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)