124 lines
5.0 KiB
Python
124 lines
5.0 KiB
Python
# ev-to-dicom
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# Copyright © 2023 Lee Yingtong Li
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU Affero General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU Affero General Public License for more details.
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#
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# You should have received a copy of the GNU Affero General Public License
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# along with this program. If not, see <https://www.gnu.org/licenses/>.
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import msgpack
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import pydicom
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from pydicom.dataset import FileDataset, FileMetaDataset
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from pydicom.encaps import encapsulate
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from datetime import datetime
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from .ev_tlv import read_ev_tlv
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def ev_files_to_dcm_file(study_uid, series_uid, series_number, image_number, input_filenames, output_filename):
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# Read Enhanced Viewer input data
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pixel_datas = []
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for filename in input_filenames:
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with open(filename, 'rb') as f:
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data = f.read()
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metadata, pixel_data = read_ev_tlv(data)
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pixel_datas.append(pixel_data)
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# Prepare DICOM file
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file_meta = FileMetaDataset()
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if metadata['metadata']['modality'] == 'US':
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if len(pixel_datas) == 0:
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file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.6.1' # Ultrasound Image Storage
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else:
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file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.3.1' # Ultrasound Multi-frame Image Storage
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else:
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raise Exception('Unknown modality {}'.format(metadata['metadata']['modality']))
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file_meta.MediaStorageSOPInstanceUID = metadata['sopInstanceUid']
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if metadata['imageFormat'] == 0:
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file_meta.TransferSyntaxUID = '1.2.840.10008.1.2.4.91' # JPEG 2000
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elif metadata['imageFormat'] == 1:
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file_meta.TransferSyntaxUID = '1.2.840.10008.1.2.4.50' # JPEG
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else:
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raise Exception('Unknown imageFormat {}'.format(metadata['metadata']['imageFormat']))
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ds = FileDataset(output_filename, {}, file_meta=file_meta, preamble=b'\0' * 128)
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ds.SOPClassUID = file_meta.MediaStorageSOPClassUID
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ds.SOPInstanceUID = metadata['sopInstanceUid']
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ds.is_little_endian = True
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ds.is_implicit_VR = False
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ds.StudyInstanceUID = study_uid
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ds.SeriesInstanceUID = series_uid
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ds.SeriesNumber = series_number
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ds.InstanceNumber = image_number
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ds.PatientName = metadata['metadata']['patientName'].replace(', ', '^')
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ds.PatientSex = metadata['metadata']['patientSex']
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ds.SeriesDescription = metadata['metadata']['seriesDescription']
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ds.Modality = metadata['metadata']['modality']
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ds.PatientID = metadata['metadata']['patientId']
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ds.StudyDate = datetime.strptime(metadata['metadata']['seriesDate'], '%Y-%m-%dT%H:%M:%S.%f').strftime('%Y%m%d')
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ds.StudyTime = datetime.strptime(metadata['metadata']['seriesDate'], '%Y-%m-%dT%H:%M:%S.%f').strftime('%H%M%S.%f')
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ds.SeriesDate = datetime.strptime(metadata['metadata']['seriesDate'], '%Y-%m-%dT%H:%M:%S.%f').strftime('%Y%m%d')
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ds.SeriesTime = datetime.strptime(metadata['metadata']['seriesDate'], '%Y-%m-%dT%H:%M:%S.%f').strftime('%H%M%S.%f')
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ds.StudyDescription = metadata['metadata']['studyDescription']
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ds.AccessionNumber = metadata['metadata']['accessionNumber']
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ds.PatientBirthDate = datetime.strptime(metadata['metadata']['patientBirthDate'], '%Y-%m-%d').strftime('%Y%m%d')
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ds.InstitutionName = metadata['metadata']['institutionName']
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ds.PatientAge = metadata['metadata']['patientAge']
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ds.SamplesPerPixel = 3 if metadata['color'] else 1
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ds.PixelRepresentation = 1 if metadata['isSigned'] else 0
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#ds.BitsAllocated = metadata['bytesPerSample'] * 8 # Incorrect value!
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#ds.BitsStored = metadata['bytesPerSample'] * 8
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ds.Columns = metadata['columns']
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ds.WindowCenter = metadata['windowCenter']
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ds.LossyImageCompression = '01' if metadata['isLossyImage'] else '00'
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ds.PixelSpacing = [metadata['rowPixelSpacing'], metadata['columnPixelSpacing']]
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ds.WindowWidth = metadata['windowWidth']
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ds.PlanarConfiguration = 1 if metadata['planarConfiguration'] else 0
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ds.Rows = metadata['rows']
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if metadata['color']:
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ds.PhotometricInterpretation = 'YBR_FULL_422' # Specify YBR as that is how JPEG compression works, even though the JSON says RGB
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else:
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ds.PhotometricInterpretation = 'MONOCHROME2'
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if len(pixel_datas) > 1:
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ds.RecommendedDisplayFrameRate = round(metadata['recommendedDisplayFrameRate'])
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ds.FrameTime = 1000 / metadata['recommendedDisplayFrameRate']
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ds.FrameIncrementPointer = (0x0018, 0x1063)
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ds.NumberOfFrames = len(pixel_datas)
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# Store copy of raw metadata
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block = ds.private_block(0x0075, 'RunasSudo ev-to-dicom', create=True)
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block.add_new(0x01, 'UL', 0) # Version
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del metadata['totalAvailableBytes']
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block.add_new(0x02, 'OB', msgpack.packb(metadata))
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if metadata['imageFormat'] == 0:
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# JPEG 2000 - For some reason, the end of codestream tag is missing
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ds.PixelData = encapsulate([pixel_data + b'\xff\xd9' for pixel_data in pixel_datas])
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else:
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ds.PixelData = encapsulate(pixel_datas)
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# Save DICOM data
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ds.save_as(output_filename)
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