🔮

.github/workflows/ci.yml

@@ -17,27 +17,6 @@ on:
     branches: [ main ]
 
 jobs:
-  test:
-    name: Unit tests
-    runs-on: ubuntu-22.04
-    steps:
-      - uses: actions/checkout@v4
-      - uses: docker/setup-buildx-action@v3
-      - name: Build
-        uses: docker/build-push-action@v5
-        with:
-          build-args: extras_require=dev
-          context: .
-          load: true
-          push: false
-          tags: "localhost/local/app:dev"
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
-      - name: Run pytest
-        run: |
-          docker run -v "$GITHUB_WORKSPACE:/app:ro" -w /app localhost/local/app:dev \
-            pytest -o cache_dir=/tmp/pytest
-
   build:
     name: Build
     if: github.event_name == 'push' || github.event_name == 'release'
@@ -106,34 +85,31 @@ jobs:
       # If you have a directory called examples/incoming/ and examples/outgoing/, then
       # run your ChRIS plugin with no parameters, and assert that it creates all the files
       # which are expected. File contents are not compared.
+      - name: Download example data
+        run: cd examples && ./download.sh incoming
       - name: Run examples
         id: run_examples
         run: |
-          if ! [ -d 'examples/incoming/' ] || ! [ -d 'examples/outgoing/' ]; then
-            echo "No examples."
-            exit 0
-          fi
-        
           dock_image=${{ steps.info.outputs.local_tag }}
           output_dir=$(mktemp -d)
           cmd=$(docker image inspect -f '{{ (index .Config.Cmd 0) }}' $dock_image)
           docker run --rm -u "$(id -u):$(id -g)" \
             -v "$PWD/examples/incoming:/incoming:ro" \
             -v "$output_dir:/outgoing:rw" \
-            $dock_image $cmd /incoming /outgoing
+            $dock_image $cmd --thresholds template.nii.gz:37.0 /incoming /outgoing
           
-          for expected_file in $(find examples/outgoing -type f); do
-            fname="${expected_file##*/}"
-            out_path="$output_dir/$fname"
-            printf "Checking output %s exists..." "$out_path"
-            if [ -f "$out_path" ]; then
-              echo "ok"
-            else
-              echo "not found"
-              exit 1
-            fi
-          done
-
+          set +e
+          diff -q examples/incoming/age34/template.nii.gz $output_dir/age34/template.nii.gz
+          if [ "$?" = "0" ]; then
+            echo "age34/template.nii.gz should have been changed, but it was not."
+            exit 1
+          fi
+          diff -q examples/incoming/age34/mask.nii.gz $output_dir/age34/mask.nii.gz
+          if [ "$?" = "1" ]; then
+            echo "age34/template.nii.gz should have been copied, but it was changed."
+            exit 1
+          fi
+          echo "tests passed"
       - name: Login to DockerHub
         if: (github.event_name == 'push' || github.event_name == 'release') && contains(steps.info.outputs.tags_csv, 'docker.io')
         uses: docker/login-action@v3
@@ -155,7 +131,7 @@ jobs:
           file: ./Dockerfile
           tags: ${{ steps.info.outputs.tags_csv }}
           # if non-x86_84 architectures are supported, add them here
-          platforms: linux/amd64  #,linux/arm64,linux/ppc64le
+          platforms: linux/amd64,linux/arm64,linux/ppc64le
           push: ${{ steps.info.outputs.push }}
           cache-to: type=gha,mode=max
 

examples/download.sh

@@ -3,11 +3,12 @@
 
 mkdir "$1"
 cd "$1"
+mkdir age24 age34
 
-wget -O template24.nii.gz https://fetalmri-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/files/307/template.nii.gz
-wget -O ventricles24.nii.gz https://fetalmri-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/files/331/ventricles.nii.gz
-wget -O mask24.nii.gz https://fetalmri-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/files/330/mask.nii.gz
+wget -O age24/template.nii.gz https://fetalmri-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/files/307/template.nii.gz
+wget -O age24/ventricles.nii.gz https://fetalmri-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/files/331/ventricles.nii.gz
+wget -O age24/mask.nii.gz https://fetalmri-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/files/330/mask.nii.gz
 
-wget -O template34.nii.gz https://fetalmri-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/files/351/template.nii.gz
-wget -O ventricles34.nii.gz https://fetalmri-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/files/350/ventricles.nii.gz
-wget -O mask34.nii.gz https://fetalmri-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/files/310/mask.nii.gz
+wget -O age34/template.nii.gz https://fetalmri-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/files/351/template.nii.gz
+wget -O age34/ventricles.nii.gz https://fetalmri-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/files/350/ventricles.nii.gz
+wget -O age34/mask.nii.gz https://fetalmri-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/files/310/mask.nii.gz

setup.py

@@ -38,11 +38,5 @@ def get_version(rel_path: str) -> str:
         'Topic :: Scientific/Engineering',
         'Topic :: Scientific/Engineering :: Bio-Informatics',
         'Topic :: Scientific/Engineering :: Medical Science Apps.'
-    ],
-    extras_require={
-        'none': [],
-        'dev': [
-            'pytest~=7.1'
-        ]
-    }
+    ]
 )

zb.py

@@ -1,10 +1,17 @@
 #!/usr/bin/env python
-
+import os
+import shutil
+import sys
 from pathlib import Path
 from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter
-from tqdm.contrib.concurrent import process_map
+from typing import Callable
+
+import numpy as np
+import nibabel as nib
 
-from chris_plugin import chris_plugin, PathMapper
+from tqdm.contrib.concurrent import process_map, thread_map
+
+from chris_plugin import chris_plugin, PathMapper, helpers
 
 __version__ = '1.0.0'
 
@@ -22,8 +29,8 @@
 
 parser = ArgumentParser(description='Set the background intensity of MRI volumes to zero.',
                         formatter_class=ArgumentDefaultsHelpFormatter)
-parser.add_argument('-t', '--threshold', required=False, type=str,
-                    default='.nii.gz:37',
+parser.add_argument('-t', '--thresholds', required=False, type=str,
+                    default='.nii.gz:37.0',
                     help='A filename glob and background intensity threshold. Multiple pairs should be comma-separated,'
                          ' i.e. GLOB1:THRESHOLD1,GLOB2:THRESHOLD2,...')
 parser.add_argument('-J', '--threads', type=int, default=0,
@@ -36,22 +43,37 @@
 @chris_plugin(
     parser=parser,
     title='Zero MRI Background',
-    category='',                 # ref. https://chrisstore.co/plugins
-    min_memory_limit='1Gi',      # supported units: Mi, Gi
-    min_cpu_limit='1000m',       # millicores, e.g. "1000m" = 1 CPU core
+    category='MRI',              # ref. https://chrisstore.co/plugins
+    min_memory_limit='4Gi',      # supported units: Mi, Gi
+    min_cpu_limit='4000m',       # millicores, e.g. "1000m" = 1 CPU core
     min_gpu_limit=0              # set min_gpu_limit=1 to enable GPU
 )
 def main(options: Namespace, inputdir: Path, outputdir: Path):
     print(DISPLAY_TITLE, flush=True)
 
-    mapper = PathMapper.file_mapper(inputdir, outputdir, glob=options.pattern, suffix='.count.txt')
-    for input_file, output_file in mapper:
-        # The code block below is a small and easy example of how to use a ``PathMapper``.
-        # It is recommended that you put your functionality in a helper function, so that
-        # it is more legible and can be unit tested.
-        data = input_file.read_text()
-        frequency = data.count(options.word)
-        output_file.write_text(str(frequency))
+    mapper = PathMapper.file_mapper(inputdir, outputdir)
+    nproc = options.threads if options.threads else len(os.sched_getaffinity(0))
+    threshold_map = {k: float(v) for k, v in helpers.parse_csv_as_dict(options.thresholds).items()}
+    results = thread_map(curry_zerobg(threshold_map), mapper, max_workers=nproc, total=mapper.count(), maxinterval=0.1)
+    if not all(results):
+        sys.exit(1)
+
+
+def curry_zerobg(threshold_map: dict[str, float]) -> Callable[[tuple[Path, Path]], bool]:
+    return lambda t: zerobg(t[0], t[1], threshold_map)
+
+
+def zerobg(input: Path, output: Path, threshold_map: dict[str, float]) -> bool:
+    threshold = next((v for k, v in threshold_map.items() if input.name.endswith(k)), None)
+    if threshold is None:
+        shutil.copy(input, output)
+        return True
+
+    vol = nib.load(input)
+    data = vol.get_fdata()
+    result = np.where(data <= threshold, 0, data)
+    output_vol = vol.__class__(result, vol.affine, header=vol.header)
+    nib.save(output_vol, output)
 
 
 if __name__ == '__main__':