Skip to content

Instantly share code, notes, and snippets.

@mhl
Created March 26, 2011 05:39
Show Gist options
  • Save mhl/888051 to your computer and use it in GitHub Desktop.
Save mhl/888051 to your computer and use it in GitHub Desktop.
Batch convert Simple Neurite Tracer's .traces files to SWC format
import os
import re
from tracing import PathAndFillManager
# An example script showing how to convert all the .traces
# files in a directory to SWC files. (The .traces format
# is the native file format of Simple Neurite Tracer.)
def run():
d = IJ.getDirectory("Choose your directory of .traces files...")
if not d:
return
for e in os.listdir(d):
if not e.endswith(".traces"):
continue
traces_filename = os.path.join(d,e)
swc_filename_prefix = re.sub(r'\.traces', '-exported', traces_filename)
IJ.log("Converting %s to %s-*.swc" % (traces_filename,
swc_filename_prefix))
pafm = PathAndFillManager()
pafm.loadGuessingType(traces_filename)
if pafm.checkOKToWriteAllAsSWC(swc_filename_prefix):
pafm.exportAllAsSWC(swc_filename_prefix)
run()
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment