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[enh] Make all process compatible with raw files #219

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[enh] Make all process compatible with raw files #219

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ebdb614
save file as raw file if input is raw
Edouard2laire Oct 22, 2023
e382115
fixing based on Raymondo data
Edouard2laire Nov 2, 2023
e69a2c0
fix
Edouard2laire Nov 2, 2023
c4d0572
use filter for motion correction
Edouard2laire Nov 8, 2023
3f8338e
wtf
Edouard2laire Nov 11, 2023
99fc0f8
working?
Edouard2laire Nov 11, 2023
6cb7058
Add extra fields
Edouard2laire Nov 11, 2023
0369e76
update process_nst_mbll
Edouard2laire Nov 11, 2023
44cb362
minor changes
Edouard2laire Nov 11, 2023
8a3d6f5
make it work [ need to duplicate channel flag]
Edouard2laire Nov 11, 2023
4d4af6f
Apply changes on motion correction
Edouard2laire Nov 11, 2023
376800c
Apply change to process_nst_remove_ssc
Edouard2laire Nov 12, 2023
05692c0
update process_nst_iir_filter
Edouard2laire Nov 12, 2023
3599165
change process_nst_detrend
Edouard2laire Nov 12, 2023
07c9cba
Load event in filter process
Edouard2laire Nov 23, 2023
685048b
improve history
Edouard2laire Nov 23, 2023
f65bfab
improve history
Edouard2laire Nov 23, 2023
12b3f53
update mex file from windows
Edouard2laire Nov 27, 2023
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76 changes: 52 additions & 24 deletions bst_plugin/mbll/process_nst_dOD.m
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Original file line number Diff line number Diff line change
Expand Up @@ -115,10 +115,12 @@
if strcmp(sInputs.FileType, 'data') % Imported data structure
sDataIn = in_bst_data(sInputs(1).FileName);
events = sDataIn.Events;
isRaw = 0;
elseif strcmp(sInputs.FileType, 'raw') % Continuous data file
sDataIn = in_bst(sInputs(1).FileName, [], 1, 1, 'no');
sDataRaw = in_bst_data(sInputs(1).FileName, 'F');
events = sDataRaw.F.events;
isRaw = 1;
end

parameters = parse_options(sProcess, sDataIn);
Expand Down Expand Up @@ -149,35 +151,61 @@
if strcmp(cond_name(1:4), '@raw')
cond_name = cond_name(5:end);
end
iStudy = db_add_condition(sInputs.SubjectName, [cond_name, '_dOD']);

if isRaw
iStudy = db_add_condition(sInputs.SubjectName, ['@raw', cond_name, '_dOD']);
else
iStudy = db_add_condition(sInputs.SubjectName, [cond_name, '_dOD']);
end
sStudy = bst_get('Study', iStudy);
%

% % Save channel definition
[tmp, iChannelStudy] = bst_get('ChannelForStudy', iStudy);
db_set_channel(iChannelStudy, ChannelMat, 0, 0);

% Save time-series data
% final_nirs = sDataIn.F;
% final_nirs(to_keep, :) = final_nirs';
sDataOut = db_template('data');
sDataOut.F = final_dOD';
sDataOut.Comment = sDataIn.Comment;
%sDataOut.ChannelFlag = sDataIn.ChannelFlag;
sDataOut.ChannelFlag = ones(size(final_dOD, 2), 1);
sDataOut.Time = sDataIn.Time;
sDataOut.DataType = 'recordings';
sDataOut.nAvg = 1;
sDataOut.Events = events;
sDataOut.History = sDataIn.History;
sDataOut = bst_history('add', sDataOut, 'process', sProcess.Comment);
sDataOut.DisplayUnits = 'delta OD';

% Generate a new file name in the same folder
OutputFile = bst_process('GetNewFilename', bst_fileparts(sStudy.FileName), 'data_OD');
sDataOut.FileName = file_short(OutputFile);
bst_save(OutputFile, sDataOut, 'v7');
% Register in database
db_add_data(iStudy, OutputFile, sDataOut);
if ~isRaw
% Save time-series data
sDataOut = db_template('data');
sDataOut.F = final_dOD';
sDataOut.Comment = sDataIn.Comment;
%sDataOut.ChannelFlag = sDataIn.ChannelFlag;
sDataOut.ChannelFlag = ones(size(final_dOD, 2), 1);
sDataOut.Time = sDataIn.Time;
sDataOut.DataType = 'recordings';
sDataOut.nAvg = 1;
sDataOut.Events = events;
sDataOut.History = sDataIn.History;
sDataOut = bst_history('add', sDataOut, 'process', sProcess.Comment);
sDataOut.DisplayUnits = 'delta OD';

sDataOut.FileName = file_short(OutputFile);
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bst_save(OutputFile, sDataOut, 'v7');
% Register in database
db_add_data(iStudy, OutputFile, sDataOut);

else

% Generate a new file name in the same folder
OutputFile = bst_process('GetNewFilename', bst_fileparts(sStudy.FileName), 'data_0raw_OD');

sFileIn = sDataRaw.F;
sFileOut = out_fopen(OutputFile, 'BST-BIN',sFileIn , ChannelMat);
% Set Output sFile structure
sOutMat.F = sFileOut;
% Save new link to raw .mat file
bst_save(OutputFile, sOutMat, 'v6');
% Create new channel file
db_set_channel(iStudy, ChannelMat, 2, 0);
% Write block
out_fwrite(sFileOut, ChannelMat, 1, [], [], final_dOD');
% Register in BST database
sFileOut.Comment = sDataIn.Comment;
db_add_data(iStudy, OutputFile, sFileOut);
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OutputFile={};
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OutputFile{1} = OutputFile;
end


end


Expand Down