Autotrace_DemoTree.py

# @LogService log
# @SNTService snt
# @UIService ui

"""
file:       Autotrace_OP_1.py
"""

import time
from sc.fiji.snt import (Path, SNT, Tree)
from sc.fiji.snt.util import PointInImage

def run():
    # Exit if SNT is already busy doing something
    if snt.isActive() and snt.getUI() and not snt.getUI().isReady():
        ui.showDialog("Please complete current operation before running this script", "Error")
        return

    # Prepare plugin for auto-tracing
    plugin = snt.initialize("demo", True)
    plugin.enableAstar(True)
    plugin.getPathAndFillManager().clear();
    #plugin.startHessian("primary", 1.15, 14)

    ref_tree = snt.demoTree()
    new_tree = Tree()
    for path in ref_tree.list():

        end_point = path.getNode(path.size() - 1)
        if path.getStartJoinsPoint() is None:
            start_point = path.getNode(0)
            primary_path = plugin.autoTrace(start_point, end_point, None)
            new_tree.add(primary_path)   
        else:
            # TODO: Simplify this. It is very confusing
            source_tree_start_point = path.getStartJoinsPoint()
            fork_path_id = path.getStartJoins().getID()
            fork_path = new_tree.get(fork_path_id)
            closest_index = fork_path.indexNearestTo(source_tree_start_point.x, source_tree_start_point.y,
                                                     source_tree_start_point.z, float('inf'))
            fork_point = fork_path.getNode(closest_index)
            child = plugin.autoTrace([fork_point, end_point], fork_point)
            new_tree.add(child)

        time.sleep(0.1) # the demo tree is really small: we need a delay


    #snt.dispose()

run()