def _singleframe_to_nifti(grouped_dicoms, output_file):
"""
This function will convert a philips singleframe series to a nifti
"""
# Create mosaic block
logger.info('Creating data block')
full_block = _singleframe_to_block(grouped_dicoms)
logger.info('Creating affine')
# Create the nifti header info
affine, slice_increment = common.create_affine(grouped_dicoms[0])
logger.info('Creating nifti')
# Convert to nifti
if full_block.ndim > 3: # do not squeeze single slice data
full_block = full_block.squeeze()
nii_image = nibabel.Nifti1Image(full_block, affine)
common.set_tr_te(nii_image, float(grouped_dicoms[0][0].RepetitionTime),
float(grouped_dicoms[0][0].EchoTime))
if output_file is not None:
# Save to disk
logger.info('Saving nifti to disk %s' % output_file)
nii_image.header.set_slope_inter(1, 0)
nii_image.header.set_xyzt_units(
2) # set units for xyz (leave t as unknown)
nii_image.to_filename(output_file)
if _is_singleframe_diffusion_imaging(grouped_dicoms):
bval_file = None
bvec_file = None
# Create the bval en bvec files
if output_file is not None:
base_name = os.path.splitext(output_file)[0]
if base_name.endswith('.nii'):
base_name = os.path.splitext(base_name)[0]
logger.info('Creating bval en bvec files')
bval_file = '%s.bval' % base_name
bvec_file = '%s.bvec' % base_name
nii_image, bval, bvec, bval_file, bvec_file = _create_singleframe_bvals_bvecs(
grouped_dicoms, bval_file, bvec_file, nii_image, output_file)
return {
'NII_FILE': output_file,
'BVAL_FILE': bval_file,
'BVEC_FILE': bvec_file,
'NII': nii_image,
'BVAL': bval,
'BVEC': bvec,
'MAX_SLICE_INCREMENT': slice_increment
}
return {
'NII_FILE': output_file,
'NII': nii_image,
'MAX_SLICE_INCREMENT': slice_increment
}
def _classic_4d_to_nifti(grouped_dicoms, output_file):
"""
This function will convert siemens 4d series to a nifti
Some inspiration on which fields can be used was taken from
http://slicer.org/doc/html/DICOMDiffusionVolumePlugin_8py_source.html
"""
# Get the sorted mosaics
all_dicoms = [i for sl in grouped_dicoms
for i in sl] # combine into 1 list for validating
common.validate_orientation(all_dicoms)
# Create mosaic block
logger.info('Creating data block')
full_block = _classic_get_full_block(grouped_dicoms)
logger.info('Creating affine')
# Create the nifti header info
affine, slice_increment = common.create_affine(grouped_dicoms[0])
logger.info('Creating nifti')
# Convert to nifti
nii_image = nibabel.Nifti1Image(full_block, affine)
common.set_tr_te(nii_image, float(grouped_dicoms[0][0].RepetitionTime),
float(grouped_dicoms[0][0].EchoTime))
logger.info('Saving nifti to disk')
# Save to disk
if output_file is not None:
nii_image.to_filename(output_file)
if _is_diffusion_imaging(grouped_dicoms[0][0]):
logger.info('Creating bval en bvec')
bval_file = None
bvec_file = None
if output_file is not None:
base_path = os.path.dirname(output_file)
base_name = os.path.splitext(
os.path.splitext(os.path.basename(output_file))[0])[0]
logger.info('Creating bval en bvec files')
bval_file = '%s/%s.bval' % (base_path, base_name)
bvec_file = '%s/%s.bvec' % (base_path, base_name)
bval = _create_bvals(grouped_dicoms, bval_file)
bvec = _create_bvecs(grouped_dicoms, bvec_file)
return {
'NII_FILE': output_file,
'BVAL_FILE': bval_file,
'BVEC_FILE': bvec_file,
'NII': nii_image,
'BVAL': bval,
'BVEC': bvec,
'MAX_SLICE_INCREMENT': slice_increment
}
return {
'NII_FILE': output_file,
'NII': nii_image,
'MAX_SLICE_INCREMENT': slice_increment
}
def _mosaic_4d_to_nifti(dicom_input, output_file):
"""
This function will convert siemens 4d series to a nifti
Some inspiration on which fields can be used was taken from
http://slicer.org/doc/html/DICOMDiffusionVolumePlugin_8py_source.html
"""
# Get the sorted mosaics
logger.info('Sorting dicom slices')
sorted_mosaics = _get_sorted_mosaics(dicom_input)
common.validate_orientation(sorted_mosaics)
# Create mosaic block
logger.info('Creating data block')
full_block = _mosaic_get_full_block(sorted_mosaics)
logger.info('Creating affine')
# Create the nifti header info
affine = _create_affine_siemens_mosaic(dicom_input)
logger.info('Creating nifti')
# Convert to nifti
if full_block.ndim > 3:
full_block = full_block.squeeze()
nii_image = nibabel.Nifti1Image(full_block, affine)
common.set_tr_te(nii_image, float(sorted_mosaics[0].RepetitionTime),
float(sorted_mosaics[0].EchoTime))
logger.info('Saving nifti to disk')
# Save to disk
if output_file is not None:
nii_image.header.set_slope_inter(1, 0)
nii_image.header.set_xyzt_units(
2) # set units for xyz (leave t as unknown)
nii_image.to_filename(output_file)
if _is_diffusion_imaging(dicom_input[0]):
# Create the bval en bvec files
logger.info('Creating bval en bvec')
bval_file = None
bvec_file = None
if output_file is not None:
base_path = os.path.dirname(output_file)
base_name = os.path.splitext(
os.path.splitext(os.path.basename(output_file))[0])[0]
logger.info('Saving bval en bvec files')
bval_file = '%s/%s.bval' % (base_path, base_name)
bvec_file = '%s/%s.bvec' % (base_path, base_name)
bvals = _create_bvals(sorted_mosaics, bval_file)
bvecs = _create_bvecs(sorted_mosaics, bvec_file)
return {
'NII_FILE': output_file,
'BVAL_FILE': bval_file,
'BVEC_FILE': bvec_file,
'NII': nii_image,
'BVAL': bvals,
'BVEC': bvecs
}
return {'NII_FILE': output_file, 'NII': nii_image}
def dicom_to_nifti(dicom_input, output_file):
"""
This function will convert an anatomical dicom series to a nifti
Examples: See unit test
:param output_file: filepath to the output nifti
:param dicom_input: directory with the dicom files for a single scan, or list of read in dicoms
"""
if len(dicom_input) <= 0:
raise ConversionError('NO_DICOM_FILES_FOUND')
# remove duplicate slices based on position and data
dicom_input = _remove_duplicate_slices(dicom_input)
# remove localizers based on image type
dicom_input = _remove_localizers_by_imagetype(dicom_input)
if settings.validate_slicecount:
# remove_localizers based on image orientation (only valid if slicecount is validated)
dicom_input = _remove_localizers_by_orientation(dicom_input)
# validate all the dicom files for correct orientations
common.validate_slicecount(dicom_input)
if settings.validate_orientation:
# validate that all slices have the same orientation
common.validate_orientation(dicom_input)
if settings.validate_orthogonal:
# validate that we have an orthogonal image (to detect gantry tilting etc)
common.validate_orthogonal(dicom_input)
# sort the dicoms
dicom_input = common.sort_dicoms(dicom_input)
if settings.validate_sliceincrement:
# validate that all slices have a consistent slice increment
common.validate_sliceincrement(dicom_input)
# Get data; originally z,y,x, transposed to x,y,z
data = common.get_volume_pixeldata(dicom_input)
affine = common.create_affine(dicom_input)
# Convert to nifti
nii_image = nibabel.Nifti1Image(data, affine)
# Set TR and TE if available
if Tag(0x0018, 0x0081) in dicom_input[0] and Tag(0x0018,
0x0081) in dicom_input[0]:
common.set_tr_te(nii_image, float(dicom_input[0].RepetitionTime),
float(dicom_input[0].EchoTime))
# Save to disk
if output_file is not None:
logger.info('Saving nifti to disk %s' % output_file)
nii_image.to_filename(output_file)
return {'NII_FILE': output_file, 'NII': nii_image}
def _multiframe_to_nifti(dicom_input, output_file):
"""
This function will convert philips 4D or anatomical multiframe series to a nifti
"""
# Read the multiframe dicom file
logger.info('Read dicom file')
multiframe_dicom = dicom_input[0]
# Create mosaic block
logger.info('Creating data block')
full_block = _multiframe_to_block(multiframe_dicom)
logger.info('Creating affine')
# Create the nifti header info
affine = _create_affine_multiframe(multiframe_dicom)
logger.info('Creating nifti')
# Convert to nifti
nii_image = nibabel.Nifti1Image(full_block, affine)
timing_parameters = multiframe_dicom.SharedFunctionalGroupsSequence[
0].MRTimingAndRelatedParametersSequence[0]
first_frame = multiframe_dicom[Tag(0x5200, 0x9230)][0]
common.set_tr_te(nii_image, float(timing_parameters.RepetitionTime),
float(first_frame[0x2005, 0x140f][0].EchoTime))
# Save to disk
if output_file is not None:
logger.info('Saving nifti to disk %s' % output_file)
nii_image.to_filename(output_file)
if _is_multiframe_diffusion_imaging(dicom_input):
bval_file = None
bvec_file = None
if output_file is not None:
# Create the bval en bvec files
base_path = os.path.dirname(output_file)
base_name = os.path.splitext(
os.path.splitext(os.path.basename(output_file))[0])[0]
logger.info('Creating bval en bvec files')
bval_file = '%s/%s.bval' % (base_path, base_name)
bvec_file = '%s/%s.bvec' % (base_path, base_name)
bval, bvec, bval_file, bvec_file = _create_bvals_bvecs(
multiframe_dicom, bval_file, bvec_file, nii_image, output_file)
return {
'NII_FILE': output_file,
'BVAL_FILE': bval_file,
'BVEC_FILE': bvec_file,
'NII': nii_image,
'BVAL': bval,
'BVEC': bvec
}
return {'NII_FILE': output_file, 'NII': nii_image}
def _multiframe_to_nifti(dicom_input, output_file):
"""
This function will convert philips 4D or anatomical multiframe series to a nifti
"""
# Read the multiframe dicom file
logger.info('Read dicom file')
multiframe_dicom = dicom_input[0]
# Create mosaic block
logger.info('Creating data block')
full_block = _multiframe_to_block(multiframe_dicom)
logger.info('Creating affine')
# Create the nifti header info
affine = _create_affine_multiframe(multiframe_dicom)
logger.info('Creating nifti')
# Convert to nifti
nii_image = nibabel.Nifti1Image(full_block, affine)
timing_parameters = multiframe_dicom.SharedFunctionalGroupsSequence[0].MRTimingAndRelatedParametersSequence[0]
first_frame = multiframe_dicom[Tag(0x5200, 0x9230)][0]
common.set_tr_te(nii_image, float(timing_parameters.RepetitionTime),
float(first_frame[0x2005, 0x140f][0].EchoTime))
# Save to disk
if output_file is not None:
logger.info('Saving nifti to disk %s' % output_file)
nii_image.to_filename(output_file)
if _is_multiframe_diffusion_imaging(dicom_input):
bval_file = None
bvec_file = None
if output_file is not None:
# Create the bval en bvec files
base_path = os.path.dirname(output_file)
base_name = os.path.splitext(os.path.splitext(os.path.basename(output_file))[0])[0]
logger.info('Creating bval en bvec files')
bval_file = '%s/%s.bval' % (base_path, base_name)
bvec_file = '%s/%s.bvec' % (base_path, base_name)
bval, bvec, bval_file, bvec_file = _create_bvals_bvecs(multiframe_dicom, bval_file, bvec_file, nii_image,
output_file)
return {'NII_FILE': output_file,
'BVAL_FILE': bval_file,
'BVEC_FILE': bvec_file,
'NII': nii_image,
'BVAL': bval,
'BVEC': bvec}
return {'NII_FILE': output_file,
'NII': nii_image}
def _singleframe_to_nifti(grouped_dicoms, output_file):
"""
This function will convert a philips singleframe series to a nifti
"""
# Create mosaic block
logger.info('Creating data block')
full_block = _singleframe_to_block(grouped_dicoms)
logger.info('Creating affine')
# Create the nifti header info
affine, slice_increment = common.create_affine(grouped_dicoms[0])
logger.info('Creating nifti')
# Convert to nifti
nii_image = nibabel.Nifti1Image(full_block, affine)
common.set_tr_te(nii_image, float(grouped_dicoms[0][0].RepetitionTime), float(grouped_dicoms[0][0].EchoTime))
if output_file is not None:
# Save to disk
logger.info('Saving nifti to disk %s' % output_file)
nii_image.to_filename(output_file)
if _is_singleframe_diffusion_imaging(grouped_dicoms):
bval_file = None
bvec_file = None
# Create the bval en bvec files
if output_file is not None:
base_name = os.path.splitext(output_file)[0]
if base_name.endswith('.nii'):
base_name = os.path.splitext(base_name)[0]
logger.info('Creating bval en bvec files')
bval_file = '%s.bval' % base_name
bvec_file = '%s.bvec' % base_name
nii_image, bval, bvec, bval_file, bvec_file = _create_singleframe_bvals_bvecs(grouped_dicoms,
bval_file,
bvec_file,
nii_image,
output_file)
return {'NII_FILE': output_file,
'BVAL_FILE': bval_file,
'BVEC_FILE': bvec_file,
'NII': nii_image,
'BVAL': bval,
'BVEC': bvec,
'MAX_SLICE_INCREMENT': slice_increment}
return {'NII_FILE': output_file,
'NII': nii_image,
'MAX_SLICE_INCREMENT': slice_increment}
def _classic_4d_to_nifti(grouped_dicoms, output_file):
"""
This function will convert siemens 4d series to a nifti
Some inspiration on which fields can be used was taken from
http://slicer.org/doc/html/DICOMDiffusionVolumePlugin_8py_source.html
"""
# Get the sorted mosaics
all_dicoms = [i for sl in grouped_dicoms for i in sl] # combine into 1 list for validating
common.validate_orientation(all_dicoms)
# Create mosaic block
logger.info('Creating data block')
full_block = _classic_get_full_block(grouped_dicoms)
logger.info('Creating affine')
# Create the nifti header info
affine, slice_increment = common.create_affine(grouped_dicoms[0])
logger.info('Creating nifti')
# Convert to nifti
nii_image = nibabel.Nifti1Image(full_block, affine)
common.set_tr_te(nii_image, float(grouped_dicoms[0][0].RepetitionTime), float(grouped_dicoms[0][0].EchoTime))
logger.info('Saving nifti to disk')
# Save to disk
if output_file is not None:
nii_image.to_filename(output_file)
if _is_diffusion_imaging(grouped_dicoms[0][0]):
logger.info('Creating bval en bvec')
bval_file = None
bvec_file = None
if output_file is not None:
base_path = os.path.dirname(output_file)
base_name = os.path.splitext(os.path.splitext(os.path.basename(output_file))[0])[0]
logger.info('Creating bval en bvec files')
bval_file = '%s/%s.bval' % (base_path, base_name)
bvec_file = '%s/%s.bvec' % (base_path, base_name)
bval = _create_bvals(grouped_dicoms, bval_file)
bvec = _create_bvecs(grouped_dicoms, bvec_file)
return {'NII_FILE': output_file,
'BVAL_FILE': bval_file,
'BVEC_FILE': bvec_file,
'NII': nii_image,
'BVAL': bval,
'BVEC': bvec,
'MAX_SLICE_INCREMENT': slice_increment}
return {'NII_FILE': output_file,
'NII': nii_image,
'MAX_SLICE_INCREMENT': slice_increment}
def _4d_to_nifti(grouped_dicoms, output_file):
"""
This function will convert ge 4d series to a nifti
"""
# Create mosaic block
logger.info('Creating data block')
full_block = _get_full_block(grouped_dicoms)
logger.info('Creating affine')
# Create the nifti header info
affine, slice_increment = common.create_affine(grouped_dicoms[0])
logger.info('Creating nifti')
# Convert to nifti
nii_image = nibabel.Nifti1Image(full_block, affine)
common.set_tr_te(nii_image, float(grouped_dicoms[0][0].RepetitionTime),
float(grouped_dicoms[0][0].EchoTime))
logger.info('Saving nifti to disk %s' % output_file)
# Save to disk
if output_file is not None:
nii_image.header.set_slope_inter(1, 0)
nii_image.header.set_xyzt_units(
2) # set units for xyz (leave t as unknown)
nii_image.to_filename(output_file)
if _is_diffusion_imaging(grouped_dicoms):
bval_file = None
bvec_file = None
# Create the bval en bevec files
if output_file is not None:
base_path = os.path.dirname(output_file)
base_name = os.path.splitext(
os.path.splitext(os.path.basename(output_file))[0])[0]
logger.info('Creating bval en bvec files')
bval_file = '%s/%s.bval' % (base_path, base_name)
bvec_file = '%s/%s.bvec' % (base_path, base_name)
bval, bvec = _create_bvals_bvecs(grouped_dicoms, bval_file, bvec_file)
return {
'NII_FILE': output_file,
'BVAL_FILE': bval_file,
'BVEC_FILE': bvec_file,
'NII': nii_image,
'BVAL': bval,
'BVEC': bvec,
'MAX_SLICE_INCREMENT': slice_increment
}
return {'NII_FILE': output_file, 'NII': nii_image}
def _mosaic_4d_to_nifti(dicom_input, output_file):
"""
This function will convert siemens 4d series to a nifti
Some inspiration on which fields can be used was taken from
http://slicer.org/doc/html/DICOMDiffusionVolumePlugin_8py_source.html
"""
# Get the sorted mosaics
logger.info('Sorting dicom slices')
sorted_mosaics = _get_sorted_mosaics(dicom_input)
common.validate_orientation(sorted_mosaics)
# Create mosaic block
logger.info('Creating data block')
full_block = _mosaic_get_full_block(sorted_mosaics)
logger.info('Creating affine')
# Create the nifti header info
affine = _create_affine_siemens_mosaic(dicom_input)
logger.info('Creating nifti')
# Convert to nifti
nii_image = nibabel.Nifti1Image(full_block, affine)
common.set_tr_te(nii_image, float(sorted_mosaics[0].RepetitionTime), float(sorted_mosaics[0].EchoTime))
logger.info('Saving nifti to disk')
# Save to disk
if output_file is not None:
nii_image.to_filename(output_file)
if _is_diffusion_imaging(dicom_input[0]):
# Create the bval en bvec files
logger.info('Creating bval en bvec')
bval_file = None
bvec_file = None
if output_file is not None:
base_path = os.path.dirname(output_file)
base_name = os.path.splitext(os.path.splitext(os.path.basename(output_file))[0])[0]
logger.info('Saving bval en bvec files')
bval_file = '%s/%s.bval' % (base_path, base_name)
bvec_file = '%s/%s.bvec' % (base_path, base_name)
bvals = _create_bvals(sorted_mosaics, bval_file)
bvecs = _create_bvecs(sorted_mosaics, bvec_file)
return {'NII_FILE': output_file,
'BVAL_FILE': bval_file,
'BVEC_FILE': bvec_file,
'NII': nii_image,
'BVAL': bvals,
'BVEC': bvecs}
return {'NII_FILE': output_file,
'NII': nii_image}
def _singleframe_to_nifti(grouped_dicoms, output_file):
"""
This function will convert a philips singleframe series to a nifti
"""
# Create mosaic block
logger.info('Creating data block')
full_block = _singleframe_to_block(grouped_dicoms)
logger.info('Creating affine')
# Create the nifti header info
affine = common.create_affine(grouped_dicoms[0])
logger.info('Creating nifti')
# Convert to nifti
nii_image = nibabel.Nifti1Image(full_block, affine)
common.set_tr_te(nii_image, float(grouped_dicoms[0][0].RepetitionTime),
float(grouped_dicoms[0][0].EchoTime))
if output_file is not None:
# Save to disk
logger.info('Saving nifti to disk %s' % output_file)
nii_image.to_filename(output_file)
if _is_singleframe_diffusion_imaging(grouped_dicoms):
bval_file = None
bvec_file = None
# Create the bval en bvec files
if output_file is not None:
base_name = os.path.splitext(output_file)[0]
if base_name.endswith('.nii'):
base_name = os.path.splitext(base_name)[0]
logger.info('Creating bval en bvec files')
bval_file = '%s.bval' % base_name
bvec_file = '%s.bvec' % base_name
nii_image, bval, bvec, bval_file, bvec_file = _create_singleframe_bvals_bvecs(
grouped_dicoms, bval_file, bvec_file, nii_image, output_file)
return {
'NII_FILE': output_file,
'BVAL_FILE': bval_file,
'BVEC_FILE': bvec_file,
'NII': nii_image,
'BVAL': bval,
'BVEC': bvec
}
return {'NII_FILE': output_file, 'NII': nii_image}
def _singleframe_to_nifti(grouped_dicoms, output_file):
"""
This function will convert a philips singleframe series to a nifti
"""
# Create mosaic block
print('Creating data block')
full_block = _singleframe_to_block(grouped_dicoms)
print('Creating affine')
# Create the nifti header info
affine = common.create_affine(grouped_dicoms[0])
print('Creating nifti')
# Convert to nifti
img = nibabel.Nifti1Image(full_block, affine)
common.set_tr_te(img, float(grouped_dicoms[0][0].RepetitionTime),
float(grouped_dicoms[0][0].EchoTime))
print('Saving nifti to disk %s' % output_file)
# Save to disk
img.to_filename(output_file)
if _is_singleframe_diffusion_imaging(grouped_dicoms):
# Create the bval en bvec files
base_name = os.path.splitext(output_file)[0]
if base_name.endswith('.nii'):
base_name = os.path.splitext(base_name)[0]
print('Creating bval en bvec files')
bval_file = '%s.bval' % base_name
bvec_file = '%s.bvec' % base_name
bval_file, bvec_file = _create_singleframe_bvals_bvecs(
grouped_dicoms, bval_file, bvec_file, img, output_file)
result = {'NII_FILE': output_file}
if bval_file is not None:
result['BVAL_FILE'] = bval_file
if bvec_file is not None:
result['BVEC_FILE'] = bvec_file
return result
return {'NII_FILE': output_file}
def _mosaic_4d_to_nifti(dicom_input, output_file):
"""
This function will convert siemens 4d series to a nifti
Some inspiration on which fields can be used was taken from
http://slicer.org/doc/html/DICOMDiffusionVolumePlugin_8py_source.html
"""
# Get the sorted mosaics
print('Sorting dicom slices')
sorted_mosaics = _get_sorted_mosaics(dicom_input)
common.validate_orientation(sorted_mosaics)
# Create mosaic block
print('Creating data block')
full_block = _mosaic_get_full_block(sorted_mosaics)
print('Creating affine')
# Create the nifti header info
affine = _create_affine_siemens_mosaic(dicom_input)
print('Creating nifti')
# Convert to nifti
img = nibabel.Nifti1Image(full_block, affine)
common.set_tr_te(img, float(sorted_mosaics[0].RepetitionTime), float(sorted_mosaics[0].EchoTime))
print('Saving nifti to disk')
# Save to disk
img.to_filename(output_file)
if _is_diffusion_imaging(dicom_input[0]):
# Create the bval en bvec files
print('Creating bval en bvec files')
base_path = os.path.dirname(output_file)
base_name = os.path.splitext(os.path.splitext(os.path.basename(output_file))[0])[0]
print('Creating bval en bvec files')
bval_file = '%s/%s.bval' % (base_path, base_name)
bvec_file = '%s/%s.bvec' % (base_path, base_name)
_create_bvals(sorted_mosaics, bval_file)
_create_bvecs(sorted_mosaics, bvec_file)
return {'NII_FILE': output_file,
'BVAL_FILE': bval_file,
'BVEC_FILE': bvec_file}
return {'NII_FILE': output_file}
def _4d_to_nifti(grouped_dicoms, output_file):
"""
This function will convert ge 4d series to a nifti
"""
# Create mosaic block
logger.info('Creating data block')
full_block = _get_full_block(grouped_dicoms)
logger.info('Creating affine')
# Create the nifti header info
affine = common.create_affine(grouped_dicoms[0])
logger.info('Creating nifti')
# Convert to nifti
img = nibabel.Nifti1Image(full_block, affine)
common.set_tr_te(img, float(grouped_dicoms[0][0].RepetitionTime),
float(grouped_dicoms[0][0].EchoTime))
logger.info('Saving nifti to disk %s' % output_file)
# Save to disk
img.to_filename(output_file)
if _is_diffusion_imaging(grouped_dicoms):
# Create the bval en bevec files
base_path = os.path.dirname(output_file)
base_name = os.path.splitext(
os.path.splitext(os.path.basename(output_file))[0])[0]
logger.info('Creating bval en bvec files')
bval_file = '%s/%s.bval' % (base_path, base_name)
bvec_file = '%s/%s.bvec' % (base_path, base_name)
_create_bvals_bvecs(grouped_dicoms, bval_file, bvec_file)
return {
'NII_FILE': output_file,
'BVAL_FILE': bval_file,
'BVEC_FILE': bvec_file
}
return {'NII_FILE': output_file}
def dicom_to_nifti(dicom_input, output_file):
"""
This function will convert an anatomical dicom series to a nifti
Examples: See unit test
:param output_file: filepath to the output nifti
:param dicom_input: directory with the dicom files for a single scan, or list of read in dicoms
"""
if len(dicom_input) <= 0:
raise ConversionError('NO_DICOM_FILES_FOUND')
# remove duplicate slices based on position and data
dicom_input = remove_duplicate_slices(dicom_input)
# remove localizers based on image type
dicom_input = remove_localizers_by_imagetype(dicom_input)
# if no dicoms remain we should raise exception
if len(dicom_input) < 1:
raise ConversionValidationError('TOO_FEW_SLICES/LOCALIZER')
if settings.validate_slicecount:
common.validate_slicecount(dicom_input)
# remove_localizers based on image orientation (only valid if slicecount is validated)
dicom_input = remove_localizers_by_orientation(dicom_input)
# validate all the dicom files for correct orientations
common.validate_slicecount(dicom_input)
if settings.validate_orientation:
# validate that all slices have the same orientation
common.validate_orientation(dicom_input)
if settings.validate_orthogonal:
# validate that we have an orthogonal image (to detect gantry tilting etc)
common.validate_orthogonal(dicom_input)
# sort the dicoms
dicom_input = common.sort_dicoms(dicom_input)
# validate slice increment inconsistent
slice_increment_inconsistent = False
if settings.validate_slice_increment:
# validate that all slices have a consistent slice increment
common.validate_slice_increment(dicom_input)
elif common.is_slice_increment_inconsistent(dicom_input):
slice_increment_inconsistent = True
if settings.validate_instance_number:
# validate that all slices have a consistent instance_number
common.validate_instance_number(dicom_input)
# if inconsistent increment and we allow resampling then do the resampling based conversion to maintain the correct geometric shape
if slice_increment_inconsistent and settings.resample:
nii_image, max_slice_increment = _convert_slice_incement_inconsistencies(dicom_input)
# do the normal conversion
else:
# Get data; originally z,y,x, transposed to x,y,z
data = common.get_volume_pixeldata(dicom_input)
affine, max_slice_increment = common.create_affine(dicom_input)
# Convert to nifti
nii_image = nibabel.Nifti1Image(data.squeeze(), affine)
# Set TR and TE if available
if Tag(0x0018, 0x0080) in dicom_input[0] and Tag(0x0018, 0x0081) in dicom_input[0]:
common.set_tr_te(nii_image, float(dicom_input[0].RepetitionTime), float(dicom_input[0].EchoTime))
# Save to disk
if output_file is not None:
logger.info('Saving nifti to disk %s' % output_file)
nii_image.header.set_slope_inter(1, 0)
nii_image.header.set_xyzt_units(2) # set units for xyz (leave t as unknown)
nii_image.to_filename(output_file)
return {'NII_FILE': output_file,
'NII': nii_image,
'MAX_SLICE_INCREMENT': max_slice_increment}
def dicom_to_nifti(dicom_input, output_file):
"""
This function will convert an anatomical dicom series to a nifti
Examples: See unit test
:param output_file: filepath to the output nifti
:param dicom_input: directory with the dicom files for a single scan, or list of read in dicoms
"""
if len(dicom_input) <= 0:
raise ConversionError('NO_DICOM_FILES_FOUND')
# remove duplicate slices based on position and data
dicom_input = _remove_duplicate_slices(dicom_input)
# remove localizers based on image type
dicom_input = _remove_localizers_by_imagetype(dicom_input)
if settings.validate_slicecount:
# remove_localizers based on image orientation (only valid if slicecount is validated)
dicom_input = _remove_localizers_by_orientation(dicom_input)
# validate all the dicom files for correct orientations
common.validate_slicecount(dicom_input)
if settings.validate_orientation:
# validate that all slices have the same orientation
common.validate_orientation(dicom_input)
if settings.validate_orthogonal:
# validate that we have an orthogonal image (to detect gantry tilting etc)
common.validate_orthogonal(dicom_input)
# sort the dicoms
dicom_input = common.sort_dicoms(dicom_input)
# validate slice increment inconsistent
slice_increment_inconsistent = False
if settings.validate_slice_increment:
# validate that all slices have a consistent slice increment
common.validate_slice_increment(dicom_input)
elif common.is_slice_increment_inconsistent(dicom_input):
slice_increment_inconsistent = True
# if inconsistent increment and we allow resampling then do the resampling based conversion to maintain the correct geometric shape
if slice_increment_inconsistent and settings.resample:
nii_image, max_slice_increment = _convert_slice_incement_inconsistencies(dicom_input)
# do the normal conversion
else:
# Get data; originally z,y,x, transposed to x,y,z
data = common.get_volume_pixeldata(dicom_input)
affine, max_slice_increment = common.create_affine(dicom_input)
# Convert to nifti
nii_image = nibabel.Nifti1Image(data, affine)
# Set TR and TE if available
if Tag(0x0018, 0x0081) in dicom_input[0] and Tag(0x0018, 0x0081) in dicom_input[0]:
common.set_tr_te(nii_image, float(dicom_input[0].RepetitionTime), float(dicom_input[0].EchoTime))
# Save to disk
if output_file is not None:
logger.info('Saving nifti to disk %s' % output_file)
nii_image.to_filename(output_file)
return {'NII_FILE': output_file,
'NII': nii_image,
'MAX_SLICE_INCREMENT': max_slice_increment}
