batchgenerators 0.25.4__tar.gz → 0.25.5__tar.gz

{batchgenerators-0.25.4 → batchgenerators-0.25.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batchgenerators
-Version: 0.25.4
+Version: 0.25.5
 Summary: Data augmentation toolkit
 Author-email: "Division of Medical Image Computing, German Cancer Research Center AND Applied Computer Vision Lab, Helmholtz Imaging Platform" <f.isensee@dkfz-heidelberg.de>
 License:                                  Apache License

{batchgenerators-0.25.4 → batchgenerators-0.25.5}/batchgenerators/augmentations/utils.py

@@ -207,6 +207,10 @@ def _resample_seg_by_argmax(labels, score_fn, nearest_fn, out_shape, dtype, seg_
     if seg_tiebreak not in SEG_TIEBREAKS:
         raise ValueError('unknown seg_tiebreak: %s. Must be one of %s' % (seg_tiebreak, str(SEG_TIEBREAKS)))
     out_shape = tuple(out_shape)
+    if len(labels) == 0:
+        # an empty input: there is nothing to sample, so every output voxel is outside the image. Returning here
+        # also keeps the nearest neighbour sample below from being asked of an empty array, which fails.
+        return np.full(out_shape, 0 if empty_value is None else empty_value, dtype=dtype)
     if len(labels) == 1 and empty_value is None:
         # nothing to interpolate, and this also keeps the loop below from having to handle a missing `best`
         return np.full(out_shape, labels[0], dtype=dtype)
@@ -764,6 +768,10 @@ def resize_segmentation(segmentation, new_shape, order=3, *, seg_tiebreak='neare
     '''
     tpe = segmentation.dtype
     assert len(segmentation.shape) == len(new_shape), "new shape must have same dimensionality as segmentation"
+    if segmentation.size == 0:
+        # skimage cannot resize an empty array (scipy's zoom divides 0 by 0), at any order. Zeros of new_shape is
+        # what orders >= 1 returned before the argmax, from their zero-initialized result.
+        return np.zeros(new_shape, dtype=tpe)
     if order == 0:
         return resize(segmentation.astype(float), new_shape, order, mode="edge", clip=True, anti_aliasing=False).astype(tpe)
     else:

{batchgenerators-0.25.4 → batchgenerators-0.25.5}/batchgenerators.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batchgenerators
-Version: 0.25.4
+Version: 0.25.5
 Summary: Data augmentation toolkit
 Author-email: "Division of Medical Image Computing, German Cancer Research Center AND Applied Computer Vision Lab, Helmholtz Imaging Platform" <f.isensee@dkfz-heidelberg.de>
 License:                                  Apache License

{batchgenerators-0.25.4 → batchgenerators-0.25.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "batchgenerators"
-version = "0.25.4"
+version = "0.25.5"
 description = "Data augmentation toolkit"
 readme = "README.md"
 license = { file = "LICENSE" }

{batchgenerators-0.25.4 → batchgenerators-0.25.5}/tests/test_seg_resampling.py

@@ -141,6 +141,26 @@ class TestResizeSegmentation(unittest.TestCase):
         with self.assertRaises(ValueError):
             resize_segmentation(seg, (4, 4), order=1, seg_tiebreak='bogus')
 
+    def test_empty_input_gives_zeros(self):
+        """
+        An empty segmentation came back as zeros of new_shape (the zero-initialized result) at orders >= 1. The
+        argmax broke that: it takes the nearest neighbour sample up front, which skimage cannot compute for an
+        empty array (scipy's zoom divides 0 by 0), and 'lowest'/'highest' indexed an empty label list. Order 0
+        failed the same way even before.
+        """
+        for order in (0, 1, 3):
+            for tiebreak in ('nearest', 'lowest', 'highest'):
+                for in_shape, out_shape in (((0, 4, 4), (0, 8, 8)), ((0, 4, 4), (2, 8, 8)), ((0, 5), (0, 10))):
+                    out = resize_segmentation(np.zeros(in_shape, dtype=np.int16), out_shape, order=order,
+                                              seg_tiebreak=tiebreak)
+                    msg = f'{in_shape} -> {out_shape}, order {order}, {tiebreak}'
+                    self.assertEqual(out.shape, out_shape, msg)
+                    self.assertEqual(out.dtype, np.int16, msg)
+                    self.assertFalse(out.any(), msg)
+                out = resize_segmentation(np.ones((4, 4, 4), dtype=np.int16), (0, 8, 8), order=order,
+                                          seg_tiebreak=tiebreak)
+                self.assertEqual(out.shape, (0, 8, 8))
+
 
 class TestInterpolateImg(unittest.TestCase):
     """interpolate_img is the same rule on the augment_spatial path, and had the same two problems."""
@@ -195,6 +215,21 @@ class TestInterpolateImg(unittest.TestCase):
         # padding modes with no 'outside' must be left alone
         self.assertTrue((interpolate_img(img, coords, order=1, mode='nearest', is_seg=True) == 2).all())
 
+    def test_empty_input_gives_the_outside_value(self):
+        """With no image to sample from every point is outside it: cval for 'constant', 0 otherwise."""
+        img = np.zeros((0, 4), dtype=np.uint8)
+        coords = self._coords([0.5, 1.5], [0.5, 2.5])
+        for order in (1, 3):
+            for tiebreak in ('nearest', 'lowest', 'highest'):
+                out = interpolate_img(img, coords, order=order, mode='nearest', is_seg=True, seg_tiebreak=tiebreak)
+                self.assertEqual(out.shape, (2, 2))
+                self.assertEqual(out.dtype, np.uint8)
+                self.assertFalse(out.any(), f'order {order}, {tiebreak}')
+                for cval in (0., 7.):
+                    out = interpolate_img(img, coords, order=order, mode='constant', cval=cval, is_seg=True,
+                                          seg_tiebreak=tiebreak)
+                    self.assertTrue((out == cval).all(), f'order {order}, {tiebreak}, cval {cval}')
+
     def test_order_zero_and_non_seg_are_untouched(self):
         img = np.arange(16, dtype=np.uint8).reshape(4, 4)
         coords = self._coords([0.5, 2.5], [0.5, 2.5])