konfai 1.2.6__py3-none-any.whl → 1.2.8__py3-none-any.whl

konfai/data/patching.py

@@ -219,7 +219,7 @@ class Patch(ABC):
         )
         slices = [s] + list(self._patch_slices[a][index][1:])
         data_sliced = data[slices_pre + slices]
-        if data_sliced.shape[len(slices_pre)] < bottom + top + 1:
+        if extend_slice > 0 and data_sliced.shape[len(slices_pre)] < bottom + top + 1:
             pad_bottom = 0
             pad_top = 0
             if self._patch_slices[a][index][0].start - bottom < 0:
@@ -335,7 +335,7 @@ class DatasetManager:
         self.data: list[torch.Tensor] = []
 
         for transform_function in transforms:
-            _shape = transform_function.transform_shape(_shape, cache_attribute)
+            _shape = transform_function.transform_shape(self.name, _shape, cache_attribute)
 
         self.patch = (
             DatasetPatch(

konfai/data/transform.py

@@ -21,7 +21,7 @@ class Transform(NeedDevice, ABC):
     def set_datasets(self, datasets: list[Dataset]):
         self.datasets = datasets
 
-    def transform_shape(self, shape: list[int], cache_attribute: Attribute) -> list[int]:
+    def transform_shape(self, name: str, shape: list[int], cache_attribute: Attribute) -> list[int]:
         return shape
 
     @abstractmethod
@@ -300,7 +300,7 @@ class Padding(TransformInverse):
         ).squeeze(0)
         return result
 
-    def transform_shape(self, shape: list[int], cache_attribute: Attribute) -> list[int]:
+    def transform_shape(self, name: str, shape: list[int], cache_attribute: Attribute) -> list[int]:
         for dim in range(len(self.padding) // 2):
             shape[-dim - 1] += sum(self.padding[dim * 2 : dim * 2 + 2])
         return shape
@@ -352,7 +352,7 @@ class Resample(TransformInverse, ABC):
         pass
 
     @abstractmethod
-    def transform_shape(self, shape: list[int], cache_attribute: Attribute) -> list[int]:
+    def transform_shape(self, name: str, shape: list[int], cache_attribute: Attribute) -> list[int]:
         pass
 
     def inverse(self, name: str, tensor: torch.Tensor, cache_attribute: Attribute) -> torch.Tensor:
@@ -368,7 +368,7 @@ class ResampleToResolution(Resample):
         super().__init__(inverse)
         self.spacing = torch.tensor([0 if s < 0 else s for s in spacing])
 
-    def transform_shape(self, shape: list[int], cache_attribute: Attribute) -> list[int]:
+    def transform_shape(self, name: str, shape: list[int], cache_attribute: Attribute) -> list[int]:
         if "Spacing" not in cache_attribute:
             TransformError(
                 "Missing 'Spacing' in cache attributes, the data is likely not a valid image.",
@@ -376,36 +376,37 @@ class ResampleToResolution(Resample):
             )
         if len(shape) != len(self.spacing):
             TransformError("Shape and spacing dimensions do not match: shape={shape}, spacing={self.spacing}")
-        image_spacing = cache_attribute.get_tensor("Spacing").flip(0)
+        image_spacing = cache_attribute.get_tensor("Spacing")
         spacing = self.spacing
 
         for i, s in enumerate(self.spacing):
             if s == 0:
                 spacing[i] = image_spacing[i]
-        resize_factor = spacing / cache_attribute.get_tensor("Spacing").flip(0)
+        resize_factor = spacing / image_spacing
         return [int(x) for x in (torch.tensor(shape) * 1 / resize_factor)]
 
     def __call__(self, name: str, tensor: torch.Tensor, cache_attribute: Attribute) -> torch.Tensor:
-        image_spacing = cache_attribute.get_tensor("Spacing").flip(0)
+        image_spacing = cache_attribute.get_tensor("Spacing")
         spacing = self.spacing
         for i, s in enumerate(self.spacing):
             if s == 0:
                 spacing[i] = image_spacing[i]
-        resize_factor = spacing / cache_attribute.get_tensor("Spacing").flip(0)
-        cache_attribute["Spacing"] = spacing.flip(0)
+        resize_factor = spacing / cache_attribute.get_tensor("Spacing")
+        cache_attribute["Spacing"] = spacing
         cache_attribute["Size"] = np.asarray([int(x) for x in torch.tensor(tensor.shape[1:])])
         size = [int(x) for x in (torch.tensor(tensor.shape[1:]) * 1 / resize_factor)]
         cache_attribute["Size"] = np.asarray(size)
         return self._resample(tensor, size)
 
 
+
 class ResampleToShape(Resample):
 
     def __init__(self, shape: list[float] = [100, 256, 256], inverse: bool = True) -> None:
         super().__init__(inverse)
         self.shape = torch.tensor([0 if s < 0 else s for s in shape])
 
-    def transform_shape(self, shape: list[int], cache_attribute: Attribute) -> list[int]:
+    def transform_shape(self, name: str, shape: list[int], cache_attribute: Attribute) -> list[int]:
         if "Spacing" not in cache_attribute:
             TransformError(
                 "Missing 'Spacing' in cache attributes, the data is likely not a valid image.",
@@ -441,7 +442,7 @@ class ResampleTransform(TransformInverse):
         super().__init__(inverse)
         self.transforms = transforms
 
-    def transform_shape(self, shape: list[int], cache_attribute: Attribute) -> list[int]:
+    def transform_shape(self, name: str, shape: list[int], cache_attribute: Attribute) -> list[int]:
         return shape
 
     def __call__(self, name: str, tensor: torch.Tensor, cache_attribute: Attribute) -> torch.Tensor:
@@ -611,7 +612,7 @@ class Flatten(Transform):
     def __init__(self) -> None:
         super().__init__()
 
-    def transform_shape(self, shape: list[int], cache_attribute: Attribute) -> list[int]:
+    def transform_shape(self, name: str, shape: list[int], cache_attribute: Attribute) -> list[int]:
         return [np.prod(np.asarray(shape))]
 
     def __call__(self, name: str, tensor: torch.Tensor, cache_attribute: Attribute) -> torch.Tensor:
@@ -624,7 +625,7 @@ class Permute(TransformInverse):
         super().__init__(inverse)
         self.dims = [0] + [int(d) + 1 for d in dims.split("|")]
 
-    def transform_shape(self, shape: list[int], cache_attribute: Attribute) -> list[int]:
+    def transform_shape(self, name: str, shape: list[int], cache_attribute: Attribute) -> list[int]:
         return [shape[it - 1] for it in self.dims[1:]]
 
     def __call__(self, name: str, tensor: torch.Tensor, cache_attribute: Attribute) -> torch.Tensor:

{konfai-1.2.6.dist-info → konfai-1.2.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: konfai
-Version: 1.2.6
+Version: 1.2.8
 Summary: Modular and configurable Deep Learning framework with YAML and PyTorch
 Author-email: Valentin Boussot <boussot.v@gmail.com>
 License-Expression: Apache-2.0

{konfai-1.2.6.dist-info → konfai-1.2.8.dist-info}/RECORD

@@ -6,8 +6,8 @@ konfai/trainer.py,sha256=g_TkPDUjToFGDGB7aaRZMn-fQllHV_I2GHFKUzDGF8o,27106
 konfai/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 konfai/data/augmentation.py,sha256=7jrWcpw61t3cCIdHtUlnekRO7JwXIM5Q6RIXY8Ya-xM,27796
 konfai/data/data_manager.py,sha256=tZ2DZHDW4UySCCzwEzR2WIL0fTp7lqAfqEbNPiEw5NE,31064
-konfai/data/patching.py,sha256=jS35OxnJagKNUnJu7TzuGZpVj9fP-6H4nc2OEYOGgt8,16494
-konfai/data/transform.py,sha256=LXzvPTgLyqojVn_sRLwU_07FiI3fLSDINKRbynZBiHQ,30318
+konfai/data/patching.py,sha256=P0TcjR4qcUWpB_Uph0-dd8bMeNVJC_IGNK_jkxStglQ,16526
+konfai/data/transform.py,sha256=DpD5bNAKji_mly2IzNb1HrCXkFMYLUVj9drjTOZHk_M,30343
 konfai/metric/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 konfai/metric/measure.py,sha256=0mOIZKTa2u0UECpoDSbdJUhttAw_e1BlsROQQpi1oBk,27804
 konfai/metric/schedulers.py,sha256=TpYMA24FMpxRnqfhMGb0i_Mm-bzT9kySbBgvkYk-6wM,1327
@@ -30,9 +30,9 @@ konfai/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 konfai/utils/config.py,sha256=a7t44CYMUT5oCDdjL94IswhCVfFbQ5FCgDWZktDDkc4,14347
 konfai/utils/dataset.py,sha256=Au22fcADKyDJMfS8Z9q8kEXLtKkoufJsH7Pwly6pALo,28288
 konfai/utils/utils.py,sha256=jCj3tZ8agQYceSY_tlVYp88UFPE5oUn6tXrqnZGrKiI,28410
-konfai-1.2.6.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-konfai-1.2.6.dist-info/METADATA,sha256=yDZpZnLUABNQK1alsMDB0m6dHjXxRyxACm1FSAB49aQ,2475
-konfai-1.2.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-konfai-1.2.6.dist-info/entry_points.txt,sha256=fG82HRN5-g39ACSOCtij_I3N6EHxfYnMR0D7TI_8pW8,81
-konfai-1.2.6.dist-info/top_level.txt,sha256=xF470dkIlFoFqTZEOlRehKJr4WU_8OKGXrJqYm9vWKs,7
-konfai-1.2.6.dist-info/RECORD,,
+konfai-1.2.8.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+konfai-1.2.8.dist-info/METADATA,sha256=CKKm-QfF05P8k86_9AbNwya6QrQX0qAitMVUIlNStwc,2475
+konfai-1.2.8.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+konfai-1.2.8.dist-info/entry_points.txt,sha256=fG82HRN5-g39ACSOCtij_I3N6EHxfYnMR0D7TI_8pW8,81
+konfai-1.2.8.dist-info/top_level.txt,sha256=xF470dkIlFoFqTZEOlRehKJr4WU_8OKGXrJqYm9vWKs,7
+konfai-1.2.8.dist-info/RECORD,,