Merge pull request #14 from andreped/post-processing

Improved morphological post-processing [no ci]

.github/workflows/build.yml

@@ -14,10 +14,10 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v1
-      - name: Set up Python 3.6
+      - name: Set up Python 3.7
         uses: actions/setup-python@v2
         with:
-          python-version: 3.6
+          python-version: 3.7
 
       - name: Install dependencies
         run: |

.github/workflows/release.yml

@@ -0,0 +1,35 @@
+name: Release
+
+on:
+  push:
+    branches: 
+      - '*'
+  pull_request:
+    branches: 
+      - '*'
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v1
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install wheel setuptools
+
+      - name: Build wheel
+        run: python setup.py bdist_wheel --universal
+
+      - name: Upload Python wheel
+        uses: actions/upload-artifact@v2
+        with:
+          name: Python wheel
+          path: ${{github.workspace}}/dist/lungtumormask-*.whl
+          if-no-files-found: error

README.md

@@ -17,7 +17,7 @@ Software has been tested against Python `3.7-3.10`.
 
 Stable latest release:
 ```
-pip install https://github.com/VemundFredriksen/LungTumorMask/releases/download/v1.1.3/lungtumormask-1.1.3-py2.py3-none-any.whl
+pip install https://github.com/VemundFredriksen/LungTumorMask/releases/download/v1.2.0/lungtumormask-1.2.0-py2.py3-none-any.whl
 ```
 
 Or from source:

lungtumormask/__main__.py

@@ -16,7 +16,7 @@ def main():
     parser.add_argument('--lung-filter', action='store_true', help='whether to apply lungmask postprocessing.')
     parser.add_argument('--threshold', metavar='threshold', type=float, default=0.5, 
                         help='which threshold to use for assigning voxel-wise classes.')
-    parser.add_argument('--radius', metavar='radius', type=int, default=5,
+    parser.add_argument('--radius', metavar='radius', type=int, default=1,
                         help='which radius to use for morphological post-processing segmentation smoothing.')
 
     argsin = sys.argv[1:]

lungtumormask/dataprocessing.py

@@ -8,7 +8,7 @@
 import numpy as np
 from monai.transforms import (Compose, LoadImaged, ToNumpyd, ThresholdIntensityd, AddChanneld, NormalizeIntensityd, SpatialCropd, DivisiblePadd, Spacingd, SqueezeDimd)
 from tqdm import tqdm
-from skimage.morphology import binary_closing, ball
+from skimage.morphology import binary_closing, disk
 
 def mask_lung(scan_path, batch_size=20):
     model = lungmask.mask.get_model('unet', 'R231')
@@ -239,6 +239,7 @@ def post_process(left, right, preprocess_dump, lung_filter, threshold, radius):
         stitched[preprocess_dump['lungmask'] == 0] = 0
 
     # final post-processing - fix fragmentation
-    stitched = binary_closing(stitched, footprint=ball(radius=radius))
+    for i in range(stitched.shape[-1]):
+        stitched[..., i] = binary_closing(stitched[..., i], footprint=disk(radius=radius))
 
     return stitched

setup.py

@@ -3,7 +3,7 @@
 setup(
     name="lungtumormask",
     packages=find_packages(),
-    version='1.1.3',
+    version='1.2.0',
     author="Svein Ole M Sevle, Vemund Fredriksen, and André Pedersen",
     url="https://github.com/VemundFredriksen/LungTumorMask",
     license="MIT",