brainglobe
Search…
core

Contents

Atlas

1
Base class to handle atlases in BrainGlobe.
2
3
Parameters
4
----------
5
path : str or Path object
6
path to folder containing data info.
Copied!

__init__ [#28]

Check the source code online
1
def __init__(self, path):
Copied!
  docstring:
no docstring

resolution [#57]

Check the source code online
1
def resolution(self):
Copied!
  docstring:
1
Make resolution more accessible from class.
Copied!

hierarchy [#63]

Check the source code online
1
def hierarchy(self):
Copied!
  docstring:
1
Returns a Treelib.tree object with structures hierarchy.
Copied!

lookup_df [#71]

Check the source code online
1
def lookup_df(self):
Copied!
  docstring:
1
Returns a dataframe with id, acronym and name for each structure.
Copied!

reference [#85]

Check the source code online
1
def reference(self):
Copied!
  docstring:
no docstring

annotation [#91]

Check the source code online
1
def annotation(self):
Copied!
  docstring:
no docstring

hemispheres [#97]

Check the source code online
1
def hemispheres(self):
Copied!
  docstring:
no docstring

hemisphere_from_coords [#122]

Check the source code online
1
def hemisphere_from_coords(self, coords, microns=False,
2
as_string=False):
Copied!
  docstring:
1
Get the hemisphere from a coordinate triplet.
2
3
Parameters
4
5
----------
6
7
coords : tuple or list or numpy array
8
9
Triplet of coordinates. Default in voxels, can be microns if
10
11
microns=True
12
13
microns : bool
14
15
If true, coordinates are interpreted in microns.
16
17
as_string : bool
18
19
If true, returns "left" or "right".
20
21
Returns
22
23
-------
24
25
int or string
26
27
Hemisphere label.
Copied!

structure_from_coords [#148]

Check the source code online
1
def structure_from_coords(self, coords, microns=False,
2
as_acronym=False, hierarchy_lev=None):
Copied!
  docstring:
1
Get the structure from a coordinate triplet.
2
3
Parameters
4
5
----------
6
7
coords : tuple or list or numpy array
8
9
Triplet of coordinates.
10
11
microns : bool
12
13
If true, coordinates are interpreted in microns.
14
15
as_acronym : bool
16
17
If true, the region acronym is returned.
18
19
hierarchy_lev : int or None
20
21
If specified, return parent node at thi hierarchy level.
22
23
Returns
24
25
-------
26
27
int or string
28
29
Structure containing the coordinates.
Copied!

_get_from_structure [#183]

Check the source code online
1
def _get_from_structure(self, structure, key):
Copied!
  docstring:
1
Internal interface to the structure dict. It support querying with a
2
3
single structure id or a list of ids.
4
5
Parameters
6
7
----------
8
9
structure : int or str or list
10
11
Valid id or acronym, or list if ids or acronyms.
12
13
key : str
14
15
Key for the Structure dictionary (eg "name" or "rgb_triplet").
16
17
Returns
18
19
-------
20
21
value or list of values
22
23
If structure is a list, returns list.
Copied!

mesh_from_structure [#205]

Check the source code online
1
def mesh_from_structure(self, structure):
Copied!
  docstring:
no docstring

meshfile_from_structure [#208]

Check the source code online
1
def meshfile_from_structure(self, structure):
Copied!
  docstring:
no docstring

root_mesh [#211]

Check the source code online
1
def root_mesh(self):
Copied!
  docstring:
no docstring

root_meshfile [#214]

Check the source code online
1
def root_meshfile(self):
Copied!
  docstring:
no docstring

_idx_from_coords [#217]

Check the source code online
1
def _idx_from_coords(self, coords, microns):
Copied!
  docstring:
no docstring

get_structure_ancestors [#224]

Check the source code online
1
def get_structure_ancestors(self, structure):
Copied!
  docstring:
1
Returns a list of acronyms for all
2
3
ancestors of a given structure
Copied!

get_structure_descendants [#235]

Check the source code online
1
def get_structure_descendants(self, structure):
Copied!
  docstring:
1
Returns a list of acronyms for all
2
3
descendants of a given structure
Copied!