Autotrace_OP_1.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


image = r"/home/tferr/code/OP_1/OP_1.tif"
gold_standard = r"/home/tferr/code/OP_1/OP_1-GS-NoRadius.swc"
traced_result = r"/home/tferr/code/OP_1/OP_1-autotrace.swc"

def run():
    # Exit if SNT is already busy doing something
    if snt.isActive() and snt.getUI():
        ui.showDialog("Please close SNT before running this headless script", "Error")
        return

    # Prepare plugin for auto-tracing
    plugin = snt.initialize(image, False) # image file path, wether ui should be displayed
    plugin.enableAstar(True)
    plugin.startHessian("primary", 1.15, 14)

    tree = Tree(gold_standard)
    #tree.scale(0.3296485, 0.3296485, 0.9988000) # uncomment ig GS swc is unscaled and image scaled
    new_tree = Tree()
    for path in 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)


    success = "File saved" if snt.save(traced_result) else "unsaved result. I/O error?"
    log.info(success)
    snt.dispose()

run()