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

def __init__(self, path):

def resolution(self):

Make resolution more accessible from class.

def hierarchy(self):

Returns a Treelib.tree object with structures hierarchy.

def lookup_df(self):

Returns a dataframe with id, acronym and name for each structure.

def reference(self):

def annotation(self):

def hemispheres(self):

def hemisphere_from_coords(self, coords, microns=False,
    as_string=False):

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

def structure_from_coords(self, coords, microns=False,
    as_acronym=False, hierarchy_lev=None):

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

def _get_from_structure(self, structure, key):

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

def mesh_from_structure(self, structure):

def meshfile_from_structure(self, structure):

def root_mesh(self):

def root_meshfile(self):

def _idx_from_coords(self, coords, microns):

def get_structure_ancestors(self, structure):

Returns a list of acronyms for all
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ancestors of a given structure

def get_structure_descendants(self, structure):

Returns a list of acronyms for all
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descendants of a given structure