def test_single_fiber_model():
# single fiber simulate (which is the assumption of our model)
fie = 0.49
ADi = 0.00099
ADe = 0.00226
RDi = 0
RDe = 0.00087
# prepare simulation:
theta = random.uniform(0, 180)
phi = random.uniform(0, 320)
angles = [(theta, phi), (theta, phi)]
mevals = np.array([[ADi, RDi, RDi], [ADe, RDe, RDe]])
frac = [fie * 100, (1 - fie) * 100]
signal, dt, kt = multi_tensor_dki(gtab_2s,
mevals,
angles=angles,
fractions=frac,
snr=None)
# DKI fit
dkiM = dki_micro.DiffusionKurtosisModel(gtab_2s, fit_method="WLS")
dkiF = dkiM.fit(signal)
# Axonal Water Fraction
sphere = get_sphere('symmetric724')
AWF = dki_micro.axonal_water_fraction(dkiF.model_params,
sphere,
mask=None,
gtol=1e-5)
assert_almost_equal(AWF, fie)
# Extra-cellular and intra-cellular components
edt, idt = dki_micro.diffusion_components(dkiF.model_params, sphere)
EDT = eig_from_lo_tri(edt)
IDT = eig_from_lo_tri(idt)
# check eigenvalues
assert_array_almost_equal(EDT[0:3], np.array([ADe, RDe, RDe]))
assert_array_almost_equal(IDT[0:3], np.array([ADi, RDi, RDi]))
# first eigenvalue should be the direction of the fibers
fiber_direction = _check_directions([(theta, phi)])
f_norm = abs(np.dot(fiber_direction, np.array((EDT[3], EDT[6], EDT[9]))))
assert_almost_equal(f_norm, 1.)
f_norm = abs(np.dot(fiber_direction, np.array((IDT[3], IDT[6], IDT[9]))))
assert_almost_equal(f_norm, 1.)
# Test model and fit objects
wmtiM = dki_micro.KurtosisMicrostructureModel(gtab_2s, fit_method="WLS")
wmtiF = wmtiM.fit(signal)
assert_almost_equal(wmtiF.awf, AWF)
assert_array_almost_equal(wmtiF.hindered_evals, np.array([ADe, RDe, RDe]))
assert_array_almost_equal(wmtiF.restricted_evals, np.array([ADi, RDi,
RDi]))
assert_almost_equal(wmtiF.hindered_ad, ADe)
assert_almost_equal(wmtiF.hindered_rd, RDe)
assert_almost_equal(wmtiF.axonal_diffusivity, ADi)
assert_almost_equal(wmtiF.tortuosity, ADe / RDe, decimal=4)
# Test diffusion_components when a kurtosis tensors is associated with
# negative kurtosis values. E.g of this cases is given below:
dkiparams = np.array([
1.67135726e-03, 5.03651205e-04, 9.35365328e-05, -7.11167583e-01,
6.23186820e-01, -3.25390313e-01, -1.75247376e-02, -4.78415563e-01,
-8.77958674e-01, 7.02804064e-01, 6.18673368e-01, -3.51154825e-01,
2.18384153, -2.76378153e-02, 2.22893297, -2.68306546e-01, -1.28411610,
-1.56557645e-01, -1.80850619e-01, -8.33152110e-01, -3.62410766e-01,
1.57775442e-01, 8.73775381e-01, 2.77188975e-01, -3.67415502e-02,
-1.56330984e-01, -1.62295407e-02
])
edt, idt = dki_micro.diffusion_components(dkiparams)
assert_(np.all(np.isfinite(edt)))
def test_single_fiber_model():
# single fiber simulate (which is the assumption of our model)
fie = 0.49
ADi = 0.00099
ADe = 0.00226
RDi = 0
RDe = 0.00087
# prepare simulation:
theta = random.uniform(0, 180)
phi = random.uniform(0, 320)
angles = [(theta, phi), (theta, phi)]
mevals = np.array([[ADi, RDi, RDi], [ADe, RDe, RDe]])
frac = [fie*100, (1 - fie)*100]
signal, dt, kt = multi_tensor_dki(gtab_2s, mevals, angles=angles,
fractions=frac, snr=None)
# DKI fit
dkiM = dki_micro.DiffusionKurtosisModel(gtab_2s, fit_method="WLS")
dkiF = dkiM.fit(signal)
# Axonal Water Fraction
sphere = get_sphere('symmetric724')
AWF = dki_micro.axonal_water_fraction(dkiF.model_params, sphere, mask=None,
gtol=1e-5)
assert_almost_equal(AWF, fie)
# Extra-cellular and intra-cellular components
edt, idt = dki_micro.diffusion_components(dkiF.model_params, sphere)
EDT = eig_from_lo_tri(edt)
IDT = eig_from_lo_tri(idt)
# check eigenvalues
assert_array_almost_equal(EDT[0:3], np.array([ADe, RDe, RDe]))
assert_array_almost_equal(IDT[0:3], np.array([ADi, RDi, RDi]))
# first eigenvalue should be the direction of the fibers
fiber_direction = _check_directions([(theta, phi)])
f_norm = abs(np.dot(fiber_direction, np.array((EDT[3], EDT[6], EDT[9]))))
assert_almost_equal(f_norm, 1.)
f_norm = abs(np.dot(fiber_direction, np.array((IDT[3], IDT[6], IDT[9]))))
assert_almost_equal(f_norm, 1.)
# Test model and fit objects
wmtiM = dki_micro.KurtosisMicrostructureModel(gtab_2s, fit_method="WLS")
wmtiF = wmtiM.fit(signal)
assert_almost_equal(wmtiF.awf, AWF)
assert_array_almost_equal(wmtiF.hindered_evals,
np.array([ADe, RDe, RDe]))
assert_array_almost_equal(wmtiF.restricted_evals,
np.array([ADi, RDi, RDi]))
assert_almost_equal(wmtiF.hindered_ad, ADe)
assert_almost_equal(wmtiF.hindered_rd, RDe)
assert_almost_equal(wmtiF.axonal_diffusivity, ADi)
assert_almost_equal(wmtiF.tortuosity, ADe/RDe, decimal=4)
# Test diffusion_components when a kurtosis tensors is associated with
# negative kurtosis values. E.g of this cases is given below:
dkiparams = np.array([1.67135726e-03, 5.03651205e-04, 9.35365328e-05,
-7.11167583e-01, 6.23186820e-01, -3.25390313e-01,
-1.75247376e-02, -4.78415563e-01, -8.77958674e-01,
7.02804064e-01, 6.18673368e-01, -3.51154825e-01,
2.18384153, -2.76378153e-02, 2.22893297,
-2.68306546e-01, -1.28411610, -1.56557645e-01,
-1.80850619e-01, -8.33152110e-01, -3.62410766e-01,
1.57775442e-01, 8.73775381e-01, 2.77188975e-01,
-3.67415502e-02, -1.56330984e-01, -1.62295407e-02])
edt, idt = dki_micro.diffusion_components(dkiparams)
assert_(np.all(np.isfinite(edt)))
def test_wmti_model_multi_voxel():
# DKI fit
dkiM = dki_micro.DiffusionKurtosisModel(gtab_2s, fit_method="WLS")
dkiF = dkiM.fit(DWIsim)
# Axonal Water Fraction
sphere = get_sphere()
AWF = dki_micro.axonal_water_fraction(dkiF.model_params,
sphere,
mask=None,
gtol=1e-5)
assert_almost_equal(AWF, FIE)
# Extra-cellular and intra-cellular components
edt, idt = dki_micro.diffusion_components(dkiF.model_params, sphere)
EDT = eig_from_lo_tri(edt)
IDT = eig_from_lo_tri(idt)
# check eigenvalues
assert_array_almost_equal(EDT[..., 0], ADE, decimal=3)
assert_array_almost_equal(EDT[..., 1], RDE, decimal=3)
assert_array_almost_equal(EDT[..., 2], RDE, decimal=3)
assert_array_almost_equal(IDT[..., 0], ADI, decimal=3)
assert_array_almost_equal(IDT[..., 1], RDI, decimal=3)
assert_array_almost_equal(IDT[..., 2], RDI, decimal=3)
# Test methods performance when a signal with all zeros is present
FIEc = FIE.copy()
RDIc = RDI.copy()
ADIc = ADI.copy()
ADEc = ADE.copy()
Torc = Tor.copy()
RDEc = RDE.copy()
DWIsimc = DWIsim.copy()
FIEc[0, 0, 0] = 0
RDIc[0, 0, 0] = 0
ADIc[0, 0, 0] = 0
ADEc[0, 0, 0] = 0
Torc[0, 0, 0] = 0
RDEc[0, 0, 0] = 0
DWIsimc[0, 0, 0, :] = 0
mask = np.ones((2, 2, 2))
mask[0, 0, 0] = 0
dkiF = dkiM.fit(DWIsimc)
awf = dki_micro.axonal_water_fraction(dkiF.model_params, sphere, gtol=1e-5)
assert_almost_equal(awf, FIEc)
# Extra-cellular and intra-cellular components
edt, idt = dki_micro.diffusion_components(dkiF.model_params,
sphere,
awf=awf)
EDT = eig_from_lo_tri(edt)
IDT = eig_from_lo_tri(idt)
assert_array_almost_equal(EDT[..., 0], ADEc, decimal=3)
assert_array_almost_equal(EDT[..., 1], RDEc, decimal=3)
assert_array_almost_equal(EDT[..., 2], RDEc, decimal=3)
assert_array_almost_equal(IDT[..., 0], ADIc, decimal=3)
assert_array_almost_equal(IDT[..., 1], RDIc, decimal=3)
assert_array_almost_equal(IDT[..., 2], RDIc, decimal=3)
# Check when mask is given
dkiF = dkiM.fit(DWIsim)
awf = dki_micro.axonal_water_fraction(dkiF.model_params,
sphere,
gtol=1e-5,
mask=mask)
assert_almost_equal(awf, FIEc, decimal=3)
# Extra-cellular and intra-cellular components
edt, idt = dki_micro.diffusion_components(dkiF.model_params,
sphere,
awf=awf,
mask=mask)
EDT = eig_from_lo_tri(edt)
IDT = eig_from_lo_tri(idt)
assert_array_almost_equal(EDT[..., 0], ADEc, decimal=3)
assert_array_almost_equal(EDT[..., 1], RDEc, decimal=3)
assert_array_almost_equal(EDT[..., 2], RDEc, decimal=3)
assert_array_almost_equal(IDT[..., 0], ADIc, decimal=3)
assert_array_almost_equal(IDT[..., 1], RDIc, decimal=3)
assert_array_almost_equal(IDT[..., 2], RDIc, decimal=3)
# Check class object
wmtiM = dki_micro.KurtosisMicrostructureModel(gtab_2s, fit_method="WLS")
wmtiF = wmtiM.fit(DWIsim, mask=mask)
assert_almost_equal(wmtiF.awf, FIEc, decimal=3)
assert_almost_equal(wmtiF.axonal_diffusivity, ADIc, decimal=3)
assert_almost_equal(wmtiF.hindered_ad, ADEc, decimal=3)
assert_almost_equal(wmtiF.hindered_rd, RDEc, decimal=3)
assert_almost_equal(wmtiF.tortuosity, Torc, decimal=3)
def test_wmti_model_multi_voxel():
# DKI fit
dkiM = dki_micro.DiffusionKurtosisModel(gtab_2s, fit_method="WLS")
dkiF = dkiM.fit(DWIsim)
# Axonal Water Fraction
sphere = get_sphere()
AWF = dki_micro.axonal_water_fraction(dkiF.model_params, sphere, mask=None,
gtol=1e-5)
assert_almost_equal(AWF, FIE)
# Extra-cellular and intra-cellular components
edt, idt = dki_micro.diffusion_components(dkiF.model_params, sphere)
EDT = eig_from_lo_tri(edt)
IDT = eig_from_lo_tri(idt)
# check eigenvalues
assert_array_almost_equal(EDT[..., 0], ADE, decimal=3)
assert_array_almost_equal(EDT[..., 1], RDE, decimal=3)
assert_array_almost_equal(EDT[..., 2], RDE, decimal=3)
assert_array_almost_equal(IDT[..., 0], ADI, decimal=3)
assert_array_almost_equal(IDT[..., 1], RDI, decimal=3)
assert_array_almost_equal(IDT[..., 2], RDI, decimal=3)
# Test methods performance when a signal with all zeros is present
FIEc = FIE.copy()
RDIc = RDI.copy()
ADIc = ADI.copy()
ADEc = ADE.copy()
Torc = Tor.copy()
RDEc = RDE.copy()
DWIsimc = DWIsim.copy()
FIEc[0, 0, 0] = 0
RDIc[0, 0, 0] = 0
ADIc[0, 0, 0] = 0
ADEc[0, 0, 0] = 0
Torc[0, 0, 0] = 0
RDEc[0, 0, 0] = 0
DWIsimc[0, 0, 0, :] = 0
mask = np.ones((2, 2, 2))
mask[0, 0, 0] = 0
dkiF = dkiM.fit(DWIsimc)
awf = dki_micro.axonal_water_fraction(dkiF.model_params, sphere,
gtol=1e-5)
assert_almost_equal(awf, FIEc)
# Extra-cellular and intra-cellular components
edt, idt = dki_micro.diffusion_components(dkiF.model_params, sphere,
awf=awf)
EDT = eig_from_lo_tri(edt)
IDT = eig_from_lo_tri(idt)
assert_array_almost_equal(EDT[..., 0], ADEc, decimal=3)
assert_array_almost_equal(EDT[..., 1], RDEc, decimal=3)
assert_array_almost_equal(EDT[..., 2], RDEc, decimal=3)
assert_array_almost_equal(IDT[..., 0], ADIc, decimal=3)
assert_array_almost_equal(IDT[..., 1], RDIc, decimal=3)
assert_array_almost_equal(IDT[..., 2], RDIc, decimal=3)
# Check when mask is given
dkiF = dkiM.fit(DWIsim)
awf = dki_micro.axonal_water_fraction(dkiF.model_params, sphere,
gtol=1e-5, mask=mask)
assert_almost_equal(awf, FIEc, decimal=3)
# Extra-cellular and intra-cellular components
edt, idt = dki_micro.diffusion_components(dkiF.model_params, sphere,
awf=awf, mask=mask)
EDT = eig_from_lo_tri(edt)
IDT = eig_from_lo_tri(idt)
assert_array_almost_equal(EDT[..., 0], ADEc, decimal=3)
assert_array_almost_equal(EDT[..., 1], RDEc, decimal=3)
assert_array_almost_equal(EDT[..., 2], RDEc, decimal=3)
assert_array_almost_equal(IDT[..., 0], ADIc, decimal=3)
assert_array_almost_equal(IDT[..., 1], RDIc, decimal=3)
assert_array_almost_equal(IDT[..., 2], RDIc, decimal=3)
# Check class object
wmtiM = dki_micro.KurtosisMicrostructureModel(gtab_2s, fit_method="WLS")
wmtiF = wmtiM.fit(DWIsim, mask=mask)
assert_almost_equal(wmtiF.awf, FIEc, decimal=3)
assert_almost_equal(wmtiF.axonal_diffusivity, ADIc, decimal=3)
assert_almost_equal(wmtiF.hindered_ad, ADEc, decimal=3)
assert_almost_equal(wmtiF.hindered_rd, RDEc, decimal=3)
assert_almost_equal(wmtiF.tortuosity, Torc, decimal=3)