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Commit 53c886d4 authored by leprob001's avatar leprob001
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Added first version of ARGO netCDF trajectory file export.

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VERSION
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View file @ 53c886d4
313 314
\ No newline at end of file \ No newline at end of file
lib/+artoa/+controller/+file/saveArgoTrajectoryFile.m 0 → 100644
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function [] = saveArgoTrajectoryFile(~, ~)
%SAVERFC Saves the argo trajectory netcdf file to disk.
% Detailed explanation goes here
global artoaWorkspace artoaConfig artoaDataInput;
%% Get selected trajectory
trajectoryIndex = artoaWorkspace.trajectoryOutput.tableGeneratedTracksSelectedRow;
trajectory = artoaWorkspace.trajectoryOutput.trajectories{trajectoryIndex};
%% Ask for filename
folder = artoa.data.getMember(artoaConfig, {'directory', 'argotraj'}, pwd());
filter = artoa.data.getMember(artoaConfig, {'filemask', 'argotraj'}, '*.nc');
[filename, pathname] = uiputfile(fullfile(folder, filter));
if filename == 0
return;
end
filepath = fullfile(pathname, filename);
artoa.save.argo_trajectory(filepath, artoaDataInput.rfb, trajectory);
end
lib/+artoa/+controller/+main/open.m
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...@@ -22,6 +22,7 @@ callbacks.loadSoundsourceFile = @artoa.controller.file.loadSoundSourceFile; ...@@ -22,6 +22,7 @@ callbacks.loadSoundsourceFile = @artoa.controller.file.loadSoundSourceFile;
callbacks.saveRfc = @artoa.controller.file.saveRfc; callbacks.saveRfc = @artoa.controller.file.saveRfc;
callbacks.saveInterim = @artoa.controller.file.saveInterim; callbacks.saveInterim = @artoa.controller.file.saveInterim;
callbacks.saveOptimumTables = @artoa.controller.file.saveOptimumTables; callbacks.saveOptimumTables = @artoa.controller.file.saveOptimumTables;
callbacks.saveArgoTrajectory = @artoa.controller.file.saveArgoTrajectoryFile;
callbacks.saveTrajectoryToProfile = @artoa.controller.file.trajectory2profile.open; callbacks.saveTrajectoryToProfile = @artoa.controller.file.trajectory2profile.open;
callbacks.loadArtoaIni = @artoa.controller.file.reloadArtoaIni; callbacks.loadArtoaIni = @artoa.controller.file.reloadArtoaIni;
callbacks.reloadSoundsourceFile = @artoa.controller.file.reloadSoundSourceFile; callbacks.reloadSoundsourceFile = @artoa.controller.file.reloadSoundSourceFile;
......
lib/+artoa/+gui/main.m
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...@@ -13,6 +13,7 @@ availableCallbacks = { ... ...@@ -13,6 +13,7 @@ availableCallbacks = { ...
'loadSoundsourceFile', ... 'loadSoundsourceFile', ...
'saveRfc', ... 'saveRfc', ...
'saveInterim', ... 'saveInterim', ...
'saveArgoTrajectory', ...
'saveOptimumTables', ... 'saveOptimumTables', ...
'saveTrajectoryToProfile', ... 'saveTrajectoryToProfile', ...
'loadArtoaIni', ... 'loadArtoaIni', ...
...@@ -133,6 +134,12 @@ uimenu( ... ...@@ -133,6 +134,12 @@ uimenu( ...
'Callback', pCallbacks.saveInterim ... 'Callback', pCallbacks.saveInterim ...
); );
uimenu( ...
artoaGui.main.menus.fileSave, ...
'Label', 'ARGO trajectory file', ...
'Callback', pCallbacks.saveArgoTrajectory ...
);
uimenu( ... uimenu( ...
artoaGui.main.menus.fileSave, ... artoaGui.main.menus.fileSave, ...
'Label', 'Optimum tables', ... 'Label', 'Optimum tables', ...
......
lib/+artoa/+save/argo_trajectory.m 0 → 100644
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− 0
View file @ 53c886d4
function [outputArg1,outputArg2] = argo_trajectory(p_filepath, p_rfb, p_trajectory)
%ARGO_TRAJECTORY Summary of this function goes here
% Detailed explanation goes here
%% Prepare required variables
%% Remove file if exists
if exist(p_filepath, 'file')
delete(p_filepath);
end
%% Create netCDF file
ncid = netcdf.create(p_filepath, 'CLOBBER');
%% Define dimensions
DIM_DATE_TIME = netcdf.defDim(ncid, 'DATE_TIME', 14);
DIM_STRING2 = netcdf.defDim(ncid, 'STRING2', 2);
DIM_STRING4 = netcdf.defDim(ncid, 'STRING4', 4);
DIM_STRING8 = netcdf.defDim(ncid, 'STRING8', 8);
DIM_STRING16 = netcdf.defDim(ncid, 'STRING16', 16);
DIM_STRING32 = netcdf.defDim(ncid, 'STRING32', 32);
DIM_STRING64 = netcdf.defDim(ncid, 'STRING64', 64);
DIM_N_PARAM = netcdf.defDim(ncid, 'N_PARAM', 2);
%DIM_N_MEASUREMENT = netcdf.defDim(ncid, 'N_MEASUREMENT', netcdf.getConstant('NC_UNLIMITED'));
DIM_N_MEASUREMENT = netcdf.defDim(ncid, 'N_MEASUREMENT', length(p_trajectory.date));
DIM_N_CYCLE = netcdf.defDim(ncid, 'N_CYCLE', 1); % TODO: needs to be determined if it is correct!
DIM_N_HISTORY = netcdf.defDim(ncid, 'N_HISTORY', 1);
%% Define variables for general trajectory file information
ID_DATA_TYPE = netcdf.defVar(ncid, 'DATA_TYPE', 'NC_CHAR', DIM_STRING16);
netcdf.putAtt(ncid, ID_DATA_TYPE, 'long_name', 'Data type');
netcdf.putAtt(ncid, ID_DATA_TYPE, 'conventions', 'Argo reference table 1');
netcdf.putAtt(ncid, ID_DATA_TYPE, '_FillValue', ' ');
ID_FORMAT_VERSION = netcdf.defVar(ncid, 'FORMAT_VERSION', 'NC_CHAR', DIM_STRING4);
netcdf.putAtt(ncid, ID_FORMAT_VERSION, 'long_name', 'File format version');
netcdf.putAtt(ncid, ID_FORMAT_VERSION, '_FillValue', ' ');
ID_HANDBOOK_VERSION = netcdf.defVar(ncid, 'HANDBOOK_VERSION', 'NC_CHAR', DIM_STRING16);
netcdf.putAtt(ncid, ID_HANDBOOK_VERSION, 'long_name', 'Data handbook version');
netcdf.putAtt(ncid, ID_HANDBOOK_VERSION, '_FillValue', ' ');
ID_REFERENCE_DATE_TIME = netcdf.defVar(ncid, 'REFERENCE_DATE_TIME', 'NC_CHAR', DIM_DATE_TIME);
netcdf.putAtt(ncid, ID_REFERENCE_DATE_TIME, 'long_name', 'Date of reference for Julian days');
netcdf.putAtt(ncid, ID_REFERENCE_DATE_TIME, 'conventions', 'YYYYMMDDHHMISS');
netcdf.putAtt(ncid, ID_REFERENCE_DATE_TIME, '_FillValue', ' ');
ID_DATE_CREATION = netcdf.defVar(ncid, 'DATE_CREATION', 'NC_CHAR', DIM_DATE_TIME);
netcdf.putAtt(ncid, ID_DATE_CREATION, 'long_name', 'Date of file creation');
netcdf.putAtt(ncid, ID_DATE_CREATION, 'conventions', 'YYYYMMDDHHMISS');
netcdf.putAtt(ncid, ID_DATE_CREATION, '_FillValue', ' ');
ID_DATE_UPDATE = netcdf.defVar(ncid, 'DATE_UPDATE', 'NC_CHAR', DIM_DATE_TIME);
netcdf.putAtt(ncid, ID_DATE_UPDATE, 'long_name', 'Date of update of this file');
netcdf.putAtt(ncid, ID_DATE_UPDATE, 'conventions', 'YYYYMMDDHHMISS');
netcdf.putAtt(ncid, ID_DATE_UPDATE, '_FillValue', ' ');
%% Define variables for general information about the float
ID_PLATFORM_NUMBER = netcdf.defVar(ncid, 'PLATFORM_NUMBER', 'NC_CHAR', DIM_STRING8);
netcdf.putAtt(ncid, ID_PLATFORM_NUMBER, 'long_name', 'Float unique identifier');
netcdf.putAtt(ncid, ID_PLATFORM_NUMBER, 'conventions', 'WMO float identifier : A9IIIII');
netcdf.putAtt(ncid, ID_PLATFORM_NUMBER, '_FillValue', ' ');
ID_PROJECT_NAME = netcdf.defVar(ncid, 'PROJECT_NAME', 'NC_CHAR', DIM_STRING64);
netcdf.putAtt(ncid, ID_PROJECT_NAME, 'long_name', 'Name of the project');
netcdf.putAtt(ncid, ID_PROJECT_NAME, '_FillValue', ' ');
ID_PI_NAME = netcdf.defVar(ncid, 'PI_NAME', 'NC_CHAR', DIM_STRING64);
netcdf.putAtt(ncid, ID_PI_NAME, 'long_name', 'Name of the principal investigator');
netcdf.putAtt(ncid, ID_PI_NAME, '_FillValue', ' ');
ID_TRAJECTORY_PARAMETERS = netcdf.defVar(ncid, 'TRAJECTORY_PARAMETERS', 'NC_CHAR', [DIM_N_PARAM, DIM_STRING16]);
netcdf.putAtt(ncid, ID_TRAJECTORY_PARAMETERS, 'long_name', 'List of available parameters for the station');
netcdf.putAtt(ncid, ID_TRAJECTORY_PARAMETERS, 'conventions', 'Argo reference table 3');
netcdf.putAtt(ncid, ID_TRAJECTORY_PARAMETERS, '_FillValue', ' ');
ID_DATA_CENTRE = netcdf.defVar(ncid, 'DATA_CENTRE', 'NC_CHAR', DIM_STRING2);
netcdf.putAtt(ncid, ID_DATA_CENTRE, 'long_name', 'Data centre in charge of float data processing');
netcdf.putAtt(ncid, ID_DATA_CENTRE, 'conventions', 'Argo reference table 4');
netcdf.putAtt(ncid, ID_DATA_CENTRE, '_FillValue', ' ');
ID_DATA_STATE_INDICATOR = netcdf.defVar(ncid, 'DATA_STATE_INDICATOR', 'NC_CHAR', DIM_STRING4);
netcdf.putAtt(ncid, ID_DATA_STATE_INDICATOR, 'long_name', 'Degree of processing the data have passed through');
netcdf.putAtt(ncid, ID_DATA_STATE_INDICATOR, 'conventions', 'Argo reference table 6');
netcdf.putAtt(ncid, ID_DATA_STATE_INDICATOR, '_FillValue', ' ');
ID_PLATFORM_TYPE = netcdf.defVar(ncid, 'PLATFORM_TYPE', 'NC_CHAR', DIM_STRING32);
netcdf.putAtt(ncid, ID_PLATFORM_TYPE, 'long_name', 'Type of float');
netcdf.putAtt(ncid, ID_PLATFORM_TYPE, 'conventions', 'Argo reference table 23');
netcdf.putAtt(ncid, ID_PLATFORM_TYPE, '_FillValue', ' ');
ID_FLOAT_SERIAL_NO = netcdf.defVar(ncid, 'FLOAT_SERIAL_NO', 'NC_CHAR', DIM_STRING32);
netcdf.putAtt(ncid, ID_FLOAT_SERIAL_NO, 'long_name', 'Serial number of the float');
netcdf.putAtt(ncid, ID_FLOAT_SERIAL_NO, '_FillValue', ' ');
ID_FIRMWARE_VERSION = netcdf.defVar(ncid, 'FIRMWARE_VERSION', 'NC_CHAR', DIM_STRING64);
netcdf.putAtt(ncid, ID_FIRMWARE_VERSION, 'long_name', 'Instrument firmware version');
netcdf.putAtt(ncid, ID_FIRMWARE_VERSION, '_FillValue', ' ');
ID_WMO_INST_TYPE = netcdf.defVar(ncid, 'WMO_INST_TYPE', 'NC_CHAR', DIM_STRING4);
netcdf.putAtt(ncid, ID_WMO_INST_TYPE, 'long_name', 'Coded instrument type');
netcdf.putAtt(ncid, ID_WMO_INST_TYPE, 'conventions', 'Argo reference table 8');
netcdf.putAtt(ncid, ID_WMO_INST_TYPE, '_FillValue', ' ');
ID_POSITIONING_SYSTEM = netcdf.defVar(ncid, 'POSITIONING_SYSTEM', 'NC_CHAR', DIM_STRING8);
netcdf.putAtt(ncid, ID_POSITIONING_SYSTEM, 'long_name', 'Positioning system');
netcdf.putAtt(ncid, ID_POSITIONING_SYSTEM, '_FillValue', ' ');
%% Create global attributes
netcdf.putAtt(ncid, netcdf.getConstant('NC_GLOBAL'), 'title', 'Argo trajectory file');
netcdf.putAtt(ncid, netcdf.getConstant('NC_GLOBAL'), 'institution', '');
netcdf.putAtt(ncid, netcdf.getConstant('NC_GLOBAL'), 'source', 'Argo float');
% prepare datetime
dt = string(datetime('now', 'Format', 'yyyy-MM-dd HH:mm:ss', 'TimeZone', 'Z'));
dt = strsplit(dt, ' ');
dt = strjoin(dt, 'T');
netcdf.putAtt(ncid, netcdf.getConstant('NC_GLOBAL'), 'history', dt + 'Z creation');
netcdf.putAtt(ncid, netcdf.getConstant('NC_GLOBAL'), 'references', 'http://www.argodatamgt.org/Documentation');
netcdf.putAtt(ncid, netcdf.getConstant('NC_GLOBAL'), 'comment', '');
netcdf.putAtt(ncid, netcdf.getConstant('NC_GLOBAL'), 'user_manual_version', '3.2');
netcdf.putAtt(ncid, netcdf.getConstant('NC_GLOBAL'), 'Conventions', 'Argo-3.1 CF-1.6');
netcdf.putAtt(ncid, netcdf.getConstant('NC_GLOBAL'), 'featureType', 'trajectory');
%% Define trajectory variables
ID_JULD = netcdf.defVar(ncid, 'JULD', 'NC_DOUBLE', DIM_N_MEASUREMENT);
netcdf.putAtt(ncid, ID_JULD, 'long_name', 'Julian day (UTC) of each measurement relative to REFERENCE_DATE_TIME');
netcdf.putAtt(ncid, ID_JULD, 'standard_name', 'time');
netcdf.putAtt(ncid, ID_JULD, 'units', 'days since 1950-01-01 00:00:00 UTC');
netcdf.putAtt(ncid, ID_JULD, 'conventions', 'Relative julian days with decimal part (as parts of day)');
netcdf.putAtt(ncid, ID_JULD, 'resolution', 'X');
netcdf.putAtt(ncid, ID_JULD, '_FillValue', 999999);
netcdf.putAtt(ncid, ID_JULD, 'axis', 'T');
ID_LATITUDE = netcdf.defVar(ncid, 'LATITUDE', 'NC_DOUBLE', DIM_N_MEASUREMENT);
netcdf.putAtt(ncid, ID_LATITUDE, 'long_name', 'Latitude of each location');
netcdf.putAtt(ncid, ID_LATITUDE, 'standard_name', 'latitude');
netcdf.putAtt(ncid, ID_LATITUDE, 'units', 'degree_north');
netcdf.putAtt(ncid, ID_LATITUDE, '_FillValue', 99999);
netcdf.putAtt(ncid, ID_LATITUDE, 'valid_min', -90);
netcdf.putAtt(ncid, ID_LATITUDE, 'valid_max', 90);
netcdf.putAtt(ncid, ID_LATITUDE, 'axis', 'Y');
ID_LONGITUDE = netcdf.defVar(ncid, 'LONGITUDE', 'NC_DOUBLE', DIM_N_MEASUREMENT);
netcdf.putAtt(ncid, ID_LONGITUDE, 'long_name', 'Longitude of each location');
netcdf.putAtt(ncid, ID_LONGITUDE, 'standard_name', 'longitude');
netcdf.putAtt(ncid, ID_LONGITUDE, 'units', 'degree_east');
netcdf.putAtt(ncid, ID_LONGITUDE, '_FillValue', 99999);
netcdf.putAtt(ncid, ID_LONGITUDE, 'valid_min', -180);
netcdf.putAtt(ncid, ID_LONGITUDE, 'valid_max', 180);
netcdf.putAtt(ncid, ID_LONGITUDE, 'axis', 'X');
ID_PRES = netcdf.defVar(ncid, 'PRES', 'NC_DOUBLE', DIM_N_MEASUREMENT);
netcdf.putAtt(ncid, ID_PRES, 'long_name', 'Sea water pressure, equals 0 at sea-level');
netcdf.putAtt(ncid, ID_PRES, 'standard_name', 'sea_water_pressure');
netcdf.putAtt(ncid, ID_PRES, 'units', 'decibar');
netcdf.putAtt(ncid, ID_PRES, 'valid_min', '0.f');
netcdf.putAtt(ncid, ID_PRES, 'valid_max', '12000.f');
ID_TEMP = netcdf.defVar(ncid, 'TEMP', 'NC_DOUBLE', DIM_N_MEASUREMENT);
netcdf.putAtt(ncid, ID_TEMP, 'long_name', 'Sea temperature in-situ ITS-90 scale');
netcdf.putAtt(ncid, ID_TEMP, 'standard_name', 'sea_water_temperature');
netcdf.putAtt(ncid, ID_TEMP, 'units', 'degree_Celsius');
netcdf.putAtt(ncid, ID_TEMP, 'valid_min', '-2.5f');
netcdf.putAtt(ncid, ID_TEMP, 'valid_max', '40.f');
%
% ID_PSAL = netcdf.defVar(ncid, 'PSAL', 'NC_CHAR', DIM_N_MEASUREMENT);
% netcdf.putAtt(ncid, ID_PSAL, 'long_name', 'Practical salinity');
% netcdf.putAtt(ncid, ID_PSAL, 'standard_name', 'sea_water_salinity');
% netcdf.putAtt(ncid, ID_PSAL, 'units', 'psu');
% netcdf.putAtt(ncid, ID_PSAL, 'valid_min', '2.f');
% netcdf.putAtt(ncid, ID_PSAL, 'valid_max', '41.f');
% ID_JULD_STATUS = netcdf.defVar(ncid, 'JULD_STATUS', 'NC_CHAR', DIM_N_MEASUREMENT);
% netcdf.putAtt(ncid, ID_JULD_STATUS, 'long_name', 'Status of the date and time');
% netcdf.putAtt(ncid, ID_JULD_STATUS, 'conventions', 'Argo reference table 19');
% netcdf.putAtt(ncid, ID_JULD_STATUS, '_FillValue', ' ');
%
% ID_JULD_QC = netcdf.defVar(ncid, 'JULD_QC', 'NC_CHAR', DIM_N_MEASUREMENT);
% netcdf.putAtt(ncid, ID_JULD_QC, 'long_name', 'Quality on date and time');
% netcdf.putAtt(ncid, ID_JULD_QC, 'conventions', 'Argo reference table 2');
% netcdf.putAtt(ncid, ID_JULD_QC, '_FillValue', ' ');
%
%
% ID_JULD_ADJUSTED = netcdf.defVar(ncid, 'JULD_ADJUSTED', 'NC_CHAR', DIM_N_MEASUREMENT);
% netcdf.putAtt(ncid, ID_JULD_ADJUSTED, 'long_name', 'Adjusted julian day (UTC) of each measurement relative to REFERENCE_DAT_TIME');
% netcdf.putAtt(ncid, ID_JULD_ADJUSTED, 'standard_name', 'time');
% netcdf.putAtt(ncid, ID_JULD_ADJUSTED, 'units', 'days since 1950-01-01 00:00:00 UTC');
% netcdf.putAtt(ncid, ID_JULD_ADJUSTED, 'conventions', 'Relative julian days with decimal part (as parts of day)');
% netcdf.putAtt(ncid, ID_JULD_ADJUSTED, 'resultion', 'X');
% netcdf.putAtt(ncid, ID_JULD_ADJUSTED, '_FillValue', 999999);
% netcdf.putAtt(ncid, ID_JULD, 'axis', 'T');
%% End defintions
netcdf.endDef(ncid);
%% Fill variables for general trajectory file information
netcdf.putVar(ncid, ID_DATA_TYPE, pad('Argo trajectory', 16, 'right', ' '));
netcdf.putVar(ncid, ID_FORMAT_VERSION, pad('3.1', 4, 'right', ' '));
netcdf.putVar(ncid, ID_HANDBOOK_VERSION, pad('3.3', 16, 'right', ' '));
netcdf.putVar(ncid, ID_REFERENCE_DATE_TIME, pad('', 14, 'right', ' ')); % TODO:
netcdf.putVar(ncid, ID_DATE_CREATION, string(datetime('now', 'Format', 'yyyyMMddHHmmss', 'TimeZone', 'Z')));
netcdf.putVar(ncid, ID_DATE_UPDATE, string(datetime('now', 'Format', 'yyyyMMddHHmmss', 'TimeZone', 'Z')));
%% Fill variables for general float information
netcdf.putVar(ncid, ID_PLATFORM_NUMBER, pad('', 8, 'right', ' ')); % TODO:
netcdf.putVar(ncid, ID_PROJECT_NAME, pad(p_rfb.FLOAT.projectname, 64, 'right', ' '));
netcdf.putVar(ncid, ID_PI_NAME, pad('', 64, 'right', ' ')); % TODO:
%netcdf.putVar(ncid, ID_TRAJECTORY_PARAMETERS, [pad('PRES', 16, 'right', ' '); pad('TEMP', 16, 'right', ' '); pad('PSAL', 16, 'right', ' ')]);
netcdf.putVar(ncid, ID_TRAJECTORY_PARAMETERS, [pad('PRES', 16, 'right', ' '); pad('TEMP', 16, 'right', ' ')]);
netcdf.putVar(ncid, ID_DATA_CENTRE, ' '); % TODO:
netcdf.putVar(ncid, ID_DATA_STATE_INDICATOR, pad('', 4, 'right', ' ')); % TODO:
netcdf.putVar(ncid, ID_PLATFORM_TYPE, pad(p_rfb.FLOAT.type, 32, 'right', ' '));
netcdf.putVar(ncid, ID_FLOAT_SERIAL_NO, pad(string(p_rfb.FLOAT.floatname), 32, 'right', ' '));
netcdf.putVar(ncid, ID_FIRMWARE_VERSION, pad('', 64, 'right', ' ')); % TODO:
netcdf.putVar(ncid, ID_WMO_INST_TYPE, pad('', 4, 'right', ' ')); % TODO:
netcdf.putVar(ncid, ID_POSITIONING_SYSTEM, pad('', 8, 'right', ' ')); % TODO:
%% Fill dataset
netcdf.putVar(ncid, ID_JULD, p_trajectory.date);
netcdf.putVar(ncid, ID_LONGITUDE, p_trajectory.longitude);
netcdf.putVar(ncid, ID_LATITUDE, p_trajectory.latitude);
netcdf.putVar(ncid, ID_PRES, p_trajectory.pressure);
netcdf.putVar(ncid, ID_TEMP, p_trajectory.temperature);
%% Close file
netcdf.close(ncid);
end
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