Merge pull request #384 from Project-MONAI/vikash/breast_density_map

A breast density monai application package

Author: GreySeaWolf

examples/apps/breast_density_classifer_app/README.md

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+## A MONAI Application Package to deploy breast density classification algorithm 
+This MAP is based on the Breast Density Model in MONAI [Model-Zoo](https://github.com/Project-MONAI/model-zoo). This model is developed at the Center for Augmented Intelligence in Imaging at the Mayo Clinic, Florida. 
+For any questions, feel free to contact Vikash Gupta ([email protected])
+Sample data and a torchscript model can be downloaded from https://drive.google.com/drive/folders/1Dryozl2MwNunpsGaFPVoaKBLkNbVM3Hu?usp=sharing
+
+
+## Run the application package
+### Python CLI 
+```
+python app.py -i <input_dir> -o <out_dir> -m <breast_density_model> 
+```
+
+### MONAI Deploy CLI
+```
+monai-deploy exec app.py -i <input_dir> -o <out_dir> -m <breast_density_model> 
+```
+Alternatively, you can go a level higher and execute 
+```
+monai-deploy exec breast_density_classification_app -i <input_dir> -o <out_dir> -m <breast_density_model>
+```
+
+
+### Packaging the monai app
+In order to build the monai app, Go a level up and execute the following command.
+```
+monai-deploy package -b nvcr.io/nvidia/pytorch:21.12-py3 breast_density_classification_app --tag breast_density:0.1.0 -m $breast_density_model
+```
+
+

examples/apps/breast_density_classifer_app/__init__.py

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+import os
+import sys
+
+_current_dir = os.path.abspath(os.path.dirname(__file__))
+if sys.path and os.path.abspath(sys.path[0]) != _current_dir:
+    sys.path.insert(0, _current_dir)
+del _current_dir

examples/apps/breast_density_classifer_app/__main__.py

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+from app import BreastClassificationApp
+
+if __name__ == "__main__":
+    BreastClassificationApp(do_run=True)

examples/apps/breast_density_classifer_app/app.py

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+from breast_density_classifier_operator import ClassifierOperator
+
+from monai.deploy.core import Application
+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
+from monai.deploy.operators.dicom_text_sr_writer_operator import DICOMTextSRWriterOperator, EquipmentInfo, ModelInfo
+
+
+class BreastClassificationApp(Application):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+    def compose(self):
+        model_info = ModelInfo(
+            "MONAI Model for Breast Density",
+            "BreastDensity",
+            "0.1",
+            "Center for Augmented Intelligence in Imaging, Mayo Clinic, Florida",
+        )
+        my_equipment = EquipmentInfo(manufacturer="MONAI Deploy App SD", manufacturer_model="DICOM SR Writer")
+        my_special_tags = {"SeriesDescription": "Not for clinical use"}
+        study_loader_op = DICOMDataLoaderOperator()
+        series_selector_op = DICOMSeriesSelectorOperator(rules="")
+        series_to_vol_op = DICOMSeriesToVolumeOperator()
+        classifier_op = ClassifierOperator()
+        sr_writer_op = DICOMTextSRWriterOperator(
+            copy_tags=False, model_info=model_info, equipment_info=my_equipment, custom_tags=my_special_tags
+        )
+
+        self.add_flow(study_loader_op, series_selector_op, {"dicom_study_list": "dicom_study_list"})
+        self.add_flow(
+            series_selector_op, series_to_vol_op, {"study_selected_series_list": "study_selected_series_list"}
+        )
+        self.add_flow(series_to_vol_op, classifier_op, {"image": "image"})
+        self.add_flow(classifier_op, sr_writer_op, {"result_text": "classification_result"})
+
+
+def main():
+    app = BreastClassificationApp()
+    image_dir = "./sampleDICOMs/1/BI_BREAST_SCREENING_BILATERAL_WITH_TOMOSYNTHESIS-2019-07-08/1/L_CC_C-View"
+
+    model_path = "./model/traced_ts_model.pt"
+    app.run(input=image_dir, output="./output", model=model_path)
+
+
+if __name__ == "__main__":
+    main()

examples/apps/breast_density_classifer_app/breast_density_classifier_operator.py

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+import json
+from typing import Dict, Text
+
+import torch
+
+import monai.deploy.core as md
+from monai.data import DataLoader, Dataset
+from monai.deploy.core import ExecutionContext, Image, InputContext, IOType, Operator, OutputContext
+from monai.deploy.operators.monai_seg_inference_operator import InMemImageReader
+from monai.transforms import (
+    Activations,
+    Compose,
+    EnsureChannelFirst,
+    EnsureType,
+    LoadImage,
+    NormalizeIntensity,
+    RepeatChannel,
+    Resize,
+    SqueezeDim,
+)
+
+
+@md.input("image", Image, IOType.IN_MEMORY)
+@md.output("result_text", Text, IOType.IN_MEMORY)
+class ClassifierOperator(Operator):
+    def __init__(self):
+        super().__init__()
+        self._input_dataset_key = "image"
+        self._pred_dataset_key = "pred"
+
+    def _convert_dicom_metadata_datatype(self, metadata: Dict):
+        if not metadata:
+            return metadata
+
+        # Try to convert data type for the well knowned attributes. Add more as needed.
+        if metadata.get("SeriesInstanceUID", None):
+            try:
+                metadata["SeriesInstanceUID"] = str(metadata["SeriesInstanceUID"])
+            except Exception:
+                pass
+        if metadata.get("row_pixel_spacing", None):
+            try:
+                metadata["row_pixel_spacing"] = float(metadata["row_pixel_spacing"])
+            except Exception:
+                pass
+        if metadata.get("col_pixel_spacing", None):
+            try:
+                metadata["col_pixel_spacing"] = float(metadata["col_pixel_spacing"])
+            except Exception:
+                pass
+
+        print("Converted Image object metadata:")
+        for k, v in metadata.items():
+            print(f"{k}: {v}, type {type(v)}")
+
+        return metadata
+
+    def compute(self, op_input: InputContext, op_output: OutputContext, context: ExecutionContext):
+        input_image = op_input.get("image")
+        _reader = InMemImageReader(input_image)
+        input_img_metadata = self._convert_dicom_metadata_datatype(input_image.metadata())
+        img_name = str(input_img_metadata.get("SeriesInstanceUID", "Img_in_context"))
+
+        output_path = context.output.get().path
+
+        device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+        model = context.models.get()
+
+        pre_transforms = self.pre_process(_reader)
+        post_transforms = self.post_process()
+
+        dataset = Dataset(data=[{self._input_dataset_key: img_name}], transform=pre_transforms)
+        dataloader = DataLoader(dataset, batch_size=10, shuffle=False, num_workers=0)
+
+        with torch.no_grad():
+            for d in dataloader:
+                image = d[0].to(device)
+                outputs = model(image)
+                out = post_transforms(outputs).data.cpu().numpy()[0]
+                print(out)
+
+        result_dict = (
+            "A " + ":" + str(out[0]) + " B " + ":" + str(out[1]) + " C " + ":" + str(out[2]) + " D " + ":" + str(out[3])
+        )
+        result_dict_out = {"A": str(out[0]), "B": str(out[1]), "C": str(out[2]), "D": str(out[3])}
+        output_folder = context.output.get().path
+        output_folder.mkdir(parents=True, exist_ok=True)
+
+        output_path = output_folder / "output.json"
+        with open(output_path, "w") as fp:
+            json.dump(result_dict, fp)
+
+        op_output.set(result_dict, "result_text")
+
+    def pre_process(self, image_reader) -> Compose:
+        return Compose(
+            [
+                LoadImage(reader=image_reader, image_only=True),
+                EnsureChannelFirst(),
+                SqueezeDim(dim=3),
+                NormalizeIntensity(),
+                Resize(spatial_size=(299, 299)),
+                RepeatChannel(repeats=3),
+                EnsureChannelFirst(),
+            ]
+        )
+
+    def post_process(self) -> Compose:
+        return Compose([EnsureType(), Activations(sigmoid=True)])