Add function to clear border in binary images

skimage/morphology/_clear_border.py

@@ -0,0 +1,36 @@
+import numpy as np
+from skimage.measure import regionprops
+from skimage.morphology import label
+
+
+def clear_border(image, buffer_size=0, bgval=0):
+    """Clear objects connected to image border.
+
+    The changes will be applied to the input image.
+
+    Parameters
+    ----------
+    image : (N, M) array
+        binary image
+    buffer_size : int, optional
+        define additional buffer around image border
+    bgval : float or int, optional
+        value for cleared objects
+
+    Returns
+    -------
+    image : (N, M) array
+        cleared binary image
+    """
+    rows, cols = image.shape
+    for prop in regionprops(label(image), ['BoundingBox', 'Image']):
+        minr, minc, maxr, maxc = prop['BoundingBox']
+        if (
+            minr <= buffer_size
+            or minc <= buffer_size
+            or maxr >= rows - buffer_size
+            or maxc >= cols - buffer_size
+        ):
+            r, c = np.nonzero(prop['Image'])
+            image[minr + r, minc + c] = bgval
+    return image

skimage/morphology/tests/test_clear_border.py

@@ -0,0 +1,32 @@
+import numpy as np
+from numpy.testing import assert_array_equal, assert_equal
+from skimage.morphology import clear_border
+
+
+def test_possible_hull():
+    image = np.array(
+        [[0, 0, 0, 0, 0, 0, 0, 1, 0],
+         [0, 0, 0, 0, 1, 0, 0, 0, 0],
+         [1, 0, 0, 1, 0, 1, 0, 0, 0],
+         [0, 0, 1, 1, 1, 1, 1, 0, 0],
+         [0, 1, 1, 1, 1, 1, 1, 1, 0],
+         [0, 0, 0, 0, 0, 0, 0, 0, 0]])
+
+    # test default case
+    result = clear_border(image.copy())
+    ref = image.copy()
+    ref[2, 0] = 0
+    ref[0, -2] = 0
+    assert_array_equal(result, ref)
+
+    # test buffer
+    result = clear_border(image.copy(), 1)
+    assert_array_equal(result, np.zeros(result.shape))
+
+    # test background value
+    result = clear_border(image.copy(), 1, 2)
+    assert_array_equal(result, 2 * image)
+
+
+if __name__ == "__main__":
+    np.testing.run_module_suite()