocessing/quality_check.m b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/quality_check.m
new file mode 100644
index 0000000..c8ef6e2
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/quality_check.m
@@ -0,0 +1,105 @@
+function [ commented_nemo_data ] = quality_check( p_nemo_data )
+%QUALITY_CHECK Does several quality checks.
+% 1) Adds two fields to the SECOND_ORDER_INFORMATION block:
+% fieldname values
+% xmit_transmittion_type nrt, delayed, unknown
+% ice_detected 0, 1
+%
+% 2) Removes profiles where the best_guess_datevec is before the
+% deployment time.
+%
+% Parameters:
+% p_nemo_data: The nemo data.
+%
+% Returns:
+% commented_nemo_data: The nemo data with applied changes.
+
+%% Check passed parameter
+parameter_error = false;
+
+if (~iscell(p_nemo_data))
+ parameter_error = true;
+end
+
+if (parameter_error)
+ disp([mfilename ': Parameter error. Please check your input parameters.']);
+end
+clear parameter_error;
+
+float_count = length(p_nemo_data);
+commented_nemo_data = p_nemo_data;
+
+for o_float = 1:float_count
+
+ profile_count = length(commented_nemo_data{o_float});
+ current_float = commented_nemo_data{o_float};
+
+ for o_profile_index = 1:profile_count % process all profiles
+
+ %% Check if profile has been sent directly after recording
+
+ if (o_profile_index < profile_count ...
+ && ~nemo.profile.verify_iridium( ...
+ current_float{o_profile_index}, ...
+ current_float{o_profile_index + 1}) ...
+ )
+
+ switch (nemo.profile.get_status(current_float{o_profile_index}))
+ case 'DONE'
+ % it has been sent later on, no clue why
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.xmit_transmission_type = 'delayed';
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.ice_detected = 0;
+ case 'ICE DETECTION'
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.xmit_transmission_type = 'delayed';
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.ice_detected = 1;
+ otherwise
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.xmit_transmission_type = 'unknown';
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.ice_detected = 0;
+ end
+ else
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.xmit_transmission_type = 'nrt';
+ switch (nemo.profile.get_status(current_float{o_profile_index}))
+ case 'DONE'
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.ice_detected = 0;
+ case 'ICE DETECTION'
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.ice_detected = 1;
+ otherwise
+ current_float{o_profile_index}.SECOND_ORDER_INFORMATION.ice_detected = 0;
+ end
+ end
+
+ %% Check if profile time is before deployment time
+ deploy_datenum = datenum([ ...
+ fliplr(current_float{o_profile_index}.DEPLOYMENT_INFO.deployment_date), ...
+ current_float{o_profile_index}.DEPLOYMENT_INFO.deployment_time, ...
+ 0 ...
+ ]);
+ profile_datenum = datenum(current_float{o_profile_index}.SECOND_ORDER_INFORMATION.best_guess_datevec);
+ if (profile_datenum < deploy_datenum)
+ disp(['Removed profile ' num2str(current_float{o_profile_index}.PROFILE_TECHNICAL_DATA.xmit_profile_number) ...
+ ' of float ' num2str(current_float{o_profile_index}.FLOAT_IDENTIFICATION.float_serial_number) ...
+ ' because it was recorded before deployment!']);
+ current_float{o_profile_index} = {};
+ end
+
+% if (nemo.profile.positions_differ_by(commented_nemo_data{o_profile_index}, 50))
+% commented_nemo_data{o_profile_index}.COMMENT.position = 'gps and iridium differ by more than 50km';
+% end
+
+ end
+
+ %% Remove all empty profiles
+ current_float = current_float(~cellfun(@(x) isempty(x), current_float));
+
+ %% Save current float
+ commented_nemo_data{o_float} = current_float;
+end
+
+%% Manual quality checks
+
+
+%% Remove all empty floats
+commented_nemo_data = commented_nemo_data(~cellfun(@(x) isempty(x), commented_nemo_data));
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+postprocessing/sort_profile_data.m b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/sort_profile_data.m
new file mode 100644
index 0000000..366b859
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+postprocessing/sort_profile_data.m
@@ -0,0 +1,27 @@
+function [ sorted_nemo_data ] = sort_profile_data( p_nemo_data )
+%SORT_PROFILE_DATA Sorts the CTD profile data of the given floats.
+% Uses nemo.float.sort_profuile_data function to sort each float
+% individually.
+%
+% Parameters:
+% p_nemo_data: The nemo data that will be sorted.
+%
+% Returns:
+% sorted_nemo_data: A copy of p_nemo_data with sorted CTD data.
+
+
+%% Initialize return variable
+sorted_nemo_data = false;
+
+%% Parameter check
+if (~iscell(p_nemo_data))
+ disp([mfilename ': Unknown input type! Please check your input parameter!']);
+ return
+end
+
+%% Sort profile data by time
+sorted_nemo_data = cellfun(@nemo.float.sort_profile_data, p_nemo_data, 'UniformOutput', false);
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/calc_rtc_software_difference.m b/lib/vendor/nemo2profilelib/+nemo/+profile/calc_rtc_software_difference.m
new file mode 100644
index 0000000..de7019e
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/calc_rtc_software_difference.m
@@ -0,0 +1,40 @@
+function [ difference_rtc_software ] = calc_rtc_software_difference( p_profile )
+%CALC_RTC_SOFTWARE_DIFFERENCE Summary of this function goes here
+% Detailed explanation goes here
+
+software_datevec = ...
+ datevec( ...
+ datetime([ ...
+ fliplr(p_profile.OVERALL_MISSION_INFORMATION.start_date), ...
+ p_profile.OVERALL_MISSION_INFORMATION.start_time 0 ...
+ ]) ...
+ + seconds(p_profile.PROFILE_TECHNICAL_DATA.xmit_ascent_start_time) ...
+);
+software_time = software_datevec(4:6);
+% get internal clock (RTC) @ 2000m
+rtc_time = p_profile.PROFILE_DATA( ...
+ p_profile.PROFILE_DATA(:, 7) == max(p_profile.PROFILE_DATA(:, 7)), ...
+ 2:4);
+% if there are multiple pressure levels get the one with the
+% earliest time
+rtc_time = sortrows(rtc_time, [1:3]);
+if isempty(rtc_time) || isempty(software_datevec) % prevent errors if empty
+ difference_rtc_software = NaN;
+ return;
+end
+rtc_time = rtc_time(end, :);
+
+rtc_datevec = datevec(datetime([software_datevec(1:3), rtc_time]));
+
+if (any(rtc_time(1) == 21:23) && any(software_time(1) == 0:3))
+ % RTC is more trustworthy, so reduce the software date by 1
+ rtc_datevec = datevec(datetime([software_datevec(1:3), rtc_time]) - days(1));
+elseif (any(rtc_time(1) == 0:3) && any(software_time(1) == 21:23))
+ % same here, but now add 1 day
+ rtc_datevec = datevec(datetime([software_datevec(1:3), rtc_time]) + days(1));
+end
+
+difference_rtc_software = etime(rtc_datevec, software_datevec) + 10;
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/compare.m b/lib/vendor/nemo2profilelib/+nemo/+profile/compare.m
new file mode 100644
index 0000000..0c2872c
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/compare.m
@@ -0,0 +1,79 @@
+function [ boolean ] = compare( p_profile_a, p_profile_b )
+%COMPARE Checks if the input profiles are equal.
+% Both input profiles are compared to each other. If one of the
+% underlying struct/cell/double values are not equal, it will return false.
+%
+% Parameters:
+% p_profile_a, p_profile_b: Profiles to be compared. Ideally they are
+% previously loaded by nemo.profile.load()
+%
+% Returns:
+% boolean: True if both profiles are equal.
+
+%% Initialize return variables
+boolean = true;
+%% TODO: Parameter check
+
+%% Comparing profiles
+
+compare_variables(p_profile_a, p_profile_b);
+
+ function compare_variables(p_a, p_b)
+
+ switch class(p_a)
+ case {'double', 'logical'}
+ if (all(all(isnan(p_a))) && all(all(isnan(p_b))))
+ return;
+ elseif (all(all(isnan(p_a))) && ~all(all(isnan(p_b))))
+ boolean = false;
+ return;
+ end
+ if (~strcmp(num2str(p_a), num2str(p_b)))
+ boolean = false;
+ return;
+ end
+ case 'char'
+ if (~strcmp(p_a, p_b))
+ boolean = false;
+ return;
+ end
+ case 'struct'
+ fieldnames_a = fieldnames(p_a);
+ fieldnames_b = fieldnames(p_b);
+ if (~isequaln(fieldnames_a, fieldnames_b))
+ boolean = false;
+ return;
+ end
+ for i = 1:length(fieldnames_a)
+ compare_variables(p_a.(fieldnames_a{i}), p_b.(fieldnames_b{i}));
+ end
+
+ case 'cell'
+ [la, ca] = size(p_a);
+ [lb, cb] = size(p_b);
+ if ((la ~= lb) || (ca ~= cb))
+ boolean = false;
+ return;
+ end
+ if ((ca > 1) && (la > 1))
+ for i = 1:la
+ for k = 1:ca
+ compare_variables(p_a{i}{k}, p_b{i}{k});
+ end
+ end
+ else
+ la = size(p_a);
+ for i = 1:la
+ compare_variables(p_a{i}, p_b{i});
+ end
+ end
+ end
+
+
+
+
+
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/find.m b/lib/vendor/nemo2profilelib/+nemo/+profile/find.m
new file mode 100644
index 0000000..8e3f442
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/find.m
@@ -0,0 +1,19 @@
+function [ profile, index ] = find( p_float, p_profile_number )
+%FIND Searches the profile with p_profile_number in the given float.
+% Returns the profile and its index in the p_float structure.
+% If not found, profile contains false.
+
+index = cellfun(@(x) x.PROFILE_TECHNICAL_DATA.xmit_profile_number == p_profile_number, p_float);
+if (~any(index))
+ profile = false;
+ return
+elseif (sum(index) > 1)
+ disp(['Multiple profiles found: ' index]);
+ profile = false;
+ return
+end
+
+profile = p_float{index};
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/get_gps.m b/lib/vendor/nemo2profilelib/+nemo/+profile/get_gps.m
new file mode 100644
index 0000000..331c589
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/get_gps.m
@@ -0,0 +1,32 @@
+function [ gps_data ] = get_gps( p_profile )
+%GET_GPS Returns gps data block of the given profile.
+%
+% Returns: Double of size 1x15 if gps coordinates are available.
+% Displays a warning if parameters are wrong, but returns false!
+%
+% Parameters:
+% p_profile: The nemo profile where gps data is being extracted.
+
+%% Initializing return variables
+gps_data = false;
+
+%% Parameter check
+
+if (~isstruct(p_profile))
+ disp([mfilename ': Wrong parameter. Please check your input. Returning false!']);
+ return
+end
+
+%% Check if GPS section is available
+if (~isfield(p_profile, 'SURFACE_GPS_DATA'))
+ gps_data = false;
+ return
+else
+ % store all values
+ gps_data = p_profile.SURFACE_GPS_DATA;
+end
+
+return;
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/get_iridium.m b/lib/vendor/nemo2profilelib/+nemo/+profile/get_iridium.m
new file mode 100644
index 0000000..4a2fea0
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/get_iridium.m
@@ -0,0 +1,32 @@
+function [ iridium_mean_data ] = get_iridium( p_profile )
+%GET_IRIDIUM Returns iridium data block of the given profile.
+%
+% Returns: Double of size 1x9 if iridium information is available.
+% Displays a warning if parameters are wrong, but returns false!
+%
+% Parameters:
+% p_profile: The nemo profile where gps data is being extracted.
+
+%% Initializing return variables
+iridium_mean_data = false;
+
+%% Parameter check
+
+if (~isstruct(p_profile))
+ disp([mfilename ': Wrong parameter. Please check your input. Returning false!']);
+ return
+end
+
+%% Check if iridium section is available
+if (~isfield(p_profile, 'IRIDIUM_DATA'))
+ iridium_mean_data = false;
+ return
+else
+ % store all values
+ iridium_mean_data = p_profile.IRIDIUM_DATA;
+end
+
+return;
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/get_rtc_datevec_of_ctd_sample.m b/lib/vendor/nemo2profilelib/+nemo/+profile/get_rtc_datevec_of_ctd_sample.m
new file mode 100644
index 0000000..2546ed0
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/get_rtc_datevec_of_ctd_sample.m
@@ -0,0 +1,84 @@
+function [ sample_datevec, rtc_datevecs ] = get_rtc_datevec_of_ctd_sample( p_profile, p_sample_index )
+%GET_TIMESTAMP_OF_CTD_SAMPLE Summary of this function goes here
+% Detailed explanation goes here
+
+%% Parameter check
+if ~exist('p_sample_index', 'var')
+ p_sample_index = 1;
+end
+
+if ~isstruct(p_profile) || ~isa(p_sample_index, 'double')
+ disp([mfilename ': Please check your input parameter!']);
+ return;
+end
+
+%% Initialize return variable
+sample_datevec = NaN(1, 6);
+
+%% Find CTD sample
+
+ctd_profile = [];
+
+if ~isempty(p_profile.PROFILE_DATA)
+ p = nemo.profile.sort_profile_data(p_profile);
+ ctd_profile = p.PROFILE_DATA;
+ clear p
+else
+ return
+end
+
+software_datevec = ...
+ datevec( ...
+ datetime([ ...
+ fliplr(p_profile.OVERALL_MISSION_INFORMATION.start_date), ...
+ p_profile.OVERALL_MISSION_INFORMATION.start_time 0 ...
+ ]) ...
+ + seconds(p_profile.PROFILE_TECHNICAL_DATA.xmit_ascent_start_time) ...
+);
+software_time = software_datevec(4:6);
+% get internal clock (RTC) @ 2000m
+rtc_time = p_profile.PROFILE_DATA( ...
+ p_profile.PROFILE_DATA(:, 7) == max(p_profile.PROFILE_DATA(:, 7)), ...
+ 2:4);
+% if there are multiple pressure levels get the one with the
+% earliest time
+rtc_time = sortrows(rtc_time, [1:3]);
+if isempty(rtc_time) || isempty(software_datevec) % prevent errors if empty
+ return;
+end
+rtc_time = rtc_time(end, :);
+
+rtc_datevec = datevec(datetime([software_datevec(1:3), rtc_time]));
+
+if (any(rtc_time(1) == 21:23) && any(software_time(1) == 0:3))
+ % RTC is more trustworthy, so reduce the software date by 1
+ rtc_datevec = datevec(datetime([software_datevec(1:3), rtc_time]) - days(1));
+elseif (any(rtc_time(1) == 0:3) && any(software_time(1) == 21:23))
+ % same here, but now add 1 day
+ rtc_datevec = datevec(datetime([software_datevec(1:3), rtc_time]) + days(1));
+end
+
+
+
+% get ctd, rtc time
+rtc_times = p_profile.PROFILE_DATA(:, 2:4);
+% add pseudo date to profile samples
+pseudo_datenums = datenum([ ...
+ zeros(size(ctd_profile, 1), 2), ...
+ flipud((1:size(ctd_profile, 1))'), ...
+ rtc_times ...
+]);
+
+diff_in_seconds = mod(flipud(diff(flipud(pseudo_datenums))), 1) * 86400;
+
+rtc_datevecs = [rtc_datevec];
+for i = 1:length(diff_in_seconds)
+ rtc_datevecs = [ rtc_datevecs; datevec(datetime(rtc_datevecs(i, :)) + seconds(diff_in_seconds(end - i + 1)))];
+end
+rtc_datevecs = flipud(rtc_datevecs);
+
+sample_datevec = rtc_datevecs(p_sample_index);
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/get_status.m b/lib/vendor/nemo2profilelib/+nemo/+profile/get_status.m
new file mode 100644
index 0000000..b4fc659
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/get_status.m
@@ -0,0 +1,13 @@
+function [ status ] = get_status( p_profile )
+%GET_STATUS Returns the xmit_upcast_status value of the given profile.
+%
+% Returns: String, containing the profiles xmit_upcast_status.
+%
+% Parameters:
+% p_profile: The nemo profile that is being checked.
+
+status = strtrim(p_profile.PROFILE_TECHNICAL_DATA.xmit_upcast_status);
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/has_best_guess.m b/lib/vendor/nemo2profilelib/+nemo/+profile/has_best_guess.m
new file mode 100644
index 0000000..fbf8b41
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/has_best_guess.m
@@ -0,0 +1,36 @@
+function [ boolean ] = has_best_guess( p_profile )
+%HAS_BEST_GUESS Checks if profile has best guess coordinates as well as time.
+%
+% Returns: True if best guess information is available.
+% Displays a warning if parameters are wrong, but returns false!
+%
+% Parameters:
+% p_profile: The nemo profile that is being checked.
+
+%% Initializing return variables
+boolean = false;
+
+%% Parameter check
+
+if (~isstruct(p_profile))
+ disp([mfilename ': Wrong parameter. Please check your input. Returning false!']);
+end
+
+%% Check if GPS section is available
+if (~isfield(p_profile, 'SECOND_ORDER_INFORMATION') ...
+ || ~isfield(p_profile.SECOND_ORDER_INFORMATION, 'best_guess_position_lat') ...
+ || ~isfield(p_profile.SECOND_ORDER_INFORMATION, 'best_guess_position_lon') ...
+ || ~isfield(p_profile.SECOND_ORDER_INFORMATION, 'best_guess_position_src'))
+ || ~isfield(p_profile.SECOND_ORDER_INFORMATION, 'best_guess_datevec'))
+ || ~isfield(p_profile.SECOND_ORDER_INFORMATION, 'best_guess_datevec_src'))
+ boolean = false;
+ return
+else
+ % check if the values are available
+ boolean = ~isnan(p_profile.SECOND_ORDER_INFORMATION.best_guess_position_lat);
+end
+
+return;
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/has_gps.m b/lib/vendor/nemo2profilelib/+nemo/+profile/has_gps.m
new file mode 100644
index 0000000..1e7a706
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/has_gps.m
@@ -0,0 +1,31 @@
+function [ boolean ] = has_gps( p_profile )
+%HAS_GPS Checks if profile has gps coordinates.
+%
+% Returns: True if gps coordinates are available.
+% Displays a warning if parameters are wrong, but returns false!
+%
+% Parameters:
+% p_profile: The nemo profile that is being checked.
+
+%% Initializing return variables
+boolean = false;
+
+%% Parameter check
+
+if (~isstruct(p_profile))
+ disp([mfilename ': Wrong parameter. Please check your input. Returning false!']);
+end
+
+%% Check if GPS section is available
+if (~isfield(p_profile, 'SURFACE_GPS_DATA'))
+ boolean = false;
+ return
+else
+ % check if the values are available
+ boolean = (~any(isnan(p_profile.SURFACE_GPS_DATA)) && ~isempty(p_profile.SURFACE_GPS_DATA));
+end
+
+return;
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/has_iridium.m b/lib/vendor/nemo2profilelib/+nemo/+profile/has_iridium.m
new file mode 100644
index 0000000..707128b
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/has_iridium.m
@@ -0,0 +1,31 @@
+function [ boolean ] = has_iridium( p_profile )
+%HAS_IRIDIUM Checks if profile has iridium coordinates.
+%
+% Returns: True if iridium coordinates are available.
+% Displays a warning if parameters are wrong, but returns false!
+%
+% Parameters:
+% p_profile: The nemo profile that is being checked.
+
+%% Initializing return variables
+boolean = false;
+
+%% Parameter check
+
+if (~isstruct(p_profile))
+ disp([mfilename ': Wrong parameter. Please check your input. Returning false!']);
+end
+
+%% Check coordinates
+if (~isfield(p_profile, 'IRIDIUM_DATA'))
+ boolean = false;
+ return
+else
+ % check if the values are available
+ boolean = (~any(isnan(p_profile.IRIDIUM_DATA)));
+end
+
+return;
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/has_no_gps_but_iridium.m b/lib/vendor/nemo2profilelib/+nemo/+profile/has_no_gps_but_iridium.m
new file mode 100644
index 0000000..7f4c56b
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/has_no_gps_but_iridium.m
@@ -0,0 +1,52 @@
+function [ boolean ] = has_no_gps_but_iridium( p_profile )
+%HAS_NO_GPS_BUT_IRIDIUM Checks if profile has iridium coordinates, but no gps.
+%
+% Returns: True if iridium but no gps coordinates are available.
+% Displays a warning if parameters are wrong, but returns false!
+%
+% Parameters:
+% p_profile: The nemo profile that is being checked.
+
+%% Initializing return variables
+boolean = false;
+
+%% Parameter check
+
+if (~isstruct(p_profile))
+ disp([mfilename ': Wrong parameter. Please check your input. Returning false!']);
+end
+
+%% Check if gps section and values are available
+if (isfield(p_profile, 'SURFACE_GPS_DATA'))
+ % check if the values are available
+ gps_available = (~any(isnan(p_profile.SURFACE_GPS_DATA))) && ~isempty(p_profile.SURFACE_GPS_DATA);
+else
+ gps_available = false;
+end
+
+%% Check if iridium is available
+if (isfield(p_profile, 'IRIDIUM_DATA') && ~isempty(p_profile.IRIDIUM_DATA))
+ % check if the values are available
+ % get indices of lat and lon
+ index_lat = find(not(cellfun('isempty', ...
+ strfind(p_profile.('IRIDIUM_DATA_FORMAT'), 'mean_lat') ...
+ )));
+ index_lon = find(not(cellfun('isempty', ...
+ strfind(p_profile.('IRIDIUM_DATA_FORMAT'), 'mean_lon') ...
+ )));
+ boolean = (~isnan(p_profile.('IRIDIUM_DATA')(index_lat)) && ~isnan(p_profile.('IRIDIUM_DATA')(index_lon)));
+
+ if (boolean && ~gps_available)
+ boolean = true;
+ return
+ else
+ boolean = false;
+ return;
+ end
+else
+ boolean = false;
+ return;
+end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/has_no_iridium_but_gps.m b/lib/vendor/nemo2profilelib/+nemo/+profile/has_no_iridium_but_gps.m
new file mode 100644
index 0000000..d2debcd
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/has_no_iridium_but_gps.m
@@ -0,0 +1,31 @@
+function [ boolean ] = has_no_iridium_but_gps( p_profile )
+%HAS_NO_IRIDIUM_BUT_GPS Checks if profile has gps coordinates, but no iridium.
+%
+% Returns: True if gps but no iridium coordinates are available.
+% Displays a warning if parameters are wrong, but returns false!
+%
+% Parameters:
+% p_profile: The nemo profile that is being checked.
+
+%% Initializing return variables
+boolean = false;
+
+%% Parameter check
+
+if (~isstruct(p_profile))
+ disp([mfilename ': Wrong parameter. Please check your input. Returning false!']);
+end
+
+%% Check coordinates
+
+boolean = ( ...
+ isnan(p_profile.iridium_mean_lat) ...
+ && isnan(p_profile.iridium_mean_lon) ...
+ && ~isnan(p_profile.gps_lat) ...
+ && ~isnan(p_profile.gps_lon) ...
+ );
+
+return;
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/has_status.m b/lib/vendor/nemo2profilelib/+nemo/+profile/has_status.m
new file mode 100644
index 0000000..16800bf
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/has_status.m
@@ -0,0 +1,36 @@
+function [ boolean ] = has_status( p_profile, p_status )
+%HAS_STATUS Returns true if given profile has given status, false otherwise.
+% Compares xmit_upcast_status of the given profile with the p_status
+% parameter.
+%
+% Returns: True or false.
+%
+% Parameters:
+% p_profile: The nemo profile that is being checked.
+% p_status: Expected xmit_upcast_status.
+
+%% Initializing return variables
+boolean = false;
+
+%% Parameter check
+
+if isempty(p_profile)
+ return; % because no values given
+end
+
+if (~isstruct(p_profile) ...
+ || ~ischar(p_status))
+ disp([mfilename ': Wrong parameter. Please check your input. Returning false!']);
+end
+
+%% Check status
+if isnan(p_profile.PROFILE_TECHNICAL_DATA.xmit_upcast_status)
+ boolean = false;
+else
+ boolean = (strcmp(p_status, strtrim(p_profile.PROFILE_TECHNICAL_DATA.xmit_upcast_status)));
+end
+
+return;
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/has_status_and_coordinates.m b/lib/vendor/nemo2profilelib/+nemo/+profile/has_status_and_coordinates.m
new file mode 100644
index 0000000..3db8a96
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/has_status_and_coordinates.m
@@ -0,0 +1,56 @@
+function [ boolean ] = has_status_and_coordinates( p_profile, p_status, p_max_coord_dist )
+%HAS_STATUS_AND_COORDINATES DEPRECATED! Not required anymore! Checks if profile has valid coordinates and given status.
+% Checks if the given profile has the given status as well as valid iridium and
+% gps coordinates. If the distance between iridium and gps exceeds
+% p_max_coord_dist, false is being returned. The distance is being
+% calculated via build in MATLAB distance function.
+%
+% Returns: True if all conditions are met. Displays a warning if
+% parameters are wrong, but returns false!
+%
+% Parameters:
+% p_profile: The nemo profile that is being checked.
+% p_status: Expected xmit_upcast_status.
+% p_max_coord_dist: Maximum distance in km between iridium and gps.
+
+%% Initializing return variables
+boolean = false;
+
+%% Parameter check
+
+if (~isstruct(p_profile) ...
+ || ~ischar(p_status) ...
+ || ~isnumeric(p_max_coord_dist))
+ disp([mfilename ': Wrong parameter. Please check your input. Returning false!']);
+end
+
+%% Check status, skip if '' is given
+if (~strcmp(p_status, strtrim(p_profile.PROFILE_TECHNICAL_DATA.xmit_upcast_status)) ...
+ && ~strcmp(p_status, ''))
+ return;
+end
+
+%% Check coordinates
+
+if (~nemo.profile.has_gps(p_profile) || ~nemo.profile.has_iridium(p_profile))
+ return;
+end
+
+% get distance in between
+difference = deg2km( ...
+ distance('gc', ... % convert to km for easier handling
+ [p_profile.SURFACE_GPS_DATA(14), p_profile.SURFACE_GPS_DATA(15)], ...
+ [p_profile.IRIDIUM_DATA(1), p_profile.IRIDIUM_DATA(2)] ...
+ ) ...
+);
+
+if (difference > p_max_coord_dist)
+ return;
+end
+
+boolean = true;
+
+return;
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/has_status_and_gps.m b/lib/vendor/nemo2profilelib/+nemo/+profile/has_status_and_gps.m
new file mode 100644
index 0000000..250b57d
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/has_status_and_gps.m
@@ -0,0 +1,42 @@
+function [ boolean ] = has_status_and_gps( p_profile, p_status )
+%HAS_STATUS_AND_GPS Checks if profile has gps coordinates and given status.
+% Checks if the given profile has the given status as well as
+% gps coordinates.
+%
+% Returns: True if all conditions are met. Displays a warning if
+% parameters are wrong, but returns false!
+%
+% Parameters:
+% p_profile: The nemo profile that is being checked.
+% p_status: Expected xmit_upcast_status.
+
+%% Initializing return variables
+boolean = false;
+
+%% Parameter check
+
+if (~isstruct(p_profile) ...
+ || ~ischar(p_status))
+ disp([mfilename ': Wrong parameter. Please check your input. Returning false!']);
+end
+
+%% Check status
+if (~strcmp(p_status, strtrim(p_profile.xmit_upcast_status)))
+ return;
+end
+
+%% Check coordinates
+
+if ( ... % one of them is NaN
+ isnan(p_profile.gps_lat) ...
+ || isnan(p_profile.gps_lon) ...
+ )
+ return;
+end
+
+boolean = true;
+
+return;
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/load.m b/lib/vendor/nemo2profilelib/+nemo/+profile/load.m
new file mode 100644
index 0000000..004318a
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/load.m
@@ -0,0 +1,165 @@
+function [ profile ] = load( p_filename )
+%LOAD Loads a .profile file into memory.
+%
+% Returns: A struct containing all parameter and data that has been read from
+% the datafile. WARNING: Does not check if something went wrong while reading
+% the file.
+%
+% Parameters:
+% p_filename: Absolute filename of the file to read.
+%
+
+%% TODO:
+% - remove sections and make this function recognize automatically which type
+% of variable should be used, same as in nemo.profile.save().
+
+%% Initialize input parameter
+profile = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~ischar(p_filename))
+ warning([mfilename ': Please check input parameter. p_filename is not a string!']);
+ parameter_error = true;
+else
+ % get filename details
+ [pathstr, name, ext] = fileparts(p_filename);
+ if (~strcmp(ext, '.profile'))
+ warning([mfilename ': Please check input parameter. Wrong file extension! Should be .profile!']);
+ parameter_error = true;
+ end
+end
+
+if parameter_error
+ return; % return if parameter check has not been passed successfully
+else
+ clear parameter_error;
+end
+
+%% Load profile into variable
+
+% initialize all required variables
+profile = {};
+current_section = '';
+comment_char = '%'; % character to indicate comments
+section_char = '['; % character indicating new section
+
+% open file
+file_id = fopen(p_filename);
+fseek(file_id, 0, 'bof');
+
+
+% read file line by line
+current_line = fgetl(file_id);
+while (ischar(current_line))
+ if length(current_line) == 0
+ current_line = fgetl(file_id);
+ continue
+ end
+
+ switch current_line(1)
+ case section_char % this indicates a new section
+ current_line = strtrim(current_line);
+ current_section = current_line(2:end-1);
+ read_section
+ otherwise
+ current_line = fgetl(file_id);
+ end
+
+end
+
+fclose(file_id);
+
+ function read_section
+ % read complete section
+ current_line = fgetl(file_id);
+
+ if isempty(current_line)
+ % initialize an empty array to prevent errors when trying to
+ % access in another function
+ profile.(current_section) = [];
+ end
+
+ while ischar(current_line) && ~isempty(current_line) ...
+ && ~strcmp(current_line(1), section_char)
+
+ if strcmp(current_line(1), comment_char) % ignore commented lines
+ current_line = fgetl(file_id);
+ continue
+ end
+
+ % if it contains a comment char anywhere, just take the string
+ % before it
+ found_comment = strfind(current_line, comment_char);
+ if ~isempty(found_comment)
+ current_line = current_line(1:found_comment(1)-1);
+ end
+
+ switch (current_section)
+ case { ...
+ 'FLOAT_IDENTIFICATION', ...
+ 'OVERALL_MISSION_INFORMATION', ...
+ 'DEPLOYMENT_INFO', ...
+ 'PROFILE_TECHNICAL_DATA', ...
+ 'BOTTOM_VALUES_DURING_DRIFT', ...
+ 'PROFILE_HEADER', ...
+ 'QUALITY_CONTROL_HEADER', ...
+ 'SECOND_ORDER_INFORMATION' ...
+ }
+ % get variable name and value
+ [token, remain] = strtok(current_line);
+ % try to convert remain to a number
+ remain_as_num = str2num(strtrim(remain));
+ if (~isempty(remain_as_num))
+ profile.(current_section).(token(2:end)) = remain_as_num;
+ else
+ profile.(current_section).(token(2:end)) = strtrim(remain);
+ end
+ case { ...
+ 'RAFOS_VALUES_FORMAT', ...
+ 'PROFILE_DATA_FORMAT', ...
+ 'SURFACE_GPS_DATA_FORMAT', ...
+ 'IRIDIUM_POSITIONS_FORMAT', ...
+ 'IRIDIUM_DATA_FORMAT', ...
+ 'PROFILE_DATA_HEADER' ...
+ }
+ % remove -format, split afterwards
+ [token, remain] = strtok(current_line);
+ if (~strcmp(token, '-format'))
+ profile.(current_section) = [ token, ...
+ strsplit(strtrim(remain), {' ', '\t'}, 'CollapseDelimiters', true)];
+ else
+ profile.(current_section) = strsplit( ...
+ strtrim(remain), {' ', '\t'}, 'CollapseDelimiters', true);
+ end
+ %break
+ case { ...
+ 'RAFOS_VALUES', ...
+ 'PROFILE_DATA', ...
+ 'SURFACE_GPS_DATA', ...
+ 'IRIDIUM_POSITIONS', ...
+ 'IRIDIUM_DATA' ...
+ }
+ % store into matrix
+ % read values and append them into the same var as long
+ % as no empty line occured (convention)
+ profile.(current_section) = [];
+ while (ischar(current_line) && ~strcmp(current_line, ''))
+ profile.(current_section) = [ ...
+ profile.(current_section); ...
+ str2double(strsplit(current_line, {'\t', ' '}, 'CollapseDelimiters', true)) ...
+ ];
+ current_line = fgetl(file_id);
+ end
+ break
+
+ end
+
+ current_line = fgetl(file_id);
+ end
+ end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/map_to.m b/lib/vendor/nemo2profilelib/+nemo/+profile/map_to.m
new file mode 100644
index 0000000..26e7317
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/map_to.m
@@ -0,0 +1,75 @@
+function [ mapped_profile ] = map_to( p_profile, p_mapping, p_skip_undefined )
+%MAP_TO Summary of this function goes here
+% Detailed explanation goes here
+
+%% Initialize return variable
+mapped_profile = false;
+
+%% Parameter check
+if ~isstruct(p_profile) || ~isstruct(p_mapping)
+ disp([mfilename ': Please check your input parameter!']);
+ return
+end
+
+%% Map parameters
+mapped_profile = struct;
+
+fnames_profile = fieldnames(p_profile);
+
+for i = 1:length(fnames_profile)
+
+ % check if mapping exists for this field
+ if ~isfield(p_mapping, fnames_profile{i})
+ if exist('p_skip_undefined', 'var') && ~p_skip_undefined
+ mapped_profile.(fnames_profile{i}) = p_profile.(fnames_profile{i});
+ end
+ continue
+ end
+
+ current_field = p_profile.(fnames_profile{i});
+
+ if ~isstruct(current_field) % we only want to modify structs atm
+ continue
+ end
+
+ mapped_profile.(fnames_profile{i}) = struct;
+
+ % get the fieldnames in the struct
+ subfnames = fieldnames(current_field);
+ for k = 1:length(subfnames)
+
+ if ~isfield(p_mapping.(fnames_profile{i}), subfnames{k})
+ if exist('p_skip_undefined', 'var') && ~p_skip_undefined
+ mapped_profile.(fnames_profile{i}).(subfnames{k}) = p_profile.(fnames_profile{i}).(subfnames{k});
+ end
+ continue
+ end
+
+ % check if the previous value is the same
+ if isfield(mapped_profile.(fnames_profile{i}), (p_mapping.(fnames_profile{i}).(subfnames{k})))
+ % append the value instead of copying
+ mapped_profile.(fnames_profile{i}).(p_mapping.(fnames_profile{i}).(subfnames{k})) = ...
+ [ ...
+ mapped_profile.(fnames_profile{i}).(p_mapping.(fnames_profile{i}).(subfnames{k})) ...
+ p_profile.(fnames_profile{i}).(subfnames{k})
+ ];
+ continue
+ end
+
+ % check if there are multiple values in the field
+ values = strsplit(p_mapping.(fnames_profile{i}).(subfnames{k}), ',');
+ if length(values) > 1
+ for m = 1:length(values)
+ mapped_profile.(fnames_profile{i}).(values{m}) = p_profile.(fnames_profile{i}).(subfnames{k})(m);
+ end
+ continue
+ end
+
+ mapped_profile.(fnames_profile{i}).(p_mapping.(fnames_profile{i}).(subfnames{k})) = p_profile.(fnames_profile{i}).(subfnames{k});
+
+ end
+
+end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/positions_differ_by.m b/lib/vendor/nemo2profilelib/+nemo/+profile/positions_differ_by.m
new file mode 100644
index 0000000..1409e19
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/positions_differ_by.m
@@ -0,0 +1,38 @@
+function [ boolean ] = positions_differ_by( p_profile, p_distance )
+%POSITIONS_DIFFER_BY Checks if gps and iridium coordinates differ by given distance.
+%
+% Returns: True if the distance exceeds p_distance [km].
+%
+% Parameters:
+% p_profile: The nemo profile that is being checked.
+% p_distance: The maximum distance that is being accepted.
+
+%% Initializing return variables
+boolean = false;
+
+%% Parameter check
+
+if (~isstruct(p_profile))
+ disp([mfilename ': Wrong parameter. Please check your input. Returning false!']);
+end
+
+%% Check coordinates
+
+if (~nemo.profile.has_gps(p_profile) || ~nemo.profile.has_iridium(p_profile))
+ return;
+end
+
+% get distance in between
+difference = deg2km( ...
+ distance('gc', ... % convert to km for easier handling
+ [p_profile.SURFACE_GPS_DATA(14), p_profile.SURFACE_GPS_DATA(15)], ...
+ [p_profile.IRIDIUM_DATA(1), p_profile.IRIDIUM_DATA(2)] ...
+ ) ...
+);
+
+if (difference > p_distance)
+ boolean = true;
+end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/save.m b/lib/vendor/nemo2profilelib/+nemo/+profile/save.m
new file mode 100644
index 0000000..1aeddea
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/save.m
@@ -0,0 +1,179 @@
+function [ boolean ] = save( p_header_filename, p_profile, p_output_file, p_overwrite )
+%SAVE Writes the input profile to the output file.
+% This function saves the p_profile structure to an ASCII textfile with
+% .profile extension. The structure of the parameter is being transferred
+% equally into the textfile so that it can be loaded by the load
+% function.
+% TO BE OPTIMIZED: This function does not recursively checks for the
+% variable type. Only up to the second level.
+%
+% Returns: Boolean variable, being false if something went wrong during
+% write.
+%
+% Parameters:
+% p_header_file: Contains the absolute filename of the header being
+% written to the output file. There is no comment
+% character being added by this function.
+% p_profile: Contains the profile structure that will be written to
+% the output file.
+% p_output_file: Absolute file path to the output file that will be
+% written.
+% p_overwrite: If set to true, the output file will be overwritten if
+% it exists.
+%
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~isstruct(p_profile) || ~ischar(p_header_filename) ...
+ || ~ischar(p_output_file))
+ parameter_error = true;
+end
+
+if (~exist('p_overwrite', 'var') || isempty(p_overwrite))
+ p_overwrite = 1; % default setting is to overwrite existing profile files
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% File existence checks
+
+if exist(p_output_file, 'file') == 2 && ~p_overwrite
+ % file will not be overwritten
+ boolean = true;
+ return
+end
+
+header_file_id = 0;
+if exist(p_header_filename, 'file') ~= 2
+ disp([mfilename ': Header file does not exist! Skipping...']);
+ return;
+else % read header file
+ header_file_id = fopen(p_header_filename, 'r');
+ header_content = fscanf(header_file_id, '%c');
+ fclose(header_file_id);
+ clear header_file_id
+end
+
+%% Write file
+
+% prepare for writing
+help_tabs = ['\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t'];
+desired_tab_count = 12;
+section_names = fieldnames(p_profile); % will be stored in between []
+section_count = length(section_names);
+output_file_id = fopen(p_output_file, 'w'); % open file for writing
+double_format = '%.15g';
+
+% write header
+fprintf(output_file_id, '%s', header_content); % write header to file
+fprintf(output_file_id, '\n\n'); % add 2 lines to separate data from header
+
+% write content
+for o_section = 1:section_count % run through every section
+
+ % write section name to file
+ fprintf(output_file_id, ['[' section_names{o_section} ']' '\n' ]);
+
+ % check which type of data it is and decide how to output
+ switch class(p_profile.(section_names{o_section}))
+ case 'struct'
+ write_struct(p_profile.(section_names{o_section}));
+
+ case 'cell'
+ write_cell(p_profile.(section_names{o_section}));
+
+ case 'double'
+ write_double(p_profile.(section_names{o_section}));
+
+ otherwise
+ end
+
+ fprintf(output_file_id, '\n');
+
+
+end
+
+% close file
+fclose(output_file_id);
+
+boolean = true; % update return variable
+
+
+ function [ tabs ] = get_tabs_to_insert(p_member_name)
+ % this function computes the required tabs to insert, making the
+ % textfile easier to read.
+ tablength = 4;
+ tab_count = desired_tab_count - floor((length(p_member_name)+1)/tablength);
+ tabs = help_tabs(1:(tab_count*2));
+ end
+
+ function write_struct(p_input_struct)
+ % get all fieldnames and write them to the file
+ member_names = fieldnames(p_input_struct);
+ member_count = length(member_names);
+ for o_member = 1:member_count % run through all members
+ % calculate how many tabs have to be inserted to have a
+ % good table layout
+ tabstring = get_tabs_to_insert(member_names{o_member});
+ fprintf(output_file_id, ['-' member_names{o_member} tabstring]);
+ current_member = p_input_struct.(member_names{o_member});
+ current_member_class = class(current_member);
+ switch current_member_class
+ case {'double', 'logical'}
+ write_double(current_member);
+ case 'char'
+ fprintf(output_file_id, [current_member '\n']);
+ otherwise
+ disp(['Unknown class in file: ' class(current_member)]);
+ end
+
+ end
+ clear o_member
+ end
+
+ function write_cell(p_input_cell)
+ % run through every cell member and check the class
+ for o_cell_line = 1:size(p_input_cell, 1)
+ for o_cell_column = 1:size(p_input_cell, 2)
+ current_value = p_input_cell{o_cell_line, o_cell_column};
+ switch class(current_value)
+ case 'char'
+ fprintf(output_file_id, current_value);
+ case {'double', 'logical'}
+ fprintf(output_file_id, double_format, current_value);
+ otherwise
+ disp(['Unknown class in file: ' class(current_value)]);
+ end
+ if (o_cell_column ~= size(p_input_cell, 2))
+ fprintf(output_file_id, '\t');
+ end
+ end
+
+ fprintf(output_file_id, '\n');
+ end
+ end
+
+ function write_double(p_input_double)
+
+ for o_double = 1:size(p_input_double, 1)
+ if length(p_input_double(o_double, :)) > 1
+ fprintf(output_file_id, sprintf([double_format '\t'], p_input_double(o_double, 1:end-1)));
+ end
+ fprintf(output_file_id, [double_format '\n'], p_input_double(o_double, end));
+ end
+ clear o_double
+
+ end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/sort_profile_data.m b/lib/vendor/nemo2profilelib/+nemo/+profile/sort_profile_data.m
new file mode 100644
index 0000000..b32f7c6
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/sort_profile_data.m
@@ -0,0 +1,27 @@
+function [ sorted_profile ] = sort_profile_data( p_profile )
+%SORT_PROFILE_DATA Sorts the CTD profile data ascending by pressure.
+% See nemo.float.sort_profile_data for more details.
+%
+% Parameters:
+% p_profile: The profile to be sorted.
+%
+% Returns:
+% sorted_profile: A copy of the profile with sorted CTD data.
+
+
+%% Initialize return variable
+sorted_profile = false;
+
+%% Parameter check
+if (~isstruct(p_profile) || ~isfield(p_profile, 'PROFILE_DATA'))
+ disp([mfilename ': Unknown input type! Please check your input parameter!']);
+ return
+end
+
+%% Sort profile data by time
+sorted_profile = p_profile;
+sorted_profile.PROFILE_DATA = sortrows(p_profile.PROFILE_DATA, 7);
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+profile/verify_iridium.m b/lib/vendor/nemo2profilelib/+nemo/+profile/verify_iridium.m
new file mode 100644
index 0000000..352fb45
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+profile/verify_iridium.m
@@ -0,0 +1,38 @@
+function [ boolean ] = verify_iridium( p_profile, p_next_profile )
+%VERIFY_IRIDIUM Checks if the Iridium data represents profile time and position.
+%
+% Returns: True if Iridium time of current profile is smaller than the
+% one of the next profile.
+%
+% Parameters:
+% p_profile: The current nemo profile.
+% p_next_profile: The nemo profile with profile no +1.
+
+%% Initializing return variables
+boolean = false;
+
+%% Parameter check
+
+if (~isstruct(p_profile) || ~isstruct(p_next_profile))
+ disp([mfilename ': Wrong parameters. Please check your input. Returning false!']);
+ return
+end
+
+%% Check if iridium section is available
+if (~isfield(p_profile, 'IRIDIUM_DATA') || ~isfield(p_next_profile, 'IRIDIUM_DATA'))
+ boolean = false;
+ return
+else % compare it to next profile
+ % the current profile datetime has to be lower than the one of the next
+ % profile
+ boolean = ( ...
+ datenum(p_profile.IRIDIUM_DATA(4:9)) ...
+ < ...
+ datenum(p_next_profile.IRIDIUM_DATA(4:9)) ...
+ );
+
+end
+
+return;
+
+end
\ No newline at end of file
diff --git a/lib/vendor/nemo2profilelib/+nemo/+rfb/create.m b/lib/vendor/nemo2profilelib/+nemo/+rfb/create.m
new file mode 100644
index 0000000..28ed1cd
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+rfb/create.m
@@ -0,0 +1,239 @@
+function [ rfb, metadata ] = create( p_nemo_float, p_float_metadata )
+%CREATE Creates the rfb structure of the given floats.
+%
+% Parameters:
+% p_nemo_float: The floats to process.
+% p_float_metadata: The floats metadata.
+%
+% Returns:
+% rfb: The rfb structure.
+% metadata: The corresponding metadata. Floats without
+% RAFOS have been sorted out.
+
+%% Initialize return variables
+rfb = false;
+
+%% Parameter check
+if (~iscell(p_nemo_float)) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+end
+
+% if it is the first profile, it is a struct, otherwise a cell
+switch (class(p_nemo_float{1}))
+ case 'cell'
+ % sort out all floats without rafos data
+% sending_floats_metadata = {};
+% for o = 1:length(p_nemo_float) % run through every float
+% current_serial = p_nemo_float{o}{1}.FLOAT_IDENTIFICATION.float_serial_number;
+% for i = 1:length(p_float_metadata)
+% if (p_float_metadata{i}.GENERAL_INFO.SERIAL == current_serial)
+% sending_floats_metadata{o} = p_float_metadata{i};
+% end
+% end
+% end
+% rfb = cellfun(@create_rfb_float, p_nemo_float, sending_floats_metadata', 'UniformOutput', false);
+ rfb = cellfun(@create_rfb_float, p_nemo_float, p_float_metadata, 'UniformOutput', false);
+% metadata = sending_floats_metadata;
+ metadata = p_float_metadata;
+ case 'struct'
+ rfb = create_rfb_float(p_nemo_float, p_float_metadata);
+ metadata = p_float_metadata;
+ otherwise
+ disp([mfilename ': Type ' class(p_nemo_float{1}) ' not supported!' ]);
+ return
+end
+
+
+ function rfb_float = create_rfb_float(float, metadata)
+
+ if(~isfield(float{1}, 'SECOND_ORDER_INFORMATION'))
+ disp([ mfilename ': Generation of rfb file requires field SECOND_ORDER_INFORMATION!']);
+ return;
+ end
+
+ rfb_float = struct();
+
+ %% Create header information
+ FLOAT = struct( ...
+ 'floatname', float{1}.FLOAT_IDENTIFICATION.float_serial_number, ...
+ 'type', '', ...
+ 'projectname', metadata.RAFOS.GENERAL_INFO.projectname, ...
+ 'pttdec', '', ...
+ 'ptthex', '', ...
+ 'pttrep', metadata.RAFOS.GENERAL_INFO.pttrep, ...
+ 'launchpos', float{1}.DEPLOYMENT_INFO.deployment_position, ...
+ 'launchtime', [ ...
+ fliplr(float{1}.DEPLOYMENT_INFO.deployment_date), ...
+ float{1}.DEPLOYMENT_INFO.deployment_time ...
+ ], ...
+ 'recoverpos', [ ...
+ float{end}.SECOND_ORDER_INFORMATION.best_guess_position_lat, ...
+ float{end}.SECOND_ORDER_INFORMATION.best_guess_position_lon ...
+ ], ...
+ 'recovertime', float{end}.SECOND_ORDER_INFORMATION.best_guess_datevec, ...
+ 'offset', float{end}.SECOND_ORDER_INFORMATION.best_guess_datevec, ...
+ 'cycle', [ ...
+ 1, ...
+ float{1}.DEPLOYMENT_INFO.deployment_position, ...
+ fliplr(float{1}.DEPLOYMENT_INFO.deployment_date), ...
+ float{1}.DEPLOYMENT_INFO.deployment_time, ...
+ float{end}.SECOND_ORDER_INFORMATION.best_guess_position_lat, ...
+ float{end}.SECOND_ORDER_INFORMATION.best_guess_position_lon, ...
+ float{end}.SECOND_ORDER_INFORMATION.best_guess_datevec ...
+ ], ...
+ 'phasespercycle', 0, ... % is being set later, not available up to this point
+ 'schedule', metadata.RAFOS.GENERAL_INFO.schedule, ...
+ 'phasereftime', metadata.RAFOS.GENERAL_INFO.phasereftime, ...
+ 'windowsperphase', metadata.RAFOS.GENERAL_INFO.windowsperphase, ...
+ 'toaperwindow', metadata.RAFOS.GENERAL_INFO.toaperwindow, ...
+ 'toaperphase', metadata.RAFOS.GENERAL_INFO.toaperphase, ...
+ 'correlationrange', metadata.RAFOS.GENERAL_INFO.correlationrange, ...
+ 'windowrange', metadata.RAFOS.GENERAL_INFO.windowrange, ...
+ 'windowstart', metadata.RAFOS.GENERAL_INFO.windowstart, ...
+ 'windowlength', metadata.RAFOS.GENERAL_INFO.windowlength, ...
+ 'progdepth', metadata.RAFOS.GENERAL_INFO.progdepth, ...
+ 'progtemp', metadata.RAFOS.GENERAL_INFO.progtemp, ...
+ 'tempequation', metadata.RAFOS.GENERAL_INFO.tempequation, ...
+ 'tempcoeff', metadata.RAFOS.GENERAL_INFO.tempcoeff, ...
+ 'presequation', metadata.RAFOS.GENERAL_INFO.presequation, ...
+ 'prescoeff', metadata.RAFOS.GENERAL_INFO.prescoeff, ...
+ 'signal_length', metadata.RAFOS.GENERAL_INFO.signal_length, ...
+ 'comment', metadata.RAFOS.GENERAL_INFO.comment, ...
+ 'edited_by', metadata.RAFOS.GENERAL_INFO.edited_by, ...
+ 'edited_on', datevec(now), ...
+ 'variables', metadata.RAFOS.GENERAL_INFO.variables ...
+ );
+
+ SAT_FORMAT = struct( ...
+ 'lat_sat', metadata.RAFOS.GPS_FORMAT.lat, ...
+ 'lon_sat', metadata.RAFOS.GPS_FORMAT.lon, ...
+ 'src', metadata.RAFOS.GPS_FORMAT.src, ...
+ 'year_sat', metadata.RAFOS.GPS_FORMAT.year, ...
+ 'month_sat', metadata.RAFOS.GPS_FORMAT.month, ...
+ 'day_sat', metadata.RAFOS.GPS_FORMAT.day, ...
+ 'hour_sat', metadata.RAFOS.GPS_FORMAT.hour, ...
+ 'minutes_sat', metadata.RAFOS.GPS_FORMAT.minutes, ...
+ 'seconds_sat', metadata.RAFOS.GPS_FORMAT.seconds, ...
+ 'year_rtc', metadata.RAFOS.GPS_FORMAT.year_rtc, ...
+ 'month_rtc', metadata.RAFOS.GPS_FORMAT.month_rtc, ...
+ 'day_rtc', metadata.RAFOS.GPS_FORMAT.day_rtc, ...
+ 'hour_rtc', metadata.RAFOS.GPS_FORMAT.hour_rtc', ...
+ 'minutes_rtc', metadata.RAFOS.GPS_FORMAT.minutes_rtc, ...
+ 'seconds_rtc', metadata.RAFOS.GPS_FORMAT.seconds_rtc ...
+ );
+
+ VARIABLE_LIST = struct( ...
+ 'line_number', metadata.RAFOS.VARIABLE_LIST.line_number, ...
+ 'start_listen_yr', metadata.RAFOS.VARIABLE_LIST.start_listen_yr, ...
+ 'start_listen_mon', metadata.RAFOS.VARIABLE_LIST.start_listen_mon, ...
+ 'start_listen_day', metadata.RAFOS.VARIABLE_LIST.start_listen_day, ...
+ 'start_listen_hr', metadata.RAFOS.VARIABLE_LIST.start_listen_hr, ...
+ 'start_listen_min', metadata.RAFOS.VARIABLE_LIST.start_listen_min, ...
+ 'start_listen_sec', metadata.RAFOS.VARIABLE_LIST.start_listen_sec, ...
+ 'time_of_arrival', metadata.RAFOS.VARIABLE_LIST.time_of_arrival, ...
+ 'correlation_height', metadata.RAFOS.VARIABLE_LIST.correlation_height, ...
+ 'pressure', metadata.RAFOS.VARIABLE_LIST.pressure, ...
+ 'temperature', metadata.RAFOS.VARIABLE_LIST.temperature, ...
+ 'pres_counts', metadata.RAFOS.VARIABLE_LIST.pres_counts, ...
+ 'temp_counts', metadata.RAFOS.VARIABLE_LIST.temp_counts ...
+ );
+
+
+ %% Collect all data information
+
+ SAT_DATA = nemo.float.collect(float, 'SURFACE_GPS_DATA', '', 'combine');
+
+ rafos_data = nemo.float.collect(float, 'RAFOS_VALUES', '', 'combine');
+ if (isempty(rafos_data))
+ rfb_float = false;
+ return;
+ end
+ % apply some corrections
+ hour_scheduled = 30;
+ travel_correction = -60 * (rafos_data(:, 6) - hour_scheduled) ...
+ + rafos_data(:, 7);
+ % the following line throws an error in 2016a
+ % rafos_data(:, 9:2:19) = rafos_data(:, 9:2:19) + travel_correction;
+ rafos_data(:, 9) = rafos_data(:, 9) + travel_correction;
+ rafos_data(:, 11) = rafos_data(:, 11) + travel_correction;
+ rafos_data(:, 13) = rafos_data(:, 13) + travel_correction;
+ rafos_data(:, 15) = rafos_data(:, 15) + travel_correction;
+ rafos_data(:, 17) = rafos_data(:, 17) + travel_correction;
+ rafos_data(:, 19) = rafos_data(:, 19) + travel_correction;
+ % remove all unknown dates
+ rafos_data = rafos_data(isfinite(datenum(rafos_data(:, 2:4))), :);
+
+ % insert NaN for every missing row (compatibility fix for artoa)
+ % time_axis = datenum( ...
+ % datestr(FLOAT.launchtime,'dd-mmm-yyyy')) ...
+ % :p_rfb_config.GENERAL_INFO.artoa_expected_cycle ...
+ % :datenum(datestr(FLOAT.recovertime,'dd-mmm-yyyy') ...
+ % - 1 ...
+ % );
+ time_axis = [ ...
+ datenum(fliplr(float{1}.DEPLOYMENT_INFO.deployment_date)) ...
+ :metadata.RAFOS.GENERAL_INFO.artoa_expected_cycle ...
+ :datenum(float{end}.SECOND_ORDER_INFORMATION.best_guess_datevec(1:3)) ...
+ ];
+ rafos_dates = datenum(rafos_data(:, 2:4));
+
+ [~, id1] = intersect(time_axis, rafos_dates);
+ [~, id2] = intersect(rafos_dates, time_axis);
+
+ if (size(rafos_data, 1) > length(time_axis))
+ disp([ mfilename ...
+ ': More RAFOS values available than possible for float number ' ...
+ num2str(float{1}.FLOAT_IDENTIFICATION.float_serial_number) '!' ...
+ ]);
+ end
+
+ if (strcmp(float{end}.SECOND_ORDER_INFORMATION.best_guess_datevec_src, 'none'))
+ % create resulting matrix
+ RAFOS_VALUES = rafos_data;
+ %RAFOS_VALUES(id1, 1) = id1;
+
+ % change order of columns and remove unnecessary ones
+ tmp = [ ...
+ RAFOS_VALUES(:, 1:19), ...
+ RAFOS_VALUES(:, 22), ...
+ RAFOS_VALUES(:, 20) ...
+ ];
+ RAFOS_VALUES = tmp;
+ clear tmp
+
+ %% Set values that were not available until now
+ FLOAT.phasespercycle = length(rafos_dates) + 1;
+ else
+ % create resulting matrix
+ RAFOS_VALUES = nan(length(time_axis), size(rafos_data, 2));
+ RAFOS_VALUES(id1, :) = rafos_data(id2, :);
+ RAFOS_VALUES(id1, 1) = id1;
+
+ % change order of columns and remove unnecessary ones
+ tmp = [ ...
+ RAFOS_VALUES(:, 1:19), ...
+ RAFOS_VALUES(:, 22), ...
+ RAFOS_VALUES(:, 20) ...
+ ];
+ RAFOS_VALUES = tmp;
+ clear tmp
+
+ %% Set values that were not available until now
+ FLOAT.phasespercycle = length(time_axis) + 1;
+ end
+
+ %% Write resulting structure
+
+ rfb_float.FLOAT = FLOAT;
+ rfb_float.VARIABLE_LIST = VARIABLE_LIST;
+ if ~isempty(SAT_DATA)
+ rfb_float.SAT_FORMAT = SAT_FORMAT;
+ rfb_float.SAT_DATA = SAT_DATA;
+ end
+ rfb_float.DATA = RAFOS_VALUES;
+ end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+rfb/create_and_save_collection.m b/lib/vendor/nemo2profilelib/+nemo/+rfb/create_and_save_collection.m
new file mode 100644
index 0000000..910ab37
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+rfb/create_and_save_collection.m
@@ -0,0 +1,49 @@
+function [ boolean, rfb_floats ] = create_and_save_collection( p_nemo_floats, p_config, p_metadata )
+%CREATE_AND_SAVE_COLLECTION Creates the rfb structure from a collection of nemo floats and saves them to disk.
+%
+% Parameters:
+% p_nemo_floats: The nemo data.
+% p_config: The nemo configuration.
+% p_metadata: The nemo metadata.
+%
+% Returns:
+% boolean: True, if successful.
+% rfb_floats: The rfb structure.
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~iscell(p_nemo_floats) || ~isstruct(p_config) || ~iscell(p_metadata))
+ parameter_error = true;
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% Collect necessary information and save all rfb files
+
+output_files = cellfun(...
+ @(x) [ p_config.RFB.output_path sprintf('%04d', x{1}.FLOAT_IDENTIFICATION.float_serial_number) '.rfb'] ...
+ , p_nemo_floats, 'UniformOutput', false);
+
+p_metadata = nemo.sync_metadata_to_nemodata(p_nemo_floats, p_metadata);
+
+[rfb_floats, ~] = nemo.rfb.create(p_nemo_floats, p_metadata);
+
+booleans = cellfun(@nemo.rfb.save, rfb_floats, output_files, cell(length(rfb_floats), 1));
+
+if (all(booleans))
+ boolean = true;
+else
+ boolean = false;
+end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+rfb/save.m b/lib/vendor/nemo2profilelib/+nemo/+rfb/save.m
new file mode 100644
index 0000000..caa105e
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+rfb/save.m
@@ -0,0 +1,174 @@
+function [ boolean ] = save( p_profile, p_output_file, p_overwrite )
+%SAVE Writes the input profile to the output file.
+% This function saves the p_profile structure to an ASCII textfile with
+% .profile extension. The structure of the parameter is being transferred
+% equally into the textfile so that it can be loaded by the load
+% function.
+% TO BE OPTIMIZED: This function does not recursively checks for the
+% variable type. Only up to the second level.
+%
+% Returns: Boolean variable, being false if something went wrong during
+% write.
+%
+% Parameters:
+% p_profile: Contains the profile structure that will be written to
+% the output file.
+% p_output_file: Absolute file path to the output file that will be
+% written.
+% p_overwrite: If set to true, the output file will be overwritten if
+% it exists.
+%
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (isa(p_profile, 'logical') && ~p_profile)
+ boolean = true;
+ return
+end
+
+if (~isstruct(p_profile) || ~ischar(p_output_file))
+ parameter_error = true;
+end
+
+if (isempty(p_overwrite))
+ p_overwrite = 1; % default setting is to overwrite existing profile files
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% File existence checks
+
+[directory, ~, ~] = fileparts(p_output_file);
+if exist(directory, 'dir') ~= 7
+ mkdir(directory)
+end
+
+if exist(p_output_file, 'file') == 2 && ~p_overwrite
+ % file will not be overwritten
+ boolean = true;
+ return
+end
+
+%% Write file
+
+% prepare for writing
+help_tabs = ['\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t', '\t'];
+desired_tab_count = 12;
+section_names = fieldnames(p_profile); % will be stored in between []
+section_count = length(section_names);
+output_file_id = fopen(p_output_file, 'w'); % open file for writing
+double_format = '%.15g';
+
+% write content
+for o_section = 1:section_count % run through every section
+
+ % write section name to file
+ fprintf(output_file_id, ['[' section_names{o_section} ']' '\n' ]);
+
+ % check which type of data it is and decide how to output
+ switch class(p_profile.(section_names{o_section}))
+ case 'struct'
+ write_struct(p_profile.(section_names{o_section}));
+
+ case 'cell'
+ write_cell(p_profile.(section_names{o_section}));
+
+ case 'double'
+ write_double(p_profile.(section_names{o_section}));
+
+ otherwise
+ end
+
+ fprintf(output_file_id, '\n');
+
+
+end
+
+% close file
+fclose(output_file_id);
+
+boolean = true; % update return variable
+
+
+ function [ tabs ] = get_tabs_to_insert(p_member_name)
+ % this function computes the required tabs to insert, making the
+ % textfile easier to read.
+ tablength = 4;
+ tab_count = desired_tab_count - floor((length(p_member_name)+1)/tablength);
+ tabs = help_tabs(1:(tab_count*2));
+ end
+
+ function write_struct(p_input_struct)
+ % get all fieldnames and write them to the file
+ member_names = fieldnames(p_input_struct);
+ member_count = length(member_names);
+ for o_member = 1:member_count % run through all members
+ % calculate how many tabs have to be inserted to have a
+ % good table layout
+ tabstring = get_tabs_to_insert(member_names{o_member});
+ fprintf(output_file_id, ['-' member_names{o_member} tabstring]);
+ current_member = p_input_struct.(member_names{o_member});
+ current_member_class = class(current_member);
+ switch current_member_class
+ case {'double', 'logical'}
+ if (isempty(current_member))
+ fprintf(output_file_id, [current_member '\n']);
+ else
+ write_double(current_member);
+ end
+ case 'char'
+ fprintf(output_file_id, [current_member '\n']);
+ otherwise
+ disp(['Unknown class in file: ' class(current_member)]);
+ end
+
+ end
+ clear o_member
+ end
+
+ function write_cell(p_input_cell)
+ % run through every cell member and check the class
+ for o_cell_line = 1:size(p_input_cell, 1)
+ for o_cell_column = 1:size(p_input_cell, 2)
+ current_value = p_input_cell{o_cell_line, o_cell_column};
+ switch class(current_value)
+ case 'char'
+ fprintf(output_file_id, current_value);
+ case {'double', 'logical'}
+ fprintf(output_file_id, double_format, current_value);
+ otherwise
+ disp(['Unknown class in file: ' class(current_value)]);
+ end
+ if (o_cell_column ~= size(p_input_cell, 2))
+ fprintf(output_file_id, '\t');
+ end
+ end
+
+ fprintf(output_file_id, '\n');
+ end
+ end
+
+ function write_double(p_input_double)
+
+ for o_double = 1:size(p_input_double, 1)
+ if length(p_input_double(o_double, :)) > 1
+ fprintf(output_file_id, sprintf([double_format '\t'], p_input_double(o_double, 1:end-1)));
+ end
+ fprintf(output_file_id, [double_format '\n'], p_input_double(o_double, end));
+ end
+ clear o_double
+
+ end
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+sbd/decode_float.m b/lib/vendor/nemo2profilelib/+nemo/+sbd/decode_float.m
new file mode 100644
index 0000000..df6b840
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+sbd/decode_float.m
@@ -0,0 +1,41 @@
+function [ decoded_sbd, sbd_messages_info ] = decode_float( p_config, p_imei )
+%DECODE_FLOAT Decodes the sbd messages of the floats that match the given IMEI.
+%
+% Parameters:
+% p_config: The nemo configuration.
+% p_imei: The IMEI of the float to be decoded.
+%
+% Returns:
+% decoded_sbd: The decoded sbd messages.
+% sbd_messages_info: The information about the sbd messages.
+
+%% Initialize return value
+decoded_sbd = false;
+sbd_messages_info = false;
+
+%% Create filepath string
+sbd = ['sbd' p_config.GENERAL.folder_separator];
+if (~ischar(p_imei))
+ imei = int2str(p_imei);
+else
+ imei = p_imei;
+end
+
+filepath = p_config.MAIL.storage_directory;
+
+% Do not change the order of the next two if conditions!
+if (p_config.MAIL.sort_by_imei)
+ filepath = [filepath imei p_config.GENERAL.folder_separator];
+end
+if (p_config.MAIL.separate_sbd_and_txt)
+ filepath = [filepath sbd];
+end
+
+if (p_config.MAIL.sort_by_imei)
+ [decoded_sbd,~,sbd_messages_info] = nemo.optimare.process_moms(filepath);
+else
+ [decoded_sbd,~,sbd_messages_info] = nemo.optimare.process_moms(filepath, imei);
+end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/+test/best_guess_nan.m b/lib/vendor/nemo2profilelib/+nemo/+test/best_guess_nan.m
new file mode 100644
index 0000000..f4dbcc2
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+test/best_guess_nan.m
@@ -0,0 +1,23 @@
+function [] = best_guess_nan(bgp_profiles)
+%BEST_GUESS_NAN Tests best guess positions for NaN's.
+
+% get size of bgp_profiles
+float_count = length(bgp_profiles);
+
+for o_floats = 1:float_count
+ profile_count = length(bgp_profiles{o_floats});
+ nan_positions = [];
+ for o_profiles = 1:profile_count
+ if isnan(bgp_profiles{o_floats}{o_profiles}.SECOND_ORDER_INFORMATION.best_guess_position_src)
+ nan_positions = [nan_positions; o_profiles];
+ end
+ end
+ if (~isempty(nan_positions))
+ disp(['Float index: ' num2str(o_floats) ' Float ID: ' num2str(bgp_profiles{o_floats}{1}.FLOAT_IDENTIFICATION.float_serial_number)]);
+ nan_positions
+ end
+ clear nan_positions
+
+end
+
+end
\ No newline at end of file
diff --git a/lib/vendor/nemo2profilelib/+nemo/+test/compare_nemo_data.m b/lib/vendor/nemo2profilelib/+nemo/+test/compare_nemo_data.m
new file mode 100644
index 0000000..b3eb77f
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+test/compare_nemo_data.m
@@ -0,0 +1,16 @@
+function compare_nemo_data(p_first_data, p_second_data)
+%COMPARE_NEMO_DATA Compares two data sets of nemo data for differences.
+
+length_a = length(p_first_data);
+length_b = length(p_second_data);
+
+for o_a = 1:length_a
+ for i = 1:length(p_first_data{o_a})
+ [bool, string] = nemo.profile.compare(p_first_data{o_a}{i}, p_second_data{o_a}{i});
+ if ~bool
+ disp(['float index ' num2str(o_a) ' profile ' num2str(i) ': ' string{:}]);
+ end
+ end
+end
+
+clear o_a i length_a length_b first_floats second_floats
\ No newline at end of file
diff --git a/lib/vendor/nemo2profilelib/+nemo/+test/mail_development.m b/lib/vendor/nemo2profilelib/+nemo/+test/mail_development.m
new file mode 100644
index 0000000..b9baf31
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+test/mail_development.m
@@ -0,0 +1,24 @@
+% config = nemo.load_config('etc\nemo2profile.conf');
+%
+% imapstore = nemo.mail.connect(config)
+% messages = nemo.mail.fetch_messages(imapstore, 'Inbox');
+%
+%
+% msg = messages(end);
+%
+%
+%
+% [from, subject, inline, attachments] = nemo.mail.extract(msg);
+% att = attachments{1,2};
+%
+%
+% nemo.mail.export_attachment(att, '\\filesrv1.awi.de\csys_ocean2\argo\data\nemo\mail\sbd.sbd')
+
+config = nemo.load.config('etc\nemo2profile.conf');
+if ~exist('metadata', 'var')
+ %metadata = nemo.load.xml_file('etc\float_metadata');
+ metadata = nemo.load.float_metadata('etc\float_metadata');
+end
+tic;
+nemo.float.fetch_process_mails(config, metadata)
+toc
\ No newline at end of file
diff --git a/lib/vendor/nemo2profilelib/+nemo/+test/process_nemo.m b/lib/vendor/nemo2profilelib/+nemo/+test/process_nemo.m
new file mode 100644
index 0000000..9005b95
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+test/process_nemo.m
@@ -0,0 +1,82 @@
+timer = tic;
+disp([mfilename ': Adding dependencies ...']);
+cd('C:\FLOAT DEPLOYMENT ON POLARSTERN\FLOAT DATA PROCESSING AND ANALYSIS');
+addpath(genpath('C:\FLOAT DEPLOYMENT ON POLARSTERN\FLOAT DATA PROCESSING AND ANALYSIS'));
+
+disp([mfilename ': Loading configuration file...']);
+% load program config
+config = nemo.load.config('etc\nemo2profile.conf');
+disp([mfilename ': ...done!']);
+disp([mfilename ': Loading float metadata files...']);
+% load all floats that have to be processed
+metadata = nemo.load.float_metadata('etc\float_metadata');
+disp([mfilename ': ...done!']);
+
+disp([mfilename ': Downloading and processing mails...']);
+% download and process mails
+nemo.float.fetch_process_mails(config, metadata);
+disp([mfilename ': ...done!']);
+disp([mfilename ': Converting sbd attachments and extracting transmission information...']);
+awi_struct = nemo.load.floats2nemostruct(config, metadata);
+disp([mfilename ': ...done!']);
+
+%% Remove logical cells (without profiles)
+awi_struct = awi_struct(~cellfun(@(x) isa(x, 'logical'), awi_struct));
+
+%% Manual quality check
+awi_struct = nemo.postprocessing.delete_profile(awi_struct, 239, 1);
+
+%% Process data
+
+disp([mfilename ': Creating second order information...']);
+% possible estimation methods:
+% 'time based': memory consumption EXTREMLY high, but most descriptive
+% 'position based': less memory consumption, positions equally split
+% 'nan': most leightweight estimation, using NaN for unknown positions
+awi_struct = ...
+ nemo.postprocessing.position.create_best_guess( ...
+ awi_struct, 'time based' ...
+ );
+awi_struct = nemo.postprocessing.datetime.create_best_guess(awi_struct);
+disp([mfilename ': ... done!' ]);
+disp([mfilename ': Doing quality check...' ]);
+awi_struct = nemo.postprocessing.quality_check(awi_struct);
+disp([mfilename ': ... done!']);
+disp([mfilename ': Generating RFB files and save to disk...']);
+[success, rfb_floats] = nemo.rfb.create_and_save_collection(awi_struct, config, metadata);
+if (~success)
+ disp([mfilename ': ... failed!']);
+else
+ save([config.OUTPUT_FILES.output_path 'rfb_floats.mat'], 'rfb_floats');
+ disp([mfilename ': ... done!']);
+end
+disp([mfilename ': Saving data to ' config.OUTPUT_FILES.output_path '...']);
+nemo.save_data(awi_struct, config);
+save([config.OUTPUT_FILES.output_path 'awi_struct.mat'], 'awi_struct');
+save([config.OUTPUT_FILES.output_path 'config.mat'], 'config');
+save([config.OUTPUT_FILES.output_path 'metadata.mat'], 'metadata');
+disp([mfilename ': ... done!']);
+
+disp([mfilename ': Generating analysis items...']);
+if ~nemo.analysis.create_csv_table(awi_struct, config)
+ warning('Creating overview table failed!');
+end
+if ~nemo.plot.floats(awi_struct, config, 'south', false)
+ warning('Creating overview south plot failed!');
+end
+if ~nemo.plot.floats(awi_struct, config, 'south', true)
+ warning('Creating plot for every single float failed!');
+end
+if ~nemo.plot.arrival_of_profiles(awi_struct, config)
+ warning('Creating arrival of profiles plot failed!');
+end
+disp([mfilename ': ... done!']);
+
+disp([mfilename ': Uploading float data to server ...']);
+% Upload data to server
+if (~nemo.ftp.upload(config))
+ disp([mfilename ': Uploading data failed!']);
+else
+ disp([mfilename ': Uploading data successful!']);
+end
+disp([mfilename ': Processing nemo data took ' num2str(toc(timer)) ' seconds!']);
\ No newline at end of file
diff --git a/lib/vendor/nemo2profilelib/+nemo/+test/sbd2nemostruct.m b/lib/vendor/nemo2profilelib/+nemo/+test/sbd2nemostruct.m
new file mode 100644
index 0000000..a125704
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/+test/sbd2nemostruct.m
@@ -0,0 +1,7 @@
+config = nemo.load.config('etc\nemo2profile.conf');
+if ~exist('metadata', 'var')
+ %metadata = nemo.load.xml_file('etc\float_metadata');
+ metadata = nemo.load.float_metadata('etc\float_metadata\sn_248_imei_300234011429370_metadata.xml');
+end
+
+nemo_struct = nemo.load.floats2nemostruct(config, metadata);
\ No newline at end of file
diff --git a/lib/vendor/nemo2profilelib/+nemo/find_float_in_metadata.m b/lib/vendor/nemo2profilelib/+nemo/find_float_in_metadata.m
new file mode 100644
index 0000000..4911163
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/find_float_in_metadata.m
@@ -0,0 +1,50 @@
+function [ float_metadata ] = find_float_in_metadata( p_metadata, p_imeis )
+%FIND_FLOAT_IN_METADATA Returns the metadata of the given IMEI
+% Searches p_metadata for the given IMEI.
+%
+% Parameters:
+% p_metadata: The metadata of the floats.
+% p_imeis: The IMEI(s) to be searched for.
+%
+% Returns:
+% float_metadata: False if not found. Returns copies of the float
+% metadata of the given IMEIs otherwise.
+
+%% Initialize return value
+float_metadata = false;
+
+%% Find the float
+
+if (isempty(p_imeis))
+ return;
+end
+booleans = cellfun(@(x) x.GENERAL_INFO.IMEI == p_imeis(1), p_metadata);
+for i=2:length(p_imeis)
+ tmp_booleans = cellfun(@(x) x.GENERAL_INFO.IMEI == p_imeis(i), p_metadata);
+ booleans = booleans + tmp_booleans;
+end
+
+booleans(booleans > 1) = 1;
+booleans = logical(booleans);
+
+float_metadata = p_metadata(booleans);
+
+if (~isempty(float_metadata))
+ return
+end
+
+% nothing has been found, so check all serials
+
+booleans = cellfun(@(x) x.GENERAL_INFO.SERIAL == p_imeis(1), p_metadata);
+for i=2:length(p_imeis)
+ tmp_booleans = cellfun(@(x) x.GENERAL_INFO.SERIAL == p_imeis(i), p_metadata);
+ booleans = booleans + tmp_booleans;
+end
+
+booleans(booleans > 1) = 1;
+booleans = logical(booleans);
+
+float_metadata = p_metadata(booleans);
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/get_data_with_setting.m b/lib/vendor/nemo2profilelib/+nemo/get_data_with_setting.m
new file mode 100644
index 0000000..e650a35
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/get_data_with_setting.m
@@ -0,0 +1,35 @@
+function [ metadata, nemo_data ] = get_data_with_setting( p_metadata, p_nemo_data, p_setting_name, p_setting_value )
+%GET_DATA_FOR_OVERVIEW_PLOTS Summary of this function goes here
+% Detailed explanation goes here
+
+%% Parameter check
+if ~iscell(p_metadata) || ~iscell(p_nemo_data) || ~ischar(p_setting_name) || ~exist('p_setting_value', 'var')
+ disp([mfilename ': Please check your input!']);
+end
+
+%% Get data that matches
+
+
+metadata = cellfun(@(x) match_float(x), p_metadata, 'UniformOutput', false);
+metadata = metadata(cellfun(@(x) ~isempty(x), metadata));
+nemo_data = cellfun(@(x) match_float_to_metadata(x), p_nemo_data, 'UniformOutput', false);
+nemo_data = nemo_data(cellfun(@(x) ~isempty(x), nemo_data));
+
+
+ function [ x ] = match_float(meta)
+ x = [];
+ if meta.SETTINGS.(p_setting_name) == p_setting_value
+ x = meta;
+ end
+ end
+
+ function [ y ] = match_float_to_metadata(x)
+ if (isempty(nemo.find_float_in_metadata(metadata, x{1}.FLOAT_IDENTIFICATION.float_serial_number)))
+ y = [];
+ else
+ y = x;
+ end
+ end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/get_profiles_in_polygon.m b/lib/vendor/nemo2profilelib/+nemo/get_profiles_in_polygon.m
new file mode 100644
index 0000000..b0c0abb
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/get_profiles_in_polygon.m
@@ -0,0 +1,88 @@
+function [ filtered_nemo_data ] = get_profiles_in_polygon( p_nemo_data, ...
+ p_xv, p_yv )
+%GET_PROFILES_IN_POLYGON Returns all profiles in the given polygon.
+% This function returns all profiles that have been found in the given
+% polygon. The check is being performed with the built in MATLAB function
+% inpolygon. Please check documentation to be sure p_xv and p_yv is being
+% set correctly. The structure of p_nemo_data is being held, all profiles
+% that are not in the polygon are being removed. If p_nemo_data is a
+% string, it reads the profiles using nemo.load_data().
+%
+% Returns: p_nemo_data with filtered profiles, false on fail.
+%
+% Requirements:
+% - read_profiles.m: Containing function that reads nemo profiles from a
+% file into a multidimensional struct.
+%
+% Parameters:
+% p_nemo_data: Either has to be a multidimensional struct (created by
+% nemo.load.data()) or a string, where the nemo float data
+% is stored.
+% p_xv, p_yv: X and Y coordinates of the polygon. To get examples how
+% they should be set up, see "help inpolygon"
+
+
+%% Initialize return variables
+
+filtered_nemo_data = {};
+
+%% Check parameters
+parameter_error = false;
+
+if (ischar(p_nemo_data)) % read profiles using read_profiles.m
+ if (~isdir(p_nemo_data)) % parameter is not a directory
+ parameter_error = true;
+ else % read profiles
+ p_nemo_data = nemo.load.data(p_nemo_data);
+ end
+else if (~iscell(p_nemo_data)) % raise error
+ parameter_error = true;
+ end
+end
+
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please provide either a ' ...
+ 'directory path or a struct created by read_profiles.m!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+
+%% Delete all profiles that are not in polygon
+
+%nemo_field_names = fieldnames(p_nemo_data); % get all float names
+
+for index_current_float = 1:length(p_nemo_data) % process every single float
+ current_profiles = p_nemo_data{index_current_float};
+ profile_count = length(current_profiles);
+ filtered_profiles = {};
+
+ % loop through current_profiles
+ index_current_profile = 1;
+ while (index_current_profile <= profile_count)
+ % get position
+ xq = current_profiles{index_current_profile}.SECOND_ORDER_INFORMATION.best_guess_position_lon;
+ yq = current_profiles{index_current_profile}.SECOND_ORDER_INFORMATION.best_guess_position_lat;
+
+ if (inpolygon(xq, yq, p_xv, p_yv))
+ % profile is not in given rectangle, so delete it
+ filtered_profiles{end + 1} = current_profiles{index_current_profile};
+ end
+
+ % increase profile index
+ index_current_profile = index_current_profile + 1;
+ end
+
+ % update return variable
+ if (~isempty(filtered_profiles)) % there are profiles to update
+ filtered_nemo_data{end + 1} = filtered_profiles;
+ end
+
+ clear current_profiles profile_field_names profile_count ...
+ index_current_profile;
+
+end
+
+end
diff --git a/lib/vendor/nemo2profilelib/+nemo/get_profiles_in_timerange.m b/lib/vendor/nemo2profilelib/+nemo/get_profiles_in_timerange.m
new file mode 100644
index 0000000..b38703b
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/get_profiles_in_timerange.m
@@ -0,0 +1,87 @@
+function [ filtered_nemo_data ] = get_profiles_in_timerange( p_nemo_data, ...
+ p_tlower, p_tupper )
+%GET_PROFILES_IN_TIMERANGE Returns all profiles in the given time range.
+% This function returns all profiles that have been found in the given
+% time range. The check is being performed with the built in MATLAB function
+% isbetween. Please check documentation to be sure p_tlower and p_tupper is being
+% set correctly. The structure of p_nemo_data is being held, all profiles
+% that are not in the timrange are being removed. If p_nemo_data is a
+% string, it reads the profiles using nemo.load_data().
+%
+% Returns: p_nemo_data with filtered profiles, false on fail.
+%
+% Requirements:
+% - read_profiles.m: Containing function that reads nemo profiles from a
+% file into a multidimensional struct.
+%
+% Parameters:
+% p_nemo_data: Either has to be a multidimensional struct (created by
+% nemo.load.data()) or a string, where the nemo float data
+% is stored.
+% p_tlower, p_tupper: Lower and upper time range boundary. To get examples how
+% they should be set up, see "help inpolygon"
+
+
+%% Initialize return variables
+
+filtered_nemo_data = {};
+
+%% Check parameters
+parameter_error = false;
+
+if (ischar(p_nemo_data)) % read profiles using read_profiles.m
+ if (~isdir(p_nemo_data)) % parameter is not a directory
+ parameter_error = true;
+ else % read profiles
+ p_nemo_data = nemo.load.data(p_nemo_data);
+ end
+else if (~iscell(p_nemo_data)) % raise error
+ parameter_error = true;
+ end
+end
+
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please provide either a ' ...
+ 'directory path or a struct created by read_profiles.m!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+
+%% Delete all profiles that are not in polygon
+
+%nemo_field_names = fieldnames(p_nemo_data); % get all float names
+
+for index_current_float = 1:length(p_nemo_data) % process every single float
+ current_profiles = p_nemo_data{index_current_float};
+ profile_count = length(current_profiles);
+ filtered_profiles = {};
+
+ % loop through current_profiles
+ index_current_profile = 1;
+ while (index_current_profile <= profile_count)
+ % get position
+ profile_time = datetime(current_profiles{index_current_profile}.SECOND_ORDER_INFORMATION.best_guess_datevec);
+
+ if (isbetween(profile_time, p_tlower, p_tupper))
+ % profile is not in given rectangle, so delete it
+ filtered_profiles{end + 1} = current_profiles{index_current_profile};
+ end
+
+ % increase profile index
+ index_current_profile = index_current_profile + 1;
+ end
+
+ % update return variable
+ if (~isempty(filtered_profiles)) % there are profiles to update
+ filtered_nemo_data{end + 1} = filtered_profiles;
+ end
+
+ clear current_profiles profile_field_names profile_count ...
+ index_current_profile;
+
+end
+
+end
diff --git a/lib/vendor/nemo2profilelib/+nemo/save_data.m b/lib/vendor/nemo2profilelib/+nemo/save_data.m
new file mode 100644
index 0000000..4841142
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/save_data.m
@@ -0,0 +1,101 @@
+function [ boolean ] = save_data( p_nemo_data, p_config )
+%SAVE_DATA Writes the input nemo data using the given config.
+% This function saves given nemo data using nemo.pofile.save(). All
+% required options have to be stored in p_config.OUTPUT_FILES.
+%
+% Returns: Boolean variable, being false if something went wrong during
+% write.
+%
+% Parameters:
+% p_nemo_data: Contains structure with all float and profile information.
+% p_config: Contains all config options that are required, such as
+% output path as well as filename format (currently not
+% implemented) of profile files.
+%
+
+%% Initialize return variables
+boolean = false;
+
+%% Parameter check
+parameter_error = false;
+
+if (~iscell(p_nemo_data) || ~isstruct(p_config))
+ parameter_error = true;
+end
+
+if (parameter_error) % display error message
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+else % do some cleanup
+ clear parameter_error;
+end
+
+%% Save all profiles
+
+output_folder = p_config.OUTPUT_FILES.output_path;
+header_filename = p_config.OUTPUT_FILES.profile_header_file;
+
+if (~exist(header_filename, 'file'))
+ warning('Specified header file does not exist. Please check your configuration!');
+ return;
+end
+
+float_count = length(p_nemo_data);
+
+if (~exist(output_folder, 'dir'))
+ if (~mkdir(output_folder))
+ warning('Could not create output folder for nemo profiles!');
+ return;
+ end
+end
+
+for o_float = 1:float_count % every float will be processed
+ profile_count = length(p_nemo_data{o_float});
+ profile_subfoldername = sprintf('%04d', p_nemo_data{o_float}{1}.FLOAT_IDENTIFICATION.float_serial_number);
+ profile_folder = [output_folder profile_subfoldername p_config.GENERAL.folder_separator];
+
+ % check if folder exists
+ if (~exist(profile_folder, 'dir'))
+ if (~mkdir(profile_folder))
+ warning(['Could not create output subfolder for nemo float number ' profile_subfoldername '!']);
+ return;
+ end
+ end
+
+ for o_profile = 1:profile_count
+ % construct desired profile filename
+ profile_number = sprintf('%04d', p_nemo_data{o_float}{o_profile}.PROFILE_TECHNICAL_DATA.xmit_profile_number);
+ if isnan(p_nemo_data{o_float}{o_profile}.PROFILE_TECHNICAL_DATA.xmit_profile_number)
+ disp([mfilename ': Float ' profile_subfoldername ...
+ ' contains a profile without xmit_profile_number!']);
+ continue
+ end
+ output_filename = [profile_folder profile_subfoldername '_' ...
+ profile_number '.profile'];
+
+ overwrite_file = 1; % if true, existing files will be overwritten
+ if (p_config.OUTPUT_FILES.update_changed_files_only) ...
+ && exist(output_filename, 'file')
+ % load existing profile
+ old_profile = nemo.profile.load(output_filename);
+ if nemo.profile.compare(old_profile, ...
+ p_nemo_data{o_float}{o_profile})
+ % profiles are the same, so do not overwrite current one
+ overwrite_file = 0;
+ end
+ clear old_profile
+ end
+
+ if ~nemo.profile.save(header_filename, ...
+ p_nemo_data{o_float}{o_profile}, output_filename, overwrite_file)
+ warning(['Writing profile ' profile_number ' of float with serial ' profile_subfoldername ' failed!' ]);
+ end
+ end
+end
+
+boolean = true;
+
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/save_startup_messages.m b/lib/vendor/nemo2profilelib/+nemo/save_startup_messages.m
new file mode 100644
index 0000000..de5ad4a
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/save_startup_messages.m
@@ -0,0 +1,29 @@
+function [ boolean ] = save_startup_messages( p_config, p_startup_messages )
+%SAVE_STARTUP_MESSAGES Summary of this function goes here
+% Detailed explanation goes here
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check
+if ~isstruct(p_config) || ~iscell(p_startup_messages)
+ disp([ mfilename ': Wrong parameter! Please check your input parameters carefully!']);
+ return;
+end
+
+%% Save all messages to the specified folder
+if ~isfield(p_config.OUTPUT_FILES, 'output_path_startup_messages')
+ disp([ mfilename ': Parameter output_path_startup_messages not specified!']);
+end
+
+output_folder = p_config.OUTPUT_FILES.output_path_startup_messages;
+
+% remove empty cells if there are some
+p_startup_messages = p_startup_messages(~cellfun(@(x) isempty(x), p_startup_messages));
+
+boolean = all(cellfun(@(x) nemo.float.save_startup_message(x, output_folder), p_startup_messages));
+
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/sort_data_by_float_serial.m b/lib/vendor/nemo2profilelib/+nemo/sort_data_by_float_serial.m
new file mode 100644
index 0000000..5f98045
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/sort_data_by_float_serial.m
@@ -0,0 +1,36 @@
+function [ sorted_nemo_data ] = sort_data_by_float_serial( p_nemo_data )
+%SORT_DATA_BY_FLOAT_SERIAL Summary of this function goes here
+% Detailed explanation goes here
+
+%% Initialize return variable
+sorted_nemo_data = {};
+
+%% Parameter check
+if ~iscell(p_nemo_data)
+ disp([mfilename ': Please check your input parameter!']);
+ return;
+end
+
+%% Sort by float serial
+
+float_serials = cellfun(@(x) x{1}.FLOAT_IDENTIFICATION.float_serial_number, p_nemo_data);
+
+[~, indices] = sort(float_serials);
+% create helping variable to check if the float is already sorted
+sorted = [1:length(float_serials)];
+if indices == sorted
+ % indeed it is, so save work and just return the input one :)
+ sorted_nemo_data = p_nemo_data;
+ return
+end
+
+% sorting required
+sorted_nemo_data = {};
+
+% indices have already been taken so just run through them
+for i = 1:length(p_nemo_data)
+ sorted_nemo_data{i} = p_nemo_data{indices(i)};
+end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/sync_metadata_to_nemodata.m b/lib/vendor/nemo2profilelib/+nemo/sync_metadata_to_nemodata.m
new file mode 100644
index 0000000..2c37411
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/sync_metadata_to_nemodata.m
@@ -0,0 +1,16 @@
+function [ metadata ] = sync_metadata_to_nemodata( p_nemo_data, p_metadata )
+%SYNC_METADATA_NEMODATA Summary of this function goes here
+% Detailed explanation goes here
+
+
+%% Initialize return variables
+metadata = {};
+
+%% Get all IMEIS of the floats of nemo data
+
+imeis = cellfun(@(x) x{1}.FLOAT_IDENTIFICATION.transmission_id_number_dec, p_nemo_data);
+metadata = nemo.find_float_in_metadata(p_metadata, imeis);
+
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+nemo/update_nemo_data_mat.m b/lib/vendor/nemo2profilelib/+nemo/update_nemo_data_mat.m
new file mode 100644
index 0000000..6c01f04
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+nemo/update_nemo_data_mat.m
@@ -0,0 +1,44 @@
+function [ boolean ] = update_nemo_data_mat( p_nemo_data_filename, p_updated_floats )
+%UPDATE_NEMO_DATA_MAT Summary of this function goes here
+% Detailed explanation goes here
+
+%% Initialize return variable
+boolean = false;
+
+%% Parameter check
+if ~ischar(p_nemo_data_filename) || ~iscell(p_updated_floats)
+ disp([mfilename 'Please check input parameter!']);
+ return
+end
+
+%% Load mat file
+if exist(p_nemo_data_filename, 'file') == 2
+ n = load(p_nemo_data_filename);
+ nemo_data = n.nemo_data;
+ clear n
+else
+ nemo_data = {};
+end
+
+%% Replace updated floats in nemo data
+for i = 1:length(p_updated_floats)
+ [~, index] = nemo.float.find(nemo_data, p_updated_floats{1}{1}.FLOAT_IDENTIFICATION.float_serial_number);
+ if index == 0 % float is not present
+ nemo_data{end + 1} = p_updated_floats{1};
+ else
+ nemo_data{index} = p_updated_floats{1};
+ p_updated_floats(1) = [];
+ end
+end
+
+%% Sort floats by serial number
+
+nemo_data = nemo.sort_data_by_float_serial(nemo_data);
+
+%% Save to file
+save(p_nemo_data_filename, 'nemo_data');
+
+boolean = true;
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/+utils/suplabel.m b/lib/vendor/nemo2profilelib/+utils/suplabel.m
new file mode 100644
index 0000000..7845259
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+utils/suplabel.m
@@ -0,0 +1,101 @@
+function [ax,h]=suplabel(text,whichLabel,supAxes)
+% PLaces text as a title, xlabel, or ylabel on a group of subplots.
+% Returns a handle to the label and a handle to the axis.
+% [ax,h]=suplabel(text,whichLabel,supAxes)
+% returns handles to both the axis and the label.
+% ax=suplabel(text,whichLabel,supAxes)
+% returns a handle to the axis only.
+% suplabel(text) with one input argument assumes whichLabel='x'
+%
+% whichLabel is any of 'x', 'y', 'yy', or 't', specifying whether the
+% text is to be the xlable, ylabel, right side y-label,
+% or title respectively.
+%
+% supAxes is an optional argument specifying the Position of the
+% "super" axes surrounding the subplots.
+% supAxes defaults to [.08 .08 .84 .84]
+% specify supAxes if labels get chopped or overlay subplots
+%
+% EXAMPLE:
+% subplot(2,2,1);ylabel('ylabel1');title('title1')
+% subplot(2,2,2);ylabel('ylabel2');title('title2')
+% subplot(2,2,3);ylabel('ylabel3');xlabel('xlabel3')
+% subplot(2,2,4);ylabel('ylabel4');xlabel('xlabel4')
+% [ax1,h1]=suplabel('super X label');
+% [ax2,h2]=suplabel('super Y label','y');
+% [ax3,h2]=suplabel('super Y label (right)','yy');
+% [ax4,h3]=suplabel('super Title' ,'t');
+% set(h3,'FontSize',30)
+%
+% SEE ALSO: text, title, xlabel, ylabel, zlabel, subplot,
+% suptitle (Matlab Central)
+
+% Author: Ben Barrowes <barrowes@alum.mit.edu>
+
+%modified 3/16/2010 by IJW to make axis behavior re "zoom" on exit same as
+%at beginning. Requires adding tag to the invisible axes
+
+
+currax=findobj(gcf,'type','axes','-not','tag','suplabel');
+
+if nargin < 3
+ supAxes=[.08 .08 .84 .84];
+ ah=findall(gcf,'type','axes');
+ if ~isempty(ah)
+ supAxes=[inf,inf,0,0];
+ leftMin=inf; bottomMin=inf; leftMax=0; bottomMax=0;
+ axBuf=.04;
+ set(ah,'units','normalized')
+ ah=findall(gcf,'type','axes');
+ for ii=1:length(ah)
+ if strcmp(get(ah(ii),'Visible'),'on')
+ thisPos=get(ah(ii),'Position');
+ leftMin=min(leftMin,thisPos(1));
+ bottomMin=min(bottomMin,thisPos(2));
+ leftMax=max(leftMax,thisPos(1)+thisPos(3));
+ bottomMax=max(bottomMax,thisPos(2)+thisPos(4));
+ end
+ end
+ supAxes=[leftMin-axBuf,bottomMin-axBuf,leftMax-leftMin+axBuf*2,bottomMax-bottomMin+axBuf*2];
+ end
+end
+if nargin < 2, whichLabel = 'x'; end
+if nargin < 1, help(mfilename); return; end
+
+if ~isstr(text) | ~isstr(whichLabel)
+ error('text and whichLabel must be strings')
+end
+whichLabel=lower(whichLabel);
+
+ax=axes('Units','Normal','Position',supAxes,'Visible','off','tag','suplabel');
+if strcmp('t',whichLabel)
+ set(get(ax,'Title'),'Visible','on')
+ title(text);
+elseif strcmp('x',whichLabel)
+ set(get(ax,'XLabel'),'Visible','on')
+ xlabel(text);
+elseif strcmp('y',whichLabel)
+ set(get(ax,'YLabel'),'Visible','on')
+ ylabel(text);
+elseif strcmp('yy',whichLabel)
+ set(get(ax,'YLabel'),'Visible','on')
+ ylabel(text);
+ set(ax,'YAxisLocation','right')
+end
+
+%for k=1:length(currax), axes(currax(k));end % restore all other axes
+
+if (nargout < 2)
+ return
+end
+if strcmp('t',whichLabel)
+ h=get(ax,'Title');
+ set(h,'VerticalAlignment','middle')
+elseif strcmp('x',whichLabel)
+ h=get(ax,'XLabel');
+elseif strcmp('y',whichLabel) | strcmp('yy',whichLabel)
+ h=get(ax,'YLabel');
+end
+
+%%%ah=findall(gcf,'type','axes');
+%%%'sssssssss',kb
\ No newline at end of file
diff --git a/lib/vendor/nemo2profilelib/+utils/xml_read.m b/lib/vendor/nemo2profilelib/+utils/xml_read.m
new file mode 100644
index 0000000..845efd0
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+utils/xml_read.m
@@ -0,0 +1,550 @@
+function [tree, RootName, DOMnode] = xml_read(xmlfile, Pref)
+%XML_READ reads xml files and converts them into Matlab's struct tree.
+%
+% DESCRIPTION
+% tree = xml_read(xmlfile) reads 'xmlfile' into data structure 'tree'
+%
+% tree = xml_read(xmlfile, Pref) reads 'xmlfile' into data structure 'tree'
+% according to your preferences
+%
+% [tree, RootName, DOMnode] = xml_read(xmlfile) get additional information
+% about XML file
+%
+% INPUT:
+% xmlfile URL or filename of xml file to read
+% Pref Preferences:
+% Pref.ItemName - default 'item' - name of a special tag used to itemize
+% cell arrays
+% Pref.ReadAttr - default true - allow reading attributes
+% Pref.ReadSpec - default true - allow reading special nodes
+% Pref.Str2Num - default 'smart' - convert strings that look like numbers
+% to numbers. Options: "always", "never", and "smart"
+% Pref.KeepNS - default true - keep or strip namespace info
+% Pref.NoCells - default true - force output to have no cell arrays
+% Pref.Debug - default false - show mode specific error messages
+% Pref.NumLevels- default infinity - how many recursive levels are
+% allowed. Can be used to speed up the function by prunning the tree.
+% Pref.RootOnly - default true - output variable 'tree' corresponds to
+% xml file root element, otherwise it correspond to the whole file.
+% Pref.CellItem - default 'true' - leave 'item' nodes in cell notation.
+% OUTPUT:
+% tree tree of structs and/or cell arrays corresponding to xml file
+% RootName XML tag name used for root (top level) node.
+% Optionally it can be a string cell array storing: Name of
+% root node, document "Processing Instructions" data and
+% document "comment" string
+% DOMnode output of xmlread
+%
+% DETAILS:
+% Function xml_read first calls MATLAB's xmlread function and than
+% converts its output ('Document Object Model' tree of Java objects)
+% to tree of MATLAB struct's. The output is in format of nested structs
+% and cells. In the output data structure field names are based on
+% XML tags, except in cases when tags produce illegal variable names.
+%
+% Several special xml node types result in special tags for fields of
+% 'tree' nodes:
+% - node.CONTENT - stores data section of the node if other fields are
+% present. Usually data section is stored directly in 'node'.
+% - node.ATTRIBUTE.name - stores node's attribute called 'name'.
+% - node.COMMENT - stores node's comment section (string). For global
+% comments see "RootName" output variable.
+% - node.CDATA_SECTION - stores node's CDATA section (string).
+% - node.PROCESSING_INSTRUCTIONS - stores "processing instruction" child
+% node. For global "processing instructions" see "RootName" output variable.
+% - other special node types like: document fragment nodes, document type
+% nodes, entity nodes, notation nodes and processing instruction nodes
+% will be treated like regular nodes
+%
+% EXAMPLES:
+% MyTree=[];
+% MyTree.MyNumber = 13;
+% MyTree.MyString = 'Hello World';
+% xml_write('test.xml', MyTree);
+% [tree treeName] = xml_read ('test.xml');
+% disp(treeName)
+% gen_object_display()
+% % See also xml_examples.m
+%
+% See also:
+% xml_write, xmlread, xmlwrite
+%
+% Written by Jarek Tuszynski, SAIC, jaroslaw.w.tuszynski_at_saic.com
+% References:
+% - Function inspired by Example 3 found in xmlread function.
+% - Output data structures inspired by xml_toolbox structures.
+
+%% default preferences
+DPref.TableName = {'tr','td'}; % name of a special tags used to itemize 2D cell arrays
+DPref.ItemName = 'item'; % name of a special tag used to itemize 1D cell arrays
+DPref.CellItem = false; % leave 'item' nodes in cell notation
+DPref.ReadAttr = true; % allow reading attributes
+DPref.ReadSpec = true; % allow reading special nodes: comments, CData, etc.
+DPref.KeepNS = true; % Keep or strip namespace info
+DPref.Str2Num = 'smart';% convert strings that look like numbers to numbers
+DPref.NoCells = true; % force output to have no cell arrays
+DPref.NumLevels = 1e10; % number of recurence levels
+DPref.PreserveSpace = false; % Preserve or delete spaces at the beggining and the end of stings?
+RootOnly = true; % return root node with no top level special nodes
+Debug = false; % show specific errors (true) or general (false)?
+tree = [];
+RootName = [];
+
+%% Check Matlab Version
+v = ver('MATLAB');
+version = str2double(regexp(v.Version, '\d.\d','match','once'));
+if (version<7.1)
+ error('Your MATLAB version is too old. You need version 7.1 or newer.');
+end
+
+%% read user preferences
+if (nargin>1)
+ if (isfield(Pref, 'TableName')), DPref.TableName = Pref.TableName; end
+ if (isfield(Pref, 'ItemName' )), DPref.ItemName = Pref.ItemName; end
+ if (isfield(Pref, 'CellItem' )), DPref.CellItem = Pref.CellItem; end
+ if (isfield(Pref, 'Str2Num' )), DPref.Str2Num = Pref.Str2Num ; end
+ if (isfield(Pref, 'NoCells' )), DPref.NoCells = Pref.NoCells ; end
+ if (isfield(Pref, 'NumLevels')), DPref.NumLevels = Pref.NumLevels; end
+ if (isfield(Pref, 'ReadAttr' )), DPref.ReadAttr = Pref.ReadAttr; end
+ if (isfield(Pref, 'ReadSpec' )), DPref.ReadSpec = Pref.ReadSpec; end
+ if (isfield(Pref, 'KeepNS' )), DPref.KeepNS = Pref.KeepNS; end
+ if (isfield(Pref, 'RootOnly' )), RootOnly = Pref.RootOnly; end
+ if (isfield(Pref, 'Debug' )), Debug = Pref.Debug ; end
+ if (isfield(Pref, 'PreserveSpace')), DPref.PreserveSpace = Pref.PreserveSpace; end
+end
+if ischar(DPref.Str2Num), % convert from character description to numbers
+ DPref.Str2Num = find(strcmpi(DPref.Str2Num, {'never', 'smart', 'always'}))-1;
+ if isempty(DPref.Str2Num), DPref.Str2Num=1; end % 1-smart by default
+end
+
+%% read xml file using Matlab function
+if isa(xmlfile, 'org.apache.xerces.dom.DeferredDocumentImpl');
+ % if xmlfile is a DOMnode than skip the call to xmlread
+ try
+ try
+ DOMnode = xmlfile;
+ catch ME
+ error('Invalid DOM node: \n%s.', getReport(ME));
+ end
+ catch %#ok<CTCH> catch for mablab versions prior to 7.5
+ error('Invalid DOM node. \n');
+ end
+else % we assume xmlfile is a filename
+ if (Debug) % in debuging mode crashes are allowed
+ DOMnode = xmlread(xmlfile);
+ else % in normal mode crashes are not allowed
+ try
+ try
+ DOMnode = xmlread(xmlfile);
+ catch ME
+ error('Failed to read XML file %s: \n%s',xmlfile, getReport(ME));
+ end
+ catch %#ok<CTCH> catch for mablab versions prior to 7.5
+ error('Failed to read XML file %s\n',xmlfile);
+ end
+ end
+end
+Node = DOMnode.getFirstChild;
+
+%% Find the Root node. Also store data from Global Comment and Processing
+% Instruction nodes, if any.
+GlobalTextNodes = cell(1,3);
+GlobalProcInst = [];
+GlobalComment = [];
+GlobalDocType = [];
+while (~isempty(Node))
+ if (Node.getNodeType==Node.ELEMENT_NODE)
+ RootNode=Node;
+ elseif (Node.getNodeType==Node.PROCESSING_INSTRUCTION_NODE)
+ data = strtrim(char(Node.getData));
+ target = strtrim(char(Node.getTarget));
+ GlobalProcInst = [target, ' ', data];
+ GlobalTextNodes{2} = GlobalProcInst;
+ elseif (Node.getNodeType==Node.COMMENT_NODE)
+ GlobalComment = strtrim(char(Node.getData));
+ GlobalTextNodes{3} = GlobalComment;
+ % elseif (Node.getNodeType==Node.DOCUMENT_TYPE_NODE)
+ % GlobalTextNodes{4} = GlobalDocType;
+ end
+ Node = Node.getNextSibling;
+end
+
+%% parse xml file through calls to recursive DOMnode2struct function
+if (Debug) % in debuging mode crashes are allowed
+ [tree RootName] = DOMnode2struct(RootNode, DPref, 1);
+else % in normal mode crashes are not allowed
+ try
+ try
+ [tree RootName] = DOMnode2struct(RootNode, DPref, 1);
+ catch ME
+ error('Unable to parse XML file %s: \n %s.',xmlfile, getReport(ME));
+ end
+ catch %#ok<CTCH> catch for mablab versions prior to 7.5
+ error('Unable to parse XML file %s.',xmlfile);
+ end
+end
+
+%% If there were any Global Text nodes than return them
+if (~RootOnly)
+ if (~isempty(GlobalProcInst) && DPref.ReadSpec)
+ t.PROCESSING_INSTRUCTION = GlobalProcInst;
+ end
+ if (~isempty(GlobalComment) && DPref.ReadSpec)
+ t.COMMENT = GlobalComment;
+ end
+ if (~isempty(GlobalDocType) && DPref.ReadSpec)
+ t.DOCUMENT_TYPE = GlobalDocType;
+ end
+ t.(RootName) = tree;
+ tree=t;
+end
+if (~isempty(GlobalTextNodes))
+ GlobalTextNodes{1} = RootName;
+ RootName = GlobalTextNodes;
+end
+
+
+%% =======================================================================
+% === DOMnode2struct Function ===========================================
+% =======================================================================
+function [s TagName LeafNode] = DOMnode2struct(node, Pref, level)
+
+%% === Step 1: Get node name and check if it is a leaf node ==============
+[TagName LeafNode] = NodeName(node, Pref.KeepNS);
+s = []; % initialize output structure
+
+%% === Step 2: Process Leaf Nodes (nodes with no children) ===============
+if (LeafNode)
+ if (LeafNode>1 && ~Pref.ReadSpec), LeafNode=-1; end % tags only so ignore special nodes
+ if (LeafNode>0) % supported leaf node types
+ try
+ try % use try-catch: errors here are often due to VERY large fields (like images) that overflow java memory
+ s = char(node.getData);
+ if (isempty(s)), s = ' '; end % make it a string
+ % for some reason current xmlread 'creates' a lot of empty text
+ % fields with first chatacter=10 - those will be deleted.
+ if (~Pref.PreserveSpace || s(1)==10)
+ if (isspace(s(1)) || isspace(s(end))), s = strtrim(s); end % trim speces is any
+ end
+ if (LeafNode==1), s=str2var(s, Pref.Str2Num, 0); end % convert to number(s) if needed
+ catch ME % catch for mablab versions 7.5 and higher
+ warning('xml_io_tools:read:LeafRead', ...
+ 'This leaf node could not be read and was ignored. ');
+ getReport(ME)
+ end
+ catch %#ok<CTCH> catch for mablab versions prior to 7.5
+ warning('xml_io_tools:read:LeafRead', ...
+ 'This leaf node could not be read and was ignored. ');
+ end
+ end
+ if (LeafNode==3) % ProcessingInstructions need special treatment
+ target = strtrim(char(node.getTarget));
+ s = [target, ' ', s];
+ end
+ return % We are done the rest of the function deals with nodes with children
+end
+if (level>Pref.NumLevels+1), return; end % if Pref.NumLevels is reached than we are done
+
+%% === Step 3: Process nodes with children ===============================
+if (node.hasChildNodes) % children present
+ Child = node.getChildNodes; % create array of children nodes
+ nChild = Child.getLength; % number of children
+
+ % --- pass 1: how many children with each name -----------------------
+ f = [];
+ for iChild = 1:nChild % read in each child
+ [cname cLeaf] = NodeName(Child.item(iChild-1), Pref.KeepNS);
+ if (cLeaf<0), continue; end % unsupported leaf node types
+ if (~isfield(f,cname)),
+ f.(cname)=0; % initialize first time I see this name
+ end
+ f.(cname) = f.(cname)+1; % add to the counter
+ end % end for iChild
+ % text_nodes become CONTENT & for some reason current xmlread 'creates' a
+ % lot of empty text fields so f.CONTENT value should not be trusted
+ if (isfield(f,'CONTENT') && f.CONTENT>2), f.CONTENT=2; end
+
+ % --- pass 2: store all the children as struct of cell arrays ----------
+ for iChild = 1:nChild % read in each child
+ [c cname cLeaf] = DOMnode2struct(Child.item(iChild-1), Pref, level+1);
+ if (cLeaf && isempty(c)) % if empty leaf node than skip
+ continue; % usually empty text node or one of unhandled node types
+ elseif (nChild==1 && cLeaf==1)
+ s=c; % shortcut for a common case
+ else % if normal node
+ if (level>Pref.NumLevels), continue; end
+ n = f.(cname); % how many of them in the array so far?
+ if (~isfield(s,cname)) % encountered this name for the first time
+ if (n==1) % if there will be only one of them ...
+ s.(cname) = c; % than save it in format it came in
+ else % if there will be many of them ...
+ s.(cname) = cell(1,n);
+ s.(cname){1} = c; % than save as cell array
+ end
+ f.(cname) = 1; % initialize the counter
+ else % already have seen this name
+ s.(cname){n+1} = c; % add to the array
+ f.(cname) = n+1; % add to the array counter
+ end
+ end
+ end % for iChild
+end % end if (node.hasChildNodes)
+
+%% === Step 4: Post-process struct's created for nodes with children =====
+if (isstruct(s))
+ fields = fieldnames(s);
+ nField = length(fields);
+
+ % Detect structure that looks like Html table and store it in cell Matrix
+ if (nField==1 && strcmpi(fields{1},Pref.TableName{1}))
+ tr = s.(Pref.TableName{1});
+ fields2 = fieldnames(tr{1});
+ if (length(fields2)==1 && strcmpi(fields2{1},Pref.TableName{2}))
+ % This seems to be a special structure such that for
+ % Pref.TableName = {'tr','td'} 's' corresponds to
+ % <tr> <td>M11</td> <td>M12</td> </tr>
+ % <tr> <td>M12</td> <td>M22</td> </tr>
+ % Recognize it as encoding for 2D struct
+ nr = length(tr);
+ for r = 1:nr
+ row = tr{r}.(Pref.TableName{2});
+ Table(r,1:length(row)) = row; %#ok<AGROW>
+ end
+ s = Table;
+ end
+ end
+
+ % --- Post-processing: convert 'struct of cell-arrays' to 'array of structs'
+ % Example: let say s has 3 fields s.a, s.b & s.c and each field is an
+ % cell-array with more than one cell-element and all 3 have the same length.
+ % Then change it to array of structs, each with single cell.
+ % This way element s.a{1} will be now accessed through s(1).a
+ vec = zeros(size(fields));
+ for i=1:nField, vec(i) = f.(fields{i}); end
+ if (numel(vec)>1 && vec(1)>1 && var(vec)==0) % convert from struct of
+ s = cell2struct(struct2cell(s), fields, 1); % arrays to array of struct
+ end % if anyone knows better way to do above conversion please let me know.
+
+end
+
+%% === Step 5: Process nodes with attributes =============================
+if (node.hasAttributes && Pref.ReadAttr)
+ if (~isstruct(s)), % make into struct if is not already
+ ss.CONTENT=s;
+ s=ss;
+ end
+ Attr = node.getAttributes; % list of all attributes
+ for iAttr = 1:Attr.getLength % for each attribute
+ name = char(Attr.item(iAttr-1).getName); % attribute name
+ name = str2varName(name, Pref.KeepNS); % fix name if needed
+ value = char(Attr.item(iAttr-1).getValue); % attribute value
+ value = str2var(value, Pref.Str2Num, 1); % convert to number if possible
+ s.ATTRIBUTE.(name) = value; % save again
+ end % end iAttr loop
+end % done with attributes
+if (~isstruct(s)), return; end %The rest of the code deals with struct's
+
+%% === Post-processing: fields of "s"
+% convert 'cell-array of structs' to 'arrays of structs'
+fields = fieldnames(s); % get field names
+nField = length(fields);
+for iItem=1:length(s) % for each struct in the array - usually one
+ for iField=1:length(fields)
+ field = fields{iField}; % get field name
+ % if this is an 'item' field and user want to leave those as cells
+ % than skip this one
+ if (strcmpi(field, Pref.ItemName) && Pref.CellItem), continue; end
+ x = s(iItem).(field);
+ if (iscell(x) && all(cellfun(@isstruct,x(:))) && numel(x)>1) % it's cell-array of structs
+ % numel(x)>1 check is to keep 1 cell-arrays created when Pref.CellItem=1
+ try % this operation fails sometimes
+ % example: change s(1).a{1}.b='jack'; s(1).a{2}.b='john'; to
+ % more convinient s(1).a(1).b='jack'; s(1).a(2).b='john';
+ s(iItem).(field) = [x{:}]'; %#ok<AGROW> % converted to arrays of structs
+ catch %#ok<CTCH>
+ % above operation will fail if s(1).a{1} and s(1).a{2} have
+ % different fields. If desired, function forceCell2Struct can force
+ % them to the same field structure by adding empty fields.
+ if (Pref.NoCells)
+ s(iItem).(field) = forceCell2Struct(x); %#ok<AGROW>
+ end
+ end % end catch
+ end
+ end
+end
+
+%% === Step 4: Post-process struct's created for nodes with children =====
+
+% --- Post-processing: remove special 'item' tags ---------------------
+% many xml writes (including xml_write) use a special keyword to mark
+% arrays of nodes (see xml_write for examples). The code below converts
+% s.item to s.CONTENT
+ItemContent = false;
+if (isfield(s,Pref.ItemName))
+ s.CONTENT = s.(Pref.ItemName);
+ s = rmfield(s,Pref.ItemName);
+ ItemContent = Pref.CellItem; % if CellItem than keep s.CONTENT as cells
+end
+
+% --- Post-processing: clean up CONTENT tags ---------------------
+% if s.CONTENT is a cell-array with empty elements at the end than trim
+% the length of this cell-array. Also if s.CONTENT is the only field than
+% remove .CONTENT part and store it as s.
+if (isfield(s,'CONTENT'))
+ if (iscell(s.CONTENT) && isvector(s.CONTENT))
+ x = s.CONTENT;
+ for i=numel(x):-1:1, if ~isempty(x{i}), break; end; end
+ if (i==1 && ~ItemContent)
+ s.CONTENT = x{1}; % delete cell structure
+ else
+ s.CONTENT = x(1:i); % delete empty cells
+ end
+ end
+ if (nField==1)
+ if (ItemContent)
+ ss = s.CONTENT; % only child: remove a level but ensure output is a cell-array
+ s=[]; s{1}=ss;
+ else
+ s = s.CONTENT; % only child: remove a level
+ end
+ end
+end
+
+
+
+%% =======================================================================
+% === forceCell2Struct Function =========================================
+% =======================================================================
+function s = forceCell2Struct(x)
+% Convert cell-array of structs, where not all of structs have the same
+% fields, to a single array of structs
+
+%% Convert 1D cell array of structs to 2D cell array, where each row
+% represents item in original array and each column corresponds to a unique
+% field name. Array "AllFields" store fieldnames for each column
+AllFields = fieldnames(x{1}); % get field names of the first struct
+CellMat = cell(length(x), length(AllFields));
+for iItem=1:length(x)
+ fields = fieldnames(x{iItem}); % get field names of the next struct
+ for iField=1:length(fields) % inspect all fieldnames and find those
+ field = fields{iField}; % get field name
+ col = find(strcmp(field,AllFields),1);
+ if isempty(col) % no column for such fieldname yet
+ AllFields = [AllFields; field]; %#ok<AGROW>
+ col = length(AllFields); % create a new column for it
+ end
+ CellMat{iItem,col} = x{iItem}.(field); % store rearanged data
+ end
+end
+%% Convert 2D cell array to array of structs
+s = cell2struct(CellMat, AllFields, 2);
+
+%% =======================================================================
+% === str2var Function ==================================================
+% =======================================================================
+function val=str2var(str, option, attribute)
+% Can this string 'str' be converted to a number? if so than do it.
+val = str;
+len = numel(str);
+if (len==0 || option==0), return; end % Str2Num="never" of empty string -> do not do enything
+if (len>10000 && option==1), return; end % Str2Num="smart" and string is very long -> probably base64 encoded binary
+digits = '(Inf)|(NaN)|(pi)|[\t\n\d\+\-\*\.ei EI\[\]\;\,]';
+s = regexprep(str, digits, ''); % remove all the digits and other allowed characters
+if (~all(~isempty(s))) % if nothing left than this is probably a number
+ if (~isempty(strfind(str, ' '))), option=2; end %if str has white-spaces assume by default that it is not a date string
+ if (~isempty(strfind(str, '['))), option=2; end % same with brackets
+ str(strfind(str, '\n')) = ';';% parse data tables into 2D arrays, if any
+ if (option==1) % the 'smart' option
+ try % try to convert to a date, like 2007-12-05
+ datenum(str); % if successful than leave it as string
+ catch %#ok<CTCH> % if this is not a date than ...
+ option=2; % ... try converting to a number
+ end
+ end
+ if (option==2)
+ if (attribute)
+ num = str2double(str); % try converting to a single number using sscanf function
+ if isnan(num), return; end % So, it wasn't really a number after all
+ else
+ num = str2num(str); %#ok<ST2NM> % try converting to a single number or array using eval function
+ end
+ if(isnumeric(num) && numel(num)>0), val=num; end % if convertion to a single was succesful than save
+ end
+elseif ((str(1)=='[' && str(end)==']') || (str(1)=='{' && str(end)=='}')) % this looks like a (cell) array encoded as a string
+ try
+ val = eval(str);
+ catch %#ok<CTCH>
+ val = str;
+ end
+elseif (~attribute) % see if it is a boolean array with no [] brackets
+ str1 = lower(str);
+ str1 = strrep(str1, 'false', '0');
+ str1 = strrep(str1, 'true' , '1');
+ s = regexprep(str1, '[01 \;\,]', ''); % remove all 0/1, spaces, commas and semicolons
+ if (~all(~isempty(s))) % if nothing left than this is probably a boolean array
+ num = str2num(str1); %#ok<ST2NM>
+ if(isnumeric(num) && numel(num)>0), val = (num>0); end % if convertion was succesful than save as logical
+ end
+end
+
+
+%% =======================================================================
+% === str2varName Function ==============================================
+% =======================================================================
+function str = str2varName(str, KeepNS)
+% convert a sting to a valid matlab variable name
+if(KeepNS)
+ str = regexprep(str,':','_COLON_', 'once', 'ignorecase');
+else
+ k = strfind(str,':');
+ if (~isempty(k))
+ str = str(k+1:end);
+ end
+end
+str = regexprep(str,'-','_DASH_' ,'once', 'ignorecase');
+if (~isvarname(str)) && (~iskeyword(str))
+ str = genvarname(str);
+end
+
+%% =======================================================================
+% === NodeName Function =================================================
+% =======================================================================
+function [Name LeafNode] = NodeName(node, KeepNS)
+% get node name and make sure it is a valid variable name in Matlab.
+% also get node type:
+% LeafNode=0 - normal element node,
+% LeafNode=1 - text node
+% LeafNode=2 - supported non-text leaf node,
+% LeafNode=3 - supported processing instructions leaf node,
+% LeafNode=-1 - unsupported non-text leaf node
+switch (node.getNodeType)
+ case node.ELEMENT_NODE
+ Name = char(node.getNodeName);% capture name of the node
+ Name = str2varName(Name, KeepNS); % if Name is not a good variable name - fix it
+ LeafNode = 0;
+ case node.TEXT_NODE
+ Name = 'CONTENT';
+ LeafNode = 1;
+ case node.COMMENT_NODE
+ Name = 'COMMENT';
+ LeafNode = 2;
+ case node.CDATA_SECTION_NODE
+ Name = 'CDATA_SECTION';
+ LeafNode = 2;
+ case node.DOCUMENT_TYPE_NODE
+ Name = 'DOCUMENT_TYPE';
+ LeafNode = 2;
+ case node.PROCESSING_INSTRUCTION_NODE
+ Name = 'PROCESSING_INSTRUCTION';
+ LeafNode = 3;
+ otherwise
+ NodeType = {'ELEMENT','ATTRIBUTE','TEXT','CDATA_SECTION', ...
+ 'ENTITY_REFERENCE', 'ENTITY', 'PROCESSING_INSTRUCTION', 'COMMENT',...
+ 'DOCUMENT', 'DOCUMENT_TYPE', 'DOCUMENT_FRAGMENT', 'NOTATION'};
+ Name = char(node.getNodeName);% capture name of the node
+ warning('xml_io_tools:read:unkNode', ...
+ 'Unknown node type encountered: %s_NODE (%s)', NodeType{node.getNodeType}, Name);
+ LeafNode = -1;
+end
+
+
diff --git a/lib/vendor/nemo2profilelib/+utils/xml_write.m b/lib/vendor/nemo2profilelib/+utils/xml_write.m
new file mode 100644
index 0000000..10a18de
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/+utils/xml_write.m
@@ -0,0 +1,447 @@
+function DOMnode = xml_write(filename, tree, RootName, Pref)
+%XML_WRITE Writes Matlab data structures to XML file
+%
+% DESCRIPTION
+% xml_write( filename, tree) Converts Matlab data structure 'tree' containing
+% cells, structs, numbers and strings to Document Object Model (DOM) node
+% tree, then saves it to XML file 'filename' using Matlab's xmlwrite
+% function. Optionally one can also use alternative version of xmlwrite
+% function which directly calls JAVA functions for XML writing without
+% MATLAB middleware. This function is provided as a patch to existing
+% bugs in xmlwrite (in R2006b).
+%
+% xml_write(filename, tree, RootName, Pref) allows you to specify
+% additional preferences about file format
+%
+% DOMnode = xml_write([], tree) same as above except that DOM node is
+% not saved to the file but returned.
+%
+% INPUT
+% filename file name
+% tree Matlab structure tree to store in xml file.
+% RootName String with XML tag name used for root (top level) node
+% Optionally it can be a string cell array storing: Name of
+% root node, document "Processing Instructions" data and
+% document "comment" string
+% Pref Other preferences:
+% Pref.ItemName - default 'item' - name of a special tag used to
+% itemize cell or struct arrays
+% Pref.XmlEngine - let you choose the XML engine. Currently default is
+% 'Xerces', which is using directly the apache xerces java file.
+% Other option is 'Matlab' which uses MATLAB's xmlwrite and its
+% XMLUtils java file. Both options create identical results except in
+% case of CDATA sections where xmlwrite fails.
+% Pref.CellItem - default 'true' - allow cell arrays to use 'item'
+% notation. See below.
+% Pref.RootOnly - default true - output variable 'tree' corresponds to
+% xml file root element, otherwise it correspond to the whole file.
+% Pref.StructItem - default 'true' - allow arrays of structs to use
+% 'item' notation. For example "Pref.StructItem = true" gives:
+% <a>
+% <b>
+% <item> ... <\item>
+% <item> ... <\item>
+% <\b>
+% <\a>
+% while "Pref.StructItem = false" gives:
+% <a>
+% <b> ... <\b>
+% <b> ... <\b>
+% <\a>
+%
+%
+% Several special xml node types can be created if special tags are used
+% for field names of 'tree' nodes:
+% - node.CONTENT - stores data section of the node if other fields
+% (usually ATTRIBUTE are present. Usually data section is stored
+% directly in 'node'.
+% - node.ATTRIBUTE.name - stores node's attribute called 'name'.
+% - node.COMMENT - create comment child node from the string. For global
+% comments see "RootName" input variable.
+% - node.PROCESSING_INSTRUCTIONS - create "processing instruction" child
+% node from the string. For global "processing instructions" see
+% "RootName" input variable.
+% - node.CDATA_SECTION - stores node's CDATA section (string). Only works
+% if Pref.XmlEngine='Xerces'. For more info, see comments of F_xmlwrite.
+% - other special node types like: document fragment nodes, document type
+% nodes, entity nodes and notation nodes are not being handled by
+% 'xml_write' at the moment.
+%
+% OUTPUT
+% DOMnode Document Object Model (DOM) node tree in the format
+% required as input to xmlwrite. (optional)
+%
+% EXAMPLES:
+% MyTree=[];
+% MyTree.MyNumber = 13;
+% MyTree.MyString = 'Hello World';
+% xml_write('test.xml', MyTree);
+% type('test.xml')
+% %See also xml_tutorial.m
+%
+% See also
+% xml_read, xmlread, xmlwrite
+%
+% Written by Jarek Tuszynski, SAIC, jaroslaw.w.tuszynski_at_saic.com
+
+%% Check Matlab Version
+v = ver('MATLAB');
+v = str2double(regexp(v.Version, '\d.\d','match','once'));
+if (v<7)
+ error('Your MATLAB version is too old. You need version 7.0 or newer.');
+end
+
+%% default preferences
+DPref.TableName = {'tr','td'}; % name of a special tags used to itemize 2D cell arrays
+DPref.ItemName = 'item'; % name of a special tag used to itemize 1D cell arrays
+DPref.StructItem = true; % allow arrays of structs to use 'item' notation
+DPref.CellItem = true; % allow cell arrays to use 'item' notation
+DPref.StructTable= 'Html';
+DPref.CellTable = 'Html';
+DPref.XmlEngine = 'Matlab'; % use matlab provided XMLUtils
+%DPref.XmlEngine = 'Xerces'; % use Xerces xml generator directly
+DPref.PreserveSpace = false; % Preserve or delete spaces at the beggining and the end of stings?
+RootOnly = true; % Input is root node only
+GlobalProcInst = [];
+GlobalComment = [];
+GlobalDocType = [];
+
+%% read user preferences
+if (nargin>3)
+ if (isfield(Pref, 'TableName' )), DPref.TableName = Pref.TableName; end
+ if (isfield(Pref, 'ItemName' )), DPref.ItemName = Pref.ItemName; end
+ if (isfield(Pref, 'StructItem')), DPref.StructItem = Pref.StructItem; end
+ if (isfield(Pref, 'CellItem' )), DPref.CellItem = Pref.CellItem; end
+ if (isfield(Pref, 'CellTable')), DPref.CellTable = Pref.CellTable; end
+ if (isfield(Pref, 'StructTable')), DPref.StructTable= Pref.StructTable; end
+ if (isfield(Pref, 'XmlEngine' )), DPref.XmlEngine = Pref.XmlEngine; end
+ if (isfield(Pref, 'RootOnly' )), RootOnly = Pref.RootOnly; end
+ if (isfield(Pref, 'PreserveSpace')), DPref.PreserveSpace = Pref.PreserveSpace; end
+end
+if (nargin<3 || isempty(RootName)), RootName=inputname(2); end
+if (isempty(RootName)), RootName='ROOT'; end
+if (iscell(RootName)) % RootName also stores global text node data
+ rName = RootName;
+ RootName = char(rName{1});
+ if (length(rName)>1), GlobalProcInst = char(rName{2}); end
+ if (length(rName)>2), GlobalComment = char(rName{3}); end
+ if (length(rName)>3), GlobalDocType = char(rName{4}); end
+end
+if(~RootOnly && isstruct(tree)) % if struct than deal with each field separatly
+ fields = fieldnames(tree);
+ for i=1:length(fields)
+ field = fields{i};
+ x = tree(1).(field);
+ if (strcmp(field, 'COMMENT'))
+ GlobalComment = x;
+ elseif (strcmp(field, 'PROCESSING_INSTRUCTION'))
+ GlobalProcInst = x;
+ elseif (strcmp(field, 'DOCUMENT_TYPE'))
+ GlobalDocType = x;
+ else
+ RootName = field;
+ t = x;
+ end
+ end
+ tree = t;
+end
+
+%% Initialize jave object that will store xml data structure
+RootName = varName2str(RootName);
+if (~isempty(GlobalDocType))
+ % n = strfind(GlobalDocType, ' ');
+ % if (~isempty(n))
+ % dtype = com.mathworks.xml.XMLUtils.createDocumentType(GlobalDocType);
+ % end
+ % DOMnode = com.mathworks.xml.XMLUtils.createDocument(RootName, dtype);
+ warning('xml_io_tools:write:docType', ...
+ 'DOCUMENT_TYPE node was encountered which is not supported yet. Ignoring.');
+end
+DOMnode = com.mathworks.xml.XMLUtils.createDocument(RootName);
+
+
+%% Use recursive function to convert matlab data structure to XML
+root = DOMnode.getDocumentElement;
+struct2DOMnode(DOMnode, root, tree, DPref.ItemName, DPref);
+
+%% Remove the only child of the root node
+root = DOMnode.getDocumentElement;
+Child = root.getChildNodes; % create array of children nodes
+nChild = Child.getLength; % number of children
+if (nChild==1)
+ node = root.removeChild(root.getFirstChild);
+ while(node.hasChildNodes)
+ root.appendChild(node.removeChild(node.getFirstChild));
+ end
+ while(node.hasAttributes) % copy all attributes
+ root.setAttributeNode(node.removeAttributeNode(node.getAttributes.item(0)));
+ end
+end
+
+%% Save exotic Global nodes
+if (~isempty(GlobalComment))
+ DOMnode.insertBefore(DOMnode.createComment(GlobalComment), DOMnode.getFirstChild());
+end
+if (~isempty(GlobalProcInst))
+ n = strfind(GlobalProcInst, ' ');
+ if (~isempty(n))
+ proc = DOMnode.createProcessingInstruction(GlobalProcInst(1:(n(1)-1)),...
+ GlobalProcInst((n(1)+1):end));
+ DOMnode.insertBefore(proc, DOMnode.getFirstChild());
+ end
+end
+% Not supported yet as the code below does not work
+% if (~isempty(GlobalDocType))
+% n = strfind(GlobalDocType, ' ');
+% if (~isempty(n))
+% dtype = DOMnode.createDocumentType(GlobalDocType);
+% DOMnode.insertBefore(dtype, DOMnode.getFirstChild());
+% end
+% end
+
+%% save java DOM tree to XML file
+if (~isempty(filename))
+ if (strcmpi(DPref.XmlEngine, 'Xerces'))
+ xmlwrite_xerces(filename, DOMnode);
+ else
+ xmlwrite(filename, DOMnode);
+ end
+end
+
+
+%% =======================================================================
+% === struct2DOMnode Function ===========================================
+% =======================================================================
+function [] = struct2DOMnode(xml, parent, s, TagName, Pref)
+% struct2DOMnode is a recursive function that converts matlab's structs to
+% DOM nodes.
+% INPUTS:
+% xml - jave object that will store xml data structure
+% parent - parent DOM Element
+% s - Matlab data structure to save
+% TagName - name to be used in xml tags describing 's'
+% Pref - preferenced
+% OUTPUT:
+% parent - modified 'parent'
+
+% perform some conversions
+if (ischar(s) && min(size(s))>1) % if 2D array of characters
+ s=cellstr(s); % than convert to cell array
+end
+% if (strcmp(TagName, 'CONTENT'))
+% while (iscell(s) && length(s)==1), s = s{1}; end % unwrap cell arrays of length 1
+% end
+TagName = varName2str(TagName);
+
+%% == node is a 2D cell array ==
+% convert to some other format prior to further processing
+nDim = nnz(size(s)>1); % is it a scalar, vector, 2D array, 3D cube, etc?
+if (iscell(s) && nDim==2 && strcmpi(Pref.CellTable, 'Matlab'))
+ s = var2str(s, Pref.PreserveSpace);
+end
+if (nDim==2 && (iscell (s) && strcmpi(Pref.CellTable, 'Vector')) || ...
+ (isstruct(s) && strcmpi(Pref.StructTable, 'Vector')))
+ s = s(:);
+end
+if (nDim>2), s = s(:); end % can not handle this case well
+nItem = numel(s);
+nDim = nnz(size(s)>1); % is it a scalar, vector, 2D array, 3D cube, etc?
+
+%% == node is a cell ==
+if (iscell(s)) % if this is a cell or cell array
+ if ((nDim==2 && strcmpi(Pref.CellTable,'Html')) || (nDim< 2 && Pref.CellItem))
+ % if 2D array of cells than can use HTML-like notation or if 1D array
+ % than can use item notation
+ if (strcmp(TagName, 'CONTENT')) % CONTENT nodes already have <TagName> ... </TagName>
+ array2DOMnode(xml, parent, s, Pref.ItemName, Pref ); % recursive call
+ else
+ node = xml.createElement(TagName); % <TagName> ... </TagName>
+ array2DOMnode(xml, node, s, Pref.ItemName, Pref ); % recursive call
+ parent.appendChild(node);
+ end
+ else % use <TagName>...<\TagName> <TagName>...<\TagName> notation
+ array2DOMnode(xml, parent, s, TagName, Pref ); % recursive call
+ end
+%% == node is a struct ==
+elseif (isstruct(s)) % if struct than deal with each field separatly
+ if ((nDim==2 && strcmpi(Pref.StructTable,'Html')) || (nItem>1 && Pref.StructItem))
+ % if 2D array of structs than can use HTML-like notation or
+ % if 1D array of structs than can use 'items' notation
+ node = xml.createElement(TagName);
+ array2DOMnode(xml, node, s, Pref.ItemName, Pref ); % recursive call
+ parent.appendChild(node);
+ elseif (nItem>1) % use <TagName>...<\TagName> <TagName>...<\TagName> notation
+ array2DOMnode(xml, parent, s, TagName, Pref ); % recursive call
+ else % otherwise save each struct separatelly
+ fields = fieldnames(s);
+ node = xml.createElement(TagName);
+ for i=1:length(fields) % add field by field to the node
+ field = fields{i};
+ x = s.(field);
+ switch field
+ case {'COMMENT', 'CDATA_SECTION', 'PROCESSING_INSTRUCTION'}
+ if iscellstr(x) % cell array of strings -> add them one by one
+ array2DOMnode(xml, node, x(:), field, Pref ); % recursive call will modify 'node'
+ elseif ischar(x) % single string -> add it
+ struct2DOMnode(xml, node, x, field, Pref ); % recursive call will modify 'node'
+ else % not a string - Ignore
+ warning('xml_io_tools:write:badSpecialNode', ...
+ ['Struct field named ',field,' encountered which was not a string. Ignoring.']);
+ end
+ case 'ATTRIBUTE' % set attributes of the node
+ if (isempty(x)), continue; end
+ if (isstruct(x))
+ attName = fieldnames(x); % get names of all the attributes
+ for k=1:length(attName) % attach them to the node
+ att = xml.createAttribute(varName2str(attName(k)));
+ att.setValue(var2str(x.(attName{k}),Pref.PreserveSpace));
+ node.setAttributeNode(att);
+ end
+ else
+ warning('xml_io_tools:write:badAttribute', ...
+ 'Struct field named ATTRIBUTE encountered which was not a struct. Ignoring.');
+ end
+ otherwise % set children of the node
+ struct2DOMnode(xml, node, x, field, Pref ); % recursive call will modify 'node'
+ end
+ end % end for i=1:nFields
+ parent.appendChild(node);
+ end
+%% == node is a leaf node ==
+else % if not a struct and not a cell than it is a leaf node
+ switch TagName % different processing depending on desired type of the node
+ case 'COMMENT' % create comment node
+ com = xml.createComment(s);
+ parent.appendChild(com);
+ case 'CDATA_SECTION' % create CDATA Section
+ cdt = xml.createCDATASection(s);
+ parent.appendChild(cdt);
+ case 'PROCESSING_INSTRUCTION' % set attributes of the node
+ OK = false;
+ if (ischar(s))
+ n = strfind(s, ' ');
+ if (~isempty(n))
+ proc = xml.createProcessingInstruction(s(1:(n(1)-1)),s((n(1)+1):end));
+ parent.insertBefore(proc, parent.getFirstChild());
+ OK = true;
+ end
+ end
+ if (~OK)
+ warning('xml_io_tools:write:badProcInst', ...
+ ['Struct field named PROCESSING_INSTRUCTION need to be',...
+ ' a string, for example: xml-stylesheet type="text/css" ', ...
+ 'href="myStyleSheet.css". Ignoring.']);
+ end
+ case 'CONTENT' % this is text part of already existing node
+ txt = xml.createTextNode(var2str(s, Pref.PreserveSpace)); % convert to text
+ parent.appendChild(txt);
+ otherwise % I guess it is a regular text leaf node
+ txt = xml.createTextNode(var2str(s, Pref.PreserveSpace));
+ node = xml.createElement(TagName);
+ node.appendChild(txt);
+ parent.appendChild(node);
+ end
+end % of struct2DOMnode function
+
+%% =======================================================================
+% === array2DOMnode Function ============================================
+% =======================================================================
+function [] = array2DOMnode(xml, parent, s, TagName, Pref)
+% Deal with 1D and 2D arrays of cell or struct. Will modify 'parent'.
+nDim = nnz(size(s)>1); % is it a scalar, vector, 2D array, 3D cube, etc?
+switch nDim
+ case 2 % 2D array
+ for r=1:size(s,1)
+ subnode = xml.createElement(Pref.TableName{1});
+ for c=1:size(s,2)
+ v = s(r,c);
+ if iscell(v), v = v{1}; end
+ struct2DOMnode(xml, subnode, v, Pref.TableName{2}, Pref ); % recursive call
+ end
+ parent.appendChild(subnode);
+ end
+ case 1 %1D array
+ for iItem=1:numel(s)
+ v = s(iItem);
+ if iscell(v), v = v{1}; end
+ struct2DOMnode(xml, parent, v, TagName, Pref ); % recursive call
+ end
+ case 0 % scalar -> this case should never be called
+ if ~isempty(s)
+ if iscell(s), s = s{1}; end
+ struct2DOMnode(xml, parent, s, TagName, Pref );
+ end
+end
+
+%% =======================================================================
+% === var2str Function ==================================================
+% =======================================================================
+function str = var2str(object, PreserveSpace)
+% convert matlab variables to a string
+switch (1)
+ case isempty(object)
+ str = '';
+ case (isnumeric(object) || islogical(object))
+ if ndims(object)>2, object=object(:); end % can't handle arrays with dimention > 2
+ str=mat2str(object); % convert matrix to a string
+ % mark logical scalars with [] (logical arrays already have them) so the xml_read
+ % recognizes them as MATLAB objects instead of strings. Same with sparse
+ % matrices
+ if ((islogical(object) && isscalar(object)) || issparse(object)),
+ str = ['[' str ']'];
+ end
+ if (isinteger(object)),
+ str = ['[', class(object), '(', str ')]'];
+ end
+ case iscell(object)
+ if ndims(object)>2, object=object(:); end % can't handle cell arrays with dimention > 2
+ [nr nc] = size(object);
+ obj2 = object;
+ for i=1:length(object(:))
+ str = var2str(object{i}, PreserveSpace);
+ if (ischar(object{i})), object{i} = ['''' object{i} '''']; else object{i}=str; end
+ obj2{i} = [object{i} ','];
+ end
+ for r = 1:nr, obj2{r,nc} = [object{r,nc} ';']; end
+ obj2 = obj2.';
+ str = ['{' obj2{:} '}'];
+ case isstruct(object)
+ str='';
+ warning('xml_io_tools:write:var2str', ...
+ 'Struct was encountered where string was expected. Ignoring.');
+ case isa(object, 'function_handle')
+ str = ['[@' char(object) ']'];
+ case ischar(object)
+ str = object;
+ otherwise
+ str = char(object);
+end
+
+%% string clean-up
+str=str(:); str=str.'; % make sure this is a row vector of char's
+if (~isempty(str))
+ str(str<32|str==127)=' '; % convert no-printable characters to spaces
+ if (~PreserveSpace)
+ str = strtrim(str); % remove spaces from begining and the end
+ str = regexprep(str,'\s+',' '); % remove multiple spaces
+ end
+end
+
+%% =======================================================================
+% === var2Namestr Function ==============================================
+% =======================================================================
+function str = varName2str(str)
+% convert matlab variable names to a sting
+str = char(str);
+p = strfind(str,'0x');
+if (~isempty(p))
+ for i=1:length(p)
+ before = str( p(i)+(0:3) ); % string to replace
+ after = char(hex2dec(before(3:4))); % string to replace with
+ str = regexprep(str,before,after, 'once', 'ignorecase');
+ p=p-3; % since 4 characters were replaced with one - compensate
+ end
+end
+str = regexprep(str,'_COLON_',':', 'once', 'ignorecase');
+str = regexprep(str,'_DASH_' ,'-', 'once', 'ignorecase');
+
diff --git a/lib/vendor/nemo2profilelib/exclude_elements.m b/lib/vendor/nemo2profilelib/exclude_elements.m
new file mode 100644
index 0000000..d3f56bc
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/exclude_elements.m
@@ -0,0 +1,38 @@
+function [ resulting_list ] = exclude_elements( p_source, p_exclude_items, p_source_type )
+%EXCLUDE_ELEMENTS Excludes items from given source.
+% Runs through the given source and excludes all given elements from it.
+% Currently only source type 'dir' is implemented.
+%
+% Parameters:
+% p_source Input source, class depends on p_source_type.
+% p_exclude_items Items to exclude from p_source.
+% p_source_type Type of given source, currently only 'dir' is implemented.
+
+%% Initialize return variables
+resulting_list = false;
+
+%% Parameter check
+if nargin ~= 3
+ warning([mfilename ': Parameter not set correctly! Returning false.']);
+ return
+end
+
+%% Switch source type
+
+switch p_source_type
+ case 'dir'
+ tmp_list = [];
+ for o_index = 1:length(p_source) % check if element is a directory
+ if ~any(strcmp(p_source(o_index).name, p_exclude_items))
+ tmp_list = [tmp_list p_source(o_index)];
+ end % ignore every other elements
+ end
+ resulting_list = tmp_list; % copy the created list to the correct variable
+ clear tmp_list o_index; % clean up
+ otherwise
+ warning([mfilename ': Unknown source type! Returning false.']);
+ return
+end
+
+end
+
diff --git a/lib/vendor/nemo2profilelib/exclude_files.m b/lib/vendor/nemo2profilelib/exclude_files.m
new file mode 100644
index 0000000..30992de
--- /dev/null
+++ b/lib/vendor/nemo2profilelib/exclude_files.m
@@ -0,0 +1,30 @@
+function [ folder_list ] = exclude_files( p_source )
+%EXCLUDE_FILES Excludes all files from a list of folders given by p_source.
+% Runs through p_source and excludes all files that are found.
+%
+% Parameters:
+% p_source List of directories.
+
+%% Initialize return variables
+folder_list = false;
+
+%% Parameter check
+if ~isstruct(p_source)
+ warning([mfilename ': Parameter not set correctly! Returning false.']);
+ return
+end
+
+%% Exclude all files
+
+tmp_list = [];
+for o_index = 1:size(p_source, 1) % check if element is a directory
+ %if isdir(p_source(o_index).name)
+ if p_source(o_index).isdir
+ tmp_list = [tmp_list p_source(o_index)];
+ end % ignore every other elements
+end
+folder_list = tmp_list; % copy the created list to the correct variable
+clear tmp_list o_index; % clean up
+
+end
+
--
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