Source code for monai.deploy.operators.dicom_data_loader_operator

# Copyright 2021-2022 MONAI Consortium
# 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
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.

import logging
import os
from pathlib import Path
from typing import List

import monai.deploy.core as md
from monai.deploy.core import DataPath, ExecutionContext, InputContext, IOType, Operator, OutputContext
from monai.deploy.core.domain.dicom_series import DICOMSeries
from monai.deploy.core.domain.dicom_study import DICOMStudy
from monai.deploy.exceptions import ItemNotExistsError
from monai.deploy.utils.importutil import optional_import

dcmread, _ = optional_import("pydicom", name="dcmread")
get_testdata_file, _ = optional_import("", name="dcmread")
FileSet, _ = optional_import("pydicom.fileset", name="FileSet")
generate_uid, _ = optional_import("pydicom.uid", name="generate_uid")
valuerep, _ = optional_import("pydicom", name="valuerep")
InvalidDicomError, _ = optional_import("pydicom.errors", name="InvalidDicomError")

[docs]@md.input("dicom_files", DataPath, IOType.DISK) @md.output("dicom_study_list", List[DICOMStudy], IOType.IN_MEMORY) @md.env(pip_packages=["pydicom >= 1.4.2"]) class DICOMDataLoaderOperator(Operator): """ This operator loads a collection of DICOM Studies in memory given a directory which contains a list of SOP Instances. """
[docs] def __init__(self, must_load: bool = True, *args, **kwargs): """Creates an instance of this class Args: must_load (bool): If true, raise exception if no study is loaded. Defaults to True. """ super().__init__(*args, **kwargs) self._must_load = must_load
[docs] def compute(self, op_input: InputContext, op_output: OutputContext, context: ExecutionContext): """Performs computation for this operator and handlesI/O.""" input_path = op_input.get().path dicom_study_list = self.load_data_to_studies(input_path) op_output.set(dicom_study_list, "dicom_study_list")
[docs] def load_data_to_studies(self, input_path: Path): """Load DICOM data from files into DICOMStudy objects in a list. It scans through the input directory for all SOP instances. It groups them by a collection of studies where each study contains one or more series. This method returns a list of studies. If there is no studies loaded, an exception will be thrown if set to must load. Args: input_path (Path): The folder containing DICOM instance files. Returns: List[DICOMStudy]: List of DICOMStudy. Raises: ValueError: If the folder to load files from does not exist. ItemNotExistsError: If no studies loaded and must_load is True. """ if not input_path.exists() or not input_path.is_dir(): raise ValueError("Required input folder does not exist.") files: List[str] = [] self._list_files(input_path, files) dicom_studies = self._load_data(files) if self._must_load and len(dicom_studies) < 1: raise ItemNotExistsError(f"No study loaded from path {input_path}.") return dicom_studies
def _list_files(self, path, files: List[str]): """Collects fully qualified names of all files recursively given a directory path. Args: path: A directory containing DICOM SOP instances. It may have nested hirerarchical directories. files: This method populates "files" with fully qualified names of files that belong to the specified directory. """ for item in os.listdir(path): item = os.path.join(path, item) if os.path.isdir(item): self._list_files(item, files) else: files.append(item) def _load_data(self, files: List[str]): """Provides a list of DICOM Studies given a list of fully qualified file names. Args: files: A list of file names that represents SOP Instances Returns: A list of DICOMStudy objects. """ study_dict = {} series_dict = {} sop_instances = [] for file in files: try: sop_instances.append(dcmread(file)) except InvalidDicomError as ex: logging.warning(f"Ignored {file}, reason being: {ex}") for sop_instance in sop_instances: study_instance_uid = sop_instance[0x0020, 0x000D] # name is the UID as str if study_instance_uid not in study_dict: study = DICOMStudy(study_instance_uid) self.populate_study_attributes(study, sop_instance) study_dict[study_instance_uid] = study series_instance_uid = sop_instance[0x0020, 0x000E] # name is the UID as str if series_instance_uid not in series_dict: series = DICOMSeries(series_instance_uid) series_dict[series_instance_uid] = series self.populate_series_attributes(series, sop_instance) study_dict[study_instance_uid].add_series(series) series_dict[series_instance_uid].add_sop_instance(sop_instance) return list(study_dict.values())
[docs] def populate_study_attributes(self, study, sop_instance): """Populates study level attributes in the study data structure. Args: study: A DICOM Study instance that needs to be filled-in with study level attribute values sop_instance: A sample DICOM SOP Instance that contains the list of attributed which will be parsed """ try: study_id_de = sop_instance[0x0020, 0x0010] if study_id_de is not None: study.StudyID = study_id_de.value except KeyError: pass try: study_date_de = sop_instance[0x0008, 0x0020] if study_date_de is not None: study.StudyDate = study_date_de.value except KeyError: pass try: study_time_de = sop_instance[0x0008, 0x0030] if study_time_de is not None: study.StudyTime = study_time_de.value except KeyError: pass try: study_desc_de = sop_instance[0x0008, 0x1030] if study_desc_de is not None: study.StudyDescription = study_desc_de.value except KeyError: pass try: accession_number_de = sop_instance[0x0008, 0x0050] if accession_number_de is not None: study.AccessionNumber = accession_number_de.value except KeyError: pass
[docs] def populate_series_attributes(self, series, sop_instance): """Populates series level attributes in the study data structure. Args: study: A DICOM Series instance that needs to be filled-in with series level attribute values sop_instance: A sample DICOM SOP Instance that contains the list of attributed which will be parsed """ try: series_date_de = sop_instance[0x0008, 0x0021] if series_date_de is not None: series.SeriesDate = series_date_de.value except KeyError: pass try: series_time_de = sop_instance[0x0008, 0x0031] if series_time_de is not None: series.SeriesTime = series_time_de.value except KeyError: pass try: series_modality_de = sop_instance[0x0008, 0x0060] if series_modality_de is not None: series.Modality = series_modality_de.value except KeyError: pass try: series_description_de = sop_instance[0x0008, 0x103E] if series_description_de is not None: series.SeriesDescription = series_description_de.value except KeyError: pass try: body_part_examined_de = sop_instance[0x0008, 0x0015] if body_part_examined_de is not None: series.BodyPartExamined = body_part_examined_de.value except KeyError: pass try: patient_position_de = sop_instance[0x0018, 0x5100] if patient_position_de is not None: series.PatientPosition = patient_position_de.value except KeyError: pass try: series_number_de = sop_instance[0x0020, 0x0011] if series_number_de is not None: val = series_number_de.value if isinstance(val, valuerep.IS): series.SeriesNumber = val.real else: series.SeriesNumber = int(val) except KeyError: pass try: laterality_de = sop_instance[0x0020, 0x0060] if laterality_de is not None: series.Laterality = laterality_de.value except KeyError: pass try: tag_pixel_spacing = "PixelSpacing" # tag (0x0028, 0x0030) tag_imager_pixel_spacing = "ImagerPixelSpacing" # tag (0x0018, 0x1164) if tag_pixel_spacing in sop_instance: pixel_spacing_de = sop_instance[tag_pixel_spacing] elif tag_imager_pixel_spacing in sop_instance: pixel_spacing_de = sop_instance[tag_imager_pixel_spacing] else: raise KeyError("Neither {tag_pixel_spacing} nor {tag_imager_pixel_spacing} in dataset header.") if pixel_spacing_de is not None: series.row_pixel_spacing = pixel_spacing_de.value[0] series.col_pixel_spacing = pixel_spacing_de.value[1] except KeyError: pass try: image_orientation_paient_de = sop_instance[0x0020, 0x0037] if image_orientation_paient_de is not None: orientation_orig = image_orientation_paient_de.value orientation = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0] for index, _ in enumerate(orientation_orig): orientation[index] = float(orientation_orig[index]) series.row_direction_cosine = orientation[0:3] series.col_direction_cosine = orientation[3:6] except KeyError: pass
def test(): current_file_dir = Path(__file__).parent.resolve() data_path = current_file_dir.joinpath("../../../examples/ai_spleen_seg_data/dcm") loader = DICOMDataLoaderOperator() study_list = loader.load_data_to_studies(data_path.absolute()) for study in study_list: print("###############################") print(study) for series in study.get_all_series(): print(series) for series in study.get_all_series(): for sop in series.get_sop_instances(): print("Demonstrating ways to access DICOM attributes in a SOP instance.") # No need to get the native_ds = sop.get_native_sop_instance() # sop = sop.get_native_sop_instance() print(f" 'StudyInstanceUID': {sop['StudyInstanceUID'].repval}") print(f" (0x0020, 0x000D): {sop[0x0020, 0x000D].repval}") print(f" 'SeriesInstanceUID': {sop['SeriesInstanceUID']}") print(f" (0x0020, 0x000E): {sop[0x0020, 0x000E]}") print(f" 'SOPInstanceUID': {sop['SOPInstanceUID']}") print(f" (0008,0018): {sop[0x0008, 0x0018]}") try: print(f" 'InstanceNumber': {sop['InstanceNumber'].repval}") print(f" (0020, 0013): {sop[0x0020, 0x0013].repval}") except KeyError: pass # Need to get pydicom dataset to use properties and get method of a dict. ds = sop.get_native_sop_instance() print(f" 'StudyInstanceUID': {ds.StudyInstanceUID if ds.StudyInstanceUID else ''}") print(f" 'SeriesDescription': {ds.SeriesDescription if ds.SeriesDescription else ''}") print( f" 'IssuerOfPatientID': {ds.get('IssuerOfPatientID', '').repval if ds.get('IssuerOfPatientID', '') else '' }" ) try: print(f" 'IssuerOfPatientID': {ds.IssuerOfPatientID if ds.IssuerOfPatientID else '' }") except AttributeError: print( " If the IssuerOfPatientID does not exist, ds.IssuerOfPatientID would throw AttributeError." ) print(" Use ds.get('IssuerOfPatientID', '') instead.") break break # Test raising exception, or not, depending on if set to must_load. non_dcm_dir = current_file_dir.parent / "utils" print(f"{non_dcm_dir}") try: loader.load_data_to_studies(non_dcm_dir) except ItemNotExistsError as ex: print(f"Tested exception when no studies loaded & must_load is True: {ex}") relaxed_loader = DICOMDataLoaderOperator(must_load=False) study_list = relaxed_loader.load_data_to_studies(non_dcm_dir) print(f"Loaded studies length of {len(study_list)} is OK when must_load is set to False.") if __name__ == "__main__": test()