def test_wfi_dualR2s():
filename = '/Users/mnd/Projects/FatParameterEstimation/data/DiagnostikBilanz/20170609_125718_0402_ImDataParams.mat'
imDataParams = h5io.load_ImDataParams_mat(filename)
imDataParams = imDataParams['ImDataParams']
filename = '/Users/mnd/Projects/FatParameterEstimation/data/DiagnostikBilanz/20170609_125718_0402_WFIparams_CSS_GANDALF2D_VL.mat'
wfiParams = h5io.load_WFIparams_mat(filename)
fieldmap_Hz = np.transpose(wfiParams['WFIparams']['fieldmap_Hz'])
fieldmap_Hz_equalized = wfi.equalize_fieldmap_periods(fieldmap_Hz,
imDataParams['TE_s'])
options = {'init_fieldmap_Hz': fieldmap_Hz_equalized,
'iSlice': slice(35, 37)}
wfiParams = wfi.wfi_css_varpro(imDataParams, options)
assert {'water', 'fat', 'fieldmap_Hz', 'R2s_Hz', 'pdff_percent'}.\
issubset(wfiParams.keys())
Cr = np.eye(len(wfiParams['Cr']), 2)
Cr[1:, 1] = 1
options2 = wfiParams.copy()
options2.pop('water')
options2.pop('fat')
options2.pop('pdff_percent')
options2.pop('fieldmap_Hz')
options2.pop('R2s_Hz')
options2.pop('param_maps')
options2.pop('resnorm')
options2.pop('iterations')
options2.update({'Cr': Cr})
wfiParams2 = wfi.wfi_css_varpro(imDataParams, options2)
close_all()
show_arr3d(np.clip(wfiParams['pdff_percent'], 0, 100))
show_arr3d(np.clip(wfiParams2['pdff_percent'], 0, 100))
close_all()
show_arr3d(np.clip(wfiParams['R2s_Hz'], 0, 400))
show_arr3d(np.clip(wfiParams2['R2s_Hz'], 0, 400))
show_arr3d(np.clip(wfiParams2['param_maps'][6], 0, 400))
close_all()
show_arr3d(np.clip(wfiParams['fieldmap_Hz'], -400, 200))
show_arr3d(np.clip(wfiParams2['fieldmap_Hz'], -400, 200))
close_all()
show_arr3d(np.clip(wfiParams['resnorm'], 0, 1e2))
show_arr3d(np.clip(wfiParams2['resnorm'], 0, 1e2))
close_all()
show_arr3d(np.clip(wfiParams['iterations'], 0, 1e2))
show_arr3d(np.clip(wfiParams2['iterations'], 0, 1e2))
def test_css_varpro():
filename = '/Users/mnd/Projects/FatParameterEstimation/data/DiagnostikBilanz/20170609_125718_0402_ImDataParams.mat'
imDataParams = load_ImDataParams_mat(filename)
imDataParams = imDataParams['ImDataParams']
iz = slice(35, 37)
imDataParams['signal'] = imDataParams['signal'][:, :, iz, :]
imDataParams['TE_s'] = imDataParams['TE_s'].ravel()
tissue_mask = wfi.calculate_tissue_mask(imDataParams['signal'])
filename = '/Users/mnd/Projects/FatParameterEstimation/data/DiagnostikBilanz/20170609_125718_0402_WFIparams_CSS_GANDALF2D_VL.mat'
h5file = h5.File(filename, 'r')
path = '/WFIparams'
f = h5.File(filename, 'r')
fieldmap_Hz = np.transpose(f['/WFIparams/fieldmap_Hz'][...])[:, :, iz]
fieldmap_Hz_equalized = wfi.equalize_fieldmap_periods(
fieldmap_Hz, imDataParams['TE_s'])
fieldmap_Hz_equalized = tissue_mask * \
wfi.equalize_fieldmap_periods(fieldmap_Hz, imDataParams['TE_s'])
F = Fatmodel()
F.set_fatmodel('Hamilton VAT')
F.set_constraints_matrices()
Cm, Cp, Cf, Cr = F.constraints_matrices
options = {}
options['Cm'] = Cm
options['Cp'] = Cp
options['Cf'] = Cf
options['Cr'] = Cr
options['Pm0'] = wfi.build_Pm0(F.get_chemical_shifts_Hz(),
fieldmap_Hz_equalized[tissue_mask])
options['mask'] = tissue_mask
options['tol'] = 1e-5
options['itermax'] = 100
outParams = css.css_varpro(imDataParams, options)
assert set(outParams.keys()) == {
'elapsed_time_s', 'iterations', 'param_maps', 'resnorm'
}
assert outParams['param_maps'][0].shape == tissue_mask.shape
def test_wfi_css_varpro_wuq():
filename = '/Users/mnd/Projects/FatParameterEstimation/data/FatParamEstimation/BMR/BMR106_EN/20171013_131406_1302_ImDataParams.mat'
imDataParams = h5io.load_ImDataParams_mat(filename)
imDataParams = imDataParams['ImDataParams']
filename = '/Users/mnd/Projects/FatParameterEstimation/data/FatParamEstimation/BMR/BMR106_EN/20171013_131406_1302_WFIparams_GANDALF3D_VL.mat'
wfiParams = h5io.load_WFIparams_mat(filename)
fieldmap_Hz = np.transpose(wfiParams['WFIparams']['fieldmap_Hz'])
fieldmap_Hz_equalized = wfi.equalize_fieldmap_periods(fieldmap_Hz,
imDataParams['TE_s'])
options = {'init_fieldmap_Hz': fieldmap_Hz_equalized,
'iSlice': slice(35, 37),
'iTE': slice(2, 20),
'uncertainty_quant': True}
wfiParams = wfi.wfi_css_varpro(imDataParams, options)
show_arr3d(wfi.calculate_echoMIP(imDataParams['signal']))
print(wfiParams.keys())
crlb = wfiParams['CRLBs'][0]
assert len(wfiParams['CRLBs']) == 6
close_all()
show_arr3d(np.log(wfiParams['CRLBs'][0]))
show_arr3d(np.log(wfiParams['CRLBs'][1]))
show_arr3d(np.log(wfiParams['CRLBs'][2]))
show_arr3d(np.log(wfiParams['CRLBs'][3]))
show_arr3d(np.log(wfiParams['CRLBs'][4]))
show_arr3d(np.log(wfiParams['CRLBs'][5]))
close_all()
show_arr3d(wfiParams['NSAs'][0])
show_arr3d(wfiParams['NSAs'][1])
show_arr3d(wfiParams['NSAs'][2])
show_arr3d(wfiParams['NSAs'][3])
show_arr3d(wfiParams['NSAs'][4])
show_arr3d(wfiParams['NSAs'][5])
trF = wfiParams['trFIM']
trInvF = wfiParams['trInvFIM']
detF = wfiParams['detFIM']
detInvF = np.divide(1, detF, out=-np.ones_like(detF), where=detF!=0)
close_all()
show_arr3d(np.log(trF))
show_arr3d(-np.log(trInvF))
show_arr3d(np.log(detF))
show_arr3d(-np.log(detInvF))
def test_dualR2s_wat():
filename = '/Users/mnd/Projects/FatParameterEstimation/data/FatParamEstimation/BMR/BMR106_EN/20171013_131406_1302_ImDataParams.mat'
imDataParams = h5io.load_ImDataParams_mat(filename)
imDataParams = imDataParams['ImDataParams']
filename = '/Users/mnd/Projects/FatParameterEstimation/data/FatParamEstimation/BMR/BMR106_EN/20171013_131406_1302_WFIparams_GANDALF3D_VL.mat'
wfiParams = h5io.load_WFIparams_mat(filename)
fieldmap_Hz = np.transpose(wfiParams['WFIparams']['fieldmap_Hz'])
fieldmap_Hz_equalized = wfi.equalize_fieldmap_periods(fieldmap_Hz,
imDataParams['TE_s'])
options = {'init_fieldmap_Hz': fieldmap_Hz_equalized,
'iSlice': slice(35, 37)}
wfiParams = wfi.wfi_css_varpro(imDataParams, options)
Cr = np.eye(len(wfiParams['Cr']), 2)
Cr[1:, 1] = 1
wfiParams2 = wfi.wfi_css_varpro(imDataParams, options2)
close_all()
show_arr3d(np.clip(wfiParams['pdff_percent'], 0, 100))
show_arr3d(np.clip(wfiParams2['pdff_percent'], 0, 100))
close_all()
show_arr3d(np.clip(wfiParams['R2s_Hz'], 0, 400))
show_arr3d(np.clip(wfiParams2['R2s_Hz'], 0, 400))
show_arr3d(np.clip(wfiParams2['param_maps'][6], 0, 400))
close_all()
show_arr3d(np.clip(wfiParams['fieldmap_Hz'], -400, 200))
show_arr3d(np.clip(wfiParams2['fieldmap_Hz'], -400, 200))
close_all()
show_arr3d(np.clip(wfiParams['resnorm'], 0, 1e2))
show_arr3d(np.clip(wfiParams2['resnorm'], 0, 1e2))
close_all()
show_arr3d(np.clip(wfiParams['iterations'], 0, 1e2))
show_arr3d(np.clip(wfiParams2['iterations'], 0, 1e2))
def test_wfi_css_varpro():
filename = '/Users/mnd/Projects/FatParameterEstimation/data/DiagnostikBilanz/20170609_125718_0402_ImDataParams.mat'
imDataParams = h5io.load_ImDataParams_mat(filename)
imDataParams = imDataParams['ImDataParams']
filename = '/Users/mnd/Projects/FatParameterEstimation/data/DiagnostikBilanz/20170609_125718_0402_WFIparams_CSS_GANDALF2D_VL.mat'
wfiParams = h5io.load_WFIparams_mat(filename)
fieldmap_Hz = np.transpose(wfiParams['WFIparams']['fieldmap_Hz'])
fieldmap_Hz_equalized = wfi.equalize_fieldmap_periods(fieldmap_Hz,
imDataParams['TE_s'])
options = {'init_fieldmap_Hz': fieldmap_Hz_equalized,
'iSlice': slice(35, 37)}
wfiParams = wfi.wfi_css_varpro(imDataParams, options)
assert {'water', 'fat', 'fieldmap_Hz', 'R2s_Hz', 'pdff_percent'}.\
issubset(wfiParams.keys())
close_all()
show_arr3d(np.clip(wfiParams['pdff_percent'], 0, 100))
Sig = ImDataParams['signal'][tissue_mask]
print(Sig.shape)
filename = '/Users/mnd/Projects/FatParameterEstimation/data/DiagnostikBilanz/20170609_125718_0402_WFIparams_CSS_GANDALF2D_VL.mat'
h5file = h5.File(filename, 'r')
path = '/WFIparams'
f = h5.File(filename, 'r')
pprint(list(f['/WFIparams'].keys()))
TE_s = ImDataParams['TE_s'].ravel()
fieldmap_Hz = np.transpose(f['/WFIparams/fieldmap_Hz'][...])
fieldmap_Hz = fieldmap_Hz[:, :, iz]
fieldmap_Hz_equalized = tissue_mask * wfi.equalize_fieldmap_periods(
fieldmap_Hz, TE_s)
fieldmap_Hz_equalized = fieldmap_Hz_equalized[tissue_mask]
F = Fatmodel(modelname='Hamilton VAT')
F.set_constraints_matrices()
Cm, Cp, Cf, Cr = F.constraints_matrices
F.set_params_matrix()
tol, itermax = 1e-3, 100
# nVoxel = Sig.shape[0]
chemical_shifts_Hz = np.concatenate(
([0], F.centerfreq_Hz * 1e-6 * F.deshielding_ppm))
wfi.build_Pm0(chemical_shifts_Hz, fieldmap_Hz_equalized)
Pm0 = np.zeros((nVoxel, len(chemical_shifts_Hz), 4))
def test_contrainedPhase():
filename = '/Users/mnd/Projects/FatParameterEstimation/data/DiagnostikBilanz/20170609_125718_0402_ImDataParams.mat'
imDataParams = h5io.load_ImDataParams_mat(filename)
imDataParams = imDataParams['ImDataParams']
filename = '/Users/mnd/Projects/FatParameterEstimation/data/DiagnostikBilanz/20170609_125718_0402_WFIparams_CSS_GANDALF2D_VL.mat'
wfiParams = h5io.load_WFIparams_mat(filename)
fieldmap_Hz = np.transpose(wfiParams['WFIparams']['fieldmap_Hz'])
fieldmap_Hz_equalized = wfi.equalize_fieldmap_periods(fieldmap_Hz,
imDataParams['TE_s'])
options = {'init_fieldmap_Hz': fieldmap_Hz_equalized,
'iSlice': slice(35, 37)}
wfiParams = wfi.wfi_css_varpro(imDataParams, options)
assert {'water', 'fat', 'fieldmap_Hz', 'R2s_Hz', 'pdff_percent'}.\
issubset(wfiParams.keys())
options2 = options.copy()
Cp = np.zeros((10, 1))
Cp[:, 0] = 1.
options2['Cp'] = Cp
wfiParams2 = wfi.wfi_css_varpro(imDataParams, options2)
close_all()
show_arr3d(np.clip(wfiParams['pdff_percent'], 0, 100))
show_arr3d(np.clip(wfiParams2['pdff_percent'], 0, 100))
show_arr3d(np.clip(wfiParams2['pdff_percent'], 0, 100) - \
np.clip(wfiParams['pdff_percent'], 0, 100))
close_all()
show_arr3d(np.angle(wfiParams['water']))
show_arr3d(np.angle(wfiParams['fat']))
show_arr3d(np.angle(wfiParams2['water']))
show_arr3d(np.angle(wfiParams2['fat']))
assert ~np.allclose(np.angle(wfiParams['water']),
np.angle(wfiParams['fat']))
assert np.allclose(np.angle(wfiParams2['water']),
np.angle(wfiParams2['fat']))
close_all()
show_arr3d(np.clip(wfiParams['R2s_Hz'], 0, 400))
show_arr3d(np.clip(wfiParams2['R2s_Hz'], 0, 400))
show_arr3d(np.clip(wfiParams2['R2s_Hz'], 0, 400) - \
np.clip(wfiParams['R2s_Hz'], 0, 400))
close_all()
show_arr3d(np.clip(wfiParams['fieldmap_Hz'], -400, 200))
show_arr3d(np.clip(wfiParams2['fieldmap_Hz'], -400, 200))
show_arr3d(np.clip(wfiParams2['R2s_Hz'], -400, 200) - \
np.clip(wfiParams['R2s_Hz'], -400, 200))
close_all()
show_arr3d(np.clip(wfiParams['resnorm'], 0, 1e2))
show_arr3d(np.clip(wfiParams2['resnorm'], 0, 1e2))
close_all()
show_arr3d(wfiParams['iterations'], )
show_arr3d(wfiParams2['iterations'])
def test_wfi_css_varpro_wuq_dualR2s():
filename = '/Users/mnd/Projects/FatParameterEstimation/data/FatParamEstimation/BMR/BMR106_EN/20171013_131406_1302_ImDataParams.mat'
imDataParams = h5io.load_ImDataParams_mat(filename)
imDataParams = imDataParams['ImDataParams']
imDataParams['TE_s'] = imDataParams['TE_s'].ravel()
filename = '/Users/mnd/Projects/FatParameterEstimation/data/FatParamEstimation/BMR/BMR106_EN/20171013_131406_1302_WFIparams_GANDALF3D_VL.mat'
wfiParams = h5io.load_WFIparams_mat(filename)
fieldmap_Hz = np.transpose(wfiParams['WFIparams']['fieldmap_Hz'])
fieldmap_Hz_equalized = wfi.equalize_fieldmap_periods(fieldmap_Hz,
imDataParams['TE_s'])
options = {'init_fieldmap_Hz': fieldmap_Hz_equalized,
'iSlice': slice(35, 37),
'iTE': slice(4, 16),
'uncertainty_quant': True}
wfiParams = wfi.wfi_css_varpro(imDataParams, options)
options2 = options.copy()
options2.update({'Cr': np.array([[1., 0.],
[0., 1.],
[0., 1.],
[0., 1.],
[0., 1.],
[0., 1.],
[0., 1.],
[0., 1.],
[0., 1.],
[0., 1.],
[0., 1.]])})
wfiParams2 = wfi.wfi_css_varpro(imDataParams, options2)
FIMparams = css.compute_FIMmaps(imDataParams['TE_s'],
wfiParams['params_matrices'],
wfiParams['Cm'],
wfiParams['Cp'],
wfiParams['Cf'],
wfiParams['Cr'],
wfiParams['mask'])
FIMparams2 = css.compute_FIMmaps(imDataParams['TE_s'],
wfiParams['params_matrices'],
wfiParams['Cm'],
wfiParams['Cp'],
wfiParams['Cf'],
wfiParams2['Cr'],
wfiParams['mask'])
close_all()
show_arr3d(np.log(FIMparams['CRLBs'][0]))
show_arr3d(np.log(FIMparams2['CRLBs'][0]))
close_all()
show_arr3d(np.log(FIMparams['trFIM']))
show_arr3d(np.log(FIMparams2['trFIM']))
show_arr3d(np.log(FIMparams['trFIM']) - np.log(FIMparams2['trFIM']))
echoMIP = wfi.calculate_echoMIP(imDataParams['signal'][:, :, 35:37, 4:16])
diff_dict = {}
for k in ['CRLBs', 'NSAs']:
diff_dict[k] = np.array(wfiParams[k]) - np.array(wfiParams2[k][:-1])
for k in ['trFIM', 'trInvFIM', 'detFIM']:
diff_dict[k] = np.array(wfiParams[k]) - np.array(wfiParams2[k])
show_arr3d(diff_dict['CRLBs'][0])
show_arr3d(diff_dict['CRLBs'][1])
show_arr3d(diff_dict['CRLBs'][2])
show_arr3d(diff_dict['CRLBs'][3])
show_arr3d(diff_dict['CRLBs'][4])
show_arr3d(diff_dict['CRLBs'][5])
show_arr3d(diff_dict['trFIM'])
close_all()
maptofuse = 'pdff_percent'
# maptofuse = 'fieldmap_Hz'
vmin, vmax = 0, 100
# vmin, vmax = -400, 200
wheretofuse = FIMparams['trFIM'] >= FIMparams2['trFIM']
# wheretofuse = FIMparams['detFIM'] >= FIMparams2['detFIM']
# wheretofuse = FIMparams['trInvFIM'] <= FIMparams2['trInvFIM']
# wheretofuse = FIMparams['detInvFIM'] <= FIMparams2['detInvFIM']
# wheretofuse = FIMparams['NSAs'][5] >= FIMparams2['NSAs'][5]
frankenstein = np.where(wheretofuse,
wfiParams[maptofuse],
wfiParams2[maptofuse])
show_arr3d(wfiParams[maptofuse])
show_arr3d(wfiParams2[maptofuse])
show_arr3d(wheretofuse * echoMIP)
show_arr3d(np.clip(frankenstein, vmin, vmax))
show_arr3d(np.clip(frankenstein, vmin, vmax) -
np.clip(wfiParams[maptofuse], vmin, vmax))
show_arr3d(wfiParams['resnorm'])
close_all()
maptofuse = 'fat'
vmin, vmax = 0, 200
wheretofuse = FIMparams['detFIM'] >= FIMparams2['detFIM']
frankenstein = np.where(wheretofuse,
wfiParams[maptofuse],
wfiParams2[maptofuse])
show_arr3d(wheretofuse * echoMIP)
show_arr3d(np.clip(wfiParams[maptofuse], vmin, vmax))
show_arr3d(np.clip(frankenstein, vmin, vmax))
show_arr3d(np.clip(frankenstein, vmin, vmax) -
np.clip(wfiParams[maptofuse], vmin, vmax))
close_all()
maptofuse = 'R2s_Hz'
maptofuse2 = 'waterR2s_Hz'
vmin, vmax = 0, 200
wheretofuse = FIMparams['detFIM'] >= FIMparams2['detFIM']
frankenstein = np.where(wheretofuse,
wfiParams[maptofuse],
wfiParams2[maptofuse2])
show_arr3d(wheretofuse * echoMIP)
show_arr3d(np.clip(wfiParams[maptofuse], vmin, vmax))
show_arr3d(np.clip(frankenstein, vmin, vmax))
show_arr3d(np.clip(frankenstein, vmin, vmax) -
np.clip(wfiParams[maptofuse], vmin, vmax))
close_all()
maptofuse = 'R2s_Hz'
maptofuse2 = 'fatR2s_Hz'
vmin, vmax = 0, 200
wheretofuse = FIMparams['detFIM'] >= FIMparams2['detFIM']
frankenstein = np.where(wheretofuse,
wfiParams[maptofuse],
wfiParams2[maptofuse2])
show_arr3d(wheretofuse * echoMIP)
show_arr3d(np.clip(wfiParams[maptofuse], vmin, vmax))
show_arr3d(np.clip(frankenstein, vmin, vmax))
show_arr3d(np.clip(frankenstein, vmin, vmax) -
np.clip(wfiParams[maptofuse], vmin, vmax))
close_all()
show_arr3d(np.log(FIMparams['detFIM']))
show_arr3d(np.log(FIMparams2['detFIM']))
show_arr3d(np.log(FIMparams['detFIM']) - np.log(FIMparams2['detFIM']))
show_arr3d(np.log(FIMparams['trFIM']) - np.log(FIMparams2['trFIM']))
show_arr3d(np.log(FIMparams['trInvFIM']) - np.log(FIMparams2['trInvFIM']))
show_arr3d(FIMparams['NSAs'][0] - FIMparams2['NSAs'][0])
show_arr3d(FIMparams['NSAs'][1] - FIMparams2['NSAs'][1])
show_arr3d(FIMparams['NSAs'][4] - FIMparams2['NSAs'][4])
show_arr3d(wfiParams['fieldmap_Hz'] - wfiParams2['fieldmap_Hz'])
import matplotlib.pyplot as plt
from utils.utils import *
from matplotlib2tikz import save as tikzsave
import deepdish as dd
# filename = '/Users/mnd/Projects/FatParameterEstimation/data/FatParamEstimation/DiagnostikBilanz/20170609_125718_0402_ImDataParams.mat'
# imDataParams = h5io.load_ImDataParams_mat(filename)
# imDataParams = imDataParams['ImDataParams']
# dd.io.save('imDataParams.h5', imDataParams)
imDataParams = dd.io.load('imDataParams.h5')
echoMIP = wfi.calculate_echoMIP(imDataParams['signal'])
filename = '/Users/mnd/Projects/FatParameterEstimation/data/FatParamEstimation/DiagnostikBilanz/20170609_125718_0402_WFIparams_CSS_GANDALF2D_VL.mat'
wfiParams = h5io.load_WFIparams_mat(filename)
fieldmap_Hz = np.transpose(wfiParams['WFIparams']['fieldmap_Hz'])
fieldmap_Hz_equalized = wfi.equalize_fieldmap_periods(fieldmap_Hz,
imDataParams['TE_s'])
# single R2*
options = {
'init_fieldmap_Hz': fieldmap_Hz_equalized,
'iSlice': slice(35, 36),
'uncertainty_quant': True
}
wfiParams = wfi.wfi_css_varpro(imDataParams, options)
dd.io.save('wfiParams.h5', wfiParams)
# wfiParams = dd.io.load('wfiParams.h5')
# show_arr3d(np.clip(wfiParams['pdff_percent'], 0, 100))
# double R2*
Cr = np.eye(len(wfiParams['Cr']), 2)