Test cropping with annotated images

bob/bio/vein/preprocessor/crop.py

@@ -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.
+  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.top:h-self.bottom, self.left:w-self.right]
+    retval = image[self.top:h-self.bottom, 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(y-self.top, 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
+        points.append((y,x))
+      retval.metadata['roi'] = points
+
+    return retval
 
 
 class NoCrop(FixedCrop):

bob/bio/vein/tests/test.py

@@ -51,6 +51,26 @@ def test_cropping():
   nose.tools.eq_(cropped.shape, (shape[0]-(top+bottom), shape[1]-(left+right)))
   nose.tools.eq_((test_image[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():