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bg-atlasapi
BG-AtlasAPI
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structure_tree_util
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utils
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core

Base class to handle atlases in BrainGlobe.
​
Parameters
----------
path : str or Path object
path to folder containing data info.

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def __init__(self, path):
  docstring:
no docstring

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def resolution(self):
  docstring:
Make resolution more accessible from class.

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def hierarchy(self):
  docstring:
Returns a Treelib.tree object with structures hierarchy.

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def lookup_df(self):
  docstring:
Returns a dataframe with id, acronym and name for each structure.

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def reference(self):
  docstring:
no docstring

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def annotation(self):
  docstring:
no docstring

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def hemispheres(self):
  docstring:
no docstring

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def hemisphere_from_coords(self, coords, microns=False,
as_string=False):
  docstring:
Get the hemisphere from a coordinate triplet.
​
Parameters
​
----------
​
coords : tuple or list or numpy array
​
Triplet of coordinates. Default in voxels, can be microns if
​
microns=True
​
microns : bool
​
If true, coordinates are interpreted in microns.
​
as_string : bool
​
If true, returns "left" or "right".
​
Returns
​
-------
​
int or string
​
Hemisphere label.

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def structure_from_coords(self, coords, microns=False,
as_acronym=False, hierarchy_lev=None):
  docstring:
Get the structure from a coordinate triplet.
​
Parameters
​
----------
​
coords : tuple or list or numpy array
​
Triplet of coordinates.
​
microns : bool
​
If true, coordinates are interpreted in microns.
​
as_acronym : bool
​
If true, the region acronym is returned.
​
hierarchy_lev : int or None
​
If specified, return parent node at thi hierarchy level.
​
Returns
​
-------
​
int or string
​
Structure containing the coordinates.

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def _get_from_structure(self, structure, key):
  docstring:
Internal interface to the structure dict. It support querying with a
​
single structure id or a list of ids.
​
Parameters
​
----------
​
structure : int or str or list
​
Valid id or acronym, or list if ids or acronyms.
​
key : str
​
Key for the Structure dictionary (eg "name" or "rgb_triplet").
​
Returns
​
-------
​
value or list of values
​
If structure is a list, returns list.

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def mesh_from_structure(self, structure):
  docstring:
no docstring

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def meshfile_from_structure(self, structure):
  docstring:
no docstring

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def root_mesh(self):
  docstring:
no docstring

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def root_meshfile(self):
  docstring:
no docstring

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def _idx_from_coords(self, coords, microns):
  docstring:
no docstring

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def get_structure_ancestors(self, structure):
  docstring:
Returns a list of acronyms for all
​
ancestors of a given structure

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def get_structure_descendants(self, structure):
  docstring:
Returns a list of acronyms for all
​
descendants of a given structure
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structure_tree_util
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Contents
Atlas
__init__ [#28]
resolution [#57]
hierarchy [#63]
lookup_df [#71]
reference [#85]
annotation [#91]
hemispheres [#97]
hemisphere_from_coords [#122]
structure_from_coords [#148]
_get_from_structure [#183]
mesh_from_structure [#205]
meshfile_from_structure [#208]
root_mesh [#211]
root_meshfile [#214]
_idx_from_coords [#217]
get_structure_ancestors [#224]
get_structure_descendants [#235]