Merge pull request #117 from CCC-members/develop

Develop

cfs_properties/functions/cfs_set.m

@@ -0,0 +1,36 @@
+function cfs_set( varargin )
+
+if ((nargin >= 2) && ischar(varargin{1}))
+    contextName = varargin{1};
+    data = varargin{2};
+else
+    return
+end
+
+% Get required context structure
+switch contextName
+    case 'cfs_dir'
+        output1 = fullfile(getUserDir(),'.CiftiStorm');
+    case 'defaults_dir'
+        cfs_db_dir = fullfile(getUserDir(),'.CiftiStorm');
+        output1 =  fullfile(cfs_db_dir,'defaults','anatomy');
+        output2 =  fullfile(cfs_db_dir,'defaults','eeg');
+        output3 =  fullfile(cfs_db_dir,'defaults','meg');
+    case 'datasets'
+        if(~isfolder(fullfile(getUserDir(),'.CiftiStorm')))
+            mkdir(fullfile(getUserDir(),'.CiftiStorm'));
+        end
+        if(~isfolder(fullfile(getUserDir(),'.CiftiStorm','Datasets')))
+            mkdir(fullfile(getUserDir(),'.CiftiStorm','Datasets'));
+        end
+        saveJSON(data,fullfile(getUserDir(),'.CiftiStorm','Datasets','Datasets.json')) 
+
+    case 'bst_default_eeg'
+        output1 = 'https://github.com/brainstorm-tools/brainstorm3/raw/master/defaults/eeg';
+
+    case 'openmeeg'
+
+    case 'duneruro'
+end
+
+end

cfs_properties/functions/check_properties.m

@@ -2,7 +2,9 @@
 %CHECK_PROPERTIES Summary of this function goes here
 %   Detailed explanation goes here
 status = true;
-reject_subjects = {};
+reject_subjects = struct;
+reject_anat = {};
+reject_nonbrain = {};
 
 disp('==========================================================================');
 disp("-->> Checking properties");
@@ -63,8 +65,8 @@
         status = false;
         return;
     end
-    if(~isfolder(fullfile(general_params.output_path,'BC-V_Structure',protocol_name)))
-        mkdir(fullfile(general_params.output_path,'BC-V_Structure',protocol_name));        
+    if(~isfolder(fullfile(general_params.output_path,'CiftiStorm',protocol_name)))
+        mkdir(fullfile(general_params.output_path,'CiftiStorm',protocol_name));        
     end
     if(~isfolder(fullfile(general_params.output_path,'BST','Subjects',protocol_name)))
         mkdir(fullfile(general_params.output_path,'BST','Subjects',protocol_name));        
@@ -128,7 +130,7 @@
             checked = check_HCP_anat_structure(structure, selected_anatomy);
             if(~checked)
                 count_HCP_structure = count_HCP_structure + 1;
-                reject_subjects{length(reject_subjects)+1} = structure.name;
+                reject_anat{end+1} = structure.name;
             end
         end
         if(~isequal(count_HCP_structure,0))
@@ -166,7 +168,7 @@
             checked = check_non_brain_surfaces(structure);
             if(~checked)
                 count_non_brain = count_non_brain + 1;
-                reject_subjects{length(reject_subjects)+1} = structure.name;
+                reject_nonbrain{end+1} = structure.name;
             end
         end
         if(~isequal(count_non_brain,0))
@@ -275,7 +277,7 @@
             raw_file = fullfile(base_path,structure.name,strrep(raw_data.file_location,'SubID',structure.name));
             if(~isfile(raw_file))
                 count_raw = count_raw + 1;
-                reject_subjects{length(reject_subjects)+1} = structure.name;
+                reject_chann{end+1} = structure.name;
             end            
         end
         if(~isequal(count_raw,0))
@@ -319,29 +321,32 @@
                 return;
             end
         end
+    end    
+
+    %% Joinning rejected subjects
+    for i=1:length(reject_anat)
+        reject_subjects(end+1).SubID                = reject_anat{i};
+        reject_subjects(end).Status                 = "Rejected";
+        reject_subjects(end).FileInfo               = "";
+        reject_subjects(end).Process(1).Name        = "Check_anat";
+        reject_subjects(end).Process(1).Status      = "Rejected";
+        reject_subjects(end).Process(1).Error       = 'The subject do not contain a correct anatomy folder';
     end
-    %%
-    %% Checking subject number in each folder
-    %%
-    anat_params = properties.anatomy_params;
-    if(isequal(lower(anat_params.anatomy_type.id),'individual'))
-        hcp_base_path = selected_anatomy.base_path;
-        hcp_subjects = dir(hcp_base_path);
-        hcp_subjects(ismember( {hcp_subjects.name}, {'.', '..'})) = [];  %remove . and ..
-        hcp_names = {hcp_subjects.name};
-
-        non_brain_path = non_brain.base_path;
-        nb_subjects = dir(non_brain_path);
-        nb_subjects(ismember( {nb_subjects.name}, {'.', '..'})) = [];  %remove . and ..
-        nb_names = {nb_subjects.name};
-
-        index1 = ismember(hcp_names,nb_names);
-        index2 = ismember(nb_names,hcp_names);
-        hcp_names(index1) = [];
-        nb_names(index2) = [];
-        reject_subjects = [reject_subjects , hcp_names, nb_names];
+    for i=1:length(reject_nonbrain)
+        idx = find(ismember({reject_subjects.Name},reject_nonbrain{i}),1);
+        if(isempty(idx))
+            reject_subjects(end+1).SubID            = reject_nonbrain{i};
+            reject_subjects(end).Status             = "Rejected";
+            reject_subjects(end).FileInfo           = "";
+            reject_subjects(end).Process(1).Name    = "Check_nonbrain";
+            reject_subjects(end).Process(1).Status  = "Rejected";
+            reject_subjects(end).Process(1).Error   = 'The subject do not contain a correct non-brain structure';
+        else            
+            reject_subjects(idx).Process(2).Name    = reject_nonbrain{i};
+            reject_subjects(idx).Process(2).Status  = "Rejected";
+            reject_subjects(idx).Process(2).Error   = 'The subject do not contain a correct non-brain structure';
+        end
     end
-    reject_subjects = unique(reject_subjects);
     if(~isempty(reject_subjects))
         disp("-->> Subjects to reject");
         disp("--------------------------------------------------------------------------");

ciftistorm.m

@@ -20,7 +20,7 @@ function ciftistorm(varargin)
 close all;
 restoredefaultpath;
 clearvars -except varargin;
-disp('-->> Starting process');
+disp('CFS -->> Starting process');
 disp('==========================================================================');
 
 %%
@@ -57,24 +57,29 @@ function ciftistorm(varargin)
     if(isequal(properties,'canceled'))
         return;
     end
-    [status, reject_subjects]     = check_properties(properties);
+    [status, reject_subjects]   = check_properties(properties);
     if(~status)
-        fprintf(2,strcat('\nBC-V-->> Error: The current configuration files are wrong \n'));
+        fprintf(2,strcat('\n-->> Error: The current configuration files are wrong \n'));
         disp('Please check the configuration files.');
         return;
     end    
 
     %% BrainStorm configuration
-    disp('-->> Preparing BrainStorm properties.');
-    disp('==========================================================================');
-    bst_path        = properties.general_params.bst_config.bst_path;
-    addpath(genpath(bst_path));
+    disp('CFS -->> Preparing BrainStorm properties.');
+    disp('==========================================================================');    
     status          = starting_brainstorm(properties);
 
     %% Calling dataset function to analysis
     if(status)
-        process_error = cfs_process_interface(properties,reject_subjects);
-        % save("process_output.mat","process_error","reject_subjects");
+        datasetFile = cfs_process_interface(properties,reject_subjects);
+        dataset = jsondecode(fileread(datasetFile));
+        datasets  = cfs_get('datasets');
+        if(isempty(datasets))            
+            datasets = dataset;
+        else
+            datasets(end+1) = dataset;
+        end
+        cfs_set('datasets',datasets);
     end
 
     %% Stopping BrainStorm

functions/cfs_process_interface.m

@@ -1,4 +1,4 @@
-function [process_error] = cfs_process_interface(properties, reject_subjects)
+function datasetFile = cfs_process_interface(properties, reject_subjects)
 % HeadModel Process Interface
 %   
 %
@@ -54,6 +54,7 @@
                 return;
             end        
         else
+
             base_path           = anatomy_type.base_path;
             subjects            = dir(base_path);
             subjects(ismember({subjects.name},{'.','..'}))           = [];  %remove . and ..
@@ -68,10 +69,9 @@
         subID        = subjects(sub).Name;
     else
         subID        = subjects(sub).name;
-    end 
-    CiftiStorm.Participants(end+1).SubID     = subID;
+    end     
     disp('==========================================================================');
-    disp(strcat('-->> Processing subject: ', subID));
+    disp(strcat('CFS -->> Processing subject: ', subID));
     disp('==========================================================================');    
 
     %%
@@ -90,7 +90,7 @@
     %% Process Import Anatomy
     %%
     disp("--------------------------------------------------------------------------");
-    disp("-->> Process Import Anatomy");
+    disp("CFS -->> Process Import Anatomy");
     disp("--------------------------------------------------------------------------");
     [CiftiStorm, CSurfaces] = process_import_anat(CiftiStorm, properties,subID);
     if(isequal(CiftiStorm.Participants(end).Status,'Rejected'));continue;end
@@ -99,7 +99,7 @@
     %% Process: Generate BEM surfaces
     %%
     disp("--------------------------------------------------------------------------");
-    disp("-->> Process Generate BEM surfaces");
+    disp("CFS -->> Process Generate BEM surfaces");
     disp("--------------------------------------------------------------------------");    
     [CiftiStorm, CSurfaces] = process_gen_bem_surfaces(CiftiStorm, properties, subID, CSurfaces);   
     if(isequal(CiftiStorm.Participants(end).Status,'Rejected'));continue;end
@@ -108,7 +108,7 @@
     %% Process: Transform surfaces
     %%
     disp("--------------------------------------------------------------------------");
-    disp("-->> Transform surfaces");
+    disp("CFS -->> Transform surfaces");
     disp("--------------------------------------------------------------------------");    
     [CiftiStorm, CSurfaces, sub_to_FSAve] = process_compute_surfaces(CiftiStorm, properties, subID, CSurfaces);
     if(isequal(CiftiStorm.Participants(end).Status,'Rejected'));continue;end
@@ -117,7 +117,7 @@
     %% Process: Import Atlas
     %%
     disp("--------------------------------------------------------------------------");
-    disp("-->> Process Import Atlas");
+    disp("CFS -->> Process Import Atlas");
     disp("--------------------------------------------------------------------------");
     CiftiStorm     = process_import_atlas(CiftiStorm, properties, subID, CSurfaces);
     if(isequal(CiftiStorm.Participants(end).Status,'Rejected'));continue;end
@@ -126,7 +126,7 @@
     %% Process: Generate SPM canonical surfaces
     %%
     disp("--------------------------------------------------------------------------");
-    disp("-->> Process Generate SPM canonical surfaces");
+    disp("CFS -->> Process Generate SPM canonical surfaces");
     disp("--------------------------------------------------------------------------");
     CiftiStorm      = process_canonical_surfaces(CiftiStorm, properties, subID);
     if(isequal(CiftiStorm.Participants(end).Status,'Rejected'));continue;end
@@ -135,7 +135,7 @@
     %% Process Import Channel
     %%
     disp("--------------------------------------------------------------------------");
-    disp("-->> Process Import Channel");
+    disp("CFS -->> Process Import Channel");
     disp("--------------------------------------------------------------------------");
     CiftiStorm   = process_import_chann(CiftiStorm, properties, subID, CSurfaces);
     if(isequal(CiftiStorm.Participants(end).Status,'Rejected'));continue;end
@@ -144,7 +144,7 @@
     %% Process: Compute Headmodel
     %%
     disp("--------------------------------------------------------------------------");
-    disp("-->> Process Compute HeadModel");
+    disp("CFS -->> Process Compute HeadModel");
     disp("--------------------------------------------------------------------------");
     CiftiStorm      = process_comp_headmodel(CiftiStorm, properties, subID, CSurfaces);
     if(isequal(CiftiStorm.Participants(end).Status,'Rejected'));continue;end
@@ -153,16 +153,24 @@
     %% Process: Export subject
     %%
     disp("--------------------------------------------------------------------------");
-    disp("-->> Process Export subject");
+    disp("CFS -->> Process Export subject");
     disp("--------------------------------------------------------------------------");
-    CiftiStorm      = process_export_subject(CiftiStorm,properties,subID);
+    CiftiStorm      = process_export_subject(CiftiStorm, properties, subID, CSurfaces, sub_to_FSAve);
     if(isequal(CiftiStorm.Participants(end).Status,'Rejected'));continue;end
 
-    disp(strcat('-->> Subject:' , subID, '. Processing finished.'));
+    disp(strcat('CFS -->> Subject:' , subID, '. Processing finished.'));
     disp('==========================================================================');    
 end
-disp(strcat('-->> Process finished....'));
+disp(strcat('CFS -->> Saving Dataset.'));
+disp('==============================================================================');
+datasetFile = fullfile(CiftiStorm.Location,'CiftiStorm.json');
+saveJSON(CiftiStorm,datasetFile);
+h = matlab.desktop.editor.openDocument(datasetFile);
+h.smartIndentContents
+h.save
+h.close
+
+disp(strcat('CFS -->> Dataset processed....'));
 disp('==============================================================================');
 disp('==============================================================================');
-save report.mat subjects_processed subjects_process_error;
 end

functions/export/export_subject_structure.m

@@ -22,10 +22,6 @@
     return;
 end
 
-%% Uploding Subject file into BrainStorm Protocol
-disp('BST-P ->> Uploading Subject file into BrainStorm Protocol.');
-disp('==========================================================================');
-
 %%
 %% Genering leadfield file
 %%
@@ -50,7 +46,7 @@
 %%
 %% Saving files in BC-VARETA Structure
 %%
-base_path = fullfile(output_path,'BC-V_Structure',ProtocolInfo.Comment);
+base_path = fullfile(output_path,'CiftiStorm',ProtocolInfo.Comment);
 save_output_files(base_path, modality, subID, HeadModels, Cdata, Shead, Sout, Sinn, Scortex);
 
 end

functions/processes/process_export_subject.m

@@ -1,15 +1,13 @@
 function CiftiStorm = process_export_subject(CiftiStorm, properties, subID, CSurfaces, sub_to_FSAve)
 
 errMessage      = [];
-ProtocolName    = general_params.bst_config.protocol_name;
-output_path     = general_params.output_path;
+ProtocolName    = properties.general_params.bst_config.protocol_name;
+output_path     = properties.general_params.output_path;
 
 %%
 %% Export subject from protocol
 %%
-disp("--------------------------------------------------------------------------");
 disp("-->> Export Subject from BST Protocol");
-disp("--------------------------------------------------------------------------");
 if(~isfolder(fullfile(output_path,'BST','Subjects',ProtocolName)))
     mkdir(fullfile(output_path,'BST','Subjects',ProtocolName));
 end
@@ -21,22 +19,15 @@
 %%
 %% Save and display report
 %%
-disp("--------------------------------------------------------------------------");
 disp("-->> Export BST Report");
-disp("--------------------------------------------------------------------------");
 report_path     = get_report_path(properties, subID);
 ReportFile      = bst_report('Save', []);
 bst_report('Export',  ReportFile, fullfile(report_path,[subID,'.html']));
-disp(strcat("-->> Process finished for subject: ",subID));
 
 %%
 %% Export Subject
 %%
-disp("--------------------------------------------------------------------------");
-disp("-->> Export to CiftiStorm");
-disp("--------------------------------------------------------------------------");
-
-disp(strcat('cfs -->> Export subject:' , subID));
+disp(strcat('-->> Export subject:' , subID));
 errMessage = export_subject_structure(properties, subID, CSurfaces, sub_to_FSAve);
 
 if(isempty(errMessage))

functions/starting_brainstorm.m

@@ -2,6 +2,8 @@
 %%
 %% Starting BrainStorm
 %%
+bst_path        = properties.general_params.bst_config.bst_path;
+addpath(genpath(bst_path));
 status = true;
 brainstorm reset
 brainstorm nogui local
@@ -16,7 +18,8 @@
 %%
 %% Loading BST modules
 %%
-disp("-->> Installing external plugins.");
+disp('==========================================================================');
+disp("CFS -->> Installing external plugins.");
 disp('==========================================================================');
 if(~isempty(bst_plugin('GetInstalled', 'spm12')))
     [isOk, errMsg, PlugDesc] = bst_plugin('Unload', 'spm12');

tools/BC-VARETA/dataConverter/download_testdata.m

@@ -7,7 +7,7 @@
 if(~isfolder(fullfile(pwd,'data')) && isequal(testDataPath,fullfile(pwd,'data')))
     mkdir(fullfile(pwd,'data'));
 end
-dafaultWorkspace = fullfile(char(java.lang.System.getProperty('user.home')),"BC-VARETA_Structure");
+dafaultWorkspace = fullfile(char(java.lang.System.getProperty('user.home')),"CiftiStorm");
 if(~isfolder(BC_V_Workspace) && ~isequal(BC_V_Workspace,dafaultWorkspace))
     disp("The Workspace path is not a folder");
     return;