Hotfix

.github/workflows/build-docs.yml

@@ -9,15 +9,15 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install Dependencies
       run: |
         pip install --upgrade pip
-        pip install .[dev]
+        pip install .[dev] --verbose
     - name: Generate Docs
       run: |
         make gen-docs

.github/workflows/build-main.yml

@@ -15,19 +15,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.9, '3.10']
         os: [ubuntu-latest, windows-latest, macOS-latest]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .[test]
+        pip install .[test] --verbose
     - name: Test with pytest
       run: |
         pytest --cov-report xml --cov=aicssegmentation aicssegmentation/tests/
@@ -36,15 +36,15 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .[test]
+        pip install .[test] --verbose
     - name: Lint with flake8
       run: |
         flake8 aicssegmentation --count --verbose --show-source --statistics

.github/workflows/publish.yml

@@ -9,11 +9,11 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/test-and-lint-manual-trigger.yml

@@ -8,19 +8,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.9, '3.10']
         os: [ubuntu-latest, windows-latest, macOS-latest]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .[test]
+        pip install .[test] --verbose
     - name: Test with pytest
       run: |
         pytest aicssegmentation/tests/
@@ -29,11 +29,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/test-and-lint.yml

@@ -7,19 +7,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.9, '3.10']
         os: [ubuntu-latest, windows-latest, macOS-latest]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .[test]
+        pip install .[test] --verbose
     - name: Test with pytest
       run: |
         pytest aicssegmentation/tests/
@@ -28,15 +28,15 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .[test]
+        pip install .[test] --verbose
     - name: Lint with flake8
       run: |
         flake8 aicssegmentation --count --verbose --show-source --statistics

aicssegmentation/structure_wrapper/seg_PCNA_lateS.py

@@ -78,13 +78,11 @@ def Workflow_PCNA_lateS(
     # smoothing with boundary preserving smoothing
     structure_img_smooth = edge_preserving_smoothing_3d(struct_img)
     structure_img_smooth_otsu = edge_preserving_smoothing_3d(struct_img_otsu)
-
 
     out_img_list.append(structure_img_smooth.copy())
     out_name_list.append("im_smooth")
     out_img_list.append(structure_img_smooth_otsu.copy())
     out_name_list.append("im_smooth_otsu")
-
 
     ###################
     # core algorithm
@@ -100,18 +98,9 @@ def Workflow_PCNA_lateS(
     response_f3 = response_f3 > vesselness_cutoff
 
     response_s3_1 = dot_3d(structure_img_smooth, log_sigma=dot_3d_sigma)
-    response_s3_3 = dot_3d(structure_img_smooth, log_sigma=3)
-
-    #bw_small_inverse = remove_small_objects(response_s3_1 > 0.035, min_size=150)
-    #bw_small = np.logical_xor(bw_small_inverse, response_s3_1 > 0.025)
-    #bw_small = response_s3_1 > 0.12
     bw_medium = response_s3_1 > 0.05
-    #bw_large =  response_s3_3 > 0.45
-    #bw_large = np.logical_or(response_s3_3 > 0.45, response_f3 > 0.5)
-    #bw_dots = np.logical_or(bw_medium, bw_large)
-    #bw = np.logical_and(bw_dots, bw_otsu_mask_removesmallobjects)
     bw = np.logical_and(bw_medium, bw_otsu_mask_removesmallobjects)
-    
+
     out_img_list.append(bw_otsu_mask.copy())
     out_name_list.append("bw_otsu_mask")
     out_img_list.append(bw_otsu_mask_removesmallobjects.copy())

aicssegmentation/structure_wrapper/seg_PCNA_lateS_hole_fill.py

@@ -16,6 +16,7 @@
 from skimage.filters import threshold_otsu
 from scipy import ndimage
 
+
 def Workflow_PCNA_lateS_hole_fill(
     struct_img: np.ndarray,
     rescale_ratio: float = -1,
@@ -75,13 +76,11 @@ def Workflow_PCNA_lateS_hole_fill(
     # smoothing with boundary preserving smoothing
     structure_img_smooth = edge_preserving_smoothing_3d(struct_img)
     structure_img_smooth_otsu = edge_preserving_smoothing_3d(struct_img_otsu)
-
 
     out_img_list.append(structure_img_smooth.copy())
     out_name_list.append("im_smooth")
     out_img_list.append(structure_img_smooth_otsu.copy())
     out_name_list.append("im_smooth_otsu")
-
 
     ###################
     # core algorithm
@@ -93,15 +92,14 @@ def Workflow_PCNA_lateS_hole_fill(
         bw_otsu_mask, min_size=otsumask_min_area, connectivity=1, in_place=False
     )
 
-
     response_s3_1 = dot_3d(structure_img_smooth, log_sigma=dot_3d_sigma)
     response_s3_2 = dot_3d(structure_img_smooth, log_sigma=2)
 
     bw_medium = response_s3_1 > 0.05
-    bw_large =  response_s3_2 > 0.095
+    bw_large = response_s3_2 > 0.095
     bw_dots = np.logical_or(bw_medium, bw_large)
     bw = np.logical_and(bw_dots, bw_otsu_mask_removesmallobjects)
-    
+
     out_img_list.append(bw_otsu_mask.copy())
     out_name_list.append("bw_otsu_mask")
     out_img_list.append(bw_otsu_mask_removesmallobjects.copy())

setup.py

@@ -72,8 +72,8 @@
         "Intended Audience :: Developers",
         "License :: Free for non-commercial use",
         "Natural Language :: English",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
     ],
     description="Part 1 of Allen Cell and Structure Segmenter",
     entry_points={