batchgeneratorsv2 0.3.2__tar.gz → 0.3.4__tar.gz

{batchgeneratorsv2-0.3.2 → batchgeneratorsv2-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batchgeneratorsv2
-Version: 0.3.2
+Version: 0.3.4
 Summary: Batchgenerators but better
 Author: Helmholtz Imaging Applied Computer Vision Lab
 Author-email: Fabian Isensee <f.isensee@dkfz-heidelberg.de>

{batchgeneratorsv2-0.3.2 → batchgeneratorsv2-0.3.4}/batchgeneratorsv2/transforms/local/brightness_gradient.py

@@ -140,6 +140,10 @@ class BrightnessGradientAdditiveTransform(ImageOnlyTransform, LocalTransform):
         return {'kernels': kernels}
 
     def _apply_to_image(self, img: torch.Tensor, **params) -> torch.Tensor:
+        if self.clip_intensities:
+            original_min = img.min()
+            original_max = img.max()
+
         for c, kernel in enumerate(params['kernels']):
             if kernel is None:
                 continue
@@ -147,7 +151,7 @@ class BrightnessGradientAdditiveTransform(ImageOnlyTransform, LocalTransform):
             img[c].add_(kernel_tensor)
 
         if self.clip_intensities:
-            img.clamp_(min=img.min(), max=img.max())
+            img.clamp_(min=original_min, max=original_max)
 
         return img
 

{batchgeneratorsv2-0.3.2 → batchgeneratorsv2-0.3.4}/batchgeneratorsv2/transforms/spatial/channel_misalignment.py

@@ -201,7 +201,10 @@ class ChannelMisalignmentTransform(ImageOnlyTransform):
             if params['elastic_offsets'] is not None:
                 grid += params['elastic_offsets']
             if params['affine'] is not None:
-                grid = torch.matmul(grid, torch.from_numpy(params['affine']).float())
+                # grid stores spatial vectors as row vectors (shape [..., dim]), whereas affine is built to act on
+                # column vectors (x' = affine @ x). We therefore multiply by affine.T so that each grid point is
+                # transformed by affine rather than its transpose (see issue #24).
+                grid = torch.matmul(grid, torch.from_numpy(params['affine'].T).float())
 
             # we center the grid around the center_location_in_pixels. We should center the mean of the grid, not the center position
             # only do this if we elastic deform

{batchgeneratorsv2-0.3.2 → batchgeneratorsv2-0.3.4}/batchgeneratorsv2/transforms/spatial/spatial.py

@@ -219,7 +219,10 @@ class SpatialTransform(BasicTransform):
             if offsets is not None:
                 grid += offsets
             if affine is not None:
-                grid = torch.matmul(grid, torch.from_numpy(affine).float())
+                # grid stores spatial vectors as row vectors (shape [..., dim]), whereas affine is built to act on
+                # column vectors (x' = affine @ x). We therefore multiply by affine.T so that each grid point is
+                # transformed by affine rather than its transpose (see issue #24).
+                grid = torch.matmul(grid, torch.from_numpy(affine.T).float())
 
             # we center the grid around the center_location_in_pixels. We should center the mean of the grid, not the center position
             # only do this if we elastic deform

{batchgeneratorsv2-0.3.2 → batchgeneratorsv2-0.3.4}/batchgeneratorsv2.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batchgeneratorsv2
-Version: 0.3.2
+Version: 0.3.4
 Summary: Batchgenerators but better
 Author: Helmholtz Imaging Applied Computer Vision Lab
 Author-email: Fabian Isensee <f.isensee@dkfz-heidelberg.de>

{batchgeneratorsv2-0.3.2 → batchgeneratorsv2-0.3.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "batchgeneratorsv2"
-version = "0.3.2"
+version = "0.3.4"
 requires-python = ">=3.9"
 description = "Batchgenerators but better"
 readme = "readme.md"