from ijutils import Roi
#from sim import *
import traceback
run ("imaging/sim")

roi=Roi(0,0,128,128)

"""
stack = load_test_stack(show=True, size=2)
ipr, ipi = complex_edge_filtering(stack, show=False) 
shifts = calculate_shifts(ipr, ipi, roi,  java_code=True)
#shifts= load_shifts("{images}/TestObjAligner/shifts.mat")
#stack = load_test_stack(show=True)
r=translate(stack, shifts, show=True)
"""




ref = "{images}/TestObjAligner/i210517_040#001.tif"
img = "{images}/TestObjAligner/i210517_041#001.tif"

ref = open_image(ref)
img = open_image(img)
#ref=ref.getBufferedImage()
#img=img.getBufferedImage()
#ref=ca.data
img=grayscale(to_ip(ca.data))
ref = grayscale(ref.crop([Roi(0,0,452,452)])[0])

def calculate_shift(ref,img, roi, upscale_factor=100, reference_slide=1):
    ref = to_ip(ref)
    img = to_ip(img)      
    stack = create_stack([ref,img])
    stack.show()
    ipr, ipi = complex_edge_filtering(stack, show=False) 
    shifts = calculate_shifts(ipr, ipi, roi,  java_code=True)
    xoff, yoff =  shifts[1][3], shifts[1][2]
    error, diffphase =  shifts[1][4], shifts[1][5]
    r=translate(stack, shifts, show=True)
    return xoff, yoff,error, diffphase

    
print calculate_shift(ref,img, roi)