sp.io.savemat('tmp_data.mat',{'pat_py': pat,'data_py': data,'csm_py': csm,'alias_img_py':alias_img,'unmix_grappa_py':unmix_grappa})
#%%
#Reload some modules
reload(show)
reload(sense)
reload(grappa)
reload(simulation)
reload(transform)
reload(coils)
#%%
reload(simulation)
matrix_size = 256
csm = simulation.generate_birdcage_sensitivities(matrix_size)
phan = simulation.phantom(matrix_size)
coil_images = np.tile(phan,(8, 1, 1)) * csm
show.imshow(abs(coil_images),tile_shape=(4,2),colorbar=True)
#%%
#Undersample
reload(simulation)
acc_factor = 2
ref_lines = 16
(data,pat) = simulation.sample_data(phan,csm,acc_factor,ref_lines)
#%%
#Add noise
noise = np.random.standard_normal(data.shape) + 1j*np.random.standard_normal(data.shape)
noise = (5.0/matrix_size)*noise
kspace = np.logical_or(pat==1,pat==3).astype('float32')*(data + noise)
def create(filename='testdata.h5', matrix_size=256, coils=8, oversampling=2, repetitions=1, acceleration=1, noise_level=0.05):
# Generate the phantom and coil sensitivity maps
phan = simulation.phantom(matrix_size)
csm = simulation.generate_birdcage_sensitivities(matrix_size, coils)
coil_images = np.tile(phan,(coils, 1, 1)) * csm
# Oversample if needed
if oversampling>1:
padding = (oversampling*phan.shape[1] - phan.shape[1])/2
phan = np.pad(phan,((0,0),(padding,padding)),mode='constant')
csm = np.pad(csm,((0,0),(0,0),(padding,padding)),mode='constant')
coil_images = np.pad(coil_images,((0,0),(0,0),(padding,padding)),mode='constant')
# The number of points in x,y,kx,ky
nx = matrix_size
ny = matrix_size
nkx = oversampling*nx
nky = ny
# Open the dataset
dset = ismrmrd.Dataset(filename, "dataset", create_if_needed=True)
# Create the XML header and write it to the file
header = ismrmrd.xsd.ismrmrdHeader()
# Experimental Conditions
exp = ismrmrd.xsd.experimentalConditionsType()
exp.H1resonanceFrequency_Hz = 128000000
header.experimentalConditions = exp
# Acquisition System Information
sys = ismrmrd.xsd.acquisitionSystemInformationType()
sys.receiverChannels = coils
header.acquisitionSystemInformation = sys
# Encoding
encoding = ismrmrd.xsd.encoding()
encoding.trajectory = ismrmrd.xsd.trajectoryType.cartesian
# encoded and recon spaces
efov = ismrmrd.xsd.fieldOfView_mm()
efov.x = oversampling*256
efov.y = 256
efov.z = 5
rfov = ismrmrd.xsd.fieldOfView_mm()
rfov.x = 256
rfov.y = 256
rfov.z = 5
ematrix = ismrmrd.xsd.matrixSize()
ematrix.x = nkx
ematrix.y = nky
ematrix.z = 1
rmatrix = ismrmrd.xsd.matrixSize()
rmatrix.x = nx
rmatrix.y = ny
rmatrix.z = 1
espace = ismrmrd.xsd.encodingSpaceType()
espace.matrixSize = ematrix
espace.fieldOfView_mm = efov
rspace = ismrmrd.xsd.encodingSpaceType()
rspace.matrixSize = rmatrix
rspace.fieldOfView_mm = rfov
# Set encoded and recon spaces
encoding.encodedSpace = espace
encoding.reconSpace = rspace
# Encoding limits
limits = ismrmrd.xsd.encodingLimitsType()
limits1 = ismrmrd.xsd.limitType()
limits1.minimum = 0
limits1.center = ny/2
limits1.maximum = ny - 1
limits.kspace_encoding_step_1 = limits1
limits_rep = ismrmrd.xsd.limitType()
limits_rep.minimum = 0
limits_rep.center = repetitions / 2
limits_rep.maximum = repetitions - 1
limits.repetition = limits_rep
limits_rest = ismrmrd.xsd.limitType()
limits_rest.minimum = 0
limits_rest.center = 0
limits_rest.maximum = 0
limits.kspace_encoding_step_0 = limits_rest
limits.slice = limits_rest
limits.average = limits_rest
limits.contrast = limits_rest
limits.kspaceEncodingStep2 = limits_rest
limits.phase = limits_rest
limits.segment = limits_rest
limits.set = limits_rest
encoding.encodingLimits = limits
header.encoding.append(encoding)
dset.write_xml_header(header.toxml('utf-8'))
# Synthesize the k-space data
Ktrue = transform.transform_image_to_kspace(coil_images,(1,2))
# Create an acquistion and reuse it
acq = ismrmrd.Acquisition()
acq.resize(nkx, coils)
acq.version = 1
acq.available_channels = coils
acq.center_sample = nkx/2
acq.read_dir[0] = 1.0
acq.phase_dir[1] = 1.0
acq.slice_dir[2] = 1.0
# Initialize an acquisition counter
counter = 0
# Write out a few noise scans
for n in range(32):
noise = noise_level * (np.random.randn(coils, nkx) + 1j * np.random.randn(coils, nkx))
# here's where we would make the noise correlated
acq.scan_counter = counter
acq.clearAllFlags()
acq.setFlag(ismrmrd.ACQ_IS_NOISE_MEASUREMENT)
acq.data[:] = noise
dset.append_acquisition(acq)
counter += 1 # increment the scan counter
# Loop over the repetitions, add noise and write to disk
# simulating a T-SENSE type scan
for rep in range(repetitions):
noise = noise_level * (np.random.randn(coils, nky, nkx) + 1j * np.random.randn(coils, nky, nkx))
# here's where we would make the noise correlated
K = Ktrue + noise
acq.idx.repetition = rep
for acc in range(acceleration):
for line in np.arange(acc,nky,acceleration):
# set some fields in the header
acq.scan_counter = counter
acq.idx.kspace_encode_step_1 = line
acq.clearAllFlags()
if line == 0:
acq.setFlag(ismrmrd.ACQ_FIRST_IN_ENCODE_STEP1)
acq.setFlag(ismrmrd.ACQ_FIRST_IN_SLICE)
acq.setFlag(ismrmrd.ACQ_FIRST_IN_REPETITION)
elif line == nky - 1:
acq.setFlag(ismrmrd.ACQ_LAST_IN_ENCODE_STEP1)
acq.setFlag(ismrmrd.ACQ_LAST_IN_SLICE)
acq.setFlag(ismrmrd.ACQ_LAST_IN_REPETITION)
# set the data and append
acq.data[:] = K[:,line,:]
dset.append_acquisition(acq)
counter += 1
# Clean up
dset.close()
def create(filename='testdata.h5',
matrix_size=256,
coils=8,
oversampling=2,
repetitions=1,
acceleration=1,
noise_level=0.05):
# Generate the phantom and coil sensitivity maps
phan = simulation.phantom(matrix_size)
csm = simulation.generate_birdcage_sensitivities(matrix_size, coils)
coil_images = np.tile(phan, (coils, 1, 1)) * csm
# Oversample if needed
if oversampling > 1:
padding = round((oversampling * phan.shape[1] - phan.shape[1]) / 2)
phan = np.pad(phan, ((0, 0), (padding, padding)), mode='constant')
csm = np.pad(csm, ((0, 0), (0, 0), (padding, padding)),
mode='constant')
coil_images = np.pad(coil_images, ((0, 0), (0, 0), (padding, padding)),
mode='constant')
# The number of points in x,y,kx,ky
nx = matrix_size
ny = matrix_size
nkx = oversampling * nx
nky = ny
# Open the dataset
dset = ismrmrd.Dataset(filename, "dataset", create_if_needed=True)
# Create the XML header and write it to the file
header = ismrmrd.xsd.ismrmrdHeader()
# Experimental Conditions
exp = ismrmrd.xsd.experimentalConditionsType()
exp.H1resonanceFrequency_Hz = 128000000
header.experimentalConditions = exp
# Acquisition System Information
sys = ismrmrd.xsd.acquisitionSystemInformationType()
sys.receiverChannels = coils
header.acquisitionSystemInformation = sys
# Encoding
encoding = ismrmrd.xsd.encoding()
encoding.trajectory = ismrmrd.xsd.trajectoryType.cartesian
# encoded and recon spaces
efov = ismrmrd.xsd.fieldOfView_mm()
efov.x = oversampling * 256
efov.y = 256
efov.z = 5
rfov = ismrmrd.xsd.fieldOfView_mm()
rfov.x = 256
rfov.y = 256
rfov.z = 5
ematrix = ismrmrd.xsd.matrixSize()
ematrix.x = nkx
ematrix.y = nky
ematrix.z = 1
rmatrix = ismrmrd.xsd.matrixSize()
rmatrix.x = nx
rmatrix.y = ny
rmatrix.z = 1
espace = ismrmrd.xsd.encodingSpaceType()
espace.matrixSize = ematrix
espace.fieldOfView_mm = efov
rspace = ismrmrd.xsd.encodingSpaceType()
rspace.matrixSize = rmatrix
rspace.fieldOfView_mm = rfov
# Set encoded and recon spaces
encoding.encodedSpace = espace
encoding.reconSpace = rspace
# Encoding limits
limits = ismrmrd.xsd.encodingLimitsType()
limits1 = ismrmrd.xsd.limitType()
limits1.minimum = 0
limits1.center = round(ny / 2)
limits1.maximum = ny - 1
limits.kspace_encoding_step_1 = limits1
limits_rep = ismrmrd.xsd.limitType()
limits_rep.minimum = 0
limits_rep.center = round(repetitions / 2)
limits_rep.maximum = repetitions - 1
limits.repetition = limits_rep
limits_rest = ismrmrd.xsd.limitType()
limits_rest.minimum = 0
limits_rest.center = 0
limits_rest.maximum = 0
limits.kspace_encoding_step_0 = limits_rest
limits.slice = limits_rest
limits.average = limits_rest
limits.contrast = limits_rest
limits.kspaceEncodingStep2 = limits_rest
limits.phase = limits_rest
limits.segment = limits_rest
limits.set = limits_rest
encoding.encodingLimits = limits
header.encoding.append(encoding)
dset.write_xml_header(header.toxml('utf-8'))
# Synthesize the k-space data
Ktrue = transform.transform_image_to_kspace(coil_images, (1, 2))
# Create an acquistion and reuse it
acq = ismrmrd.Acquisition()
acq.resize(nkx, coils)
acq.version = 1
acq.available_channels = coils
acq.center_sample = round(nkx / 2)
acq.read_dir[0] = 1.0
acq.phase_dir[1] = 1.0
acq.slice_dir[2] = 1.0
# Initialize an acquisition counter
counter = 0
# Write out a few noise scans
for n in range(32):
noise = noise_level * (np.random.randn(coils, nkx) +
1j * np.random.randn(coils, nkx))
# here's where we would make the noise correlated
acq.scan_counter = counter
acq.clearAllFlags()
acq.setFlag(ismrmrd.ACQ_IS_NOISE_MEASUREMENT)
acq.data[:] = noise
dset.append_acquisition(acq)
counter += 1 # increment the scan counter
# Loop over the repetitions, add noise and write to disk
# simulating a T-SENSE type scan
for rep in range(repetitions):
noise = noise_level * (np.random.randn(coils, nky, nkx) +
1j * np.random.randn(coils, nky, nkx))
# here's where we would make the noise correlated
K = Ktrue + noise
acq.idx.repetition = rep
for acc in range(acceleration):
for line in np.arange(acc, nky, acceleration):
# set some fields in the header
acq.scan_counter = counter
acq.idx.kspace_encode_step_1 = line
acq.clearAllFlags()
if line == 0:
acq.setFlag(ismrmrd.ACQ_FIRST_IN_ENCODE_STEP1)
acq.setFlag(ismrmrd.ACQ_FIRST_IN_SLICE)
acq.setFlag(ismrmrd.ACQ_FIRST_IN_REPETITION)
elif line == nky - 1:
acq.setFlag(ismrmrd.ACQ_LAST_IN_ENCODE_STEP1)
acq.setFlag(ismrmrd.ACQ_LAST_IN_SLICE)
acq.setFlag(ismrmrd.ACQ_LAST_IN_REPETITION)
# set the data and append
acq.data[:] = K[:, line, :]
dset.append_acquisition(acq)
counter += 1
# Clean up
dset.close()
# -*- coding: utf-8 -*-
#%%
#Basic setup
import time
import numpy as np
from ismrmrdtools import simulation, coils, show
matrix_size = 256
csm = simulation.generate_birdcage_sensitivities(matrix_size)
phan = simulation.phantom(matrix_size)
coil_images = phan[np.newaxis, :, :] * csm
show.imshow(abs(coil_images), tile_shape=(4, 2))
tstart = time.time()
(csm_est, rho) = coils.calculate_csm_walsh(coil_images)
print("Walsh coil estimation duration: {}s".format(time.time() - tstart))
combined_image = np.sum(csm_est * coil_images, axis=0)
show.imshow(abs(csm_est), tile_shape=(4, 2), scale=(0, 1))
show.imshow(abs(combined_image), scale=(0, 1))
tstart = time.time()
(csm_est2, rho2) = coils.calculate_csm_inati_iter(coil_images)
print("Inati coil estimation duration: {}s".format(time.time() - tstart))
combined_image2 = np.sum(csm_est2 * coil_images, axis=0)
show.imshow(abs(csm_est2), tile_shape=(4, 2), scale=(0, 1))
show.imshow(abs(combined_image2), scale=(0, 1))