feat: binary_dijkstra for binary images (#40)

* feat: binary_dijkstra for binary images

* fix: get it working with a few tests

* docs: add some examples

* test: check that black is treated as background

* test: use GHA

Author: william-silversmith

.github/workflows/test.yaml

@@ -0,0 +1,38 @@
+name: Tests
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - "*"
+
+jobs:
+  run_tests:
+    name: Test ${{ matrix.os }} Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macos-latest, windows-2019]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          package-dir: ./python
+
+      - uses: actions/checkout@v2
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pytest -r requirements.txt -r requirements_dev.txt
+
+      - name: Compile
+        run: python setup.py develop
+
+      - name: Test with pytest
+        run: pytest -v -x automated_test.py

.gitignore

@@ -136,4 +136,6 @@ ENV/
 .pytest_cache
 
 test.py
-test
+test
+
+dijkstra3d.cpp

.travis.yml

@@ -11,6 +11,15 @@ field = np.ones((512, 512, 512), dtype=np.int32)
 source = (0,0,0)
 target = (511, 511, 511)
 
+
+# If you're working with a binary image with one color considered
+# foreground the other background, use this function.
+path = dijkstra3d.binary_dijkstra(field, source, target, background_color=0)
+path = dijkstra3d.binary_dijkstra(
+  field, source, target, 
+  anisotropy=(2.0, 2.0, 1.0),
+)
+
 # path is an [N,3] numpy array i.e. a list of x,y,z coordinates
 # terminates early, default is 26 connected
 path = dijkstra3d.dijkstra(field, source, target, connectivity=26) 

README.md

@@ -112,6 +112,107 @@ def test_dijkstra2d_10x10_26(dtype, bidirectional, connectivity, compass):
     [5,5,0],
   ]))
 
+@pytest.mark.parametrize("connectivity", [ 18, 26 ])
+def test_binary_dijkstra2d_10x10_26(connectivity):
+  values = np.ones((10,10,1), dtype=bool)
+
+  path = dijkstra3d.binary_dijkstra(
+    values, (1,1,0), (1,1,0), 
+    connectivity=connectivity,
+  )
+  assert len(path) == 1
+  assert np.all(path == np.array([ [1,1,0] ]))
+  
+  path = dijkstra3d.binary_dijkstra(
+    values, (0,0,0), (3,0,0), 
+    connectivity=connectivity,
+  )
+
+  assert len(path) == 4
+  assert np.all(path == np.array([
+    [0,0,0],
+    [1,1,0],
+    [2,1,0],
+    [3,0,0],
+  ])) or np.all(path == np.array([
+    [0,0,0],
+    [1,1,0],
+    [2,0,0],
+    [3,0,0],    
+  ])) or np.all(path == np.array([
+    [0,0,0],
+    [1,0,0],
+    [2,1,0],
+    [3,0,0],    
+  ])) or np.all(path == np.array([
+    [0,0,0],
+    [1,0,0],
+    [2,0,0],
+    [3,0,0],    
+  ])) 
+
+  path = dijkstra3d.binary_dijkstra(
+    values, (0,0,0), (5,5,0), 
+    connectivity=connectivity
+  )
+
+  assert len(path) == 6
+  assert np.all(path == np.array([
+    [0,0,0],
+    [1,1,0],
+    [2,2,0],
+    [3,3,0],
+    [4,4,0],
+    [5,5,0],
+  ]))
+
+  path = dijkstra3d.binary_dijkstra(
+    values, (0,0,0), (9,9,0), 
+    connectivity=connectivity,
+  )
+  
+  assert len(path) == 10
+  assert np.all(path == np.array([
+    [0,0,0],
+    [1,1,0],
+    [2,2,0],
+    [3,3,0],
+    [4,4,0],
+    [5,5,0],
+    [6,6,0],
+    [7,7,0],
+    [8,8,0],
+    [9,9,0]
+  ]))
+
+  path = dijkstra3d.binary_dijkstra(values, (2,1,0), (3,0,0), connectivity=connectivity)
+
+  assert len(path) == 2
+  assert np.all(path == np.array([
+    [2,1,0],
+    [3,0,0],
+  ]))
+
+  path = dijkstra3d.binary_dijkstra(values, (9,9,0), (5,5,0), connectivity=connectivity)
+
+  assert len(path) == 5
+  assert np.all(path == np.array([
+    [9,9,0],
+    [8,8,0],
+    [7,7,0],
+    [6,6,0],
+    [5,5,0],
+  ]))
+
+  values[5:,5:] = 0
+  path = dijkstra3d.binary_dijkstra(values, (9,9,0), (5,5,0), connectivity=connectivity)
+  assert path.size == 0
+  path = dijkstra3d.binary_dijkstra(values, (9,9,0), (9,9,0), connectivity=connectivity)
+  assert path.size == 0
+
+  path = dijkstra3d.binary_dijkstra(values, (9,9,0), (9,9,0), connectivity=connectivity, background_color=1)
+  assert np.all(path == np.array([[9,9,0]]))
+
 @pytest.mark.parametrize("dtype", TEST_TYPES)
 @pytest.mark.parametrize("connectivity", [ 18, 26 ])
 def test_value_target_dijkstra2d_10x10_26(dtype, connectivity):