def test_MFI_given_im(self):
# Test correction given image data
or_corr_im = ORC.MFI(dataIn=raw_data[:, :, 0], dataInType='raw', kt=ktraj, df=field_map[:,:,0], Lx=1,
nonCart=1, params=acq_params)
or_corr_im2 = ORC.MFI(dataIn=or_corr_im, dataInType='im', kt=ktraj, df=field_map[:,:,0], Lx=1, nonCart=1, params=acq_params)
self.assertEqual(or_corr_im2.shape, field_map.shape[:-1])
self.assertEqual(or_corr_im2.all(), or_corr_im.all())
def test_MFI_wrongtype(self):
# Error when dataIn is raw data but dataInType is 'im'
with self.assertRaises(ValueError): ORC.MFI(dataIn=raw_data[:, :, 0], dataInType='im', kt=ktraj,
df=field_map, Lx=1, nonCart=1, params=acq_params)
or_corr_im = ORC.MFI(dataIn=raw_data[:, :, 0], dataInType='raw', kt=ktraj, df=field_map[:,:,0], Lx=1, nonCart=1,
params=acq_params)
# Error when dataIn is image data but dataInType is 'raw'
with self.assertRaises(ValueError): ORC.MFI(dataIn=or_corr_im, dataInType='raw', kt=ktraj,
df=field_map, Lx=1, nonCart=1, params=acq_params)
# Error when dataInType is other than 'raw' or 'im'
with self.assertRaises(ValueError): ORC.MFI(dataIn=raw_data[:, :, 0], dataInType='other', kt=ktraj,
df=field_map, Lx=1, nonCart=1, params=acq_params)
def test_Npoints(self):
params_dict = acq_params.copy()
params_dict['Npoints'] = 10
with self.assertRaises(ValueError): ORC.CPR(dataIn=raw_data[:, :, 0], dataInType='raw', kt=ktraj,
df=field_map_CPR, nonCart=1, params=params_dict)
with self.assertRaises(ValueError): ORC.fs_CPR(dataIn=raw_data[:, :, 0], dataInType='raw', kt=ktraj,
df=field_map_CPR, Lx=1, nonCart=1, params=params_dict)
with self.assertRaises(ValueError): ORC.MFI(dataIn=raw_data[:, :, 0], dataInType='raw', kt=ktraj,
df=field_map_CPR, Lx=1, nonCart=1, params=params_dict)
def test_N(self):
# Test that an error is raised if N specified in the parameters dictionary does not match the image dimensions
params_dict = acq_params.copy()
params_dict['N'] = 1
with self.assertRaises(ValueError): ORC.CPR(dataIn=raw_data[:, :, 0], dataInType='raw', kt=ktraj,
df=field_map_CPR, nonCart=1, params=params_dict)
with self.assertRaises(ValueError): ORC.fs_CPR(dataIn=raw_data[:, :, 0], dataInType='raw', kt=ktraj,
df=field_map_CPR, Lx=1, nonCart=1, params=params_dict)
with self.assertRaises(ValueError): ORC.MFI(dataIn=raw_data[:, :, 0], dataInType='raw', kt=ktraj,
df=field_map_CPR, Lx=1, nonCart=1, params=params_dict)
def test_MFI_given_rawData(self):
# Test correction given raw data
or_corr_im = ORC.MFI(dataIn=raw_data[:, :, 0], dataInType='raw', kt=ktraj, df=field_map[:,:,0], Lx=1,
nonCart=1, params=acq_params)
self.assertEqual(or_corr_im.shape, field_map.shape[:-1]) # Dimensions agree
def numsim_cartesian():
N = 192
ph = resize(shepp_logan_phantom(), (N, N))
ph = ph.astype(complex)
plt.imshow(np.abs(ph), cmap='gray')
plt.title('Original phantom')
plt.axis('off')
plt.colorbar()
plt.show()
brain_mask = mask_by_threshold(ph)
# Floodfill from point (0, 0)
ph_holes = ~(flood_fill(brain_mask, (0, 0), 1).astype(int)) + 2
mask = brain_mask + ph_holes
##
# Cartesian k-space trajectory
##
dt = 10e-6 # grad raster time
ktraj_cart = np.arange(0, N * dt, dt).reshape(1, N)
ktraj_cart = np.tile(ktraj_cart, (N, 1))
plt.imshow(ktraj_cart, cmap='gray')
plt.title('Cartesian trajectory')
plt.show()
##
# Simulated field map
##
fmax_v = [1600, 3200, 4800] # Hz correspontig to 25, 50 and 75 ppm at 3T
i = 0
or_corrupted = np.zeros((N, N, len(fmax_v)), dtype='complex')
or_corrected_CPR = np.zeros((N, N, len(fmax_v)), dtype='complex')
or_corrected_fsCPR = np.zeros((N, N, len(fmax_v)), dtype='complex')
or_corrected_MFI = np.zeros((N, N, len(fmax_v)), dtype='complex')
for fmax in fmax_v:
field_map = fieldmap_sim.realistic(np.abs(ph), mask, fmax)
plt.imshow(field_map, cmap='gray')
plt.title('Field Map')
plt.colorbar()
plt.axis('off')
plt.show()
##
# Corrupted images
##
or_corrupted[:, :, i], _ = ORC.add_or_CPR(ph, ktraj_cart, field_map)
corrupt = (np.abs(or_corrupted[:, :, i]) -
np.abs(or_corrupted[..., i]).min()) / (
np.abs(or_corrupted[:, :, i]).max() -
np.abs(or_corrupted[..., i]).min())
#plt.imshow(np.abs(or_corrupted[:,:,i]),cmap='gray')
plt.imshow(corrupt, cmap='gray')
plt.colorbar()
plt.title('Corrupted Image')
plt.axis('off')
plt.show()
###
# Corrected images
###
or_corrected_CPR[:, :, i] = ORC.CPR(or_corrupted[:, :, i], 'im',
ktraj_cart, field_map)
or_corrected_fsCPR[:, :, i] = ORC.fs_CPR(or_corrupted[:, :, i], 'im',
ktraj_cart, field_map, 2)
or_corrected_MFI[:, :, i] = ORC.MFI(or_corrupted[:, :, i], 'im',
ktraj_cart, field_map, 2)
i += 1
##
# Plot
##
im_stack = np.stack(
(np.squeeze(or_corrupted), np.squeeze(or_corrected_CPR),
np.squeeze(or_corrected_fsCPR), np.squeeze(or_corrected_MFI)))
cols = ('Corrupted Image', 'CPR Correction', 'fs-CPR Correction',
'MFI Correction')
row_names = ('-/+ 1600 Hz', '-/+ 3200 Hz', '-/+ 4800 Hz')
plot_correction_results(im_stack, cols, row_names)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("path", help="Path containing the input data")
parser.add_argument(
"datain",
help=
"Corrupted data with dimensions [Npoints OR N(Cartesian), Nshots OR N(Cartesian), Nslices, Nchannels]"
)
parser.add_argument(
"ktraj",
help=
"K-space trajectory: [Npoints OR N(Cartesian), Nshots OR N(Cartesian)]"
)
parser.add_argument("fmap", help="Field map in rad/s")
parser.add_argument("ORCmethod",
choices=['CPR', 'fsCPR', 'MFI'],
help="Correction method")
parser.add_argument("--cart",
default=0,
choices=[0, 1],
dest="cart_opt",
help="0: non-cartesian data, 1: cartesian data")
parser.add_argument(
'--Lx',
default=2,
dest='Lx',
help="L(frequency bins) factor with respect to minimum L")
parser.add_argument('--grad_raster',
default=10e-6,
dest='grad_raster',
help="Gradient raster time")
parser.add_argument('--TE', default=0, dest='TE', help="Echo time")
parser.add_argument(
'--dcf',
default=None,
dest='dcf',
help="Density compensation factor for non-cartesian trajectories")
args = parser.parse_args()
data_in = get_data_from_file(os.path.join(args.path, args.datain))
ktraj = get_data_from_file(os.path.join(args.path, args.ktraj))
fmap = get_data_from_file(os.path.join(args.path,
args.fmap)) / (2 * math.pi)
## Dimensions check
print('Checking dimensions...')
if data_in.shape[0] != ktraj.shape[0] or data_in.shape[1] != ktraj.shape[1]:
raise ValueError(
'The raw data does not agree with the k-space trajectory')
if fmap.shape[0] != fmap.shape[1]:
raise ValueError(
'Image and field map should have square dimensions (NxN)')
if len(fmap.shape) > 2:
if fmap.shape[-1] != data_in.shape[2]:
raise ValueError(
'The field map dimensions do not agree with the raw data')
if len(fmap.shape) == 2:
fmap = np.expand_dims(fmap, -1)
if data_in.shape[2] != 1:
raise ValueError(
'The field map dimensions do not agree with the raw data')
print('OK')
## Sequence parameters
N = fmap.shape[0]
Npoints = data_in.shape[0]
Nshots = data_in.shape[1]
Nslices = data_in.shape[-2]
Nchannels = data_in.shape[-1]
t_ro = Npoints * args.grad_raster
T = np.linspace(args.TE, args.TE + t_ro, Npoints).reshape((Npoints, 1))
if args.cart_opt == 0:
seq_params = {
'N': N,
'Npoints': Npoints,
'Nshots': Nshots,
't_vector': T,
't_readout': t_ro
}
if args.dcf is not None:
dcf = get_data_from_file(os.path.join(args.path,
args.dcf)).flatten()
seq_params.update({'dcf': dcf})
ORC_result = np.zeros((N, N, Nslices, Nchannels), dtype=complex)
if args.ORCmethod == 'MFI':
for ch in tqdm(range(Nchannels)):
for sl in range(Nslices):
if args.cart_opt == 0:
ORC_result[:, :, sl,
ch] = ORC.MFI(np.squeeze(data_in[:, :, sl, ch]),
'raw', ktraj,
np.squeeze(fmap[:, :, sl]),
args.Lx, 1, seq_params)
elif args.cart_opt == 1:
ORC_result[:, :, sl,
ch] = ORC.MFI(np.squeeze(data_in[:, :, sl, ch]),
'raw', ktraj,
np.squeeze(fmap[:, :,
sl]), args.Lx)
elif args.ORCmethod == 'fsCPR':
for ch in tqdm(range(Nchannels)):
for sl in range(Nslices):
if args.cart == 0:
ORC_result[:, :, sl, ch] = ORC.fs_CPR(
np.squeeze(data_in[:, :, sl, ch]), 'raw', ktraj,
np.squeeze(fmap[:, :, sl]), args.Lx, 1, seq_params)
elif args.cart == 1:
ORC_result[:, :, sl, ch] = ORC.fs_CPR(
np.squeeze(data_in[:, :, sl, ch]), 'raw', ktraj,
np.squeeze(fmap[:, :, sl]), args.Lx)
elif args.ORCmethod == 'CPR':
for ch in tqdm(range(Nchannels)):
for sl in range(Nslices):
if args.cart == 0:
ORC_result[:, :, sl,
ch] = ORC.CPR(np.squeeze(data_in[:, :, sl, ch]),
'raw', ktraj,
np.squeeze(fmap[:, :, sl]), 1,
seq_params)
elif args.cart == 1:
ORC_result[:, :, sl,
ch] = ORC.CPR(np.squeeze(data_in[:, :, sl, ch]),
'raw', ktraj,
np.squeeze(fmap[:, :, sl]))
np.save(os.path.join(args.path, 'ORC_result_' + args.ORCmethod),
ORC_result)
fsCPR_result[:, :, sl,
ch] = ORC.fs_CPR(np.squeeze(rawdata[:, :, sl,
ch]), 'raw', ktraj,
np.squeeze(fmap[:, :, sl]), Lx, 1,
seq_params)
fsCPR_timing += time.time() - before
print('fsCPR: Done with slice:' + str(sl + 1) + ', channel:' +
str(ch + 1))
np.save(outputs['path_correction_folder'] + 'fsCPR_Lx' + str(Lx),
fsCPR_result)
before = time.time()
MFI_result[:, :, sl,
ch] = ORC.MFI(np.squeeze(rawdata[:, :, sl,
ch]), 'raw', ktraj,
np.squeeze(fmap[:, :, sl]), Lx, 1, seq_params)
MFI_timing += time.time() - before
print('MFI: Done with slice:' + str(sl + 1) + ', channel:' +
str(ch + 1))
np.save(outputs['path_correction_folder'] + 'MFI_Lx' + str(Lx),
MFI_result)
##
# Display the results
##
print('\nCPR correction took ' + str(CPR_timing) + ' seconds.')
print('\nFs-CPR correction took ' + str(fsCPR_timing) + ' seconds.')
print('\nMFI correction took ' + str(MFI_timing) + ' seconds.')