🌼

Dockerfile

@@ -1,18 +1,20 @@
-# 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-skimage-mcubes-mni" \
+      org.opencontainers.image.description="A ChRIS ds plugin wrapper around scikit-image's implementation of marching-cubes"
 
-WORKDIR /usr/local/src/app
+WORKDIR /usr/local/src/ep-skimage-mcubes-mni
+
+# Install binary Python packages using conda, but install
+# nibabel using pip for ppc64le support
+
+RUN conda install -y -c conda-forge h5py=3.6.0 scikit-image=0.19.1
 
 COPY requirements.txt .
 RUN pip install -r requirements.txt
 
 COPY . .
 RUN pip install .
 
-CMD ["commandname", "--help"]
+CMD ["skimc", "--help"]

README.md

@@ -1,82 +1,9 @@
-# _ChRIS_ ds Plugin Template
+# ep-skimage-mcubes-mni
 
-<!--
-[![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-skimage-mcubes-mni?sort=semver)](https://hub.docker.com/r/fnndsc/ep-skimage-mcubes-mni)
+[![MIT License](https://img.shields.io/github/license/fnndsc/ep-skimage-mcubes-mni)](https://github.com/FNNDSC/ep-skimage-mcubes-mni/blob/main/LICENSE)
+[![Build](https://github.com/FNNDSC/ep-skimage-mcubes-mni/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/ep-skimage-mcubes-mni/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/" '{}' \;
-}
-
-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-skimage-mcubes-mni` is a _ChRIS_ _ds_ plugin that performs the
+[marching-cubes](https://scikit-image.org/docs/stable/auto_examples/edges/plot_marching_cubes.html)
+algorithm on binary `.mnc` masks, producing surfaces in the `.obj` file format.

requirements.txt

@@ -1 +1,5 @@
 chris_plugin~=0.0.10
+pybicpl~=0.3.0
+numpy~=1.22.2
+nibabel~=3.2.2
+loguru~=0.6.0

setup.py

@@ -1,19 +1,19 @@
 from setuptools import setup
 
 setup(
-    name             = 'chris-plugin-template',
+    name             = 'ep-skimage-mcubes-mni',
     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'],
+    description      = 'Marching-cubes implementation from scikit-image',
+    author           = 'Jennings Zhang',
+    author_email     = '[email protected]',
+    url              = 'https://github.com/jennydaman/ep-skimage-mcubes-mni',
+    py_modules       = ['skimc'],
+    install_requires = ['chris_plugin', 'pybicpl', 'nibabel', 'scikit-image', 'h5py', 'loguru'],
     license          = 'MIT',
-    python_requires  = '>=3.8.2',
+    python_requires  = '>=3.10.2',
     entry_points     = {
         'console_scripts': [
-            'commandname = app:main'
+            'skimc = skimc:main'
             ]
         },
     classifiers      = [

skimc.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python
+
+import os
+import nibabel as nib
+from nibabel.affines import apply_affine
+from skimage import measure
+from bicpl import PolygonObj
+
+from pathlib import Path
+from argparse import ArgumentParser, Namespace
+from concurrent.futures import ThreadPoolExecutor
+from loguru import logger
+from chris_plugin import chris_plugin, PathMapper
+
+parser = ArgumentParser(description='cli description')
+parser.add_argument('--spacing', default='1,1,1',
+                    help='Voxel spacing in spatial dimensions corresponding'
+                         ' to numpy array indexing dimensions (M, N, P).')
+parser.add_argument('-s', '--step-size', default=1, type=int,
+                    help='Step size in voxels. '
+                         'Larger steps yield faster but coarser results. '
+                         'The result will always be topologically correct though.')
+parser.add_argument('-m', '--method', default='lewiner',
+                    choices=('lewiner', 'lorensen'),
+                    help='Specify which of Lewiner et al. or Lorensen et al.'
+                         ' method will be used.')
+parser.add_argument('-p', '--pattern', default='**/*.mnc',
+                    help='pattern for file names to include')
+
+
+def mcubes(mask_path: Path, surface_path: Path,
+           spacing: tuple[float, float, float],
+           step_size: int,
+           method: str):
+    mask = nib.load(mask_path)
+    data = mask.get_fdata()
+    verts, faces, normals, values = measure.marching_cubes(
+        data, spacing=spacing, step_size=step_size, method=method, allow_degenerate=False
+    )
+    transformed_verts = apply_affine(mask.affine, verts)
+    obj = PolygonObj.from_data(transformed_verts, faces, normals)
+    obj.save(surface_path)
+    logger.info('Completed: {} => {}', mask_path, surface_path)
+
+
+@chris_plugin(
+    parser=parser,
+    title='Scikit-Image Marching Cubes',
+    category='Surface Extraction',
+    min_memory_limit='200Mi',
+    min_cpu_limit='1000m',
+)
+def main(options: Namespace, inputdir: Path, outputdir: Path):
+    spacing = tuple(float(n) for n in options.spacing.split(','))
+
+    logger.info('scikit-image marching_cubes: spacing={} step_size={} method={}',
+                spacing, options.step_size, options.method)
+
+    results = []
+    with ThreadPoolExecutor(max_workers=len(os.sched_getaffinity(0))) as pool:
+        mapper = PathMapper(inputdir, outputdir, glob=options.pattern, suffix='.obj')
+        for mnc, obj in mapper:
+            results.append(pool.submit(mcubes, mnc, obj, spacing, options.step_size, options.method))
+
+    for future in results:
+        future.exception()
+
+
+if __name__ == '__main__':
+    main()