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mrd2dicom.py
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#!/usr/bin/python3
import os
import re
import argparse
import h5py
import ismrmrd
import numpy as np
import pydicom
import base64
# Lookup table between DICOM and MRD mrdImg types
imtype_map = {ismrmrd.IMTYPE_MAGNITUDE : 'M',
ismrmrd.IMTYPE_PHASE : 'P',
ismrmrd.IMTYPE_REAL : 'R',
ismrmrd.IMTYPE_IMAG : 'I',
0 : 'M'} # Fallback for unset value
# Lookup table between DICOM and Siemens flow directions
venc_dir_map = {'FLOW_DIR_R_TO_L' : 'rl',
'FLOW_DIR_L_TO_R' : 'lr',
'FLOW_DIR_A_TO_P' : 'ap',
'FLOW_DIR_P_TO_A' : 'pa',
'FLOW_DIR_F_TO_H' : 'fh',
'FLOW_DIR_H_TO_F' : 'hf',
'FLOW_DIR_TP_IN' : 'in',
'FLOW_DIR_TP_OUT' : 'out'}
def main(args):
dset = h5py.File(args.filename, 'r')
if not dset:
print("Not a valid dataset: %s" % (args.filename))
return
dsetNames = dset.keys()
print("File %s contains %d groups:" % (args.filename, len(dset.keys())))
print(" ", "\n ".join(dsetNames))
if not args.in_group:
if len(dset.keys()) > 1:
print("Input group not specified -- selecting most recent")
args.in_group = list(dset.keys())[-1]
if not args.out_folder:
args.out_folder = re.sub('.h5$', '', args.filename)
print("Output folder not specified -- using %s" % args.out_folder)
if args.in_group not in dset:
print("Could not find group %s" % (args.in_group))
return
if not os.path.exists(args.out_folder):
os.makedirs(args.out_folder)
group = dset.get(args.in_group)
print("Reading data from group '%s' in file '%s'" % (args.in_group, args.filename))
# mrdImg data is stored as:
# /group/config text of recon config parameters (optional)
# /group/xml text of ISMRMRD flexible data header (optional)
# /group/image_0/data array of IsmrmrdImage data
# /group/image_0/header array of ImageHeader
# /group/image_0/attributes text of mrdImg MetaAttributes
isImage = True
imageNames = group.keys()
print("Found %d mrdImg sub-groups: %s" % (len(imageNames), ", ".join(imageNames)))
for imageName in imageNames:
if ((imageName == 'xml') or (imageName == 'config') or (imageName == 'config_file')):
continue
mrdImg = group[imageName]
if not (('data' in mrdImg) and ('header' in mrdImg) and ('attributes' in mrdImg)):
isImage = False
dset.close()
if (isImage is False):
print("File does not contain properly formatted MRD raw or mrdImg data")
return
dset = ismrmrd.Dataset(args.filename, args.in_group, False)
groups = dset.list()
if ('xml' in groups):
xml_header = dset.read_xml_header()
xml_header = xml_header.decode("utf-8")
mrdHead = ismrmrd.xsd.CreateFromDocument(xml_header)
else:
mrdHead = ismrmrd.xsd.ismrmrdHeader()
filesWritten = 0
for group in groups:
if ( (group == 'config') or (group == 'config_file') or (group == 'xml') ):
continue
print("Reading images from '/" + args.in_group + "/" + group + "'")
for imgNum in range(0, dset.number_of_images(group)):
mrdImg = dset.read_image(group, imgNum)
meta = ismrmrd.Meta.deserialize(mrdImg.attribute_string)
if ((mrdImg.data.shape[0] == 3) and (mrdImg.getHead().image_type == 6)):
# RGB images
print("RGB data not yet supported")
continue
else:
if (mrdImg.data.shape[1] != 1):
print("Multi-slice data not yet supported")
continue
if (mrdImg.data.shape[0] != 1):
print("Multi-channel data not yet supported")
continue
# Use previously JSON serialized header as a starting point, if available
if meta.get('DicomJson') is not None:
dicomDset = pydicom.dataset.Dataset.from_json(base64.b64decode(meta['DicomJson']))
else:
dicomDset = pydicom.dataset.Dataset()
dicomDset = pydicom.dataset.Dataset()
# Enforce explicit little endian for written DICOM files
dicomDset.file_meta = pydicom.dataset.FileMetaDataset()
dicomDset.file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian
dicomDset.file_meta.MediaStorageSOPClassUID = pydicom.uid.MRImageStorage
dicomDset.file_meta.MediaStorageSOPInstanceUID = pydicom.uid.generate_uid()
pydicom.dataset.validate_file_meta(dicomDset.file_meta)
# FileMetaInformationGroupLength is still missing?
dicomDset.is_little_endian = True
dicomDset.is_implicit_VR = False
# ----- Update DICOM header from MRD header -----
try:
if mrdHead.measurementInformation is None:
pass
# print(" MRD header does not contain measurementInformation section")
else:
# print("---------- Old -------------------------")
# print("SeriesInstanceUID : %s" % dicomDset.SeriesInstanceUID )
# print("PatientPosition : %s" % dicomDset.PatientPosition )
# print("SeriesDescription : %s" % dicomDset.SeriesDescription )
# print("FrameOfReferenceUID: %s" % dicomDset.FrameOfReferenceUID )
if mrdHead.measurementInformation.measurementID is not None: dicomDset.SeriesInstanceUID = mrdHead.measurementInformation.measurementID
if mrdHead.measurementInformation.patientPosition is not None: dicomDset.PatientPosition = mrdHead.measurementInformation.patientPosition.name
if mrdHead.measurementInformation.protocolName is not None: dicomDset.SeriesDescription = mrdHead.measurementInformation.protocolName
if mrdHead.measurementInformation.frameOfReferenceUID is not None: dicomDset.FrameOfReferenceUID = mrdHead.measurementInformation.frameOfReferenceUID
# print("---------- New -------------------------")
# print("SeriesInstanceUID : %s" % dicomDset.SeriesInstanceUID )
# print("PatientPosition : %s" % dicomDset.PatientPosition )
# print("SeriesDescription : %s" % dicomDset.SeriesDescription )
# print("FrameOfReferenceUID: %s" % dicomDset.FrameOfReferenceUID )
except:
print("Error setting header information from MRD header's measurementInformation section")
try:
if mrdHead.acquisitionSystemInformation is None:
pass
else:
# print("---------- Old -------------------------")
# print("mrdHead.acquisitionSystemInformation.systemVendor : %s" % mrdHead.acquisitionSystemInformation.systemVendor )
# print("mrdHead.acquisitionSystemInformation.systemModel : %s" % mrdHead.acquisitionSystemInformation.systemModel )
# print("mrdHead.acquisitionSystemInformation.systemFieldStrength_T: %s" % mrdHead.acquisitionSystemInformation.systemFieldStrength_T )
# print("mrdHead.acquisitionSystemInformation.institutionName : %s" % mrdHead.acquisitionSystemInformation.institutionName )
# print("mrdHead.acquisitionSystemInformation.stationName : %s" % mrdHead.acquisitionSystemInformation.stationName )
if mrdHead.acquisitionSystemInformation.systemVendor is not None: dicomDset.Manufacturer = mrdHead.acquisitionSystemInformation.systemVendor
if mrdHead.acquisitionSystemInformation.systemModel is not None: dicomDset.ManufacturerModelName = mrdHead.acquisitionSystemInformation.systemModel
if mrdHead.acquisitionSystemInformation.systemFieldStrength_T is not None: dicomDset.MagneticFieldStrength = mrdHead.acquisitionSystemInformation.systemFieldStrength_T
if mrdHead.acquisitionSystemInformation.institutionName is not None: dicomDset.InstitutionName = mrdHead.acquisitionSystemInformation.institutionName
if mrdHead.acquisitionSystemInformation.stationName is not None: dicomDset.StationName = mrdHead.acquisitionSystemInformation.stationName
# print("---------- New -------------------------")
# print("mrdHead.acquisitionSystemInformation.systemVendor : %s" % mrdHead.acquisitionSystemInformation.systemVendor )
# print("mrdHead.acquisitionSystemInformation.systemModel : %s" % mrdHead.acquisitionSystemInformation.systemModel )
# print("mrdHead.acquisitionSystemInformation.systemFieldStrength_T: %s" % mrdHead.acquisitionSystemInformation.systemFieldStrength_T )
# print("mrdHead.acquisitionSystemInformation.institutionName : %s" % mrdHead.acquisitionSystemInformation.institutionName )
# print("mrdHead.acquisitionSystemInformation.stationName : %s" % mrdHead.acquisitionSystemInformation.stationName )
except:
print("Error setting header information from MRD header's acquisitionSystemInformation section")
# Set mrdImg pixel data from MRD mrdImg
dicomDset.PixelData = np.squeeze(mrdImg.data).tobytes() # mrdImg.data is [cha z y x] -- squeeze to [y x] for [row col]
dicomDset.Rows = mrdImg.data.shape[2]
dicomDset.Columns = mrdImg.data.shape[3]
if (mrdImg.data.dtype == 'uint16') or (mrdImg.data.dtype == 'int16'):
dicomDset.BitsAllocated = 16
dicomDset.BitsStored = 16
dicomDset.HighBit = 15
elif (mrdImg.data.dtype == 'uint32') or (mrdImg.data.dtype == 'int') or (mrdImg.data.dtype == 'float32'):
dicomDset.BitsAllocated = 32
dicomDset.BitsStored = 32
dicomDset.HighBit = 31
elif (mrdImg.data.dtype == 'float64'):
dicomDset.BitsAllocated = 64
dicomDset.BitsStored = 64
dicomDset.HighBit = 63
else:
print("Unsupported data type: ", mrdImg.data.dtype)
dicomDset.SeriesNumber = mrdImg.image_series_index
dicomDset.InstanceNumber = mrdImg.image_index
# ----- Set some mandatory default values -----
if not 'SamplesPerPixel' in dicomDset:
dicomDset.SamplesPerPixel = 1
if not 'PhotometricInterpretation' in dicomDset:
dicomDset.PhotometricInterpretation = 'MONOCHROME2'
if not 'PixelRepresentation' in dicomDset:
dicomDset.PixelRepresentation = 0 # Unsigned integer
if not 'ImageType' in dicomDset:
dicomDset.ImageType = ['ORIGINAL', 'PRIMARY', 'M']
if not 'SeriesNumber' in dicomDset:
dicomDset.SeriesNumber = 1
if not 'SeriesDescription' in dicomDset:
dicomDset.SeriesDescription = ''
if not 'InstanceNumber' in dicomDset:
dicomDset.InstanceNumber = 1
# ----- Update DICOM header from MRD ImageHeader -----
dicomDset.ImageType[2] = imtype_map[mrdImg.image_type]
dicomDset.PixelSpacing = [float(mrdImg.field_of_view[0]) / mrdImg.data.shape[2], float(mrdImg.field_of_view[1]) / mrdImg.data.shape[3]]
dicomDset.SliceThickness = mrdImg.field_of_view[2]
dicomDset.ImagePositionPatient = [mrdImg.position[0], mrdImg.position[1], mrdImg.position[2]]
dicomDset.ImageOrientationPatient = [mrdImg.read_dir[0], mrdImg.read_dir[1], mrdImg.read_dir[2], mrdImg.phase_dir[0], mrdImg.phase_dir[1], mrdImg.phase_dir[2]]
time_sec = mrdImg.acquisition_time_stamp/1000/2.5
hour = int(np.floor(time_sec/3600))
min = int(np.floor((time_sec - hour*3600)/60))
sec = time_sec - hour*3600 - min*60
dicomDset.AcquisitionTime = "%02.0f%02.0f%09.6f" % (hour, min, sec)
dicomDset.TriggerTime = mrdImg.physiology_time_stamp[0] / 2.5
# ----- Update DICOM header from MRD Image MetaAttributes -----
if meta.get('SeriesDescription') is not None:
dicomDset.SeriesDescription = meta['SeriesDescription']
if meta.get('SeriesDescriptionAdditional') is not None:
dicomDset.SeriesDescription = dicomDset.SeriesDescription + meta['SeriesDescriptionAdditional']
if meta.get('ImageComment') is not None:
dicomDset.ImageComment = "_".join(meta['ImageComment'])
if meta.get('ImageType') is not None:
dicomDset.ImageType = meta['ImageType']
if (meta.get('ImageRowDir') is not None) and (meta.get('ImageColumnDir') is not None):
dicomDset.ImageOrientationPatient = [float(meta['ImageRowDir'][0]), float(meta['ImageRowDir'][1]), float(meta['ImageRowDir'][2]), float(meta['ImageColumnDir'][0]), float(meta['ImageColumnDir'][1]), float(meta['ImageColumnDir'][2])]
if meta.get('RescaleIntercept') is not None:
dicomDset.RescaleIntercept = meta['RescaleIntercept']
if meta.get('RescaleSlope') is not None:
dicomDset.RescaleSlope = meta['RescaleSlope']
if meta.get('WindowCenter') is not None:
dicomDset.WindowCenter = meta['WindowCenter']
if meta.get('WindowWidth') is not None:
dicomDset.WindowWidth = meta['WindowWidth']
if meta.get('EchoTime') is not None:
dicomDset.EchoTime = meta['EchoTime']
if meta.get('InversionTime') is not None:
dicomDset.InversionTime = meta['InversionTime']
# Unhandled fields:
# LUTFileName
# ROI
# Write DICOM files
fileName = "%02.0f_%s_%03.0f.dcm" % (dicomDset.SeriesNumber, dicomDset.SeriesDescription, dicomDset.InstanceNumber)
print(" Writing file %s" % fileName)
dicomDset.save_as(os.path.join(args.out_folder, fileName), enforce_file_format=True)
filesWritten += 1
print("Wrote %d DICOM files to %s" % (filesWritten, args.out_folder))
return
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Convert MRD image file to DICOM files',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('filename', help='Input file')
parser.add_argument('-g', '--in-group', help='Input data group')
parser.add_argument('-o', '--out-folder', help='Output folder')
args = parser.parse_args()
main(args)