def edit_actors(self, actors, **kwargs): """ edits a list of actors (e.g. render as wireframe or solid) :param actors: list of actors :param **kwargs: """ if not isinstance(actors, list): actors = [actors] for actor in actors: actors_funcs.edit_actor(actor, **kwargs)
def test_edit_actors(scene):
actor = scene.add_brain_regions("TH")
edit_actor(
actor,
wireframe=True,
color="red",
line=True,
line_kwargs={"lw": 2},
upsample=True,
downsample=False,
)
edit_actor(
actor,
solid=True,
downsample=True,
smooth=True,
)
def get_brain_regions(
self,
brain_regions,
add_labels=False,
colors=None,
use_original_color=True,
alpha=None,
hemisphere=None,
verbose=False,
**kwargs,
):
"""
Gets brain regions meshes for rendering
Many parameters can be passed to specify how the regions should be rendered.
To treat a subset of the rendered regions, specify which regions are VIP.
Use the kwargs to specify more detailes on how the regins should be rendered (e.g. wireframe look)
:param brain_regions: str list of acronyms of brain regions
:param colors: str, color of rendered brian regions (Default value = None)
:param use_original_color: bool, if True, the allen's default color for the region is used. (Default value = False)
:param alpha: float, transparency of the rendered brain regions (Default value = None)
:param hemisphere: str (Default value = None)
:param add_labels: bool (default False). If true a label is added to each regions' actor. The label is visible when hovering the mouse over the actor
:param **kwargs: used to determine a bunch of thigs, including the look and location of lables from scene.add_labels
"""
# Parse arguments
if alpha is None:
alpha = brainrender.DEFAULT_STRUCTURE_ALPHA
# check that we have a list
if not isinstance(brain_regions, list):
brain_regions = [brain_regions]
# check the colors input is correct
if colors is not None:
if isinstance(colors, (list, tuple)):
if not len(colors) == len(brain_regions):
raise ValueError(
"when passing colors as a list, the number of colors must match the number of brain regions"
)
for col in colors:
if not check_colors(col):
raise ValueError(
"Invalide colors in input: {}".format(col))
else:
if not check_colors(colors):
raise ValueError(
"Invalide colors in input: {}".format(colors))
colors = [colors for i in range(len(brain_regions))]
# loop over all brain regions
actors = {}
for i, region in enumerate(brain_regions):
if verbose:
print("Rendering: ({})".format(region))
# get the structure and check if we need to download the object file
if region not in self.lookup_df.acronym.values:
print(
f"The region {region} doesn't seem to belong to the atlas being used: {self.atlas_name}. Skipping"
)
continue
# Get path to .obj file
obj_file = str(self.meshfile_from_structure(region))
# check which color to assign to the brain region
if use_original_color:
color = [
x / 255
for x in self._get_from_structure(region, "rgb_triplet")
]
else:
if colors is None:
color = brainrender.DEFAULT_STRUCTURE_COLOR
elif isinstance(colors, list):
color = colors[i]
else:
color = colors
# Load the object file as a mesh and store the actor
if hemisphere is not None:
if (hemisphere.lower() == "left"
or hemisphere.lower() == "right"):
obj = self.get_region_unilateral(region,
hemisphere=hemisphere,
color=color,
alpha=alpha)
else:
raise ValueError(
f"Invalid hemisphere argument: {hemisphere}")
else:
obj = load_mesh_from_file(obj_file, color=color, alpha=alpha)
if obj is not None:
actors_funcs.edit_actor(obj, **kwargs)
actors[region] = obj
else:
print(
f"Something went wrong while loading mesh data for {region}, skipping."
)
return actors
def get_brain_regions(self, brain_regions, VIP_regions=None, VIP_color=None,
add_labels=False,
colors=None, use_original_color=True,
alpha=None, hemisphere=None, verbose=False, **kwargs):
"""
Gets brain regions meshes for rendering
Many parameters can be passed to specify how the regions should be rendered.
To treat a subset of the rendered regions, specify which regions are VIP.
Use the kwargs to specify more detailes on how the regins should be rendered (e.g. wireframe look)
:param brain_regions: str list of acronyms of brain regions
:param VIP_regions: if a list of brain regions are passed, these are rendered differently compared to those in brain_regions (Default value = None)
:param VIP_color: if passed, this color is used for the VIP regions (Default value = None)
:param colors: str, color of rendered brian regions (Default value = None)
:param use_original_color: bool, if True, the allen's default color for the region is used. (Default value = False)
:param alpha: float, transparency of the rendered brain regions (Default value = None)
:param hemisphere: str (Default value = None)
:param add_labels: bool (default False). If true a label is added to each regions' actor. The label is visible when hovering the mouse over the actor
:param **kwargs: used to determine a bunch of thigs, including the look and location of lables from scene.add_labels
"""
# Check that the atlas has brain regions data
if self.region_acronyms is None:
print(f"The atlas {self.atlas_name} has no brain regions data")
return
# Parse arguments
if VIP_regions is None:
VIP_regions = brainrender.DEFAULT_VIP_REGIONS
if VIP_color is None:
VIP_color = brainrender.DEFAULT_VIP_COLOR
if alpha is None:
_alpha = brainrender.DEFAULT_STRUCTURE_ALPHA
else: _alpha = alpha
# check that we have a list
if not isinstance(brain_regions, list):
brain_regions = [brain_regions]
# check the colors input is correct
if colors is not None:
if isinstance(colors[0], (list, tuple)):
if not len(colors) == len(brain_regions):
raise ValueError("when passing colors as a list, the number of colors must match the number of brain regions")
for col in colors:
if not check_colors(col): raise ValueError("Invalide colors in input: {}".format(col))
else:
if not check_colors(colors): raise ValueError("Invalide colors in input: {}".format(colors))
colors = [colors for i in range(len(brain_regions))]
# loop over all brain regions
actors = {}
for i, region in enumerate(brain_regions):
self._check_valid_region_arg(region)
if region in self.ignore_regions: continue
if verbose: print("Rendering: ({})".format(region))
# get the structure and check if we need to download the object file
if region not in self.region_acronyms:
print(f"The region {region} doesn't seem to belong to the atlas being used: {self.atlas_name}. Skipping")
continue
obj_file = os.path.join(self.meshes_folder, "{}.{}".format(region, self.mesh_format))
if not self._check_obj_file(region, obj_file):
print("Could not render {}, maybe we couldn't get the mesh?".format(region))
continue
# check which color to assign to the brain region
if use_original_color:
color = [x/255 for x in self.get_region_color(region)]
else:
if region in VIP_regions:
color = VIP_color
else:
if colors is None:
color = brainrender.DEFAULT_STRUCTURE_COLOR
elif isinstance(colors, list):
color = colors[i]
else:
color = colors
if region in VIP_regions:
alpha = 1
else:
alpha = _alpha
# Load the object file as a mesh and store the actor
if hemisphere is not None:
if hemisphere.lower() == "left" or hemisphere.lower() == "right":
obj = self.get_region_unilateral(region, hemisphere=hemisphere, color=color, alpha=alpha)
else:
raise ValueError(f'Invalid hemisphere argument: {hemisphere}')
else:
obj = load(obj_file, c=color, alpha=alpha)
if obj is not None:
actors_funcs.edit_actor(obj, **kwargs)
actors[region] = obj
else:
print(f"Something went wrong while loading mesh data for {region}")
return actors