fixed overwriting old contours and added tests

ripplemapper/analyse.py

@@ -20,14 +20,24 @@ def add_boundary_contours(ripple_images: list[RippleImage] | RippleImage | Rippl
  ripple_images = [ripple_images]
  for ripple_image in ripple_images:
  if len(ripple_image.contours) > 0:
- for contour in ripple_image.contours:
- if 'Upper Boundary' in contour.method or 'Lower Boundary' in contour.method:
- if overwrite:
- warnings.warn(f"Overwriting boundary contour for image: {ripple_image.source_file}")
- ripple_image.contours.remove(contour)
- else:
- warnings.warn(f"Boundary contour already exists, skipping image: {ripple_image.source_file}")
- continue
+ indexes = []
+ for i in range(len(ripple_image.contours)):
+ if ripple_image.contours[i].method == 'Upper Boundary':
+ indexes.append(i)
+ if ripple_image.contours[i].method == 'Lower Boundary':
+ indexes.append(i)
+ if len(indexes) > 0:
+ if overwrite:
+ warnings.warn(f"Overwriting boundary contours for image: {ripple_image.source_file}")
+ if len(indexes) == 1:
+ ripple_image.contours.pop(indexes[0])
+ if len(indexes) == 2:
+ ripple_image.contours.pop(indexes[0])
+ # they have now moved by 1.
+ ripple_image.contours.pop(indexes[1]-1)
+ else:
+ warnings.warn(f"Boundary contours already exist, skipping image: {ripple_image.source_file}")
+ continue
  edges = detect_edges(ripple_image.image)
  processed_edges = process_edges(edges)
  contours = find_contours(processed_edges, level=level)
@@ -47,14 +57,20 @@ def add_a_star_contours(ripple_images: list[RippleImage] | RippleImage | RippleI
  if len(ripple_image.contours) < 2:
  warnings.warn(f"RippleImage object must have at least two contours, skipping image: {ripple_image.source_file}")
  continue
- for contour in ripple_image.contours:
- if 'A* traversal' in contour.method:
- if overwrite:
- warnings.warn(f"Overwriting A* contour for image: {ripple_image.source_file}")
- ripple_image.contours.remove(contour)
- else:
- warnings.warn(f"A* contour already exists, skipping image: {ripple_image.source_file}")
- continue
+ methods = [contour.method for contour in ripple_image.contours]
+ if 'A* traversal' in methods:
+ if overwrite:
+ warnings.warn(f"Overwriting A* contour for image: {ripple_image.source_file}")
+ # find me the method index that matches 'A* traversal'
+ for contour in ripple_image.contours:
+ print(contour.method)
+ if contour.method == 'A* traversal':
+ ripple_image.contours.remove(contour)
+ print(ripple_image.contours)
+ else:
+ warnings.warn(f"A* contour already exists, skipping image: {ripple_image.source_file}")
+ continue
+
  cont1 = np.flip(ripple_image.contours[contour_index[0]].values).astype(np.int32).T
  cont2 = np.flip(ripple_image.contours[contour_index[1]].values).astype(np.int32).T
  contour = combine_contours(cont1, cont2)
@@ -76,14 +92,16 @@ def add_chan_vese_contours(ripple_images: list[RippleImage] | RippleImage | Ripp
  ripple_images = [ripple_images]
  for ripple_image in ripple_images:
  if len(ripple_image.contours) > 0:
- for contour in ripple_image.contours:
- if 'Chan-Vese' in contour.method:
- if overwrite:
- warnings.warn(f"Overwriting Chan-Vese contour for image: {ripple_image.source_file}")
- ripple_image.contours.remove(contour)
- else:
- warnings.warn(f"Chan-Vese contour already exists, skipping image: {ripple_image.source_file}")
- continue
+ methods = [contour.method for contour in ripple_image.contours]
+ if 'Chan-Vese' in methods:
+ if overwrite:
+ warnings.warn(f"Overwriting Chan-Vese contour for image: {ripple_image.source_file}")
+ for contour in ripple_image.contours:
+ if contour.method == 'Chan-Vese':
+ ripple_image.contours.remove(contour)
+ else:
+ warnings.warn(f"Chan-Vese contour already exists, skipping image: {ripple_image.source_file}")
+ continue
  if use_gradients:
  grad = np.sum(np.abs(np.gradient(ripple_image.image)), axis=0)
  img = cv2.GaussianBlur(grad / np.max(grad), (7,7), 0)+(1-(ripple_image.image/np.max(ripple_image.image)))

ripplemapper/io.py

@@ -7,7 +7,7 @@
 
 __all__ = ["load_image", "load_tif", "load_dir", "load_dir_to_obj", "load"]
 
-def load(file: str | PosixPath):
+def load(file: str | PosixPath | WindowsPath):
  """Load a file into a ripplemapper object based on file extension."""
  from ripplemapper.classes import (RippleContour, RippleImage,
  RippleImageSeries)
@@ -26,7 +26,7 @@ def load(file: str | PosixPath):
 
 # TODO (ADW): Add support for other image file types just use load_tif for now.
 # should probably be looping in this function rather than the dispatched functions but... it's fine for now.
-def load_image(file: str | PosixPath) -> np.ndarray:
+def load_image(file: str | PosixPath | WindowsPath) -> np.ndarray:
  """Load an image file based on file extension."""
  # TODO (ADW): this needs to be refactored to allow lists.
  if isinstance(file, PosixPath) | isinstance(file, WindowsPath):

ripplemapper/tests/test_analyse.py

@@ -11,17 +11,50 @@ def test_add_boundary_contours(loaded_example_image):
  assert loaded_example_image.contours[0].method == 'Upper Boundary'
  assert loaded_example_image.contours[1].method == 'Lower Boundary'
 
+def test_overwrite_boundary_contours(loaded_example_image):
+ add_boundary_contours(loaded_example_image)
+ with pytest.warns(UserWarning, match="Overwriting boundary contour"):
+ add_boundary_contours(loaded_example_image, overwrite=True)
+ assert len(loaded_example_image.contours) == 2
+ assert loaded_example_image.contours[0].method == 'Upper Boundary'
+ assert loaded_example_image.contours[1].method == 'Lower Boundary'
+
+def test_overwrite_single_boundary_contour(loaded_example_image):
+ add_boundary_contours(loaded_example_image)
+ loaded_example_image.contours.pop(0)
+ assert len(loaded_example_image.contours) == 1
+ with pytest.warns(UserWarning, match="Overwriting boundary contour"):
+ add_boundary_contours(loaded_example_image, overwrite=True)
+ assert len(loaded_example_image.contours) == 2
+ assert loaded_example_image.contours[0].method == 'Upper Boundary'
+ assert loaded_example_image.contours[1].method == 'Lower Boundary'
+
 def test_add_a_star_contours(loaded_example_image):
  add_boundary_contours(loaded_example_image)
  add_a_star_contours(loaded_example_image)
  assert len(loaded_example_image.contours) == 3
  assert loaded_example_image.contours[2].method == 'A* traversal'
 
+def test_overwrite_a_star_contours(loaded_example_image):
+ add_boundary_contours(loaded_example_image)
+ add_a_star_contours(loaded_example_image)
+ with pytest.warns(UserWarning, match="Overwriting A"):
+ add_a_star_contours(loaded_example_image, overwrite=True)
+ assert len(loaded_example_image.contours) == 3
+ assert loaded_example_image.contours[2].method == 'A* traversal'
+
 def test_add_chan_vese_contours(loaded_example_image):
  add_chan_vese_contours(loaded_example_image)
  assert len(loaded_example_image.contours) == 1
  assert loaded_example_image.contours[0].method == 'Chan-Vese'
 
+def test_overwrite_chan_vese_contours(loaded_example_image):
+ add_chan_vese_contours(loaded_example_image)
+ with pytest.warns(UserWarning, match="Overwriting Chan-Vese contour"):
+ add_chan_vese_contours(loaded_example_image, overwrite=True)
+ assert len(loaded_example_image.contours) == 1
+ assert loaded_example_image.contours[0].method == 'Chan-Vese'
+
 def test_remove_small_bumps(loaded_example_contour):
  smoothed_contour = remove_small_bumps(loaded_example_contour)
  assert smoothed_contour.values.shape[1] <= loaded_example_contour.values.shape[1]
@@ -57,5 +90,29 @@ def test_remove_small_bumps_from_image_series(loaded_example_image_series):
  for image in loaded_example_image_series.images:
  assert len(image.contours) == 2
 
+def test_add_boundary_contours_emits_warning(loaded_example_image):
+ add_boundary_contours(loaded_example_image)
+ with pytest.warns(UserWarning, match="Boundary contours already exist, skipping image"):
+ add_boundary_contours(loaded_example_image)
+ assert len(loaded_example_image.contours) == 2
+
+def test_add_a_star_contours_emits_warning(loaded_example_image):
+ with pytest.warns(UserWarning, match="RippleImage object must have at least two contours, skipping image:"):
+ add_a_star_contours(loaded_example_image)
+ assert len(loaded_example_image.contours) == 0
+
+def test_add_a_star_overwrite_warning(loaded_example_image):
+ add_boundary_contours(loaded_example_image)
+ add_a_star_contours(loaded_example_image)
+ with pytest.warns(UserWarning, match="contour already exists, skipping image"):
+ add_a_star_contours(loaded_example_image, overwrite=False)
+ assert len(loaded_example_image.contours) == 3
+
+def test_add_chan_vese_contours_emits_warning(loaded_example_image):
+ add_chan_vese_contours(loaded_example_image)
+ with pytest.warns(UserWarning, match="Chan-Vese contour already exists, skipping image:"):
+ add_chan_vese_contours(loaded_example_image)
+ assert len(loaded_example_image.contours) == 1
+
 if __name__ == '__main__':
  pytest.main()

ripplemapper/tests/test_vis.py

@@ -30,6 +30,13 @@ def test_plot_image_calls_imshow(loaded_example_image):
  assert plt.imshow.called
  plt.imshow.assert_called_with(loaded_example_image.image, cmap='gray')
 
+def test_plot_image_without_data(loaded_example_image):
+ plt.imshow = MagicMock()
+ with pytest.warns(UserWarning, match="Image not loaded for image: "):
+ loaded_example_image.image = None
+ plot_image(loaded_example_image, include_contours=False)
+ assert plt.imshow.called
+
 def test_plot_image_with_contours_calls_plot(loaded_example_image_with_contours):
  plt.imshow = MagicMock()
  plt.plot = MagicMock()

ripplemapper/visualisation.py

@@ -39,6 +39,10 @@ def plot_image(ripple_image, include_contours: bool=True, cmap: str='gray', **k
  x_min = min(x_min, np.min(contour.values[1]))
  y_max = max(y_max, np.max(contour.values[0]))
  y_min = min(y_min, np.min(contour.values[0]))
+ if x_min == np.inf:
+ x_min = 0
+ if y_min == np.inf:
+ y_min = 0
  x_min, x_max, y_min, y_max = int(np.floor(x_min)), int(np.ceil(x_max)), int(np.floor(y_min)), int(np.ceil(y_max))
  plt.imshow(np.zeros((y_max, x_max)), cmap=cmap, **kwargs)
  plt.xlim(x_min, x_max)