run ("imaging/sim")
    
stack = load_test_stack(show=True)
ipr, ipi = complex_edge_filtering(stack, complex=True, g_sigma = 3.0, show=False) 


#complex_edge_filter = get_context().getClassByName("Align_ComplexEdgeFiltering").newInstance()
#translation_filter = get_context().getClassByName("Align_TranslationFilter2").newInstance()
#compute_shifts_filter = get_context().getClassByName("Align_ComputeShifts2").newInstance()

"""
ip_list = []
for index in range(40,49):
    ip_list.append(open_image(expand_path("{images}/TestObjAligner/i210517_0" + str(index) + "#001.tif")))
stack =  create_stack(ip_list, title = "Test")
stack.show()

complex_edge_filter.setup("2,True,False", stack)   #Gaussian blur radius, Complex (True) or Real (False), show dialog = False
complex_edge_filter.r"un(stack.getProcessor())
imp_r, imp_i = complex_edge_filter.output

#imp_r.show()
#imp_i.show()
roi=Roi(258,0,256,256)
compute_shifts_filter.setup(10, False, ipr, ipi, 1, roi)
compute_shifts_filter.run(None)
shifts = compute_shifts_filter.shifts

translation_filter.shifts = shifts
translation_filter.setup("",stack)
translation_filter.run(stack.getProcessor())

translation_filter.registred.show();
translation_filter.registred.updateAndDraw();

"""

roi=Roi(258,0,256,256)
shifts = calculate_shifts(ipr, ipi, roi, 2)
r=translate(stack, shifts, True)