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_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))
def test_fucl_bat():
filename = '/Users/mnd/Projects/FatParameterEstimation/data/FatParamEstimation/BMR/BMR106_EN/20171013_124742_0502_ImDataParams.mat'
imDataParams = h5io.load_ImDataParams_mat(filename)
imDataParams = imDataParams['ImDataParams']
filename = '/Users/mnd/Projects/FatParameterEstimation/data/FatParamEstimation/BMR/BMR106_EN/20171013_124742_0502_WFIparams_GANDALF3D_VL.mat'
wfiParams = h5io.load_WFIparams_mat(filename)
for k in wfiParams['WFIparams'].keys():
print(k)
fieldmap_Hz = np.transpose(wfiParams['WFIparams']['fieldmap_Hz'])
echoMIP = wfi.calculate_echoMIP(imDataParams['signal'])
options = {'init_fieldmap_Hz': fieldmap_Hz,
'iSlice': slice(17, 21),
'fatmodel': 'Hamilton sSAT',
'tol': 1e-3,
'itermax': 20}
F = Fatmodel(modelname='Berglund 10 peaks')
F.compute_fatmodel(cl=18.5, ndb=2.73, nmidb=0.76)
F.set_constraints_matrices()
Cm = np.array([[1, 0, 0, 0, 0],
[0, 1, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 2/3, 0, 0, 0],
[0, 0, 0, 1, 0],
[0, 2/3, 0, 0, 0],
[0, 0, 0, 0, 1],
[0, 2/9, 0, 0, 0],
[0, 2/9, 0, 0, 0],
[0, 1/9, 0, 0, 0],
[0, 0, 0, 1/2, 1]])
Cp = (Cm > 0).astype(float)
options['fatmodel'] = 'Berglund 10 peaks'
options['Cm'] = Cm
options['Cp'] = Cp
fuclParams = wfi.wfi_css_varpro(imDataParams, options)
close_all()
show_arr3d(echoMIP)
W = fuclParams['param_maps'][0] * np.exp(1.j * fuclParams['param_maps'][5])
F1 = fuclParams['param_maps'][1] * np.exp(1.j * fuclParams['param_maps'][6])
F2 = fuclParams['param_maps'][2] * np.exp(1.j * fuclParams['param_maps'][7])
F3 = fuclParams['param_maps'][3] * np.exp(1.j * fuclParams['param_maps'][8])
F4 = fuclParams['param_maps'][4] * np.exp(1.j * fuclParams['param_maps'][9])
show_arr3d(np.abs(W))
show_arr3d(np.abs(F1))
show_arr3d(np.abs(F2))
show_arr3d(np.abs(F3))
show_arr3d(np.abs(F4))
fieldmap_Hz = fuclParams['param_maps'][10]
R2s_Hz = fuclParams['param_maps'][11]
show_arr3d(fieldmap_Hz)
show_arr3d(R2s_Hz)
show_arr3d(fuclParams['resnorm'])
show_arr3d(fuclParams['iterations'])
F1nonzero = F1 != 0
null = np.zeros_like(F1nonzero, dtype=np.complex128)
CL = 4 + np.abs(np.divide((F2 + 4 * F3 + 3 * F4) / 3, F1,
out=null, where=F1nonzero))
UD = np.abs(np.divide(F3 + F4, F1, out=null, where=F1nonzero))
SF = 1 - np.abs(np.divide(F3 / 3, F1, out=null, where=F1nonzero))
PUD = np.abs(np.divide(F4, F1, out=null, where=F1nonzero))
PUF = PUD / 3
UF = np.abs(np.divide(F3 / 3, F1, out=null, where=F1nonzero))
MUF = UF - PUF
show_arr3d(CL)
show_arr3d(UD)
show_arr3d(SF)
show_arr3d(PUD)
show_arr3d(PUF)
show_arr3d(UF)
show_arr3d(MUF)
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 numpy as np
import matplotlib.pyplot as plt
from utils.utils import *
import SimpleITK as sitk
import matplotlib.pyplot as plt
from Fatmodel import Fatmodel
import css
import wfi
import h5io
import sim
import deepdish as dd
from matplotlib2tikz import save as tikzsave
import subprocess
filename = '/Users/mnd/Projects/FatParameterEstimation/data/FatParamEstimation/BMR/BMR106_EN/20171013_131406_1302_ImDataParams_corr.mat'
imDataParams = h5io.load_ImDataParams_mat(filename)
imDataParams = imDataParams['ImDataParams']
# imDataParams = dd.io.load('imDataParams.h5')
echoMIP = wfi.calculate_echoMIP(imDataParams['signal'])
# 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'])
# options = {'init_fieldmap_Hz': fieldmap_Hz,
# 'iSlice': slice(39, 40),
# # 'iTE': slice(3, 18),
# 'fatmodel': 'Hamilton sSAT'}
# # wfiParams = wfi.wfi_css_varpro(imDataParams, options)
# # dd.io.save('wfiParams.h5', wfiParams)