Skip to content
Snippets Groups Projects
Commit 6f00d2f9 authored by Michiel Cottaar's avatar Michiel Cottaar
Browse files

Made the dtifit tests deterministic 

The random element of running GPS is taken out by using precomputed gradient orientations.
The old implementation set a random subset of bvecs to b=0 (or to b=2000).
This is now fixed ensuring that the full bvecs are used for each shell.
parent 4434d234
No related branches found
No related tags found
1 merge request!28Made the dtifit tests deterministic
Pipeline #10400 passed
Stage: fsl-ci-build
Hide whitespace changes
Inline Side-by-side
unit_tests/fdt/dtifit/bvecs 0 → 100644
+ 100
− 0
View file @ 6f00d2f9
1 0 0
-0.5759015626 -0.7557308713 -0.3117823605
0.365980027 -0.7618208505 0.5344975318
0.8266615166 -0.1676571833 0.5371422586
-0.05315328551 0.9970703725 0.05500364094
-0.892798637 -0.417852473 -0.1682554742
0.3087651681 -0.9424873375 -0.127990975
0.7332427031 0.4098806082 -0.5425431092
-0.1825675796 -0.5151226918 -0.8374471275
0.09477098885 0.2595515517 0.9610678705
0.4475465206 -0.1412286865 0.8830382608
0.2530429794 -0.9593392114 0.1250501023
0.7354607419 0.5792546654 -0.3515132
-0.5011088611 0.8646571561 -0.03546705109
-0.3494413307 -0.8410040687 -0.4130410546
0.5847739281 -0.673936579 0.451496335
-0.02897174538 -0.6915161468 -0.721779784
-0.4770470052 0.5391935114 0.6940435952
0.4255848778 0.5245407073 0.7373835896
0.009732249087 0.9778708631 -0.2089829141
-0.744303127 -0.5609345609 -0.3624434763
0.9602209556 -0.2697422875 0.07221367413
0.1393337386 0.9597085901 0.2440195309
0.7522079351 0.1906474061 0.6307430451
-0.3567824679 0.728888815 0.5843178638
-0.7286370555 0.6829724737 0.05134823829
-0.5349212614 -0.4088516965 0.7393913269
0.529750921 0.7762409725 -0.3417805061
-0.569654883 -0.3145360974 -0.7593157167
0.6217432613 -0.06371685415 -0.7806250569
0.3453124252 0.7834611175 -0.5166701137
-0.8535268378 -0.5129379489 0.09157836941
-0.5587028258 -0.6151797057 0.5562419277
0.8519057956 0.3209637223 0.4138101066
0.7595775019 -0.2538503571 -0.5988338791
-0.07088030006 -0.2600860223 0.9629803965
0.1887815711 -0.9086574383 0.3724287559
0.3395785924 0.3083633785 0.8885934989
0.7939510312 -0.004256524139 -0.60796681
0.9655440027 0.09666497466 -0.2416209045
-0.4870237311 -0.1400514288 0.8620867025
-0.6162092547 0.2793353638 -0.7363816326
-0.8894556659 0.3184317103 -0.3278259663
0.07781834695 0.8865281032 -0.4560835748
0.5172584768 0.09327887008 0.850730698
-0.2525751629 -0.07009201098 0.9650351792
-0.1623217266 0.2030117623 0.9656282315
-0.9618908747 0.08459748658 -0.2600177119
0.4390180431 -0.8494682801 0.2926889115
-0.5639861908 0.696073956 0.4442979005
0.5206750927 0.6613037007 0.5399767247
-0.3735930616 -0.9135138536 -0.160998955
0.9657303691 -0.1908806804 -0.1758676206
0.2130723856 -0.6134846857 -0.7604187655
-0.05575164709 0.6279947277 -0.776217995
0.2012065496 0.9790943217 -0.02983678162
0.6831070125 -0.488981839 -0.5424588192
0.5649523258 -0.3142452495 -0.7629408842
0.7622387032 0.6365113381 0.1176667999
0.7470292555 -0.5960070066 -0.2944875881
-0.1310894929 0.4209333665 -0.8975692986
0.9622650553 0.2686836542 -0.04307037652
0.1061646581 -0.9424636145 -0.3170037867
-0.1291652717 0.8215637452 0.555292126
-0.5834669993 -0.8093404121 -0.06733764226
-0.1192284364 0.7942416415 -0.5957892201
0.8518057006 -0.5121976914 0.1099116614
-0.6837200427 -0.2064174643 0.6999419502
0.6851120126 0.7141287529 -0.1436720377
0.6585541815 -0.7279225646 0.1908798837
0.1957313245 -0.1849897966 0.9630514128
-0.06212628167 0.4530442329 0.8893206667
-0.2695387498 -0.06120002388 -0.9610428812
-0.3833288505 0.383118637 -0.8404041304
0.9090382753 -0.09865802712 -0.4048654194
-0.4058148335 0.1340505374 0.9040712219
-0.8626199411 -0.1899531769 0.4688332622
0.1080390675 0.863494933 0.4926500387
0.5327300523 -0.5300131134 0.659761162
0.3265434473 0.3324700658 -0.8847785216
-0.8871676959 -0.06216033205 -0.4572412628
0.3023205804 -0.6078512357 0.7342473302
-0.8859213785 0.4451050057 0.1304792892
0.7313288468 -0.4074607226 0.5469313278
0.3546148915 0.5889792358 -0.7261898777
-0.1470996957 -0.7322905532 0.6649152015
0.3241330104 -0.3892888966 -0.8622018015
-4.417301429e-10 4.004270839e-06 1
0.6761752544 0.4542177365 0.5800631631
-0.1433995357 -0.4987553831 0.8547980118
0.884545539 0.363778833 -0.2919660085
0.8552783312 -0.3584224946 -0.3742088875
0.9626357675 0.1700108002 0.2107811826
0.4405758073 0.88966168 -0.1199793859
0.7666600818 -0.5445902196 0.3400791258
0.2683263442 0.9167243162 -0.2960025356
0.2733316952 0.7152873417 0.6431592363
0.5569962534 -0.8043659644 -0.2067621074
-0.3508023035 0.8620202068 0.3658673351
0.6952687261 -0.03853288858 0.7177162496
unit_tests/fdt/dtifit/feedsRun
+ 20
− 11
View file @ 6f00d2f9
......@@ -56,24 +56,33 @@ def gen_data():
diffusion_tensor = (eigen_values[..., None] * eigen_vectors[..., None, :] * eigen_vectors[..., :, None]).sum(-3)
partial_bvecs = np.genfromtxt('bvecs')
for multi_shell in (False, True): # we should get the same results for single or multi-shell data
directory[1] = 'multi' if multi_shell else 'single'
if multi_shell:
bvals = np.zeros(210)
bvals[10:110] = 1000.
bvals[110:] = 2000.
bvecs = np.concatenate((
np.zeros((10, 3)),
partial_bvecs,
partial_bvecs,
), axis=0)
else:
bvals = np.zeros(110)
bvals[10:] = 1000.
bvecs = np.concatenate((
np.zeros((10, 3)),
partial_bvecs,
), axis=0)
for kurt in (0, 1, 2): # 0: no kurtosis; 1: single kurtosis; 2: parallel and perpendicular kurtosis
if kurt != 0 and not multi_shell:
continue
directory[2] = ['', 'kurt', 'kurtdir'][kurt]
bvals = np.full(50, 1000.)
if multi_shell:
bvals[25:] = 2000.
bvals[::10] = 0.
bvecs_fn = os.path.join(OUTDIR, "bvecs")
run(['gps', '--ndir=50', '--out={}'.format(bvecs_fn)], check=True)
bvecs = np.genfromtxt(bvecs_fn)
assert bvecs.shape == (50, 3), f"GPS produced bvecs-file with shape {bvecs.shape} rather than the expected (50, 3)"
testing.assert_allclose((bvecs ** 2).sum(-1), 1.)
if kurt == 2:
kvec = np.array([0.1, 0.05, 0.2])
beig = (
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment