From a099464fa2dc5f9743545452e0cacc14c3482a00 Mon Sep 17 00:00:00 2001 From: Dylan Hall Date: Wed, 17 Jul 2024 09:09:56 -0400 Subject: [PATCH] dicom fundus photos --- .../python/coherent-data/associate_images.py | 222 ++++++++++-------- 1 file changed, 126 insertions(+), 96 deletions(-) diff --git a/src/main/python/coherent-data/associate_images.py b/src/main/python/coherent-data/associate_images.py index 424228b816..8170404b14 100644 --- a/src/main/python/coherent-data/associate_images.py +++ b/src/main/python/coherent-data/associate_images.py @@ -11,6 +11,8 @@ import shutil import uuid + +import pydicom from pydicom.dataset import Dataset, FileMetaDataset from pydicom.sequence import Sequence @@ -157,8 +159,9 @@ def process_file(file, fundus_index, oct_index, output): dicom = create_dicom(image, imaging_study, context) dicom_uid = imaging_study['identifier'][0]['value'][8:] # cut off urn:uuid: pat_name = Path(file).stem - # dicom.save_as(f'{output}/dicom/{pat_name}_{dicom_uid}.dcm') - image.save(f'{output}/dicom/{pat_name}_{dicom_uid}.jpg') + if dicom: + dicom.save_as(f'{output}/dicom/{pat_name}_{dicom_uid}.dcm') + image.save(f'{output}/images/{pat_name}_{dicom_uid}.jpg') media = create_fhir_media(context, imaging_study, image, dicom) bundle['entry'].append(wrap_in_entry(media)) @@ -212,7 +215,7 @@ def get_stage(observations, encounter_id): stage = DR_STAGE_VALUE_CODES.index(stage_obs['valueCodeableConcept']['coding'][0]['code']) - return stage + return str(stage) def pick_image(fundus_index, oct_index, context): @@ -316,117 +319,144 @@ def ref(resource): def create_dicom(image, imaging_study, context): # run `pydicom codify ` to build this + # for now only dicomify the fundus photos + if context['code'] == OCT_PROCEDURE_CODE: + return None + + # File meta info data elements file_meta = FileMetaDataset() - file_meta.FileMetaInformationGroupLength = 192 + file_meta.FileMetaInformationGroupLength = 196 file_meta.FileMetaInformationVersion = b'\x00\x01' - file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2' - file_meta.MediaStorageSOPInstanceUID = '1.3.6.1.4.1.5962.1.1.1.1.1.20040119072730.12322' + file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.77.1.5.1' + file_meta.MediaStorageSOPInstanceUID = '1.2.392.200106.1651.6.2.1803921148151.3911546542.14' file_meta.TransferSyntaxUID = '1.2.840.10008.1.2.1' - file_meta.ImplementationClassUID = '1.3.6.1.4.1.5962.2' - file_meta.ImplementationVersionName = 'DCTOOL100' - file_meta.SourceApplicationEntityTitle = 'CLUNIE1' + file_meta.ImplementationClassUID = '1.2.392.200106.1651.6.2' + file_meta.ImplementationVersionName = 'TP_STO_IM6_100' # Main data elements ds = Dataset() ds.SpecificCharacterSet = 'ISO_IR 100' - ds.ImageType = ['ORIGINAL', 'PRIMARY', 'AXIAL'] - ds.InstanceCreationDate = '20040119' - ds.InstanceCreationTime = '072731' - ds.InstanceCreatorUID = '1.3.6.1.4.1.5962.3' - ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.2' - ds.SOPInstanceUID = '1.3.6.1.4.1.5962.1.1.1.1.1.20040119072730.12322' - ds.StudyDate = '20040119' - ds.SeriesDate = '19970430' - ds.AcquisitionDate = '19970430' - ds.ContentDate = '19970430' - ds.StudyTime = '072730' - ds.SeriesTime = '112749' - ds.AcquisitionTime = '112936' - ds.ContentTime = '113008' + ds.ImageType = ['ORIGINAL', 'PRIMARY', '3D Wide'] + ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.77.1.5.1' + ds.SOPInstanceUID = '1.2.392.200106.1651.6.2.1803921148151.3911546542.14' + + image_date = imaging_study['started'][0:10].replace('-', '') + image_time = imaging_study['started'][11:19].replace(':', '') + '.000000' + ds.StudyDate = image_date + ds.SeriesDate = image_date + ds.AcquisitionDate = image_date + ds.ContentDate = image_date + ds.AcquisitionDateTime = image_date + image_time + ds.StudyTime = image_time + ds.SeriesTime = image_time + ds.AcquisitionTime = image_time + ds.ContentTime = image_time ds.AccessionNumber = '' - ds.Modality = 'CT' - ds.Manufacturer = 'GE MEDICAL SYSTEMS' - ds.InstitutionName = 'JFK IMAGING CENTER' + ds.Modality = 'OP' + ds.ConversionType = 'WSD' + ds.Manufacturer = 'Topcon Healthcare' + ds.InstitutionName = 'THINC' ds.ReferringPhysicianName = '' - ds.TimezoneOffsetFromUTC = '-0500' - ds.StationName = 'CT01_OC0' - ds.StudyDescription = 'e+1' - ds.ManufacturerModelName = 'RHAPSODE' - ds.PatientName = 'CompressedSamples^CT1' - ds.PatientID = '1CT1' - ds.PatientBirthDate = '' - ds.PatientSex = 'O' - - # Other Patient IDs Sequence - other_patient_i_ds_sequence = Sequence() - ds.OtherPatientIDsSequence = other_patient_i_ds_sequence - - # Other Patient IDs Sequence: Other Patient IDs 1 - other_patient_i_ds1 = Dataset() - other_patient_i_ds_sequence.append(other_patient_i_ds1) - other_patient_i_ds1.PatientID = 'ABCD1234' - other_patient_i_ds1.TypeOfPatientID = 'TEXT' - - # Other Patient IDs Sequence: Other Patient IDs 2 - other_patient_i_ds2 = Dataset() - other_patient_i_ds_sequence.append(other_patient_i_ds2) - other_patient_i_ds2.PatientID = '1234ABCD' - other_patient_i_ds2.TypeOfPatientID = 'TEXT' - - ds.PatientAge = '000Y' - ds.PatientWeight = '0.0' - ds.AdditionalPatientHistory = '' - ds.ContrastBolusAgent = 'ISOVUE300/100' - ds.ScanOptions = 'HELICAL MODE' - ds.SliceThickness = '5.0' - ds.KVP = '120.0' - ds.SpacingBetweenSlices = '5.0' - ds.DataCollectionDiameter = '480.0' - ds.SoftwareVersions = '05' - ds.ContrastBolusRoute = 'IV' - ds.ReconstructionDiameter = '338.6716' - ds.DistanceSourceToDetector = '1099.3100585938' - ds.DistanceSourceToPatient = '630.0' - ds.GantryDetectorTilt = '0.0' - ds.TableHeight = '133.699997' - ds.ExposureTime = '1601' - ds.XRayTubeCurrent = '170' - ds.Exposure = '170' - ds.FilterType = 'LARGE BOWTIE FIL' - ds.FocalSpots = '0.7' - ds.ConvolutionKernel = 'STANDARD' - ds.PatientPosition = 'FFS' - ds.StudyInstanceUID = '1.3.6.1.4.1.5962.1.2.1.20040119072730.12322' - ds.SeriesInstanceUID = '1.3.6.1.4.1.5962.1.3.1.1.20040119072730.12322' - ds.StudyID = '1CT1' + ds.SeriesDescription = 'Fundus' + ds.ManufacturerModelName = 'Maestro2' + + # Anatomic Region Sequence + anatomic_region_sequence = Sequence() + ds.AnatomicRegionSequence = anatomic_region_sequence + + # Anatomic Region Sequence: Anatomic Region 1 + anatomic_region1 = Dataset() + anatomic_region_sequence.append(anatomic_region1) + anatomic_region1.CodeValue = 'T-AA610' + anatomic_region1.CodingSchemeDesignator = 'SRT' + anatomic_region1.CodeMeaning = 'Retina' + + patient = context['patient'] + name_obj = patient['name'][0] + ds.PatientName = f"{name_obj['family']}^{name_obj['given'][0]}" + ds.PatientID = patient['id'] + ds.PatientBirthDate = patient['birthDate'].replace('-', '') + ds.PatientSex = patient['gender'][0].upper() + ds.DeviceSerialNumber = '3070395' + ds.SoftwareVersions = '2.54.24153' + ds.FrameTime = '0.0' + ds.SynchronizationTrigger = 'NO TRIGGER' + ds.DateOfLastCalibration = '20220822' + ds.TimeOfLastCalibration = '093900' + ds.AcquisitionTimeSynchronized = 'N' + ds.StudyInstanceUID = imaging_study['series'][0]['uid'] + ds.SeriesInstanceUID = imaging_study['series'][0]['instance'][0]['uid'] + ds.StudyID = '1' ds.SeriesNumber = '1' - ds.AcquisitionNumber = '2' + ds.AcquisitionNumber = '1' ds.InstanceNumber = '1' - ds.ImagePositionPatient = [-158.135803, -179.035797, -75.699997] - ds.ImageOrientationPatient = [1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000] - ds.FrameOfReferenceUID = '1.3.6.1.4.1.5962.1.4.1.1.20040119072730.12322' - ds.Laterality = '' - ds.PositionReferenceIndicator = 'SN' - ds.SliceLocation = '-77.2040634155' - ds.ImageComments = 'Uncompressed' + ds.PatientOrientation = ['L', 'F'] + ds.ImageLaterality = 'R' + ds.SynchronizationFrameOfReferenceUID = '1.2.392.200106.1651.6.2.1803921148151.3911546542' + ds.PatientEyeMovementCommanded = '' + ds.EmmetropicMagnification = None + ds.IntraOcularPressure = None + ds.HorizontalFieldOfView = None + ds.PupilDilated = '' + + # Acquisition Device Type Code Sequence + acquisition_device_type_code_sequence = Sequence() + ds.AcquisitionDeviceTypeCodeSequence = acquisition_device_type_code_sequence + + # Acquisition Device Type Code Sequence: Acquisition Device Type Code 1 + acquisition_device_type_code1 = Dataset() + acquisition_device_type_code_sequence.append(acquisition_device_type_code1) + acquisition_device_type_code1.CodeValue = 'R-1021A' + acquisition_device_type_code1.CodingSchemeDesignator = 'SRT' + acquisition_device_type_code1.CodeMeaning = 'Fundus Camera' + + + # Illumination Type Code Sequence + illumination_type_code_sequence = Sequence() + ds.IlluminationTypeCodeSequence = illumination_type_code_sequence + + + # Light Path Filter Type Stack Code Sequence + light_path_filter_type_stack_code_sequence = Sequence() + ds.LightPathFilterTypeStackCodeSequence = light_path_filter_type_stack_code_sequence + + + # Image Path Filter Type Stack Code Sequence + image_path_filter_type_stack_code_sequence = Sequence() + ds.ImagePathFilterTypeStackCodeSequence = image_path_filter_type_stack_code_sequence + + + # Lenses Code Sequence + lenses_code_sequence = Sequence() + ds.LensesCodeSequence = lenses_code_sequence + + + # Refractive State Sequence + refractive_state_sequence = Sequence() + ds.RefractiveStateSequence = refractive_state_sequence + + + np_image = np.array(image.getdata(), dtype=np.uint8)[:,:3] + ds.SamplesPerPixel = 3 - # ds.PhotometricInterpretation = 'RGB' + ds.PhotometricInterpretation = 'RGB' + ds.PlanarConfiguration = 0 + ds.NumberOfFrames = '1' + ds.FrameIncrementPointer = (0x0018, 0x1063) ds.Rows = image.height ds.Columns = image.width - # ds.PixelSpacing = [0.661468, 0.661468] + ds.PhotometricInterpretation = "RGB" + ds.PixelSpacing = [0, 0] ds.BitsAllocated = 8 ds.BitsStored = 8 ds.HighBit = 7 - ds.PixelRepresentation = 1 - ds.PixelPaddingValue = -2000 - ds.RescaleIntercept = '-1024.0' - ds.RescaleSlope = '1.0' - image_data = np.array(image.getdata(), dtype=np.uint8)[:, :3] - # ds.PixelData = image_data.tobytes() - # ds.DataSetTrailingPadding = # XXX Array of 126 bytes excluded - - ds.file_meta = file_meta + ds.PixelRepresentation = 0 + ds.BurnedInAnnotation = 'NO' + ds.LossyImageCompression = '00' + ds.PixelData = image.tobytes() + + # ds.file_meta = file_meta ds.is_implicit_VR = False ds.is_little_endian = True return ds