|
| 1 | +import datetime |
| 2 | +import logging |
| 3 | +import os |
| 4 | +import time |
| 5 | + |
| 6 | +import numpy as np |
| 7 | +from PIL import Image |
| 8 | +from pydicom.dataset import Dataset, FileMetaDataset |
| 9 | +from pydicom.uid import ExplicitVRLittleEndian, generate_uid |
| 10 | +from pynetdicom import AE |
| 11 | +from pynetdicom.sop_class import ( |
| 12 | + DigitalMammographyXRayImageStorageForPresentation, # type: ignore |
| 13 | + ModalityWorklistInformationFind, # type: ignore |
| 14 | +) |
| 15 | + |
| 16 | +from environment import Environment |
| 17 | +from services.dicom import PENDING, PENDING_WARNING, SUCCESS |
| 18 | +from services.mwl import MWLStatus |
| 19 | +from services.storage import MWLStorage |
| 20 | + |
| 21 | +logging.basicConfig( |
| 22 | + level=os.getenv("LOG_LEVEL", "INFO").upper(), |
| 23 | + format=os.getenv("LOG_FORMAT", "%(asctime)s - %(name)s - %(levelname)s - %(message)s"), |
| 24 | +) |
| 25 | + |
| 26 | +logger = logging.getLogger(__name__) |
| 27 | + |
| 28 | + |
| 29 | +DICOM_LATERALITIES = ["L", "R"] |
| 30 | +DICOM_VIEWS = ["CC", "MLO"] |
| 31 | +EMULATED_PROCEDURE_DURATION_SECONDS = int(os.getenv("EMULATED_PROCEDURE_DURATION_SECONDS", "5")) |
| 32 | +MODALITY = "MG" |
| 33 | +MWL_AET = os.getenv("MWL_AET", "SCREENING_MWL") |
| 34 | +MWL_DB_PATH = os.getenv("MWL_DB_PATH", "/var/lib/pacs/worklist.db") |
| 35 | +MWL_HOST = os.getenv("MWL_HOST", "localhost") |
| 36 | +MWL_PORT = int(os.getenv("MWL_PORT", "4243")) |
| 37 | +PACS_AET = os.getenv("PACS_AET", "SCREENING_PACS") |
| 38 | +PACS_DB_PATH = os.getenv("PACS_DB_PATH", "/var/lib/pacs/pacs.db") |
| 39 | +PACS_HOST = os.getenv("PACS_HOST", "localhost") |
| 40 | +PACS_PORT = int(os.getenv("PACS_PORT", "4244")) |
| 41 | +SAMPLE_IMAGES_PATH = os.getenv("SAMPLE_IMAGES_PATH", "sample_images") |
| 42 | + |
| 43 | + |
| 44 | +class DicomExample: |
| 45 | + def __init__( |
| 46 | + self, dataset: Dataset | None, laterality: str, view: str, study_instance_uid: str, series_number: int |
| 47 | + ): |
| 48 | + self.dataset = dataset |
| 49 | + self.laterality = laterality |
| 50 | + self.view = view |
| 51 | + self.study_instance_uid = study_instance_uid |
| 52 | + self.series_number = series_number |
| 53 | + self.data = self.generate_dicom() |
| 54 | + |
| 55 | + def generate_dicom(self) -> Dataset: |
| 56 | + ds = Dataset() |
| 57 | + if not self.dataset: |
| 58 | + logger.error("No dataset provided for DICOM generation") |
| 59 | + return ds |
| 60 | + |
| 61 | + img_path = f"{SAMPLE_IMAGES_PATH}/L{self.view}.jpg" |
| 62 | + img = Image.open(img_path).convert("L") |
| 63 | + if self.laterality == "R": |
| 64 | + img = img.transpose(Image.Transpose.FLIP_LEFT_RIGHT) |
| 65 | + columns, rows = img.size |
| 66 | + pixel_array = np.array(img, dtype=np.uint8) |
| 67 | + pixel_bytes = pixel_array.tobytes() |
| 68 | + if len(pixel_bytes) % 2 != 0: |
| 69 | + pixel_bytes += b"\x00" |
| 70 | + |
| 71 | + file_meta = FileMetaDataset() |
| 72 | + file_meta.MediaStorageSOPClassUID = DigitalMammographyXRayImageStorageForPresentation |
| 73 | + file_meta.MediaStorageSOPInstanceUID = generate_uid() |
| 74 | + file_meta.ImplementationClassUID = generate_uid() |
| 75 | + file_meta.TransferSyntaxUID = ExplicitVRLittleEndian |
| 76 | + |
| 77 | + ds.SOPClassUID = file_meta.MediaStorageSOPClassUID |
| 78 | + ds.SOPInstanceUID = file_meta.MediaStorageSOPInstanceUID |
| 79 | + ds.SamplesPerPixel = 1 |
| 80 | + ds.PhotometricInterpretation = "MONOCHROME2" |
| 81 | + ds.Rows = rows |
| 82 | + ds.Columns = columns |
| 83 | + ds.BitsAllocated = 8 |
| 84 | + ds.BitsStored = 8 |
| 85 | + ds.HighBit = 7 |
| 86 | + ds.PixelRepresentation = 0 |
| 87 | + ds.PixelData = pixel_bytes |
| 88 | + ds.ImageLaterality = self.laterality |
| 89 | + ds.ViewPosition = self.view |
| 90 | + |
| 91 | + ds.AccessionNumber = self.dataset.AccessionNumber |
| 92 | + ds.PatientID = self.dataset.PatientID |
| 93 | + ds.PatientName = self.dataset.PatientName |
| 94 | + ds.PatientBirthDate = self.dataset.PatientBirthDate |
| 95 | + ds.PatientSex = self.dataset.PatientSex |
| 96 | + scheduled_step = self.dataset.ScheduledProcedureStepSequence[0] |
| 97 | + ds.StudyDate = scheduled_step.ScheduledProcedureStepStartDate |
| 98 | + ds.StudyTime = scheduled_step.ScheduledProcedureStepStartTime |
| 99 | + ds.StudyInstanceUID = self.study_instance_uid |
| 100 | + ds.StudyID = f"STUDY{self.study_instance_uid[-8:]}" |
| 101 | + ds.SeriesInstanceUID = generate_uid() |
| 102 | + ds.SeriesNumber = self.series_number |
| 103 | + ds.Modality = MODALITY |
| 104 | + ds.InstanceNumber = 1 |
| 105 | + ds.file_meta = file_meta |
| 106 | + |
| 107 | + logger.debug(f"Generated DICOM for worklist item {self.dataset.AccessionNumber} - {self.laterality}{self.view}") |
| 108 | + logger.debug(f"{ds}") |
| 109 | + |
| 110 | + return ds |
| 111 | + |
| 112 | + |
| 113 | +class ModalityEmulator: |
| 114 | + def __init__(self, mwl_storage: MWLStorage): |
| 115 | + self.mwl_storage = mwl_storage |
| 116 | + self.processed_items = set() |
| 117 | + |
| 118 | + def process_worklist_items(self, ae: AE): |
| 119 | + """ |
| 120 | + Queries the MWL for items scheduled for today and sends generated DICOM files to the PACS server for each item. |
| 121 | + """ |
| 122 | + mwl_assoc = ae.associate(MWL_HOST, MWL_PORT, ae_title=MWL_AET) |
| 123 | + pacs_assoc = ae.associate(PACS_HOST, PACS_PORT, ae_title=PACS_AET) |
| 124 | + |
| 125 | + if mwl_assoc.is_established and pacs_assoc.is_established: |
| 126 | + logger.info(f"Connected to MWL server {MWL_HOST}:{MWL_PORT} ({MWL_AET})") |
| 127 | + logger.info(f"Connected to PACS server {PACS_HOST}:{PACS_PORT} ({PACS_AET})") |
| 128 | + |
| 129 | + logger.info("Querying MWL for scheduled items...") |
| 130 | + responses = mwl_assoc.send_c_find(self.c_find_dataset, query_model=ModalityWorklistInformationFind) |
| 131 | + for status, ds in responses: |
| 132 | + status_code = getattr(status, "Status", SUCCESS) |
| 133 | + |
| 134 | + if status_code in (PENDING, PENDING_WARNING): |
| 135 | + accession_number = getattr(ds, "AccessionNumber", "UNKNOWN") |
| 136 | + |
| 137 | + if accession_number in self.processed_items: |
| 138 | + logger.info(f"Skipping already processed worklist item {accession_number}") |
| 139 | + continue |
| 140 | + |
| 141 | + self.processed_items.add(accession_number) |
| 142 | + study_instance_uid = generate_uid() |
| 143 | + series_number = 1 |
| 144 | + for laterality in DICOM_LATERALITIES: |
| 145 | + for view in DICOM_VIEWS: |
| 146 | + logger.info( |
| 147 | + f"Processing worklist item {accession_number} - generating DICOM for {laterality}{view}" |
| 148 | + ) |
| 149 | + dicom_example = DicomExample(ds, laterality, view, study_instance_uid, series_number) |
| 150 | + dataset = dicom_example.data |
| 151 | + |
| 152 | + if getattr(dataset, "SOPInstanceUID", None) is None: |
| 153 | + logger.error( |
| 154 | + f"Skipping DICOM generation for {laterality}{view} of worklist item {accession_number}" |
| 155 | + ) |
| 156 | + continue |
| 157 | + |
| 158 | + pacs_assoc.send_c_store(dataset) |
| 159 | + logger.info( |
| 160 | + f"Sent DICOM for {laterality}{view} of worklist item {accession_number}. Series# {series_number}" |
| 161 | + ) |
| 162 | + series_number += 1 |
| 163 | + |
| 164 | + time.sleep(1) # Allow C-STORE operations to complete before updating status |
| 165 | + |
| 166 | + self.mwl_storage.update_status(accession_number, MWLStatus.COMPLETED.value) |
| 167 | + logger.info(f"Completed processing for worklist item {accession_number}") |
| 168 | + elif status_code == SUCCESS: |
| 169 | + logger.info("C-FIND query completed successfully") |
| 170 | + else: |
| 171 | + logger.error(f"C-FIND query failed with status: 0x{status_code:04X}") |
| 172 | + |
| 173 | + else: |
| 174 | + logger.error("Failed to make MWL and PACS associations") |
| 175 | + |
| 176 | + mwl_assoc.release() |
| 177 | + pacs_assoc.release() |
| 178 | + |
| 179 | + @property |
| 180 | + def c_find_dataset(self) -> Dataset: |
| 181 | + date_today = datetime.date.today() |
| 182 | + ds = Dataset() |
| 183 | + sps_dataset = Dataset() |
| 184 | + sps_dataset.Modality = MODALITY |
| 185 | + sps_dataset.ScheduledProcedureStepStartDate = date_today.strftime("%Y%m%d") |
| 186 | + sps_dataset.ScheduledProcedureStepStartTime = "000000-" |
| 187 | + ds.ScheduledProcedureStepSequence = [sps_dataset] |
| 188 | + return ds |
| 189 | + |
| 190 | + |
| 191 | +def main(): |
| 192 | + if Environment().production: |
| 193 | + raise RuntimeError("Modality Emulator should not be run in production environment") |
| 194 | + |
| 195 | + logger.info("Modality Emulator Starting...") |
| 196 | + mwl_storage = MWLStorage(db_path=MWL_DB_PATH) |
| 197 | + emulator = ModalityEmulator(mwl_storage) |
| 198 | + ae = AE(ae_title="ModalityEmulator") |
| 199 | + ae.add_requested_context(DigitalMammographyXRayImageStorageForPresentation) |
| 200 | + ae.add_requested_context(ModalityWorklistInformationFind) |
| 201 | + |
| 202 | + while True: |
| 203 | + try: |
| 204 | + time.sleep(EMULATED_PROCEDURE_DURATION_SECONDS) |
| 205 | + emulator.process_worklist_items(ae) |
| 206 | + except KeyboardInterrupt: |
| 207 | + logger.warning("\n Modality Emulator shutting down...") |
| 208 | + break |
| 209 | + except Exception: |
| 210 | + logger.exception("Error in Modality Emulator") |
| 211 | + time.sleep(5) # Wait before retrying to avoid tight error loop |
| 212 | + |
| 213 | + |
| 214 | +if __name__ == "__main__": |
| 215 | + main() |
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