Added descriptions to all scripts, checked functioning

demonstration scripts/fixing_things.py

@@ -1,23 +0,0 @@
-import numpy as np
-import sys
-sys.path.insert(0, '/Users/joost/Dropbox/Werk/PhD/Documents/Published/FourierOptics GitHub release/')
-# sys.path.insert(0, '/Users/joost/Dropbox/Werk/PhD/Analyses/Python/Analytical/Fourier Optics')
-from fourierOptics import *
-
-if __name__ == '__main__':
-	# Initiate MICADO paraxial model
-	mcd = ParaxialMICADO()
-	# mcd.plot_ray_trace()
-
-	print(mcd.platescale)
-	# Initiate WFE object
-	wfe = WavefrontError(mcd.n, mcd.m)
-
-	# Generate PSD surfaces
-	psd = wfe.generate_height_map(200e-6, 2, 1)
-
-	# Add it to ADC-P1
-	mcd.ELT_ADC.p1.add_wavefront_error(psd)
-
-	# Generate the PSF and plot it
-	E, x, y = mcd.propagate(l=1.35e-3,surface=-1, zoom=True, show=True) # image_output=[-.4,.4,-.4,.4]

demonstration scripts/generate_PSF_with_WFE.py

@@ -1,8 +1,16 @@
 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 *
 
+'''
+	Description:
+	This script generates a point spread function of the MICADO optical model.
+	During the setup a wavefront error of 200 nm RMS is added to the first 
+	prisms of the MICADO atmospheric dispersion corrector.
+'''
+
+
 if __name__ == '__main__':
 	# Initiate MICADO paraxial model
 	mcd = ParaxialMICADO()

demonstration scripts/generate_bahtinov_dispersion.py

@@ -1,9 +1,21 @@
 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 *
 
 
+'''
+	Description:
+	This script generates a point spread function of the MICADO optical model.
+	Here we apply a Bahtinov mask to the pupil and simulate a broadband PSF,
+	done through the summation of multiple (here: 15) wavelength slices. 
+	When there is atmospheric dispersion, the diffraction speckles created by the 
+	Bahtinov mask will start to point to a location outside the zeroth order 
+	PSF core.
+	Here, atmospheric dispersion is modelled as a wavelength dependent phase
+	tilt.
+'''
+
 if __name__ == '__main__':
 	# Initiate MICADO paraxial model
 	mcd = ParaxialMICADO()

demonstration scripts/generate_field.py

@@ -1,8 +1,17 @@
 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 *
-from pdb import set_trace
+
+
+'''
+	Description:
+	This script generates nine points in a small field to illustrate the 
+	most basic form of off-axis propagation. 
+	For larger off-axis distances the hx and hy values should directly
+	be supplied to the propagate function.
+'''
+
 
 def field_angle(hx, hy):
 	fx = hx * 0.0075
@@ -14,14 +23,6 @@ if __name__ == '__main__':
 	# Initializing MICADO paraxial model
 	mcd = ParaxialMICADO()
 	wfe = WavefrontError(mcd.n, mcd.m)
-
-	# Uncomment to load in WFE (coma)
-	# Problem here is that the field of view is too small to see 
-	# a radial effect...
-	# xin, yin = load_variable('../adc_data_coordinates.pkl')
-	# adcObj = ADC_surfaces(xin,yin)
-	# zern = wfe.zernike_cartesian([0,0,0,0,0,0,0,100e-5], adcObj.xz, adcObj.yz, rescale=False)
-	# mcd.ELT_ADC.p1.add_wavefront_error(zern)
 	
 	# Setup
 	l = 1.49e-3

demonstration scripts/generate_propagation_figures.py

@@ -1,9 +1,14 @@
 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 *
 import matplotlib.pyplot as plt
-from pdb import set_trace
+
+'''
+	Description:
+	This script generates the amplitude and phase information of all surfaces
+	in the MICADO paraxial model in a nicely presented form.
+'''
 
 if __name__ == '__main__':
 	plt.rc('font', family='serif')

demonstration scripts/thesis_propagation_figures.py

@@ -1,10 +1,16 @@
 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 *
 import matplotlib.pyplot as plt
-from pdb import set_trace
+
+'''
+	Description:
+	This script generates the amplitude and phase information of all surfaces
+	in the MICADO paraxial model in a nicely presented form.
+'''
+
+
 
 if __name__ == '__main__':
 	plt.rc('font', family='serif')
@@ -13,13 +19,9 @@ if __name__ == '__main__':
 	# Initiate MICADO paraxial model
 	mcd = ParaxialMICADO(n=3001, m=3001, dpix=50)
 
-	# Generate the PSF and plot it
-	# E, x, y = mcd.propagate(l=1.35e-3,surface=-1, zoom=True, show=True, save='all')
-
 	confList = [ ( 1, [-0.4, 0.4, -0.4, 0.4], 	'02_fourier_ELT-IFP.pdf'),
 				 ( 2, [-50, 50, -50, 50], 		'03_fourier_ELT-COL.pdf'),
 				 ( 4, [-50, 50, -50, 50], 		'04_fourier_ELT-MCD-ADC-P2.pdf'),
-				 # (-1, [-1.2, 1.2, -1.2, 1.2], 	'05_fourier_ELT-MCD-DET.pdf')]
 				 (-1, [-1.2/2.669, 1.2/2.669, -1.2/2.669, 1.2/2.669], 	'05_fourier_ELT-MCD-DET.pdf')]
 
 
@@ -50,4 +52,4 @@ if __name__ == '__main__':
 	_fig.colorbar(_im2, ax=_ax2, label='Phase')
 	plt.tight_layout()
 	# plt.savefig('01_fourier_ELT-M1.pdf', bbox_inches='tight', transparent=True)
-	plt.close()#show()
+	plt.show()