def test_gadgetron_grappa_coil_output(self):
config = GadgetronConfig()
config.add_reader('1008', 'GadgetIsmrmrdAcquisitionMessageReader')
config.add_reader('1026', 'GadgetIsmrmrdWaveformMessageReader')
config.add_writer('1022', 'MRIImageWriter')
config.add_gadget('RemoveROOversampling')
config.add_gadget('Grappa',
props=[('target_coils', '8'), ('use_gpu', 'false'),
('uncombined_channels',
'1,2,3,4,5,6,7,8,9,10,11,12')])
config.add_gadget('GrappaUnmixing')
config.add_gadget('Extract',
props=[('extract_magnitude', 'false')('extract_real',
'true'),
('extract_imag', 'true')])
config.add_gadget('ImageFinish')
data, header = client(self.filename, config_local=config.tostring())
data = data[0, ...] + 1j * data[1, ...]
view(data, montage_axis=0)
('use_gpu', 'false'),
('uncombined_channels',
','.join(str(x) for x in range(num_coils))),
])
config.add_gadget('GrappaUnmixing')
# config.add_gadget('PassthroughPython', 'PythonGadget', props=[
# ('python_module', 'passthrough'),
# ('python_class', 'Passthrough'),
# ('error_ignored_mode', 'true'),
# ])
# config.add_gadget('GS', 'PythonGadget', props=[
# ('error_ignored_mode', 'true'),
# ('python_path', '/usr/local/share/gadgetron'),
# ('python_module', 'gs_recon'),
# ('python_class', 'ArrayImagePassThrough')
# ])
config.add_gadget('Extract',
props=[
('extract_real', 'true'),
('extract_imag', 'true'),
])
config.add_gadget('AutoScale')
# config.add_gadget('FloatToShort', 'FloatToUShortGadget')
config.add_gadget('ImageFinish')
print(config.tostring())
im, hdr = client(data, config_local=config.tostring(), verbose=True)
print(im.shape)
view(im[0, ...] + 1j * im[1, ...], montage_axis=0)
('python_path', default_dir),
('python_module', 'accumulate_and_recon'),
('python_class', 'AccumulateAndRecon'),
])
config.add_gadget('CoilCombinePython',
'PythonGadget',
props=[
('python_path', script_dir),
('python_module', 'rms_coil_combine'),
('python_class', 'RMSCoilCombine'),
])
config.add_gadget('Extract')
config.add_gadget('AutoScale')
config.add_gadget('FloatToShort', 'FloatToUShortGadget')
config.add_gadget('ImageFinish')
# Get the path to the script we want to send over
script_path = os.path.join(ROOT_DIR, 'mr_utils', 'gadgetron', 'gadgets',
'rms_coil_combine.py')
# from mr_utils.utils import package_script
# test = ROOT_DIR + '/mr_utils/utils/mi_ssfp.py'
# print(package_script(test, existing_modules=['numpy', 'scipy']))
im, hdr = client(data,
config_local=config.tostring(),
script=script_path,
script_dir=script_dir,
verbose=True)
view(im)
'''Example of how to programmatically generate a config file.'''
from mr_utils.gadgetron import GadgetronConfig
if __name__ == '__main__':
config = GadgetronConfig()
config.add_reader(1008, 'GadgetIsmrmrdAcquisitionMessageReader')
config.add_writer(1004, 'MRIImageWriterCPLX')
config.add_writer(1005, 'MRIImageWriterFLOAT')
config.add_writer(1006, 'MRIImageWriterUSHORT')
config.add_gadget('Acc', 'AccumulatorGadget')
config.add_gadget('FFT')
config.add_gadget('Extract')
config.add_gadget('ImageFinishFLOAT', 'ImageFinishGadgetFLOAT')
print(config.tostring())
