poly_bg

#!/usr/bin/python3

# Copyright (C) 2017 Vladimir Nadvornik
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.


import numpy as np
import cv2

import tifffile
import argparse
import sys
from astro_utils import normalize, noise_level, poly_bg


parser = argparse.ArgumentParser()
parser.add_argument("outfile",
                    help="output tiff file")
parser.add_argument("infile",
                    help="input tiff file")

parser.add_argument('--zero', type=int, default = 1024,
                   help='output zero level')

parser.add_argument('--offset', type=int, default = 1,
                   help='zero offset')

parser.add_argument('--poly-bg', type=int, default = 0,
                   help='poly_bg_order')
parser.add_argument('--poly-bg-iter', type=int, default = 10,
                   help='poly_bg_iter')
parser.add_argument('--poly-bg-kappa', type=float, default = 2,
                   help='poly_bg_kappa')
args = parser.parse_args()



eps = 1.0 / 65536.0
zero = args.zero / 65535.0
offset = args.offset / 65535.0
img_in = tifffile.imread(args.infile)
img_in = np.atleast_3d(img_in)
h, w, channels = img_in.shape
	
col = [1,1,1,3,3][channels]

if img_in.dtype == np.uint16:
	img = np.array(img_in[:,:, 0:col], np.float32)
	img /= 65535.0
else:
	img = np.array(img_in[:,:, 0:col], np.float32)

if args.poly_bg > 0:
	bg = poly_bg(cv2.medianBlur(img, 3), order = args.poly_bg, scale = 2, erode = 1, kappa = args.poly_bg_kappa, it = args.poly_bg_iter, save_mask = "mask")
	bg -= zero
	img -= bg

img += offset
img[img < zero] = zero

np.save("lin.npy", img)

h, w, nchannels = img.shape



#img = np.clip(img * 65535.0, 0, 65535.0)
#img = np.array(img, dtype = np.uint16) 
print("check img", cv2.minMaxLoc(img[:,:,1]))

if args.outfile is not None:
	tifffile.imsave(args.outfile, img)