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@couppeym
couppeym committed Nov 24, 2022
1 parent da68ec3 commit ea8a9ae
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Showing 4 changed files with 910 additions and 217 deletions.
215 changes: 138 additions & 77 deletions decArgo_soft/soft/util/nc_create_synthetic_profile.m
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,9 @@
% this new version generates S-PROF file (possibly
% empty) even when 'c' PROF or 'b' PROF file is
% missing
% 07/10/2020 - RNU - V 1.10: correction in processing of PROFILE_<PARAM>_QC
% (the input Qcs used depend on PARAMATER_DATA_MODE
% information)
% ------------------------------------------------------------------------------
function nc_create_synthetic_profile(varargin)

Expand Down Expand Up @@ -102,11 +105,15 @@ function nc_create_synthetic_profile(varargin)

% program version
global g_cocs_ncCreateSyntheticProfileVersion;
g_cocs_ncCreateSyntheticProfileVersion = '1.9 (version 30.06.2020 for ARGO_simplified_profile)';
g_cocs_ncCreateSyntheticProfileVersion = '1.10 (version 30.06.2020 for ARGO_simplified_profile)';

% current float and cycle identification
global g_cocs_floatNum;

% output CSV file Id
global g_cocs_fidCsvFile;
g_cocs_fidCsvFile = -1;


% default values initialization
init_default_values;
Expand Down Expand Up @@ -190,6 +197,22 @@ function nc_create_synthetic_profile(varargin)
end

if (errorFlag == 0)

% output CSV file name
[~, logFileName, ~] = fileparts(logFile);
csvFileName = [DIR_CSV_FILE '/' logFileName '.csv'];

% create CSV file
g_cocs_fidCsvFile = fopen(csvFileName, 'wt');
if (g_cocs_fidCsvFile == -1)
fprintf('ERROR: Unable to create output CSV file: %s\n', csvFileName);
return
end

% put header
header = 'dac, type, float code, cycle number, message, file';
fprintf(g_cocs_fidCsvFile, '%s\n', header);

if (~isempty(floatList))

% process floats of the FLOAT_LIST_FILE_NAME file (or provided in input
Expand Down Expand Up @@ -238,12 +261,14 @@ function nc_create_synthetic_profile(varargin)
end
end

fclose(g_cocs_fidCsvFile);

diary off;

if (~isempty(DIR_CSV_FILE))
% generate CSV file (from log file contents)
generate_csv_file(logFile, DIR_CSV_FILE);
end
% if (~isempty(DIR_CSV_FILE))
% % generate CSV file (from log file contents)
% generate_csv_file(logFile, DIR_CSV_FILE);
% end

return

Expand Down Expand Up @@ -279,17 +304,46 @@ function process_one_float(a_floatDir, a_outputDir, ...
global g_cocs_floatNum;
global g_cocs_cycleNum;
global g_cocs_cycleDir;

g_cocs_cycleDir = '';

% output CSV file information
global g_cocs_fidCsvFile;
global g_cocs_dacName;
g_cocs_dacName = '-';
global g_cocs_floatWmoStr;
g_cocs_floatWmoStr = num2str(g_cocs_floatNum);
global g_cocs_cycleNumStr;
g_cocs_cycleNumStr = '-';
global g_cocs_inputFile;
g_cocs_inputFile = '-';

floatWmoStr = num2str(g_cocs_floatNum);


% META data file
metaFileName = [a_floatDir '/' floatWmoStr '_meta.nc'];
if ~(exist(metaFileName, 'file') == 2)
fprintf('ERROR: Float %d: META file not found: %s\n', g_cocs_floatNum, metaFileName);

% CSV output
msgType = 'error';
message = 'File not found.';
[~, fileName, fileExt] = fileparts(metaFileName);
g_cocs_inputFile = [fileName fileExt];
fprintf(g_cocs_fidCsvFile, '%s,%s,%s,%s%s,%s,%s\n', ...
g_cocs_dacName, msgType, g_cocs_floatWmoStr, g_cocs_cycleNumStr, g_cocs_cycleDir, message, g_cocs_inputFile);

return
end

% retrieve DATA_CENTRE from META file
wantedVars = [ ...
{'DATA_CENTRE'} ...
];
[metaData] = get_data_from_nc_file(metaFileName, wantedVars);
dataCentre = get_data_from_name('DATA_CENTRE', metaData);
g_cocs_dacName = dataCentre(:, 1)';

% create the list of available cycle numbers (from PROF files)
profileDir = [a_floatDir '/profiles'];
files = dir([profileDir '/' '*' floatWmoStr '_' '*.nc']);
Expand All @@ -315,6 +369,7 @@ function process_one_float(a_floatDir, a_outputDir, ...
for idCy = 1:length(cyNumList)

g_cocs_cycleNum = cyNumList(idCy);
g_cocs_cycleNumStr = num2str(g_cocs_cycleNum);

createMultiProfFlag = 0;
if (idCy == length(cyNumList))
Expand Down Expand Up @@ -450,101 +505,107 @@ function process_one_float(a_floatDir, a_outputDir, ...
return

% ------------------------------------------------------------------------------
% Generate the output CSV file (from INFO/WARNING/ERROR messages of the log
% file).
% Get data from name in a {var_name}/{var_data} list.
%
% SYNTAX :
% generate_csv_file(a_logFileName, a_csvDirName)
% [o_dataValues] = get_data_from_name(a_dataName, a_dataList)
%
% INPUT PARAMETERS :
% a_logFileName : log file path name of the run
% a_csvDirName : directory of CSV files
% a_dataName : name of the data to retrieve
% a_dataList : {var_name}/{var_data} list
%
% OUTPUT PARAMETERS :
% o_dataValues : concerned data
%
% EXAMPLES :
%
% SEE ALSO :
% AUTHORS : Jean-Philippe Rannou (Altran)([email protected])
% ------------------------------------------------------------------------------
% RELEASES :
% 04/22/2020 - RNU - creation
% 06/15/2018 - RNU - creation
% ------------------------------------------------------------------------------
function generate_csv_file(a_logFileName, a_csvDirName)

% output CSV file name
[~, logFileName, ~] = fileparts(a_logFileName);
csvFileName = [a_csvDirName '/' logFileName '.csv'];
function [o_dataValues] = get_data_from_name(a_dataName, a_dataList)

% output parameters initialization
o_dataValues = [];

% create CSV file
fidOut = fopen(csvFileName, 'wt');
if (fidOut == -1)
fprintf('ERROR: Unable to create output file: %s\n', csvFileName);
return
idVal = find(strcmp(a_dataName, a_dataList(1:2:end)) == 1, 1);
if (~isempty(idVal))
o_dataValues = a_dataList{2*idVal};
end

% put header
header = 'MESSAGE TYPE;MESSAGE SOURCE;MESSAGE CONTENT';
fprintf(fidOut, '%s\n', header);
return

if (~isempty(a_logFileName))
% read log file
fId = fopen(a_logFileName, 'r');
if (fId == -1)
sprintf('ERROR: Unable to open file: %s\n', a_logFileName);
% ------------------------------------------------------------------------------
% Retrieve data from NetCDF file.
%
% SYNTAX :
% [o_ncData] = get_data_from_nc_file(a_ncPathFileName, a_wantedVars)
%
% INPUT PARAMETERS :
% a_ncPathFileName : NetCDF file name
% a_wantedVars : NetCDF variables to retrieve from the file
%
% OUTPUT PARAMETERS :
% o_ncData : retrieved data
%
% EXAMPLES :
%
% SEE ALSO :
% AUTHORS : Jean-Philippe Rannou (Altran)([email protected])
% ------------------------------------------------------------------------------
% RELEASES :
% 06/15/2018 - RNU - creation
% ------------------------------------------------------------------------------
function [o_ncData] = get_data_from_nc_file(a_ncPathFileName, a_wantedVars)

% output parameters initialization
o_ncData = [];

% output CSV file information
global g_cocs_fidCsvFile;
global g_cocs_dacName;
global g_cocs_floatWmoStr;
global g_cocs_cycleNumStr;
global g_cocs_cycleDir;
global g_cocs_inputFile;


if (exist(a_ncPathFileName, 'file') == 2)

% open NetCDF file
fCdf = netcdf.open(a_ncPathFileName, 'NC_NOWRITE');
if (isempty(fCdf))
fprintf('ERROR: Unable to open NetCDF input file: %s\n', a_ncPathFileName);

% CSV output
msgType = 'error';
message = 'Unable to open file.';
[~, fileName, fileExt] = fileparts(a_ncPathFileName);
g_cocs_inputFile = [fileName fileExt];
fprintf(g_cocs_fidCsvFile, '%s,%s,%s,%s%s,%s,%s\n', ...
g_cocs_dacName, msgType, g_cocs_floatWmoStr, g_cocs_cycleNumStr, g_cocs_cycleDir, message, g_cocs_inputFile);

return
end
fileContents = textscan(fId, '%s', 'delimiter', '\n');
fclose(fId);

if (~isempty(fileContents) && ~isempty(fileContents{:}))
% retrieve wanted messages
fileContents = fileContents{:};
idLine = 1;
while (1)
line = fileContents{idLine};
msgType = '';
msgSource = '';
msg = '';
if (strncmp(line, 'INFO: ', length('INFO: ')))
msgType = 'INFO';
msgSource = 'nc_create_synthetic_profile';
msg = line(length('INFO: ')+1:end);
elseif (strncmp(line, 'WARNING: ', length('WARNING: ')))
msgType = 'WARNING';
msgSource = 'nc_create_synthetic_profile';
msg = line(length('WARNING: ')+1:end);
elseif (strncmp(line, 'ERROR: ', length('ERROR: ')))
msgType = 'ERROR';
msgSource = 'nc_create_synthetic_profile';
msg = line(length('ERROR: ')+1:end);
elseif (strncmp(line, 'S-PROF_INFO: ', length('S-PROF_INFO: ')))
msgType = 'INFO';
msgSource = 'ARGO_simplified_profile';
msg = line(length('S-PROF_INFO: ')+1:end);
elseif (strncmp(line, 'S-PROF_WARNING: ', length('S-PROF_WARNING: ')))
msgType = 'WARNING';
msgSource = 'ARGO_simplified_profile';
msg = line(length('S-PROF_WARNING: ')+1:end);
elseif (strncmp(line, 'S-PROF_ERROR: ', length('S-PROF_ERROR: ')))
msgType = 'ERROR';
msgSource = 'ARGO_simplified_profile';
msg = line(length('S-PROF_ERROR: ')+1:end);
end

if (~isempty(msgType))
fprintf(fidOut, '%s;%s;%s\n', msgType, msgSource, msg);
end

idLine = idLine + 1;
if (idLine > length(fileContents))
break
end
% retrieve variables from NetCDF file
for idVar = 1:length(a_wantedVars)
varName = a_wantedVars{idVar};

if (var_is_present_dec_argo(fCdf, varName))
varValue = netcdf.getVar(fCdf, netcdf.inqVarID(fCdf, varName));
o_ncData = [o_ncData {varName} {varValue}];
else
% fprintf('WARNING: Variable %s not present in file : %s\n', ...
% varName, a_ncPathFileName);
o_ncData = [o_ncData {varName} {' '}];
end

end

netcdf.close(fCdf);
end

fclose(fidOut);

return
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