Added descriptions to all scripts, checked functioning

scripts/SPIE/Thesis/generate_fp_wfe_phase_array.py

@@ -1,11 +1,8 @@
 import numpy as np
 import matplotlib.pyplot as plt
 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

scripts/SPIE/Thesis/geometric_distortions.py

@@ -1,7 +1,5 @@
 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 *
 

scripts/SPIE/Thesis/geometric_distortions_fp_wfe.py

@@ -1,7 +1,5 @@
 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
@@ -17,14 +15,6 @@ from pdb import set_trace
 '''
 
 def plot_distortions(xe, ye, xf, yf):
-	# Coordinates without WFEs
-	# xe = load_variable('../data/GD_IFP_zoom93_obscured_PSF_xcentroid_expected_zern_psd.pkl')
-	# ye = load_variable('../data/GD_IFP_zoom93_obscured_PSF_ycentroid_expected_zern_psd.pkl')
-
-	# # Coordinates with WFEs
-	# xf = load_variable('../data/GD_IFP_zoom93_obscured_PSF_xcentroid_found_with_wfe_airy_zern_psd.pkl')
-	# yf = load_variable('../data/GD_IFP_zoom93_obscured_PSF_ycentroid_found_with_wfe_airy_zern_psd.pkl')
-
 	mcd = ParaxialMICADO(n=3001, m=3001, dpix=50, l=1.49e-3)
 
 	n = xe.shape[0]

scripts/SPIE/Thesis/geometric_distortions_fp_wfe_continuous.py

@@ -1,7 +1,5 @@
 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

scripts/SPIE/Thesis/geometric_distortions_incl_rotations.py

@@ -1,6 +1,5 @@
 import numpy as np
 import sys
-# sys.path.insert(0, '/Users/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 *
 

scripts/SPIE/Thesis/plotting_detectors.py

@@ -8,7 +8,6 @@ import pandas as pd
 import sys
 sys.path.insert(0, '/Users/joost/Dropbox/Werk/PhD/Documents/Published/FourierOptics GitHub release/')
 from fourierOptics import *
-from pdb import set_trace
 
 '''
 	Date: 			2022-06-20

scripts/SPIE/Thesis/plotting_geometric_distortions_IFP.py

@@ -1,4 +1,3 @@
-
 import numpy as np
 import matplotlib.pyplot as plt
 import matplotlib.patches as patches
@@ -8,7 +7,6 @@ import pandas as pd
 import sys
 sys.path.insert(0, '/Users/joost/Dropbox/Werk/PhD/Documents/Published/FourierOptics GitHub release/')
 from fourierOptics import *
-from pdb import set_trace
 from matplotlib.colors import Normalize, LogNorm
 
 '''

scripts/SPIE/Thesis/plotting_geometric_distortions_IFP_zern.py

@@ -8,7 +8,6 @@ import pandas as pd
 import sys
 sys.path.insert(0, '/Users/joost/Dropbox/Werk/PhD/Documents/Published/FourierOptics GitHub release/')
 from fourierOptics import *
-from pdb import set_trace
 from matplotlib.colors import Normalize, LogNorm
 
 '''

scripts/SPIE/Thesis/retrieving_average_tilt.py

@@ -4,7 +4,14 @@ from numpy.polynomial import polynomial
 import sys
 sys.path.insert(0, '/Users/joost/Dropbox/Werk/PhD/Documents/Published/FourierOptics GitHub release/')
 from fourierOptics import *
-from pdb import set_trace
+
+'''
+	Description: This script loads the already generated WFEs and performs a 
+				 linear fit on them. This is then used to find the average tilt
+				 over the beam footprint.
+				 Used for the discussion section of Ch. 3 in my PhD Dissertation.
+'''	
+
 
 def polyfit2d(x, y, z, deg):
 	x = np.asarray(x)