Merge pull request #21 from neuro-ml/fix-starter-example

remove bad formatting

.github/workflows/release.yml

@@ -4,15 +4,18 @@ on:
   release:
     types: [ released ]
 
+env:
+  MODULE_NAME: dicom_csv
+
 jobs:
   build:
 
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
 
@@ -24,7 +27,7 @@ jobs:
         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 $VERSION) || echo
+          MATCH=$(pip index versions $MODULE_NAME | 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

.github/workflows/tests.yml

@@ -1,28 +1,34 @@
 name: Python package
 
-on: [ push, pull_request ]
+on: [ pull_request ]
+
+env:
+  MODULE_NAME: dicom_csv
 
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: [ 3.6, 3.7, 3.8, 3.9 ]
+        python-version: [ '3.6', '3.7', '3.8', '3.9', '3.10', '3.11' ]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Check the version and build the package
+      - name: Check the version
+        if: "! github.event.pull_request.head.repo.fork "
         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 $VERSION) || echo
+          MATCH=$(pip index versions $MODULE_NAME | grep "Available versions:" | grep $VERSION) || echo
           echo $MATCH
           if [ "$GITHUB_BASE_REF" = "master" ] && [ "$MATCH" != "" ]; then exit 1; fi
+      - name: Build the package
+        run: |
           python setup.py sdist
 
       - name: Install

README.md

@@ -35,22 +35,22 @@ pip install -e .
 from a series of dicom files (each containing 2D image)
 
 ```python
->>> from dicom_csv import join_tree, order_series, stack_images
->>> from pydicom import dcmread
->>> from pathlib import Path
->>>
->>> # 1. Collect metadata from all dicom files
->>> folder = Path('/path/to/folder/')
->>> meta = join_tree(folder, verbose=2)
->>>
->>> # 2. Select series to load
->>> uid = '...' # unique identifier of a series you want to load,
->>>             # you could list them by `meta.SeriesInstanceUID.unique()`
->>> series = meta.query("SeriesInstanceUID==@uid")
->>>
->>> # 3. Read files & combine them into a single volume
->>> images2d = [dcmread(folder / row[1].PathToFolder / row[1].FileName) for row in series.iterrows()] 
->>> image3d = stack_images(order_series(images2d))
+from dicom_csv import join_tree, order_series, stack_images
+from pydicom import dcmread
+from pathlib import Path
+
+# 1. Collect metadata from all dicom files
+folder = Path('/path/to/folder/')
+meta = join_tree(folder, verbose=2)
+
+# 2. Select series to load
+uid = '...' # unique identifier of a series you want to load,
+            # you could list them by `meta.SeriesInstanceUID.unique()`
+series = meta.query("SeriesInstanceUID==@uid")
+
+# 3. Read files & combine them into a single volume
+images2d = [dcmread(folder / row[1].PathToFolder / row[1].FileName) for row in series.iterrows()] 
+image3d = stack_images(order_series(images2d))
 ```
 
 # Documentation

dicom_csv/__version__.py

@@ -1 +1 @@
-__version__ = '0.2.5'
+__version__ = '0.2.6'

dicom_csv/spatial.py

@@ -210,7 +210,7 @@ def get_image_size(series: Series) -> Tuple[int, int, int]:
     rows = get_common_tag(series, 'Rows')
     columns = get_common_tag(series, 'Columns')
     slices = len(series)
-    return rows, columns, slices
+    return int(rows), int(columns), slices
 
 
 def drop_duplicated_slices(series: Series, tolerance_hu=1) -> Series: