Merge pull request #25 from cpp-lln-lab/fix_metadata

[FIX] various bug fixes in metadata creation

Author: Remi-Gau

.gitignore

@@ -12,6 +12,7 @@ lib/JSONio
 coverage_html
 coverage.xml
 test_report.log
+mapping.md
 
 ## MATLAB / OCTAVE gitignore template
 

miss_hit.cfg

@@ -17,5 +17,5 @@ copyright_entity: "spm_2_bids developers"
 # metric for code quality
 metric "cnest": limit 5
 metric "file_length": limit 500
-metric "cyc": limit 16
+metric "cyc": limit 20
 metric "parameters": limit 6

src/spm_2_bids.m

@@ -148,9 +148,20 @@
 
     json = bids.derivatives_json(bf.filename);
 
+    if strcmp(bf.suffix, 'probseg')
+        json.content.Manual = false;
+    end
+
     content = json.content;
+
     content.RawSources = identify_rawsources(file, verbose);
-    content.Sources = identify_sources(file, map, verbose);
+
+    Sources = identify_sources(file, map, verbose);
+    if ~isempty(Sources)
+        content.Sources = Sources;
+    elseif isfield(content, 'Sources')
+        content = rmfield(content, 'Sources');
+    end
 
     if isfield(bf.entities, 'space') && strcmp(bf.entities.space, 'IXI549Space')
         content.SpatialReference  = struct('IXI549Space', ...

src/utils/identify_rawsources.m

@@ -39,7 +39,7 @@
         derivatives = strrep(derivatives, '_uw.mat', '.nii');
     end
 
-    bf = bids.File(derivatives, 'verbose', verbose);
+    bf = bids.File(derivatives, 'verbose', verbose, 'use_schema', false);
 
     bf.prefix = '';
 

src/utils/identify_sources.m

@@ -102,7 +102,23 @@
         else
             % remove the prefix of the last step
 
-            if startsWith(bf.prefix, 's') || startsWith(bf.prefix, 'u')
+            if startsWith(bf.prefix, 's')
+
+                % in case the prefix includes a number to denotate the FXHM used
+                % for smoothing
+                starts_with_fwhm = regexp(bf.prefix, '^s[0-9]*', 'match');
+                if ~isempty(starts_with_fwhm)
+                    bf.prefix = bf.prefix(length(starts_with_fwhm{1}) + 1:end);
+                else
+                    bf.prefix = bf.prefix(2:end);
+                end
+
+            elseif ismember(bf.prefix(1:2), {'c1', 'c2', 'c3', 'c4', 'c5'})
+                % TODO bias corrected image
+                sources = 'TODO';
+                return
+
+            elseif startsWith(bf.prefix, 'u')
                 bf.prefix = bf.prefix(2:end);
 
             elseif startsWith(bf.prefix, 'w')
@@ -120,10 +136,12 @@
                 %                 'meanu'
                 %                 'meanua'
                 %                };
+                sources = 'TODO';
                 return
 
             else
                 % no idea
+                sources = 'TODO';
                 return
 
             end
@@ -136,6 +154,7 @@
 
     sources{1, 1} = fullfile(bf.bids_path, new_filename);
 
+    % for normalized images
     if add_deformation_field
 
         % for anatomical data we assume that

tests/test_identify_sources.m

@@ -8,6 +8,29 @@
     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'
+                     'wc1', 'sub-01/sub-01_space-individual_label-GM_probseg.nii'
+                    };
+
+    map = default_mapping();
+
+    for i  = 1:size(prefix_output, 1)
+
+        sources = identify_sources([prefix_output{i, 1} anat_file], map, false);
+
+        assertEqual(sources{1}, prefix_output{i, 2});
+
+    end
+
+end
+
 function test_identify_sources_func()
 
     func_file = 'sub-01_task-auditory_bold.nii';
@@ -60,28 +83,6 @@ function test_identify_sources_mean()
 
 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'
-                    };
-
-    map = default_mapping();
-
-    for i  = 1:size(prefix_output, 1)
-
-        sources = identify_sources([prefix_output{i, 1} anat_file], map, false);
-
-        assertEqual(sources{1}, prefix_output{i, 2});
-
-    end
-
-end
-
 function test_identify_sources_suffix()
 
     input_output = {'msub-01_T1w_seg8.mat', ...

tests/test_spm_2_bids_metadata.m

@@ -8,6 +8,49 @@
     initTestSuite;
 end
 
+function test_spm_2_bids_metadata_probseg()
+
+    file = 'c1sub-01_T1w.nii';
+
+    [~, ~, 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.Manual, false);
+
+    bids.util.jsonencode(json.filename, json.content);
+
+end
+
+function test_spm_2_bids_metadata_smoothed_data()
+
+    file = 's6wusub-01_task-auditory_bold.nii';
+
+    [~, ~, 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.Sources{1}, ...
+                'sub-01/sub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii');
+
+    bids.util.jsonencode(json.filename, json.content);
+
+end
+
+function test_spm_2_bids_metadata_source_must_be_empty()
+
+    file = 'msub-01_T1w.nii';
+
+    [~, ~, json] = spm_2_bids(file, [], false);
+
+    assertEqual(fieldnames(json), {'filename'; 'content'});
+    assertEqual(fieldnames(json.content), {'Description'; 'RawSources'; 'SpatialReference'});
+    assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_T1w.nii');
+
+    bids.util.jsonencode(json.filename, json.content);
+
+end
+
 function test_spm_2_bids_metadata_anat()
 
     file = 'wmsub-01_T1w.nii';