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.github/workflows/build.yml

@@ -0,0 +1,114 @@
+# Automatically build multi-architectural tagged container images and push them to DockerHub
+# https://github.com/FNNDSC/cookiecutter-chrisapp/wiki/Automatic-Builds
+
+name: build
+
+on:
+  push:
+    branches: [ main ]
+    tags: [ '**' ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  publish:
+    if: github.event_name == 'push' || github.event_name == 'release'
+    runs-on: ubuntu-20.04
+
+    services:
+      registry:
+        image: registry:2
+        ports:
+          - 5000:5000
+
+    steps:
+      - name: Get git tag
+        id: git_info
+        if: startsWith(github.ref, 'refs/tags/')
+        run: echo "::set-output name=tag::${GITHUB_REF##*/}"
+      - name: Decide image tag name
+        id: determine
+        env:
+          git_tag: ${{ steps.git_info.outputs.tag }}
+        run: |
+          repo="${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
+      - uses: docker/setup-qemu-action@v1
+      - uses: docker/setup-buildx-action@v1
+        with:
+          driver-opts: network=host
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        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
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v1 
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push
+        uses: docker/build-push-action@v2
+        id: docker_build
+        with:
+          context: .
+          file: ./Dockerfile
+          tags: |
+            ${{ steps.determine.outputs.dock_image }}
+            localhost:5000/${{ steps.determine.outputs.dock_image }}
+            ghcr.io/${{ steps.determine.outputs.dock_image }}
+          platforms: linux/amd64,linux/arm64,linux/ppc64le
+          push: true
+          cache-from: type=local,src=/tmp/.buildx-cache
+          cache-to: type=local,dest=/tmp/.buildx-cache
+
+      - name: Get plugin meta
+        id: pluginmeta
+        run: |
+          repo=${{ steps.determine.outputs.repo }}
+          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)"
+
+      - name: Update DockerHub description
+        uses: peter-evans/dockerhub-description@v2
+        continue-on-error: true  # it is not crucial that this works
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+          short-description: ${{ steps.pluginmeta.outputs.title }}
+          readme-filepath: ./README.md
+          repository: ${{ steps.determine.outputs.repo }}
+
+      - name: Upload to ChRIS Store
+        if: "!endsWith(steps.determine.outputs.dock_image, ':latest')"
+        uses: FNNDSC/chrisstore-action@master
+        with:
+          descriptor_file: /tmp/description.json
+          auth: ${{ secrets.CHRIS_STORE_USER }}

Dockerfile

@@ -1,18 +1,15 @@
-# Python version can be changed, e.g.
-# FROM python:3.8
-# FROM docker.io/fnndsc/conda:python3.10.2-cuda11.6.0
-FROM docker.io/python:3.10.2-slim-buster
+FROM docker.io/fnndsc/mni-conda-base:civet2.1.1-python3.10.2
 
 LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \
-      org.opencontainers.image.title="ChRIS Plugin Title" \
-      org.opencontainers.image.description="A ChRIS ds plugin that..."
+      org.opencontainers.image.title="ep-interpolate-surface-with-sphere" \
+      org.opencontainers.image.description="Resample surface meshes to have 81,920 triangles."
 
-WORKDIR /usr/local/src/app
+WORKDIR /usr/local/src/ep-interpolate-surface-with-sphere
 
 COPY requirements.txt .
 RUN pip install -r requirements.txt
 
 COPY . .
 RUN pip install .
 
-CMD ["commandname", "--help"]
+CMD ["isws", "--help"]

README.md

@@ -1,82 +1,8 @@
-# _ChRIS_ ds Plugin Template
+# ep-interpolate-surface-with-sphere
 
-<!--
-[![Version](https://img.shields.io/docker/v/fnndsc/pl-appname?sort=semver)](https://hub.docker.com/r/fnndsc/pl-appname)
-[![MIT License](https://img.shields.io/github/license/fnndsc/pl-appname)](https://github.com/FNNDSC/pl-appname/blob/main/LICENSE)
-[![Build](https://github.com/FNNDSC/pl-appname/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-appname/actions)
--->
+[![Version](https://img.shields.io/docker/v/fnndsc/ep-interpolate-surface-with-sphere?sort=semver)](https://hub.docker.com/r/fnndsc/ep-interpolate-surface-with-sphere)
+[![MIT License](https://img.shields.io/github/license/fnndsc/ep-interpolate-surface-with-sphere)](https://github.com/FNNDSC/ep-interpolate-surface-with-sphere/blob/main/LICENSE)
+[![Build](https://github.com/FNNDSC/ep-interpolate-surface-with-sphere/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/ep-interpolate-surface-with-sphere/actions)
 
-
-This is a minimal template repository for _ChRIS_ _ds_ plugin applications.
-For a more comprehensive boilerplate, use
-
-https://github.com/fnndsc/cookiecutter-chrisapp
-
-## How to Use This Template
-
-1. Click "Use this template"
-2. Clone the newly created repository
-3. Replace placeholder text
-
-```shell
-function replace () {
-  find . -type f -not -path '*/\.*/*' -not -path '*/\venv/*' -exec sed -i -e "s/$1/$2/g" '{}' \;
-}
-
-replace commandname my_command_name
-replace pl-appname pl-my-plugin-name
-replace fnndsc my_username
-```
-
-### Template Examples
-
-Here are some good, complete examples of _ChRIS_ plugins created from this template.
-
-- https://github.com/FNNDSC/pl-nums2mask
-- https://github.com/FNNDSC/pl-nii2mnc-u8
-
-Advanced users can `cp -rv .github/workflows` into their own repositories to enable
-automatic builds.
-
-## Abstract
-
-PROGRAMNAME is a [_ChRIS_](https://chrisproject.org/)
-_ds_ plugin which takes in ...  as input files and
-creates ... as output files.
-
-## Usage
-
-```shell
-singularity exec docker://fnndsc/pl-appname commandname [--args values...] input/ output/
-```
-
-## Examples
-
-```shell
-mkdir incoming/ outgoing/
-mv some.dat other.dat incoming/
-singularity exec docker://fnndsc/pl-appname:latest commandname [--args] incoming/ outgoing/
-```
-
-## Development
-
-### Building
-
-```shell
-docker build -t localhost/fnndsc/pl-appname .
-```
-
-### Get JSON Representation
-
-```shell
-docker run --rm localhost/fnndsc/pl-appname chris_plugin_info > MyProgram.json
-```
-
-### Local Test Run
-
-```shell
-docker run --rm -it --userns=host -u $(id -u):$(id -g) \
-    -v $PWD/app.py:/usr/local/lib/python3.10/site-packages/app.py:ro \
-    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
-    localhost/fnndsc/pl-appname commandname /incoming /outgoing
-```
+`ep-interpolate-surface-with-sphere` resamples surface meshes
+created by the marching-cubes algorithm to have 81,920 triangles.

isws.py

@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+
+import os
+import sys
+from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter
+from concurrent.futures import ThreadPoolExecutor
+from pathlib import Path
+
+from typing import BinaryIO, Sequence, Literal, Optional
+import subprocess
+from loguru import logger
+from chris_plugin import chris_plugin, PathMapper
+from civet.extraction import Side, IrregularSurface
+
+SIDE_OPTIONS = ('left', 'right', 'auto', 'none')
+SideStr = Literal['left', 'right', 'auto', 'none']
+
+
+parser = ArgumentParser(description='Resample surface mesh to have 81,920 triangles.',
+                        formatter_class=ArgumentDefaultsHelpFormatter)
+parser.add_argument('-s', '--side', default='auto', choices=SIDE_OPTIONS,
+                    help='brain hemisphere side. "auto" => infer from file name')
+parser.add_argument('-p', '--pattern', default='**/*.obj',
+                    help='pattern for file names to include')
+parser.add_argument('-q', '--quiet', action='store_true',
+                    help='disable status messages')
+
+
+def isws(surface: Path, output: Path, side: SideStr) -> None:
+    log_path = output.with_suffix('.log')
+    try:
+        logger.info('Processing {} to {}, log: {}', surface, output, log_path)
+        with log_path.open('wb') as log:
+            IrregularSurface(surface)\
+                .interpolate_with_sphere(pick_side(surface, side))\
+                .save(output, shell=curry_log(log))
+        logger.info('Completed {}', output)
+    except Exception as e:
+        logger.exception('Failed to process {}', surface)
+        raise e
+
+
+def curry_log(log: BinaryIO):
+    def run_with_log(cmd: Sequence[str | os.PathLike]) -> None:
+        subprocess.run(cmd, stderr=log, stdout=log, check=True)
+    return run_with_log
+
+
+def pick_side(input_path: Path, side: SideStr) -> Optional[Side]:
+    if side == 'left':
+        return Side.LEFT
+    if side == 'right':
+        return Side.RIGHT
+    if side == 'auto':
+        path = str(input_path).lower()
+        if 'left' in path:
+            return Side.LEFT
+        if 'right' in path:
+            return Side.RIGHT
+        raise ValueError(f'Substring "left" nor "right" found in: {path}')
+    if side == 'none':
+        return None
+    raise ValueError(f'side must be one of: {SIDE_OPTIONS}')
+
+
+@chris_plugin(
+    parser=parser,
+    category='MRI Processing',
+    min_memory_limit='100Mi',
+    min_cpu_limit='1000m',
+)
+def main(options: Namespace, inputdir: Path, outputdir: Path):
+    if options.quiet:
+        logger.remove()
+        logger.add(sys.stderr, level='WARNING')
+
+    nproc = len(os.sched_getaffinity(0))
+    logger.debug('Using {} threads.', nproc)
+
+    results = []
+    with ThreadPoolExecutor(max_workers=nproc) as pool:
+        mapper = PathMapper(inputdir, outputdir, glob=options.pattern, suffix='._81920.obj')
+        for mc_surface, output in mapper:
+            results.append(pool.submit(isws, mc_surface, output, options.side))
+
+    for future in results:
+        e = future.exception()
+        if e is not None:
+            raise e
+
+
+if __name__ == '__main__':
+    main()

requirements.txt

@@ -1 +1,3 @@
-chris_plugin~=0.0.12
+chris_plugin~=0.0.13
+pycivet==0.0.6
+loguru~=0.6.0

setup.py

@@ -1,21 +1,21 @@
 from setuptools import setup
 
 setup(
-    name             = 'chris-plugin-template',
-    version          = '1.0.0',
-    description      = 'A ChRIS DS plugin template',
-    author           = 'FNNDSC',
-    author_email     = '[email protected]',
-    url              = 'https://github.com/FNNDSC/python-chrisapp-template',
-    py_modules       = ['app'],
-    install_requires = ['chris_plugin'],
+    name             = 'interpolate-surface-with-sphere',
+    version          = '0.1.0',
+    description      = 'Resample a surface mesh to have 81,920 triangles.',
+    author           = 'Jennings Zhang',
+    author_email     = '[email protected]',
+    url              = 'https://github.com/FNNDSC/ep-interpolate-surface-with-sphere',
+    py_modules       = ['isws'],
+    install_requires = ['chris_plugin', 'pycivet', 'loguru'],
     license          = 'MIT',
-    python_requires  = '>=3.8.2',
+    python_requires  = '>=3.10.2',
     entry_points     = {
         'console_scripts': [
-            'commandname = app:main'
-            ]
-        },
+            'isws = isws:main'
+        ]
+    },
     classifiers      = [
         'License :: OSI Approved :: MIT License',
         'Programming Language :: Python :: 3.10',