Thresholding and measuring circles for scope calibration

threshold_and_measure_circles.fiji.py

from ij import IJ
from ij.measure import ResultsTable
from ij.plugin.filter import ParticleAnalyzer
import time


def analyze(path):
	IJ.open(path)
	IJ.run("16-bit");
	IJ.run("Auto Threshold", "method=Minimum");
	IJ.run("Invert");
	
	IJ.run("Set Measurements...", "area centroid bounding redirect=None decimal=3");
	IJ.run("Analyze Particles...", "size=100-Infinity circularity=0.50-1.00 show=Outlines display clear");
	time.sleep(1)
	
	rt = ResultsTable.getResultsTable()
	return rt


def main():
	file_nums = range(128,184)
	for count, n in enumerate(file_nums):
		path = '/path/to/%05d.JPG' % n
		rt = analyze(path)
		if count == 0:
			print(rt.getColumnHeadings())
		for i in range(0,rt.size()):
			s = rt.getRowAsString(i)
			cs = s.split('\t')
			if -300 < (float(cs[2]) - 640) < 300 and -200 < (float(cs[3]) - 480) < 200:
				cs[0] = n
				print('\t'.join(map(str,cs)))
		IJ.run('Close All')


main()