Slicer · jcfr · Aug 17, 2023 · Aug 17, 2023 · Aug 17, 2023 · Aug 17, 2023
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,32 +1,32 @@
-<!--
-Thank you for contributing to 3D Slicer!
-- To add a new extension with this pull request: Please keep content of "New extension" section and put an 'x' in the brackets for each todo item to indicate that you have accomplished that prerequisite.
-- To update an existing extension with this pull request: Please delete all text in this template and just describe which extension is updated and optionally tell us in a sentence what has been changed. To make extension updates easier in the future you may consider replacing specific git hash in your s4ext file by a branch name (for example: `main` for Slicer Preview Releases; `(majorVersion).(minorVersion)` such as `4.10` for Slicer Stable Releases).
--->
-
-# New extension
-
-<!-- To make sure users can find your extension, understand what it is intended for and how to use it, please complete the checklist below. You do not need to complete all the item by the time you submit the pull request, but most likely the changes will only be merged if all the tasks are done. See more information about the submission process here: https://slicer.readthedocs.io/en/latest/developer_guide/extensions.html -->
-
-- [ ] Extension has a reasonable name (not too general, not too narrow, suggests what the extension is for)
-- [ ] Repository name is Slicer+ExtensionName
-- [ ] Repository is associated with `3d-slicer-extension` GitHub topic so that it is listed [here](https://github.com/topics/3d-slicer-extension). To edit topics, click the settings icon in the right side of "About" section header and enter `3d-slicer-extension` in "Topics" and click "Save changes". To learn more about topics, read https://help.github.com/en/articles/about-topics
-- [ ] Extension description summarizes in 1-2 sentences what the extension is usable (should be understandable for non-experts)
-- [ ] Any known related patents must be mentioned in the extension description.
-- [ ] LICENSE.txt is present in the repository root. MIT  (https://choosealicense.com/licenses/mit/) or Apache (https://choosealicense.com/licenses/apache-2.0/) license is recommended. If source code license is more restrictive for users than MIT, BSD, Apache, or 3D Slicer license then the name of the used license must be mentioned in the extension description.
-- [ ] Extension URL and revision (scmurl, scmrevision) is correct, consider using a branch name (main, release, ...) instead of a specific git has to avoid re-submitting pull request whenever the extension is updated
-- [ ] Extension icon URL is correct (do not use the icon's webpage but the raw data download URL that you get from the download button - it should look something like this: https://raw.githubusercontent.com/user/repo/main/SomeIcon.png)
-- [ ] Screenshot URLs (screenshoturls) are correct, contains at least one
-- [ ] Homepage URL points to valid webpage containing the following:
-  - [ ] Extension name
-  - [ ] Short description: 1-2 sentences, which summarizes what the extension is usable for
-  - [ ] At least one nice, informative image, that illustrates what the extension can do. It may be a screenshot.
-  - [ ] Description of contained modules: at one sentence for each module
-  - [ ] Tutorial: step-by-step description of at least the most typical use case, include a few screenshots, provide download links to sample input data set
-  - [ ] Publication: link to publication and/or to PubMed reference (if available)
-  - [ ] License: We suggest you use a permissive license that includes patent and contribution clauses.  This will help protect developers and ensure the code remains freely available.  We suggest you use the [Slicer License](https://github.com/Slicer/Slicer/blob/main/License.txt) or the [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0). Always mention in your README file the license you have chosen.  If you choose a different license, explain why to the extension maintainers. Depending on the license we may not be able to host your work. Read [here](https://opensource.guide/legal/#which-open-source-license-is-appropriate-for-my-project) to learn more about licenses.
-  - [ ] Content of submitted s4ext file is consistent with the top-level CMakeLists.txt file in the repository (description, URLs, dependencies, etc. are the same)
-- Hide unused features in the repository to reduce noise/irrelevant information:
-  - [ ] Click `Settings` and in repository settings uncheck `Wiki`, `Projects`, and `Discussions` (if they are currently not used)
-  - [ ] Click the settings icon next to `About` in the top-right corner of the repository main page and uncheck `Releases` and `Packages` (if they are currently not used)
-<!-- If you have any questions or comments then please describe them here. -->
+<!--
+Thank you for contributing to 3D Slicer!
+- To add a new extension with this pull request: Please keep content of "New extension" section and put an 'x' in the brackets for each todo item to indicate that you have accomplished that prerequisite.
+- To update an existing extension with this pull request: Please delete all text in this template and just describe which extension is updated and optionally tell us in a sentence what has been changed. To make extension updates easier in the future you may consider replacing specific git hash in your s4ext file by a branch name (for example: `main` for Slicer Preview Releases; `(majorVersion).(minorVersion)` such as `4.10` for Slicer Stable Releases).
+-->
+
+# New extension
+
+<!-- To make sure users can find your extension, understand what it is intended for and how to use it, please complete the checklist below. You do not need to complete all the item by the time you submit the pull request, but most likely the changes will only be merged if all the tasks are done. See more information about the submission process here: https://slicer.readthedocs.io/en/latest/developer_guide/extensions.html -->
+
+- [ ] Extension has a reasonable name (not too general, not too narrow, suggests what the extension is for)
+- [ ] Repository name is Slicer+ExtensionName
+- [ ] Repository is associated with `3d-slicer-extension` GitHub topic so that it is listed [here](https://github.com/topics/3d-slicer-extension). To edit topics, click the settings icon in the right side of "About" section header and enter `3d-slicer-extension` in "Topics" and click "Save changes". To learn more about topics, read https://help.github.com/en/articles/about-topics
+- [ ] Extension description summarizes in 1-2 sentences what the extension is usable (should be understandable for non-experts)
+- [ ] Any known related patents must be mentioned in the extension description.
+- [ ] LICENSE.txt is present in the repository root. MIT  (https://choosealicense.com/licenses/mit/) or Apache (https://choosealicense.com/licenses/apache-2.0/) license is recommended. If source code license is more restrictive for users than MIT, BSD, Apache, or 3D Slicer license then the name of the used license must be mentioned in the extension description.
+- [ ] Extension URL and revision (scmurl, scmrevision) is correct, consider using a branch name (main, release, ...) instead of a specific git has to avoid re-submitting pull request whenever the extension is updated
+- [ ] Extension icon URL is correct (do not use the icon's webpage but the raw data download URL that you get from the download button - it should look something like this: https://raw.githubusercontent.com/user/repo/main/SomeIcon.png)
+- [ ] Screenshot URLs (screenshoturls) are correct, contains at least one
+- [ ] Homepage URL points to valid webpage containing the following:
+  - [ ] Extension name
+  - [ ] Short description: 1-2 sentences, which summarizes what the extension is usable for
+  - [ ] At least one nice, informative image, that illustrates what the extension can do. It may be a screenshot.
+  - [ ] Description of contained modules: at one sentence for each module
+  - [ ] Tutorial: step-by-step description of at least the most typical use case, include a few screenshots, provide download links to sample input data set
+  - [ ] Publication: link to publication and/or to PubMed reference (if available)
+  - [ ] License: We suggest you use a permissive license that includes patent and contribution clauses.  This will help protect developers and ensure the code remains freely available.  We suggest you use the [Slicer License](https://github.com/Slicer/Slicer/blob/main/License.txt) or the [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0). Always mention in your README file the license you have chosen.  If you choose a different license, explain why to the extension maintainers. Depending on the license we may not be able to host your work. Read [here](https://opensource.guide/legal/#which-open-source-license-is-appropriate-for-my-project) to learn more about licenses.
+  - [ ] Content of submitted s4ext file is consistent with the top-level CMakeLists.txt file in the repository (description, URLs, dependencies, etc. are the same)
+- Hide unused features in the repository to reduce noise/irrelevant information:
+  - [ ] Click `Settings` and in repository settings uncheck `Wiki`, `Projects`, and `Discussions` (if they are currently not used)
+  - [ ] Click the settings icon next to `About` in the top-right corner of the repository main page and uncheck `Releases` and `Packages` (if they are currently not used)
+<!-- If you have any questions or comments then please describe them here. -->
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,3 +7,12 @@ repos:
   - id: check-case-conflict
   - id: check-merge-conflict
   - id: check-symlinks
+  - id: end-of-file-fixer
+  - id: mixed-line-ending
+  - id: trailing-whitespace
+
+- repo: https://github.com/Lucas-C/pre-commit-hooks
+  rev: "v1.5.4"
+  hooks:
+    - id: forbid-tabs
+    - id: remove-tabs
diff --git a/ABLTemporalBoneSegmentation.s4ext b/ABLTemporalBoneSegmentation.s4ext
@@ -32,7 +32,7 @@ iconurl https://raw.githubusercontent.com/Auditory-Biophysics-Lab/Slicer-ABLTemp
 
 # Give people an idea what to expect from this code
 #  - Is it just a test or something you stand behind?
-status 
+status
 
 # One line stating what the module does
 description Temporal bone deep-learning segmentation and pre-processing module.

diff --git a/ARCHIVE/ABC.s4ext b/ARCHIVE/ABC.s4ext
@@ -38,7 +38,7 @@ status Beta
 description Utah atlas based segmentation pipeline. Generates output images after bias correction and co-registration along with segmentation label image.
 
 # Space separated list of urls
-screenshoturls 
+screenshoturls
 
 # 0 or 1: Define if the extension should be enabled after its installation.
 enabled 1
diff --git a/ARCHIVE/AutoTract.s4ext b/ARCHIVE/AutoTract.s4ext
@@ -38,7 +38,7 @@ status beta
 description Automated tractography in diffusion tensor images and fiber tract classification using a deep learning approach
 
 # Space separated list of urls
-screenshoturls https://www.nitrc.org/project/screenshot.php?group_id=948&screenshot_id=934 
+screenshoturls https://www.nitrc.org/project/screenshot.php?group_id=948&screenshot_id=934
 
 # 0 or 1: Define if the extension should be enabled after its installation.
 enabled 1
diff --git a/ARCHIVE/CBC_3D_I2MConversion.s4ext b/ARCHIVE/CBC_3D_I2MConversion.s4ext
@@ -32,7 +32,7 @@ iconurl     http://wiki.slicer.org/slicerWiki/images/3/3e/I2M_logo.jpg
 
 # Give people an idea what to expect from this code
 #  - Is it just a test or something you stand behind?
-status      
+status
 
 # One line stating what the module does
 description CBC 3D (CRTC's BCC & Compression) I2M (Image-To-Mesh) Conversion for Image Guided Therapy. The extension encapsulates two CLI modules: (1) Body Centric Cubic (BCC) Mesh Generation. This module generates a Body Centric Cubic (BCC) mesh from a labeled image. Initially the generated mesh is homogeneous, that means does not distinguish different tissues. Later the component specifies which tissue each tetrahedron belongs to. Each tissue is capable of automatically adjusting its resolution based on its geometric complexity and the predefined subdivision criterion. (2) Mesh Compression (MC). This module deforms an input tetrahedral mesh towards the boundaries of the input labeled image. Two point sets are extracted for the mesh deformation. The first (source point set) consists of the surface vertices of the input mesh. The second (target point set) consists of the surface edge points in the input labeled image. Then the input mesh is deformed by registering the source to the target point set using a Physics-Based Non-Rigid Registration method.

diff --git a/ARCHIVE/DTIAtlasFiberAnalyzer.s4ext b/ARCHIVE/DTIAtlasFiberAnalyzer.s4ext
@@ -29,7 +29,7 @@ category Diffusion
 iconurl http://www.nitrc.org/project/screenshot.php?group_id=403&screenshot_id=606
 
 # Extension development status
-status 
+status
 
 # One line stating what the module does
 description DTIAtlasFiberAnalyzer allows the user to study the behavior of water diffusion (using DTI data) along the length of the white matter fiber-tracts.

diff --git a/ARCHIVE/DTIPrep.s4ext b/ARCHIVE/DTIPrep.s4ext
@@ -32,7 +32,7 @@ iconurl    http://www.nitrc.org/project/screenshot.php?group_id=283&screenshot_i
 
 # Give people an idea what to expect from this code
 #  - Is it just a test or something you stand beind?
-status      
+status
 
 # One line stating what the module does description This extension provides the tool DTIProcess integrated in Slicer
 

diff --git a/ARCHIVE/DTIProcess.s4ext b/ARCHIVE/DTIProcess.s4ext
@@ -32,7 +32,7 @@ iconurl    http://www.nitrc.org/project/screenshot.php?group_id=312&screenshot_i
 
 # Give people an idea what to expect from this code
 #  - Is it just a test or something you stand beind?
-status      
+status
 
 # One line stating what the module does
 description This extension provides the tool DTIProcess integrated in Slicer

diff --git a/ARCHIVE/DeepInfer.s4ext b/ARCHIVE/DeepInfer.s4ext
@@ -18,7 +18,7 @@ depends     NA
 build_subdirectory .
 
 # homepage
-homepage   https://www.slicer.org/wiki/Documentation/Nightly/Modules/DeepInfer 
+homepage   https://www.slicer.org/wiki/Documentation/Nightly/Modules/DeepInfer
 
 contributors Alireza Mehrtash(UBC, BWH, SPL), Mehran Pesteie(UBC)
 
@@ -30,7 +30,7 @@ iconurl    https://www.slicer.org/w/images/a/a9/Deepinfer-256.png
 
 # Give people an idea what to expect from this code
 #  - Is it just a test or something you stand beind?
-status      
+status
 
 # One line stating what the module does
 description Deep learning deployment toolkit for medical imaging.

diff --git a/ARCHIVE/Eigen3.s4ext b/ARCHIVE/Eigen3.s4ext
@@ -25,6 +25,3 @@ status      Release
 
 # One line stating what the module does
 description a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
-
-
-
diff --git a/ARCHIVE/FiberViewerLight.s4ext b/ARCHIVE/FiberViewerLight.s4ext
@@ -32,7 +32,7 @@ iconurl    http://www.nitrc.org/project/screenshot.php?group_id=534&screenshot_i
 
 # Give people an idea what to expect from this code
 #  - Is it just a test or something you stand behind?
-status      
+status
 
 # One line stating what the module does
 description FiberViewerLight is an open-source software to visualize and edit fibers

diff --git a/ARCHIVE/GraphCutSegment.s4ext b/ARCHIVE/GraphCutSegment.s4ext
@@ -32,7 +32,7 @@ iconurl http://www.example.com/Slicer/Extensions/GraphCutSegment.png
 
 # Give people an idea what to expect from this code
 #  - Is it just a test or something you stand behind?
-status 
+status
 
 # One line stating what the module does
 description Graph cut algorithm based segmentation tool.

diff --git a/ARCHIVE/IASEM.s4ext b/ARCHIVE/IASEM.s4ext
@@ -36,7 +36,7 @@ iconurl     http://raw.github.com/blowekamp/Slicer-IASEM/master/IASEM.png
 status      Experimental
 
 # One line stating what the module does
-description 
+description
 
 # Space separated list of urls
 screenshoturls http://www.slicer.org/slicerWiki/images/c/cd/IASEM-Screenshot1.png

diff --git a/ARCHIVE/LAScarSegmenter.s4ext b/ARCHIVE/LAScarSegmenter.s4ext
@@ -22,7 +22,7 @@ homepage     http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Ex
 
 # Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
 # For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Liangjia Zhu (SBU), Yi Gao (UAB), Josh Cates (Utah), Alan Morris (Utah), Danny Perry (Utah), Greg Gardner (Utah), Rob MacLeod (Utah), Allen Tannenbaum (SBU) 
+contributors Liangjia Zhu (SBU), Yi Gao (UAB), Josh Cates (Utah), Alan Morris (Utah), Danny Perry (Utah), Greg Gardner (Utah), Rob MacLeod (Utah), Allen Tannenbaum (SBU)
 
 # Match category in the xml description of the module (where it shows up in Modules menu)
 category    Segmentation

diff --git a/ARCHIVE/LASegmenter.s4ext b/ARCHIVE/LASegmenter.s4ext
@@ -22,7 +22,7 @@ homepage http://www.slicer.org/slicerWiki/index.php?title=Documentation/Nightly/
 
 # Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
 # For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Liangjia Zhu (SBU), Yi Gao (UAB), Josh Cates (Utah), Alan Morris (Utah), Danny Perry (Utah), Greg Gardner (Utah), Rob MacLeod (Utah), Allen Tannenbaum (SBU) 
+contributors Liangjia Zhu (SBU), Yi Gao (UAB), Josh Cates (Utah), Alan Morris (Utah), Danny Perry (Utah), Greg Gardner (Utah), Rob MacLeod (Utah), Allen Tannenbaum (SBU)
 
 # Match category in the xml description of the module (where it shows up in Modules menu)
 category Segmentation
@@ -32,7 +32,7 @@ iconurl http://www.slicer.org/slicerWiki/images/0/0b/LASegmenter.png
 
 # Give people an idea what to expect from this code
 #  - Is it just a test or something you stand behind?
-status 
+status
 
 # One line stating what the module does
 description This module performs segmentation of the left atrium from MR images

diff --git a/ARCHIVE/LesionSimulator.s4ext b/ARCHIVE/LesionSimulator.s4ext
@@ -32,7 +32,7 @@ iconurl https://www.slicer.org/w/images/d/d5/LesionSimulator-logo.png
 
 # Give people an idea what to expect from this code
 #  - Is it just a test or something you stand behind?
-status 
+status
 
 # One line stating what the module does
 description This extension offer a set of tools for brain lesion simulation, based on MRI images. At moment, the modules MS Lesion Simulator and MS Longitudinal Lesion Simulator are available, where it can simulate both baseline scan lesion volumes (given a lesion load) and longitudinal image simulations, respectively. In summary, a statistical lesion database is generated based on a set of manual lesion mark-ups, being non-linearly registered to MNI152 space (isotropic 1mm of voxel resolution). Using a small set of parameters (lesion load, lesion homogeneity, lesion intensity indenpendence and lesion variability), it is possible to generate a broad range of MS lesions patterns in multimodal MRI imaging techniques (at moment, T1, T2, T2-FLAIR, PD, DTI-FA and DTI-ADC images are provided). For more details about this project, please see the original paper (DOI: 10.1088/2057-1976/ab08fc ) and the wiki page.

diff --git a/ARCHIVE/LesionSpotlight.s4ext b/ARCHIVE/LesionSpotlight.s4ext
@@ -32,7 +32,7 @@ iconurl https://www.slicer.org/w/images/7/71/LesionSpotlight-logo.png
 
 # Give people an idea what to expect from this code
 #  - Is it just a test or something you stand behind?
-status 
+status
 
 # One line stating what the module does
 description This extension provides an recent image segmentation and enhancement approaches in order to highlight abnormal white matter voxels in magnetic resonance images. At moment, there are available the LS Segmenter module (specific for hyperintense Multiple Sclerosis lesion segmentation on T2-FLAIR images) and LS Contrast Enhancement Module (specific to increase the contrast of abnormal voxels of the same T2-FLAIR images). The LS Segmenter module implements a hyperintense T2-FLAIR lesion segmentation based on a hybrid segmentation algorithm, published by Senra Filho, A.C. (http://dx.doi.org/10.1007/s11517-017-1747-2). In addition, a simple implementation of another recent MS lesion segmentation algorithm is provided, being the method described in Cabezas M. et al. (http://dx.doi.org/10.1016/j.cmpb.2014.04.006)

diff --git a/ARCHIVE/LightWeightRobotIGT.s4ext b/ARCHIVE/LightWeightRobotIGT.s4ext
@@ -32,7 +32,7 @@ iconurl     http://www.slicer.org/slicerWiki/images/5/58/LightWeightRobotIGT.png
 
 # Give people an idea what to expect from this code
 #  - Is it just a test or something you stand behind?
-status      
+status
 
 # One line stating what the module does
 description 3D Slicer module for communication between 3D Slicer and LightWeight robot.

diff --git a/ARCHIVE/LongitudinalPETCT.s4ext b/ARCHIVE/LongitudinalPETCT.s4ext
@@ -32,7 +32,7 @@ iconurl     http://www.slicer.org/slicerWiki/images/0/08/LongitudinalPETCTLogo.p
 
 # Give people an idea what to expect from this code
 #  - Is it just a test or something you stand beind?
-status      
+status
 
 # One line stating what the module does
 description The purpose of the Longitudinal PET/CT Analysis module is to provide a user friendly Slicer interface for quantification of DICOM PET/CT image data by computing the standardized uptake value (SUV) based on bodyweight for different regions of interest and for different timepoints.