def test_pdb_from_fg():
"""
Test writing a fiber-group to file
"""
coords1 = np.arange(900).reshape(3,300)
coords2 = np.arange(900).reshape(3,300) + 100
fiber_stats = dict(foo=1,bar=2)
node_stats = dict(ecc=np.arange(300))
fg = mtf.FiberGroup([mtf.Fiber(coords1,
fiber_stats=fiber_stats,
node_stats=node_stats),
mtf.Fiber(coords2,
fiber_stats=fiber_stats,
node_stats=node_stats)])
temp_dir = tempfile.gettempdir()
mio.pdb_from_fg(fg, os.path.join(temp_dir,'fg.pdb'))
# Test that the properties are preserved upon reloading:
fg2 = mio.fg_from_pdb(os.path.join(temp_dir,'fg.pdb'))
npt.assert_equal(fg2[0].coords, fg[0].coords)
npt.assert_equal(fg2[1].coords, fg[1].coords)
npt.assert_equal(fg2[0].node_stats, fg[0].node_stats)
npt.assert_equal(fg2[1].node_stats, fg[1].node_stats)
npt.assert_equal(fg2.fiber_stats, fg.fiber_stats)
def test_fg_from_pdb():
"""
Test initialization of the FiberGroup from pdb file
Benchmark was generated using vistasoft in Matlab as follows:
>> fg = mtrImportFibers('FG_w_stats.pdb')
"""
pdb_files = ['FG_w_stats.pdb', 'pdb_version2.pdb']
mat_files = ['fg_from_matlab.mat', 'pdb_version2.mat']
for ii in range(len(pdb_files)):
file_name = data_path + pdb_files[ii]
fg = mio.fg_from_pdb(file_name)
# Get the same fiber group as saved in matlab:
mat_fg = sio.loadmat(data_path + mat_files[ii],
squeeze_me=True)["fg"]
k = [d[0] for d in mat_fg.dtype.descr]
v = mat_fg.item()
mat_fg_dict = dict(zip(k,v))
npt.assert_equal(fg.name, mat_fg_dict["name"])
npt.assert_equal(fg.fibers[0].coords, mat_fg_dict["fibers"][0])
if ii==0:
npt.assert_equal(fg.fibers[0].node_stats["eccentricity"],
mat_fg_dict["params"][0].item()[-1][0])
mio.pdb_from_fg(fg, data_path + 'fg_new.pdb')
def test_pdb_from_fg():
"""
Test writing a fiber-group to file
"""
coords1 = np.arange(900).reshape(3, 300)
coords2 = np.arange(900).reshape(3, 300) + 100
fiber_stats = dict(foo=1, bar=2)
node_stats = dict(ecc=np.arange(300))
fg = mtf.FiberGroup([
mtf.Fiber(coords1, fiber_stats=fiber_stats, node_stats=node_stats),
mtf.Fiber(coords2, fiber_stats=fiber_stats, node_stats=node_stats)
])
temp_dir = tempfile.gettempdir()
mio.pdb_from_fg(fg, os.path.join(temp_dir, 'fg.pdb'))
# Test that the properties are preserved upon reloading:
fg2 = mio.fg_from_pdb(os.path.join(temp_dir, 'fg.pdb'))
npt.assert_equal(fg2[0].coords, fg[0].coords)
npt.assert_equal(fg2[1].coords, fg[1].coords)
npt.assert_equal(fg2[0].node_stats, fg[0].node_stats)
npt.assert_equal(fg2[1].node_stats, fg[1].node_stats)
npt.assert_equal(fg2.fiber_stats, fg.fiber_stats)
def test_fg_from_pdb():
"""
Test initialization of the FiberGroup from pdb file
Benchmark was generated using vistasoft in Matlab as follows:
>> fg = mtrImportFibers('FG_w_stats.pdb')
"""
pdb_files = ['FG_w_stats.pdb', 'pdb_version2.pdb']
mat_files = ['fg_from_matlab.mat', 'pdb_version2.mat']
for ii in range(len(pdb_files)):
file_name = data_path + pdb_files[ii]
fg = mio.fg_from_pdb(file_name)
# Get the same fiber group as saved in matlab:
mat_fg = sio.loadmat(data_path + mat_files[ii], squeeze_me=True)["fg"]
k = [d[0] for d in mat_fg.dtype.descr]
v = mat_fg.item()
mat_fg_dict = dict(zip(k, v))
npt.assert_equal(fg.name, mat_fg_dict["name"])
npt.assert_equal(fg.fibers[0].coords, mat_fg_dict["fibers"][0])
if ii == 0:
npt.assert_equal(fg.fibers[0].node_stats["eccentricity"],
mat_fg_dict["params"][0].item()[-1][0])
mio.pdb_from_fg(fg, data_path + 'fg_new.pdb')
def test_fg2volume():
data_path = os.path.split(oz.__file__)[0] + '/data/'
pdb_file = data_path + 'FG_w_stats.pdb'
nii_file = data_path + 'fp20110912_ecc.nii.gz'
fg = ozv.nii2fg(oio.fg_from_pdb(pdb_file), nii_file)
# Smoke testing this:
vol = ozv.fg2volume(fg, 'fp20110912_ecc.nii.gz',
shape=ni.load(nii_file).get_shape())
def test_nii2fg():
"""
Testing the addition of information from a nifti volume to fiber groups
nii2fg
"""
data_path = os.path.split(oz.__file__)[0] + '/data/'
pdb_file = data_path + 'FG_w_stats.pdb'
nii_file = data_path + 'fp20110912_ecc.nii.gz'
# Smoke testing this:
fg = ozv.nii2fg(oio.fg_from_pdb(pdb_file), nii_file)
def test_FiberModel():
"""
Test the initialization of FiberModel class instances
"""
ad = 1.5
rd = 0.5
FG = mio.fg_from_pdb(data_path + "FG_w_stats.pdb", verbose=False)
M = FiberModel(data_path + "dwi.nii.gz", data_path + "dwi.bvecs", data_path + "dwi.bvals", FG, ad, rd)
npt.assert_equal(M.matrix[0].shape[0], np.prod(M.voxel_signal.shape))
npt.assert_equal(M.matrix[0].shape[-1], len(FG.fibers))
npt.assert_equal(M.matrix[1].shape[0], np.prod(M.voxel_signal.shape))
npt.assert_equal(M.matrix[1].shape[-1], len(M.fg_idx_unique.T))
def test_FiberModel():
"""
Test the initialization of FiberModel class instances
"""
ad = 1.5
rd = 0.5
FG = mio.fg_from_pdb(data_path + 'FG_w_stats.pdb', verbose=False)
M = FiberModel(data_path + 'dwi.nii.gz', data_path + 'dwi.bvecs',
data_path + 'dwi.bvals', FG, ad, rd)
npt.assert_equal(M.matrix[0].shape[0], np.prod(M.voxel_signal.shape))
npt.assert_equal(M.matrix[0].shape[-1], len(FG.fibers))
npt.assert_equal(M.matrix[1].shape[0], np.prod(M.voxel_signal.shape))
npt.assert_equal(M.matrix[1].shape[-1], len(M.fg_idx_unique.T))
