Merge pull request #15 from neuro-ml/dev

added to_color_space to stack images

.github/workflows/release.yml

@@ -0,0 +1,36 @@
+name: Python package
+
+on:
+  release:
+    types: [ released ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - id: get_version
+        name: Get the release version
+        uses: battila7/get-version-action@v2
+
+      - name: Check the version and build the package
+        run: |
+          RELEASE=${{ steps.get_version.outputs.version-without-v }}
+          VERSION=$(python -c "from pathlib import Path; import runpy; folder, = {d.parent for d in Path().resolve().glob('*/__init__.py') if d.parent.is_dir() and (d.parent / '__version__.py').exists()}; print(runpy.run_path(folder / '__version__.py')['__version__'])")
+          MATCH=$(pip index versions dicom-csv | grep "Available versions:" | grep $VERSION) || echo
+          echo $MATCH
+          if [ "$GITHUB_BASE_REF" = "master" ] && [ "$MATCH" != "" ]; then echo "Version $VERSION already present" && exit 1; fi
+          if [ "$VERSION" != "$RELEASE" ]; then echo "$VERSION vs $RELEASE" && exit 1; fi
+          python setup.py sdist
+
+      - name: Publish to PyPi
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/tests.yml

@@ -0,0 +1,30 @@
+name: Python package
+
+on: [ push, pull_request ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ 3.6, 3.7, 3.8, 3.9 ]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Check the version and build the package
+        run: |
+          VERSION=$(python -c "from pathlib import Path; import runpy; folder, = {d.parent for d in Path().resolve().glob('*/__init__.py') if d.parent.is_dir() and (d.parent / '__version__.py').exists()}; print(runpy.run_path(folder / '__version__.py')['__version__'])")
+          MATCH=$(pip index versions dicom-csv | grep "Available versions:" | grep $VERSION) || echo
+          echo $MATCH
+          if [ "$GITHUB_BASE_REF" = "master" ] && [ "$MATCH" != "" ]; then exit 1; fi
+          python setup.py sdist
+
+      - name: Install
+        run: |
+          pip install dist/*

dicom_csv/__version__.py

@@ -1 +1 @@
-__version__ = '0.2.1'
+__version__ = '0.2.2'

dicom_csv/misc.py

@@ -1,22 +1,29 @@
 import os
 import warnings
+from functools import partial
 from operator import itemgetter
 from os.path import join as jp
+from typing import Optional
 
 import numpy as np
+from pydicom.pixel_data_handlers import convert_color_space
 
 from .utils import *
 
 __all__ = 'get_image', 'stack_images'
 
 
-def get_image(instance: Dataset):
+def get_image(instance: Dataset, to_color_space: Optional[str] = None):
     def _to_int(x):
+        # this little trick helps to avoid unneeded type casting
         if x == int(x):
             x = int(x)
         return x
 
     array = instance.pixel_array
+    if to_color_space is not None:
+        array = convert_color_space(array, instance.PhotometricInterpretation, to_color_space)
+
     slope, intercept = instance.get('RescaleSlope'), instance.get('RescaleIntercept')
     if slope is not None and slope != 1:
         array = array * _to_int(slope)
@@ -26,8 +33,8 @@ def _to_int(x):
     return array
 
 
-def stack_images(series: Series, axis: int = -1):
-    return np.stack(list(map(get_image, series)), axis)
+def stack_images(series: Series, axis: int = -1, to_color_space: Optional[str] = None):
+    return np.stack(list(map(partial(get_image, to_color_space=to_color_space), series)), axis)
 
 
 # TODO: legacy support