import unittest
import connectome
import fibers
import nibabel
fib = fibers.read('test_data/fibers/CMTK_scale33.trk')
roi = nibabel.load('test_data/images/CMTK_roi.nii.gz')
node_info = 'test_data/connectome/freesurfer_node_info.graphml'
class Test_TNConnectome(unittest.TestCase):
def setUp(self):
pass
def tearDown(self):
pass
def test_can_generate_connectome_from_fibers_and_rois(self):
assert connectome.generate_connectome(fib, roi) is not None
def test_node_info(self):
my_connectome = connectome.generate_connectome(fib,
roi,
node_info=node_info)
assert my_connectome.node[82]['name'] == 'Left-Amygdala'
assert my_connectome.node[82]['region'] == 'subcortical'
assert my_connectome.node[82]['hemisphere'] == 'left'
def test_can_set_clinical_info(self):
test_info = dict(group='foo', gender='F', a_score=114.56, b_score=5)
my_connectome = connectome.generate_connectome(fib, roi)
import unittest
import fibers
FIBERS_DIR = 'test_data/fibers'
IMAGES_DIR = 'test_data/images'
# load trackvis files up front and share between all tests, otherwise,
# tests take too long to run
f_cmtk = fibers.read("%s/CMTK_scale33.trk" % FIBERS_DIR) # CMTK
f_dtk = fibers.read("%s/DTK_RungeKutta.trk" % FIBERS_DIR) # DTK
class Test_TNImages(unittest.TestCase):
def setUp(self):
pass
def tearDown(self):
pass
def test_can_get_sum_of_inverse_lengths(self):
# TODO: I need a better test for this, basically I need to
# generate well-defined NIFTI images w/ more complexity than I
# currently have and test the results
pass
def test_can_load_trackvis(self):
global f_cmtk
assert f_cmtk is not None
def test_can_get_data(self):
# test trackfile has a fiber count of 230814 according to
import unittest
import connectome
import fibers
import nibabel
fib = fibers.read('test_data/fibers/CMTK_scale33.trk')
roi = nibabel.load('test_data/images/CMTK_roi.nii.gz')
node_info = 'test_data/connectome/freesurfer_node_info.graphml'
class Test_TNConnectome(unittest.TestCase):
def setUp(self):
pass
def tearDown(self):
pass
def test_can_generate_connectome_from_fibers_and_rois(self):
assert connectome.generate_connectome(fib, roi) is not None
def test_node_info(self):
my_connectome = connectome.generate_connectome(fib, roi, node_info=node_info)
assert my_connectome.node[82]['name'] == 'Left-Amygdala'
assert my_connectome.node[82]['region'] == 'subcortical'
assert my_connectome.node[82]['hemisphere'] == 'left'
def test_can_set_clinical_info(self):
test_info = dict( group='foo',
gender='F',
a_score=114.56,
b_score=5 )
import unittest
import fibers
FIBERS_DIR = 'test_data/fibers'
IMAGES_DIR = 'test_data/images'
# load trackvis files up front and share between all tests, otherwise,
# tests take too long to run
f_cmtk = fibers.read("%s/CMTK_scale33.trk" % FIBERS_DIR) # CMTK
f_dtk = fibers.read("%s/DTK_RungeKutta.trk" % FIBERS_DIR) # DTK
class Test_TNImages(unittest.TestCase):
def setUp(self):
pass
def tearDown(self):
pass
def test_can_get_sum_of_inverse_lengths(self):
# TODO: I need a better test for this, basically I need to
# generate well-defined NIFTI images w/ more complexity than I
# currently have and test the results
pass
def test_can_load_trackvis(self):
global f_cmtk
assert f_cmtk is not None
def test_can_get_data(self):
# test trackfile has a fiber count of 230814 according to
