[INFRA] add tests

.gitignore

@@ -19,16 +19,20 @@ demos/MoAE/output/*
 demos/spm*/raw
 demos/spm*/source
 
-# test folder
+# test folder and dummy data
 tests/sub-01/*
 tests/group/*
 tests/models/*.json
+tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.nii
+tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.tsv
+tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.txt
+tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.json
+tests/dummyData/derivatives/cpp_spm/sub-*/stats/*/*/*.nii
 
 # ignore content of the build folder of the doc
 docs/build/*
 
 # ignore virtual env
-cpp_bids_spm/*
 cpp_spm/*
 
 # visual studio code stuff

.travis.yml

@@ -69,7 +69,12 @@ jobs:
         - mkdir $output_folder
         - curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $output_folder'MoAEpilot.zip'
         - unzip $output_folder'MoAEpilot.zip' -d $output_folder
-
+
+        # generate dummy data
+        - cd tests
+        - sh createDummyDataSet.sh
+        - cd ..
+
       script:
         - octave $OCTFLAGS --eval "runTests"
         - cat test_report.log | grep 0

docs/source/conf.py

@@ -17,9 +17,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'CPP BIDS SPM'
-copyright = '2020, the CPP BIDS SPM pipeline dev team'
-author = 'the CPP BIDS SPM pipeline dev team'
+project = 'CPP SPM'
+copyright = '2020, the CPP SPM pipeline dev team'
+author = 'the CPP SPM pipeline dev team'
 
 # The full version, including alpha/beta/rc tags
 release = 'v0.1.0'

manualTests/test_setBatchCoregistrationFmap.m

@@ -0,0 +1,63 @@
+function test_suite = test_setBatchCoregistrationFmap %#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_setBatchCoregistrationFmapBasic()
+
+  subID = '01';
+
+  opt.taskName = 'vismotion';
+  opt.derivativesDir = fullfile(fileparts(mfilename('fullpath')), 'dummyData');
+
+  opt = checkOptions(opt);
+
+  [~, opt, BIDS] = getData(opt);
+
+  matlabbatch = [];
+  matlabbatch = setBatchCoregistrationFmap(matlabbatch, BIDS, opt, subID);
+
+  directory = fullfile(opt.derivativesDir, ...
+                       'sub-01', ...
+                       'ses-01');
+  ref = fullfile(directory, ...
+                 'func', ...
+                 'mean_sub-01_ses-01_task-vismotion_run-1_bold.nii');
+
+  expectedbatch = [];
+
+  src = fullfile(directory, ...
+                 'fmap', ...
+                 'sub-01_ses-01_run-2_magnitude1.nii');
+  other = {fullfile(directory, ...
+                    'fmap', ...
+                    'sub-01_ses-01_run-2_magnitude2.nii'); ...
+           fullfile(directory, ...
+                    'fmap', ...
+                    'sub-01_ses-01_run-2_phasediff.nii')};
+  expectedbatch{end + 1}.spm.spatial.coreg.estimate.ref = { ref };
+  expectedbatch{end}.spm.spatial.coreg.estimate.source = { src };
+  expectedbatch{end}.spm.spatial.coreg.estimate.other = other;
+
+  directory = fullfile(opt.derivativesDir, ...
+                       'sub-01', ...
+                       'ses-02');
+  src = fullfile(directory, ...
+                 'fmap', ...
+                 'sub-01_ses-02_run-2_magnitude1.nii');
+  other = {fullfile(directory, ...
+                    'fmap', ...
+                    'sub-01_ses-02_run-2_magnitude2.nii'); ...
+           fullfile(directory, ...
+                    'fmap', ...
+                    'sub-01_ses-02_run-2_phasediff.nii')};
+  expectedbatch{end + 1}.spm.spatial.coreg.estimate.ref = { ref };
+  expectedbatch{end}.spm.spatial.coreg.estimate.source = { src };
+  expectedbatch{end}.spm.spatial.coreg.estimate.other = other;
+
+  assertEqual(matlabbatch, expectedbatch);
+
+end

manualTests/test_setBatchCreateVDMs.m

@@ -0,0 +1,30 @@
+function test_suite = test_setBatchCreateVDMs %#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_setBatchCreateVDMsBasic()
+
+  subID = '01';
+
+  opt.taskName = 'vismotion';
+  opt.derivativesDir = fullfile(fileparts(mfilename('fullpath')), 'dummyData');
+  opt.taskName = 'vismotion';
+
+  opt = checkOptions(opt);
+
+  [~, opt, BIDS] = getData(opt);
+
+  matlabbatch = [];
+  matlabbatch = setBatchCreateVDMs(matlabbatch, BIDS, opt, subID);
+
+  %   matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj
+
+  %   expectedBatch = returnExpectedBatch(refImage);
+  %
+  %   assertEqual(matlabbatch, expectedBatch);
+
+end

src/batches/setBatch3Dto4D.m

@@ -1,30 +1,52 @@
 % (C) Copyright 2020 CPP BIDS SPM-pipeline developers
 
-function matlabbatch = setBatch3Dto4D(volumesList, outputName, dataType, RT)
+function matlabbatch = setBatch3Dto4D(matlabbatch, volumesList, RT, outputName, dataType)
   %
   % Set the batch for 3D to 4D conversion
   %
   % USAGE::
   %
-  %   matlabbatch = setBatch3Dto4D(volumesList, outputName, dataType, RT)
+  %   matlabbatch = setBatch3Dto4D(matlabbatch, volumesList, RT, [outputName], [dataType])
   %
+  % :param matlabbatch:
+  % :type matlabbatch: structure
   % :param volumesList: List of volumes to be converted in a single 4D brain
   % :type volumesList: array
-  % :param outputName: Obligatory argument. The string that will be used to save the 4D brain
+  % :param outputName: The string that will be used to save the 4D brain
   % :type outputName: string
-  % :param dataType: Obligatory argument. It identifies the data format conversion
+  % :param dataType: It identifies the data format conversion
   % :type dataType: integer
-  % :param RT: Obligatory argument. It identifies the TR in secof the volumes to be written in the
-  %            4D file header
+  % :param RT: It identifies the TR in seconds of the volumes
+  %            to be written in the 4D file header
   % :type RT: float
   %
   % :returns: - :matlabbatch: (structure) The matlabbatch ready to run the spm job
+  %
+  % ``dataType``:
+  %
+  %   - 0:  SAME
+  %   - 2:  UINT8   - unsigned char
+  %   - 4:  INT16   - signed short
+  %   - 8:  INT32   - signed int
+  %   - 16: FLOAT32 - single prec. float
+  %   - 64: FLOAT64 - double prec. float
+  %
+
+  if nargin < 5 || isempty(dataType)
+    dataType = 0;
+  end
+
+  if nargin < 4 || isempty(outputName)
+    outputName = deblank(volumesList(1, :));
+    [pth, filename, ext] = spm_fileparts(outputName);
+    outputName = fullfile(pth, [filename, '_4D', ext]);
+  end
 
-  fprintf(1, 'PREPARING: 3D to 4D conversion\n');
+  printBatchName('3D to 4D conversion');
 
-  matlabbatch{1}.spm.util.cat.vols = volumesList;
-  matlabbatch{1}.spm.util.cat.name = outputName;
-  matlabbatch{1}.spm.util.cat.dtype = dataType;
-  matlabbatch{1}.spm.util.cat.RT = RT;
+  matlabbatch{end + 1}.spm.util.cat.vols = volumesList;
+  matlabbatch{end}.spm.util.cat.name = outputName;
+  matlabbatch{end}.spm.util.cat.dtype = dataType;
+  matlabbatch{end}.spm.util.cat.RT = RT;
 
 end

src/batches/setBatchComputeVDM.m

@@ -6,7 +6,7 @@
   %
   % USAGE::
   %
-  %   [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3])
+  %   matlabbatch = setBatchComputeVDM(matlabbatch, fmapType, refImage)
   %
   % :param matlabbatch: list of SPM batches
   % :type matlabbatch: structure
@@ -28,7 +28,7 @@
       matlabbatch{end}.spm.tools.fieldmap.calculatevdm.subj(1).data.presubphasemag.magnitude = '';
 
     case 'phase&mag'
-      matlabbatch{end}.spm.tools.fieldmap.calculatevdm.subj(1).data.phasemag.shortphase = '';
+      matlabbatch{end + 1}.spm.tools.fieldmap.calculatevdm.subj(1).data.phasemag.shortphase = '';
       matlabbatch{end}.spm.tools.fieldmap.calculatevdm.subj(1).data.phasemag.shortmag = '';
       matlabbatch{end}.spm.tools.fieldmap.calculatevdm.subj(1).data.phasemag.longphase = '';
       matlabbatch{end}.spm.tools.fieldmap.calculatevdm.subj(1).data.phasemag.longmag = '';

src/batches/setBatchContrasts.m

@@ -0,0 +1,27 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
+
+function matlabbatch = setBatchContrasts(matlabbatch, spmMatFile, consess)
+  %
+  % Short description of what the function does goes here.
+  %
+  % USAGE::
+  %
+  %   matlabbatch = setBatchContrasts(matlabbatch, spmMatFile, consess)
+  %
+  % :param matlabbatch:
+  % :type matlabbatch: structure
+  % :param spmMatFile:
+  % :type spmMatFile: string
+  % :param consess:
+  % :type consess: cell
+  %
+  % :returns: - :matlabbatch: (structure)
+  %
+
+  printBatchName('contrasts specification');
+
+  matlabbatch{end + 1}.spm.stats.con.spmmat = spmMatFile;
+  matlabbatch{end}.spm.stats.con.consess = consess;
+  matlabbatch{end}.spm.stats.con.delete = 1;
+
+end

src/batches/setBatchCoregistrationFmap.m

@@ -1,70 +1,71 @@
 % (C) Copyright 2020 CPP BIDS SPM-pipeline developers
 
-function matlabbatch = setBatchCoregistrationFmap(BIDS, opt, subID)
-  %
-  % Set the batch for the coregistration of field maps
-  %
-  % USAGE::
-  %
-  %   [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3])
-  %
-  % :param BIDS: BIDS layout returned by ``getData``.
-  % :type BIDS: structure
-  % :param opt: structure or json filename containing the options. See
-  %             ``checkOptions()`` and ``loadAndCheckOptions()``.
-  % :type opt: structure
-  % :param subID: subject ID
-  % :type subID: string
-  %
-  % :returns: - :matlabbatch: (structure) The matlabbatch ready to run the spm job
-  %
-
-  % TODO
-  % assumes all the fieldmap relate to the current task
-  % - use the "for" metadata field
-  % - implement for 'phase12', 'fieldmap', 'epi'
-
-  printBatchName('coregister fieldmaps data to functional');
-
-  % Create rough mean of the 1rst run to improve SNR for coregistration
-  % TODO use the slice timed EPI if STC was used ?
-  [sessions, nbSessions] = getInfo(BIDS, subID, opt, 'Sessions');
-  runs = getInfo(BIDS, subID, opt, 'Runs', sessions{1});
-  [fileName, subFuncDataDir] = getBoldFilename(BIDS, subID, sessions{1}, runs{1}, opt);
-
-  spmup_basics(fullfile(subFuncDataDir, fileName), 'mean');
-
-  refImage = fullfile(subFuncDataDir, ['mean_', fileName]);
-
-  matlabbatch = [];
-
-  for iSes = 1:nbSessions
-
-    runs = bids.query(BIDS, 'runs', ...
-                      'modality', 'fmap', ...
-                      'sub', subID, ...
-                      'ses', sessions{iSes});
-
-    for iRun = 1:numel(runs)
-
-      % TODO
-      % - Move to getInfo
-      fmapFiles = bids.query(BIDS, 'data', ...
-                             'modality', 'fmap', ...
-                             'sub', subID, ...
-                             'ses', sessions{iSes}, ...
-                             'run', runs{iRun});
-
-      srcImage = strrep(fmapFiles{1}, 'phasediff', 'magnitude1');
-
-      otherImages = cell(2, 1);
-      otherImages{1} = strrep(fmapFiles{1}, 'phasediff', 'magnitude2');
-      otherImages{2} = fmapFiles{1};
-
-      matlabbatch = setBatchCoregistration(matlabbatch, refImage, srcImage, otherImages);
-
+function matlabbatch = setBatchCoregistrationFmap(matlabbatch, BIDS, opt, subID)
+    %
+    % Set the batch for the coregistration of field maps
+    %
+    % USAGE::
+    %
+    %   matlabbatch = setBatchCoregistrationFmap(matlabbatch, BIDS, opt, subID)
+    %
+    % :param BIDS: BIDS layout returned by ``getData``.
+    % :type BIDS: structure
+    % :param opt: structure or json filename containing the options. See
+    %             ``checkOptions()`` and ``loadAndCheckOptions()``.
+    % :type opt: structure
+    % :param subID: subject ID
+    % :type subID: string
+    %
+    % :returns: - :matlabbatch: (structure) The matlabbatch ready to run the spm job
+    %
+
+    % TODO
+    % - implement for 'phase12', 'fieldmap', 'epi'
+
+    printBatchName('coregister fieldmaps data to functional');
+
+    % Use a rough mean of the 1rst run to improve SNR for coregistration
+    % created by spmup
+    [sessions, nbSessions] = getInfo(BIDS, subID, opt, 'Sessions');
+    runs = getInfo(BIDS, subID, opt, 'Runs', sessions{1});
+    [fileName, subFuncDataDir] = getBoldFilename(BIDS, subID, sessions{1}, runs{1}, opt);
+    refImage = validationInputFile(subFuncDataDir, fileName, 'mean_');
+
+    for iSes = 1:nbSessions
+
+        runs = bids.query(BIDS, 'runs', ...
+            'modality', 'fmap', ...
+            'sub', subID, ...
+            'ses', sessions{iSes});
+
+        for iRun = 1:numel(runs)
+
+            metadata = bids.query(BIDS, 'metadata', ...
+                'modality', 'fmap', ...
+                'sub', subID, ...
+                'ses', sessions{iSes}, ...
+                'run', runs{iRun});
+
+            if strfind(metadata.IntendedFor, opt.taskName)
+
+                fmapFiles = bids.query(BIDS, 'data', ...
+                    'modality', 'fmap', ...
+                    'sub', subID, ...
+                    'ses', sessions{iSes}, ...
+                    'run', runs{iRun});
+
+                srcImage = strrep(fmapFiles{1}, 'phasediff', 'magnitude1');
+
+                otherImages = cell(2, 1);
+                otherImages{1} = strrep(fmapFiles{1}, 'phasediff', 'magnitude2');
+                otherImages{2} = fmapFiles{1};
+
+                matlabbatch = setBatchCoregistration(matlabbatch, refImage, srcImage, otherImages);
+
+            end
+
+        end
+
     end
-
-  end
-
+
 end