auto updates (#5322)

Signed-off-by: monai-bot <[email protected]>

Signed-off-by: monai-bot <[email protected]>
Signed-off-by: KumoLiu <[email protected]>

Author: monai-bot

monai/apps/auto3dseg/__main__.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from monai.apps.auto3dseg.auto_runner import AutoRunner
 from monai.apps.auto3dseg.bundle_gen import BundleAlgo, BundleGen
 from monai.apps.auto3dseg.data_analyzer import DataAnalyzer

monai/apps/auto3dseg/ensemble_builder.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 import json
 import os
 from abc import ABC, abstractmethod

monai/apps/deepedit/transforms.py

@@ -28,7 +28,6 @@
 
 logger = logging.getLogger(__name__)
 
-
 distance_transform_cdt, _ = optional_import("scipy.ndimage.morphology", name="distance_transform_cdt")
 
 

monai/apps/detection/metrics/coco.py

@@ -56,7 +56,6 @@
 # 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.
-
 """
 This script is almost same with https://github.com/MIC-DKFZ/nnDetection/blob/main/nndet/evaluator/detection/coco.py
 The changes include 1) code reformatting, 2) docstrings.

monai/apps/detection/metrics/matching.py

@@ -56,7 +56,6 @@
 # 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.
-
 """
 This script is almost same with https://github.com/MIC-DKFZ/nnDetection/blob/main/nndet/evaluator/detection/matching.py
 The changes include 1) code reformatting, 2) docstrings,

monai/apps/detection/networks/retinanet_detector.py

@@ -32,7 +32,6 @@
 # * Neither the name of the copyright holder nor the names of its
 #   contributors may be used to endorse or promote products derived from
 #   this software without specific prior written permission.
-
 """
 Part of this script is adapted from
 https://github.com/pytorch/vision/blob/main/torchvision/models/detection/retinanet.py

monai/apps/detection/networks/retinanet_network.py

@@ -32,7 +32,6 @@
 # * Neither the name of the copyright holder nor the names of its
 #   contributors may be used to endorse or promote products derived from
 #   this software without specific prior written permission.
-
 """
 Part of this script is adapted from
 https://github.com/pytorch/vision/blob/main/torchvision/models/detection/retinanet.py

monai/apps/detection/utils/ATSS_matcher.py

@@ -59,7 +59,6 @@
 # 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 functions in this script are adapted from nnDetection,
 https://github.com/MIC-DKFZ/nnDetection/blob/main/nndet/core/boxes/matcher.py

monai/apps/detection/utils/anchor_utils.py

@@ -32,7 +32,6 @@
 # * Neither the name of the copyright holder nor the names of its
 #   contributors may be used to endorse or promote products derived from
 #   this software without specific prior written permission.
-
 """
 This script is adapted from
 https://github.com/pytorch/vision/blob/release/0.12/torchvision/models/detection/anchor_utils.py

monai/apps/detection/utils/box_coder.py

@@ -43,7 +43,6 @@
 # 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.
-
 """
 This script is modified from torchvision to support N-D images,
 

monai/apps/detection/utils/box_selector.py

@@ -32,7 +32,6 @@
 # * Neither the name of the copyright holder nor the names of its
 #   contributors may be used to endorse or promote products derived from
 #   this software without specific prior written permission.
-
 """
 Part of this script is adapted from
 https://github.com/pytorch/vision/blob/main/torchvision/models/detection/retinanet.py

monai/apps/detection/utils/hard_negative_sampler.py

@@ -24,7 +24,6 @@
 # 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.
-
 """
 The functions in this script are adapted from nnDetection,
 https://github.com/MIC-DKFZ/nnDetection/blob/main/nndet/core/boxes/sampler.py

monai/apps/mmars/mmars.py

@@ -8,7 +8,6 @@
 # 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.
-
 """
 Utilities for accessing Nvidia MMARs
 

monai/apps/mmars/model_desc.py

@@ -8,7 +8,6 @@
 # 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.
-
 """
 Collection of the remote MMAR descriptors
 

monai/apps/reconstruction/transforms/array.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from abc import abstractmethod
 from typing import Sequence
 

monai/apps/reconstruction/transforms/dictionary.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from typing import Dict, Hashable, Mapping, Optional, Sequence
 
 import numpy as np

monai/apps/tcia/label_desc.py

@@ -9,12 +9,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from typing import Dict
 
 __all__ = ["TCIA_LABEL_DICT"]
 
-
 TCIA_LABEL_DICT: Dict[str, Dict[str, int]] = {
     "C4KC-KiTS": {"Kidney": 0, "Renal Tumor": 1},
     "NSCLC-Radiomics": {

monai/bundle/__main__.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from monai.bundle.scripts import ckpt_export, download, init_bundle, run, verify_metadata, verify_net_in_out
 
 if __name__ == "__main__":

monai/bundle/utils.py

@@ -21,13 +21,11 @@
 
 __all__ = ["ID_REF_KEY", "ID_SEP_KEY", "EXPR_KEY", "MACRO_KEY"]
 
-
 ID_REF_KEY = "@"  # start of a reference to a ConfigItem
 ID_SEP_KEY = "#"  # separator for the ID of a ConfigItem
 EXPR_KEY = "$"  # start of a ConfigExpression
 MACRO_KEY = "%"  # start of a macro of a config
 
-
 _conf_values = get_config_values()
 
 DEFAULT_METADATA = {

monai/config/type_definitions.py

@@ -41,7 +41,6 @@
     "SequenceStr",
 ]
 
-
 #: KeysCollection
 #
 # The KeyCollection type is used to for defining variables

monai/data/box_utils.py

@@ -8,7 +8,6 @@
 # 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.
-
 """
 This utility module mainly supports rectangular bounding boxes with a few
 different parameterizations and methods for converting between them. It
@@ -36,7 +35,6 @@
 # We support 2-D or 3-D bounding boxes
 SUPPORTED_SPATIAL_DIMS = [2, 3]
 
-
 # TO_REMOVE = 0.0 if the bottom-right corner pixel/voxel is not included in the boxes,
 #      i.e., when xmin=1., xmax=2., we have w = 1.
 # TO_REMOVE = 1.0  if the bottom-right corner pixel/voxel is included in the boxes,

monai/data/dataset.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 import collections.abc
 import math
 import pickle

monai/data/image_writer.py

@@ -46,7 +46,6 @@
     nib, _ = optional_import("nibabel")
     PILImage, _ = optional_import("PIL.Image")
 
-
 __all__ = [
     "ImageWriter",
     "ITKWriter",

monai/data/thread_buffer.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from multiprocessing.context import SpawnContext
 from queue import Empty, Full, Queue
 from threading import Thread

monai/data/utils.py

@@ -52,7 +52,6 @@
 DataFrame, _ = optional_import("pandas", name="DataFrame")
 nib, _ = optional_import("nibabel")
 
-
 __all__ = [
     "AFFINE_TOL",
     "SUPPORTED_PICKLE_MOD",

monai/handlers/logfile_handler.py

@@ -22,7 +22,6 @@
 else:
     Engine, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Engine")
 
-
 __all__ = ["LogfileHandler"]
 
 

monai/handlers/nvtx_handlers.py

@@ -24,7 +24,6 @@
     Engine, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Engine")
     Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
 
-
 __all__ = ["RangeHandler", "RangePushHandler", "RangePopHandler", "MarkHandler"]
 
 

monai/losses/contrastive.py

@@ -19,7 +19,6 @@
 
 
 class ContrastiveLoss(_Loss):
-
     """
     Compute the Contrastive loss defined in:
 

monai/losses/giou_loss.py

@@ -19,7 +19,6 @@
 
 
 class BoxGIoULoss(_Loss):
-
     """
     Compute the generalized intersection over union (GIoU) loss of a pair of boxes.
     The two inputs should have the same shape. giou_loss = 1.0 - giou

monai/losses/ssim_loss.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 import torch
 import torch.nn.functional as F
 from torch import nn

monai/losses/tversky.py

@@ -20,7 +20,6 @@
 
 
 class TverskyLoss(_Loss):
-
     """
     Compute the Tversky loss defined in:
 

monai/metrics/froc.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from typing import List, Optional, Tuple, Union
 
 import numpy as np

monai/networks/blocks/backbone_fpn_utils.py

@@ -43,7 +43,6 @@
 # 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.
-
 """
 This script is modified from from torchvision to support N-D images,
 by overriding the definition of convolutional layers and pooling layers.

monai/networks/blocks/dints_block.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from typing import Tuple, Union
 
 import torch

monai/networks/blocks/feature_pyramid_network.py

@@ -43,7 +43,6 @@
 # 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.
-
 """
 This script is modified from from torchvision to support N-D images,
 by overriding the definition of convolutional layers and pooling layers.

monai/networks/blocks/unetr_block.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from typing import Sequence, Tuple, Union
 
 import torch

monai/networks/layers/factories.py

@@ -8,7 +8,6 @@
 # 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.
-
 """
 Defines factories for creating layers in generic, extensible, and dimensionally independent ways. A separate factory
 object is created for each type of layer, and factory functions keyed to names are added to these objects. Whenever
@@ -70,7 +69,6 @@ def use_factory(fact_args):
 
 InstanceNorm3dNVFuser, has_nvfuser = optional_import("apex.normalization", name="InstanceNorm3dNVFuser")
 
-
 __all__ = ["LayerFactory", "Dropout", "Norm", "Act", "Conv", "Pool", "Pad", "split_args"]
 
 

monai/networks/nets/dints.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 import warnings
 from typing import List, Optional, Tuple, Union
 

monai/networks/nets/dynunet.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from typing import List, Optional, Sequence, Tuple, Union
 
 import torch

monai/networks/nets/senet.py

@@ -34,7 +34,6 @@
     "SE_NET_MODELS",
 ]
 
-
 SE_NET_MODELS = {
     "senet154": "http://data.lip6.fr/cadene/pretrainedmodels/senet154-c7b49a05.pth",
     "se_resnet50": "http://data.lip6.fr/cadene/pretrainedmodels/se_resnet50-ce0d4300.pth",

monai/networks/nets/torchvision_fc.py

@@ -16,7 +16,6 @@
 
 models, _ = optional_import("torchvision.models")
 
-
 __all__ = ["TorchVisionFCModel"]
 
 

monai/networks/nets/vit.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from typing import Sequence, Union
 
 import torch

monai/networks/nets/vitautoenc.py

@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from typing import Sequence, Union
 
 import torch

monai/transforms/adaptors.py

@@ -8,7 +8,6 @@
 # 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.
-
 """
 How to use the adaptor function
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

monai/transforms/signal/array.py

@@ -34,7 +34,6 @@
 central_frequency, has_central_frequency = optional_import("pywt", name="central_frequency")
 cwt, has_cwt = optional_import("pywt", name="cwt")
 
-
 __all__ = [
     "SignalRandDrop",
     "SignalRandScale",

monai/transforms/smooth_field/array.py

@@ -8,7 +8,6 @@
 # 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.
-
 """Transforms using a smooth spatial field generated by interpolating from smaller randomized fields."""
 
 from typing import Any, Optional, Sequence, Union