[ENH] add model selection to CLI (#1121)

* update submod * [DATALAD] Recorded changes * [DATALAD] Recorded changes * minor work on cli * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix some tests * more fixes * add folders * start implementing bms * fix system test * loop over models * rm models * generate models * update bids matlab * Apply suggestions from code review * fix bug * fix test * refacrtor * refactor * add basic error handling * fix test * fix and doc * fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * move space to each action cli * add use_dummy_regressor arg * [DATALAD] Recorded changes * move space to each action cli * [DATALAD] Recorded changes * update fields name, fix failing tests, add arg displaying function * refactor CI * FCI * smooth bms data * use the proper task * use dummy regressor argument * [DATALAD] Recorded changes * use proper argument * fix passing or use fummy argument --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
cpp-lln-lab · Aug 11, 2023 · b7ebdc9 · b7ebdc9
1 parent 0d1ecae
commit b7ebdc9
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Showing 75 changed files with 1,038 additions and 373 deletions.
diff --git a/.github/workflows/system_tests_bms.m b/.github/workflows/system_tests_bms.m
@@ -0,0 +1,12 @@
+%
+% (C) Copyright 2023 bidspm developers
+
+root_dir = getenv('GITHUB_WORKSPACE');
+
+fprintf('\nroot dir is %s\n', root_dir);
+
+addpath(fullfile(root_dir, 'spm12'));
+
+cd(fullfile(root_dir, 'demos', 'bayes'));
+
+run ds000114_run;
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -43,6 +43,10 @@ jobs:
         os: [ubuntu-latest, macos-latest]
         matlab: [R2022b]
         include:
+        - test_type: system
+          script: bms
+          os: ubuntu-latest
+          matlab: R2022b
         - test_type: unit
           os: ubuntu-latest
           matlab: R2022b
@@ -59,12 +63,6 @@ jobs:
       if: matrix.test_type == 'system'
       run: echo ${{ matrix.test_type }} test ${{ matrix.script }}
 
-    - name: Install dependencies
-      if: matrix.os == 'ubuntu-latest'
-      run: |
-        sudo apt-get -y -qq update
-        sudo apt-get -y install unzip wget
-
     - name: Install Node
       uses: actions/setup-node@v3
       with:
@@ -75,6 +73,14 @@ jobs:
       with:
         python-version: '3.11'
 
+    - name: Install dependencies
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        sudo apt-get -y -qq update
+        sudo apt-get -y install unzip wget git-annex
+        python -m pip install --upgrade pip setuptools
+        pip install datalad
+
     - name: Clone bidspm
       uses: actions/checkout@v3
       with:
@@ -104,6 +110,10 @@ jobs:
         cd tests
         make data
 
+    - name: Get data for BMS
+      if: matrix.script == 'bms'
+      run: make -C demos/bayes data_ds000114
+
     - name: Install Moxunit and MOcov
       run: |
         git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
@@ -130,7 +140,6 @@ jobs:
         fail_ci_if_error: false
       # token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits
 
-
     - name: Run system tests MATLAB ${{ matrix.script }}
       if: matrix.test_type == 'system'
       uses: matlab-actions/run-command@v1.2.1

diff --git a/bidspm.m b/bidspm.m
@@ -6,7 +6,12 @@
   % (C) Copyright 2022 bidspm developers
 
   args = defaultInputParser();
-  parse(args, varargin{:});
+  try
+    parse(args, varargin{:});
+  catch ME
+    displayArguments(varargin{:});
+    rethrow(ME);
+  end
 
   action = args.Results.action;
 
@@ -45,7 +50,7 @@
 
     case 'help'
       system('bidspm --help');
-      help(fullfile(fileparts(mfilename('fullpath')), 'src', 'messages', 'bidspmHelp.m'));
+      help(fullfile(rootDir(), 'src', 'messages', 'bidspmHelp.m'));
 
     case 'version'
       versionBidspm();
@@ -77,9 +82,12 @@
     case 'default_model'
       cliDefaultModel(varargin{2:end});
 
-    case {'stats', 'contrasts', 'results'}
+    case {'stats', 'contrasts', 'results', 'specify_only'}
       cliStats(varargin{2:end});
 
+    case {'bms'}
+      cliBayesModel(varargin{2:end});
+
     case 'meaning_of_life'
       fprintf('\n42\n\n');
 
@@ -94,12 +102,25 @@
 
 end
 
+function displayArguments(varargin)
+  disp('arguments passed were :');
+  for i = 1:numel(varargin)
+    fprintf('- ');
+    disp(varargin{i});
+  end
+  fprintf(1, '\n');
+end
+
+function value = rootDir()
+  value = fullfile(fileparts(mfilename('fullpath')));
+end
+
 %% low level actions
 function versionBidspm()
   try
     versionNumber = getVersion();
   catch
-    versionNumber = fileread(fullfile(fileparts(mfilename('fullpath')), 'version.txt'));
+    versionNumber = fileread(rootDir(), 'version.txt');
     versionNumber = versionNumber(1:end - 1);
   end
   fprintf(1, '%s\n', versionNumber);
@@ -130,8 +151,6 @@ function initBidspm(dev)
   % octave packages
   installlist = {'io', 'statistics', 'image'};
 
-  thisDirectory = fileparts(mfilename('fullpath'));
-
   global BIDSPM_INITIALIZED
   global BIDSPM_PATHS
 
@@ -143,27 +162,27 @@ function initBidspm(dev)
     end
 
     % add bidspm source code
-    BIDSPM_PATHS = fullfile(thisDirectory);
+    BIDSPM_PATHS = fullfile(rootDir());
     BIDSPM_PATHS = cat(2, BIDSPM_PATHS, ...
                        pathSep, ...
-                       genpath(fullfile(thisDirectory, 'src')));
+                       genpath(fullfile(rootDir(), 'src')));
     if dev
       BIDSPM_PATHS = cat(2, BIDSPM_PATHS, pathSep, ...
-                         fullfile(thisDirectory, 'tests', 'utils'));
+                         fullfile(rootDir(), 'tests', 'utils'));
     end
 
     % for some reasons this folder was otherwise not added to the path in Octave
     BIDSPM_PATHS = cat(2, BIDSPM_PATHS, ...
                        pathSep, ...
-                       genpath(fullfile(thisDirectory, 'src', 'workflows', 'stats')));
+                       genpath(fullfile(rootDir(), 'src', 'workflows', 'stats')));
 
     % add library that do not have an set up script
     libList = {'spmup'};
 
     for i = 1:numel(libList)
       BIDSPM_PATHS = cat(2, BIDSPM_PATHS, ...
                          pathSep, ...
-                         genpath(fullfile(thisDirectory, 'lib', libList{i})));
+                         genpath(fullfile(rootDir(), 'lib', libList{i})));
     end
 
     libList = {'mancoreg', ...
@@ -173,23 +192,23 @@ function initBidspm(dev)
                'utils'};
     for i = 1:numel(libList)
       BIDSPM_PATHS = cat(2, BIDSPM_PATHS, pathSep, ...
-                         fullfile(thisDirectory, 'lib', libList{i}));
+                         fullfile(rootDir(), 'lib', libList{i}));
     end
 
     BIDSPM_PATHS = cat(2, BIDSPM_PATHS, pathSep, ...
-                       fullfile(thisDirectory, 'lib', 'brain_colours', 'code'));
+                       fullfile(rootDir(), 'lib', 'brain_colours', 'code'));
 
     BIDSPM_PATHS = cat(2, BIDSPM_PATHS, pathSep, ...
-                       fullfile(thisDirectory, 'lib', 'riksneurotools', 'GLM'));
+                       fullfile(rootDir(), 'lib', 'riksneurotools', 'GLM'));
 
     addpath(BIDSPM_PATHS, '-begin');
 
     silenceOctaveWarning();
 
     % add library that have a set up script
-    run(fullfile(thisDirectory, 'lib', 'CPP_ROI', 'initCppRoi'));
-    run(fullfile(thisDirectory, 'lib', 'spm_2_bids', 'init_spm_2_bids'));
-    run(fullfile(thisDirectory, 'lib', 'octache', 'setup'));
+    run(fullfile(rootDir(), 'lib', 'CPP_ROI', 'initCppRoi'));
+    run(fullfile(rootDir(), 'lib', 'spm_2_bids', 'init_spm_2_bids'));
+    run(fullfile(rootDir(), 'lib', 'octache', 'setup'));
 
     checkDependencies(opt);
     printCredits(opt);
@@ -248,8 +267,6 @@ function uninitBidspm()
 
   % (C) Copyright 2021 bidspm developers
 
-  thisDirectory = fileparts(mfilename('fullpath'));
-
   global BIDSPM_INITIALIZED
   global BIDSPM_PATHS
 
@@ -258,7 +275,7 @@ function uninitBidspm()
     return
 
   else
-    run(fullfile(thisDirectory, 'lib', 'CPP_ROI', 'uninitCppRoi'));
+    run(fullfile(rootDir(), 'lib', 'CPP_ROI', 'uninitCppRoi'));
     rmpath(BIDSPM_PATHS);
     spm('Clean');
     spm('Quit');
@@ -350,7 +367,9 @@ function update()
            'default_model'; ...
            'stats'; ...
            'contrasts'; ...
-           'results'};
+           'results'; ...
+           'specify_only', ...
+           'bms'};
 
 end
 

diff --git a/demos/MoAE/moae_01_bids_app.m b/demos/MoAE/moae_01_bids_app.m
@@ -124,7 +124,7 @@
 bidspm(bids_dir, output_dir, 'subject', ...
        'participant_label', {subject_label}, ...
        'action', 'preprocess', ...
-       'task', {'auditory'}, ...
+       'task', 'auditory', ...
        'ignore', {'unwarp', 'slicetiming'}, ...
        'space', {'IXI549Space'}, ...
        'fwhm', 6, ...

diff --git a/demos/MoAE/test_moae.m b/demos/MoAE/test_moae.m
@@ -24,7 +24,7 @@
 
 bidspm();
 if download_data
-  download_moae_ds(download_data, clean);
+  download_moae_ds(download_data, clean); %#ok<*UNRCH>
 end
 
 warning('off', 'SPM:noDisplay');
@@ -52,12 +52,12 @@
   %% preproc
   bids_dir = fullfile(WD, 'inputs', 'raw');
   output_dir = fullfile(tempname, 'outputs', 'derivatives');
-  mkdir(output_dir);
+  spm_mkdir(output_dir);
 
   bidspm(bids_dir, output_dir, 'subject', ...
          'participant_label', {'01'}, ...
          'action', 'preprocess', ...
-         'task', {'auditory'}, ...
+         'task', 'auditory', ...
          'ignore', ignore{iOption}, ...
          'space', space(iOption), ...
          'options', optionsFile);

diff --git a/demos/bayes/Makefile b/demos/bayes/Makefile
@@ -0,0 +1,11 @@
+.PHONY: clean data data_ds000001
+
+data_ds000114:
+	mkdir -p inputs
+	cd inputs && datalad install ///openneuro/ds000114
+	cd inputs && datalad install ///openneuro-derivatives/ds000114-fmriprep
+	cd inputs/ds000114-fmriprep && datalad get sub-*/anat/*MNI152NLin2009cAsym*desc-preproc*.nii.gz -J 12
+	cd inputs/ds000114-fmriprep && datalad get sub-*/ses-*/func/*tsv -J 12
+	cd inputs/ds000114-fmriprep && datalad get sub-*/ses-*/func/*json -J 12
+	cd inputs/ds000114-fmriprep && datalad get sub-*/ses-*/func/*overtverbgeneration*MNI152NLin2009cAsym*_mask.nii.gz -J 12
+	cd inputs/ds000114-fmriprep && datalad get sub-*/ses-*/func/*overtverbgeneration*MNI152NLin2009cAsym*desc-preproc*bold.nii.gz -J 12