Merge branch '0002_cleanup' into main

nndet/evaluator/detection/froc.py

@@ -32,7 +32,6 @@ from nndet.utils.info import experimental
 
 
 class FROCMetric(DetectionMetric):
-    @experimental
     def __init__(self,
                  classes: Sequence[str],
                  iou_thresholds: Sequence[float] = (0.1, 0.5),

nndet/evaluator/detection/matching.py

-"""
-Some parts are adapted from https://github.com/cocodataset/cocoapi :
-
-Copyright (c) 2014, Piotr Dollar and Tsung-Yi Lin
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met: 
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer. 
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution. 
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-The views and conclusions contained in the software and documentation are those
-of the authors and should not be interpreted as representing official policies, 
-either expressed or implied, of the FreeBSD Project.
-"""
-"""
-For the remaining parts:
-
-Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-   http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-"""
+# Modifications licensed under:
+# SPDX-FileCopyrightText: 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+# SPDX-License-Identifier: Apache-2.0
+#
+# Parts of this code are from cocoapi licensed under
+# SPDX-FileCopyrightText: 2014, Piotr Dollar and Tsung-Yi Lin
+# SPDX-License-Identifier: BSD-2-Clause-Views
+
 
 import numpy as np
 from typing import Callable, Sequence, List, Dict

nndet/io/transforms/instances.py

@@ -190,8 +190,8 @@ def get_instance_class_from_properties(
     Returns:
         Tensor: extracted instance classes
     """
-    instance_idx, _ = instance_idx.sort()
-    classes = [int(map_dict[str(int(idx.detach().item()))]) for idx in instance_idx]
+    _map_dict = {int(k): int(i) for k, i in map_dict.items()}
+    classes = [int(_map_dict[int(idx.detach().item())]) for idx in instance_idx]
     return torch.tensor(classes, device=instance_idx.device)
 
 
@@ -207,8 +207,8 @@ def get_instance_class_from_properties_seq(
     Returns:
         Sequence[int]: extracted instance classes
     """
-    instance_idx = sorted(instance_idx)
-    classes = [int(map_dict[str(int(idx))]) for idx in instance_idx]
+    _map_dict = {int(k): int(i) for k, i in map_dict.items()}
+    classes = [int(_map_dict[int(idx)]) for idx in instance_idx]
     return classes
 
 

nndet/losses/regression.py

+# Modifications licensed under:
+# SPDX-FileCopyrightText: 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+# SPDX-License-Identifier: Apache-2.0
+#
+# L1 loss from fvcore (https://github.com/facebookresearch/fvcore) licensed under
+# SPDX-FileCopyrightText: 2019, Facebook, Inc
+# SPDX-License-Identifier: Apache-2.0
+
+
 from typing import Optional
 
 import torch

nndet/utils/check.py

+# SPDX-FileCopyrightText: 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+# SPDX-License-Identifier: Apache-2.0
+
+
 import functools
 import os
 import warnings
@@ -264,7 +268,7 @@ def _full_check(
 def _check_itk_params(
     img_seq: Sequence[sitk.Image],
     paths: Sequence[Path],
-    ) -> None:
+) -> None:
     """
     Check Dimension, Origin, Direction and Spacing of a Sequence of images
 
@@ -279,15 +283,31 @@ def _check_itk_params(
         ValueError: raised if spacing does not match
     """
     for idx, img in enumerate(img_seq[1:], start=1):
-        if not (np.asarray(img_seq[0].GetDimension()) == \
-            np.asarray(img.GetDimension())).all():
-            raise ValueError(f"Expected {paths[idx]} and {paths[0]} to have same dimensions!")
-        if not (np.asarray(img_seq[0].GetOrigin()) == \
-            np.asarray(img.GetOrigin())).all():
-            raise ValueError(f"Expected {paths[idx]} and {paths[0]} to have same origin!")
-        if not (np.asarray(img_seq[0].GetDirection()) == \
-            np.asarray(img.GetDirection())).all():
-            raise ValueError(f"Expected {paths[idx]} and {paths[0]} to have same direction!")
-        if not (np.asarray(img_seq[0].GetSpacing()) == \
-            np.asarray(img.GetSpacing())).all():
-            raise ValueError(f"Expected {paths[idx]} and {paths[0]} to have same spacing!")
+        if not (
+            np.asarray(img_seq[0].GetDimension()) == np.asarray(img.GetDimension())
+        ).all():
+            raise ValueError(
+                f"Expected {paths[idx]} and {paths[0]} to have same dimensions!"
+            )
+        if not ((np.asarray(img_seq[0].GetSize()) == np.asarray(img.GetSize()))).all():
+            raise ValueError(
+                f"Expected {paths[idx]} and {paths[0]} to have same dimensions!"
+            )
+        if not np.allclose(
+            np.asarray(img_seq[0].GetOrigin()), np.asarray(img.GetOrigin())
+        ):
+            raise ValueError(
+                f"Expected {paths[idx]} and {paths[0]} to have same origin!"
+            )
+        if not np.allclose(
+            np.asarray(img_seq[0].GetDirection()), np.asarray(img.GetDirection())
+        ):
+            raise ValueError(
+                f"Expected {paths[idx]} and {paths[0]} to have same direction!"
+            )
+        if not np.allclose(
+            np.asarray(img_seq[0].GetSpacing()), np.asarray(img.GetSpacing())
+        ):
+            raise ValueError(
+                f"Expected {paths[idx]} and {paths[0]} to have same spacing!"
+            )

nndet/utils/registry.py

+# Modifications licensed under:
+# SPDX-FileCopyrightText: 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+# SPDX-License-Identifier: Apache-2.0
+#
+# L1 loss from fvcore (https://github.com/facebookresearch/fvcore) licensed under
+# SPDX-FileCopyrightText: 2019, Facebook, Inc
+# SPDX-License-Identifier: Apache-2.0
+
+
 import inspect
 import shutil
 import os

nndet/utils/tensor.py

+# SPDX-FileCopyrightText: 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+# SPDX-License-Identifier: Apache-2.0
+
 from collections import defaultdict
 
 import torch

nndet/utils/timer.py

+# SPDX-FileCopyrightText: 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+# SPDX-License-Identifier: Apache-2.0
+
 import time
 
 from loguru import logger

scripts/train.py

@@ -177,7 +177,7 @@ def _train(
         do_sweep: determine best emprical parameters for run
     """
     print(f"Overwrites: {ov}")
-    initialize_config_module(config_module="nndet.conf")
+    initialize_config_module(config_module="nndet.conf", version_base="1.1")
     cfg = compose(task, "config.yaml", overrides=ov if ov is not None else [])
 
     assert cfg.host.parent_data is not None, 'Parent data can not be None'