add function to identifyu source data

Author: Remi-Gau

src/spm_2_bids.m

@@ -56,7 +56,7 @@
 
     spec = [];
 
-    % TODO se if some of the bids-query machinery cannot be kept for identifying
+    % TODO see if some of the bids-query machinery cannot be kept for identifying
     % the right mapping
 
     % look for the right prefix in the mapping
@@ -136,7 +136,7 @@
     new_filename = bf.filename;
 
     json = bids.derivatives_json(bf.filename);
-    json.content.RawSources{1} = strrep(bf.filename, bf.prefix, '');
+    json.content.RawSources{1} = identify_rawsources(file, false);
 
 end
 

src/utils/identify_sources.m

@@ -0,0 +1,85 @@
+function sources = identify_sources(derivatives)
+    %
+    % finds the most likely files in the detrivatives that was used to create
+    % this file
+    %
+    % USAGE::
+    %
+    %   sources = identify_sources(derivatives, verbose)
+    %
+    % :param file: SPM preprocessed filename (can be fullpath);
+    %              for example ``wmsub-01_ses-01_T1w.nii``
+    % :type file: string
+    %
+    %
+    % (C) Copyright 2021 spm_2_bids developers
+
+    % "r" could mean realigned or resliced...
+    %     'sr'
+    %     'sra'
+    %     'wr'
+    %     'wra'
+
+    % TODO mean may involve several files from the source (across runs
+    % and sessions
+    %     prefixes = {
+    %                 'mean'
+    %                 'meanu'
+    %                 'meanua'
+    %                 'wmeanu'
+    %                };
+
+    sources = '';
+
+    prefix_based = true;
+
+    if nargin < 1 || isempty(derivatives)
+        return
+    end
+
+    if endsWith(derivatives, '_seg8.mat')
+
+        prefix_based = false;
+
+        derivatives = strrep(derivatives, '_seg8.mat', '.nii');
+
+    elseif endsWith(derivatives, '_uw.mat')
+
+        prefix_based = false;
+
+        derivatives = strrep(derivatives, '_uw.mat', '.nii');
+
+    end
+
+    bf = bids.File(derivatives);
+
+    if prefix_based
+        if numel(bf.prefix) < 2
+            % needs at least 2 characters for this file to have some provenance in the
+            % derivatives
+            return
+
+        else
+            % remove the prefix of the last step
+
+            if startsWith(bf.prefix, 's') || startsWith(bf.prefix, 'w')
+                bf.prefix = bf.prefix(2:end);
+
+            elseif startsWith(bf.prefix, 'rp_a')
+                bf.prefix = bf.prefix(4:end);
+
+            else
+                % no idea
+                return
+
+            end
+
+        end
+    end
+
+    % call spm_2_bids what is the filename from the previous step
+    [new_filename] = spm_2_bids(bf.filename);
+
+    sources = fullfile(bf.bids_path, new_filename);
+
+end

tests/test_identify_sources.m

@@ -0,0 +1,73 @@
+% (C) Copyright 2022 spm_2_bids developers
+
+function test_suite = test_identify_sources %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
+
+function test_identify_sources_anat()
+
+    anat_file = 'sub-01_T1w.nii';
+
+    prefix_output = {'wm', 'sub-01/sub-01_space-individual_desc-biascor_T1w.nii'
+                     'wc1', 'sub-01/sub-01_space-individual_label-GM_probseg.nii'
+                     'wc2', 'sub-01/sub-01_space-individual_label-WM_probseg.nii'
+                     'wc3', 'sub-01/sub-01_space-individual_label-CSF_probseg.nii'
+                    };
+
+    for i  = 1:size(prefix_output, 1)
+
+        sources = identify_sources([prefix_output{i, 1} anat_file]);
+
+        assertEqual(sources, prefix_output{i, 2});
+
+    end
+
+end
+
+function test_identify_sources_func()
+
+    func_file = 'sub-01_task-auditory_bold.nii';
+
+    prefix_output = {
+                     'rp_a', 'sub-01_task-auditory_space-individual_desc-stc_bold.nii'
+                     'wua', 'sub-01_task-auditory_space-individual_desc-realignUnwarp_bold.nii'
+                     'wu', 'sub-01_task-auditory_space-individual_desc-realignUnwarp_bold.nii'
+                     'sw', 'sub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii'
+                     'swua', 'sub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii'
+                     'swu', 'sub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii'
+                     'swr', 'sub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii'
+                     'swra', 'sub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii'
+                     'sua', 'sub-01_task-auditory_space-individual_desc-realignUnwarp_bold.nii'
+                     'su', 'sub-01_task-auditory_space-individual_desc-realignUnwarp_bold.nii'
+                    };
+
+    for i  = 1:size(prefix_output, 1)
+
+        sources = identify_sources([prefix_output{i, 1} func_file]);
+
+        assertEqual(sources, fullfile('sub-01', prefix_output{i, 2}));
+
+    end
+
+end
+
+function test_identify_sources_suffix()
+
+    input_output = {'msub-01_T1w_seg8.mat', ...
+                    'sub-01_space-individual_desc-biascor_T1w.nii'
+                    'asub-01_task-foo_bold_uw.mat', ...
+                    'sub-01_task-foo_space-individual_desc-stc_bold.nii'};
+
+    for i = 1:size(input_output, 1)
+
+        sources = identify_sources(input_output{i, 1});
+
+        assertEqual(sources, ['sub-01/' input_output{i, 2}]);
+
+    end
+
+end

tests/test_spm_2_bids_metadata.m

@@ -0,0 +1,21 @@
+% (C) Copyright 2021 spm_2_bids developers
+
+function test_suite = test_spm_2_bids_metadata %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
+
+function test_spm_2_bids_metadata_basic()
+
+    file = 'wmsub-01_T1w.nii';
+
+    [~, ~, json] = spm_2_bids(file);
+
+    assertEqual(fieldnames(json), {'filename'; 'content'});
+    assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_T1w.nii');
+    assertEqual(json.content.Sources{1}, {'sub-01_desc-biasCorected_T1w.nii'});
+
+end