analyse tests

pyproject.toml

@@ -65,7 +65,7 @@ local_scheme = "no-local-version"
 
 [tool.pytest.ini_options]
 norecursedirs = ['examples']
-testpaths = ['tests', 'docs']
+testpaths = ['ripplemapper/tests', 'docs']
 text_file_format = "rst"
 addopts = [
     "--doctest-glob=*.rst"

ripplemapper/analyse.py

@@ -99,6 +99,8 @@ def remove_small_bumps(contour: RippleContour, **kwargs) -> RippleContour:
 
 def remove_small_bumps_from_images(ripple_images: list[RippleImage] | RippleImage, **kwargs) -> list[RippleImage]:
     """Remove small bumps from a list of RippleImage objects."""
+    if isinstance(ripple_images, RippleImageSeries):
+        ripple_images = ripple_images.images
     if isinstance(ripple_images, RippleImage):
         ripple_images = [ripple_images]
     for ripple_image in ripple_images:

ripplemapper/image.py

@@ -33,7 +33,10 @@ def preprocess_image(image: np.ndarray, roi_x: list[int]=False, roi_y: list[int]
     Returns:
         numpy.ndarray: Preprocessed image.
     """
-    gray_image = color.rgb2gray(image)
+    if len(image.shape) == 3 and image.shape[2] == 3:
+        gray_image = color.rgb2gray(image)
+    else:
+        gray_image = image
     blurred_gray_image = filters.gaussian(gray_image, sigma=sigma)
     # crop the image
     if roi_x:

ripplemapper/tests/test_analyse.py

@@ -0,0 +1,61 @@
+import pytest
+
+from ripplemapper.analyse import (add_a_star_contours, add_boundary_contours,
+                                  add_chan_vese_contours, remove_small_bumps,
+                                  remove_small_bumps_from_images)
+
+
+def test_add_boundary_contours(loaded_example_image):
+    add_boundary_contours(loaded_example_image)
+    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_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_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]
+
+def test_remove_small_bumps_from_images(loaded_example_image):
+    add_boundary_contours(loaded_example_image)
+    remove_small_bumps_from_images(loaded_example_image)
+    assert len(loaded_example_image.contours) == 2
+
+def test_add_boundary_contours_image_series(loaded_example_image_series):
+    add_boundary_contours(loaded_example_image_series)
+    for image in loaded_example_image_series.images:
+        assert len(image.contours) == 2
+        assert image.contours[0].method == 'Upper Boundary'
+        assert image.contours[1].method == 'Lower Boundary'
+
+def test_add_a_star_contours_image_series(loaded_example_image_series):
+    add_boundary_contours(loaded_example_image_series)
+    add_a_star_contours(loaded_example_image_series)
+    for image in loaded_example_image_series.images:
+        assert len(image.contours) == 3
+        assert image.contours[2].method == 'A* traversal'
+
+def test_add_chan_vese_contours_image_series(loaded_example_image_series):
+    add_chan_vese_contours(loaded_example_image_series)
+    for image in loaded_example_image_series.images:
+        assert len(image.contours) == 1
+        assert image.contours[0].method == 'Chan-Vese'
+
+def test_remove_small_bumps_from_image_series(loaded_example_image_series):
+    add_boundary_contours(loaded_example_image_series)
+    remove_small_bumps_from_images(loaded_example_image_series)
+    for image in loaded_example_image_series.images:
+        assert len(image.contours) == 2
+
+if __name__ == '__main__':
+    pytest.main()