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dicom fundus photos
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@dehall
dehall committed Jul 17, 2024
1 parent 032b5c9 commit a099464
Showing 1 changed file with 126 additions and 96 deletions.
222 changes: 126 additions & 96 deletions src/main/python/coherent-data/associate_images.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,8 @@
import shutil
import uuid


import pydicom
from pydicom.dataset import Dataset, FileMetaDataset
from pydicom.sequence import Sequence

Expand Down Expand Up @@ -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))
Expand Down Expand Up @@ -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):
Expand Down Expand Up @@ -316,117 +319,144 @@ def ref(resource):
def create_dicom(image, imaging_study, context):
# run `pydicom codify <path-to-dcm>` 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
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