- Base
__init__[#18]get_plane_at_point[#26]get_sagittal_plane[#42]get_horizontal_plane[#69]get_coronal_plane[#96]get_region_CenterOfMass[#124]_get_structure_mesh[#167]get_brain_regions[#171]get_structure_ancestors[#286]get_structure_descendants[#328]get_structure_parent[#333]get_region_unilateral[#359]mirror_point_across_hemispheres[#398]get_colors_from_coordinates[#403]
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def __init__(self):
docstring:
no docstring
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def get_plane_at_point(self, pos, norm, sx, sy, color='lightgray',
alpha=0.25, **kwargs):
docstring:
Returns a plane going through a point at pos, oriented
orthogonally to the vector norm and of width and height
sx, sy.
:param pos: 3-tuple or list with x,y,z, coords of point the plane goes
through
:param sx, sy: int, width and height of the plane
:param norm: 3-tuple or list with 3d vector the plane is orthogonal to
:param color, alpha: plane color and transparency
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def get_sagittal_plane(self, pos=None, **kwargs):
docstring:
Creates a Plane actor centered at the midpoint of root (or a user
given locatin)
and oriented along the sagittal axis
:param pos: if not None, passe a list of 3 xyz defining the position
of the
point the plane goes through.
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def get_horizontal_plane(self, pos=None, **kwargs):
docstring:
Creates a Plane actor centered at the midpoint of root (or a user
given locatin)
and oriented along the horizontal axis
:param pos: if not None, passe a list of 3 xyz defining the position
of the
point the plane goes through.
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def get_coronal_plane(self, pos=None, **kwargs):
docstring:
Creates a Plane actor centered at the midpoint of root (or a user
given locatin)
and oriented along the coronal axis
:param pos: if not None, passe a list of 3 xyz defining the position
of the
point the plane goes through.
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def get_region_CenterOfMass(self, regions, unilateral=True,
hemisphere='right'):
docstring:
Get the center of mass of the 3d mesh of one or multiple brain
regions.
:param regions: str, list of brain regions acronyms
:param unilateral: bool, if True, the CoM is relative to one
hemisphere (Default value = True)
:param hemisphere: str, if unilteral=True, specifies which hemisphere
to use ['left' or 'right'] (Default value = "right")
:returns: coms = {list, dict} -- [if only one regions is passed, then
just returns the CoM coordinates for that region.
If a list is passed then a dictionary is returned. ]
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def _get_structure_mesh(self, acronym, **kwargs):
docstring:
no docstring
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def get_brain_regions(self, brain_regions, add_labels=False,
colors=None, use_original_color=True, alpha=None, hemisphere=None,
verbose=False, **kwargs):
docstring:
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
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def get_structure_ancestors(self, regions, ancestors=True,
descendants=False):
docstring:
Get's the ancestors of the region(s) passed as arguments
:param regions: str, list of str with acronums of regions of interest
:param ancestors: if True, returns the ancestors of the region
(Default value = True)
:param descendants: if True, returns the descendants of the region
(Default value = False)
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def get_structure_descendants(self, regions):
docstring:
no docstring
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def get_structure_parent(self, acronyms):
docstring:
Gets the parent of a brain region (or list of regions) from the
hierarchical structure of the
Allen Brain Atals.
:param acronyms: list of acronyms of brain regions.
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def get_region_unilateral(self, region, hemisphere='both', color=None,
alpha=None):
docstring:
Regions meshes are loaded with both hemispheres' meshes by default.
This function splits them in two.
:param region: str, actors of brain region
:param hemisphere: str, which hemisphere to return ['left', 'right' or
'both'] (Default value = "both")
:param color: color of each side's mesh. (Default value = None)
:param alpha: transparency of each side's mesh. (Default value =
None)
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def mirror_point_across_hemispheres(self, point):
docstring:
no docstring
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def get_colors_from_coordinates(self, p0):
docstring:
Given a point or a list of points returns a list of colors where
each item is the color of the brain region each point is in