auto updates (#294)

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

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

prostate-mri-lesion-seg/LICENSE

@@ -1,54 +1,54 @@
-Prostate-MRI_Lesion_Detection, v2.0 (Release date: August 2, 2023)
-•	DEFINITIONS: AUTHOR(S) NVIDIA Corp. and National Cancer Institute, NIH
-
-•	PROVIDER: the National Cancer Institute (NCI), a participating institute of the
-National Institutes of Health (NIH), and an agency of the United States Government.
-
-•	SOFTWARE: the machine readable, binary, object code form,
-and the related documentation for the modules of the Prostate-MRI_Lesion_Detection, v2.0
-software package, which is a collection of operators which accept (T2, ADC, and High
-b-value DICOM images) and produce prostate organ and lesion segmentation files
-
-•	RECIPIENT: the party that downloads the software.
-
-By downloading or otherwise receiving the SOFTWARE, RECIPIENT may
-use and/or redistribute the SOFTWARE, with or without modification,
-subject to RECIPIENT’s agreement to the following terms:
-
-1. THE SOFTWARE SHALL NOT BE USED IN THE TREATMENT OR DIAGNOSIS
-OF HUMAN SUBJECTS.  RECIPIENT is responsible for
-compliance with all laws and regulations applicable to the use
-of the SOFTWARE.
-
-2. THE SOFTWARE is distributed for NON-COMMERCIAL RESEARCH PURPOSES ONLY. RECIPIENT is
-responsible for appropriate-use compliance.
-
-3.	RECIPIENT agrees to acknowledge PROVIDER’s contribution and
-the name of the author of the SOFTWARE in all written publications
-containing any data or information regarding or resulting from use
-of the SOFTWARE.
-
-4.	THE SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESS OR IMPLIED
-WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
-OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
-ARE DISCLAIMED. IN NO EVENT SHALL THE PROVIDER OR THE INDIVIDUAL DEVELOPERS
-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.
-
-5.	RECIPIENT agrees not to use any trademarks, service marks, trade names,
-logos or product names of NVIDIA, NCI or NIH to endorse or promote products derived
-from the SOFTWARE without specific, prior and written permission.
-
-6.	For sake of clarity, and not by way of limitation, RECIPIENT may add its
-own copyright statement to its modifications or derivative works of the SOFTWARE
-and may provide additional or different license terms and conditions in its
-sublicenses of modifications or derivative works of the SOFTWARE provided that
-RECIPIENT’s use, reproduction, and distribution of the SOFTWARE otherwise complies
-with the conditions stated in this Agreement. Whenever Recipient distributes or
-redistributes the SOFTWARE, a copy of this Agreement must be included with
-each copy of the SOFTWARE.
+Prostate-MRI_Lesion_Detection, v2.0 (Release date: August 2, 2023)
+•	DEFINITIONS: AUTHOR(S) NVIDIA Corp. and National Cancer Institute, NIH
+
+•	PROVIDER: the National Cancer Institute (NCI), a participating institute of the
+National Institutes of Health (NIH), and an agency of the United States Government.
+
+•	SOFTWARE: the machine readable, binary, object code form,
+and the related documentation for the modules of the Prostate-MRI_Lesion_Detection, v2.0
+software package, which is a collection of operators which accept (T2, ADC, and High
+b-value DICOM images) and produce prostate organ and lesion segmentation files
+
+•	RECIPIENT: the party that downloads the software.
+
+By downloading or otherwise receiving the SOFTWARE, RECIPIENT may
+use and/or redistribute the SOFTWARE, with or without modification,
+subject to RECIPIENT’s agreement to the following terms:
+
+1. THE SOFTWARE SHALL NOT BE USED IN THE TREATMENT OR DIAGNOSIS
+OF HUMAN SUBJECTS.  RECIPIENT is responsible for
+compliance with all laws and regulations applicable to the use
+of the SOFTWARE.
+
+2. THE SOFTWARE is distributed for NON-COMMERCIAL RESEARCH PURPOSES ONLY. RECIPIENT is
+responsible for appropriate-use compliance.
+
+3.	RECIPIENT agrees to acknowledge PROVIDER’s contribution and
+the name of the author of the SOFTWARE in all written publications
+containing any data or information regarding or resulting from use
+of the SOFTWARE.
+
+4.	THE SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+ARE DISCLAIMED. IN NO EVENT SHALL THE PROVIDER OR THE INDIVIDUAL DEVELOPERS
+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.
+
+5.	RECIPIENT agrees not to use any trademarks, service marks, trade names,
+logos or product names of NVIDIA, NCI or NIH to endorse or promote products derived
+from the SOFTWARE without specific, prior and written permission.
+
+6.	For sake of clarity, and not by way of limitation, RECIPIENT may add its
+own copyright statement to its modifications or derivative works of the SOFTWARE
+and may provide additional or different license terms and conditions in its
+sublicenses of modifications or derivative works of the SOFTWARE provided that
+RECIPIENT’s use, reproduction, and distribution of the SOFTWARE otherwise complies
+with the conditions stated in this Agreement. Whenever Recipient distributes or
+redistributes the SOFTWARE, a copy of this Agreement must be included with
+each copy of the SOFTWARE.

prostate-mri-lesion-seg/prostate_mri_lesion_seg_app/__main__.py

@@ -1,4 +1,4 @@
-'''
+"""
 Prostate-MRI_Lesion_Detection, v2.0 (Release date: August 2, 2023)
 DEFINITIONS: AUTHOR(S) NVIDIA Corp. and National Cancer Institute, NIH
 
@@ -52,7 +52,7 @@
 RECIPIENT’s use, reproduction, and distribution of the SOFTWARE otherwise complies
 with the conditions stated in this Agreement. Whenever Recipient distributes or
 redistributes the SOFTWARE, a copy of this Agreement must be included with
-each copy of the SOFTWARE.'''
+each copy of the SOFTWARE."""
 
 from app import AIProstateLesionSegApp
 

prostate-mri-lesion-seg/prostate_mri_lesion_seg_app/app.py

@@ -1,4 +1,4 @@
-'''
+"""
 Prostate-MRI_Lesion_Detection, v2.0 (Release date: August 2, 2023)
 DEFINITIONS: AUTHOR(S) NVIDIA Corp. and National Cancer Institute, NIH
 
@@ -52,20 +52,21 @@
 RECIPIENT’s use, reproduction, and distribution of the SOFTWARE otherwise complies
 with the conditions stated in this Agreement. Whenever Recipient distributes or
 redistributes the SOFTWARE, a copy of this Agreement must be included with
-each copy of the SOFTWARE.'''
+each copy of the SOFTWARE."""
 
 import logging
 
+from custom_lesion_seg_operator import CustomProstateLesionSegOperator
+
+# Local imports
+from organ_seg_operator import ProstateSegOperator
+
 # MONAI Deploy SDK imports
 from monai.deploy.core import Application, resource
 from monai.deploy.operators.dicom_data_loader_operator import DICOMDataLoaderOperator
 from monai.deploy.operators.dicom_series_selector_operator import DICOMSeriesSelectorOperator
 from monai.deploy.operators.dicom_series_to_volume_operator import DICOMSeriesToVolumeOperator
 
-# Local imports
-from organ_seg_operator import ProstateSegOperator
-from custom_lesion_seg_operator import CustomProstateLesionSegOperator
-
 # This is a sample series selection rule in JSON, simply selecting MRI series.
 # Please see more details in DICOMSeriesSelectorOperator.
 # Sample_Rules_Text = """
@@ -140,6 +141,7 @@
 }
 """
 
+
 @resource(cpu=1, gpu=1, memory="7Gi")
 class AIProstateLesionSegApp(Application):
     def __init__(self, *args, **kwargs):
@@ -178,10 +180,17 @@ def compose(self):
         self.add_flow(study_loader_op, series_selector_T2_op, {"dicom_study_list": "dicom_study_list"})
         self.add_flow(study_loader_op, series_selector_ADC_op, {"dicom_study_list": "dicom_study_list"})
         self.add_flow(study_loader_op, series_selector_HIGHB_op, {"dicom_study_list": "dicom_study_list"})
-        self.add_flow(series_selector_T2_op, series_to_vol_T2_op, {"study_selected_series_list": "study_selected_series_list"})
-        self.add_flow(series_selector_ADC_op, series_to_vol_ADC_op, {"study_selected_series_list": "study_selected_series_list"})
-        self.add_flow(series_selector_HIGHB_op, series_to_vol_HIGHB_op, {"study_selected_series_list": "study_selected_series_list"})
-
+        self.add_flow(
+            series_selector_T2_op, series_to_vol_T2_op, {"study_selected_series_list": "study_selected_series_list"}
+        )
+        self.add_flow(
+            series_selector_ADC_op, series_to_vol_ADC_op, {"study_selected_series_list": "study_selected_series_list"}
+        )
+        self.add_flow(
+            series_selector_HIGHB_op,
+            series_to_vol_HIGHB_op,
+            {"study_selected_series_list": "study_selected_series_list"},
+        )
 
         # Organ inference
         self.add_flow(series_to_vol_T2_op, organ_seg_op, {"image": "image"})
@@ -195,6 +204,7 @@ def compose(self):
 
         self._logger.debug(f"End {self.compose.__name__}")
 
+
 if __name__ == "__main__":
     # Creates the app and test it standalone. When running is this mode, please note the following:
     #     -i <DICOM folder>, for input DICOM CT series folder

prostate-mri-lesion-seg/prostate_mri_lesion_seg_app/custom_lesion_seg_operator.py

@@ -1,4 +1,4 @@
-'''
+"""
 Prostate-MRI_Lesion_Detection, v2.0 (Release date: August 2, 2023)
 DEFINITIONS: AUTHOR(S) NVIDIA Corp. and National Cancer Institute, NIH
 
@@ -52,31 +52,33 @@
 RECIPIENT’s use, reproduction, and distribution of the SOFTWARE otherwise complies
 with the conditions stated in this Agreement. Whenever Recipient distributes or
 redistributes the SOFTWARE, a copy of this Agreement must be included with
-each copy of the SOFTWARE.'''
+each copy of the SOFTWARE."""
 
-import os
 import copy
 import logging
+import os
 from typing import Optional
+
+import nibabel as nib
 import numpy as np
 
+# AI/CV imports
+import SimpleITK as sitk
+import torch
+
+# Local imports
+from network import RRUNet3D
+from skimage.transform import resize
+from torch.utils.data import Dataset
+
 # MONAI Deploy App SDK imports
 import monai.deploy.core as md
-from monai.deploy.core import ExecutionContext, Image, InputContext, IOType, Operator, OutputContext
 
 # MONAI imports
 from monai.data import MetaTensor
+from monai.deploy.core import ExecutionContext, Image, InputContext, IOType, Operator, OutputContext
 from monai.transforms import SaveImage
 
-# AI/CV imports
-import SimpleITK as sitk
-from skimage.transform import resize
-import nibabel as nib
-import torch
-from torch.utils.data import Dataset
-
-# Local imports
-from network import RRUNet3D
 
 def bbox2_3D(img):
     r = np.any(img, axis=(1, 2))
@@ -89,6 +91,7 @@ def bbox2_3D(img):
 
     return [rmin, rmax, cmin, cmax, zmin, zmax]
 
+
 def standard_normalization_multi_channel(nda):
     for _i in range(nda.shape[0]):
         if np.amax(np.abs(nda[_i, ...])) < 1e-7:
@@ -97,6 +100,7 @@ def standard_normalization_multi_channel(nda):
 
     return nda
 
+
 class SegmentationDataset(Dataset):
     def __init__(self, output_path, data_purpose):
         self.data_purpose = data_purpose
@@ -232,14 +236,12 @@ class CustomProstateLesionSegOperator(Operator):
     """Performs Prostate Lesion segmentation with a 3D image converted from a mp-DICOM MRI series."""
 
     def __init__(self, model_name: Optional[str] = ""):
-
         self.logger = logging.getLogger("{}.{}".format(__name__, type(self).__name__))
         super().__init__()
 
         self._model_name = model_name.strip() if isinstance(model_name, str) else ""
 
     def compute(self, op_input: InputContext, op_output: OutputContext, context: ExecutionContext):
-
         output_path = context.output.get().path
 
         # Load inputs
@@ -411,7 +413,6 @@ def custom_inference(self, data, inputs, inputs_shape, net, output_path, tag, mo
             for rx in ranges_x:
                 for ry in ranges_y:
                     for rz in ranges_z:
-
                         output_patch = net(inputs[..., rx[0] : rx[1], ry[0] : ry[1], rz[0] : rz[1]])
                         output_patch = output_patch.cpu().detach().numpy()
                         output_patch = np.squeeze(output_patch)

prostate-mri-lesion-seg/prostate_mri_lesion_seg_app/network.py

@@ -1,4 +1,4 @@
-'''
+"""
 Prostate-MRI_Lesion_Detection, v2.0 (Release date: August 2, 2023)
 DEFINITIONS: AUTHOR(S) NVIDIA Corp. and National Cancer Institute, NIH
 
@@ -52,26 +52,24 @@
 RECIPIENT’s use, reproduction, and distribution of the SOFTWARE otherwise complies
 with the conditions stated in this Agreement. Whenever Recipient distributes or
 redistributes the SOFTWARE, a copy of this Agreement must be included with
-each copy of the SOFTWARE.'''
+each copy of the SOFTWARE."""
 
 import numpy as np
 import torch
 import torch.nn as nn
 import torch.nn.functional as F
 
-__all__ = [
-    "RRUNet3D"
-]
+__all__ = ["RRUNet3D"]
 
 
 class RecurrentBlock(nn.Module):
     def __init__(self, out_channels, t=2):
-        super(RecurrentBlock,self).__init__()
+        super(RecurrentBlock, self).__init__()
         self.t = t
         self.conv = nn.Sequential(
-            nn.Conv3d(out_channels, out_channels,kernel_size=3,stride=1,padding=1,bias=True),
-		    nn.BatchNorm3d(out_channels),
-			nn.ReLU(inplace=True)
+            nn.Conv3d(out_channels, out_channels, kernel_size=3, stride=1, padding=1, bias=True),
+            nn.BatchNorm3d(out_channels),
+            nn.ReLU(inplace=True),
         )
 
     def forward(self, x):
@@ -223,7 +221,6 @@ def __init__(
         self.output_conv = nn.Conv3d(num_init_kernels, out_channels, 1, stride=1, padding=0, bias=False)
         self.output_activation = nn.Softmax(dim=1)
 
-
         self.blocks_down = list(map(int, blocks_down.split(",")))
         self.blocks_up = list(map(int, blocks_up.split(",")))
         self.blocks_up = self.blocks_up[::-1]
@@ -243,7 +240,6 @@ def __init__(
         self.levels_down = len(self.blocks_down)
         self.encoders = []
         for _i in range(self.levels_down):
-
             in_c = num_init_kernels * 2**_i if _i == 0 else num_init_kernels * 2 ** (_i - 1)
             out_c = num_init_kernels * 2**_i
             # if self.debug:

prostate-mri-lesion-seg/prostate_mri_lesion_seg_app/organ_seg_operator.py

@@ -1,4 +1,4 @@
-'''
+"""
 Prostate-MRI_Lesion_Detection, v2.0 (Release date: August 2, 2023)
 DEFINITIONS: AUTHOR(S) NVIDIA Corp. and National Cancer Institute, NIH
 
@@ -52,7 +52,7 @@
 RECIPIENT’s use, reproduction, and distribution of the SOFTWARE otherwise complies
 with the conditions stated in this Agreement. Whenever Recipient distributes or
 redistributes the SOFTWARE, a copy of this Agreement must be included with
-each copy of the SOFTWARE.'''
+each copy of the SOFTWARE."""
 
 import logging
 from os import path
@@ -88,15 +88,13 @@ class ProstateSegOperator(Operator):
     """Performs Prostate segmentation with a 3D image converted from a DICOM MRI (T2) series."""
 
     def __init__(self, model_name: Optional[str] = ""):
-
         self.logger = logging.getLogger("{}.{}".format(__name__, type(self).__name__))
         super().__init__()
         self._input_dataset_key = "image"
         self._pred_dataset_key = "label"
         self._model_name = model_name.strip() if isinstance(model_name, str) else ""
 
     def compute(self, op_input: InputContext, op_output: OutputContext, context: ExecutionContext):
-
         input_image = op_input.get("image")
         if not input_image:
             raise ValueError("Input image is not found.")