add parfor loop into bidsSpatialPrep

.all-contributorsrc

@@ -17,6 +17,7 @@
         "doc"
       ]
     },
+    {
       "login": "anege",
       "name": "anege",
       "avatar_url": "https://avatars0.githubusercontent.com/u/50317099?v=4",
@@ -26,6 +27,7 @@
         "design"
       ]
     },
+    {
       "login": "mohmdrezk",
       "name": "Mohamed Rezk",
       "avatar_url": "https://avatars2.githubusercontent.com/u/9597815?v=4",
@@ -36,6 +38,7 @@
         "design"
       ]
     },
+    {
       "login": "marcobarilari",
       "name": "marcobarilari",
       "avatar_url": "https://avatars3.githubusercontent.com/u/38101692?v=4",
@@ -44,7 +47,9 @@
         "code",
         "design",
         "review",
-        "doc"
+        "doc",
+        "test",
+        "bug"
       ]
     },
     {
@@ -57,13 +62,35 @@
         "doc",
         "infra",
         "design",
-        "review"
+        "review",
+        "bug"
+      ]
+    },
+    {
+      "login": "fedefalag",
+      "name": "Fede F.",
+      "avatar_url": "https://avatars2.githubusercontent.com/u/50373329?v=4",
+      "profile": "https://github.com/fedefalag",
+      "contributions": [
+        "bug"
+      ]
+    },
+    {
+      "login": "CerenB",
+      "name": "CerenB",
+      "avatar_url": "https://avatars1.githubusercontent.com/u/10451654?v=4",
+      "profile": "https://github.com/CerenB",
+      "contributions": [
+        "bug",
+        "content",
+        "doc"
       ]
     }
   ],
   "contributorsPerLine": 7,
-  "projectName": "CPP_BIDS_SPM_pipeline",
+  "projectName": "CPP_SPM",
   "projectOwner": "cpp-lln-lab",
   "repoType": "github",
-  "repoHost": "https://github.com"
+  "repoHost": "https://github.com",
+  "skipCi": true
 }

README.md

@@ -21,9 +21,7 @@
 **Contributors**
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-
-[![All Contributors](https://img.shields.io/badge/all_contributors-5-orange.svg?style=flat-square)](#contributors)
-
+[![All Contributors](https://img.shields.io/badge/all_contributors-7-orange.svg?style=flat-square)](#contributors-)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 <!-- lint enable -->
@@ -101,17 +99,22 @@ Thanks goes to these wonderful people
 ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
 
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
-<!-- lint disable -->
+<!-- prettier-ignore-start -->
+<!-- markdownlint-disable -->
 <table>
   <tr>
-    <td align="center"><a href="https://cpplab.be"><img src="https://avatars0.githubusercontent.com/u/55407947?v=4" width="100px;" alt="OliColli"/><br /><sub><b>OliColli</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline/commits?author=OliColli" title="Code">💻</a> <a href="#design-OliColli" title="Design">🎨</a> <a href="https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline/commits?author=OliColli" title="Documentation">📖</a></td>
-    <td align="center"><a href="https://github.com/anege"><img src="https://avatars0.githubusercontent.com/u/50317099?v=4" width="100px;" alt="anege"/><br /><sub><b>anege</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline/commits?author=anege" title="Code">💻</a> <a href="#design-anege" title="Design">🎨</a></td>
-    <td align="center"><a href="https://github.com/mohmdrezk"><img src="https://avatars2.githubusercontent.com/u/9597815?v=4" width="100px;" alt="Mohamed Rezk"/><br /><sub><b>Mohamed Rezk</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline/commits?author=mohmdrezk" title="Code">💻</a> <a href="#review-mohmdrezk" title="Reviewed Pull Requests">👀</a> <a href="#design-mohmdrezk" title="Design">🎨</a></td>
-    <td align="center"><a href="https://github.com/marcobarilari"><img src="https://avatars3.githubusercontent.com/u/38101692?v=4" width="100px;" alt="marcobarilari"/><br /><sub><b>marcobarilari</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline/commits?author=marcobarilari" title="Code">💻</a> <a href="#design-marcobarilari" title="Design">🎨</a> <a href="#review-marcobarilari" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline/commits?author=marcobarilari" title="Documentation">📖</a></td>
-    <td align="center"><a href="https://remi-gau.github.io/"><img src="https://avatars3.githubusercontent.com/u/6961185?v=4" width="100px;" alt="Remi Gau"/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline/commits?author=Remi-Gau" title="Code">💻</a> <a href="https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline/commits?author=Remi-Gau" title="Documentation">📖</a> <a href="#infra-Remi-Gau" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#design-Remi-Gau" title="Design">🎨</a> <a href="#review-mohmdrezk" title="Reviewed Pull Requests">👀</a></td>
+    <td align="center"><a href="https://cpplab.be"><img src="https://avatars0.githubusercontent.com/u/55407947?v=4" width="100px;" alt=""/><br /><sub><b>OliColli</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=OliColli" title="Code">💻</a> <a href="#design-OliColli" title="Design">🎨</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=OliColli" title="Documentation">📖</a></td>
+    <td align="center"><a href="https://github.com/anege"><img src="https://avatars0.githubusercontent.com/u/50317099?v=4" width="100px;" alt=""/><br /><sub><b>anege</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=anege" title="Code">💻</a> <a href="#design-anege" title="Design">🎨</a></td>
+    <td align="center"><a href="https://github.com/mohmdrezk"><img src="https://avatars2.githubusercontent.com/u/9597815?v=4" width="100px;" alt=""/><br /><sub><b>Mohamed Rezk</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=mohmdrezk" title="Code">💻</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/pulls?q=is%3Apr+reviewed-by%3Amohmdrezk" title="Reviewed Pull Requests">👀</a> <a href="#design-mohmdrezk" title="Design">🎨</a></td>
+    <td align="center"><a href="https://github.com/marcobarilari"><img src="https://avatars3.githubusercontent.com/u/38101692?v=4" width="100px;" alt=""/><br /><sub><b>marcobarilari</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=marcobarilari" title="Code">💻</a> <a href="#design-marcobarilari" title="Design">🎨</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/pulls?q=is%3Apr+reviewed-by%3Amarcobarilari" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=marcobarilari" title="Documentation">📖</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=marcobarilari" title="Tests">⚠️</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/issues?q=author%3Amarcobarilari" title="Bug reports">🐛</a></td>
+    <td align="center"><a href="https://remi-gau.github.io/"><img src="https://avatars3.githubusercontent.com/u/6961185?v=4" width="100px;" alt=""/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=Remi-Gau" title="Code">💻</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=Remi-Gau" title="Documentation">📖</a> <a href="#infra-Remi-Gau" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#design-Remi-Gau" title="Design">🎨</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/pulls?q=is%3Apr+reviewed-by%3ARemi-Gau" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/issues?q=author%3ARemi-Gau" title="Bug reports">🐛</a></td>
+    <td align="center"><a href="https://github.com/fedefalag"><img src="https://avatars2.githubusercontent.com/u/50373329?v=4" width="100px;" alt=""/><br /><sub><b>Fede F.</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_SPM/issues?q=author%3Afedefalag" title="Bug reports">🐛</a></td>
+    <td align="center"><a href="https://github.com/CerenB"><img src="https://avatars1.githubusercontent.com/u/10451654?v=4" width="100px;" alt=""/><br /><sub><b>CerenB</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_SPM/issues?q=author%3ACerenB" title="Bug reports">🐛</a> <a href="#content-CerenB" title="Content">🖋</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=CerenB" title="Documentation">📖</a></td>
   </tr>
 </table>
-<!-- lint enable -->
+
+<!-- markdownlint-enable -->
+<!-- prettier-ignore-end -->
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
 This project follows the

src/utils/manageWorkersPool.m

@@ -20,7 +20,12 @@ function manageWorkersPool(action, opt)
   %    opt.parallelize.killOnExit = true;
   %
 
-  if ~isOctave() && opt.parallelize.do
+  if ~opt.parallelize.do
+    opt.parallelize.nbWorkers = 1;
+    opt.parallelize.killOnExit = true;
+  end
+
+  if ~isOctave()
 
     matlabVer = version('-release');
 
@@ -56,7 +61,11 @@ function manageWorkersPool(action, opt)
         if opt.parallelize.killOnExit
 
           if str2double(matlabVer(1:4)) > 2013
-            delete(gcp);
+
+            pool = gcp('nocreate');
+            if ~isempty(pool)
+              delete(gcp);
+            end
 
           else
             matlabpool close;

src/workflows/bidsSpatialPrepro.m

@@ -44,12 +44,20 @@ function bidsSpatialPrepro(opt)
 
   [BIDS, opt, group] = setUpWorkflow(opt, 'spatial preprocessing');
 
+  opt.orderBatches.selectAnat = 1;
+  opt.orderBatches.realign = 2;
+  opt.orderBatches.coregister = 3;
+  opt.orderBatches.saveCoregistrationMatrix = 4;
+  opt.orderBatches.segment = 5;
+  opt.orderBatches.skullStripping = 6;
+  opt.orderBatches.skullStrippingMask = 7;
+
   %% Loop through the groups, subjects, and sessions
   for iGroup = 1:length(group)
 
     groupName = group(iGroup).name;
 
-    for iSub = 1:group(iGroup).numSub
+    parfor iSub = 1:group(iGroup).numSub
 
       matlabbatch = [];
       % Get the ID of the subject
@@ -60,25 +68,21 @@ function bidsSpatialPrepro(opt)
       printProcessingSubject(groupName, iSub, subID);
 
       matlabbatch = setBatchSelectAnat(matlabbatch, BIDS, opt, subID);
-      opt.orderBatches.selectAnat = 1;
 
       % if action is emtpy then only realign will be done
       action = [];
       if ~opt.realign.useUnwarp
         action = 'realign';
       end
       [matlabbatch, voxDim] = setBatchRealign(matlabbatch, action, BIDS, opt, subID);
-      opt.orderBatches.realign = 2;
 
       % dependency from file selector ('Anatomical')
       matlabbatch = setBatchCoregistrationFuncToAnat(matlabbatch, BIDS, opt, subID);
-      opt.orderBatches.coregister = 3;
 
       matlabbatch = setBatchSaveCoregistrationMatrix(matlabbatch, BIDS, opt, subID);
 
       % dependency from file selector ('Anatomical')
       matlabbatch = setBatchSegmentation(matlabbatch, opt);
-      opt.orderBatches.segment = 5;
 
       matlabbatch = setBatchSkullStripping(matlabbatch, BIDS, opt, subID);
 

tests/test_manageWorkersPool.m

@@ -0,0 +1,69 @@
+function test_suite = test_manageWorkersPool %#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_manageWorkersPoolBasic()
+
+  opt.parallelize.do = true;
+  opt.parallelize.nbWorkers = 3;
+  opt.parallelize.killOnExit = true;
+
+  matlabVer = version('-release');
+
+  manageWorkersPool('close', opt);
+
+  manageWorkersPool('open', opt);
+
+  if ~isOctave()
+    if str2double(matlabVer(1:4)) > 2013
+
+      pool = gcp('nocreate');
+      nbWorkers = pool.NumWorkers;
+
+    else
+      nbWorkers = matlabpool('size'); %#ok<DPOOL>
+
+    end
+
+    manageWorkersPool('close', opt);
+
+    assertEqual(nbWorkers, opt.parallelize.nbWorkers);
+
+  end
+
+end
+
+function test_manageWorkersPoolNoParallel()
+
+  opt.parallelize.do = false;
+  opt.parallelize.nbWorkers = 3;
+  opt.parallelize.killOnExit = true;
+
+  matlabVer = version('-release');
+
+  manageWorkersPool('close', opt);
+
+  manageWorkersPool('open', opt);
+
+  if ~isOctave()
+    if str2double(matlabVer(1:4)) > 2013
+
+      pool = gcp('nocreate');
+      nbWorkers = pool.NumWorkers;
+
+    else
+      nbWorkers = matlabpool('size'); %#ok<DPOOL>
+
+    end
+
+    manageWorkersPool('close', opt);
+
+    assertEqual(nbWorkers, 1);
+
+  end
+
+end