diff --git a/tests/test_dtifit.py b/tests/test_dtifit.py
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+++ b/tests/test_dtifit.py
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+#!/usr/bin/env python
+#
+# test_dtifit.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import os.path as op
+import numpy as np
+
+import pytest
+
+import tests
+import fsl.data.dtifit as dtifit
+import fsl.data.image as fslimage
+
+
+def test_getDTIFitDataPrefix_and_isDTIFitPath():
+
+ def make_dtifit_dir(dir, prefix, suffixes):
+ for s in suffixes:
+ path = op.join(dir, '{}{}'.format(prefix, s))
+ with open(path, 'wt') as f:
+ f.write(path)
+
+ prefixes = ['dti', 'blob', 'random-prefix', '01234']
+ suffixes = ['_V1.nii', '_V2.nii', '_V3.nii',
+ '_L1.nii', '_L2.nii', '_L3.nii']
+ badSuffixes = ['_V1.txt', '_V2.nii', '_V3.nii',
+ '_L1.txt', '_L2.tar', '_L3.nii']
+
+
+ # Valid dtifit directories
+ with tests.testdir() as testdir:
+ for p in prefixes:
+
+ tests.cleardir(testdir)
+ make_dtifit_dir(testdir, p, suffixes)
+ assert dtifit.getDTIFitDataPrefix(testdir) == p
+ assert dtifit.isDTIFitPath(testdir)
+
+ # Invalid dtifit dir - one file missing
+ with tests.testdir() as testdir:
+ make_dtifit_dir(testdir, 'dti', suffixes[:-1])
+ assert dtifit.getDTIFitDataPrefix(testdir) is None
+ assert not dtifit.isDTIFitPath(testdir)
+
+ # Invalid dtifit dir - non-nifti files
+ with tests.testdir() as testdir:
+ make_dtifit_dir(testdir, 'dti', badSuffixes)
+ assert dtifit.getDTIFitDataPrefix(testdir) is None
+ assert not dtifit.isDTIFitPath(testdir)
+
+ # Ambiguous dtifit dir - multiple
+ # potential prefixes. Should return
+ # the first (alphabetical) one.
+ with tests.testdir() as testdir:
+ make_dtifit_dir(testdir, 'dti1', suffixes)
+ make_dtifit_dir(testdir, 'dti2', suffixes)
+ assert dtifit.getDTIFitDataPrefix(testdir) == 'dti1'
+ assert dtifit.isDTIFitPath(testdir)
+
+
+def test_looksLikeTensorImage():
+ # dtifit outputs one of two formats:
+ # - the eigenvectors/values of the tensor matrix
+ # - the raw values of the tensor matrix
+ #
+ # looksLikeTensorImage tests for the latter
+
+ testcases = [((10, 10, 10), False),
+ ((10, 10, 10, 5), False),
+ ((10, 10, 10, 6), True)]
+
+ with tests.testdir() as testdir:
+
+ fname = op.join(testdir, 'tensor_image.nii')
+
+ for dims, expected in testcases:
+
+ tests.make_random_image(fname, dims=dims)
+ img = fslimage.Image(fname)
+
+ assert dtifit.looksLikeTensorImage(img) == expected
+
+
+def test_decomposeTensorMatrix():
+
+ # A few tensor matrices
+ tensorMatrices = np.array([
+ [ 0.0032335606, -0.0000166876, 0.0000524589, 0.0032367723, 0.0000392826, 0.0028319934],
+ [ 0.0016628219, 0.0001651855, 0.0000678183, 0.0001300842, -0.0000293543, 0.0000450112],
+ [ 0.0006679352, -0.0000149214, 0.0000335666, 0.0007552942, -0.0003789219, 0.0008345888]])
+
+ # Expected eigenvalues and vectors
+ expEigVals = np.array([
+ [0.003252062, 0.0032290765, 0.002821188],
+ [0.0016829496, 0.00012794147, 0.000027026183],
+ [0.0011783227, 0.00066605647, 0.00041343897]])
+
+ expEigVecs = np.array([
+ [[ 0.701921939849854, -0.711941838264465, 0.021080270409584],
+ [-0.700381875038147, -0.695301055908203, -0.16131255030632 ],
+ [-0.129502296447754, -0.098464585840702, 0.986678183078766]],
+ [[-0.993700802326202, -0.104962401092052, -0.039262764155865],
+ [-0.081384353339672, 0.916762292385101, -0.391054302453995],
+ [-0.077040620148182, 0.385395616292953, 0.919529736042023]],
+ [[ 0.068294189870358, -0.666985750198364, 0.741933941841125],
+ [ 0.996652007102966, 0.079119503498077, -0.020613647997379],
+ [ 0.044952429831028, -0.740857720375061, -0.670156061649323]]])
+
+ tensorMatrices = tensorMatrices.reshape(1, 1, 3, 6)
+ expEigVals = expEigVals .reshape(1, 1, 3, 3)
+ expEigVecs = expEigVecs .reshape(1, 1, 3, 3, 3)
+
+ v1, v2, v3, l1, l2, l3 = dtifit.decomposeTensorMatrix(tensorMatrices)
+
+ expV1 = expEigVecs[:, :, :, 0]
+ expV2 = expEigVecs[:, :, :, 1]
+ expV3 = expEigVecs[:, :, :, 2]
+ expL1 = expEigVals[:, :, :, 0]
+ expL2 = expEigVals[:, :, :, 1]
+ expL3 = expEigVals[:, :, :, 2]
+
+ assert np.all(np.isclose(l1, expL1))
+ assert np.all(np.isclose(l2, expL2))
+ assert np.all(np.isclose(l3, expL3))
+
+ # Vector signs are arbitrary
+ for vox in range(3):
+ for resvec, expvec in zip([v1, v2, v3], [expV1, expV2, expV3]):
+
+ resvec = resvec[:, :, vox]
+ expvec = expvec[:, :, vox]
+
+ assert np.all(np.isclose(resvec, expvec)) or \
+ np.all(np.isclose(resvec, -expvec))
+
+
+def test_DTIFitTensor():
+
+ with tests.testdir() as testdir:
+
+ with pytest.raises(Exception):
+ dtifit.DTIFitTensor(testdir)
+
+ v1file = op.join(testdir, 'dti_V1.nii')
+ v2file = op.join(testdir, 'dti_V2.nii')
+ v3file = op.join(testdir, 'dti_V3.nii')
+ l1file = op.join(testdir, 'dti_L1.nii')
+ l2file = op.join(testdir, 'dti_L2.nii')
+ l3file = op.join(testdir, 'dti_L3.nii')
+
+ v1 = tests.make_random_image(v1file, (5, 5, 5, 3)).get_data()
+ v2 = tests.make_random_image(v2file, (5, 5, 5, 3)).get_data()
+ v3 = tests.make_random_image(v3file, (5, 5, 5, 3)).get_data()
+ l1 = tests.make_random_image(l1file, (5, 5, 5)) .get_data()
+ l2 = tests.make_random_image(l2file, (5, 5, 5)) .get_data()
+ l3 = tests.make_random_image(l3file, (5, 5, 5)) .get_data()
+
+ dtiobj = dtifit.DTIFitTensor(testdir)
+
+ assert np.all(np.isclose(dtiobj.V1()[:], v1))
+ assert np.all(np.isclose(dtiobj.V2()[:], v2))
+ assert np.all(np.isclose(dtiobj.V3()[:], v3))
+ assert np.all(np.isclose(dtiobj.L1()[:], l1))
+ assert np.all(np.isclose(dtiobj.L2()[:], l2))
+ assert np.all(np.isclose(dtiobj.L3()[:], l3))
+
+ v1 = fslimage.Image(v1file)
+
+ assert np.all(np.isclose(dtiobj.voxToWorldMat, v1.voxToWorldMat))
+ assert np.all(np.isclose(dtiobj.shape[:3], v1.shape[:3]))
+ assert np.all(np.isclose(dtiobj.pixdim[:3], v1.pixdim[:3]))