#@File[] (label="ROI folder", style="file") roi_files

#@File (label="Results folder", style="directory") csvPath

# Bootstrap to extend modules search path #

from sys import path

import os.path

from java.lang.System import getProperty

jython_scripts = os.path.join(getProperty('user.home'), 'Jython_scripts')

path.append(jython_scripts)

#=========================================#

from ij import (IJ, ImagePlus)

from ij.gui import Roi

from ij.io import Opener

from IBPlib.ij.Utils.Files import buildList

def normalized_roi_length(roi_path, pixel_scaling, normalization_fn=None):

return measure

if __name__ in ("__builtin__", "__main__"):

'''

Use case where multiple rois are measured, scaled and normalized.

Measurements being saved then to a csv file.

'''

rois = []

for i in roi_files:

if i.isDirectory():

rois.append(buildList(i.getPath(), ".roi"))

elif i.isFile() and i.getName().lower().endswith(".roi"):

rois.append(i.getPath())

scale = 3.1 # pixels/micrometers

cutdistance = 50 # distance from cell body in micrometers

lengths = (normalized_roi_length(roi, scale, lambda x: x-cutdistance) for roi in rois)

resultspath = os.path.join(csvPath.getPath(),"regrowth_1.csv")

with open(resultspath, "w") as csvfile:

for row in lengths:

line = "{0}\n".format(row)

csvfile.write(line)

IJ.log("Results were saved to {0}".format(resultspath))