Atlas
Base class to handle atlases in BrainGlobe.Parameters----------path : str or Path objectpath to folder containing data info.
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def __init__(self, path):
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no docstring
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def resolution(self):
docstring:
Make resolution more accessible from class.
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def hierarchy(self):
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Returns a Treelib.tree object with structures hierarchy.
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def lookup_df(self):
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Returns a dataframe with id, acronym and name for each structure.
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def reference(self):
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no docstring
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def annotation(self):
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no docstring
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def hemispheres(self):
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no docstring
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def hemisphere_from_coords(self, coords, microns=False,as_string=False):
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Get the hemisphere from a coordinate triplet.Parameters----------coords : tuple or list or numpy arrayTriplet of coordinates. Default in voxels, can be microns ifmicrons=Truemicrons : boolIf true, coordinates are interpreted in microns.as_string : boolIf true, returns "left" or "right".Returns-------int or stringHemisphere label.
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def structure_from_coords(self, coords, microns=False,as_acronym=False, hierarchy_lev=None):
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Get the structure from a coordinate triplet.Parameters----------coords : tuple or list or numpy arrayTriplet of coordinates.microns : boolIf true, coordinates are interpreted in microns.as_acronym : boolIf true, the region acronym is returned.hierarchy_lev : int or NoneIf specified, return parent node at thi hierarchy level.Returns-------int or stringStructure containing the coordinates.
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def _get_from_structure(self, structure, key):
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Internal interface to the structure dict. It support querying with asingle structure id or a list of ids.Parameters----------structure : int or str or listValid id or acronym, or list if ids or acronyms.key : strKey for the Structure dictionary (eg "name" or "rgb_triplet").Returns-------value or list of valuesIf structure is a list, returns list.
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def mesh_from_structure(self, structure):
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no docstring
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def meshfile_from_structure(self, structure):
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no docstring
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def root_mesh(self):
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no docstring
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def root_meshfile(self):
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no docstring
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def _idx_from_coords(self, coords, microns):
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no docstring
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def get_structure_ancestors(self, structure):
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Returns a list of acronyms for allancestors of a given structure
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def get_structure_descendants(self, structure):
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Returns a list of acronyms for alldescendants of a given structure