Commit 19e4980d authored by André Anjos's avatar André Anjos 💬

Test cropping with annotated images

parent d3f2e266
......@@ -43,7 +43,9 @@ class FixedCrop(Cropper):
"""Implements cropping using a fixed suppression of border pixels
The defaults supress no lines from the image and returns an image like the
original. If an :py:class:`..database.AnnotatedArray` is passed, then we also
check for its ``.metadata['roi']`` component and correct it so that annotated
RoI points are consistent on the cropped image.
.. note::
......@@ -97,7 +99,22 @@ class FixedCrop(Cropper):
# this should work even if limits are zeros
h, w = image.shape
return image[, self.left:w-self.right]
retval = image[, self.left:w-self.right]
if hasattr(retval, 'metadata') and 'roi' in retval.metadata:
# adjust roi points to new cropping
retval = retval.copy() #don't override original
h, w = retval.shape
points = []
for y, x in retval.metadata['roi']:
y = max(, 0) #adjust
y = min(y, h-1) #verify it is not over the limits
x = max(x-self.left, 0) #adjust
x = min(x, w-1) #verify it is not over the limits
retval.metadata['roi'] = points
return retval
class NoCrop(FixedCrop):
......@@ -51,6 +51,26 @@ def test_cropping():, (shape[0]-(top+bottom), shape[1]-(left+right)))[top:-bottom,left:-right]-cropped).sum(), 0)
# tests metadata survives after cropping (and it is corrected)
from ..database import AnnotatedArray
annotations = [
(top-2, left+2), #slightly above and to the right
(top+3, shape[1]-(right+1)+3), #slightly down and to the right
(shape[0]-(bottom+1)+4, shape[1]-(right+1)-2),
(shape[0]-(bottom+1)+1, left),
annotated_image = AnnotatedArray(test_image, metadata=dict(roi=annotations))
assert hasattr(annotated_image, 'metadata')
cropped = fixed_crop(annotated_image)
assert hasattr(cropped, 'metadata')
import ipdb; ipdb.set_trace()
assert numpy.allclose(cropped.metadata['roi'], [
(0, 2),
(3, cropped.shape[1]-1),
(cropped.shape[0]-1, 4),
(cropped.shape[0]-1, 0),
def test_masking():
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