roi in Fiji/ImageJ

from ij import IJ
from ij.io import DirectoryChooser, OpenDialog
from ij.gui import GenericDialog
import csv
import os


def run(image_filename, roi_filename=None, orientation_filename=None):
    imp = IJ.openImage(image_filename)
    roi = load_roi(roi_filename)
    imp.setRoi(roi)
    measure_area(imp)
    imp.show()

def load_roi(roi_filename):
    f = open(roi_filename, 'r')
    x = []
    y = []
    reader = csv.DictReader(f, delimiter='\t')
    for row in reader:
        x.append(float(row['X']))
        y.append(float(row['Y']))
    f.close()
    polygon = FloatPolygon(x,y)
    roi = PolygonRoi(polygon, PolygonRoi.POLYGON)
    return roi

def measure_area(imp):
    pix = imp.getProcessor().getPixels()
    total_pixels = len(pix)
    roi = imp.getProcessor().getRoi()
    w = imp.getWidth()
    total = 0
    above_thresh = 0
    total_intensity = 0.
    for i, p in enumerate(pix):
        x = i % w
        y = i / w # integer division
        if roi.contains(x,y):
            total += 1
            if p > 100:
                above_thresh += 1
            total_intensity += float(p)
        IJ.showProgress(i, total_pixels)
    if total == 0:
        print 'total pixels inside roi = 0'
        total = 1
    IJ.showProgress(1)
    stats = imp.getStatistics(Measurements.STD_DEV |
        Measurements.CENTROID |
        Measurements.CENTER_OF_MASS |
        Measurements.MEAN)
    print """Pixel count via stats: %d
Pixel count via iterating over pixels: %d""" % (stats.pixelCount, total)

def get_options():
    # Get image
    i_od = OpenDialog("Choose image file", None)
    image_filename = os.path.join(i_od.getDirectory(), i_od.getFileName())
    # Get Region of Interest (roi)
    r_od = OpenDialog("Choose roi file", None)
    roi_filename = os.path.join(r_od.getDirectory(), r_od.getFileName())
    # Get threshold value
    gd = GenericDialog("Options")
    gd.addNumericField("Threshold - just ignore, still hardcoded", 500, 0) # 500 default and zero d.p.
    gd.showDialog()
    if (image_filename is None) or \
            (roi_filename is None) or \
            gd.wasCanceled():
        raise Exception("User canceled the dialog")
    else:
        threshold = gd.getNextNumber()
        return (image_filename, roi_filename)

options = get_options()
run(*options)