def _filter_from_roi_trackvis_style(tracts_fname, roi_fname, out_tracts_fname,
include, mode, tol):
tracts, hdr = nb.trackvis.read(tracts_fname,
as_generator=True,
points_space='voxel')
img = nb.load(roi_fname)
aff = np.eye(4)
filtered_strl = []
mask = img.get_data()
for chunk in ichunk(tracts, 100000):
logging.debug("Starting new loop")
# Need to "unshift" because Dipy shifts them back to fit in voxel grid.
# However, to mimic the way TrackVis filters, we need to "unshift" it.
# TODO check no negative coordinates
strls = [s[0] - 0.5 for s in chunk]
# Interpretation from @mdesco code:
# target is used for this case because we want to support
# include=False.
if mode == 'any_part' and tol == 0:
target_strl_gen = target(strls, mask, aff, include=include)
target_strl = list(target_strl_gen)
if len(target_strl) > 0:
filtered_strl.extend(target_strl)
else:
corner_dist = dist_to_corner(aff)
# Tolerance is considered to be in mm. Rescale wrt voxel size.
tol = tol / min(img.get_header().get_zooms())
# Check this to avoid Dipy's warning and scare users.
if tol < corner_dist:
logging.debug(
"Setting tolerance to minimal distance to corner")
tol = corner_dist
if mode == 'any_part':
strls_ind = near_roi(strls, mask, aff, tol=tol, mode='any')
else:
strls_ind = near_roi(strls, mask, aff, tol=tol, mode=mode)
for i in np.where(strls_ind)[0]:
filtered_strl.append(strls[i])
logging.info("Original nb: {0}, kept: {1}".format(hdr['n_count'],
len(filtered_strl)))
# Remove the unshift
final_strls = [(s + 0.5, None, None) for s in filtered_strl]
new_hdr = np.copy(hdr)
new_hdr['n_count'] = len(filtered_strl)
nb.trackvis.write(out_tracts_fname,
final_strls,
new_hdr,
points_space="voxel")
# Compute streamlines and store as a list.
streamlines = list(streamlines)
"""
In order to select only the fibers that enter into the LGN, another ROI is
created from a cube of size 5x5x5 voxels. The near_roi command is used to find
the fibers that traverse through this ROI.
"""
# Set a mask for the lateral geniculate nucleus (LGN)
mask_lgn = np.zeros(data.shape[:-1], 'bool')
rad = 5
mask_lgn[35-rad:35+rad, 42-rad:42+rad, 28-rad:28+rad] = True
# Select all the fibers that enter the LGN and discard all others
filtered_fibers2 = utils.near_roi(streamlines, mask_lgn, tol=1.8,
affine=affine)
sfil = []
for i in range(len(streamlines)):
if filtered_fibers2[i]:
sfil.append(streamlines[i])
streamlines = list(sfil)
"""
Inspired by [Paulo_Eurographics]_, a lookup-table is created, containing
rotated versions of the fiber propagation kernel :math:`P_t`
[DuitsAndFranken_IJCV]_ rotated over a discrete set of orientations. See the
`Contextual enhancement example <http://nipy.org/dipy/examples_built/contextual_enhancement.html>`_
for more details regarding the kernel. In order to ensure rotationally
invariant processing, the discrete orientations are required to be equally
distributed over a sphere. By default, a sphere with 100 directions is used
obtained from electrostatic repulsion in DIPY.
# Compute streamlines and store as a list.
streamlines = list(streamlines)
"""
In order to select only the fibers that enter into the LGN, another ROI is
created from a cube of size 5x5x5 voxels. The near_roi command is used to find
the fibers that traverse through this ROI.
"""
# Set a mask for the lateral geniculate nucleus (LGN)
mask_lgn = np.zeros(data.shape[:-1], 'bool')
rad = 5
mask_lgn[35-rad:35+rad, 42-rad:42+rad, 28-rad:28+rad] = True
# Select all the fibers that enter the LGN and discard all others
filtered_fibers2 = utils.near_roi(streamlines, mask_lgn, tol=1.8,
affine=affine)
sfil = []
for i in range(len(streamlines)):
if filtered_fibers2[i]:
sfil.append(streamlines[i])
streamlines = list(sfil)
"""
Inspired by [Paulo_Eurographics]_, a lookup-table is created, containing
rotated versions of the fiber propagation kernel :math:`P_t`
[DuitsAndFranken_IJCV]_ rotated over a discrete set of orientations. See the
`Contextual enhancement example <http://nipy.org/dipy/examples_built/contextual_enhancement.html>`_
for more details regarding the kernel. In order to ensure rotationally
invariant processing, the discrete orientations are required to be equally
distributed over a sphere. By default, a sphere with 100 directions is used
obtained from electrostatic repulsion in DIPY.
def test_near_roi():
streamlines = [
np.array([[0., 0., 0.9], [1.9, 0., 0.], [3, 2., 2.]]),
np.array([[0.1, 0., 0], [0, 1., 1.], [0, 2., 2.]]),
np.array([[2, 2, 2], [3, 3, 3]])
]
mask = np.zeros((4, 4, 4), dtype=bool)
mask[0, 0, 0] = True
mask[1, 0, 0] = True
npt.assert_array_equal(near_roi(streamlines, np.eye(4), mask, tol=1),
np.array([True, True, False]))
npt.assert_array_equal(near_roi(streamlines, np.eye(4), mask),
np.array([False, True, False]))
# If there is an affine, we need to use it:
affine = np.eye(4)
affine[:, 3] = [-1, 100, -20, 1]
# Transform the streamlines:
x_streamlines = [sl + affine[:3, 3] for sl in streamlines]
npt.assert_array_equal(near_roi(x_streamlines, affine, mask, tol=1),
np.array([True, True, False]))
npt.assert_array_equal(near_roi(x_streamlines, affine, mask, tol=None),
np.array([False, True, False]))
# Test for use of the 'all' mode:
npt.assert_array_equal(
near_roi(x_streamlines, affine, mask, tol=None, mode='all'),
np.array([False, False, False]))
mask[0, 1, 1] = True
mask[0, 2, 2] = True
# Test for use of the 'all' mode, also testing that setting the tolerance
# to a very small number gets overridden:
with warnings.catch_warnings():
warnings.simplefilter("ignore")
npt.assert_array_equal(
near_roi(x_streamlines, affine, mask, tol=0.1, mode='all'),
np.array([False, True, False]))
mask[2, 2, 2] = True
mask[3, 3, 3] = True
npt.assert_array_equal(
near_roi(x_streamlines, affine, mask, tol=None, mode='all'),
np.array([False, True, True]))
# Test for use of endpoints as selection criteria:
mask = np.zeros((4, 4, 4), dtype=bool)
mask[0, 1, 1] = True
mask[3, 2, 2] = True
npt.assert_array_equal(
near_roi(streamlines, np.eye(4), mask, tol=0.87, mode="either_end"),
np.array([True, False, False]))
npt.assert_array_equal(
near_roi(streamlines, np.eye(4), mask, tol=0.87, mode="both_end"),
np.array([False, False, False]))
mask[0, 0, 0] = True
mask[0, 2, 2] = True
npt.assert_array_equal(
near_roi(streamlines, np.eye(4), mask, mode="both_end"),
np.array([False, True, False]))
# Test with a generator input:
def generate_sl(streamlines):
for sl in streamlines:
yield sl
npt.assert_array_equal(
near_roi(generate_sl(streamlines), np.eye(4), mask, mode="both_end"),
np.array([False, True, False]))
def test_near_roi():
streamlines = [np.array([[0., 0., 0.9],
[1.9, 0., 0.],
[3, 2., 2.]]),
np.array([[0.1, 0., 0],
[0, 1., 1.],
[0, 2., 2.]]),
np.array([[2, 2, 2],
[3, 3, 3]])]
affine = np.eye(4)
mask = np.zeros((4, 4, 4), dtype=bool)
mask[0, 0, 0] = True
mask[1, 0, 0] = True
assert_array_equal(near_roi(streamlines, mask, tol=1),
np.array([True, True, False]))
assert_array_equal(near_roi(streamlines, mask),
np.array([False, True, False]))
# If there is an affine, we need to use it:
affine[:, 3] = [-1, 100, -20, 1]
# Transform the streamlines:
x_streamlines = [sl + affine[:3, 3] for sl in streamlines]
assert_array_equal(near_roi(x_streamlines, mask, affine=affine, tol=1),
np.array([True, True, False]))
assert_array_equal(near_roi(x_streamlines, mask, affine=affine,
tol=None),
np.array([False, True, False]))
# Test for use of the 'all' mode:
assert_array_equal(near_roi(x_streamlines, mask, affine=affine, tol=None,
mode='all'), np.array([False, False, False]))
mask[0, 1, 1] = True
mask[0, 2, 2] = True
# Test for use of the 'all' mode, also testing that setting the tolerance
# to a very small number gets overridden:
assert_array_equal(near_roi(x_streamlines, mask, affine=affine, tol=0.1,
mode='all'), np.array([False, True, False]))
mask[2, 2, 2] = True
mask[3, 3, 3] = True
assert_array_equal(near_roi(x_streamlines, mask, affine=affine,
tol=None,
mode='all'),
np.array([False, True, True]))
# Test for use of endpoints as selection criteria:
mask = np.zeros((4, 4, 4), dtype=bool)
mask[0, 1, 1] = True
mask[3, 2, 2] = True
assert_array_equal(near_roi(streamlines, mask, tol=0.87,
mode="either_end"),
np.array([True, False, False]))
assert_array_equal(near_roi(streamlines, mask, tol=0.87,
mode="both_end"),
np.array([False, False, False]))
mask[0, 0, 0] = True
mask[0, 2, 2] = True
assert_array_equal(near_roi(streamlines, mask, mode="both_end"),
np.array([False, True, False]))
# Test with a generator input:
def generate_sl(streamlines):
for sl in streamlines:
yield sl
assert_array_equal(near_roi(generate_sl(streamlines),
mask, mode="both_end"),
np.array([False, True, False]))
def track_ensemble(target_samples,
atlas_data_wm_gm_int,
labels_im_file,
recon_path,
sphere,
traversal,
curv_thr_list,
step_list,
track_type,
maxcrossing,
roi_neighborhood_tol,
min_length,
waymask,
B0_mask,
t1w2dwi,
gm_in_dwi,
vent_csf_in_dwi,
wm_in_dwi,
tiss_class,
BACKEND='threading'):
"""
Perform native-space ensemble tractography, restricted to a vector of ROI
masks.
Parameters
----------
target_samples : int
Total number of streamline samples specified to generate streams.
atlas_data_wm_gm_int : str
File path to Nifti1Image in T1w-warped native diffusion space,
restricted to wm-gm interface.
parcels : list
List of 3D boolean numpy arrays of atlas parcellation ROI masks from a
Nifti1Image in T1w-warped native diffusion space.
recon_path : str
File path to diffusion reconstruction model.
tiss_classifier : str
Tissue classification method.
sphere : obj
DiPy object for modeling diffusion directions on a sphere.
traversal : str
The statistical approach to tracking. Options are: det (deterministic),
closest (clos), and prob (probabilistic).
curv_thr_list : list
List of integer curvature thresholds used to perform ensemble tracking.
step_list : list
List of float step-sizes used to perform ensemble tracking.
track_type : str
Tracking algorithm used (e.g. 'local' or 'particle').
maxcrossing : int
Maximum number if diffusion directions that can be assumed per voxel
while tracking.
roi_neighborhood_tol : float
Distance (in the units of the streamlines, usually mm). If any
coordinate in the streamline is within this distance from the center
of any voxel in the ROI, the filtering criterion is set to True for
this streamline, otherwise False. Defaults to the distance between
the center of each voxel and the corner of the voxel.
min_length : int
Minimum fiber length threshold in mm.
waymask_data : ndarray
Tractography constraint mask array in native diffusion space.
B0_mask_data : ndarray
B0 brain mask data.
n_seeds_per_iter : int
Number of seeds from which to initiate tracking for each unique
ensemble combination. By default this is set to 250.
max_length : int
Maximum number of steps to restrict tracking.
particle_count
pft_back_tracking_dist : float
Distance in mm to back track before starting the particle filtering
tractography. The total particle filtering tractography distance is
equal to back_tracking_dist + front_tracking_dist. By default this is
set to 2 mm.
pft_front_tracking_dist : float
Distance in mm to run the particle filtering tractography after the
the back track distance. The total particle filtering tractography
distance is equal to back_tracking_dist + front_tracking_dist. By
default this is set to 1 mm.
particle_count : int
Number of particles to use in the particle filter.
min_separation_angle : float
The minimum angle between directions [0, 90].
Returns
-------
streamlines : ArraySequence
DiPy list/array-like object of streamline points from tractography.
References
----------
.. [1] Takemura, H., Caiafa, C. F., Wandell, B. A., & Pestilli, F. (2016).
Ensemble Tractography. PLoS Computational Biology.
https://doi.org/10.1371/journal.pcbi.1004692
"""
import os
import gc
import time
import warnings
import time
import tempfile
from joblib import Parallel, delayed, Memory
import itertools
import pickle5 as pickle
from pynets.dmri.track import run_tracking
from colorama import Fore, Style
from pynets.dmri.utils import generate_sl
from nibabel.streamlines.array_sequence import concatenate, ArraySequence
from pynets.core.utils import save_3d_to_4d
from nilearn.masking import intersect_masks
from nilearn.image import math_img
from pynets.core.utils import load_runconfig
from dipy.tracking import utils
warnings.filterwarnings("ignore")
pickle.HIGHEST_PROTOCOL = 5
joblib_dir = tempfile.mkdtemp()
os.makedirs(joblib_dir, exist_ok=True)
hardcoded_params = load_runconfig()
nthreads = hardcoded_params["omp_threads"][0]
os.environ['MKL_NUM_THREADS'] = str(nthreads)
os.environ['OPENBLAS_NUM_THREADS'] = str(nthreads)
n_seeds_per_iter = \
hardcoded_params['tracking']["n_seeds_per_iter"][0]
max_length = \
hardcoded_params['tracking']["max_length"][0]
pft_back_tracking_dist = \
hardcoded_params['tracking']["pft_back_tracking_dist"][0]
pft_front_tracking_dist = \
hardcoded_params['tracking']["pft_front_tracking_dist"][0]
particle_count = \
hardcoded_params['tracking']["particle_count"][0]
min_separation_angle = \
hardcoded_params['tracking']["min_separation_angle"][0]
min_streams = \
hardcoded_params['tracking']["min_streams"][0]
seeding_mask_thr = hardcoded_params['tracking']["seeding_mask_thr"][0]
timeout = hardcoded_params['tracking']["track_timeout"][0]
all_combs = list(itertools.product(step_list, curv_thr_list))
# Construct seeding mask
seeding_mask = f"{os.path.dirname(labels_im_file)}/seeding_mask.nii.gz"
if waymask is not None and os.path.isfile(waymask):
waymask_img = math_img(f"img > {seeding_mask_thr}",
img=nib.load(waymask))
waymask_img.to_filename(waymask)
atlas_data_wm_gm_int_img = intersect_masks(
[
waymask_img,
math_img("img > 0.001", img=nib.load(atlas_data_wm_gm_int)),
math_img("img > 0.001", img=nib.load(labels_im_file))
],
threshold=1,
connected=False,
)
nib.save(atlas_data_wm_gm_int_img, seeding_mask)
else:
atlas_data_wm_gm_int_img = intersect_masks(
[
math_img("img > 0.001", img=nib.load(atlas_data_wm_gm_int)),
math_img("img > 0.001", img=nib.load(labels_im_file))
],
threshold=1,
connected=False,
)
nib.save(atlas_data_wm_gm_int_img, seeding_mask)
tissues4d = save_3d_to_4d([
B0_mask, labels_im_file, seeding_mask, t1w2dwi, gm_in_dwi,
vent_csf_in_dwi, wm_in_dwi
])
# Commence Ensemble Tractography
start = time.time()
stream_counter = 0
all_streams = []
ix = 0
memory = Memory(location=joblib_dir, mmap_mode='r+', verbose=0)
os.chdir(f"{memory.location}/joblib")
@memory.cache
def load_recon_data(recon_path):
import h5py
with h5py.File(recon_path, 'r') as hf:
recon_data = hf['reconstruction'][:].astype('float32')
hf.close()
return recon_data
recon_shelved = load_recon_data.call_and_shelve(recon_path)
@memory.cache
def load_tissue_data(tissues4d):
return nib.load(tissues4d)
tissue_shelved = load_tissue_data.call_and_shelve(tissues4d)
try:
while float(stream_counter) < float(target_samples) and \
float(ix) < 0.50*float(len(all_combs)):
with Parallel(n_jobs=nthreads,
backend=BACKEND,
mmap_mode='r+',
verbose=0) as parallel:
out_streams = parallel(
delayed(run_tracking)
(i, recon_shelved, n_seeds_per_iter, traversal,
maxcrossing, max_length, pft_back_tracking_dist,
pft_front_tracking_dist, particle_count,
roi_neighborhood_tol, min_length, track_type,
min_separation_angle, sphere, tiss_class, tissue_shelved)
for i in all_combs)
out_streams = list(filter(None, out_streams))
if len(out_streams) > 1:
out_streams = concatenate(out_streams, axis=0)
else:
continue
if waymask is not None and os.path.isfile(waymask):
try:
out_streams = out_streams[utils.near_roi(
out_streams,
np.eye(4),
np.asarray(
nib.load(waymask).dataobj).astype("bool"),
tol=int(round(roi_neighborhood_tol * 0.50, 1)),
mode="all")]
except BaseException:
print(f"\n{Fore.RED}No streamlines generated in "
f"waymask vacinity\n")
print(Style.RESET_ALL)
return None
if len(out_streams) < min_streams:
ix += 1
print(f"\n{Fore.YELLOW}Fewer than {min_streams} "
f"streamlines tracked "
f"on last iteration...\n")
print(Style.RESET_ALL)
if ix > 5:
print(f"\n{Fore.RED}No streamlines generated\n")
print(Style.RESET_ALL)
return None
continue
else:
ix -= 1
stream_counter += len(out_streams)
all_streams.extend([generate_sl(i) for i in out_streams])
del out_streams
print("%s%s%s%s" % (
"\nCumulative Streamline Count: ",
Fore.CYAN,
stream_counter,
"\n",
))
gc.collect()
print(Style.RESET_ALL)
if time.time() - start > timeout:
print(f"\n{Fore.RED}Warning: Tractography timed "
f"out: {time.time() - start}")
print(Style.RESET_ALL)
memory.clear(warn=False)
return None
except RuntimeError as e:
print(f"\n{Fore.RED}Error: Tracking failed due to:\n{e}\n")
print(Style.RESET_ALL)
memory.clear(warn=False)
return None
print("Tracking Complete: ", str(time.time() - start))
memory.clear(warn=False)
del parallel, all_combs
gc.collect()
if stream_counter != 0:
print('Generating final ...')
return ArraySequence([ArraySequence(i) for i in all_streams])
else:
print(f"\n{Fore.RED}No streamlines generated!")
print(Style.RESET_ALL)
return None
def run_tracking(step_curv_combinations,
recon_path,
n_seeds_per_iter,
directget,
maxcrossing,
max_length,
pft_back_tracking_dist,
pft_front_tracking_dist,
particle_count,
roi_neighborhood_tol,
waymask,
min_length,
track_type,
min_separation_angle,
sphere,
tiss_class,
tissues4d,
cache_dir,
min_seeds=100):
import gc
import os
import h5py
from dipy.tracking import utils
from dipy.tracking.streamline import select_by_rois
from dipy.tracking.local_tracking import LocalTracking, \
ParticleFilteringTracking
from dipy.direction import (ProbabilisticDirectionGetter,
ClosestPeakDirectionGetter,
DeterministicMaximumDirectionGetter)
from nilearn.image import index_img
from pynets.dmri.track import prep_tissues
from nibabel.streamlines.array_sequence import ArraySequence
from nipype.utils.filemanip import copyfile, fname_presuffix
import uuid
from time import strftime
run_uuid = f"{strftime('%Y%m%d_%H%M%S')}_{uuid.uuid4()}"
recon_path_tmp_path = fname_presuffix(
recon_path,
suffix=f"_{'_'.join([str(i) for i in step_curv_combinations])}_"
f"{run_uuid}",
newpath=cache_dir)
copyfile(recon_path, recon_path_tmp_path, copy=True, use_hardlink=False)
tissues4d_tmp_path = fname_presuffix(
tissues4d,
suffix=f"_{'_'.join([str(i) for i in step_curv_combinations])}_"
f"{run_uuid}",
newpath=cache_dir)
copyfile(tissues4d, tissues4d_tmp_path, copy=True, use_hardlink=False)
if waymask is not None:
waymask_tmp_path = fname_presuffix(
waymask,
suffix=f"_{'_'.join([str(i) for i in step_curv_combinations])}_"
f"{run_uuid}",
newpath=cache_dir)
copyfile(waymask, waymask_tmp_path, copy=True, use_hardlink=False)
else:
waymask_tmp_path = None
tissue_img = nib.load(tissues4d_tmp_path)
# Order:
B0_mask = index_img(tissue_img, 0)
atlas_img = index_img(tissue_img, 1)
seeding_mask = index_img(tissue_img, 2)
t1w2dwi = index_img(tissue_img, 3)
gm_in_dwi = index_img(tissue_img, 4)
vent_csf_in_dwi = index_img(tissue_img, 5)
wm_in_dwi = index_img(tissue_img, 6)
tiss_classifier = prep_tissues(t1w2dwi, gm_in_dwi, vent_csf_in_dwi,
wm_in_dwi, tiss_class, B0_mask)
B0_mask_data = np.asarray(B0_mask.dataobj).astype("bool")
seeding_mask = np.asarray(
seeding_mask.dataobj).astype("bool").astype("int16")
with h5py.File(recon_path_tmp_path, 'r+') as hf:
mod_fit = hf['reconstruction'][:].astype('float32')
print("%s%s" % ("Curvature: ", step_curv_combinations[1]))
# Instantiate DirectionGetter
if directget.lower() in ["probabilistic", "prob"]:
dg = ProbabilisticDirectionGetter.from_shcoeff(
mod_fit,
max_angle=float(step_curv_combinations[1]),
sphere=sphere,
min_separation_angle=min_separation_angle,
)
elif directget.lower() in ["closestpeaks", "cp"]:
dg = ClosestPeakDirectionGetter.from_shcoeff(
mod_fit,
max_angle=float(step_curv_combinations[1]),
sphere=sphere,
min_separation_angle=min_separation_angle,
)
elif directget.lower() in ["deterministic", "det"]:
maxcrossing = 1
dg = DeterministicMaximumDirectionGetter.from_shcoeff(
mod_fit,
max_angle=float(step_curv_combinations[1]),
sphere=sphere,
min_separation_angle=min_separation_angle,
)
else:
raise ValueError("ERROR: No valid direction getter(s) specified.")
print("%s%s" % ("Step: ", step_curv_combinations[0]))
# Perform wm-gm interface seeding, using n_seeds at a time
seeds = utils.random_seeds_from_mask(
seeding_mask > 0,
seeds_count=n_seeds_per_iter,
seed_count_per_voxel=False,
affine=np.eye(4),
)
if len(seeds) < min_seeds:
print(
UserWarning(
f"<{min_seeds} valid seed points found in wm-gm interface..."))
return None
# print(seeds)
# Perform tracking
if track_type == "local":
streamline_generator = LocalTracking(dg,
tiss_classifier,
seeds,
np.eye(4),
max_cross=int(maxcrossing),
maxlen=int(max_length),
step_size=float(
step_curv_combinations[0]),
fixedstep=False,
return_all=True,
random_seed=42)
elif track_type == "particle":
streamline_generator = ParticleFilteringTracking(
dg,
tiss_classifier,
seeds,
np.eye(4),
max_cross=int(maxcrossing),
step_size=float(step_curv_combinations[0]),
maxlen=int(max_length),
pft_back_tracking_dist=pft_back_tracking_dist,
pft_front_tracking_dist=pft_front_tracking_dist,
pft_max_trial=20,
particle_count=particle_count,
return_all=True,
random_seed=42)
else:
raise ValueError("ERROR: No valid tracking method(s) specified.")
# Filter resulting streamlines by those that stay entirely
# inside the brain
try:
roi_proximal_streamlines = utils.target(streamline_generator,
np.eye(4),
B0_mask_data.astype('bool'),
include=True)
except BaseException:
print('No streamlines found inside the brain! ' 'Check registrations.')
return None
del mod_fit, seeds, tiss_classifier, streamline_generator, \
B0_mask_data, seeding_mask, dg
B0_mask.uncache()
atlas_img.uncache()
t1w2dwi.uncache()
gm_in_dwi.uncache()
vent_csf_in_dwi.uncache()
wm_in_dwi.uncache()
atlas_img.uncache()
tissue_img.uncache()
gc.collect()
# Filter resulting streamlines by roi-intersection
# characteristics
atlas_data = np.array(atlas_img.dataobj).astype("uint16")
# Build mask vector from atlas for later roi filtering
parcels = []
i = 0
intensities = [i for i in np.unique(atlas_data) if i != 0]
for roi_val in intensities:
parcels.append(atlas_data == roi_val)
i += 1
parcel_vec = list(np.ones(len(parcels)).astype("bool"))
try:
roi_proximal_streamlines = \
nib.streamlines.array_sequence.ArraySequence(
select_by_rois(
roi_proximal_streamlines,
affine=np.eye(4),
rois=parcels,
include=parcel_vec,
mode="any",
tol=roi_neighborhood_tol,
)
)
print("%s%s" % ("Filtering by: \nNode intersection: ",
len(roi_proximal_streamlines)))
except BaseException:
print('No streamlines found to connect any parcels! '
'Check registrations.')
return None
try:
roi_proximal_streamlines = nib.streamlines. \
array_sequence.ArraySequence(
[
s for s in roi_proximal_streamlines
if len(s) >= float(min_length)
]
)
print(f"Minimum fiber length >{min_length}mm: "
f"{len(roi_proximal_streamlines)}")
except BaseException:
print('No streamlines remaining after minimal length criterion.')
return None
if waymask is not None and os.path.isfile(waymask_tmp_path):
waymask_data = np.asarray(
nib.load(waymask_tmp_path).dataobj).astype("bool")
try:
roi_proximal_streamlines = roi_proximal_streamlines[utils.near_roi(
roi_proximal_streamlines,
np.eye(4),
waymask_data,
tol=int(round(roi_neighborhood_tol * 0.50, 1)),
mode="all")]
print("%s%s" %
("Waymask proximity: ", len(roi_proximal_streamlines)))
del waymask_data
except BaseException:
print('No streamlines remaining in waymask\'s vacinity.')
return None
hf.close()
del parcels, atlas_data
tmp_files = [tissues4d_tmp_path, waymask_tmp_path, recon_path_tmp_path]
for j in tmp_files:
if j is not None:
if os.path.isfile(j):
os.system(f"rm -f {j} &")
if len(roi_proximal_streamlines) > 0:
return ArraySequence(
[s.astype("float32") for s in roi_proximal_streamlines])
else:
return None
def track_ensemble(dwi_data,
target_samples,
atlas_data_wm_gm_int,
parcels,
mod_fit,
tiss_classifier,
sphere,
directget,
curv_thr_list,
step_list,
track_type,
maxcrossing,
max_length,
roi_neighborhood_tol,
min_length,
waymask,
n_seeds_per_iter=100,
pft_back_tracking_dist=2,
pft_front_tracking_dist=1,
particle_count=15):
"""
Perform native-space ensemble tractography, restricted to a vector of ROI masks.
dwi_data : array
4D array of dwi data.
target_samples : int
Total number of streamline samples specified to generate streams.
atlas_data_wm_gm_int : array
3D int32 numpy array of atlas parcellation intensities from Nifti1Image in T1w-warped native diffusion space,
restricted to wm-gm interface.
parcels : list
List of 3D boolean numpy arrays of atlas parcellation ROI masks from a Nifti1Image in T1w-warped native
diffusion space.
mod : obj
Connectivity reconstruction model.
tiss_classifier : str
Tissue classification method.
sphere : obj
DiPy object for modeling diffusion directions on a sphere.
directget : str
The statistical approach to tracking. Options are: det (deterministic), closest (clos), boot (bootstrapped),
and prob (probabilistic).
curv_thr_list : list
List of integer curvature thresholds used to perform ensemble tracking.
step_list : list
List of float step-sizes used to perform ensemble tracking.
track_type : str
Tracking algorithm used (e.g. 'local' or 'particle').
maxcrossing : int
Maximum number if diffusion directions that can be assumed per voxel while tracking.
max_length : int
Maximum fiber length threshold in mm to restrict tracking.
roi_neighborhood_tol : float
Distance (in the units of the streamlines, usually mm). If any
coordinate in the streamline is within this distance from the center
of any voxel in the ROI, the filtering criterion is set to True for
this streamline, otherwise False. Defaults to the distance between
the center of each voxel and the corner of the voxel.
min_length : int
Minimum fiber length threshold in mm.
waymask : str
Path to a Nifti1Image in native diffusion space to constrain tractography.
n_seeds_per_iter : int
Number of seeds from which to initiate tracking for each unique ensemble combination.
By default this is set to 200.
particle_count
pft_back_tracking_dist : float
Distance in mm to back track before starting the particle filtering
tractography. The total particle filtering tractography distance is
equal to back_tracking_dist + front_tracking_dist. By default this is set to 2 mm.
pft_front_tracking_dist : float
Distance in mm to run the particle filtering tractography after the
the back track distance. The total particle filtering tractography
distance is equal to back_tracking_dist + front_tracking_dist. By
default this is set to 1 mm.
particle_count : int
Number of particles to use in the particle filter.
Returns
-------
streamlines : ArraySequence
DiPy list/array-like object of streamline points from tractography.
"""
from colorama import Fore, Style
from dipy.tracking import utils
from dipy.tracking.streamline import Streamlines, select_by_rois
from dipy.tracking.local_tracking import LocalTracking, ParticleFilteringTracking
from dipy.direction import ProbabilisticDirectionGetter, BootDirectionGetter, ClosestPeakDirectionGetter, DeterministicMaximumDirectionGetter
if waymask:
waymask_data = nib.load(waymask).get_fdata().astype('bool')
# Commence Ensemble Tractography
parcel_vec = list(np.ones(len(parcels)).astype('bool'))
streamlines = nib.streamlines.array_sequence.ArraySequence()
ix = 0
circuit_ix = 0
stream_counter = 0
while int(stream_counter) < int(target_samples):
for curv_thr in curv_thr_list:
print("%s%s" % ('Curvature: ', curv_thr))
# Instantiate DirectionGetter
if directget == 'prob':
dg = ProbabilisticDirectionGetter.from_shcoeff(
mod_fit, max_angle=float(curv_thr), sphere=sphere)
elif directget == 'boot':
dg = BootDirectionGetter.from_data(dwi_data,
mod_fit,
max_angle=float(curv_thr),
sphere=sphere)
elif directget == 'clos':
dg = ClosestPeakDirectionGetter.from_shcoeff(
mod_fit, max_angle=float(curv_thr), sphere=sphere)
elif directget == 'det':
dg = DeterministicMaximumDirectionGetter.from_shcoeff(
mod_fit, max_angle=float(curv_thr), sphere=sphere)
else:
raise ValueError(
'ERROR: No valid direction getter(s) specified.')
for step in step_list:
print("%s%s" % ('Step: ', step))
# Perform wm-gm interface seeding, using n_seeds at a time
seeds = utils.random_seeds_from_mask(
atlas_data_wm_gm_int > 0,
seeds_count=n_seeds_per_iter,
seed_count_per_voxel=False,
affine=np.eye(4))
if len(seeds) == 0:
raise RuntimeWarning(
'Warning: No valid seed points found in wm-gm interface...'
)
print(seeds)
# Perform tracking
if track_type == 'local':
streamline_generator = LocalTracking(
dg,
tiss_classifier,
seeds,
np.eye(4),
max_cross=int(maxcrossing),
maxlen=int(max_length),
step_size=float(step),
return_all=True)
elif track_type == 'particle':
streamline_generator = ParticleFilteringTracking(
dg,
tiss_classifier,
seeds,
np.eye(4),
max_cross=int(maxcrossing),
step_size=float(step),
maxlen=int(max_length),
pft_back_tracking_dist=pft_back_tracking_dist,
pft_front_tracking_dist=pft_front_tracking_dist,
particle_count=particle_count,
return_all=True)
else:
raise ValueError(
'ERROR: No valid tracking method(s) specified.')
# Filter resulting streamlines by roi-intersection characteristics
roi_proximal_streamlines = Streamlines(
select_by_rois(streamline_generator,
affine=np.eye(4),
rois=parcels,
include=parcel_vec,
mode='any',
tol=roi_neighborhood_tol))
print("%s%s" %
('Qualifying Streamlines by node intersection: ',
len(roi_proximal_streamlines)))
roi_proximal_streamlines = nib.streamlines.array_sequence.ArraySequence(
[
s for s in roi_proximal_streamlines
if len(s) > float(min_length)
])
print("%s%s" %
('Qualifying Streamlines by minimum length criterion: ',
len(roi_proximal_streamlines)))
if waymask:
roi_proximal_streamlines = roi_proximal_streamlines[
utils.near_roi(roi_proximal_streamlines,
np.eye(4),
waymask_data,
tol=roi_neighborhood_tol,
mode='any')]
print("%s%s" %
('Qualifying Streamlines by waymask proximity: ',
len(roi_proximal_streamlines)))
# Repeat process until target samples condition is met
ix = ix + 1
for s in roi_proximal_streamlines:
stream_counter = stream_counter + len(s)
streamlines.append(s)
if int(stream_counter) >= int(target_samples):
break
else:
continue
# Cleanup memory
del seeds, roi_proximal_streamlines, streamline_generator
del dg
circuit_ix = circuit_ix + 1
print(
"%s%s%s%s%s" %
('Completed hyperparameter circuit: ', circuit_ix,
'...\nCumulative Streamline Count: ', Fore.CYAN, stream_counter))
print(Style.RESET_ALL)
print('\n')
return streamlines
0, len(subjectSpaceTractCoords))]
# obtain that data array as bool
sphereNifti = WMA_pyFuncs.createSphere(testRadius, testCentroid,
testT1)
# add that and a True to the list vector for each
roisData.append(sphereNifti.get_fdata().astype(bool))
roisNifti.append(sphereNifti)
# randomly select include or exclude
include.append(bool(random.getrandbits(1)))
operations.append('any')
# start timing
t1_start = time.process_time()
# specify segmentation
dipySegmented1 = ut.near_roi(testTractogram.streamlines,
testT1.affine,
roisData[0],
mode='any')
dipySegmented2 = ut.near_roi(testTractogram.streamlines,
testT1.affine,
roisData[1],
mode='any')
#now we have to manually match the implicit logic of the wma Seg function
#both true
if np.all(include):
netDipySegmented = np.logical_and(dipySegmented1, dipySegmented2)
# 1 true 2 false
elif not include[0]:
netDipySegmented = np.logical_and(np.logical_not(dipySegmented1),
dipySegmented2)
#1 false and 2 True
elif not include[1]:
def track_ensemble(target_samples, atlas_data_wm_gm_int, parcels, mod_fit, tiss_classifier, sphere, directget,
curv_thr_list, step_list, track_type, maxcrossing, roi_neighborhood_tol, min_length, waymask,
B0_mask, max_length=1000, n_seeds_per_iter=500, pft_back_tracking_dist=2, pft_front_tracking_dist=1,
particle_count=15, min_separation_angle=20):
"""
Perform native-space ensemble tractography, restricted to a vector of ROI masks.
target_samples : int
Total number of streamline samples specified to generate streams.
atlas_data_wm_gm_int : array
3D int32 numpy array of atlas parcellation intensities from Nifti1Image in T1w-warped native diffusion space,
restricted to wm-gm interface.
parcels : list
List of 3D boolean numpy arrays of atlas parcellation ROI masks from a Nifti1Image in T1w-warped native
diffusion space.
mod : obj
Connectivity reconstruction model.
tiss_classifier : str
Tissue classification method.
sphere : obj
DiPy object for modeling diffusion directions on a sphere.
directget : str
The statistical approach to tracking. Options are: det (deterministic), closest (clos), boot (bootstrapped),
and prob (probabilistic).
curv_thr_list : list
List of integer curvature thresholds used to perform ensemble tracking.
step_list : list
List of float step-sizes used to perform ensemble tracking.
track_type : str
Tracking algorithm used (e.g. 'local' or 'particle').
maxcrossing : int
Maximum number if diffusion directions that can be assumed per voxel while tracking.
roi_neighborhood_tol : float
Distance (in the units of the streamlines, usually mm). If any
coordinate in the streamline is within this distance from the center
of any voxel in the ROI, the filtering criterion is set to True for
this streamline, otherwise False. Defaults to the distance between
the center of each voxel and the corner of the voxel.
min_length : int
Minimum fiber length threshold in mm.
waymask : str
Path to a Nifti1Image in native diffusion space to constrain tractography.
B0_mask : str
File path to B0 brain mask.
max_length : int
Maximum number of steps to restrict tracking.
n_seeds_per_iter : int
Number of seeds from which to initiate tracking for each unique ensemble combination.
By default this is set to 200.
particle_count
pft_back_tracking_dist : float
Distance in mm to back track before starting the particle filtering
tractography. The total particle filtering tractography distance is
equal to back_tracking_dist + front_tracking_dist. By default this is set to 2 mm.
pft_front_tracking_dist : float
Distance in mm to run the particle filtering tractography after the
the back track distance. The total particle filtering tractography
distance is equal to back_tracking_dist + front_tracking_dist. By
default this is set to 1 mm.
particle_count : int
Number of particles to use in the particle filter.
min_separation_angle : float
The minimum angle between directions [0, 90].
Returns
-------
streamlines : ArraySequence
DiPy list/array-like object of streamline points from tractography.
References
----------
.. [1] Takemura, H., Caiafa, C. F., Wandell, B. A., & Pestilli, F. (2016).
Ensemble Tractography. PLoS Computational Biology.
https://doi.org/10.1371/journal.pcbi.1004692
"""
import gc
import time
from colorama import Fore, Style
from dipy.tracking import utils
from dipy.tracking.streamline import Streamlines, select_by_rois
from dipy.tracking.local_tracking import LocalTracking, ParticleFilteringTracking
from dipy.direction import (ProbabilisticDirectionGetter, ClosestPeakDirectionGetter,
DeterministicMaximumDirectionGetter)
start = time.time()
B0_mask_data = nib.load(B0_mask).get_fdata()
if waymask:
waymask_data = np.asarray(nib.load(waymask).dataobj).astype('bool')
# Commence Ensemble Tractography
parcel_vec = list(np.ones(len(parcels)).astype('bool'))
streamlines = nib.streamlines.array_sequence.ArraySequence()
circuit_ix = 0
stream_counter = 0
while int(stream_counter) < int(target_samples):
for curv_thr in curv_thr_list:
print("%s%s" % ('Curvature: ', curv_thr))
# Instantiate DirectionGetter
if directget == 'prob':
dg = ProbabilisticDirectionGetter.from_shcoeff(mod_fit, max_angle=float(curv_thr), sphere=sphere,
min_separation_angle=min_separation_angle)
elif directget == 'clos':
dg = ClosestPeakDirectionGetter.from_shcoeff(mod_fit, max_angle=float(curv_thr), sphere=sphere,
min_separation_angle=min_separation_angle)
elif directget == 'det':
dg = DeterministicMaximumDirectionGetter.from_shcoeff(mod_fit, max_angle=float(curv_thr), sphere=sphere,
min_separation_angle=min_separation_angle)
else:
raise ValueError('ERROR: No valid direction getter(s) specified.')
for step in step_list:
print("%s%s" % ('Step: ', step))
# Perform wm-gm interface seeding, using n_seeds at a time
seeds = utils.random_seeds_from_mask(atlas_data_wm_gm_int > 0, seeds_count=n_seeds_per_iter,
seed_count_per_voxel=False, affine=np.eye(4))
if len(seeds) == 0:
raise RuntimeWarning('Warning: No valid seed points found in wm-gm interface...')
# print(seeds)
# Perform tracking
if track_type == 'local':
streamline_generator = LocalTracking(dg, tiss_classifier, seeds, np.eye(4),
max_cross=int(maxcrossing), maxlen=int(max_length),
step_size=float(step), fixedstep=False, return_all=True)
elif track_type == 'particle':
streamline_generator = ParticleFilteringTracking(dg, tiss_classifier, seeds, np.eye(4),
max_cross=int(maxcrossing),
step_size=float(step),
maxlen=int(max_length),
pft_back_tracking_dist=pft_back_tracking_dist,
pft_front_tracking_dist=pft_front_tracking_dist,
particle_count=particle_count,
return_all=True)
else:
raise ValueError('ERROR: No valid tracking method(s) specified.')
# Filter resulting streamlines by those that stay entirely inside the brain
roi_proximal_streamlines = utils.target(streamline_generator, np.eye(4), B0_mask_data,
include=True)
# Filter resulting streamlines by roi-intersection characteristics
roi_proximal_streamlines = Streamlines(select_by_rois(roi_proximal_streamlines, affine=np.eye(4),
rois=parcels, include=parcel_vec,
mode='both_end',
tol=roi_neighborhood_tol))
print("%s%s" % ('Filtering by: \nnode intersection: ', len(roi_proximal_streamlines)))
if str(min_length) != '0':
roi_proximal_streamlines = nib.streamlines.array_sequence.ArraySequence([s for s in
roi_proximal_streamlines
if len(s) >=
float(min_length)])
print("%s%s" % ('Minimum length criterion: ', len(roi_proximal_streamlines)))
if waymask:
roi_proximal_streamlines = roi_proximal_streamlines[utils.near_roi(roi_proximal_streamlines,
np.eye(4),
waymask_data,
tol=roi_neighborhood_tol,
mode='any')]
print("%s%s" % ('Waymask proximity: ', len(roi_proximal_streamlines)))
out_streams = [s.astype('float32') for s in roi_proximal_streamlines]
streamlines.extend(out_streams)
stream_counter = stream_counter + len(out_streams)
# Cleanup memory
del seeds, roi_proximal_streamlines, streamline_generator, out_streams
gc.collect()
del dg
circuit_ix = circuit_ix + 1
print("%s%s%s%s%s%s" % ('Completed Hyperparameter Circuit: ', circuit_ix,
'\nCumulative Streamline Count: ', Fore.CYAN, stream_counter, "\n"))
print(Style.RESET_ALL)
print('Tracking Complete:\n', str(time.time() - start))
return streamlines
def run_tracking(step_curv_combinations, recon_path, n_seeds_per_iter,
directget, maxcrossing, max_length, pft_back_tracking_dist,
pft_front_tracking_dist, particle_count, roi_neighborhood_tol,
waymask, min_length, track_type, min_separation_angle, sphere,
tiss_class, tissues4d, cache_dir):
import gc
import os
import h5py
from dipy.tracking import utils
from dipy.tracking.streamline import select_by_rois
from dipy.tracking.local_tracking import LocalTracking, \
ParticleFilteringTracking
from dipy.direction import (ProbabilisticDirectionGetter,
ClosestPeakDirectionGetter,
DeterministicMaximumDirectionGetter)
from nilearn.image import index_img
from pynets.dmri.track import prep_tissues
from nibabel.streamlines.array_sequence import ArraySequence
from nipype.utils.filemanip import copyfile, fname_presuffix
recon_path_tmp_path = fname_presuffix(recon_path,
suffix=f"_{step_curv_combinations}",
newpath=cache_dir)
copyfile(recon_path, recon_path_tmp_path, copy=True, use_hardlink=False)
if waymask is not None:
waymask_tmp_path = fname_presuffix(waymask,
suffix=f"_{step_curv_combinations}",
newpath=cache_dir)
copyfile(waymask, waymask_tmp_path, copy=True, use_hardlink=False)
else:
waymask_tmp_path = None
tissue_img = nib.load(tissues4d)
# Order:
B0_mask = index_img(tissue_img, 0)
atlas_img = index_img(tissue_img, 1)
atlas_data_wm_gm_int = index_img(tissue_img, 2)
t1w2dwi = index_img(tissue_img, 3)
gm_in_dwi = index_img(tissue_img, 4)
vent_csf_in_dwi = index_img(tissue_img, 5)
wm_in_dwi = index_img(tissue_img, 6)
tiss_classifier = prep_tissues(t1w2dwi, gm_in_dwi, vent_csf_in_dwi,
wm_in_dwi, tiss_class, B0_mask)
B0_mask_data = np.asarray(B0_mask.dataobj).astype("bool")
atlas_data = np.array(atlas_img.dataobj).astype("uint16")
atlas_data_wm_gm_int_data = np.asarray(
atlas_data_wm_gm_int.dataobj).astype("bool").astype("int16")
# Build mask vector from atlas for later roi filtering
parcels = []
i = 0
intensities = [i for i in np.unique(atlas_data) if i != 0]
for roi_val in intensities:
parcels.append(atlas_data == roi_val)
i += 1
del atlas_data
parcel_vec = list(np.ones(len(parcels)).astype("bool"))
with h5py.File(recon_path_tmp_path, 'r+') as hf:
mod_fit = hf['reconstruction'][:].astype('float32')
hf.close()
print("%s%s" % ("Curvature: ", step_curv_combinations[1]))
# Instantiate DirectionGetter
if directget == "prob" or directget == "probabilistic":
dg = ProbabilisticDirectionGetter.from_shcoeff(
mod_fit,
max_angle=float(step_curv_combinations[1]),
sphere=sphere,
min_separation_angle=min_separation_angle,
)
elif directget == "clos" or directget == "closest":
dg = ClosestPeakDirectionGetter.from_shcoeff(
mod_fit,
max_angle=float(step_curv_combinations[1]),
sphere=sphere,
min_separation_angle=min_separation_angle,
)
elif directget == "det" or directget == "deterministic":
maxcrossing = 1
dg = DeterministicMaximumDirectionGetter.from_shcoeff(
mod_fit,
max_angle=float(step_curv_combinations[1]),
sphere=sphere,
min_separation_angle=min_separation_angle,
)
else:
raise ValueError("ERROR: No valid direction getter(s) specified.")
print("%s%s" % ("Step: ", step_curv_combinations[0]))
# Perform wm-gm interface seeding, using n_seeds at a time
seeds = utils.random_seeds_from_mask(
atlas_data_wm_gm_int_data > 0,
seeds_count=n_seeds_per_iter,
seed_count_per_voxel=False,
affine=np.eye(4),
)
if len(seeds) == 0:
print(
UserWarning("No valid seed points found in wm-gm "
"interface..."))
return None
# print(seeds)
# Perform tracking
if track_type == "local":
streamline_generator = LocalTracking(
dg,
tiss_classifier,
seeds,
np.eye(4),
max_cross=int(maxcrossing),
maxlen=int(max_length),
step_size=float(step_curv_combinations[0]),
fixedstep=False,
return_all=True,
)
elif track_type == "particle":
streamline_generator = ParticleFilteringTracking(
dg,
tiss_classifier,
seeds,
np.eye(4),
max_cross=int(maxcrossing),
step_size=float(step_curv_combinations[0]),
maxlen=int(max_length),
pft_back_tracking_dist=pft_back_tracking_dist,
pft_front_tracking_dist=pft_front_tracking_dist,
particle_count=particle_count,
return_all=True,
)
else:
try:
raise ValueError("ERROR: No valid tracking method(s) specified.")
except ValueError:
import sys
sys.exit(0)
# Filter resulting streamlines by those that stay entirely
# inside the brain
try:
roi_proximal_streamlines = utils.target(streamline_generator,
np.eye(4),
B0_mask_data,
include=True)
except BaseException:
print('No streamlines found inside the brain! ' 'Check registrations.')
return None
# Filter resulting streamlines by roi-intersection
# characteristics
try:
roi_proximal_streamlines = \
nib.streamlines.array_sequence.ArraySequence(
select_by_rois(
roi_proximal_streamlines,
affine=np.eye(4),
rois=parcels,
include=parcel_vec,
mode="%s" % ("any" if waymask is not None else
"both_end"),
tol=roi_neighborhood_tol,
)
)
print("%s%s" % ("Filtering by: \nNode intersection: ",
len(roi_proximal_streamlines)))
except BaseException:
print('No streamlines found to connect any parcels! '
'Check registrations.')
return None
try:
roi_proximal_streamlines = nib.streamlines. \
array_sequence.ArraySequence(
[
s for s in roi_proximal_streamlines
if len(s) >= float(min_length)
]
)
print(f"Minimum fiber length >{min_length}mm: "
f"{len(roi_proximal_streamlines)}")
except BaseException:
print('No streamlines remaining after minimal length criterion.')
return None
if waymask is not None and os.path.isfile(waymask_tmp_path):
from nilearn.image import math_img
mask = math_img("img > 0.0075", img=nib.load(waymask_tmp_path))
waymask_data = np.asarray(mask.dataobj).astype("bool")
try:
roi_proximal_streamlines = roi_proximal_streamlines[utils.near_roi(
roi_proximal_streamlines,
np.eye(4),
waymask_data,
tol=roi_neighborhood_tol,
mode="all")]
print("%s%s" %
("Waymask proximity: ", len(roi_proximal_streamlines)))
except BaseException:
print('No streamlines remaining in waymask\'s vacinity.')
return None
out_streams = [s.astype("float32") for s in roi_proximal_streamlines]
del dg, seeds, roi_proximal_streamlines, streamline_generator, \
atlas_data_wm_gm_int_data, mod_fit, B0_mask_data
os.remove(recon_path_tmp_path)
gc.collect()
try:
return ArraySequence(out_streams)
except BaseException:
return None