def test_can_extract_hagmann_density(self):
global f_cmtk
f_cmtk.set_spacing('mm')
import nibabel
roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR)
wm_img = nibabel.load("%s/CMTK_wm_1mm.nii.gz" % IMAGES_DIR)
my_connectome = fibers.generate_connectome(f_cmtk, roi_img)
fibers.extract_hagmann_density(my_connectome, roi_img, wm_img)
for i,j in my_connectome.edges_iter():
assert my_connectome[i][j]['hagmann_density'] > 0
def test_can_extract_hagmann_density(self):
global f_cmtk
f_cmtk.set_spacing('mm')
import nibabel
roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR)
wm_img = nibabel.load("%s/CMTK_wm_1mm.nii.gz" % IMAGES_DIR)
my_connectome = fibers.generate_connectome(f_cmtk, roi_img)
fibers.extract_hagmann_density(my_connectome, roi_img, wm_img)
for i, j in my_connectome.edges_iter():
assert my_connectome[i][j]['hagmann_density'] > 0
def test_can_get_cmat_for_key(self):
global f_cmtk
f_cmtk.set_spacing('mm')
import nibabel
roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR)
my_connectome = fibers.generate_connectome(f_cmtk, roi_img)
fiber_cmat = fibers.cmat_for_key(my_connectome, 'number_of_fibers')
for i,j in my_connectome.edges_iter():
expected_fibers = my_connectome[i][j]['number_of_fibers']
assert fiber_cmat[i-1][j-1] == expected_fibers
assert fiber_cmat[j-1][i-1] == expected_fibers
def test_can_get_cmat_for_key(self):
global f_cmtk
f_cmtk.set_spacing('mm')
import nibabel
roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR)
my_connectome = fibers.generate_connectome(f_cmtk, roi_img)
fiber_cmat = fibers.cmat_for_key(my_connectome, 'number_of_fibers')
for i, j in my_connectome.edges_iter():
expected_fibers = my_connectome[i][j]['number_of_fibers']
assert fiber_cmat[i - 1][j - 1] == expected_fibers
assert fiber_cmat[j - 1][i - 1] == expected_fibers
def test_can_map_vertices_to_roi(self):
global f_cmtk
f_cmtk.set_spacing('mm')
import nibabel
roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR)
my_connectome = fibers.generate_connectome(f_cmtk, roi_img)
import networkx
expected_connectome = networkx.read_gpickle(
"%s/CMTK_connectome_scale33.gpickle" % FIBERS_DIR)
for i,j in my_connectome.edges_iter():
assert my_connectome[i][j]['number_of_fibers'] == \
expected_connectome[i][j]['number_of_fibers']
assert rms(my_connectome[i][j]['fiber_length_mean'],
expected_connectome[i][j]['fiber_length_mean']) < 10**-4
def test_can_map_vertices_to_roi(self):
global f_cmtk
f_cmtk.set_spacing('mm')
import nibabel
roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR)
my_connectome = fibers.generate_connectome(f_cmtk, roi_img)
import networkx
expected_connectome = networkx.read_gpickle(
"%s/CMTK_connectome_scale33.gpickle" % FIBERS_DIR)
for i, j in my_connectome.edges_iter():
assert my_connectome[i][j]['number_of_fibers'] == \
expected_connectome[i][j]['number_of_fibers']
assert rms(my_connectome[i][j]['fiber_length_mean'],
expected_connectome[i][j]['fiber_length_mean']) < 10**-4
def test_can_extract_scalars(self):
global f_cmtk
f_cmtk.set_spacing('mm')
import nibabel
roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR)
my_connectome = fibers.generate_connectome(f_cmtk, roi_img)
fa_img = nibabel.load("%s/CMTK_fa.nii.gz" % IMAGES_DIR)
fibers.extract_scalars(f_cmtk, my_connectome, fa_img, 'fa', scale_factor=[2.,2.,2.])
import networkx
expected_connectome = networkx.read_gpickle(
"%s/CMTK_connectome_scale33.gpickle" % FIBERS_DIR)
for i,j in my_connectome.edges_iter():
print i, j
assert rms(my_connectome[i][j]['fa_mean'],
expected_connectome[i][j]['fa_mean']) < 10**-4
def test_can_extract_scalars(self):
global f_cmtk
f_cmtk.set_spacing('mm')
import nibabel
roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR)
my_connectome = fibers.generate_connectome(f_cmtk, roi_img)
fa_img = nibabel.load("%s/CMTK_fa.nii.gz" % IMAGES_DIR)
fibers.extract_scalars(f_cmtk,
my_connectome,
fa_img,
'fa',
scale_factor=[2., 2., 2.])
import networkx
expected_connectome = networkx.read_gpickle(
"%s/CMTK_connectome_scale33.gpickle" % FIBERS_DIR)
for i, j in my_connectome.edges_iter():
print i, j
assert rms(my_connectome[i][j]['fa_mean'],
expected_connectome[i][j]['fa_mean']) < 10**-4