konfai 1.2.4__py3-none-any.whl → 1.2.5__py3-none-any.whl

konfai/data/transform.py

@@ -48,12 +48,13 @@ class Clip(Transform):
 
     def __init__(
         self,
-        min_value: float = -1024,
-        max_value: float = 1024,
+        min_value: float | str = -1024,
+        max_value: float | str = 1024,
         save_clip_min: bool = False,
         save_clip_max: bool = False,
+        mask: str | None = None
     ) -> None:
-        if max_value <= min_value:
+        if isinstance(min_value, float) and isinstance(max_value, float) and max_value <= min_value:
             raise ValueError(
                 f"[Clip] Invalid clipping range: max_value ({max_value}) must be greater than min_value ({min_value})"
             )
@@ -61,14 +62,56 @@ class Clip(Transform):
         self.max_value = max_value
         self.save_clip_min = save_clip_min
         self.save_clip_max = save_clip_max
+        self.mask = mask
 
     def __call__(self, name: str, tensor: torch.Tensor, cache_attribute: Attribute) -> torch.Tensor:
-        tensor[torch.where(tensor < self.min_value)] = self.min_value
-        tensor[torch.where(tensor > self.max_value)] = self.max_value
+        mask = None
+        if self.mask is not None:
+            for dataset in self.datasets:
+                if dataset.is_dataset_exist(self.mask, name):
+                    mask, _ = dataset.read_data(self.mask, name)
+                    break
+        if mask is None and self.mask is not None:
+            raise ValueError(f"Requested mask '{self.mask}' is not present in any dataset. Check your dataset group names or configuration.")
+        if mask is None:
+            tensor_masked = tensor
+        else:
+            tensor_masked = tensor[mask == 1]
+
+        if isinstance(self.min_value, str):
+            if self.min_value == "min":
+                min_value = torch.min(tensor_masked)
+            elif self.min_value.startswith("percentile:"):
+                try:
+                    percentile = float(self.min_value.split(":")[1])
+                    min_value = np.percentile(tensor_masked, percentile)
+                except (IndexError, ValueError):
+                    raise ValueError(f"Invalid format for min_value: '{self.min_value}'. Expected 'percentile:<float>'")
+            else:
+                raise TypeError(f"Unsupported string for min_value: '{self.min_value}'. Must be a float, 'min', or 'percentile:<float>'.")
+        else:
+            min_value = self.min_value
+
+        if isinstance(self.max_value, str):
+            if self.max_value == "max":
+                max_value = torch.max(tensor_masked)
+            elif self.max_value.startswith("percentile:"):
+                try:
+                    percentile = float(self.max_value.split(":")[1])
+                    max_value = np.percentile(tensor_masked, percentile)
+                except (IndexError, ValueError):
+                    raise ValueError(f"Invalid format for max_value: '{self.max_value}'. Expected 'percentile:<float>'")
+            else:
+                raise TypeError(f"Unsupported string for max_value: '{self.max_value}'. Must be a float, 'max', or 'percentile:<float>'.")
+        else:
+            max_value = self.max_value
+        
+        tensor[torch.where(tensor < min_value)] = min_value
+        tensor[torch.where(tensor > max_value)] = max_value
         if self.save_clip_min:
-            cache_attribute["Min"] = self.min_value
+            cache_attribute["Min"] = min_value
         if self.save_clip_max:
-            cache_attribute["Max"] = self.max_value
+            cache_attribute["Max"] = max_value
         return tensor
 
     def inverse(self, name: str, tensor: torch.Tensor, cache_attribute: Attribute) -> torch.Tensor:
@@ -143,36 +186,42 @@ class Standardize(Transform):
         lazy: bool = False,
         mean: list[float] | None = None,
         std: list[float] | None = None,
+        mask: str | None = None
     ) -> None:
         self.lazy = lazy
         self.mean = mean
         self.std = std
+        self.mask = mask
 
     def __call__(self, name: str, tensor: torch.Tensor, cache_attribute: Attribute) -> torch.Tensor:
+        mask = None
+        if self.mask is not None:
+            for dataset in self.datasets:
+                if dataset.is_dataset_exist(self.mask, name):
+                    mask, _ = dataset.read_data(self.mask, name)
+                    break
+        if mask is None and self.mask is not None:
+            raise ValueError(f"Requested mask '{self.mask}' is not present in any dataset. Check your dataset group names or configuration.")
+        if mask is None:
+            tensor_masked = tensor
+        else:
+            tensor_masked = tensor[mask == 1]
+
         if "Mean" not in cache_attribute:
-            cache_attribute["Mean"] = (
-                torch.mean(
-                    tensor.type(torch.float32),
-                    dim=[i + 1 for i in range(len(tensor.shape) - 1)],
-                )
-                if self.mean is None
-                else torch.tensor([self.mean])
-            )
+            cache_attribute["Mean"] = torch.tensor([torch.mean(tensor_masked.type(torch.float32))]) if self.mean is None else torch.tensor([self.mean])
+            
         if "Std" not in cache_attribute:
             cache_attribute["Std"] = (
-                torch.std(
-                    tensor.type(torch.float32),
-                    dim=[i + 1 for i in range(len(tensor.shape) - 1)],
-                )
+                torch.tensor([torch.std(
+                    tensor_masked.type(torch.float32))])
                 if self.std is None
                 else torch.tensor([self.std])
             )
-
         if self.lazy:
             return tensor
         else:
-            mean = cache_attribute.get_tensor("Mean").view(-1, *[1 for _ in range(len(tensor.shape) - 1)])
-            std = cache_attribute.get_tensor("Std").view(-1, *[1 for _ in range(len(tensor.shape) - 1)])
+            mean = cache_attribute.get_tensor("Mean")
+            std = cache_attribute.get_tensor("Std")
             return (tensor - mean) / std
 
     def inverse(self, name: str, tensor: torch.Tensor, cache_attribute: Attribute) -> torch.Tensor:

konfai/network/network.py

@@ -6,8 +6,7 @@ from collections import OrderedDict
 from collections.abc import Callable, Iterable, Iterator, Sequence
 from enum import Enum
 from functools import partial
-from typing import Any
-from typing_extensions import Self
+from typing import Any, Self
 
 import numpy as np
 import torch

konfai/predictor.py

@@ -715,7 +715,9 @@ class Predictor(DistributedObject):
                         path = models_directory() + self.name + "/StateDict/"
                         name = sorted(os.listdir(path))[-1]
                 if os.path.exists(path + name):
-                    state_dicts.append(torch.load(path + name, map_location=torch.device('cpu'), weights_only=False))
+                    state_dicts.append(
+                        torch.load(path + name, map_location=torch.device("cpu"), weights_only=False)  # nosec B614
+                    )  # nosec B614
                 else:
                     raise Exception(f"Model : {path + name} does not exist !")
         return state_dicts

{konfai-1.2.4.dist-info → konfai-1.2.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: konfai
-Version: 1.2.4
+Version: 1.2.5
 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-1.2.4.dist-info → konfai-1.2.5.dist-info}/RECORD

@@ -1,13 +1,13 @@
 konfai/__init__.py,sha256=qjE9Rqxo1sMrkqGS8I5xlGQMZnjIfU-CGgSI5Wmbmbs,1231
 konfai/evaluator.py,sha256=xAKWUDvdSxqYRUsKqH6ieQF06LWa785aE4zLv4I3_i4,17850
 konfai/main.py,sha256=Fc4HcJEhPmgunj_f-QYyvQNvjHrKHSUv27Okgu6V5_A,3842
-konfai/predictor.py,sha256=S-KlITnyxcAMHmd7aLsoKlJSiZym63yBsJd404HWp9o,34632
+konfai/predictor.py,sha256=TTMB-PowpLef-iLOaQv0X5AXV0q8n7XBEXCS0nJJBTg,34706
 konfai/trainer.py,sha256=g_TkPDUjToFGDGB7aaRZMn-fQllHV_I2GHFKUzDGF8o,27106
 konfai/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 konfai/data/augmentation.py,sha256=vcJE7mosvUkwbpbTN_lGP0S1uJrJYGjlLrt9VnDdJYY,27792
 konfai/data/data_manager.py,sha256=I5YG2HIRWQtP_6Lu9KsEWEJzAFFMTMWOYv7dzlcdUN4,31100
 konfai/data/patching.py,sha256=jS35OxnJagKNUnJu7TzuGZpVj9fP-6H4nc2OEYOGgt8,16494
-konfai/data/transform.py,sha256=YCldsqTTBFFCqc_VdvyuNVs2kmV56CxQBN5XhEoPxho,27745
+konfai/data/transform.py,sha256=_Mih41rpITQo19Y-fFsGdIaztL6CESrATrGQanu3uqU,30210
 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
@@ -24,15 +24,15 @@ konfai/models/segmentation/NestedUNet.py,sha256=W4uauwF0HY8ybi49iYiTlKLdJEyD7SaC
 konfai/models/segmentation/UNet.py,sha256=Pu_LiQdO4Mrzyn0HRE6rwxUjHGH4OG-JpzWB_U1K46g,5602
 konfai/network/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 konfai/network/blocks.py,sha256=l70_oOcz5Hmol2xmxruG0kke_2SVgO3rXYXVTMSdAS8,15645
-konfai/network/network.py,sha256=0G3goIopB_r4PHj4ohOkbov344mVYxZjq5PH57QETmc,54829
+konfai/network/network.py,sha256=PWI6W4sz7G5Pbb-79l7mL61AoyHWlQytRtBzvwh3Ro0,54800
 konfai/utils/ITK.py,sha256=HVed4Z96X1jTaWrrQNdoBMqOtVK9InAPlDBJu-5uv3g,15476
 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-1.2.4.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-konfai-1.2.4.dist-info/METADATA,sha256=y505AGDJqf-U3tO8uj9jQ4bo3g_fqdROVA-T4JZ96d8,2451
-konfai-1.2.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-konfai-1.2.4.dist-info/entry_points.txt,sha256=fG82HRN5-g39ACSOCtij_I3N6EHxfYnMR0D7TI_8pW8,81
-konfai-1.2.4.dist-info/top_level.txt,sha256=xF470dkIlFoFqTZEOlRehKJr4WU_8OKGXrJqYm9vWKs,7
-konfai-1.2.4.dist-info/RECORD,,
+konfai-1.2.5.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+konfai-1.2.5.dist-info/METADATA,sha256=IuUBngJ6PCmGk3uSVBpGBfOYfptSfgkjLkGpLEwbb4w,2451
+konfai-1.2.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+konfai-1.2.5.dist-info/entry_points.txt,sha256=fG82HRN5-g39ACSOCtij_I3N6EHxfYnMR0D7TI_8pW8,81
+konfai-1.2.5.dist-info/top_level.txt,sha256=xF470dkIlFoFqTZEOlRehKJr4WU_8OKGXrJqYm9vWKs,7
+konfai-1.2.5.dist-info/RECORD,,