def test_bssfp_data(self):
'''Sample bSSFP data set.'''
dset = pyport(file=self.sample, debug=False)
import numpy as np
import ismrmrd
import ismrmrd.xsd
from ismrmrdtools import show, transform
header = ismrmrd.xsd.CreateFromDocument(dset.read_xml_header())
enc = header.encoding[0]
# Matrix size
eNx = enc.encodedSpace.matrixSize.x
eNy = enc.encodedSpace.matrixSize.y
eNz = enc.encodedSpace.matrixSize.z
rNx = enc.reconSpace.matrixSize.x
_rNy = enc.reconSpace.matrixSize.y
_rNz = enc.reconSpace.matrixSize.z
# Field of View
_eFOVx = enc.encodedSpace.fieldOfView_mm.x
_eFOVy = enc.encodedSpace.fieldOfView_mm.y
_eFOVz = enc.encodedSpace.fieldOfView_mm.z
_rFOVx = enc.reconSpace.fieldOfView_mm.x
_rFOVy = enc.reconSpace.fieldOfView_mm.y
_rFOVz = enc.reconSpace.fieldOfView_mm.z
# Number of Slices, Reps, Contrasts, etc.
ncoils = header.acquisitionSystemInformation.receiverChannels
if enc.encodingLimits.slice is not None:
nslices = enc.encodingLimits.slice.maximum + 1
else:
nslices = 1
if enc.encodingLimits.average is not None:
nreps = enc.encodingLimits.average.maximum + 1
else:
nreps = 1
if enc.encodingLimits.contrast is not None:
ncontrasts = enc.encodingLimits.contrast.maximum + 1
else:
ncontrasts = 1
# TODO loop through the acquisitions looking for noise scans
firstacq = 0
for acqnum in range(dset.number_of_acquisitions()):
acq = dset.read_acquisition(acqnum)
# TODO: Currently ignoring noise scans
if acq.isFlagSet(ismrmrd.ACQ_IS_NOISE_MEASUREMENT):
print("Found noise scan at acq ", acqnum)
continue
else:
firstacq = acqnum
print("Imaging acquisition starts acq ", acqnum)
break
# Initialiaze a storage array
all_data = np.zeros(
(nreps, ncontrasts, nslices, ncoils, eNz, eNy, rNx),
dtype=np.complex64) #pylint: disable=E1101
# Loop through the rest of the acquisitions and stuff
for acqnum in range(firstacq, dset.number_of_acquisitions()):
acq = dset.read_acquisition(acqnum)
# TODO: this is where we would apply noise pre-whitening
# Remove oversampling if needed
if eNx != rNx:
xline = transform.transform_kspace_to_image(acq.data, [1])
x0 = int((eNx - rNx) / 2)
x1 = int((eNx - rNx) / 2 + rNx)
xline = xline[:, x0:x1]
acq.resize(rNx, acq.active_channels, acq.trajectory_dimensions) #pylint: disable=E1101
acq.center_sample = int(rNx / 2)
# need to use the [:] notation here to fill the data
acq.data[:] = transform.transform_image_to_kspace(xline, [1])
# Stuff into the buffer
rep = acq.idx.average #pylint: disable=E1101
contrast = acq.idx.contrast #pylint: disable=E1101
slise = acq.idx.slice #pylint: disable=E1101
y = acq.idx.kspace_encode_step_1 #pylint: disable=E1101
z = acq.idx.kspace_encode_step_2 #pylint: disable=E1101
all_data[rep, contrast, slise, :, z, y, :] = acq.data
# Reconstruct images
images = np.zeros((nreps, ncontrasts, nslices, eNz, eNy, rNx),
dtype=np.float32) #pylint: disable=E1101
for rep in range(nreps):
for contrast in range(ncontrasts):
for slise in range(nslices):
# FFT
if eNz > 1:
#3D
im = transform.transform_kspace_to_image(
all_data[rep, contrast, slise, ...], [1, 2, 3])
else:
#2D
im = transform.transform_kspace_to_image(
all_data[rep, contrast, slise, :, 0, ...], [1, 2])
# Sum of squares
im = np.sqrt(np.sum(np.abs(im)**2, 0))
# Stuff into the output
if eNz > 1:
#3D
images[rep, contrast, slise, ...] = im
else:
#2D
images[rep, contrast, slise, 0, ...] = im
# Show an image
show.imshow(np.squeeze(images[0, 0, 0, ...]))
def test_invalid_pmapstyle(self):
'''Make sure we break on invalid pMapStyle.'''
with self.assertRaises(IOError):
pyport(file=self.emptydat, pMapStyle='invalidfile')
def test_supplied_user_style_sheet_and_pMapStyle(self):
'''Make sure we can't supply a param map AND an embedded file.'''
with self.assertRaises(ValueError):
pyport(file=self.emptydat,
pMapStyle='file.xsl',
user_stylesheet='file.xml')
def test_invalid_user_style_sheet(self):
'''Make sure we raise an exception if user stylesheet is not valud.'''
with self.assertRaises(IOError):
pyport(file=self.emptydat, user_stylesheet='myFile.xsl')
def test_require_filename(self):
'''If we don't have a filename, we need to stop!'''
with self.assertRaises(ValueError):
pyport()
with self.assertRaises(ValueError):
pyport(file=None)
def test_extract_file_not_valid(self):
'''Make sure we raise an error when embedded file is not valid.'''
with self.assertRaises(ValueError):
pyport(extract='myFile.xml')