def testEmptyData(self):
obss = bss.BSS()
data = None
mask = 'mask.nii.gz'
params = {'max_sources': 2}
with self.assertRaises(bss.BssException) as context:
results = obss.factorize(data, mask, params, '/')
self.assertIsNone(results, 'Unexpected result')
self.assertTrue('Missing data' in context.exception)
def testNoTEData(self):
obss = bss.BSS()
dwi = ['data_TE1.nii.gz', 'data_TE2.nii.gz']
data = {'dwi': dwi}
mask = 'mask.nii.gz'
params = {'max_sources': 2}
with self.assertRaises(bss.BssException) as context:
results = obss.factorize(data, mask, params, '/')
self.assertIsNone(results, 'Unexpected result')
self.assertTrue('Missing TE data' in context.exception)
def testNoDwiData(self):
obss = bss.BSS()
TE = [60, 120]
data = {'te': TE}
mask = 'mask.nii.gz'
params = {'max_sources': 2}
with self.assertRaises(bss.BssException) as context:
results = obss.factorize(data, mask, params, '/')
self.assertIsNone(results, 'Unexpected result')
self.assertTrue('Missing diffusion data' in context.exception)
def testNoMask(self):
obss = bss.BSS()
dwi = ['data_TE1.nii.gz', 'data_TE2.nii.gz']
TE = [60, 120]
data = {'dwi': dwi, 'te': TE}
mask = []
params = {'max_sources': 2}
with self.assertRaises(bss.BssException) as context:
results = obss.factorize(data, mask, params, '/')
self.assertIsNone(results, 'Unexpected result')
self.assertTrue('Missing mask' in context.exception)
def testFweNonB0(self):
obss = bss.BSS()
dwi = ['data_TE1.nii.gz', 'data_TE2.nii.gz']
TE = [60, 120]
data = {'dwi': dwi, 'te': TE}
mask = 'mask.nii.gz'
cwd = os.path.join(os.getcwd(), '..', 'examples', 'data')
b_values = os.path.join(cwd, 'test_no_B0.bval')
with self.assertRaises(bss.BssException) as context:
results = obss.fwe(data, mask, b_values, self.out_path)
self.assertIsNone(results, 'Unexpected result')
self.assertTrue('At least one b0 is required' in context.exception)
def testFweWrongBval(self):
obss = bss.BSS()
dwi = ['data_TE1.nii.gz', 'data_TE2.nii.gz']
TE = [60, 120]
data = {'dwi': dwi, 'te': TE}
mask = 'mask.nii.gz'
b_values = '/test.bval'
with self.assertRaises(bss.BssException) as context:
results = obss.fwe(data, mask, b_values, self.out_path)
self.assertIsNone(results, 'Unexpected result')
self.assertTrue(
'b_values is a mandatory parameter' in context.exception)
def testInvalidOutpath(self):
obss = bss.BSS()
dwi = ['data_TE1.nii.gz', 'data_TE2.nii.gz']
TE = [60, 120]
data = {'dwi': dwi, 'te': TE}
mask = 'mask.nii.gz'
params = {'max_sources': 2}
out_path = '/bss_test_doesnt_exist'
with self.assertRaises(bss.BssException) as context:
results = obss.factorize(data, mask, params, out_path)
self.assertIsNone(results, 'Unexpected result')
self.assertTrue('Non existing out_path.' in context.exception)
def testMissmatchingTeData(self):
obss = bss.BSS()
dwi = ['data_TE1.nii.gz', 'data_TE2.nii.gz']
TE = [60]
data = {'dwi': dwi, 'te': TE}
mask = 'mask.nii.gz'
params = {'max_sources': 2}
with self.assertRaises(bss.BssException) as context:
results = obss.factorize(data, mask, params, '/')
self.assertIsNone(results, 'Unexpected result')
self.assertTrue(
'Number of TE values and diffusion files do not match' in
context.exception)
def testComputeActualA3ExisitingSources(self):
t2 = np.array([0.075, 0.15, 2])
tes = np.array([0.07, 0.13, 0.2])
tes = tes[:, np.newaxis]
f = np.array([0.5, 0.3, 0.2])
(A, _) = utils.build_A(t2, tes, f)
S = np.random.random((3, 30))
S[:, 0] = 1
X = np.dot(A, S)
params = {'max_sources': 3}
obss = bss.BSS()
result = obss._compute_actual_A(X, A, tes, params)
np.testing.assert_array_almost_equal(result['t2'], t2, 6,
'Wrong T2 values')
np.testing.assert_array_almost_equal(result['f'], f, 6,
'Wrong f values')
self.assertEqual(result['s0'], 1, 'Wrong S0 value')
def testComputeActualAwithZero(self):
t2 = np.array([0.075, 2])
tes = np.array([0.07, 0.13])
tes = tes[:, np.newaxis]
f = np.array([1, 0])
(A, _) = utils.build_A(t2, tes, f)
S = np.random.random((2, 30))
S[:, 0] = 1
X = np.dot(A, S)
params = {'max_sources': 2}
obss = bss.BSS()
result = obss._compute_actual_A(X, A, tes, params)
np.testing.assert_array_almost_equal(result['t2'], [0.075, 0], 6,
'Wrong T2 values')
np.testing.assert_array_almost_equal(result['f'], [1, 0], 6,
'Wrong f values')
np.testing.assert_array_almost_equal(result['s0'], 1, 6,
'Wrong S0 value')
def test__volume_factorization_ParallelFalse(self):
obss = bss.BSS()
max_sources = 2
params = {'max_sources': max_sources}
cwd = os.path.join(os.getcwd(), '..', 'examples', 'data')
dwi = [
os.path.join(cwd, 'data_TE1.nii.gz'),
os.path.join(cwd, 'data_TE2.nii.gz')
]
TE = [0.0751, 0.1351]
data = {'dwi': dwi, 'te': TE}
mask = os.path.join(cwd, 'mask.nii.gz')
niiout = obss._volume_factorization(data, mask, params, self.out_path,
None, None, False)
self.assertIsNotNone(niiout, 'Missing Result')
self.assertEqual(len(niiout['T2']), max_sources,
'Incorrect number of T2 files')
self.assertEqual(len(niiout['f']), max_sources,
'Incorrect number of volume fraction files')
self.assertEqual(len(niiout['sources']), max_sources,
'Incorrect number of source files')
self.assertIsNotNone(niiout['pd'], 'No Proton Density file')
self.assertIsNotNone(niiout['rel_error'], 'No Relative Error file')
self.assertTrue(os.path.isfile(niiout['pd']),
'Non existing proton density file')
self.assertTrue(os.path.isfile(niiout['rel_error']),
'Non existing relative error file')
for i in range(max_sources):
self.assertTrue(os.path.isfile(niiout['T2'][i]),
'Non existing T2 file')
self.assertTrue('T2_' in niiout['T2'][i], 'Wrong Name for T2 file')
self.assertTrue(os.path.isfile(niiout['f'][i]),
'Non existing volume fraction file')
self.assertTrue('f_' in niiout['f'][i],
'Wrong Name for volume fraction file')
self.assertTrue(os.path.isfile(niiout['sources'][i]),
'Non existing source file')
self.assertTrue('source_' in niiout['sources'][i],
'Wrong Name for source file')
def testComputeActualANonExisitngSource(self):
t2 = np.array([0.075, 2])
tes = np.array([0.07, 0.13])
tes = tes[:, np.newaxis]
f = np.array([1, 0])
A = np.exp(-tes * (1. / t2))
S = np.random.random(30)
S[0] = 1
S = np.stack((S, np.zeros(30)))
X = np.dot(A, S)
params = {'max_sources': 2}
obss = bss.BSS()
result = obss._compute_actual_A(X, A, tes, params)
np.testing.assert_array_almost_equal(result['t2'], [0.075, 0], 6,
'Wrong T2 values')
np.testing.assert_array_almost_equal(result['f'], [1, 0], 6,
'Wrong f values')
np.testing.assert_array_almost_equal(result['s0'], 1, 6,
'Wrong S0 value')