Reanalysis for thesis (incl. plate scale change)

scripts/SPIE/Thesis/geometric_distortions_fp_wfe.py

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+import numpy as np
+import sys
+# sys.path.insert(0, '/Users/joost/Dropbox/Werk/PhD/Analyses/Python/Analytical/Fourier Optics')
+# sys.path.insert(0, '/home/joost/Dropbox/Werk/PhD/Analyses/Python/Analytical/Fourier Optics')
+sys.path.insert(0, '/Users/joost/Dropbox/Werk/PhD/Documents/Published/FourierOptics GitHub release/')
+from fourierOptics import *
+from pdb import set_trace
+
+'''
+	Author: 		Joost van den Born, PhD student at University of Groningen
+	Contact: 		born@astro.rug.nl
+	Description: 	Script to generate the geometric distortions due to WFEs
+					off the ADC prisms. The distortions are produced by measuring
+					the offset of the PSF centroid with and without WFE as a
+					function of field position.
+	 				Script made for the SPIE manuscript.
+'''
+
+def plot_distortions():
+	# Coordinates without WFEs
+	xe = load_variable('../data/GD_IFP_obscured_PSF_xcentroid_expected_zern.pkl')
+	ye = load_variable('../data/GD_IFP_obscured_PSF_ycentroid_expected_zern.pkl')
+
+	# Coordinates with WFEs
+	xf = load_variable('../data/GD_IFP_obscured_PSF_xcentroid_found_with_wfe_airy_zern.pkl')
+	yf = load_variable('../data/GD_IFP_obscured_PSF_ycentroid_found_with_wfe_airy_zern.pkl')
+
+	mcd = ParaxialMICADO(n=3001, m=3001, dpix=50, l=1.49e-3)
+
+	n = xe.shape[0]
+	X = xe.flatten()
+	Y = ye.flatten()
+	dX = xf - xe
+	dY = yf - ye
+	dx = dX.flatten()
+	dy = dY.flatten()
+
+	# Magnitude of the distortions
+	R = np.sqrt(dx**2 + dy**2) * mcd.platescale * 1e6
+
+	# Dummy figure, used for the colorbar colors in the quiver plot
+	im = plt.imshow(np.reshape(R, (n,n)))
+	plt.close()
+
+	fig = plt.figure()
+	ax = fig.add_subplot()
+	for i in range(len(xe)):
+	    ax.plot(xe[:,i], ye[:,i], 'k-', alpha=0.2, linewidth=.5)
+	    ax.plot(xe[i,:], ye[i,:], 'k-', alpha=0.2, linewidth=.5)
+	ax.quiver(X,Y,dx,dy, angles='xy', edgecolor='k', facecolor='None', linewidth=.5, units='dots')
+	ax.quiver(X,Y,dx,dy,R, alpha=.5, units='dots')
+	ax.set_aspect('equal', adjustable='box')
+	ax.set_xlabel('x (mm)')
+	ax.set_ylabel('y (mm)')
+	fig.colorbar(im, ax=ax, label='PSF centroid shift ($\\mu$as)')
+	plt.savefig('../figures/UPDATED_GD_focal_plane_zern.pdf', bbox_inches='tight', transparent=True)
+	plt.savefig('../figures/UPDATED_GD_focal_plane_zern.png', bbox_inches='tight', transparent=True)
+	plt.tight_layout()
+	plt.show()
+
+
+if __name__ == '__main__':
+	# plt.rc('text', usetex=True)
+	# plt.rc('font', family='serif')
+	
+	# Setup of simulation
+	l = 1.49e-3
+	mcd = ParaxialMICADO(n=3001, m=3001, dpix=50)
+	# mcd.plot_ray_trace()
+	wfe = WavefrontError(mcd.n, mcd.m)
+
+	# Get x3 and y3 (the coordinates to apply the ADC WFE to):
+	# The focal plane area is about 200x200 mm, so we apply the wavefront error to an area
+	# of 200x200 mm.
+	xfp, yfp = np.meshgrid(np.linspace(-150, 150, mcd.n), np.linspace(-150, 150, mcd.m))	
+	# _, xfp, yfp = mcd.propagate(l=l,surface=1, zoom=False, show=False, 
+	# 							print_progress=False)
+
+	# Generate a wavefront error for the intermediate focal plane.
+	print('\nSetting the wavefront errors...')
+	wfe_fp 		= WavefrontError(mcd.n,mcd.m)
+	wfe_rms = 50e-6
+	#PSD Wavefront error
+	# surface_map_fp = wfe_fp.generate_height_map(wfe_rms, 2, 1)
+	# plot_real_valued_results(surface_map_fp*1e6, xfp, yfp, logscale=False, fig_size=(8,6.4), grid=False, show=True, 
+							# colormap='jet', labeltext='Surface height (nm)')
+	# save_variable('../data/MCD_IFP_wfe_object_PSD_50nm.pkl', wfe_fp)
+	# wfe_fp = load_variable('../data/MCD_IFP_wfe_object_PSD_50nm.pkl')
+	# surface_map_fp = wfe_fp.data
+
+	# Zernike wavefront error
+	# We re0se the ADC_surface classes because it can be applicable to any surface, if used properly
+	ifp_wfe = ADC_surfaces(xfp, yfp, clearAperture=300)
+	ifp_wfe.generate_ADC_wfe(zernRMS=wfe_rms, psdRMS=0.)
+	mask = np.sqrt(ifp_wfe.xz**2 + ifp_wfe.yz**2) > 1
+	
+	# Plot the wfe
+	# surf_ifp = ifp_wfe.latest_surface.copy()
+	# surf_ifp[mask]=np.nan
+	
+	# surface_map_fp = surf_ifp
+	# wfe_fp.data = surf_ifp
+	wfe_fp = load_variable('../data/MCD_IFP_wfe_object_zern_50nm.pkl')
+	surface_map_fp = wfe_fp.data
+	# save_variable('../data/MCD_IFP_wfe_object_zern_50nm.pkl', wfe_fp)
+	# figp1, axp1 = plot_real_valued_results(surface_map_fp*1e6, xfp, yfp,
+	#  						 				colormap='jet', labeltext='Surface height (nm)', fig_size=None, show=True)
+	plt.show()
+	
+
+	Elist, Eplist = [], []
+	xlist, ylist = [], []
+	xplist, yplist = [], []
+	x_expected_list, y_expected_list = [], []
+	x_centroid_list, y_centroid_list = [], []
+
+	# Set field points
+	hxList, hyList = np.mgrid[-1:1:11j,-1:1:11j]-(1/300)
+	# hxList, hyList = np.mgrid[-.1/11:.1/11:11j,-.1/11:.1/11:11j]-(1/300) # Zoomed in to central area
+	hxList = hxList.flatten()
+	hyList = hyList.flatten()
+
+	# List of performed simulations
+	# Defined by PSD
+	## GD_IFP : -1:1
+	## GD_IFP_zoom  : -1/11 :1/11
+	## GD_IFP_zoom2 : -.5/11:.5/11
+	## GD_IFP_zoom3 : -.1/11:.1/11
+
+	# Defined by zernikes
+	## GD_IFP_obscured_PSF_xcentroid_expected_zern : 50 nm rms 19 zernike modes : -1 : 1
+	## To do; check PSF shape at center field with zern wfe
+	## To do; check interpolated WFE at any zoomed in field point.
+
+	# Propagate through the field positions without any WFEs	
+	for i in range(len(hxList)):
+		hx = hxList[i]
+		hy = hyList[i]
+		print('hx: {}	- 	hy: {}'.format(hx,hy) )
+
+		# Initializing MICADO paraxial model
+		mcd = ParaxialMICADO(n=3001, m=3001, dpix=50, entrance_pupil='obscured')
+
+		# Propagate through the MICADO system
+		E, x, y = mcd.propagate(l=l,surface=-1, zoom=False, show=False, 
+								print_progress=False, hx=hx, hy=hy)
+
+		# Find approximation for the centroid and amplitude as a first 
+		# guess for the Obscured Airy pattern fit.
+		amplitude_guess = np.max(np.abs(E))**2
+		xbc, ybc, _, _ = mcd.centroid_shift(method='Barycenter')
+		print('Barycenter guess: ', xbc, ybc)
+
+		# Do the Obscured Airy Pattern Fit for the unperturbed PSF
+		xe, ye, _, _ = mcd.centroid_shift(method='Obscured Airy', initialGuess=(amplitude_guess, xbc, ybc, 0.0, 0.03))
+		print('Airy result: ', xe,  ye)
+		x_expected_list.append(xe)
+		y_expected_list.append(ye)
+
+	
+
+		# Load in the WFEs and set them to the corresponding ADC surfaces
+		print('\nSetting the wavefront errors...')
+		# null_wfe = np.zeros((3001,3001))
+		mcd.ELT_FP.add_wavefront_error(surface_map_fp, xfp, yfp, wfe=wfe_fp)
+
+
+		# Propagate through the MICADO system
+		print('Propagating with Wavefront Errors applied...')
+		Ep, xp, yp = mcd.propagate(l=l,surface=-1, zoom=False, show=False, 
+								print_progress=False, hx=hx, hy=hy)
+		
+
+		# Do the Obscured Airy Pattern Fit for the perturbed PSF
+		xf, yf, _, _ = mcd.centroid_shift(method='Obscured Airy', initialGuess=(amplitude_guess, xe, ye, 0.0, 0.03))
+
+		# Resulting centroid shift due to the WFE
+		x_centroid_list.append(xf)
+		y_centroid_list.append(yf)
+		R = np.sqrt( (xf-xe)**2 + (yf-ye)**2 ) * mcd.platescale * 1e6
+		print('xf: {}, yf: {}, shift (uas): {}'.format(xf,yf, R))
+
+		# Clear the memory by emptying the large arrays
+		mcd = None
+		wfe = None
+		E, x, y = None, None, None
+		Ep, xp, yp = None, None, None
+
+
+	# Reshaping the arrays
+	shape = (int(np.sqrt(len(x_expected_list))), int(np.sqrt(len(x_expected_list))))
+	x_expected = np.asarray(x_expected_list).reshape(shape)
+	y_expected = np.asarray(y_expected_list).reshape(shape)#.T
+
+	# Saving the arrays
+	save_variable('../data/GD_IFP_obscured_PSF_xcentroid_expected_zern.pkl', x_expected)
+	save_variable('../data/GD_IFP_obscured_PSF_ycentroid_expected_zern.pkl', y_expected)
+
+
+	# Reshaping the arrays
+	shape = (int(np.sqrt(len(x_centroid_list))), int(np.sqrt(len(x_centroid_list))))
+	x_centroid = np.asarray(x_centroid_list).reshape(shape)
+	y_centroid = np.asarray(y_centroid_list).reshape(shape)
+	
+	# Saving the arrays
+	save_variable('../data/GD_IFP_obscured_PSF_xcentroid_found_with_wfe_airy_zern.pkl', x_centroid)
+	save_variable('../data/GD_IFP_obscured_PSF_ycentroid_found_with_wfe_airy_zern.pkl', y_centroid)
+
+	plot_distortions()
+	
+
+