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Commit 381190a2 authored by jacques.grelet_ird.fr's avatar jacques.grelet_ird.fr
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deplace les fichiers de lecture/ecriture sous tsg_io

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tsg_io/readBucketData.m 0 → 100644
+ 70
− 0
View file @ 381190a2
function [error] = readBucketData( hTsgGUI, filename)
% Function to read Bucket data in ASCII format.
%
% Input
% -----
% hTsgGUI ............ Handel to the main user interface
% filename ........... Data filename
%
% Output
% ------
% error .............. 1: OK - -1 : an error occured
%
% @The data are store using setappdata - Variable name : 'bucketASCII'
%
% Caution : replace the fill-value with NaN
% $Id$
% Open the file
% -------------
fid = fopen( filename, 'r' );
error = -1;
if fid ~= -1
% Get the tsg structure from application GUI
% ------------------------------------------
tsg = getappdata( hTsgGUI, 'tsg_data');
% Read the file - skip 2 lines
% ----------------------------
fgetl( fid ); fgetl( fid );
bucketData = fscanf(fid,'%d %d %d %d %d %d %f %f %f', [9 Inf])';
% Every variable are put in a structure
% -------------------------------------
tsg.DAYD_WS = datenum(bucketData(:,1), bucketData(:,2), ...
bucketData(:,3), bucketData(:,4), ...
bucketData(:,5), bucketData(:,6));
% save original date
% ------------------
tsg.DATE_WS = datestr( tsg.DAYD_WS, 'yyyymmddHHMMSS' );
tsg.LATX_WS = bucketData(:,7);
tsg.LONX_WS = bucketData(:,8);
tsg.SSPS_WS = bucketData(:,9);
tsg.SSPS_WS_QC = zeros(size(tsg.SSPS_WS));
%@ completer ces 2 champs !!!!!!!!
%tsg.PSAL_WS_ANALDATE = ;
%tsg.PSAL_WS_BOTTLE = ;
% remplace pour l'instant sample.TYPE !!!!!!
%tsg.SSPS_WS_TYPE = ones(size(tsg.SSPS_WS));
% Save the data in the application GUI
% ------------------------------------
setappdata( hTsgGUI, 'tsg_data', tsg );
% Clear the Workspace
% -------------------
clear bucketData
% Close the file
% --------------
fclose( fid );
% Everything OK
% -------------
error = 1;
end
tsg_io/readTsgDataNetCDF.m 0 → 100644
+ 187
− 0
View file @ 381190a2
function [error] = readTsgDataNetCDF( hTsgGUI, filename)
% Function to read the TSG data. Should be a NetCDF file
% GOSUD data format TSG V1.4
%
% Input
% -----
% hTsgGUI ............ Handel to the main user interface
% filename ........... Data filename
%
% Output
% ------
% error .............. 1: OK - -1 : an error occured
%
% The data are store using setappdata - Variable name : 'tsg_data'
%
% $Id$
% Get the data from the application GUI
% -------------------------------------
tsg = getappdata( hTsgGUI, 'tsg_data');
% Display read file info on console
% ---------------------------------
fprintf('\nREAD_NETCDF_FILE\n'); tic;
% Open netCDF file
% ----------------
nc = netcdf(filename,'read');
if isempty(nc)
msg_error = ['TSG_GOSUD file_lecture : Open file error : ' filename];
warndlg( msg_error, 'NetCDF error dialog');
sprintf('...cannot locate %s\n', filename);
error = -1;
return;
end
% Display more info about read file on console
% --------------------------------------------
fprintf('...reading %s : ', filename);
% Read global attributes: meta data
% ----------------------------------
tsg.PLATFORM_NAME = nc.PLATFORM_NAME(:);
tsg.SHIP_CALL_SIGN = nc.SHIP_CALL_SIGN(:);
tsg.SHIP_MMSI = nc.SHIP_MMSI(:);
tsg.TSG_TYPE = nc.TSG_TYPE(:);
tsg.TSG_NUMBER = nc.TSG_NUMBER(:);
tsg.TINT_TYPE = nc.TINT_TYPE(:);
tsg.TINT_NUMBER = nc.TINT_NUMBER(:);
tsg.DATA_TYPE = nc.DATA_TYPE(:);
tsg.DATA_MODE = nc.DATA_MODE(:);
tsg.SAMPLING_PERIOD = nc.SAMPLING_PERIOD(:);
tsg.PROCESSING_STATUS = nc.PROCESSING_STATUS(:);
tsg.DATE_START = nc.DATE_START(:);
tsg.DATE_END = nc.DATE_END(:);
tsg.SOUTH_LATX = nc.SOUTH_LATX(:);
tsg.NORTH_LATX = nc.NORTH_LATX(:);
tsg.WEST_LONX = nc.WEST_LONX(:);
tsg.EAST_LONX = nc.EAST_LONX(:);
tsg.FORMAT_VERSION = nc.FORMAT_VERSION(:);
tsg.DATE_CREATION = nc.DATE_CREATION(:);
tsg.DATE_UPDATE = nc.DATE_UPDATE(:);
tsg.DATA_RESTRICTIONS = nc.DATA_RESTRICTIONS(:);
tsg.CITATION = nc.CITATION(:);
tsg.COMMENT = nc.COMMENT(:);
tsg.PROJECT_NAME = nc.PROJECT_NAME(:);
tsg.PI_NAME = nc.PI_NAME(:);
tsg.DATA_CENTRE = nc.DATA_CENTRE(:);
tsg.DATA_ACQUISITION = nc.DATA_ACQUISITION(:);
tsg.PROCESSING_CENTRE = nc.PROCESSING_CENTRE(:);
tsg.PROCESSING_STATE = nc.PROCESSING_STATE(:);
% read variables describing TSG installation
% ------------------------------------------
tsg.SSJT_DEPH = nc{'SSJT_DEPH'}(:);
tsg.SSJT_DEPH_MIN = nc{'SSJT_DEPH_MIN'}(:);
tsg.SSJT_DEPH_MAX = nc{'SSJT_DEPH_MAX'}(:);
tsg.CNDC_CALCOEF = nc{'CNDC_CALCOEF'}(:);
tsg.CNDC_LINCOEF = nc{'CNDC_LINCOEF'}(:);
tsg.SSJT_CALCOEF = nc{'SSJT_CALCOEF'}(:);
tsg.SSJT_LINCOEF = nc{'SSJT_LINCOEF'}(:);
% read variables describing Temperature sensor at intake (TINT) installation
% --------------------------------------------------------------------------
tsg.SSTP_DEPH = nc{'SSTP_DEPH'}(:);
tsg.SSTP_DEPH_MIN = nc{'SSTP_DEPH_MIN'}(:);
tsg.SSTP_DEPH_MAX = nc{'SSTP_DEPH_MAX'}(:);
tsg.SSTP_CALCOEF = nc{'SSTP_CALCOEF'}(:);
tsg.SSTP_LINCOEF = nc{'SSTP_LINCOEF'}(:);
% Coordinates
%------------
tsg.DATE = nc{'DATE'}(:,:);
tsg.DAYD = nc{'DAYD'}(:);
tsg.LATX = nc{'LATX'}(:);
tsg.LONX = nc{'LONX'}(:);
tsg.POSITION_QC = nc{'POSITION_QC'}(:);
tsg.SPDC = nc{'SPDC'}(:);
tsg.REFERENCE_DATE_TIME = nc{'REFERENCE_DATE_TIME'}(:);
% Convert julian day with origin 1950 to Matlab datenum in memory
% ---------------------------------------------------------------
tsg.DAYD = julianToDatenum( tsg.DAYD );
% Variables holding data from the main TSG
% data series 1
%-----------------------------------------
% measured variables
%-----------------------------------------
%if isempty(tsg.PRES)
tsg.PRES = nc{'PRES'}(:);
%end
%if isempty(tsg.SSJT)
tsg.SSJT = nc{'SSJT'}(:);
tsg.SSJT_STD = nc{'SSJT_STD'}(:);
tsg.SSJT_STD_CAL = nc{'TEMP_STD_CAL'}(:);
%end
%if isempty(tsg.CNDC)
tsg.CNDC = nc{'CNDC'}(:);
tsg.CNDC_STD = nc{'CNDC_STD'}(:);
tsg.CNDC_CAL = nc{'CNDC_CAL'}(:);
%end
% intake temperature variable
%-----------------------------------------
tsg.SSTP = nc{'SSTP'}(:);
tsg.SSTP_QC = nc{'SSTP_QC'}(:);
tsg.SSTP_CAL = nc{'SSTP_CAL'}(:);
tsg.SSTP_ADJUSTED = nc{'SSTP_ADJUSTED'}(:);
tsg.SSTP_ADJUSTED_ERROR = nc{'SSTP_ADJUSTED_ERROR'}(:);
tsg.SSTP_ADJUSTED_QC = nc{'SSTP_ADJUSTED_QC'}(:);
tsg.SSTP_ADJUSTED_HIST = nc{'HIST_SSTP_ADJUSTED'}(:);
% derived variables
%-----------------------------------------
tsg.SSPS = nc{'SSPS'}(:);
tsg.SSPS_QC = nc{'SSPS_QC'}(:);
tsg.SSPS_CAL = nc{'SSPS_CAL'}(:);
tsg.SSPS_ADJUSTED = nc{'SSPS_ADJUSTED'}(:);
tsg.SSPS_ADJUSTED_ERROR = nc{'SSPS_ADJUSTED_ERROR'}(:);
tsg.SSPS_ADJUSTED_QC = nc{'SSPS_ADJUSTED_QC'}(:);
tsg.SSPS_ADJUSTED_HIST = nc{'HIST_SSPS_ADJUSTED'}(:);
% data series 2
%-----------------------------------------
% water samples
%-----------------------------------------
tsg.DATE_WS = nc{'DATE_WS'}(:,:);
tsg.DAYD_WS = julianToDatenum(nc{'DAYD_WS'}(:));
tsg.LATX_WS = nc{'LATX_WS'}(:);
tsg.LONX_WS = nc{'LONX_WS'}(:);
tsg.SSPS_WS = nc{'SSPS_WS'}(:);
tsg.SSPS_WS_QC = nc{'SSPS_WS_QC'}(:);
tsg.SSPS_WS_ANALDATE = nc{'SSPS_WS_ANALDATE'}(:,:);
tsg.SSPS_WS_BOTTLE = nc{'SSPS_WS_BOTTLE'}(:,:);
% Save the data in the application GUI
% ------------------------------------
setappdata( hTsgGUI, 'tsg_data', tsg );
% Clear the Workspace
% -------------------
clear tsgdata
% Close the file
% --------------
%endef(nc)
close(nc);
% Display time to read file on console
% ------------------------------------
t = toc; fprintf('...done (%6.2f sec).\n\n',t);
% Everything OK
% -------------
error = 1;
end
tsg_io/readTsgDataTxt.m 0 → 100644
+ 105
− 0
View file @ 381190a2
function [error] = readTsgDataTxt( hTsgGUI, filename)
% Function to read the TSG data. Should be a NetCDF file
%
% Input
% -----
% hTsgGUI ............ Handle to the main user interface
% filename ........... Data filename
%
% Output
% ------
% error .............. 1: OK - -1 : an error occured
%
% The data are store using setappdata - Variable name : 'tsg_data'
%
%
% Caution : replace the fill-value with NaN
% $Id$
% Get the data from the application GUI
% -------------------------------------
tsg = getappdata( hTsgGUI, 'tsg_data');
% Display read file info on console
% ---------------------------------
fprintf('\nREAD_ASCII_FILE\n'); tic;
% Open the file
% -------------
fid = fopen( filename, 'r' );
% Check file
% -----------
if fid == -1
msg_error = ['TSG_GOSUD file_lecture : Open file error : ' filename];
warndlg( msg_error, 'ASCII error dialog');
sprintf('...cannot locate %s\n', filename);
error = -1;
return;
end
% Display more info about read file on console
% --------------------------------------------
fprintf('...reading %s : ', filename);
% Read the file
% -------------
tsgData = fscanf(fid, '%d/%d/%d %d:%d:%d %f %f %f %f %d %f %f', ...
[13 Inf])';
% Every variable are put in a structure
% -------------------------------------
tsg.DAYD = datenum(tsgData(:,3), tsgData(:,2),tsgData(:,1), ...
tsgData(:,4),tsgData(:,5),tsgData(:,6));
% save original date
% ------------------
tsg.DATE = datestr( tsg.DAYD, 'yyyymmddHHMMSS' );
% convert with julian day with origin 1950
% -----------------------------------------
%% a supprimer !!!!!!!
% tsg.TIME_TSG = datenumToJulian(tsg.TIME_TSG);
tsg.LATX = tsgData(:,7);
tsg.LONX = tsgData(:,8);
tsg.SSJT = tsgData(:,9);
tsg.SSPS = tsgData(:,10);
tsg.SSPS_QC = tsgData(:,11);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
tsg.SSPS_ADJ = tsgData(:,12);
tsg.SSPS_ERR = tsgData(:,13);
% Compute ship velocity from positions if sog not available
% ---------------------------------------------------------
if isempty(tsg.SPDC)
range = m_lldist(tsg.LONX,tsg.LATX);
ind = size(tsg.DAYD);
tsg.SPDC = zeros(size(ind));
for i=1:length(tsg.DAYD)-1
tsg.SPDC(i) = range(i) / ((tsg.DAYD(i+1)-tsg.DAYD(i)) * 24 * 1.854);
end
tsg.SPDC = [tsg.SPDC';0];
end
% Save the data in the application GUI
% ------------------------------------
setappdata( hTsgGUI, 'tsg_data', tsg );
% Clear the Workspace
% -------------------
clear tsgdata
% Close the file
% --------------
fclose( fid );
% Display time to read file on console
% ------------------------------------
t = toc; fprintf('...done (%6.2f sec).\n\n',t);
% Everything OK
% -------------
error = 1;
tsg_io/readTsgDataXML.m 0 → 100644
+ 58
− 0
View file @ 381190a2
function [error] = readTsgDataXML( hTsgGUI, filename)
% Function to read the TSG data XML file
%
% Input
% -----
% hTsgGUI ............ Handel to the main user interface
% filename ........... Data filename
%
% Output
% ------
% error .............. 1: OK - -1 : an error occured
%
% The data are store using setappdata - Variable name : 'tsg_data'
%
% Function not yet implemented
% Caution : replace the fill-value with NaN
% $Id$
% Open the file
% -------------
fid = fopen( filename, 'r' );
error = -1;
if fid ~= -1
disp('Read XML file, not yet implemeted ...');
% % Read the file
% % -------------
% tsgData = fscanf(fid, '%d/%d/%d %d:%d:%d %f %f %f %f %d %f %f', ...
% [13 Inf])';
%
% % Every variable are put in a structure
% % -------------------------------------
% tsg.TIME = datenum(tsgData(:,3), tsgData(:,2),tsgData(:,1), ...
% tsgData(:,4),tsgData(:,5),tsgData(:,6));
% tsg.LATITUDE = tsgData(:,7);
% tsg.LONGITUDE = tsgData(:,8);
% tsg.TEMP_TSG = tsgData(:,9);
% tsg.PSAL = tsgData(:,10);
% tsg.PSAL_QC = tsgData(:,11);
% tsg.PSAL_ADJ = tsgData(:,12);
% tsg.PSAL_ERR = tsgData(:,13);
%
% % Save the data in the application GUI
% % ------------------------------------
% setappdata( hTsgGUI, 'tsg_data', tsg );
% Clear the Workspace
% -------------------
clear tsgdata
% Close the file
% --------------
fclose( fid );
% Everything is not OK
% -------------
error = -1;
end
tsg_io/writeTSGDataNetCDF.m 0 → 100644
+ 147
− 0
View file @ 381190a2
function [error] = tsg_writeTSGDataNetCDF( hTsgGUI, filename)
% Function to write TSG data in NetCDF file.
%
% Input
% -----
% hTsgGUI ............ Handel to the main user interface
% filename ........... Data filename
%
% Output
% ------
% error ............. 1 : OK
% ............. -1 : an error occured
%
% The data are store using setappdata - Variable name : 'tsg_data'
%
% Caution : replace the fill-value with NaN
% $Id$
% Open the file
% -------------
nc = netcdf(filename, 'clobber');
if isempty(nc)
msg_error = ['TSG_GOSUD file_lecture : Open file error : ' filename];
warndlg( msg_error, 'NetCDF write dialog');
error = -1;
return;
end
% Initialize loading NetCDF file waitbar
% --------------------------------------
wb = waitbar(0, 'Initializing NetCDF file. Please wait...');
% We cannot change title property to 'none' (default set as 'tex') inside
% waitbar function (line 81), see
% http://www.mathworks.co.uk/matlabcentral/newsreader/view_thread/115725
% -----------------------------------------------------------------------
hchild = get(wb,'children');
htitle = get(hchild,'title');
set(htitle,'Interpreter','None');
% Get the data from the application GUI
% -------------------------------------
tsg = getappdata( hTsgGUI, 'tsg_data');
% Get global attributes list from class tsg_nc with file 'tsg_ncattr.csv'
% -----------------------------------------------------------------------
nca = tsg_nc('tsg_ncattr.csv');
nca_keys = keys(nca);
% Get GF3 variables list codes from class tsg_nc with file 'tsg_ncvar.csv'
% -----------------------------------------------------------------------
ncv = tsg_nc('tsg_ncvar.csv');
ncv_keys = keys(ncv);
ncv_fieldNames = get_fieldnames(ncv);
% Create NetCDF file:
% -------------------
% Variable dimensions
% -------------------
nc('DAYD') = numel(tsg.DAYD); % number of TSG measurements
nc('DAYD_WS') = numel(tsg.DAYD_WS); % number of water samples
nc('DAYD_EXT') = numel(tsg.DAYD_EXT); % number of external SSPS or SSTP comparison
nc('NCOEF_CAL') = 5; % number of calibration coefficients
nc('NCOEF_LIN') = 2; % number of linearisation coefficients
% Fixed dimensions
% ----------------
nc('STRING256') = 256;
nc('STRING14') = 14;
nc('STRING4') = 4;
nc('N1') = 1;
% display filename after 'Interpreter','None' initialization to prevent
% display console warning
% ---------------------------------------------------------------------
waitbar(1/50,wb,['Writing file: ' filename ' Please wait...']);
% Create NetCDF global attributes
% -------------------------------
for i=1:numel(nca_keys)
nc.(nca_keys{i}) = tsg.(nca_keys{i});
end
% Create NetCDF variables and attributes
% ---------------------------------------------------
for i=1:numel(ncv_keys)
for j=1:numel(ncv_fieldNames)
fn = ncv_fieldNames{j};
% define dimension
if strcmp(fn,'dimension')
nc{ncv_keys{i}} = ncfloat(get(ncv, ncv_keys{i}, fn));
% define variable atributes
elseif ~isempty(get(ncv, ncv_keys{i}, fn))
if ischar(get(ncv, ncv_keys{i}, fn))
nc{ncv_keys{i}}.(fn) = ncchar(get(ncv, ncv_keys{i}, fn));
else
nc{ncv_keys{i}}.(fn) = ncfloat(get(ncv, ncv_keys{i}, fn));
end
end
end
end
% Create data to NetCDF file:
% ---------------------------
% Write global attributes
% -----------------------
for i=1:numel(nca_keys)
nc.(nca_keys{i}) = tsg.(nca_keys{i});
end
% Convert Matlab julian days (datenum) to 1950 reference
% ------------------------------------------------------
d = strmatch('DAYD',ncv_keys);
for i=1:numel(d)
tsg.(ncv_keys{d(i)}) = datenumToJulian(tsg.(ncv_keys{d(i)}));
end
% Write measurements (variables)
% -------------------------------
for i=1:numel(ncv_keys)
% display waitbar
waitbar( i/numel(ncv_keys), wb, ['writing ' ncv_keys{i} ' variable']);
% DATE as two dimension
if strmatch('DATE',ncv_keys(i))
nc{ncv_keys{i}}(:,:) = tsg.(ncv_keys{i});
else
% other one dimension
nc{ncv_keys{i}}(:) = tsg.(ncv_keys{i});
end
end
% Close waitbar
% -------------
close(wb)
% Close NetCDF file
% -----------------
endef(nc)
close(nc)
% Everything OK
% -------------
error = 1;
end
tsg_io/writeTsgData.m 0 → 100644
+ 55
− 0
View file @ 381190a2
function [error] = tsg_writeTsgData( hTsgGUI, filename)
% Function to write the TSG data. Should be a NetCDF file
%
% Input
% -----
% hTsgGUI ............ Handel to the main user interface
% filename ........... Data filename
%
% Output
% ------
% error .............. 1: OK - -1 : an error occured
%
% The data are store using setappdata - Variable name : 'tsg_data'
%
% Function to be rewritten when the NetCDF format will be in use
% Caution : replace the fill-value with NaN
%$Id$
% Open the file
% -------------
fid = fopen( filename, 'w' );
error = -1;
if fid ~= -1
% Get the data from the application GUI
% -------------------------------------
tsg = getappdata( hTsgGUI, 'tsg_data');
[year, month, day, hour, min, sec] = datevec( tsg.TIME );
tsg_data = [day month year hour min fix(sec) tsg.LATITUDE ...
tsg.LONGITUDE tsg.TEMP_TSG ...
tsg.PSAL tsg.PSAL_QC ...
tsg.PSAL_ADJ tsg.PSAL_ERR ...
];
% Write the file
% -------------
fprintf(fid,...
'%02d/%02d/%04d %02d:%02d:%02d %11.6f %11.6f %6.3f %6.3f %1d %6.3f %6.3f\n',...
tsg_data');
% Clear the Workspace
% -------------------
clear tsgdata
% Close the file
% --------------
fclose( fid );
% Everything OK
% -------------
error = 1;
end
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