Handle .txt and add test

.github/workflows/ci.yml

@@ -82,13 +82,41 @@ jobs:
           tags: ${{ steps.info.outputs.local_tag }}
           load: true
           cache-from: type=gha
-      # If you have a directory called examples/incoming/ and examples/outgoing/, then
-      # run your ChRIS plugin with no parameters, and assert that it creates all the files
-      # which are expected. File contents are not compared.
+      - name: Download example data
+        run: examples/download.sh
       - name: Run examples
         id: run_examples
         run: |
-          echo TODO
+          mkdir /tmp/outgoing
+          docker run --rm -u "$(id -u):$(id -g)" \
+            -v "${{ github.workspace }}/examples/incoming:/incoming:ro" \
+            -v "/tmp/outgoing"/outgoing:rw" \
+            ${{ steps.info.outputs.local_tag }}
+            mni2common /incoming /outgoing
+      - name: Assert example outputs are found
+        run: |
+          expected_outputs=(
+            outgoing/colin27_t1_tal_lin.mnc2nii.log
+            outgoing/colin27_t1_tal_lin.nii
+            outgoing/colin27_t1_tal_lin_headmask.mnc2nii.log
+            outgoing/colin27_t1_tal_lin_headmask.nii
+            outgoing/colin27_t1_tal_lin_mask.mnc2nii.log
+            outgoing/colin27_t1_tal_lin_mask.nii
+            outgoing/colin_white_mc_left.mz3
+            outgoing/colin_white_mc_mask_left.mz3
+            outgoing/colin_white_mc_mask_right.mz3
+            outgoing/colin_white_mc_right.mz3
+          )
+
+          for expected_output in "${expected_outputs[@]}"; do
+            if ! [ -f "$1" ]; then
+              echo "expected $1 to be a file, but it does not."
+              parent_dir="$(dirname "$1")"
+              set -ex
+              ls -lh "$parent_dir"
+              exit 1
+            fi
+          done
 
       - name: Login to DockerHub
         if: (github.event_name == 'push' || github.event_name == 'release') && contains(steps.info.outputs.tags_csv, 'docker.io')

Dockerfile

@@ -1,26 +1,27 @@
-FROM docker.io/fnndsc/pl-mni2common:base-1
+FROM docker.io/fnndsc/pl-mni2common:base-2 AS base
 
-LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \
-      org.opencontainers.image.title="pl-mnc2common" \
-      org.opencontainers.image.description="A ChRIS plugin to convert MINC volume and MNI .obj surface file formats to NIFTI and Wavefront OBJ respectively."
+FROM base AS mni2mz3-installer
+
+RUN apt-get update \
+    && apt-get install -y curl
 
-# use micromamba to install binary python dependencies for multiarch build
-RUN \
-    --mount=type=cache,sharing=private,target=/home/mambauser/.mamba/pkgs,uid=57439,gid=57439 \
-    --mount=type=cache,sharing=private,target=/opt/conda/pkgs,uid=57439,gid=57439 \
-    micromamba install -y -n base -c conda-forge python=3.11.5 numpy=1.26.0
+RUN curl --proto '=https' --tlsv1.2 -LsSf 'https://github.com/FNNDSC/mni2mz3/releases/download/v1.0.0-rc.5/installer.sh' | bash
+
+FROM base
+
+LABEL org.opencontainers.image.authors="Jennings.Zhang <[email protected]>" \
+      org.opencontainers.image.title="pl-mnc2common" \
+      org.opencontainers.image.description="A ChRIS plugin to convert MINC volume, .txt surface data, and MNI .obj surface file formats to NIFTI and MZ3."
 
 ARG SRCDIR=/usr/local/src/pl-mni2common
 WORKDIR ${SRCDIR}
 
-COPY --chown=57439:57439 requirements.txt .
-RUN --mount=type=cache,sharing=private,target=/home/mambauser/.cache/pip,uid=57439,gid=57439 \
-    pip install -r requirements.txt
-
-COPY --chown=mambauser:mambauser . .
+COPY . .
 ARG extras_require=none
 RUN pip install ".[${extras_require}]" \
     && cd / && rm -rf ${SRCDIR}/*
 WORKDIR /
 
+COPY --from=mni2mz3-installer /usr/local/bin/mni2mz3 /usr/local/bin/mni2mz3
+
 CMD ["mni2common"]

README.md

@@ -5,12 +5,11 @@
 [![ci](https://github.com/FNNDSC/pl-mni2common/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-mni2common/actions/workflows/ci.yml)
 
 `pl-mni2common` is a [_ChRIS_](https://chrisproject.org/)
-_ds_ plugin which takes in ...  as input files and
-creates ... as output files.
-
-## Abstract
-
-...
+_ds_ plugin wrapper around the programs
+[mnc2nii](https://bic-mni.github.io/man-pages/man/mnc2nii.html)
+and [mni2mz3](https://github.com/FNNDSC/mni2mz3).
+It converts MINC volumes to NIFTI, surfaces to MZ3, and surface data to MZ3.
+The output file formats NIFTI and MZ3 are convenient for visualization by [niivue](https://github.com/niivue/niivue).
 
 ## Installation
 

base/Dockerfile

@@ -2,9 +2,9 @@ FROM docker.io/fnndsc/microminc-builder:latest as builder
 
 RUN microminc.sh mnc2nii /microminc
 
-FROM ghcr.io/mamba-org/micromamba:1.5.1-bookworm-slim
+FROM python:3.12.0-slim-bullseye
 COPY --from=builder /microminc /opt/microminc
-ENV PATH=/opt/conda/bin:/opt/microminc/bin:$PATH \
+ENV PATH=/opt/microminc/bin:$PATH \
     LD_LIBRARY_PATH=/opt/microminc/lib:$LD_LIBRARY_PATH \
     MINC_FORCE_V2=1 MINC_COMPRESS=4 VOLUME_CACHE_THRESHOLD=-1 \
     MNI_DATAPATH=/opt/microminc/share

base/build.sh

@@ -2,4 +2,4 @@
 
 exec docker buildx build --push \
     --platform linux/amd64,linux/arm64,linux/ppc64le \
-    -t docker.io/fnndsc/pl-mni2common:base-1 .
+    -t docker.io/fnndsc/pl-mni2common:base-2 .

examples/.gitignore

@@ -0,0 +1,2 @@
+/incoming
+/outgoing

examples/download.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+HERE="$(dirname "$(readlink -f "$0")")"
+
+urls=(
+  https://github.com/aces/CIVET/raw/9818b3cbe8308249e7c373ef1a2a53956512143e/models/colin/colin_white_mc_mask_left.txt
+  https://github.com/aces/CIVET/raw/9818b3cbe8308249e7c373ef1a2a53956512143e/models/colin/colin_white_mc_mask_right.txt
+  https://github.com/aces/CIVET/raw/9818b3cbe8308249e7c373ef1a2a53956512143e/models/colin/colin_white_mc_left.obj
+  https://github.com/aces/CIVET/raw/9818b3cbe8308249e7c373ef1a2a53956512143e/models/colin/colin_white_mc_right.obj
+  https://github.com/aces/mni-models_colin27-lin/raw/60787485e2ed4e012bda4da8fc2b163384fc3431/colin27_t1_tal_lin.mnc.gz
+  https://github.com/aces/mni-models_colin27-lin/raw/60787485e2ed4e012bda4da8fc2b163384fc3431/colin27_t1_tal_lin_headmask.mnc.gz
+  https://github.com/aces/mni-models_colin27-lin/raw/60787485e2ed4e012bda4da8fc2b163384fc3431/colin27_t1_tal_lin_mask.mnc.gz
+)
+
+set -ex
+
+cd "$HERE"
+mkdir -v incoming
+cd incoming
+
+parallel wget -q ::: ${urls[@]}
+find -type f -name '*.gz' | parallel gzip -d

mni2common.py

@@ -9,7 +9,6 @@
 from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter
 from tqdm.contrib.concurrent import thread_map
 from tqdm.contrib.logging import logging_redirect_tqdm
-from bicpl import PolygonObj, WavefrontObj
 
 from chris_plugin import chris_plugin, PathMapper
 
@@ -27,7 +26,7 @@
 """
 
 
-parser = ArgumentParser(description='Convert MINC and .obj to NIFTI and Wavefront respectively',
+parser = ArgumentParser(description='Convert MINC and .obj to NIFTI and MZ3 respectively',
                         formatter_class=ArgumentDefaultsHelpFormatter)
 parser.add_argument('-p', '--pattern', default='**/*', type=str,
                     help='Path filter')
@@ -60,12 +59,15 @@ def main(options: Namespace, inputdir: Path, outputdir: Path):
 
 def convert_file(file_pair: tuple[Path, Path]) -> bool:
     input_file, output_file = file_pair
-    if input_file.suffix == '.mnc':
-        return convert_minc(input_file, output_file.with_suffix('.nii'))
-    elif input_file.suffix == '.obj':
-        return convert_obj(input_file, output_file.with_suffix('.wf.obj'))
-    shutil.copy2(input_file, output_file)
-    return True
+    match input_file.suffix:
+        case '.mnc':
+            return convert_minc(input_file, output_file.with_suffix('.nii'))
+        case '.obj' | '.txt':
+            return mni2mz3(input_file, output_file.with_suffix('.mz3'))
+        case _:
+            if os.path.realpath(input_file) != os.path.realpath(output_file):
+                shutil.copy2(input_file, output_file)
+            return True
 
 
 def convert_minc(mnc, nii) -> bool:
@@ -79,16 +81,19 @@ def convert_minc(mnc, nii) -> bool:
     return False
 
 
-def convert_obj(mniobj_path, wavefront_path) -> bool:
-    try:
-        obj = PolygonObj.from_file(mniobj_path)
-        wf = WavefrontObj.from_mni(obj)
-        with wavefront_path.open('w') as f:
-            wf.write_to(f)
+def mni2mz3(input_path, output_path) -> bool:
+    cmd = ('mni2mz3', str(input_path), str(output_path))
+    proc = sp.run(cmd, stderr=sp.PIPE, stdout=sp.DEVNULL)
+    if proc.returncode == 0:
+        return True
+    # is a .txt file, but not a vertex-wise surface data file
+    if input_path.suffix == '.txt' and b'Could not parse 0th value as float' in proc.stderr:
+        output_txt = output_path.with_suffix(input_path.suffix)
+        if os.path.realpath(input_path) != os.path.realpath(output_txt):
+            shutil.copy2(input_path, output_txt)
         return True
-    except Exception as e:
-        LOG.error(str(e))
-        return False
+    LOG.error(f'Command failed: {shlex.join(cmd)}')
+    return False
 
 
 if __name__ == '__main__':

setup.py

@@ -21,12 +21,12 @@ def get_version(rel_path: str) -> str:
 setup(
     name='mni2common',
     version=get_version('mni2common.py'),
-    description='A ChRIS plugin to convert MINC volume and MNI .obj surface file formats to NIFTI and Wavefront OBJ respectively.',
+    description='A ChRIS plugin to convert MINC volume and MNI .obj surface file formats to NIFTI and MZ3 OBJ respectively.',
     author='FNNDSC',
     author_email='[email protected]',
     url='https://github.com/FNNDSC/pl-mni2common',
     py_modules=['mni2common'],
-    install_requires=['chris_plugin', 'pybicpl', 'tqdm'],
+    install_requires=['chris_plugin==0.3.1', 'tqdm~=4.66'],
     license='MIT',
     entry_points={
         'console_scripts': [