ayarmarkovich · ayarmarkovich · Sep 6, 2019 · Sep 6, 2019 · Sep 12, 2019 · Oct 11, 2019
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -0,0 +1,68 @@
+
+version: 2
+jobs:
+  check-filenames:
+    docker:
+      - image: circleci/python:3.7.0-stretch
+    steps:
+      - checkout
+      - run:
+          name: Check filenames
+          command: |
+            ./scripts/check_filenames.sh
+
+  check-description-files:
+    docker:
+      - image: circleci/python:3.7.0-stretch
+    steps:
+      - checkout
+      - run:
+          name: Check description files
+          command: |
+            python ./scripts/check_description_files.py --check-dependencies . $(find . -name "*.s4ext")
+
+  check-new-description-files:
+    docker:
+      - image: circleci/python:3.7.0-stretch
+    steps:
+      - checkout
+      - run:
+          name: Lookup base branch (Workaround the lack of CIRCLE_BASE_BRANCH env. variable)
+          # See https://discuss.circleci.com/t/how-to-get-the-pull-request-upstream-branch/5496/2
+          command: |
+            if [[ $CIRCLE_PULL_REQUEST != "" ]]; then
+              for base_branch in origin/master $(git branch -r | grep -E "origin\/[0-9](\.[0-9])+" | sort -r); do
+                differences=$(git diff $base_branch --name-only)
+                if [[ $differences != "" ]]; then
+                  break
+                fi
+              done
+            else
+              base_branch=$CIRCLE_BRANCH
+            fi
+            echo "export BASE_BRANCH=\"$base_branch\"" >> $BASH_ENV
+      - run:
+          name: Check new description files
+          command: |
+            # ignore grep exit code if no description files were added
+            set +e
+
+            echo "BASE_BRANCH is [$BASE_BRANCH]"
+            echo "CIRCLE_BRANCH is [$CIRCLE_BRANCH]"
+
+            # Collect list of new *.s4ext files
+            added=$(git diff $BASE_BRANCH --diff-filter=A --name-only | grep -E "^[^\/]+\.s4ext$")
+            echo "added [$added]"
+
+            # Run checks
+            if [[ $added != "" ]]; then
+              python ./scripts/check_description_files.py --check-git-repository-name $added
+            fi
+
+workflows:
+  version: 2
+  test:
+    jobs:
+      - check-filenames
+      - check-description-files
+      - check-new-description-files
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,30 @@
+<!--
+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: `master` 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.
+- [ ] If source code license is more restrictive for users than BSD, MIT, 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, master, 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/master/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)
+
+<!-- If you have any questions or comments then please describe them here. -->
diff --git a/ABLTemporalBoneSegmentation.s4ext b/ABLTemporalBoneSegmentation.s4ext
@@ -0,0 +1,44 @@
+#
+# First token of each non-comment line is the keyword and the rest of the line
+# (including spaces) is the value.
+# - the value can be blank
+#
+
+# This is source code manager (i.e. svn)
+scm git
+scmurl https://github.com/Auditory-Biophysics-Lab/Slicer-ABLTemporalBoneSegmentation
+scmrevision master
+
+# list dependencies
+# - These should be names of other modules that have .s4ext files
+# - The dependencies will be built first
+depends SlicerElastix
+
+# Inner build directory (default is ".")
+build_subdirectory inner-build
+
+# homepage
+homepage https://github.com/Auditory-Biophysics-Lab/Slicer-ABLTemporalBoneSegmentation
+
+# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
+# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
+contributors Evan Simpson (ABL at UWO), Ben Connors (ABL at UWO)
+
+# Match category in the xml description of the module (where it shows up in Modules menu)
+category Otolaryngology
+
+# url to icon (png, size 128x128 pixels)
+iconurl https://raw.githubusercontent.com/Auditory-Biophysics-Lab/Slicer-ABLTemporalBoneSegmentation/master/ABLTemporalBoneSegmentationModule/Resources/Icons/ABLTemporalBoneSegmentationModule.png
+
+# Give people an idea what to expect from this code
+#  - Is it just a test or something you stand behind?
+status 
+
+# One line stating what the module does
+description Temporal bone deep-learning segmentation and pre-processing module.
+
+# Space separated list of urls
+screenshoturls https://raw.githubusercontent.com/Auditory-Biophysics-Lab/Slicer-ABLTemporalBoneSegmentation/master/Images/main.png
+
+# 0 or 1: Define if the extension should be enabled after its installation.
+enabled 1
diff --git a/ARCHIVE/ABC.s4ext b/ARCHIVE/ABC.s4ext
@@ -0,0 +1,44 @@
+#
+# First token of each non-comment line is the keyword and the rest of the line
+# (including spaces) is the value.
+# - the value can be blank
+#
+
+# This is source code manager (i.e. svn)
+scm git
+scmurl https://github.com/NIRALUser/ABC
+scmrevision dcd757f4d6723c5658dd3197a20f7984fb1cf8ea
+
+# list dependencies
+# - These should be names of other modules that have .s4ext files
+# - The dependencies will be built first
+depends NA
+
+# Inner build directory (default is ".")
+build_subdirectory .
+
+# homepage
+homepage http://www.nitrc.org/projects/abc
+
+# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
+# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
+contributors Marcel Prastawa (Utah)
+
+# Match category in the xml description of the module (where it shows up in Modules menu)
+category Segmentation
+
+# url to icon (png, size 128x128 pixels)
+iconurl https://github.com/NIRALUser/ABC/raw/master/ABC.png
+
+# Give people an idea what to expect from this code
+#  - Is it just a test or something you stand behind?
+status Beta
+
+# One line stating what the module does
+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 
+
+# 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
@@ -0,0 +1,44 @@
+#
+# First token of each non-comment line is the keyword and the rest of the line
+# (including spaces) is the value.
+# - the value can be blank
+#
+
+# This is source code manager (i.e. svn)
+scm git
+scmurl https://github.com/NIRALUser/AutoTract.git
+scmrevision release
+
+# list dependencies
+# - These should be names of other modules that have .s4ext files
+# - The dependencies will be built first
+depends DTIProcess DTIAtlasFiberAnalyzer ResampleDTIlogEuclidean DTI-Reg SlicerDMRI
+
+# Inner build directory (default is .)
+build_subdirectory .
+
+# homepage
+homepage  https://www.nitrc.org/projects/autotract/
+
+# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
+# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
+contributors Jean Yves, François Budin, Prince Ngattai Lam, Adrien Boucaud, Martin Styner, Juan Carlos Prieto
+
+# Match category in the xml description of the module (where it shows up in Modules menu)
+category    Diffusion
+
+# url to icon (png, size 128x128 pixels)
+iconurl https://www.nitrc.org/project/screenshot.php?thumbnail=true&group_id=948&screenshot_id=935
+
+# Give people an idea what to expect from this code
+#  - Is it just a test or something you stand beind?
+status beta
+
+# One line stating what the module does
+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 
+
+# 0 or 1: Define if the extension should be enabled after its installation.
+enabled 1
diff --git a/CBC_3D_I2MConversion.s4ext → ARCHIVE/CBC_3D_I2MConversion.s4ext b/CBC_3D_I2MConversion.s4ext → ARCHIVE/CBC_3D_I2MConversion.s4ext
@@ -6,7 +6,7 @@
 
 # This is source code manager (i.e. svn)
 scm git
-scmurl git://github.com/fdrakopo/ImageToMeshConversion.git
+scmurl https://github.com/jbest002/CBC3D_I2M_Conversion_SlicerExtension.git
 scmrevision 1f490c6
 
 # list dependencies
@@ -22,7 +22,7 @@ homepage    http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Ext
 
 # Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
 # For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)
+contributors Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC), Joi Best (CRTC)
 
 # Match category in the xml description of the module (where it shows up in Modules menu)
 category    Mesh Generation

diff --git a/CardiacAgastonMeasures.s4ext → ARCHIVE/CardiacAgatstonMeasures.s4ext b/CardiacAgastonMeasures.s4ext → ARCHIVE/CardiacAgatstonMeasures.s4ext
@@ -7,7 +7,7 @@ enabled 1
 homepage http://brainsia.github.io/CardiacAgatstonMeasures/
 iconurl http://www.na-mic.org/Wiki/images/b/b5/CardiacAgatstonModuleIamge.png
 scm git
-scmrevision 2bbc87c3aa7bc28288eedfe390ca6a344b1914de
-scmurl git://github.com/BRAINSia/CardiacAgatstonMeasures.git
+scmrevision 1e5413ca66849942fa89985677faf72a26c2b5f2
+scmurl https://github.com/BRAINSia/CardiacAgatstonMeasures.git
 screenshoturls http://www.na-mic.org/Wiki/images/6/63/CardiacAgatstonMeasuresModuleScreenshot.jpg
 status
diff --git a/Cardiac_MRI_Toolkit.s4ext → ARCHIVE/Cardiac_MRI_Toolkit.s4ext b/Cardiac_MRI_Toolkit.s4ext → ARCHIVE/Cardiac_MRI_Toolkit.s4ext
@@ -6,8 +6,8 @@
 
 # This is source code manager (i.e. svn)
 scm git
-scmurl git://github.com/carma-center/carma_slicer_extension.git
-scmrevision fbead7a
+scmurl https://github.com/carma-center/carma_slicer_extension.git
+scmrevision 4e01680
 
 # list dependencies
 # - These should be names of other modules that have .s4ext files

diff --git a/ARCHIVE/CornerAnnotation.s4ext b/ARCHIVE/CornerAnnotation.s4ext
@@ -0,0 +1,13 @@
+build_subdirectory .
+category IGT
+contributors Atsushi Yamada (Shiga University of Medical Science, Japan)
+depends NA
+description This is an module to display annotations, time count, node elements on each panels on the Slicer user interface
+enabled 1
+homepage http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/CornerAnnotation
+iconurl http://www.slicer.org/slicerWiki/images/e/e1/CornerAnnotationIcon.png
+scm git
+scmrevision ae11992a4860b01b69b05548d99e1f666cf80d13
+scmurl https://github.com/ayamada0614/CornerAnnotation.git
+screenshoturls http://www.slicer.org/slicerWiki/images/2/2a/CA-1.png
+status
diff --git a/ARCHIVE/DTI-Reg.s4ext b/ARCHIVE/DTI-Reg.s4ext
@@ -0,0 +1,44 @@
+#
+# First token of each non-comment line is the keyword and the rest of the line
+# (including spaces) is the value.
+# - the value can be blank
+#
+
+# This is source code manager (i.e. svn)
+scm git
+scmurl https://github.com/NIRALUser/DTI-Reg.git
+scmrevision release
+
+# list dependencies
+# - These should be names of other modules that have .s4ext files
+# - The dependencies will be built first
+depends     DTIProcess ResampleDTIlogEuclidean
+
+# Inner build directory (default is .)
+build_subdirectory .
+
+# homepage
+homepage    http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/DTI-Reg
+
+# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
+# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
+contributors Francois Budin (UNC), Clement Vachet (SCI), Martin Styner (UNC)
+
+# Match category in the xml description of the module (where it shows up in Modules menu)
+category    Diffusion
+
+# url to icon (png, size 128x128 pixels)
+iconurl   https://raw.githubusercontent.com/NIRALUser/DTI-Reg/master/DTI-Reg-icon.png
+
+# Give people an idea what to expect from this code
+#  - Is it just a test or something you stand beind?
+status      Release
+
+# One line stating what the module does
+description DTI-Reg is an extension that performs pair-wise DTI registration, using scalar FA map to drive the registration.
+
+# Space separated list of urls
+screenshoturls http://www.slicer.org/slicerWiki/images/c/c5/DTI-Reg_-_Misaligned_DTIs.png http://www.slicer.org/slicerWiki/images/1/12/DTI-Reg_-_Aligned_DTIs_-_Coronal.png
+
+# 0 or 1: Define if the extension should be enabled after its installation.
+enabled 1
diff --git a/DTIAtlasBuilder.s4ext → ARCHIVE/DTIAtlasBuilder.s4ext b/DTIAtlasBuilder.s4ext → ARCHIVE/DTIAtlasBuilder.s4ext
@@ -6,23 +6,23 @@
 
 # This is source code manager (i.e. svn)
 scm git
-scmurl git://github.com/NIRALUser/DTIAtlasBuilder.git
-scmrevision fe47ddefe0ee6ca7817a10682c75dd567617aeef
+scmurl https://github.com/NIRALUser/DTIAtlasBuilder.git
+scmrevision release
 
 # list dependencies
 # - These should be names of other modules that have .s4ext files
 # - The dependencies will be built first
-depends     NA
+depends     DTIProcess ResampleDTIlogEuclidean DTI-Reg
 
 # Inner build directory (default is .)
-build_subdirectory DTIAtlasBuilder-build
+build_subdirectory .
 
 # homepage
 homepage    http://www.nitrc.org/projects/dtiatlasbuilder
 
 # Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
 # For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Adrien Kaiser (UNC)
+contributors Adrien Kaiser (UNC), Francois Budin (UNC)
 
 # Match category in the xml description of the module (where it shows up in Modules menu)
 category    Diffusion

diff --git a/DTIAtlasFiberAnalyzer.s4ext → ARCHIVE/DTIAtlasFiberAnalyzer.s4ext b/DTIAtlasFiberAnalyzer.s4ext → ARCHIVE/DTIAtlasFiberAnalyzer.s4ext
@@ -5,19 +5,17 @@
 #
 
 # This is source code manager (i.e. svn)
-scm svn
-scmurl https://www.nitrc.org/svn/dti_tract_stat/trunk/
-scmrevision 140
-svnusername slicerbot
-svnpassword slicer
+scm git
+scmurl https://github.com/NIRALUser/DTIFiberTractStatistics.git
+scmrevision release
 
 #list dependencies
 # - These should be names of other modules that have .s4ext files
 # - The dependencies will be built first
-depends  NA
+depends  DTIProcess
 
 # Inner build directory (default is .)
-build_subdirectory dti_tract_stat-build
+build_subdirectory .
 
 #homepage
 homepage http://www.nitrc.org/projects/dti_tract_stat
@@ -31,7 +29,7 @@ category Diffusion
 iconurl http://www.nitrc.org/project/screenshot.php?group_id=403&screenshot_id=606
 
 # Extension development status
-status Beta
+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.