How to use ismrmrd - 2 common examples
To help you get started, we’ve selected a few ismrmrd examples, based on popular ways it is used in public projects.
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MRSRL / dl-cs / data_prep.py View on Github 
def ismrmrd_to_np(filename):
"""Read ISMRMRD data file to numpy array"""
logger.debug('Loading file {}...'.format(filename))
dataset = ismrmrd.Dataset(filename, create_if_needed=False)
header = ismrmrd.xsd.CreateFromDocument(dataset.read_xml_header())
num_kx = header.encoding[0].encodedSpace.matrixSize.x
num_ky = header.encoding[0].encodingLimits.kspace_encoding_step_1.maximum
num_slices = header.encoding[0].encodingLimits.slice.maximum + 1
num_channels = header.acquisitionSystemInformation.receiverChannels
try:
rec_std = dataset.read_array('rec_std', 0)
rec_weight = 1.0 / (rec_std**2)
rec_weight = np.sqrt(rec_weight / np.sum(rec_weight))
logger.debug(' Using rec std...')
except Exception:
rec_weight = np.ones(num_channels)
opt_mat = np.diag(rec_weight)
kspace = np.zeros([num_channels, num_slices, num_ky, num_kx],
dtype=np.complex64)def ismrmrd_to_np(filename):
"""Read ISMRMRD data file to numpy array"""
logger.debug('Loading file {}...'.format(filename))
dataset = ismrmrd.Dataset(filename, create_if_needed=False)
header = ismrmrd.xsd.CreateFromDocument(dataset.read_xml_header())
num_kx = header.encoding[0].encodedSpace.matrixSize.x
num_ky = header.encoding[0].encodingLimits.kspace_encoding_step_1.maximum
num_slices = header.encoding[0].encodingLimits.slice.maximum + 1
num_channels = header.acquisitionSystemInformation.receiverChannels
try:
rec_std = dataset.read_array('rec_std', 0)
rec_weight = 1.0 / (rec_std**2)
rec_weight = np.sqrt(rec_weight / np.sum(rec_weight))
logger.debug(' Using rec std...')
except Exception:
rec_weight = np.ones(num_channels)
opt_mat = np.diag(rec_weight)
kspace = np.zeros([num_channels, num_slices, num_ky, num_kx],
dtype=np.complex64)
num_acq = dataset.number_of_acquisitions()ismrmrd
Python implementation of the ISMRMRD
Public-Domain
Latest version published 12 months ago