def main(imp, tolerance, window_radius, pixel_size_nm, out_dir):
# set output dir
out_dir = str(out_dir)
# Find maxima
excludeOnEdge = True
polygon = MaximumFinder().getMaxima(imp.getProcessor(), tolerance, excludeOnEdge)
roi = PointRoi(polygon)
# get RoiManager
rm = RoiManager.getInstance();
if rm is None:
rm = RoiManager()
# Check if output table is writable
out_table_fn = os.path.join(out_dir, "fwhm_values.txt")
try:
file_handle = open(out_table_fn, 'w')
except IOError:
IJ.showMessage("Output file '' not writeable. Check if file is open in Excel...")
sys.exit(0)
# iterate and write output
with file_handle as csvfile:
writer = csv.DictWriter(csvfile,
fieldnames=["id", "peak_id", "x_pos", "y_pos",
"type", "fwhm", "fwhm_nm", "r2_GoF",
"avg_fwhm", "area_profile", "area_gauss"], delimiter="\t", lineterminator='\n')
writer.writeheader()
id_ = 0
# over all peaks
for i, p in list(enumerate(roi)):
IJ.showProgress(i, roi.getNCounters() +1)
# Horizontal
lroi = Line(p.x+0.5-window_radius, p.y+0.5,
p.x+0.5+window_radius, p.y+0.5)
output = fit_gauss(lroi, imp, p, i, id_, "H", rm)
writer.writerow(output)
id_+=1
# Vertical
lroi = Line(p.x+0.5, p.y+0.5-window_radius,
p.x+0.5, p.y+0.5+window_radius)
output = fit_gauss(lroi, imp, p, i, id_, "V", rm)
writer.writerow(output)
id_+=1
# Diagonal 1
lroi = Line(p.x+0.5-MN*window_radius, p.y+0.5+MN*window_radius,
p.x+0.5+MN*window_radius, p.y+0.5-MN*window_radius)
output = fit_gauss(lroi, imp, p, i, id_, "D1", rm)
writer.writerow(output)
id_+=1
# Diagonal 2
lroi = Line(p.x+0.5-MN*window_radius, p.y+0.5-MN*window_radius,
p.x+0.5+MN*window_radius, p.y+0.5+MN*window_radius)
output = fit_gauss(lroi, imp, p, i, id_, "D2", rm)
writer.writerow(output)
id_+=1
IJ.showProgress(1)
rm.runCommand("Deselect"); # deselect ROIs to save them all
rm.runCommand("Save", os.path.join(out_dir, "fwhm_fiji_rois.zip"))
IJ.showMessage("FWHM on Spots: Done")
