remove derivative entities for RawSources and assume they were gunzipped

Author: Remi-Gau

src/spm_2_bids.m

@@ -154,7 +154,7 @@
 
     content = json.content;
 
-    content.RawSources = identify_rawsources(file, verbose);
+    content.RawSources = identify_rawsources(file, map, verbose);
 
     Sources = identify_sources(file, map, verbose);
     if ~isempty(Sources)

src/utils/identify_rawsources.m

@@ -1,4 +1,4 @@
-function rawsource = identify_rawsources(derivatives, verbose)
+function rawsource = identify_rawsources(derivatives, map, verbose)
     %
     % find the most likely files in the raw dataset
     % that was used to create this derivatives
@@ -41,9 +41,21 @@
         derivatives = strrep(derivatives, '_uw.mat', '.nii');
     end
 
+    % - remove prefix
+    % - remove eventual derivatives entities
+    % - use only .nii.gz
     bf = bids.File(derivatives, 'verbose', verbose, 'use_schema', false);
 
     bf.prefix = '';
+    
+    entities = fieldnames(bf.entities);
+    idx = find(ismember(entities, map.cfg.entity_order));
+    for i = 1:numel(idx)
+      bf.entities.(entities{idx(i)}) = '';
+    end
+    if strcmp(bf.extension, '.nii')
+      bf.extension = '.nii.gz';
+    end
 
     rawsource{1} = fullfile(bf.bids_path, bf.filename);
 

tests/test_identify_rawsources.m

@@ -8,16 +8,36 @@
     initTestSuite;
 end
 
+function test_identify_rawsources_when_der_entities()
+
+    input_output = {'sub-01_desc-skullstripped_T1w.nii', 'sub-01_T1w.nii.gz'};
+
+    verbose = false;
+    
+    map = default_mapping();
+
+    for i = 1:size(input_output, 1)
+
+        rawsource = identify_rawsources(input_output{i, 1}, map, verbose);
+
+        assertEqual(rawsource, {['sub-01/' input_output{i, 2}]});
+
+    end
+
+end
+
 function test_identify_rawsources_suffix()
 
-    input_output = {'sub-01_T1w_seg8.mat', 'sub-01_T1w.nii'
-                    'sub-01_task-foo_bold_uw.mat', 'sub-01_task-foo_bold.nii'};
+    input_output = {'sub-01_T1w_seg8.mat', 'sub-01_T1w.nii.gz'
+                    'sub-01_task-foo_bold_uw.mat', 'sub-01_task-foo_bold.nii.gz'};
 
     verbose = false;
+    
+        map = default_mapping();
 
     for i = 1:size(input_output, 1)
 
-        rawsource = identify_rawsources(input_output{i, 1}, verbose);
+        rawsource = identify_rawsources(input_output{i, 1},  map, verbose);
 
         assertEqual(rawsource, {['sub-01/' input_output{i, 2}]});
 
@@ -43,14 +63,16 @@ function test_identify_rawsources_anat()
                };
 
     verbose = false;
+    
+        map = default_mapping();
 
     for i = 1:numel(prefixes)
 
         file = [prefixes{i} anat_file];
 
-        rawsource = identify_rawsources(fullfile(pwd, 'sub-01', file), verbose);
+        rawsource = identify_rawsources(fullfile(pwd, 'sub-01', file), map,  verbose);
 
-        assertEqual(rawsource, {'sub-01/sub-01_T1w.nii'});
+        assertEqual(rawsource, {'sub-01/sub-01_T1w.nii.gz'});
 
     end
 
@@ -82,14 +104,16 @@ function test_identify_rawsources_func()
                };
 
     verbose = false;
+    
+        map = default_mapping();
 
     for i = 1:numel(prefixes)
 
         file = [prefixes{i} func_file];
 
-        rawsource = identify_rawsources(file, verbose);
+        rawsource = identify_rawsources(file, map, verbose);
 
-        assertEqual(rawsource, {'sub-01/ses-02/sub-01_ses-02_task-foo_bold.nii'});
+        assertEqual(rawsource, {'sub-01/ses-02/sub-01_ses-02_task-foo_bold.nii.gz'});
 
     end
 

tests/test_spm_2_bids_metadata.m

@@ -15,7 +15,7 @@ function test_spm_2_bids_metadata_probseg()
     [~, ~, json] = spm_2_bids(file, [], false);
 
     assertEqual(fieldnames(json), {'filename'; 'content'});
-    assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_T1w.nii');
+    assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_T1w.nii.gz');
     assertEqual(json.content.Manual, false);
 
     bids.util.jsonencode(json.filename, json.content);
@@ -29,7 +29,7 @@ function test_spm_2_bids_metadata_smoothed_data()
     [~, ~, json] = spm_2_bids(file, [], false);
 
     assertEqual(fieldnames(json), {'filename'; 'content'});
-    assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_task-auditory_bold.nii');
+    assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_task-auditory_bold.nii.gz');
     assertEqual(json.content.Sources{1}, ...
                 'sub-01/sub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii');
 
@@ -45,7 +45,7 @@ function test_spm_2_bids_metadata_source_must_be_empty()
 
     assertEqual(fieldnames(json), {'filename'; 'content'});
     assertEqual(fieldnames(json.content), {'Description'; 'RawSources'; 'SpatialReference'});
-    assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_T1w.nii');
+    assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_T1w.nii.gz');
 
     bids.util.jsonencode(json.filename, json.content);
 
@@ -58,7 +58,7 @@ function test_spm_2_bids_metadata_anat()
     [~, ~, json] = spm_2_bids(file, [], false);
 
     assertEqual(fieldnames(json), {'filename'; 'content'});
-    assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_T1w.nii');
+    assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_T1w.nii.gz');
     assertEqual(json.content.Sources{1}, ...
                 'sub-01/sub-01_space-individual_desc-biascor_T1w.nii');
     assertEqual(json.content.Sources{2}, ...
@@ -75,7 +75,7 @@ function test_spm_2_bids_metadata_func()
     [~, ~, json] = spm_2_bids(file, [], false);
 
     assertEqual(fieldnames(json), {'filename'; 'content'});
-    assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_task-foo_bold.nii');
+    assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_task-foo_bold.nii.gz');
     assertEqual(json.content.Sources{1}, ...
                 'sub-01/sub-01_task-foo_space-individual_desc-realignUnwarp_bold.nii');
     assertEqual(json.content.Sources{2}, 'TODO: add deformation field');