from pathlib import Path
from neuralib.atlas.data import load_bg_structure_tree
from neuralib.typing import PathLike
__all__ = ['plot_sunburst_acronym',
'plot_structure_tree']
[docs]
def plot_sunburst_acronym(output: PathLike | None = None):
"""
Plot allen brain structure tree interactive plot
:param output: figure output path, otherwise, render interactively
:return:
"""
from plotly import express as px
data = load_bg_structure_tree(paired=True)
data = dict(names=data['names'], parents=data['parents'])
#
fig = px.sunburst(
data,
names='names',
parents='parents',
)
if output is not None:
fig.write_image(output)
else:
fig.show()
[docs]
def plot_structure_tree(starting_node: str | None = None, output: PathLike | None = None) -> None:
"""Show tree for the brain structure
:param starting_node: starting node for rendering the tree. If None, then plot all
:param output: output file txt. print if None
"""
from anytree import Node, RenderTree
df = load_bg_structure_tree(paired=True)
nodes = {}
for it in df.iter_rows(named=True):
name = it['acronym']
parent = it['parent_acronym']
if name not in nodes:
nodes[name] = Node(name)
if parent not in nodes:
nodes[parent] = Node(parent)
nodes[name].parent = nodes[parent]
#
start = starting_node if starting_node is not None else 'root'
if start not in nodes:
raise ValueError(f'{starting_node} not find in the structure tree')
#
for pre, fill, node in RenderTree(nodes[start]):
if output is not None:
output = Path(output)
if not output.exists():
with Path(output).open('a') as file:
print("%s%s" % (pre, node.name), file=file)
else:
raise FileExistsError(f'{output}')
else:
print("%s%s" % (pre, node.name))