core - brainglobe

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]​
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!