fix header process by date, add store log when killed, modularize workflow function
This commit is contained in:
mario
391
main.py
391
main.py
@@ -15,6 +15,7 @@ from utils.cleanup import register_exit_handlers, register_cleanup_dir
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from services.dicom_finder import DicomFinder
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from services.dicom_retriever import DicomRetriever
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from services.dicom_sender import DicomSender
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import signal
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def parse_args():
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"""Parse command line arguments."""
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@@ -362,6 +363,142 @@ def send_file(args):
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logger.error(f"Error sending file: {str(e)}")
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sys.exit(1)
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def process_single_study(study_uid, accession_number=None, log_dir=None):
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"""
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Process a single study: retrieve it, send to destination PACS,
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and create detailed JSON logs.
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Args:
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study_uid: Study Instance UID
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accession_number: Optional accession number
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log_dir: Directory to save logs
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Returns:
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dict: Result information
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"""
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log_dir = log_dir or settings.JSON_OUTPUT_DIR
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# Create services
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finder = DicomFinder()
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retriever = DicomRetriever()
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sender = DicomSender()
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# First, get the study metadata with a query if not provided
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if not accession_number:
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study_metadata = finder.find_study_by_uid(study_uid)
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if not study_metadata:
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logger.error(f"Study not found: {study_uid}")
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return {'success': False, 'error': 'Study not found'}
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accession_number = getattr(study_metadata, 'AccessionNumber', '')
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else:
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study_metadata = None
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logger.info(f"Processing study: {accession_number} with Study_IUID ({study_uid})")
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# STEP 1: Retrieve the study
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retrieve_result = retriever.retrieve_study(study_uid, accession_number=accession_number)
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if not retrieve_result['success']:
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logger.error(f"Failed to retrieve study {study_uid}: {retrieve_result['status']}")
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return {'success': False, 'error': f"Failed to retrieve study: {retrieve_result['status']}"}
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logger.info(f"Retrieved {retrieve_result['successful_instances']} instances for study {study_uid}")
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# STEP 2: Send the study to destination PACS
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send_result = sender.send_study(os.path.join(settings.DICOM_STORE_DIR, study_uid))
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if not send_result['success']:
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logger.error(f"Failed to send study {study_uid}: {send_result.get('error', 'Unknown error')}")
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logger.info(f"Sent {send_result['successful_sends']} of {send_result['total_files']} files to destination PACS")
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# STEP 3: Find all series and create detailed logs
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series_list = finder.find_series_for_study(study_uid, accession_number=accession_number)
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# Get metadata from study_metadata if available, otherwise from the first element of study list
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if study_metadata:
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study_date = getattr(study_metadata, 'StudyDate', '')
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study_time = getattr(study_metadata, 'StudyTime', '000000')
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patient_id = getattr(study_metadata, 'PatientID', '')
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study_description = getattr(study_metadata, 'StudyDescription', '')
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else:
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# We need to query for it again
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study_details = finder.find_study_by_uid(study_uid)
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study_date = getattr(study_details, 'StudyDate', '') if study_details else ''
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study_time = getattr(study_details, 'StudyTime', '000000') if study_details else '000000'
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patient_id = getattr(study_details, 'PatientID', '') if study_details else ''
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study_description = getattr(study_details, 'StudyDescription', '') if study_details else ''
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study_datetime = f"{study_date}{study_time}"
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study_log = {
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'Study_IUID': study_uid,
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'AccessionNumber': accession_number,
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'PatientID': patient_id,
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'StudyDescription': study_description,
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'StudyDateTime': study_datetime,
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'CstoreSuccess': send_result['success'],
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'Series': []
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}
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for series in series_list:
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series_uid = series.SeriesInstanceUID
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# Get first instance for the series
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instance = finder.find_first_instance_for_series(study_uid, series_uid)
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series_info = {
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'Series_IUID': getattr(series, 'SeriesInstanceUID', ''),
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'SeriesNumber': getattr(series, 'SeriesNumber', ''),
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'SeriesDescription': getattr(series, 'SeriesDescription', ''),
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'NumberOfInstances': getattr(series, 'NumberOfSeriesRelatedInstances', ''),
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'SOP_IUID': getattr(instance, 'SOPInstanceUID', '') if instance else ''
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}
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study_log['Series'].append(series_info)
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# STEP 4: Send study_log to HIS API
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his_url = f"http://{settings.HIS_HOST}{settings.HIS_URL}"
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try:
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headers = {
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'id': 'Vmtaa2MySnRUblJTYWtKb1ZucHNNVlZVU2pSaFIwNTBZa1JDYkZaV1NtOWFSV1JIVmxkSmQxSnJUbFpTVlZwRlZsaGpPVkJSUFQwPQ==',
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'Content-Type': 'application/json'
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}
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response = requests.post(his_url, json=study_log, headers=headers)
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# Add response data to the log
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study_log['HisApiResponse'] = {
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'StatusCode': response.status_code,
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'ResponseText': response.text,
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'Success': False,
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'Timestamp': datetime.now().strftime('%Y-%m-%d %H:%M:%S')
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}
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# Safer JSON parsing
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try:
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response_data = response.json() if response.content else {}
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study_log['HisApiResponse']['ResponseData'] = response_data
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if response.status_code == 200 and response_data.get('OK') == "1":
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study_log['HisApiResponse']['Success'] = True
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logger.info(f"Successfully sent JSON {accession_number} to HIS API")
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return {'success': True, 'study_log': study_log, 'his_success': True}
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else:
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error_msg = response_data.get('message', 'Unknown error')
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logger.error(f"Failed to send JSON for {accession_number} to HIS API: {error_msg}. Study_IUID: {study_uid}")
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return {'success': True, 'study_log': study_log, 'his_success': False}
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except ValueError:
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study_log['HisApiResponse']['ParseError'] = "Invalid JSON response"
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logger.error(f"Failed to parse response for {accession_number}, invalid JSON response. Status code: {response.status_code}")
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return {'success': True, 'study_log': study_log, 'his_success': False}
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except Exception as e:
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study_log['HisApiResponse'] = {
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'Success': False,
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'Error': str(e),
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'Timestamp': datetime.now().strftime('%Y-%m-%d %H:%M:%S')
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}
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logger.error(f"Error sending study for {accession_number} to HIS API: {str(e)}")
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return {'success': True, 'study_log': study_log, 'his_success': False, 'error': str(e)}
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def process_workflow(args):
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"""
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Process the full workflow: find studies by date range, retrieve them, and send to destination PACS.
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@@ -387,11 +524,10 @@ def process_workflow(args):
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# Create services
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finder = DicomFinder()
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retriever = DicomRetriever()
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sender = DicomSender()
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# Create directory for logs
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create_directory_if_not_exists(log_dir)
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create_directory_if_not_exists("logs")
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# STEP 1: Find studies in the date range
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try:
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@@ -411,12 +547,30 @@ def process_workflow(args):
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save_json_data(studies_summary, f"studies_{start_date}_to_{end_date}.json", log_dir)
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# STEP 2, 3, 4: For each study, retrieve, send, and log details
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his_log_filename = f"sendtohis_{start_date}_{end_date}.json"
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his_log_path = os.path.join("logs", his_log_filename)
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his_log = []
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his_fail_log_filename = f"fail_sendtohis_{start_date}_{end_date}.json"
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his_fail_log_path = os.path.join("logs", his_fail_log_filename)
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his_fail_log = []
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his_log_filename = f"sendtohis_{start_date}_{end_date}.json"
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his_fail_log_filename = f"fail_sendtohis_{start_date}_{end_date}.json"
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# Register signal handler for SIGINT
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original_sigint_handler = signal.getsignal(signal.SIGINT)
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def sigint_handler(sig, frame):
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logger.warning("Process interrupted by user. Saving logs before exiting...")
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# Save HIS logs
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if his_log:
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save_json_data(his_log, his_log_filename, "logs")
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logger.info(f"Saved {len(his_log)} successful logs to {his_log_filename}")
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if his_fail_log:
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save_json_data(his_fail_log, his_fail_log_filename, "logs")
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logger.info(f"Saved {len(his_fail_log)} failed logs to {his_fail_log_filename}")
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# Restore original signal handler and raise KeyboardInterrupt
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signal.signal(signal.SIGINT, original_sigint_handler)
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sys.exit(1)
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# Set up our custom signal handler
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signal.signal(signal.SIGINT, sigint_handler)
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for i, study in enumerate(studies):
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accession_number = study.AccessionNumber
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@@ -429,86 +583,35 @@ def process_workflow(args):
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logger.info(f"Skipping study {study_uid} - log file already exists")
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continue
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# STEP 2: Retrieve the study
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try:
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retrieve_result = retriever.retrieve_study(study_uid, accession_number=accession_number)
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if not retrieve_result['success']:
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logger.error(f"Failed to retrieve study {study_uid}: {retrieve_result['status']}")
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result = process_single_study(study_uid, accession_number, log_dir)
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if not result['success']:
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logger.error(f"Failed to process study {study_uid}: {result.get('error', 'Unknown error')}")
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continue
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logger.info(f"Retrieved {retrieve_result['successful_instances']} instances for study {study_uid}")
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# Record results for HIS logs
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if result.get('his_success', False):
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his_log.append(result['study_log'])
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else:
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his_fail_log.append(result['study_log'])
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# STEP 3: Send the study to destination PACS
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send_result = sender.send_study(os.path.join(settings.DICOM_STORE_DIR, study_uid))
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if not send_result['success']:
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logger.error(f"Failed to send study {study_uid}: {send_result.get('error', 'Unknown error')}")
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logger.info(f"Sent {send_result['successful_sends']} of {send_result['total_files']} files to destination PACS")
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# STEP 4: Find all series and create detailed logs
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series_list = finder.find_series_for_study(study_uid, accession_number=accession_number)
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study_date = getattr(study, 'StudyDate', '')
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study_time = getattr(study, 'StudyTime', '000000') # Default to midnight if StudyTime is not available
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study_datetime = f"{study_date}{study_time}"
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study_log = {
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'Study_IUID': study_uid,
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'AccessionNumber': getattr(study, 'AccessionNumber', ''),
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'PatientID': getattr(study, 'PatientID', ''), # MedrecID
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'StudyDescription': getattr(study, 'StudyDescription', ''),
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'StudyDateTime': study_datetime,
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'CstoreSuccess': send_result['success'],
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'Series': []
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}
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for series in series_list:
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series_uid = series.SeriesInstanceUID
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# Save progress incrementally every 5 studies
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if (i + 1) % 5 == 0:
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if his_log:
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save_json_data(his_log, his_log_filename, "logs")
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if his_fail_log:
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save_json_data(his_fail_log, his_fail_log_filename, "logs")
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logger.info(f"Saved progress after processing {i+1} studies")
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# Get first instance for the series
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instance = finder.find_first_instance_for_series(study_uid, series_uid)
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series_info = {
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'Series_IUID': getattr(series, 'SeriesInstanceUID', ''),
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'SeriesNumber': getattr(series, 'SeriesNumber', ''),
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'SeriesDescription': getattr(series, 'SeriesDescription', ''),
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'NumberOfInstances': getattr(series, 'NumberOfSeriesRelatedInstances', ''),
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'SOP_IUID': getattr(instance, 'SOPInstanceUID', '') if instance else ''
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}
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study_log['Series'].append(series_info)
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# Save the detailed log
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# save_json_data(study_log, f"{study_uid}.json", log_dir)
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# logger.info(f"Created detailed log for study {study_uid}")
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# STEP 5: Send study_log to HIS API
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his_url = f"http://{settings.HIS_HOST}{settings.HIS_URL}"
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try:
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# Header tembak API HIS
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headers = {
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'id': 'Vmtaa2MySnRUblJTYWtKb1ZucHNNVlZVU2pSaFIwNTBZa1JDYkZaV1NtOWFSV1JIVmxkSmQxSnJUbFpTVlZwRlZsaGpPVkJSUFQwPQ==',
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'Content-Type': 'application/json'
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}
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response = requests.post(his_url, json=study_log, headers=headers)
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# Gunakan ini untuk development
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# response = requests.post(his_url, json=study_log)
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if response.status_code == 200 and response.json().get('OK') == "1":
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his_log.append(study_log)
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logger.info(f"Successfully sent JSON {accession_number} to HIS API")
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else:
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his_fail_log.append(study_log)
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logger.error(f"Failed to send JSON for {accession_number} to HIS API: {response.msg}. Study_IUID: {study_uid}")
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except Exception as e:
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logger.error(f"Error sending study for {accession_number} to HIS API: {str(e)}")
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except Exception as e:
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logger.error(f"Error processing study {accession_number}: {str(e)}")
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continue
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# Save HIS log
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# Restore original signal handler
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signal.signal(signal.SIGINT, original_sigint_handler)
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# Final Save HIS logs
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if his_log:
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save_json_data(his_log, his_log_filename, "logs")
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if his_fail_log:
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@@ -522,8 +625,7 @@ def process_workflow(args):
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def process_workflow_by_study(args):
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"""
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Process the full workflow for a specific study: retrieve it, send to destination PACS,
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and create detailed JSON logs.
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Process the full workflow for a specific study.
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Args:
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args: Command line arguments
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@@ -533,103 +635,64 @@ def process_workflow_by_study(args):
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logger.info(f"Starting full workflow process for study: {study_uid}")
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# Create services
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finder = DicomFinder()
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retriever = DicomRetriever()
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sender = DicomSender()
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# Create directory for logs
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create_directory_if_not_exists(log_dir)
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create_directory_if_not_exists("logs")
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# Process the study
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try:
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# First, get the study metadata with a query
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study_metadata = finder.find_study_by_uid(study_uid)
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if not study_metadata:
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logger.error(f"Study not found: {study_uid}")
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sys.exit(1)
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accession_number = getattr(study_metadata, 'AccessionNumber', '')
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logger.info(f"Processing study: {accession_number} with Study_IUID ({study_uid})")
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# STEP 1: Retrieve the study
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retrieve_result = retriever.retrieve_study(study_uid, accession_number=accession_number)
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if not retrieve_result['success']:
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logger.error(f"Failed to retrieve study {study_uid}: {retrieve_result['status']}")
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sys.exit(1)
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logger.info(f"Retrieved {retrieve_result['successful_instances']} instances for study {study_uid}")
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# STEP 2: Send the study to destination PACS
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send_result = sender.send_study(os.path.join(settings.DICOM_STORE_DIR, study_uid))
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if not send_result['success']:
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logger.error(f"Failed to send study {study_uid}: {send_result.get('error', 'Unknown error')}")
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logger.info(f"Sent {send_result['successful_sends']} of {send_result['total_files']} files to destination PACS")
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# STEP 3: Find all series and create detailed logs
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series_list = finder.find_series_for_study(study_uid, accession_number=accession_number)
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study_date = getattr(study_metadata, 'StudyDate', '')
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study_time = getattr(study_metadata, 'StudyTime', '000000') # Default to midnight if StudyTime is not available
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study_datetime = f"{study_date}{study_time}"
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# Register signal handler for SIGINT
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original_sigint_handler = signal.getsignal(signal.SIGINT)
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# Create empty containers for logs
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his_log = []
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his_fail_log = []
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his_log_filename = f"sendtohis_study_{study_uid}.json"
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his_fail_log_filename = f"fail_sendtohis_study_{study_uid}.json"
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study_log = {
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'Study_IUID': study_uid,
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'AccessionNumber': getattr(study_metadata, 'AccessionNumber', ''),
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'PatientID': getattr(study_metadata, 'PatientID', ''), # MedrecID
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'StudyDescription': getattr(study_metadata, 'StudyDescription', ''),
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'StudyDateTime': study_datetime,
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'CstoreSuccess': send_result['success'],
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'Series': []
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}
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for series in series_list:
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series_uid = series.SeriesInstanceUID
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def sigint_handler(sig, frame):
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logger.warning("Process interrupted by user. Saving logs before exiting...")
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# Save individual study log
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if 'result' in locals() and result.get('success', False):
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save_json_data(result['study_log'], f"{study_uid}.json", log_dir)
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# Get first instance for the series
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instance = finder.find_first_instance_for_series(study_uid, series_uid)
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series_info = {
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'Series_IUID': getattr(series, 'SeriesInstanceUID', ''),
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'SeriesNumber': getattr(series, 'SeriesNumber', ''),
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'SeriesDescription': getattr(series, 'SeriesDescription', ''),
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'NumberOfInstances': getattr(series, 'NumberOfSeriesRelatedInstances', ''),
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'SOP_IUID': getattr(instance, 'SOPInstanceUID', '') if instance else ''
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}
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study_log['Series'].append(series_info)
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# STEP 4: Send study_log to HIS API
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his_url = f"http://{settings.HIS_HOST}{settings.HIS_URL}"
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try:
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# Header tembak API HIS
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headers = {
|
||||
'id': 'Vmtaa2MySnRUblJTYWtKb1ZucHNNVlZVU2pSaFIwNTBZa1JDYkZaV1NtOWFSV1JIVmxkSmQxSnJUbFpTVlZwRlZsaGpPVkJSUFQwPQ==',
|
||||
'Content-Type': 'application/json'
|
||||
}
|
||||
response = requests.post(his_url, json=study_log, headers=headers)
|
||||
|
||||
# Pakai ini untuk Development
|
||||
# response = requests.post(his_url, json=study_log)
|
||||
|
||||
if response.status_code == 200 and response.json().get('OK') == "1":
|
||||
logger.info(f"Successfully sent JSON {accession_number} to HIS API")
|
||||
# Save successful log
|
||||
save_json_data([study_log], f"sendtohis_study_{study_uid}.json", "logs")
|
||||
# Save HIS logs
|
||||
if result.get('his_success', False):
|
||||
save_json_data([result['study_log']], his_log_filename, "logs")
|
||||
logger.info(f"Saved successful log to {his_log_filename}")
|
||||
else:
|
||||
logger.error(f"Failed to send JSON for {accession_number} to HIS API. Study_IUID: {study_uid}")
|
||||
# Save failed log
|
||||
save_json_data([study_log], f"fail_sendtohis_study_{study_uid}.json", "logs")
|
||||
except Exception as e:
|
||||
logger.error(f"Error sending study for {accession_number} to HIS API: {str(e)}")
|
||||
save_json_data([result['study_log']], his_fail_log_filename, "logs")
|
||||
logger.info(f"Saved failed log to {his_fail_log_filename}")
|
||||
|
||||
# Restore original signal handler and exit
|
||||
signal.signal(signal.SIGINT, original_sigint_handler)
|
||||
sys.exit(1)
|
||||
|
||||
# Set up our custom signal handler
|
||||
signal.signal(signal.SIGINT, sigint_handler)
|
||||
|
||||
try:
|
||||
result = process_single_study(study_uid, log_dir=log_dir)
|
||||
|
||||
if not result['success']:
|
||||
logger.error(f"Failed to process study {study_uid}: {result.get('error', 'Unknown error')}")
|
||||
sys.exit(1)
|
||||
|
||||
# Save individual study log
|
||||
save_json_data(result['study_log'], f"{study_uid}.json", log_dir)
|
||||
|
||||
# Save logs
|
||||
if result.get('his_success', False):
|
||||
save_json_data([result['study_log']], his_log_filename, "logs")
|
||||
else:
|
||||
save_json_data([result['study_log']], his_fail_log_filename, "logs")
|
||||
|
||||
logger.info(f"Completed processing study: {study_uid}")
|
||||
|
||||
except Exception as e:
|
||||
logger.error(f"Error during study processing: {str(e)}")
|
||||
sys.exit(1)
|
||||
finally:
|
||||
# Restore original signal handler
|
||||
signal.signal(signal.SIGINT, original_sigint_handler)
|
||||
|
||||
def main():
|
||||
"""Main function."""
|
||||
|
||||
@@ -39,6 +39,7 @@ class DicomRetriever:
|
||||
# Add storage presentation contexts (needed for receiving the images)
|
||||
# for context in StoragePresentationContexts:
|
||||
# self.ae.add_requested_context(context.abstract_syntax)
|
||||
|
||||
storage_uids = [
|
||||
'1.2.840.10008.5.1.4.1.1.1', # CR Storage
|
||||
'1.2.840.10008.5.1.4.1.1.1.1', # Digital X-Ray Image Storage
|
||||
|
||||
@@ -6,11 +6,15 @@ import glob
|
||||
import pydicom
|
||||
import shutil
|
||||
from pydicom.dataset import Dataset
|
||||
from pynetdicom import AE, StoragePresentationContexts, evt
|
||||
from pynetdicom import AE, StoragePresentationContexts, evt, build_role
|
||||
from config import settings
|
||||
from utils.logger import main_logger as logger
|
||||
from utils.error_handler import DicomStoreError, dicom_retry
|
||||
from utils.dicom_utils import create_directory_if_not_exists
|
||||
from pynetdicom.sop_class import (
|
||||
StudyRootQueryRetrieveInformationModelGet,
|
||||
PatientRootQueryRetrieveInformationModelGet
|
||||
)
|
||||
|
||||
class DicomSender:
|
||||
"""
|
||||
@@ -27,9 +31,32 @@ class DicomSender:
|
||||
self.pacs_config = pacs_config or settings.DESTINATION_PACS
|
||||
self.ae = AE(ae_title=settings.SOURCE_AET)
|
||||
|
||||
# Add storage presentation contexts (all standard transfer syntaxes for each SOP class)
|
||||
for context in StoragePresentationContexts:
|
||||
self.ae.add_requested_context(context.abstract_syntax)
|
||||
# Add the Query/Retrieve SOP classes
|
||||
self.ae.add_requested_context(StudyRootQueryRetrieveInformationModelGet)
|
||||
self.ae.add_requested_context(PatientRootQueryRetrieveInformationModelGet)
|
||||
|
||||
# Add storage presentation contexts (needed for receiving the images)
|
||||
# for context in StoragePresentationContexts:
|
||||
# self.ae.add_requested_context(context.abstract_syntax)
|
||||
|
||||
storage_uids = [
|
||||
'1.2.840.10008.5.1.4.1.1.1', # CR Storage
|
||||
'1.2.840.10008.5.1.4.1.1.1.1', # Digital X-Ray Image Storage
|
||||
'1.2.840.10008.5.1.4.1.1.2', # CT Image Storage
|
||||
'1.2.840.10008.5.1.4.1.1.4', # MR Image Storage
|
||||
'1.2.840.10008.5.1.4.1.1.7', # Secondary Capture Image Storage
|
||||
'1.2.840.10008.5.1.4.1.1.6.1', # Ultrasound Image Storage
|
||||
'1.2.840.10008.5.1.4.1.1.128', # PET Image Storage
|
||||
'1.2.840.10008.5.1.4.1.1.20', # Nuclear Medicine Image Storage
|
||||
'1.2.840.10008.5.1.4.1.1.9.1.1', # 12-lead ECG Waveform Storage
|
||||
'1.2.840.10008.5.1.4.1.1.9.1.2', # General ECG Waveform Storage
|
||||
]
|
||||
self.ext_neg = []
|
||||
for uid in storage_uids:
|
||||
self.ae.add_requested_context(uid)
|
||||
role = build_role(uid, scp_role=True)
|
||||
self.ext_neg.append(role)
|
||||
|
||||
|
||||
logger.info(f"DicomSender initialized with destination PACS: {self.pacs_config['aet']}@{self.pacs_config['host']}:{self.pacs_config['port']}")
|
||||
|
||||
|
||||
Reference in New Issue
Block a user