Creating skeletons¶
Note
This notebook requires pcg_skel to be installed. You can install it with pip install pcg_skel or upon installing paleo with pip install paleo[skeleton].
from caveclient import CAVEclient
from paleo import (
get_initial_graph,
get_root_level2_edits,
get_nucleus_supervoxel,
get_node_aliases,
)
root_id = 864691135639556411
client = CAVEclient("minnie65_public", version=1078)
Collect edit history information¶
edits = get_root_level2_edits(root_id, client)
initial_graph = get_initial_graph(root_id, client)
nuc_supervoxel_id = get_nucleus_supervoxel(root_id, client)
anchor_nodes = get_node_aliases(nuc_supervoxel_id, client, stop_layer=2)
Extracting level2 edits: 0%| | 0/693 [00:00<?, ?it/s]
Getting initial graph: 0%| | 0/309 [00:00<?, ?it/s]
Apply edit history¶
from paleo import apply_edit_sequence
graphs_by_state = apply_edit_sequence(
initial_graph,
edits,
anchor_nodes,
return_graphs=True,
include_initial=True,
verbose=True,
)
graphs_by_state[9028]
0%| | 0/694 [00:00<?, ?it/s]
<networkx.classes.graph.Graph at 0x2db3636b0>
Skeletonize states¶
from paleo import skeletonize_sequence
skeletons_by_state = skeletonize_sequence(
graphs_by_state, root_id=root_id, client=client
)
skeletons_by_state[9028]
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<meshparty.skeleton.Skeleton at 0x2f2640230>
import pandas as pd
skeleton_info = []
for i, (operation_id, skeleton) in enumerate(skeletons_by_state.items()):
skeleton_info.append(
{
"state": i,
"operation_id": operation_id,
"n_vertices": len(skeleton.vertices),
"n_edges": len(skeleton.edges),
"path_length": skeleton.path_length(),
"n_branch_points": len(skeleton.branch_points),
"n_end_points": len(skeleton.end_points),
}
)
skeleton_info = pd.DataFrame(skeleton_info)
import matplotlib.pyplot as plt
import seaborn as sns
sns.set_context("talk")
fig, axs = plt.subplots(1, 3, figsize=(15, 5), layout="constrained")
for i, feature in enumerate(["path_length", "n_branch_points", "n_end_points"]):
sns.lineplot(data=skeleton_info, x="state", y=feature, ax=axs[i])
axs[i].set_ylabel(feature.capitalize().replace("_", " "))
axs[i].set_xlabel("State")
