Added descriptions to all scripts, checked functioning

scripts/annular_mask_lens.py

@@ -1,12 +1,21 @@
 #!/usr/bin/env Python3
 import numpy as np
-from pdb import set_trace
 import matplotlib.pyplot as plt
 from matplotlib.ticker import FormatStrFormatter
 from matplotlib.colors import LogNorm
 import time
+import sys
+sys.path.insert(0, '/Users/joost/Dropbox/Werk/PhD/Documents/Published/FourierOptics GitHub release/')
 from fourierOptics import *
 
+'''
+	Description:
+	This script looks how the PSF behaves for an annular lens.
+	Specifically at 30 microns. After plotting the PSF at the 
+	focal length, a cross section of the intensity profile
+	at different distances from the lens is shown.
+'''
+
 if __name__ == '__main__':
 	plt.rc('font', family='serif')
 	plt.rc('axes', labelsize='large')
@@ -27,30 +36,27 @@ if __name__ == '__main__':
 	
 	# Initiate the profiles class and pick a profile (tophat, obscured tophat or spider)
 	prof = Profiles()
-	A = prof.obscured_top_hat(2.5, 2.3, n, m, dpix=dpix, oversample=1)
+	A = prof.obscured_top_hat(2.5, 2.3, n, m, dpix=dpix)
 	plt.imshow(A); plt.show()
 
 	
 	# Create an input grid
 	x, y = np.meshgrid(np.linspace(-n/2*dpix, n/2*dpix, n), np.linspace(-m/2*dpix, m/2*dpix, m))
 	
-
-
 	# Create a lens with a focal length ~100 mm, with a clear aperture radius of 4 mm and thickness of 1 mm.
-	L1 = LensObject('N-BK7', 50, 1e99, 1, 4, name='L1')
+	L1 = SphericalLens('N-BK7', R1=50, R2=1e99, thickness=1, CA=8, name='L1')
 	print('Focal length of lens {} is {:.1f} mm.'.format(L1.name, L1.f))
 
 	# Calculate the phase delay introduced by the lens
 	t_l = L1.phase_delay(x,y,l, paraxial=True)
 	U_in = A * t_l
-	
+
 	# Performing the propagation using Fresnel approximation to the focal plane.
 	oC = [x.min(), x.max(), y.min(), y.max()]
 	savename = False
 	Exyz_og,_,_ = fou.fresnel_propagation(U_in, x, y, dz=L1.f, show=True, save=savename, outputCoordinates=oC)
 
-	
-
+	# Plotting the Modulation Transfer Function of this lens system
 	E1, fx1, fy1 = fou.modulation_transfer_function(np.abs(Exyz_og)**2, x,y,dpix)
 	plt.figure()
 	plt.plot(fx1[1000:], E1[1000, 1000:],'b-')