Merge pull request #204 from Medical-Image-Analysis-Laboratory/v2.1.0

REL: MIALSRTK v2.1.0
Medical-Image-Analysis-Laboratory · Feb 2, 2023 · ecd37d5 · ecd37d5
2 parents e5626f6 + cce7cfc
commit ecd37d5
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -12,10 +12,13 @@
       "profile": "https://github.com/sebastientourbier",
       "contributions": [
         "design",
-        "test",
         "code",
+        "infra",
+        "test",
+        "bug",
         "example",
         "doc",
+        "ideas",
         "review"
       ]
     },
@@ -25,10 +28,13 @@
       "avatar_url": "https://avatars2.githubusercontent.com/u/19345763?v=4",
       "profile": "https://github.com/pdedumast",
       "contributions": [
+        "design",
         "example",
         "test",
         "code",
-        "doc"
+        "doc",
+        "ideas",
+        "review"
       ]
     },
     {
@@ -40,16 +46,23 @@
         "example",
         "test",
         "code",
-        "doc"
+        "doc",
+        "ideas"
       ]
     },
     {
-      "login": "meribach",
-      "name": "Meritxell Bach",
-      "avatar_url": "https://avatars3.githubusercontent.com/u/2786897?v=4",
-      "profile": "https://github.com/meribach",
+      "login": "t-sanchez",
+      "name": "Thomas Sanchez",
+      "avatar_url": "https://avatars.githubusercontent.com/u/14288440?v=4",
+      "profile": "http://t-sanchez.github.io",
       "contributions": [
-        "fundingFinding"
+        "bug",
+        "code",
+        "doc",
+        "example",
+        "ideas",
+        "infra",
+        "review"
       ]
     },
     {
@@ -72,12 +85,22 @@
         "data",
         "fundingFinding"
       ]
+    },
+    {
+      "login": "meribach",
+      "name": "Meritxell Bach",
+      "avatar_url": "https://avatars3.githubusercontent.com/u/2786897?v=4",
+      "profile": "https://github.com/meribach",
+      "contributions": [
+        "fundingFinding"
+      ]
     }
   ],
   "contributorsPerLine": 7,
   "projectName": "mialsuperresolutiontoolkit",
   "projectOwner": "Medical-Image-Analysis-Laboratory",
   "repoType": "github",
   "repoHost": "https://github.com",
-  "skipCi": true
+  "skipCi": true,
+  "commitConvention": "angular"
 }
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -807,14 +807,14 @@ workflows:
             tags:
               only: /^v.*/
 
-#      - deploy-singularity-latest:
-#          requires:
-#            - build-singularity
-#            # - build_docs
-#            - test-singularity
-#            - codacy-coverage-report
-#          filters:
-#            # ignore any commit on any branch by default
-#            branches:
-#              only: master
+      - deploy-singularity-latest:
+          requires:
+            - build-singularity
+            # - build_docs
+            - test-singularity
+            - codacy-coverage-report
+          filters:
+            # ignore any commit on any branch by default
+            branches:
+              only: master
 
diff --git a/.circleci/test-01_outputs.txt b/.circleci/test-01_outputs.txt
diff --git a/.circleci/test-02_outputs.txt b/.circleci/test-02_outputs.txt
diff --git a/.circleci/test-03_outputs.txt b/.circleci/test-03_outputs.txt
diff --git a/.circleci/test-04_outputs.txt b/.circleci/test-04_outputs.txt
diff --git a/.zenodo.json b/.zenodo.json
@@ -10,31 +10,40 @@
       "BIDS",
       "bids-apps"
     ],
-    "publication_date": "2020-12-24",
     "creators": [
       {
         "name": "Tourbier, Sebastien",
-        "affiliation": "Department of Radiology, Lausanne University Hospital (CHUV), Switzerland",
+        "affiliation": "Department of Clinical Neuroscience, Lausanne University Hospital (CHUV), Switzerland",
         "orcid": "0000-0002-4441-899X"
       },
       {
         "name": "De Dumast, Priscille",
-        "affiliation": "Department of Radiology, Lausanne University Hospital (CHUV), Switzerland",
+        "affiliation": "Department of Diagnostic and Interventional Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Switzerland; Center for Biomedical Imaging (CIBM), Switzerland",
         "orcid": "0000-0003-0359-9365"
       },
       {
         "name": "Kebiri, Hamza",
-        "affiliation": "Department of Radiology, Lausanne University Hospital (CHUV), Switzerland",
+        "affiliation": "Department of Diagnostic and Interventional Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Switzerland; Center for Biomedical Imaging (CIBM), Switzerland",
         "orcid": "0000-0001-7592-3166"
       },
+      {
+        "name": "Sanchez, Thomas",
+        "affiliation": "Department of Diagnostic and Interventional Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Switzerland; Center for Biomedical Imaging (CIBM), Switzerland",
+        "orcid": "0000-0003-3668-5155"
+      },
+      {
+        "name": "Lajous, Helene",
+        "affiliation": "Department of Diagnostic and Interventional Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Switzerland; Center for Biomedical Imaging (CIBM), Switzerland",
+        "orcid": "0000-0001-7729-6274"
+      },
       {
         "name": "Hagmann, Patric",
-        "affiliation": "Department of Radiology, Lausanne University Hospital (CHUV), Switzerland",
+        "affiliation": "Department of Diagnostic and Interventional Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Switzerland",
         "orcid": "0000-0002-2854-6561"
       },
       {
         "name": "Bach Cuadra, Meritxell",
-        "affiliation": "Department of Radiology, Lausanne University Hospital (CHUV), Switzerland",
+        "affiliation": "Department of Diagnostic and Interventional Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Switzerland; Center for Biomedical Imaging (CIBM), Switzerland",
         "orcid": "0000-0003-2730-4285"
       }
     ],

diff --git a/Dockerfile b/Dockerfile
@@ -68,8 +68,12 @@ WORKDIR /opt/mialsuperresolutiontoolkit/build
 # You can increase the number of cores used by make ("make -jN")
 # to speed up local build. However, make sure that it is
 # set back to make -j2 before pushing any change to GitHub.
-RUN cmake -D CMAKE_BUILD_TYPE=Release -D CMAKE_INSTALL_PREFIX=/usr/local -D USE_OMP:BOOL=ON ../src \
-    && make -j6 && make install
+RUN cmake \
+    -D CMAKE_BUILD_TYPE=Release \
+    -D CMAKE_INSTALL_PREFIX=/usr/local \
+    -D USE_OMP:BOOL=ON ../src && \
+    make -j6 && \
+    make install
 
 ##############################################################
 # Python cache setup and creation of conda environment

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # ![MIALSRTK logo](https://raw.githubusercontent.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/dev-pgd-hk/documentation/images/mialsrtk-logo.png)
 ---
 
-Copyright © 2016-2020 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland 
+Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland 
 
 This software is distributed under the open-source BSD 3-Clause License. See [LICENSE](LICENSE.txt) file for details.
 
@@ -47,14 +47,16 @@ All these design considerations allow us not only to (1) represent the entire pr
     $ mialsuperresolutiontoolkit_[docker|singularity] -h
 
     usage: mialsuperresolutiontoolkit_[docker|singularity] [-h]
+                                         [--run_type {sr,preprocessing}]
                                          [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                                          [--param_file PARAM_FILE]
                                          [--openmp_nb_of_cores OPENMP_NB_OF_CORES]
                                          [--nipype_nb_of_cores NIPYPE_NB_OF_CORES]
                                          [--memory MEMORY]
                                          [--masks_derivatives_dir MASKS_DERIVATIVES_DIR]
-                                         [-v]
-                                         [--codecarbon_output_dir CODECARBON_OUTPUT_DIR]
+                                         [--labels_derivatives_dir LABELS_DERIVATIVES_DIR]
+                                         [--all_outputs] [-v] [--verbose]
+                                         [--track_carbon_footprint]
                                          bids_dir output_dir {participant}
 
     Argument parser of the MIALSRTK BIDS App Python wrapper
@@ -71,6 +73,10 @@ All these design considerations allow us not only to (1) represent the entire pr
 
     optional arguments:
       -h, --help            show this help message and exit
+      --run_type {sr,preprocessing}
+                            Type of pipeline that is run. Can choose between
+                            running the super-resolution pipeline (`sr`) or only
+                            preprocessing (`preprocessing`).
       --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
                             The label(s) of the participant(s) that should be
                             analyzed. The label corresponds to
@@ -101,27 +107,36 @@ All these design considerations allow us not only to (1) represent the entire pr
       --masks_derivatives_dir MASKS_DERIVATIVES_DIR
                             Use manual brain masks found in
                             ``<output_dir>/<masks_derivatives_dir>/`` directory
-      --codecarbon_output_dir CODECARBON_OUTPUT_DIR
-                            Directory path in which `codecarbon` saves a CSV file
-                            called `emissions.csv` reporting carbon footprint
-                            details of the overall run (Defaults to user’s home
-                            directory)
+      --labels_derivatives_dir LABELS_DERIVATIVES_DIR
+                            Use low-resolution labelmaps found in
+                            ``<output_dir>/<labels_derivatives_dir>/`` directory.
+      --all_outputs         Whether or not all outputs should be kept(e.g.
+                            preprocessed LR images)
       -v, --version         show program's version number and exit
+      --verbose             Verbose mode
+      --track_carbon_footprint
+                            Track carbon footprint with `codecarbon
+                            <https://codecarbon.io/>`_ and save results in a CSV
+                            file called ``emissions.csv`` in the
+                            ``<bids_dir>/code`` directory.
 
 ## Credits 
 
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
 <!-- prettier-ignore-start -->
 <!-- markdownlint-disable -->
 <table>
-  <tr>
-    <td align="center"><a href="https://github.com/sebastientourbier"><img src="https://avatars3.githubusercontent.com/u/22279770?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Sébastien Tourbier</b></sub></a><br /><a href="#design-sebastientourbier" title="Design">🎨</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=sebastientourbier" title="Tests">⚠️</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=sebastientourbier" title="Code">💻</a> <a href="#example-sebastientourbier" title="Examples">💡</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=sebastientourbier" title="Documentation">📖</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/pulls?q=is%3Apr+reviewed-by%3Asebastientourbier" title="Reviewed Pull Requests">👀</a></td>
-    <td align="center"><a href="https://github.com/pdedumast"><img src="https://avatars2.githubusercontent.com/u/19345763?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Priscille de Dumast</b></sub></a><br /><a href="#example-pdedumast" title="Examples">💡</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=pdedumast" title="Tests">⚠️</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=pdedumast" title="Code">💻</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=pdedumast" title="Documentation">📖</a></td>
-    <td align="center"><a href="https://github.com/hamzake"><img src="https://avatars2.githubusercontent.com/u/27707790?v=4?s=100" width="100px;" alt=""/><br /><sub><b>hamzake</b></sub></a><br /><a href="#example-hamzake" title="Examples">💡</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=hamzake" title="Tests">⚠️</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=hamzake" title="Code">💻</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=hamzake" title="Documentation">📖</a></td>
-    <td align="center"><a href="https://github.com/helenelajous"><img src="https://avatars.githubusercontent.com/u/58977568?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Hélène Lajous</b></sub></a><br /><a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/issues?q=author%3Ahelenelajous" title="Bug reports">🐛</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=helenelajous" title="Tests">⚠️</a></td>
-    <td align="center"><a href="https://wp.unil.ch/connectomics"><img src="https://avatars.githubusercontent.com/u/411192?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Patric Hagmann</b></sub></a><br /><a href="#data-pahagman" title="Data">🔣</a> <a href="#fundingFinding-pahagman" title="Funding Finding">🔍</a></td>
-    <td align="center"><a href="https://github.com/meribach"><img src="https://avatars3.githubusercontent.com/u/2786897?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Meritxell Bach</b></sub></a><br /><a href="#fundingFinding-meribach" title="Funding Finding">🔍</a></td>
-  </tr>
+  <tbody>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/sebastientourbier"><img src="https://avatars3.githubusercontent.com/u/22279770?v=4?s=100" width="100px;" alt="Sébastien Tourbier"/><br /><sub><b>Sébastien Tourbier</b></sub></a><br /><a href="#design-sebastientourbier" title="Design">🎨</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=sebastientourbier" title="Code">💻</a> <a href="#infra-sebastientourbier" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=sebastientourbier" title="Tests">⚠️</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/issues?q=author%3Asebastientourbier" title="Bug reports">🐛</a> <a href="#example-sebastientourbier" title="Examples">💡</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=sebastientourbier" title="Documentation">📖</a> <a href="#ideas-sebastientourbier" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/pulls?q=is%3Apr+reviewed-by%3Asebastientourbier" title="Reviewed Pull Requests">👀</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/pdedumast"><img src="https://avatars2.githubusercontent.com/u/19345763?v=4?s=100" width="100px;" alt="Priscille de Dumast"/><br /><sub><b>Priscille de Dumast</b></sub></a><br /><a href="#design-pdedumast" title="Design">🎨</a> <a href="#example-pdedumast" title="Examples">💡</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=pdedumast" title="Tests">⚠️</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=pdedumast" title="Code">💻</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=pdedumast" title="Documentation">📖</a> <a href="#ideas-pdedumast" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/pulls?q=is%3Apr+reviewed-by%3Apdedumast" title="Reviewed Pull Requests">👀</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/hamzake"><img src="https://avatars2.githubusercontent.com/u/27707790?v=4?s=100" width="100px;" alt="hamzake"/><br /><sub><b>hamzake</b></sub></a><br /><a href="#example-hamzake" title="Examples">💡</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=hamzake" title="Tests">⚠️</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=hamzake" title="Code">💻</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=hamzake" title="Documentation">📖</a> <a href="#ideas-hamzake" title="Ideas, Planning, & Feedback">🤔</a></td>
+       <td align="center" valign="top" width="14.28%"><a href="http://t-sanchez.github.io"><img src="https://avatars.githubusercontent.com/u/14288440?v=4?s=100" width="100px;" alt="Thomas Sanchez"/><br /><sub><b>Thomas Sanchez</b></sub></a><br /><a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/issues?q=author%3At-sanchez" title="Bug reports">🐛</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=t-sanchez" title="Code">💻</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=t-sanchez" title="Documentation">📖</a> <a href="#example-t-sanchez" title="Examples">💡</a> <a href="#ideas-t-sanchez" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-t-sanchez" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/pulls?q=is%3Apr+reviewed-by%3At-sanchez" title="Reviewed Pull Requests">👀</a></td>
+       <td align="center" valign="top" width="14.28%"><a href="https://github.com/helenelajous"><img src="https://avatars.githubusercontent.com/u/58977568?v=4?s=100" width="100px;" alt="Hélène Lajous"/><br /><sub><b>Hélène Lajous</b></sub></a><br /><a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/issues?q=author%3Ahelenelajous" title="Bug reports">🐛</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/commits?author=helenelajous" title="Tests">⚠️</a> <a href="https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/pulls?q=is%3Apr+reviewed-by%3Ahelenelajous" title="Reviewed Pull Requests">👀</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://wp.unil.ch/connectomics"><img src="https://avatars.githubusercontent.com/u/411192?v=4?s=100" width="100px;" alt="Patric Hagmann"/><br /><sub><b>Patric Hagmann</b></sub></a><br /><a href="#data-pahagman" title="Data">🔣</a> <a href="#fundingFinding-pahagman" title="Funding Finding">🔍</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/meribach"><img src="https://avatars3.githubusercontent.com/u/2786897?v=4?s=100" width="100px;" alt="Meritxell Bach"/><br /><sub><b>Meritxell Bach</b></sub></a><br /><a href="#fundingFinding-meribach" title="Funding Finding">🔍</a></td>
+    </tr>
+  </tbody>
 </table>
 
 <!-- markdownlint-restore -->

diff --git a/docker/bidsapp/environment.yml b/docker/bidsapp/environment.yml
@@ -10,14 +10,14 @@ dependencies:
 - python=3.7.10
 - pip=21.0.1
 - pandas=1.1.5
-- nipype=1.8.3
-- nilearn=0.8.1
+- nipype=1.8.4
+- nilearn=0.8.0
 - pydotplus=2.0.2
 - pandoc=2.14.2
 - seaborn=0.11.2
 - matplotlib=3.4
 - tensorflow==1.13.1
-- scikit-learn=1.0.1
+- scikit-learn=0.21.3
 - scikit-image=0.16.2
 - ants=2.2.0
 

diff --git a/docker/bidsapp/run.py b/docker/bidsapp/run.py
@@ -1,4 +1,4 @@
-# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland
+# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland
 #
 #  This software is distributed under the open-source license Modified BSD.
 

diff --git a/documentation/api_pipelines.rst b/documentation/api_pipelines.rst
@@ -4,6 +4,14 @@
 Pipelines module
 ******************
 
+.. automodule:: pymialsrtk.pipelines.anatomical.abstract
+   :members:
+   :show-inheritance:
+
+.. automodule:: pymialsrtk.pipelines.anatomical.preprocessing
+   :members:
+   :show-inheritance:
+
 .. automodule:: pymialsrtk.pipelines.anatomical.srr
    :members:
    :show-inheritance: