[enh] Make all process compatible with raw files

bst_plugin/GLM/nst_glm_add_regressors.m

@@ -203,7 +203,7 @@
  if strcmp(sFile.FileType, 'data') % Imported data structure
  sDataIn = in_bst_data(sFile.FileName);
  elseif strcmp(sFile.FileType, 'raw') % Continuous data file
- sDataIn = in_bst(sFileFileName, [], 1, 1, 'no');
+ sDataIn = in_bst(sFile.FileName, [], 1, 1, 'no');
  end
 
  ChannelMat = in_bst_channel(sFile.ChannelFile);

bst_plugin/mbll/process_nst_dOD.m

@@ -18,7 +18,7 @@
 % For more information type "brainstorm license" at command prompt.
 % =============================================================================@
 %
-% Authors: Thomas Vincent (2015-2016)
+% Authors: Thomas Vincent (2015-2016), Edouard Delaire (2023)
 
 eval(macro_method);
 end
@@ -36,7 +36,7 @@
  % Definition of the input accepted by this process
  sProcess.InputTypes = {'data', 'raw'};
  % Definition of the outputs of this process
- sProcess.OutputTypes = {'data', 'data'}; 
+ sProcess.OutputTypes = {'data', 'raw'}; 
  sProcess.nInputs = 1;
  sProcess.nMinFiles = 1;
 
@@ -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);
@@ -149,35 +151,78 @@
  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
+ newCondition = ['@raw', cond_name, '_dOD'];
+ else
+ newCondition = [cond_name, '_dOD'];
+ end
+
+ iStudy = db_add_condition(sInputs.SubjectName, newCondition);
  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);
+ % Generate a new file name in the same folder
+ OutputFile = bst_process('GetNewFilename', bst_fileparts(sStudy.FileName), 'data_0raw_OD');
+
+ if ~isRaw
+
+ % Save time-series data
+ sDataOut = db_template('data');
+ sDataOut.F = final_dOD';
+ sDataOut.Comment = [sDataIn.Comment ' | OD '];
+ 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);
+ bst_save(OutputFile, sDataOut, 'v7');
+ % Register in database
+ db_add_data(iStudy, OutputFile, sDataOut);
+
+ else
+ ProtocolInfo = bst_get('ProtocolInfo');
+
+ newStudyPath = bst_fullfile(ProtocolInfo.STUDIES, sInputs.SubjectName, newCondition);
+
+ [tmp, rawBaseOut, rawBaseExt] = bst_fileparts(newStudyPath);
+ rawBaseOut = strrep([rawBaseOut rawBaseExt], '@raw', '');
+ % Full output filename
+ RawFileOut = bst_fullfile(newStudyPath, [rawBaseOut '.bst']);
+
+ sFileIn = sDataRaw.F;
+ sFileIn.channelflag = ones(size(final_dOD, 2), 1);
+ sFileIn.ChannelFlag = ones(size(final_dOD, 2), 1);
+
+ [sFileOut, errMsg] = out_fopen(RawFileOut, 'BST-BIN', sFileIn, ChannelMat);
+
+ % Set Output sFile structure
+ sOutMat.format = 'BST-BIN';
+ sOutMat.F = sFileOut;
+ sOutMat.DataType = 'raw'; 
+ sOutMat.History = sDataIn.History;
+ sOutMat = bst_history('add', sOutMat, 'process', sProcess.Comment);
+ sOutMat.ChannelFlag = ones(size(final_dOD, 2), 1);
+ sOutMat.DisplayUnits = 'delta OD';
+
+ sOutMat.Comment = [sDataIn.Comment ' | OD ']; 
+ % 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
+ db_add_data(iStudy, OutputFile, sOutMat);
+ end
 end
 
 

bst_plugin/mbll/process_nst_mbll.m

@@ -18,7 +18,7 @@
 % For more information type "brainstorm license" at command prompt.
 % =============================================================================@
 %
-% Authors: Thomas Vincent (2015-2020)
+% Authors: Thomas Vincent (2015-2020), Edouard Delaire (2023)
 
 eval(macro_method);
 end
@@ -36,7 +36,7 @@
  % Definition of the input accepted by this process
  sProcess.InputTypes = {'data', 'raw'};
  % Definition of the outputs of this process
- sProcess.OutputTypes = {'data', 'data'}; %TODO: 'raw' -> 'raw' or 'raw' -> 'data'?
+ sProcess.OutputTypes = {'data', 'raw'}; 
  sProcess.nInputs = 1;
  sProcess.nMinFiles = 1;
  % Definition of the options
@@ -72,10 +72,8 @@
 function OutputFile = Run(sProcess, sInputs) %#ok<DEFNU>
  OutputFile = {};
 
- % TODO: check for negative values
  % Get option values 
  age = sProcess.options.option_age.Value{1};
-
  do_plp_corr = sProcess.options.option_do_plp_corr.Value;
  pvf = sProcess.options.option_pvf.Value{1};
  dpf_method = sProcess.options.option_dpf_method.Value{1};
@@ -87,11 +85,14 @@
  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
+
 
  dOD_params = process_nst_dOD('parse_options', sProcess, sDataIn);
  if isempty(dOD_params)
@@ -114,7 +115,6 @@
 
 
  % Apply MBLL
- % TODO: add baseline window and expose it
  [nirs_hb, channels_hb] = Compute(fnirs, fchannel_def, age, dOD_params, do_plp_corr, pvf, dpf_method); 
 
  % Re-add other channels that were not changed during MBLL
@@ -125,32 +125,75 @@
  if length(cond_name)>=4 && strcmp(cond_name(1:4), '@raw')
  cond_name = cond_name(5:end);
  end
- iStudy = db_add_condition(sInputs.SubjectName, [cond_name, '_Hb']);
+
+
+ if isRaw
+ newCondition = ['@raw', cond_name, '_Hb'];
+ else
+ newCondition = [cond_name, '_Hb'];
+ end
+
+ iStudy = db_add_condition(sInputs.SubjectName, newCondition);
  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
- sDataOut = db_template('data');
- sDataOut.F = final_nirs'; 
- sDataOut.Comment = [sInputs(1).Comment ' | Hb [Topo]'];
- sDataOut.ChannelFlag = ones(size(final_nirs, 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 = 'mol.l-1';
 
  % Generate a new file name in the same folder
- OutputFile = bst_process('GetNewFilename', bst_fileparts(sStudy.FileName), 'data_hb');
- sDataOut.FileName = file_short(OutputFile);
- bst_save(OutputFile, sDataOut, 'v7');
- % Register in database
- db_add_data(iStudy, OutputFile, sDataOut);
+ OutputFile = bst_process('GetNewFilename', bst_fileparts(sStudy.FileName), 'data_0raw_hb');
+ if ~isRaw
+ % Save time-series data
+ sDataOut = db_template('data');
+ sDataOut.F = final_nirs'; 
+ sDataOut.Comment = [sInputs(1).Comment ' | Hb [Topo]'];
+ sDataOut.ChannelFlag = ones(size(final_nirs, 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 = 'mol.l-1';
+
+ % Generate a new file name in the same folder
+ OutputFile = bst_process('GetNewFilename', bst_fileparts(sStudy.FileName), 'data_hb');
+ sDataOut.FileName = file_short(OutputFile);
+ bst_save(OutputFile, sDataOut, 'v7');
+ % Register in database
+ db_add_data(iStudy, OutputFile, sDataOut);
+ else
+ ProtocolInfo = bst_get('ProtocolInfo');
+ newStudyPath = bst_fullfile(ProtocolInfo.STUDIES, sInputs.SubjectName, newCondition);
+
+ [tmp, rawBaseOut, rawBaseExt] = bst_fileparts(newStudyPath);
+ rawBaseOut = strrep([rawBaseOut rawBaseExt], '@raw', '');
+ % Full output filename
+ RawFileOut = bst_fullfile(newStudyPath, [rawBaseOut '.bst']);
+
+ sFileIn = sDataRaw.F;
+ sFileIn.channelflag = ones(size(final_nirs, 2), 1);
+ [sFileOut, errMsg] = out_fopen(RawFileOut, 'BST-BIN', sFileIn, ChannelMat);
+
+ % Set Output sFile structure
+ sOutMat.format = 'BST-BIN';
+ sOutMat.F = sFileOut;
+ sOutMat.DataType = 'raw'; 
+ sOutMat.History = sDataIn.History;
+ sOutMat = bst_history('add', sOutMat, 'process', sProcess.Comment);
+ sOutMat.ChannelFlag = ones(size(final_nirs, 2), 1);
+ sOutMat.DisplayUnits = 'mol.l-1';
+ sOutMat.Comment = [sInputs(1).Comment ' | Hb [Topo]'];
+
+ % 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_nirs');
+ % Register in BST database
+ db_add_data(iStudy, OutputFile, sOutMat);
+ end
 end
 
 function [fdata, fchannel_def] = ...