Merging updated master into dev

.github/workflows/docmd-wiki.yml

@@ -0,0 +1,60 @@
+name: Generate and Push Docs to Wiki
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  generate-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout wiki repo
+        uses: actions/checkout@v4
+        with:
+            repository: ${{ github.repository }}.wiki
+            path: wiki
+
+      - name: Checkout PyPlaque repo
+        uses: actions/checkout@v4
+        with:
+            repository: ${{ github.repository }}
+            path: PyPlaque
+
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install docmd
+        run: pip install docmd
+
+      - name: Check existing paths
+        run: |
+          pwd
+          ls
+
+      - name: Create MD files from PyPlaque docstrings
+        run: |
+          cd PyPlaque
+          pwd
+          pip install -e .
+          docmd PyPlaque.experiment --out ../wiki
+          docmd PyPlaque.phenotypes --out ../wiki
+          docmd PyPlaque.specimen --out ../wiki
+          docmd PyPlaque.utils --out ../wiki
+          docmd PyPlaque.view --out ../wiki
+
+      - name: Check existing paths
+        run: |
+          pwd
+          ls
+
+      - name: Run script to update wiki
+        run: |
+          cd wiki
+          git config --global user.email "noreply@github.com"
+          git config --global user.name "gh_actions_runner"
+          git add .
+          git commit -m "Updated wiki with a new page"
+          git push

PyPlaque/utils/picks.py

@@ -1,10 +1,23 @@
 import numpy as np
 from scipy import ndimage as ndi
 
-STREL_4 = np.array([[0, 1, 0],
+def get_strel(neighbourhood):
+    """
+    **get_strel Function**
+        This function returns structural elements of the defined neighbourhood.
+
+    Args:
+        neighbourhood (int, required): Neighbourhood value of 4 or 8.
+
+    Returns:
+        np.uint8 array of the structural element.
+    """
+    if neighbourhood == 4:
+        return np.array([[0, 1, 0],
                     [1, 1, 1],
                     [0, 1, 0]], dtype=np.uint8)
-STREL_8 = np.ones((3, 3), dtype=np.uint8)
+    elif neighbourhood == 8:
+        return np.ones((3, 3), dtype=np.uint8)
 
 def picks_area(image, neighbourhood=4):
     """
@@ -31,10 +44,7 @@ def picks_area(image, neighbourhood=4):
         TypeError: If `image` is not a 2D numpy array or `neighbourhood` is not an integer.
         ValueError: If `neighbourhood` is not either 4 or 8.
     """
-    if neighbourhood == 4:
-        strel = STREL_4
-    elif neighbourhood == 8:
-        strel = STREL_8
+    strel = get_strel(neighbourhood)
     image = image.astype(np.uint8)
     eroded_image = ndi.binary_erosion(image, strel, border_value=0)
     border_image = image - eroded_image
@@ -86,10 +96,7 @@ def picks_perimeter(image, neighbourhood=4):
         TypeError: If `image` is not a 2D numpy array or `neighbourhood` is not an integer.
         ValueError: If `neighbourhood` is not either 4 or 8.
     """
-    if neighbourhood == 4:
-        strel = STREL_4
-    else:
-        strel = STREL_8
+    strel = get_strel(neighbourhood)
     image = image.astype(np.uint8)
 
     (w, h) = image.shape