Feature: Graph And Paths¶

Status¶

Entry point	Status	Notes
GUI	Supported	includes interactive graph editing for single-group cases
CLI	Supported	generated in batch order
Python API	Supported	through pipeline execution

What It Does¶

Graph and path generation converts the skeleton into nodes, edges, branches, forks, and path objects used by planes and downstream metrics. When segmentation is grouped, graph generation runs per group, then combines path endpoints, fork nodes, fork roles, and path indices into one workspace-wide numbering while preserving each path group_name.

GUI edits now invalidate dependent artifacts explicitly: skeleton edits clear graph, paths, planes, and metrics; graph edits clear paths, planes, and metrics. Run the next centerline action after finishing an edit.

When To Use It¶

use it after a valid skeleton exists
use it before plane generation
use GUI editing when automatic graph structure needs correction

Quick Use¶

GUI¶

run Generate Skeleton
click Generate Graph
inspect grouped graph, fork, and path objects in the browser and 3D view
if needed, click Edit Graph when exactly one segmentation group is active

Graph edit mode hides unrelated scene layers and shows the graph controls in the step area. Select and drag nodes with the orange sphere; click an edge and press Delete/Backspace to remove it. Press E, or click Edge Mode, then click two nodes to add or remove their edge. Save Changes clears dependent paths, planes, and metrics; Cancel or Esc leaves the graph unchanged.

CLI¶

autoflow-run case.h5 --output-dir results/case

Python API¶

Use the standard batch or single-case pipeline. Graph generation is part of the normal order.

Inputs¶

Input	Required	Meaning
skeleton	yes	centerline input for graph construction
segmentation	indirectly yes	needed to build the skeleton first

Parameters¶

Parameter	Type	Default	Where set	Effect	Code owner
graph step trigger	step	fixed	GUI step or batch order	build nodes, edges, branches, and paths	`autoflow/core/pipeline.py`
edit mode	GUI mode	off	GUI only	drag nodes, toggle edges, delete nodes or edges	`autoflow/ui/app.py`

Outputs¶

Output file or object	Created when	Meaning
graph data in workspace	graph step succeeds	nodes and edges
branches and paths in workspace	graph step succeeds	branch and path topology; nearest-path labels are assigned in one vectorized operation, and grouped endpoints, fork nodes, and fork roles use global ids
graph scene objects	GUI graph step succeeds	grouped graph objects such as `graph_aorta_systemic_branches` and `smooth_path_aorta_systemic_branches_3`

Limitations¶

depends on usable skeleton quality
there is no dedicated public CLI parameter family just for graph tuning in the current docs set
interactive graph editing is only available when exactly one segmentation group is active

Where To Change Code¶

Change you want	Edit here	Also check	Tests
graph construction	`autoflow/algorithms/graph.py`	`autoflow/core/pipeline.py`	`tests/test_smoke_phantoms.py`
branches or paths logic	`autoflow/algorithms/branch.py`, `autoflow/algorithms/paths.py`	`autoflow/core/pipeline.py`	`tests/test_smoke_phantoms.py`
interactive graph editing	`autoflow/ui/app.py`, `autoflow/ui/editors.py`	`autoflow/ui/viewer.py`	GUI smoke coverage

Tests¶

~/miniconda3/envs/ryy/bin/python -m pytest tests/test_smoke_phantoms.py -q

Common Problems¶

Symptom	Likely cause	Fix
graph step is skipped	no skeleton	run `Generate Skeleton` first
graph and fork objects are listed but absent from the 3D view while paths remain visible	an older viewer did not resolve grouped `graph_<group>` and `forks_<group>` data keys	install the current editable build and run `Generate Graph` again
path structure looks wrong	skeleton topology is noisy	improve segmentation or edit graph manually
`Edit Graph` is unavailable	more than one segmentation group is active	use a single-group case, or change group configuration