def test_orient2rgb():
e2 = [0.70710678, 0, 0, 0, 0.70710678, 0]
v = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
v2 = np.array([1, 0, 0, 0, 1, 0])
npt.assert_equal(colormap.orient2rgb(v), v)
npt.assert_almost_equal(colormap.orient2rgb(v2), e2)
npt.assert_raises(IOError, colormap.orient2rgb, np.array(1))
def _orientation_colors(points, cmap='rgb_standard'):
"""
Parameters
----------
points : (N, 3) array or ndarray
points coordinates array.
cmap : string ('rgb_standard', 'boys_standard'), optional
colormap.
Returns
-------
colors_list : ndarray
list of Kx3 colors. Where K is the number of lines.
"""
if cmap.lower() == 'rgb_standard':
col_list = [
orient2rgb(points[i + 1] - points[i])
for i in range(0, len(points), 2)
]
elif cmap.lower() == 'boys_standard':
col_list = [
boys2rgb(points[i + 1] - points[i])
for i in range(0, len(points), 2)
]
else:
raise ValueError("Invalid colormap. The only available options are "
"'rgb_standard' and 'boys_standard'.")
return np.asarray(col_list)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
# Make sure the colors are consistent between executions
if args.random_coloring is not None:
random.seed(int(args.random_coloring))
# Handle bundle filenames. 3 cases are possible:
# A list of files was passed as arguments
# A directory was passed as argument
# A single-file or path containing wildcard was specified
bundle_filenames = args.in_bundles
if len(args.in_bundles) == 1:
# If only one file is specified, it may be a whole folder or
# a single file, or a wildcard usage
in_path = args.in_bundles[0]
if os.path.isdir(in_path):
# Load the folder
bundle_filenames = [
os.path.join(in_path, f) for f in os.listdir(in_path)
]
else:
# Load the file/wildcard
bundle_filenames = glob.glob(in_path)
assert_inputs_exist(parser, bundle_filenames, args.color_dict)
scene = window.Scene()
scene.background(tuple(map(int, args.background)))
def subsample(list_obj):
""" Lazily subsample a list
"""
return list(itertools.islice(list_obj, 0, None, args.subsample))
# Load each bundle, subsample and downsample it if needed
for filename in bundle_filenames:
try:
# Lazy-load streamlines to minimize ram usage
tractogram_gen = nib.streamlines.load(filename,
lazy_load=True).tractogram
streamlines_gen = tractogram_gen.streamlines
except ValueError:
# Not a file loadable by nibabel's streamline API
print('Skipping {}'.format(filename))
continue
# Actually load streamlines according to the subsample argument
streamlines = subsample(streamlines_gen)
if args.downsample:
streamlines = set_number_of_points(streamlines, args.downsample)
# Handle bundle colors. Either assign a random bright color to each
# bundle, or load a color specific to each bundle, or let the bundles
# be colored according to their local orientation
if args.random_coloring:
color = random_rgb()
elif args.color_dict:
with open(args.color_dict) as json_file:
# Color dictionary
color_dict = json.load(json_file)
# Extract filenames to compare against the color dictionary
basename = os.path.splitext(os.path.basename(filename))[0]
# Load colors
color = color_dict[basename] \
if basename in color_dict.keys() \
else color_dict['default']
elif args.color_from_streamlines:
color = subsample(tractogram_gen.data_per_streamline[
args.color_from_streamlines])
elif args.color_from_points:
color = subsample(
tractogram_gen.data_per_point[args.color_from_points])
elif args.uniform_coloring: # Assign uniform coloring to streamlines
color = tuple(map(int, args.uniform_coloring))
elif args.local_coloring: # Compute coloring from local orientations
# Compute segment orientation
diff = [np.diff(list(s), axis=0) for s in streamlines]
# Repeat first segment so that the number of segments matches
# the number of points
diff = [[d[0]] + list(d) for d in diff]
# Flatten the list of segments
orientations = np.asarray([o for d in diff for o in d])
# Turn the segments into colors
color = colormap.orient2rgb(orientations)
else: # Streamline color will depend on the streamlines' endpoints.
color = None
# TODO: Coloring from a volume of local orientations
line_actor = streamline_actor[args.shape](streamlines,
colors=color,
linewidth=args.width)
scene.add(line_actor)
# If there's actually streamlines to display
if len(bundle_filenames):
# Showtime !
showm = window.ShowManager(scene, reset_camera=True)
showm.initialize()
showm.start()