init: tested on hangtuah to cloud
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mario
359
services/dicom_retriever.py
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359
services/dicom_retriever.py
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"""
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DICOM retriever service - Implements getscu functionality using pynetdicom.
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"""
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import os
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import tempfile
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from pydicom.dataset import Dataset
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from pynetdicom import AE, evt, build_role, StoragePresentationContexts
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from pynetdicom.sop_class import (
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StudyRootQueryRetrieveInformationModelGet,
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PatientRootQueryRetrieveInformationModelGet
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)
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from config import settings
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from utils.logger import main_logger as logger
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from utils.error_handler import DicomRetrieveError, dicom_retry
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from utils.dicom_utils import create_directory_if_not_exists
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from utils.cleanup import register_cleanup_dir
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class DicomRetriever:
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"""
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Class to perform DICOM C-GET operations to retrieve studies.
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"""
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def __init__(self, pacs_config=None, store_dir=None):
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"""
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Initialize DicomRetriever with PACS settings.
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Args:
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pacs_config (dict, optional): PACS configuration dict containing host, port, aet
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store_dir (str, optional): Directory to store retrieved DICOM files
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"""
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self.pacs_config = pacs_config or settings.SOURCE_PACS
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self.store_dir = store_dir or settings.DICOM_STORE_DIR
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self.ae = AE(ae_title=settings.SOURCE_AET)
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# Add the Query/Retrieve SOP classes
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self.ae.add_requested_context(StudyRootQueryRetrieveInformationModelGet)
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self.ae.add_requested_context(PatientRootQueryRetrieveInformationModelGet)
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# Add storage presentation contexts (needed for receiving the images)
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# for context in StoragePresentationContexts:
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# self.ae.add_requested_context(context.abstract_syntax)
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storage_uids = [
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'1.2.840.10008.5.1.4.1.1.1', # CR Storage
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'1.2.840.10008.5.1.4.1.1.1.1', # Digital X-Ray Image Storage
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'1.2.840.10008.5.1.4.1.1.2', # CT Image Storage
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'1.2.840.10008.5.1.4.1.1.4', # MR Image Storage
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'1.2.840.10008.5.1.4.1.1.7', # Secondary Capture Image Storage
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'1.2.840.10008.5.1.4.1.1.6.1', # Ultrasound Image Storage
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'1.2.840.10008.5.1.4.1.1.128', # PET Image Storage
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'1.2.840.10008.5.1.4.1.1.20', # Nuclear Medicine Image Storage
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'1.2.840.10008.5.1.4.1.1.9.1.1', # 12-lead ECG Waveform Storage
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'1.2.840.10008.5.1.4.1.1.9.1.2', # General ECG Waveform Storage
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]
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self.ext_neg = []
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for uid in storage_uids:
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self.ae.add_requested_context(uid)
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role = build_role(uid, scp_role=True)
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self.ext_neg.append(role)
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# Create storage directory if it doesn't exist
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create_directory_if_not_exists(self.store_dir)
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logger.info(f"DicomRetriever initialized with PACS: {self.pacs_config['aet']}@{self.pacs_config['host']}:{self.pacs_config['port']}")
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logger.info(f"DICOM files will be stored in: {self.store_dir}")
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def _handle_store(self, event):
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"""
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Handle C-STORE operations during a C-GET association.
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Args:
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event: DICOM C-STORE event
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Returns:
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int: Status code (0 = Success)
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"""
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dataset = event.dataset
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# Get the study, series, and instance UIDs
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study_uid = dataset.StudyInstanceUID
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series_uid = dataset.SeriesInstanceUID
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instance_uid = dataset.SOPInstanceUID
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# Create nested directory structure: StudyInstanceUID/SeriesInstanceUID/
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study_dir = os.path.join(self.store_dir, study_uid)
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series_dir = os.path.join(study_dir, series_uid)
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create_directory_if_not_exists(series_dir)
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# Save the dataset to file
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filename = f"{instance_uid}.dcm"
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file_path = os.path.join(series_dir, filename)
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try:
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dataset.save_as(file_path, write_like_original=False)
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logger.debug(f"Stored instance {instance_uid} to {file_path}")
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return 0x0000 # Success status
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except Exception as e:
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logger.error(f"Error storing instance {instance_uid}: {str(e)}")
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return 0xC001 # Failed - Unable to store
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@dicom_retry(exception_types=(DicomRetrieveError, ConnectionError))
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def retrieve_study(self, study_instance_uid, accession_number=None):
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"""
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Retrieve a complete study using C-GET.
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Args:
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study_instance_uid (str): StudyInstanceUID to retrieve
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accession_number (str, optional): AccessionNumber to filter the study
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Returns:
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dict: Summary of retrieved data with counts and status
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"""
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logger.info(f"Retrieving study: {accession_number} with Study_IUID {study_instance_uid}")
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# Create study-specific directory
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study_dir = os.path.join(self.store_dir, study_instance_uid)
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create_directory_if_not_exists(study_dir)
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# Register this directory for cleanup on exit
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register_cleanup_dir(study_dir)
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# Create query dataset
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ds = Dataset()
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ds.QueryRetrieveLevel = 'STUDY'
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ds.StudyInstanceUID = study_instance_uid
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# Create association
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# Bind the evt.EVT_C_STORE handler to our _handle_store function
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handlers = [(evt.EVT_C_STORE, self._handle_store)]
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assoc = self.ae.associate(
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self.pacs_config['host'],
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self.pacs_config['port'],
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ae_title=self.pacs_config['aet'],
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evt_handlers=handlers,
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ext_neg=self.ext_neg, # No extended negotiation
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)
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result = {
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'success': False,
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'study_uid': study_instance_uid,
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'total_instances': 0,
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'successful_instances': 0,
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'failed_instances': 0,
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'status': '',
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'error': '',
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'study_dir': study_dir
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}
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if assoc.is_established:
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try:
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logger.debug(f"Association established, sending C-GET request for study {study_instance_uid}")
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# Send C-GET request
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responses = assoc.send_c_get(
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ds,
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StudyRootQueryRetrieveInformationModelGet )
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# Track progress
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for (status, identifier) in responses:
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if status:
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# Update status information
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result['total_instances'] = getattr(status, 'NumberOfRemainingSuboperations', 0) + \
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getattr(status, 'NumberOfCompletedSuboperations', 0) + \
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getattr(status, 'NumberOfFailedSuboperations', 0) + \
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getattr(status, 'NumberOfWarningSuboperations', 0)
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result['successful_instances'] = getattr(status, 'NumberOfCompletedSuboperations', 0)
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result['failed_instances'] = getattr(status, 'NumberOfFailedSuboperations', 0)
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# Log progress for large retrievals
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if status.Status == 0xFF00: # Pending
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if hasattr(status, 'NumberOfRemainingSuboperations'):
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logger.debug(f"C-GET progress: {result['successful_instances']}/{result['total_instances']} instances received")
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# Check if operation was successful
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if status.Status == 0x0000: # Success
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result['success'] = True
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result['status'] = 'Success'
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elif status.Status == 0xB000: # Warning
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result['success'] = True
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result['status'] = 'Warning - Suboperations Complete with Failures'
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else:
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result['status'] = f"Error - Status code: {status.Status:04x}"
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logger.info(f"C-GET completed: {result['successful_instances']}/{result['total_instances']} instances retrieved")
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except Exception as e:
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error_msg = f"Error during C-GET: {str(e)}"
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logger.error(error_msg)
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result['error'] = error_msg
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raise DicomRetrieveError(error_msg)
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finally:
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# Release the association
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assoc.release()
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logger.debug("Association released")
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else:
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error_msg = f"Association rejected, aborted or never connected to {self.pacs_config['aet']}"
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logger.error(error_msg)
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result['error'] = error_msg
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raise DicomRetrieveError(error_msg)
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return result
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@dicom_retry(exception_types=(DicomRetrieveError, ConnectionError))
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def retrieve_series(self, study_instance_uid, series_instance_uid):
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"""
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Retrieve a specific series using C-GET.
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Args:
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study_instance_uid (str): StudyInstanceUID
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series_instance_uid (str): SeriesInstanceUID to retrieve
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Returns:
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dict: Summary of retrieved data with counts and status
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"""
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logger.info(f"Retrieving series: {series_instance_uid} from study: {study_instance_uid}")
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# Create series-specific directory
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study_dir = os.path.join(self.store_dir, study_instance_uid)
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series_dir = os.path.join(study_dir, series_instance_uid)
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create_directory_if_not_exists(series_dir)
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# Register directories for cleanup on exit
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register_cleanup_dir(study_dir)
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register_cleanup_dir(series_dir)
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# Create query dataset
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ds = Dataset()
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ds.QueryRetrieveLevel = 'SERIES'
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ds.StudyInstanceUID = study_instance_uid
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ds.SeriesInstanceUID = series_instance_uid
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# Create association
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# Bind the evt.EVT_C_STORE handler to our _handle_store function
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handlers = [(evt.EVT_C_STORE, self._handle_store)]
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assoc = self.ae.associate(
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self.pacs_config['host'],
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self.pacs_config['port'],
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ae_title=self.pacs_config['aet'],
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evt_handlers=handlers,
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ext_neg=self.ext_neg, # No extended negotiation
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)
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result = {
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'success': False,
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'study_uid': study_instance_uid,
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'series_uid': series_instance_uid,
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'total_instances': 0,
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'successful_instances': 0,
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'failed_instances': 0,
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'status': '',
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'error': '',
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'series_dir': series_dir
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}
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if assoc.is_established:
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try:
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logger.debug(f"Association established, sending C-GET request for series {series_instance_uid}")
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# Send C-GET request
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responses = assoc.send_c_get(
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ds,
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StudyRootQueryRetrieveInformationModelGet )
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# Track progress
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for (status, identifier) in responses:
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if status:
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# Update status information
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result['total_instances'] = getattr(status, 'NumberOfRemainingSuboperations', 0) + \
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getattr(status, 'NumberOfCompletedSuboperations', 0) + \
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getattr(status, 'NumberOfFailedSuboperations', 0) + \
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getattr(status, 'NumberOfWarningSuboperations', 0)
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result['successful_instances'] = getattr(status, 'NumberOfCompletedSuboperations', 0)
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result['failed_instances'] = getattr(status, 'NumberOfFailedSuboperations', 0)
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# Check if operation was successful
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if status.Status == 0x0000: # Success
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result['success'] = True
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result['status'] = 'Success'
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elif status.Status == 0xB000: # Warning
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result['success'] = True
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result['status'] = 'Warning - Suboperations Complete with Failures'
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else:
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result['status'] = f"Error - Status code: {status.Status:04x}"
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logger.info(f"C-GET completed: {result['successful_instances']}/{result['total_instances']} instances retrieved")
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except Exception as e:
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error_msg = f"Error during C-GET: {str(e)}"
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logger.error(error_msg)
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result['error'] = error_msg
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raise DicomRetrieveError(error_msg)
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finally:
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# Release the association
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assoc.release()
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logger.debug("Association released")
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else:
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error_msg = f"Association rejected, aborted or never connected to {self.pacs_config['aet']}"
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logger.error(error_msg)
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result['error'] = error_msg
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raise DicomRetrieveError(error_msg)
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return result
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def get_retrieved_file_count(self, study_uid, series_uid=None):
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"""
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Count the number of files retrieved for a study or series.
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Args:
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study_uid (str): StudyInstanceUID
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series_uid (str, optional): SeriesInstanceUID. If None, count all files in the study.
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Returns:
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int: Number of DICOM files found
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"""
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study_dir = os.path.join(self.store_dir, study_uid)
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if not os.path.exists(study_dir):
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logger.warning(f"Study directory does not exist: {study_dir}")
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return 0
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file_count = 0
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if series_uid:
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# Count files in a specific series
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series_dir = os.path.join(study_dir, series_uid)
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if os.path.exists(series_dir):
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# Count only .dcm files
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file_count = len([f for f in os.listdir(series_dir) if f.endswith('.dcm')])
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else:
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# Count files in all series of the study
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for series_name in os.listdir(study_dir):
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series_dir = os.path.join(study_dir, series_name)
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if os.path.isdir(series_dir):
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file_count += len([f for f in os.listdir(series_dir) if f.endswith('.dcm')])
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return file_count
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def is_study_complete(self, study_uid, expected_instance_count=None):
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"""
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Check if a study has been completely retrieved.
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Args:
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study_uid (str): StudyInstanceUID
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expected_instance_count (int, optional): Expected number of instances.
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Returns:
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bool: True if study is complete, False otherwise
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"""
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if expected_instance_count is None:
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logger.warning("No expected instance count provided, can't determine if study is complete")
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return False
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actual_count = self.get_retrieved_file_count(study_uid)
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logger.info(f"Study {study_uid} completeness: {actual_count}/{expected_instance_count} instances")
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return actual_count >= expected_instance_count
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