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additional updates
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@dehall
dehall committed Aug 30, 2024
1 parent 49f16a0 commit 83507ad
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Showing 3 changed files with 55 additions and 175 deletions.
5 changes: 3 additions & 2 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 @@ -4,6 +4,7 @@
import glob
import json
import os
import numpy as np
import pandas as pd
from pathlib import Path
from PIL import Image
Expand Down Expand Up @@ -169,8 +170,8 @@ def process_file(file, fundus_index, oct_index, output):

pat_name = Path(file).stem
if dicom:
dicom.save_as(f'{output}/dicom/{pat_name}_{dicom_uid}_{instance_uid}.dcm')
image.save(f'{output}/images/{pat_name}_{dicom_uid}_{instance_uid}.jpg')
dicom.save_as(f'{output}/dicom/{pat_name}_{img_type}_{dicom_uid}_{instance_uid}.dcm', write_like_original=False)
image.save(f'{output}/images/{pat_name}_{img_type}_{dicom_uid}_{instance_uid}.jpg')

media = create_fhir_media(context, imaging_study, image, dicom)
bundle['entry'].append(wrap_in_entry(media))
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75 changes: 51 additions & 24 deletions src/main/python/coherent-data/dicom.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,12 +21,12 @@ def create_dataset_common(image, imaging_study, context):
image_time = imaging_study['started'][11:19].replace(':', '') + '.000000'
ds.StudyDate = image_date
ds.SeriesDate = image_date
ds.AcquisitionDate = 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.AcquisitionTime = image_time
ds.ContentTime = image_time

patient = context['patient']
Expand All @@ -42,10 +42,28 @@ def create_dataset_common(image, imaging_study, context):
ds.SeriesNumber = '1'
ds.AcquisitionNumber = '1'
ds.InstanceNumber = str(context['instance']['number'])
ds.ImageLaterality = 'L' if context['laterality'] == 'OS' else 'OD'
ds.AccessionNumber = ''

ds.PupilDilated = 'YES'
ds.MydriaticAgentSequence = None
ds.DegreeOfDilation = None
ds.IntraOcularPressure = None
ds.HorizontalFieldOfView = None
ds.EmmetropicMagnification = None
ds.RefractiveStateSequence = None

ds.Rows = image.height
ds.Columns = image.width
ds.PixelData = image.tobytes()
if context['type'] == 'OCT':
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = 'MONOCHROME2'
np_image = np.array(image.getdata(), dtype=np.uint8)[:,0]
ds.PixelData = np_image.tobytes()
else:
ds.SamplesPerPixel = 3
ds.PhotometricInterpretation = 'RGB'
ds.PixelData = image.tobytes()

return ds

Expand All @@ -63,20 +81,25 @@ def create_oct_dicom(image, imaging_study, context):

# Main data elements
ds = create_dataset_common(image, imaging_study, context)
ds.file_meta = file_meta
# import pdb; pdb.set_trace()
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.ImageType = ['ORIGINAL', 'PRIMARY', '']
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.77.1.5.4'
ds.SOPInstanceUID = '1.2.392.200106.1651.6.2.1803921148151.3911546542.17'

ds.LightPathFilterTypeStackCodeSequence = None
ds.AcquisitionContextSequence = None

ds.Modality = 'OPT'
ds.Manufacturer = 'Topcon Healthcare'
ds.InstitutionName = 'THINC'
ds.Manufacturer = 'GenericMfr'
ds.InstitutionName = 'Generic'
ds.ReferringPhysicianName = ''
ds.StationName = 'VM'
ds.SeriesDescription = 'OCT'
ds.InstitutionalDepartmentName = 'GPM'
ds.OperatorsName = 'admin'
ds.ManufacturerModelName = 'Maestro2'
ds.ManufacturerModelName = 'GenericDevice'

# Anatomic Region Sequence
anatomic_region_sequence = Sequence()
Expand Down Expand Up @@ -105,9 +128,11 @@ def create_oct_dicom(image, imaging_study, context):
ds.SOPInstanceUIDOfConcatenationSource = '1.2.392.200106.1651.6.2.1803921148151.45272.2.2'
ds.PositionReferenceIndicator = ''
ds.ConcatenationUID = '1.2.392.200106.1651.6.2.1803921148151.45272.2.2'
ds.ConcatenationFrameOffsetNumber = 0
ds.InConcatenationNumber = 1
ds.InConcatenationTotalNumber = 1

ds.PresentationLUTShape = 'IDENTITY'

# Acquisition Device Type Code Sequence
acquisition_device_type_code_sequence = Sequence()
Expand All @@ -120,7 +145,6 @@ def create_oct_dicom(image, imaging_study, context):
acquisition_device_type_code1.CodingSchemeDesignator = 'SRT'
acquisition_device_type_code1.CodeMeaning = 'Optical Coherence Tomography Scanner'


ds.AxialLengthOfTheEye = None
ds.DepthSpatialResolution = 6.0
ds.MaximumDepthDistortion = 0.5
Expand All @@ -131,11 +155,7 @@ def create_oct_dicom(image, imaging_study, context):
ds.IlluminationWaveLength = 840.0
ds.IlluminationPower = 650.0
ds.IlluminationBandwidth = 50.0
ds.SamplesPerPixel = 3
ds.PhotometricInterpretation = 'RGB' # TODO: should be 'MONOCHROME2'
ds.NumberOfFrames = '1'
# ds.Rows = 885
# ds.Columns = 512
ds.BitsAllocated = 8
ds.BitsStored = 8
ds.HighBit = 7
Expand Down Expand Up @@ -244,6 +264,14 @@ def create_oct_dicom(image, imaging_study, context):
frame_content1.InStackPositionNumber = 1
frame_content1.DimensionIndexValues = [1, 1]

# Dimension Organization Sequence
dimension_organization_sequence = Sequence()
ds.DimensionOrganizationSequence = dimension_organization_sequence

# Dimension Organization Sequence: Dimension Organization 1
dimension_organization1 = Dataset()
dimension_organization_sequence.append(dimension_organization1)
dimension_organization1.DimensionOrganizationUID = '@@@'

# Plane Position Sequence
plane_position_sequence = Sequence()
Expand Down Expand Up @@ -289,7 +317,7 @@ def create_oct_dicom(image, imaging_study, context):
purpose_of_ref_code1.CodingSchemeDesignator = 'DCM'
purpose_of_ref_code1.CodeMeaning = 'Localizer'

# ds.file_meta = file_meta

ds.is_implicit_VR = False
ds.is_little_endian = True

Expand All @@ -310,19 +338,25 @@ def create_fundus_dicom(image, imaging_study, context):

# Main data elements
ds = create_dataset_common(image, imaging_study, context)
ds.file_meta = file_meta
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.ImageType = ['ORIGINAL', 'PRIMARY', '3D Wide']
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'

ds.Modality = 'OP'
ds.ConversionType = 'WSD'
# ds.ConversionType = 'WSD'
ds.Manufacturer = 'Topcon Healthcare'
ds.InstitutionName = 'THINC'
ds.ReferringPhysicianName = ''
ds.SeriesDescription = 'Fundus'
ds.ManufacturerModelName = 'Maestro2'

ds.IlluminationTypeCodeSequence = None
ds.LightPathFilterTypeStackCodeSequence = None
ds.ImagePathFilterTypeStackCodeSequence = None
ds.LensesCodeSequence = None

# Anatomic Region Sequence
anatomic_region_sequence = Sequence()
ds.AnatomicRegionSequence = anatomic_region_sequence
Expand All @@ -344,14 +378,9 @@ def create_fundus_dicom(image, imaging_study, context):
ds.AcquisitionTimeSynchronized = 'N'

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 = ''

ds.PatientEyeMovementCommanded = 'NO'
ds.DetectorType = ''
# Acquisition Device Type Code Sequence
acquisition_device_type_code_sequence = Sequence()
ds.AcquisitionDeviceTypeCodeSequence = acquisition_device_type_code_sequence
Expand All @@ -363,8 +392,7 @@ def create_fundus_dicom(image, imaging_study, context):
acquisition_device_type_code1.CodingSchemeDesignator = 'SRT'
acquisition_device_type_code1.CodeMeaning = 'Fundus Camera'

ds.SamplesPerPixel = 3
ds.PhotometricInterpretation = 'RGB'

ds.PlanarConfiguration = 0
ds.NumberOfFrames = '1'
ds.FrameIncrementPointer = (0x0018, 0x1063)
Expand All @@ -377,7 +405,6 @@ def create_fundus_dicom(image, imaging_study, context):
ds.BurnedInAnnotation = 'NO'
ds.LossyImageCompression = '00'

# ds.file_meta = file_meta
ds.is_implicit_VR = False
ds.is_little_endian = True
return ds
150 changes: 1 addition & 149 deletions src/main/resources/modules/eye/ophthalmic_tomography.json
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Original file line number Diff line number Diff line change
Expand Up @@ -50,161 +50,13 @@
]
}
],
"direct_transition": "Quantitative_Report",
"direct_transition": "Qualitative_Report",
"remarks": [
"Body site \"entire retina\" has child codes for left/right eye; sibling codes for other parts",
"",
"DICOM notes: https://www.dicomstandard.org/News-dir/ftsup/docs/sups/sup110.pdf"
]
},
"Quantitative_Report": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "57119-0",
"display": "Optical coherence tomography panel"
}
],
"observations": [
{
"category": "laboratory",
"unit": "um",
"codes": [
{
"system": "LOINC",
"code": "57108-3",
"display": "Macular grid.center point thickness by OCT"
}
],
"attribute": "oct_center_point_thickness"
},
{
"category": "laboratory",
"unit": "um",
"codes": [
{
"system": "LOINC",
"code": "57109-1",
"display": "Macular grid.center subfield thickness by OCT"
}
],
"attribute": "oct_center_subfield_thickness"
},
{
"category": "laboratory",
"unit": "um",
"codes": [
{
"system": "LOINC",
"code": "57110-9",
"display": "Macular grid.inner superior subfield thickness by OCT"
}
],
"attribute": "oct_inner_superior_subfield_thickness"
},
{
"category": "laboratory",
"unit": "um",
"codes": [
{
"system": "LOINC",
"code": "57111-7",
"display": "Macular grid.inner nasal subfield thickness by OCT"
}
],
"attribute": "oct_inner_nasal_subfield_thickness"
},
{
"category": "laboratory",
"unit": "um",
"codes": [
{
"system": "LOINC",
"code": "57112-5",
"display": "Macular grid.inner inferior subfield thickness by OCT"
}
],
"attribute": "oct_inner_inferior_subfield_thickness"
},
{
"category": "laboratory",
"unit": "um",
"codes": [
{
"system": "LOINC",
"code": "57113-3",
"display": "Macular grid.inner temporal subfield thickness by OCT"
}
],
"attribute": "oct_inner_temporal_subfield_thickness"
},
{
"category": "laboratory",
"unit": "um",
"codes": [
{
"system": "LOINC",
"code": "57114-1",
"display": "Macular grid.outer superior subfield thickness by OCT"
}
],
"attribute": "oct_outer_superior_subfield_thickness"
},
{
"category": "laboratory",
"unit": "um",
"codes": [
{
"system": "LOINC",
"code": "57115-8",
"display": "Macular grid.outer nasal subfield thickness by OCT"
}
],
"attribute": "oct_outer_nasal_subfield_thickness"
},
{
"category": "laboratory",
"unit": "um",
"codes": [
{
"system": "LOINC",
"code": "57116-6",
"display": "Macular grid.outer inferior subfield thickness by OCT"
}
],
"attribute": "oct_outer_inferior_subfield_thickness"
},
{
"category": "laboratory",
"unit": "um",
"codes": [
{
"system": "LOINC",
"code": "57117-4",
"display": "Macular grid.outer temporal subfield thickness by OCT"
}
],
"attribute": "oct_outer_temporal_subfield_thickness"
},
{
"category": "laboratory",
"unit": "uL",
"codes": [
{
"system": "LOINC",
"code": "57118-2",
"display": "Macular grid.total volume by OCT"
}
],
"attribute": "oct_total_volume"
}
],
"direct_transition": "Qualitative_Report",
"remarks": [
"https://build.fhir.org/ig/HL7/fhir-eyecare-ig/StructureDefinition-diagnostic-report-oct-macula.html"
]
},
"Qualitative_Report": {
"type": "DiagnosticReport",
"codes": [
Expand Down

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