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TrackCropper.py
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TrackCropper.py
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# The TrackCropper script is designed to crop a region of interest from
# an input hyperstack. The size of the ROI can be set manually, and will
# be centered around the x,y position of each individual track. The
# resulting cropped stacks will be saved in the chosen output directory.
#
# Jorik van Rijn <jorik.vanrijn@gmail.com> - 2020
import ij.IJ as IJ
import ij.WindowManager as WindowManager
from FijiTools2020.fileHandling import opencsv, getresults
from FijiTools2020.impActions import croptracks, combinestacks
def main():
# Get the wanted output directory and prepare subdirectories for
# output.
outdir = IJ.getDirectory("output directory")
# Open the 'Track statistics.csv' input file and format as
# getresults() dictionary.
rt = opencsv()
rt = getresults(rt)
# Retrieve the current image as input (source) image.
imp = WindowManager.getCurrentImage()
# Run the main crop function on the source image.
croptracks(imp, tracks=rt, outdir=outdir, roi_x=150, roi_y=150)
crop
# Combine all output stacks into one movie.
combinestacks(outdir, height=8)
# Execute main()
main()