Merge branch 'main' of github.com:FNNDSC/pl-fetal-surface-extract

FNNDSC · Feb 20, 2023 · 2670592 · 2670592
2 parents 9c4005f + d7e405f
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -20,7 +20,7 @@ jobs:
   build:
     name: Build
     if: github.event_name == 'push' || github.event_name == 'release'
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     # A local registry helps us reuse the built image between steps
     services:
@@ -33,7 +33,7 @@ jobs:
       - name: Get git tag
         id: git_info
         if: startsWith(github.ref, 'refs/tags/')
-        run: echo "::set-output name=tag::${GITHUB_REF##*/}"
+        run: echo "tag=${GITHUB_REF##*/}" >> $GITHUB_OUTPUT
       - name: Get project info
         id: determine
         env:
@@ -42,49 +42,45 @@ jobs:
           repo="${GITHUB_REPOSITORY,,}"  # to lower case
           # if build triggered by tag, use tag name
           tag="${git_tag:-latest}"
-
           # if tag is a version number prefixed by 'v', remove the 'v'
           if [[ "$tag" =~ ^v[0-9].* ]]; then
             tag="${tag:1}"
           fi
-
           dock_image=$repo:$tag
           echo $dock_image
-          echo "::set-output name=dock_image::$dock_image"
-          echo "::set-output name=repo::$repo"
-
-      - uses: actions/checkout@v2
+          echo "dock_image=$dock_image" >> $GITHUB_OUTPUT
+          echo "repo=$repo" >> $GITHUB_OUTPUT
+      - uses: actions/checkout@v3
         # QEMU is used for non-x86_64 builds
-      - uses: docker/setup-qemu-action@v1
+      - uses: docker/setup-qemu-action@v2
         # buildx adds additional features to docker build
-      - uses: docker/setup-buildx-action@v1
+      - uses: docker/setup-buildx-action@v2
         with:
           driver-opts: network=host
         # cache slightly improves rebuild time
       - name: Cache Docker layers
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /tmp/.buildx-cache
           key: ${{ runner.os }}-buildx-${{ github.sha }}
           restore-keys: |
             ${{ runner.os }}-buildx-
-
       - name: Login to DockerHub
         id: dockerhub_login
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
 
       - name: Login to GitHub Container Registry
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v2
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Build and push
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v3
         id: docker_build
         with:
           context: .
@@ -105,10 +101,9 @@ jobs:
           dock_image=${{ steps.determine.outputs.dock_image }}
           docker run --rm localhost:5000/$dock_image chris_plugin_info > /tmp/description.json
           jq < /tmp/description.json  # pretty print in log
-          echo "::set-output name=title::$(jq -r '.title' < /tmp/description.json)"
-
+          echo "title=$(jq -r '.title' < /tmp/description.json)" >> $GITHUB_OUTPUT
       - name: Update DockerHub description
-        uses: peter-evans/dockerhub-description@v2
+        uses: peter-evans/dockerhub-description@v3
         continue-on-error: true  # it is not crucial that this works
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
@@ -118,7 +113,7 @@ jobs:
           repository: ${{ steps.determine.outputs.repo }}
 
       - name: Upload to ChRIS Store
-        if: github.event_name == 'release'
+        if: steps.git_info.outcome != 'skipped'
         uses: FNNDSC/chrisstore-action@master
         with:
           descriptor_file: /tmp/description.json

diff --git a/README.md b/README.md
@@ -1,16 +1,16 @@
 # Fetal CP Surface Extraction
 
-[![Version](https://img.shields.io/docker/v/fnndsc/pl-fetal-cp-surface-extract?sort=semver)](https://hub.docker.com/r/fnndsc/pl-fetal-cp-surface-extract)
-[![MIT License](https://img.shields.io/github/license/fnndsc/pl-fetal-cp-surface-extract)](https://github.com/FNNDSC/pl-fetal-cp-surface-extract/blob/main/LICENSE)
-[![ci](https://github.com/FNNDSC/pl-fetal-cp-surface-extract/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-fetal-cp-surface-extract/actions/workflows/ci.yml)
+[![Version](https://img.shields.io/docker/v/fnndsc/pl-fetal-surface-extract?sort=semver)](https://hub.docker.com/r/fnndsc/pl-fetal-surface-extract)
+[![MIT License](https://img.shields.io/github/license/fnndsc/pl-fetal-surface-extract)](https://github.com/FNNDSC/pl-fetal-surface-extract/blob/main/LICENSE)
+[![ci](https://github.com/FNNDSC/pl-fetal-surface-extract/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-fetal-surface-extract/actions/workflows/ci.yml)
 
 Fetal brain cortical plate surface extraction using CIVET marching-cubes (`sphere_mesh`).
 
 ![Figure](docs/fig.png)
 
 ## Abstract
 
-`pl-fetal-cp-surface-extract` consumes binary volumetric `.mnc` brain masks to produce
+`pl-fetal-surface-extract` consumes binary volumetric `.mnc` brain masks to produce
 surfaces as `.obj` files with standard connectivity (81,920 triangles). This program is
 suitable for targeting the **inner cortical plate** surface (gray-white matter boundary)
 of high-quality human fetal brain MRI segmentation for subjects between 23-35 gestational
@@ -21,29 +21,29 @@ weeks of age.
 Polygonal surface mesh representations of brain hemispheres are useful for measuring cortical
 thickness, image registration, and quantitative regional analysis.
 
-## Marching Cubes
+## Surface Extraction Algorithm
+
+1. Preprocess mask using `mincmorph` to fill in disconnected voxels (improve mask quality)
+2. Marching-cubes -> spherical topology surface mesh with unknown number of triangles
+3. Calculate distance error
+4. _If_ maximum distance error is too large, _then_ redo marching-cubes with subsampling
+5. Sphere-to-sphere interpolation -> resample mesh to standard connectivity of 81,920 triangles, preserving morphology
+6. Calculate smoothness error
+7. Run `adapt_object_mesh` to achieve desired smoothness. Number of iterations is predicted by a regression
+
+### Marching Cubes
 
 We have evaluated two implementations of marching-cubes:
 
-- [scikit-image](https://github.com/FNNDSC/pl-fetal-cp-surface-extract)
+- [scikit-image](https://github.com/FNNDSC/pl-fetal-surface-extract)
 - [CIVET](https://github.com/FNNDSC/ep-sphere_mesh)
 
 We found that CIVET's implementation of the marching-cubes algorithm, `sphere_mesh`, is
 [more accurate](docs/compare_civet_skimage.md)
 than scikit-image's implementation, which requires FWHM blurring of the volume.
 Moreover, `sphere_mesh` guarantees a spherical topology.
 
-## Surface Extraction Algorithm
-
-1. Preprocess mask using `mincmorph` to fill in disconnected voxels (improve mask quality)
-2. Marching-cubes -> spherical topology surface mesh with unknown number of triangles
-3. Calculate distance error
-4. _If_ maximum distance error is too large, _then_ redo marching-cubes with subsampling
-5. Sphere-to-sphere interpolation -> resample mesh to standard connectivity of 81,920 triangles, preserving morphology
-6. Calculate smoothness error
-7. Run `adapt_object_mesh` to achieve desired smoothness. Number of iterations is predicted by a regression model
-
-### Estimation of: How much smoothing?
+### How much Smoothing? Estimation
 
 We developed a model which predicts the number of `adapt_object_mesh` smoothing iterations necessary, given a desired smoothness error threshold.
 The model was created from the experiment described here:
@@ -55,7 +55,7 @@ The model was created from the experiment described here:
 1. https://github.com/FNNDSC/ep-premc-mincmorph
 2. https://github.com/FNNDSC/pl-nums2mask
 3. https://github.com/FNNDSC/pl-subdiv-minc TODO
-4. pl-fetal-cp-surface-extract
+4. pl-fetal-surface-extract
 5. pl-extracted-surface-asp TODO
 
 <!--
@@ -67,10 +67,10 @@ without the extra step the accuracy is nonetheless sufficient.
 
 ## Installation
 
-`pl-fetal-cp-surface-extract` is a _[ChRIS](https://chrisproject.org/) plugin_, meaning it can
+`pl-fetal-surface-extract` is a _[ChRIS](https://chrisproject.org/) plugin_, meaning it can
 run from either within _ChRIS_ or the command-line.
 
-[![Get it from chrisstore.co](https://raw.githubusercontent.com/FNNDSC/ChRIS_store_ui/963938c241636e4c3dc4753ee1327f56cb82d8b5/src/assets/public/badges/light.svg)](https://chrisstore.co/plugin/pl-fetal-cp-surface-extract)
+[![Get it from chrisstore.co](https://raw.githubusercontent.com/FNNDSC/ChRIS_store_ui/963938c241636e4c3dc4753ee1327f56cb82d8b5/src/assets/public/badges/light.svg)](https://chrisstore.co/plugin/pl-fetal-surface-extract)
 
 ## Usage
 
@@ -98,31 +98,31 @@ values shouldn't do any harm, and would help compensate for larger brain sizes.
 
 Copy input mask file to output directory.
 
-`--keep-mask` is a workaround for using `pl-fetal-cp-surface-extract` as part of a
+`--keep-mask` is a workaround for using `pl-fetal-surface-extract` as part of a
 _ChRIS_ pipeline. It eliminates the need for an extra _ts_ plugin step.
 
 ## Local Usage
 
 To get started with local command-line usage, use [Apptainer](https://apptainer.org/)
-to run `pl-fetal-cp-surface-extract` as a container:
+to run `pl-fetal-surface-extract` as a container:
 
 ```shell
-apptainer exec docker://fnndsc/pl-fetal-cp-surface-extract extract_cp input/ output/
+apptainer exec docker://fnndsc/pl-fetal-surface-extract extract_cp input/ output/
 ```
 
 To print its available options, run:
 
 ```shell
-apptainer exec docker://fnndsc/pl-fetal-cp-surface-extract extract_cp --help
+apptainer exec docker://fnndsc/pl-fetal-surface-extract extract_cp --help
 ```
 
 ## Suggested Software
 
-### Before `pl-fetal-cp-surface-extract`
+### Before `pl-fetal-surface-extract`
 
 - [`pl-nums2mask`](https://chrisstore.co/plugin/pl-nums2mask): create input masks
 
-### After `pl-fetal-cp-surface-extract`
+### After `pl-fetal-surface-extract`
 
 - [`pl-surfdisterr`](https://chrisstore.co/plugin/pl-surfdisterr): QC
 - [`pl-smoothness-error`](https://chrisstore.co/plugin/pl-smoothness-error): QC
@@ -136,7 +136,7 @@ Instructions for developers.
 Build a local container image:
 
 ```shell
-docker build -t localhost/fnndsc/pl-fetal-cp-surface-extract .
+docker build -t localhost/fnndsc/pl-fetal-surface-extract .
 ```
 
 ### Get JSON Representation
@@ -145,7 +145,7 @@ Run [`chris_plugin_info`](https://github.com/FNNDSC/chris_plugin#usage)
 to produce a JSON description of this plugin, which can be uploaded to a _ChRIS Store_.
 
 ```shell
-docker run --rm localhost/fnndsc/pl-fetal-cp-surface-extract chris_plugin_info > chris_plugin_info.json
+docker run --rm localhost/fnndsc/pl-fetal-surface-extract chris_plugin_info > chris_plugin_info.json
 ```
 
 ### Local Test Run
@@ -156,5 +156,5 @@ Mount the source code `extract_cp.py` into a container to test changes without r
 docker run --rm -it --userns=host -u $(id -u):$(id -g) \
     -v $PWD/extract_cp:/opt/conda/lib/python3.10/site-packages/extract_cp:ro \
     -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
-    localhost/fnndsc/pl-fetal-cp-surface-extract extract_cp /incoming /outgoing
+    localhost/fnndsc/pl-fetal-surface-extract extract_cp /incoming /outgoing
 ```
diff --git a/docs/compare_civet_skimage.md b/docs/compare_civet_skimage.md
@@ -1,5 +1,5 @@
 Brief comparison of marching-cubes implementations between
-[scikit-image](https://github.com/FNNDSC/pl-fetal-cp-surface-extract)
+[scikit-image](https://github.com/FNNDSC/pl-fetal-surface-extract)
 and [CIVET](https://github.com/FNNDSC/ep-sphere_mesh).
 
 Cost function is mean

diff --git a/setup.py b/setup.py
@@ -1,13 +1,13 @@
-from setuptools import setup
+from setuptools import setup, find_packages
 
 setup(
     name='extract_cp',
     version='2.0.1',
     description='Fetal brain MRI CP surface extraction using CIVET marching-cubes',
     author='Jennings Zhang',
     author_email='[email protected]',
-    url='https://github.com/FNNDSC/pl-fetal-cp-surface-extract',
-    packages=['extract_cp'],
+    url='https://github.com/FNNDSC/pl-fetal-surface-extract',
+    packages=find_packages(exclude=['tests']),
     install_requires=['chris_plugin', 'loguru', 'pycivet', 'pybicpl', 'numpy'],
     license='MIT',
     entry_points={