Jython script to fit paths automatically from a traces file and image in SNT

fit_paths.py

# @SNTService sntService
# script to fit paths from previous tracing session programatically via Jython and SNT
# single threaded fitting and slow. Will refactor to multithreaded in future....
# see: https://forum.image.sc/t/fit-paths-with-simple-neurite-tracer-api/30139/

# test traces file
traces_test = "path/to/traces_file.traces"
# test img file
image_test = "path/to/image_file.tif"


import os
from java.io import File
from sc.fiji.snt import Path
from sc.fiji.snt import PathFitter
from sc.fiji.snt import PathAndFillManager
from sc.fiji.snt import Tree

print("starting")


snt = sntService.initialize(image_test, False) # No GUI
sntService.loadTracings(traces_test)
loaded_tree = sntService.getTree(False)

pfm = PathAndFillManager() # for later quick export. 
pfm.addTree(loaded_tree) # add tree to manager instance

for p in loaded_tree.list():
    pf = PathFitter(snt, p)
    pf.setMaxRadius(10) # option for path fitting. 
    pf.setScope(PathFitter.RADII_AND_MIDPOINTS) # another option for path fitting. 
    pf.setReplaceNodes(True)
    pf.call()
    print("fitting {}  : {}".format(p, str(pf.getSucceeded())))

new_traces_fname = os.path.join(os.path.dirname(traces_test), "new_traces.traces")
new_properties_fname = os.path.join(os.path.dirname(traces_test), "new_properties.csv")
print("saving csv properties: {}".format(new_properties_fname))
pfm.exportToCSV(File(new_properties_fname)) # export quick measurements to csv, using Java IO file. 
print("saving traces properties: {}".format(new_traces_fname))
sntService.save(new_traces_fname) # save traces file for csv
print("done")