From 6f00d2f9f3c7b58b26ba4973ca36ac5f21723a1d Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Mon, 16 Aug 2021 13:16:19 +0100
Subject: [PATCH] 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.
---
unit_tests/fdt/dtifit/bvecs | 100 +++++++++++++++++++++++++++++++++
unit_tests/fdt/dtifit/feedsRun | 31 ++++++----
2 files changed, 120 insertions(+), 11 deletions(-)
create mode 100644 unit_tests/fdt/dtifit/bvecs
diff --git a/unit_tests/fdt/dtifit/bvecs b/unit_tests/fdt/dtifit/bvecs
new file mode 100644
index 0000000..01bd597
--- /dev/null
+++ b/unit_tests/fdt/dtifit/bvecs
@@ -0,0 +1,100 @@
+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
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+0.7332427031 0.4098806082 -0.5425431092
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+-0.5011088611 0.8646571561 -0.03546705109
+-0.3494413307 -0.8410040687 -0.4130410546
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+-0.02897174538 -0.6915161468 -0.721779784
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+-0.744303127 -0.5609345609 -0.3624434763
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+-0.3567824679 0.728888815 0.5843178638
+-0.7286370555 0.6829724737 0.05134823829
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+-4.417301429e-10 4.004270839e-06 1
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+-0.3508023035 0.8620202068 0.3658673351
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diff --git a/unit_tests/fdt/dtifit/feedsRun b/unit_tests/fdt/dtifit/feedsRun
index bea1b60..a0b3c18 100755
--- a/unit_tests/fdt/dtifit/feedsRun
+++ b/unit_tests/fdt/dtifit/feedsRun
@@ -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 = (
--
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