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Added scripts folder with old scripts
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#!/usr/bin/env Python3
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import numpy as np
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from pdb import set_trace
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import matplotlib.pyplot as plt
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from matplotlib import cm, colors
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from cmath import sqrt as csqrt
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from scipy import interpolate
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from scipy.optimize import leastsq
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from matplotlib.ticker import FormatStrFormatter
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from matplotlib.colors import LogNorm
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import pyfftw
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# import glassCatalog
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from tabulate import tabulate
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import types
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import time
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from math import ceil
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import sys
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from mpl_toolkits import mplot3d
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sys.path.insert(0, '../../') # where fourieroptics.py is located, so that it can be imported
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import fourierOptics as fouOpt
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class FourierOptics:
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def __init__(self, l):
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self.l = l # Wavelength
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def plane_wave_propagation_rotation(self, A, dpix=None, Rx=None, Ry=None, oversample=None, show=False, save=False, scaleInputArray=False, outputLimits=False):
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'''
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Propagation through the Fresnel approximation, which is valid in many different situations.
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A separate code for the Fraunhofer propagation is not striclty necessary, as the exponent
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converges to 1 for large z values in any case.
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Input parameters:
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A - [array] (Complex) Input field
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dpix - [float] pixel scale at which the calculations are done
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dz - [float] propagation distance
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oversample - [bool] Apply padding on the outside of A, increasing the size of A
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by the given factor.
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show - [bool] Show the resulting amplitude and phase map after propagation
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save - [bool] Save the figure
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scaleInputArray - [tuple] Rescale the resolution of the input array using interpolation.
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outputCoordinates - [list] list the corners of the desired output coordinate plane.
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Order: [xmin, xmax, ymin, ymax]
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Output:
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E_out - [array] (Complex) Output field distribution
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x, y - [array] Output coordinates
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'''
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if scaleInputArray:
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A = np.asarray(A)
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_n, _m = A.shape
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_nA, _mA = np.linspace(-1, 1, _n), np.linspace(-1, 1, _m)
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A_ip_real = interpolate.interp2d(_nA, _mA, A.real, kind='cubic')
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A_ip_imag = interpolate.interp2d(_nA, _mA, A.imag, kind='linear')
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_a, _b = scaleInputArray
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_nx, _my = np.linspace(-1, 1, _a), np.linspace(-1, 1, _b)
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A_out_ip_real = A_ip_real(_nx, _my)
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A_out_ip_imag = A_ip_imag(_nx, _my)
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A_out_ip = A_out_ip_real + A_out_ip_imag*1j
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A = np.rint(A_out_ip_real)
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if oversample:
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_Aos = np.zeros((np.shape(A)[0]*oversample, np.shape(A)[1]*oversample))
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_Aos[int(len(_Aos)/2-len(A)/2): int(len(_Aos)/2+len(A)/2), int(len(_Aos)/2-len(A)/2): int(len(_Aos)/2+len(A)/2)] = A
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A = _Aos
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_n, _m = np.shape(A)
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# A at z=0 is then
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_E_xy0 = pyfftw.empty_aligned((_n,_m), dtype='complex128')
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_E_xy0[:] = np.fft.ifftshift(A) # use ifftshift to shift origin to start array
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_IntensityNormFactor = np.sum(np.abs(_E_xy0)**2) # Factor to scale the intensity after the FFTs
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_Az0 = pyfftw.empty_aligned((_n,_m), dtype='complex128')
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_FFTW_Obj = pyfftw.FFTW( _E_xy0, _Az0, axes=(0,1), direction='FFTW_BACKWARD', threads=6, flags=('FFTW_ESTIMATE',))
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_FFTW_Obj()
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# E-field at z=dz is the fourier transform of A(z=0)*e^(-ikz)
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_fx_l = np.fft.fftfreq(_n, d=dpix)
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_fy_l = np.fft.fftfreq(_m, d=dpix)
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_fx, _fy = np.meshgrid(_fx_l, _fy_l)
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_fz = np.sqrt( (self.l**(-2) - _fx**2 - _fy**2).astype('complex128') )
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# Rotation about the x and y axis from radians to degrees
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Rx = np.deg2rad(Rx)
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Ry = np.deg2rad(Ry)
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# Rotation matrices
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_Rx = np.array([[1,0,0],
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[0, np.cos(Rx), -np.sin(Rx)],
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[0, np.sin(Rx), np.cos(Rx)]])
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_Ry = np.array([[np.cos(Ry), 0, np.sin(Ry)],
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[0,1,0],
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[-np.sin(Ry), 0, np.cos(Ry)]])
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_R = np.dot(_Rx,_Ry)
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# Rotation in k-space
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_fxr = (_R[0,0]*_fx + _R[1,0]*_fy + _R[2,0]*_fz)
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_fyr = (_R[0,1]*_fx + _R[1,1]*_fy + _R[2,1]*_fz)
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_fzr = np.sqrt( (self.l**(-2) - _fxr**2 - _fyr**2).astype('complex128') )
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# Carrier frequency
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_u0 = _R[2,0]*1/self.l
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_v0 = _R[2,1]*1/self.l
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# Recenter the new rotated frequencies at 0,0
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_fxr_c = (_fxr - _u0)
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_fyr_c = (_fyr - _v0)
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_fzr_c = np.sqrt( (self.l**(-2) - _fxr_c**2 - _fyr_c**2).astype('complex128') )
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# Calculation of the Jacobian
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# _J = (_R[0,0]*_R[1,1] - _R[0,1]*_R[1,0]) + (_R[0,1]*_R[1,2] - _R[0,2]*_R[1,1])*_fxr_c/_fzr_c + (_R[0,2]*_R[1,0]-_R[0,0]*_R[1,2])*_fyr_c/_fzr_c
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_J = (_R[0,0]*_R[1,1] - _R[0,1]*_R[1,0]) + (_R[1,0]*_R[2,0] - _R[2,0]*_R[1,1])*_fxr_c/_fzr_c + (_R[0,2]*_R[2,0]-_R[0,0]*_R[2,1])*_fyr_c/_fzr_c
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# Fourier transform of the input distribution, _A_in
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_E_rot = pyfftw.empty_aligned((_n,_m), dtype='complex128')
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_A_in = pyfftw.empty_aligned((_n,_m), dtype='complex128')
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_A_in[:] = _Az0 * np.abs(_J)
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_FFTW_Obj2 = pyfftw.FFTW( _A_in, _E_rot, axes=(0,1), direction='FFTW_BACKWARD', threads=6, flags=('FFTW_ESTIMATE',))
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_FFTW_Obj2()
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# Coordinates of E_rot
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_y, _x = np.mgrid[-_n / 2 * dpix : _n / 2 * dpix : 1j*_n, -_m / 2 * dpix : _m / 2 * dpix : 1j * _m]
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# Multiplication with the phase contribution due to frequency shift,
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# i.e. shift theorem.
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_carr_freq = np.exp(1j * 2 * np.pi * (_u0 * _x + _v0 * _y))
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_E_rot = np.fft.fftshift(_E_rot) # use fftshift to move the origin from edge to center
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_E_rot *= _carr_freq
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_E_rot /= np.sqrt(_IntensityNormFactor) # Normalization back to initial energy.
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if Rx or Ry:
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# A rotation requires interpolation over the output
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# Performing interpolation to get to the required final plane, done for real and imaginary part.
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_xs = np.linspace(-_n/2*dpix, _n/2*dpix, _n)
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_ys = np.linspace(-_m/2*dpix, _m/2*dpix, _m)
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_zs = np.zeros(_xs.shape)
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_xr = _R[0,0]*_xs + _R[1,0]*_ys + _R[2,0]*_zs # Rotated original coordinates
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_yr = _R[0,1]*_xs + _R[1,1]*_ys + _R[2,1]*_zs # Rotated original coordinates
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_f_ip_real = interpolate.interp2d(_xs, _ys, _E_rot.real, kind='linear')
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_f_ip_imag = interpolate.interp2d(_xs, _ys, _E_rot.imag, kind='linear')
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# _f_ip_real = interpolate.interp2d(_xr, _yr, _E_rot.real, kind='linear')
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# _f_ip_imag = interpolate.interp2d(_xr, _yr, _E_rot.imag, kind='linear')
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_xi = np.linspace(_xr.min(), _xr.max(), _n)
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_yi = np.linspace(_yr.min(), _yr.max(), _m)
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# _xi = _xs
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# _yi = _ys
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_E_out_ip_real = _f_ip_real(_xi, _yi)
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_E_out_ip_imag = _f_ip_imag(_xi, _yi)
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_E_rot = _E_out_ip_real + _E_out_ip_imag*1j
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_y, _x = np.meshgrid(_yi, _xi)
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if show or save:
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# Plot the amplitude and phase
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_E_rot_extent = [np.min(_x), np.max(_x), np.min(_x), np.max(_x)]
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fig = plt.figure(figsize=(8,3))
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ax = fig.add_subplot(121)
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im = ax.imshow(np.abs(_E_rot), cmap='hot', extent=_E_rot_extent)#, vmax=1, vmin=0)
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ax.set_xlabel('x [mm]')
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ax.set_ylabel('y [mm]')
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fig.colorbar(im, ax=ax, label='Normalized intensity')
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ax2 = fig.add_subplot(122)
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im2 = ax2.imshow(np.angle(_E_rot), cmap='hot', extent=_E_rot_extent)
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ax2.set_xlabel('x [mm]')
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ax2.set_ylabel('y [mm]')
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ax.set_xlim([-0.4,0.4])
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ax.set_ylim([-0.4,0.4])
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ax2.set_xlim([-0.4,0.4])
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ax2.set_ylim([-0.4,0.4])
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fig.colorbar(im2, ax=ax2)
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plt.tight_layout()
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if save:
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plt.savefig(save, bbox_inches='tight', transparent=True)
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if show:
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plt.show()
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elif not show:
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plt.close()
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return np.array([_E_rot, _x, _y])
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def phase_exponent(self, fx, fy, l):
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k = 2*np.pi / l
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kx = np.asarray(2*np.pi * fx)
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ky = np.asarray(2*np.pi * fy)
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K_squared = (kx**2 + ky**2)
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kA = np.ones(K_squared.shape) * k
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K_1 = np.sqrt((kA**2-K_squared).astype('complex128'))
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kz = K_1.real + -1j*K_1.imag
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return kz
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def coordinate_rotation(self, Rx, Ry, n=5, m=5):
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# Visualisation of the rotation matrix and projection.
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#
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# A circle C is plotted on the source frame (dark blue),
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# the rotation of C onto the reference plane is shown in red
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# and C is also projected from the source frame onto the
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# reference frame in black.
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#
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_n = n
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_m = m
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Rx = np.deg2rad(Rx)
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Ry = np.deg2rad(Ry)
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dpix = 1/30 * self.l * 1000
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_Rx = np.array([[1,0,0],
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[0, np.cos(Rx), -np.sin(Rx)],
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[0, np.sin(Rx), np.cos(Rx)]])
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_Ry = np.array([[np.cos(Ry), 0, np.sin(Ry)],
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[0,1,0],
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[-np.sin(Ry), 0, np.cos(Ry)]])
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_R = np.dot(_Rx,_Ry)
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# A grid in the source frame, coordinates (xs, ys, zs)
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_ys, _xs = np.mgrid[-_n / 2 * dpix : _n / 2 * dpix : 1j*_n, -_m / 2 * dpix : _m / 2 * dpix : 1j * _m]
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_zs = np.zeros(_xs.shape)
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# Rotated coordinates of the grid in the reference frame, coordinates (xr, yr, zr)
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_xr = _R[0,0]*_xs + _R[1,0]*_ys + _R[2,0]*_zs # Rotated original coordinates
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_yr = _R[0,1]*_xs + _R[1,1]*_ys + _R[2,1]*_zs # Rotated original coordinates
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_zr = _R[0,2]*_xs + _R[1,2]*_ys + _R[2,2]*_zs
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# The circle C in the source frame.
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theta = range(360)
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_xcirc = 1.2 * np.cos(np.deg2rad(theta))
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_ycirc = 1.2 * np.sin(np.deg2rad(theta))
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_zcirc = np.zeros(_xcirc.shape)
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# Rotated coordinates
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_xcirc_r = _R[0,0]*_xcirc + _R[1,0]*_ycirc + _R[2,0]*_zcirc # Rotated original coordinates
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_ycirc_r = _R[0,1]*_xcirc + _R[1,1]*_ycirc + _R[2,1]*_zcirc # Rotated original coordinates
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_zcirc_r = _R[0,2]*_xcirc + _R[1,2]*_ycirc + _R[2,2]*_zcirc
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# Projected coordinates
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_xcirc_p = _xcirc
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_ycirc_p = _ycirc
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_zcirc_p = (-_R[2,0]*_xcirc_p - _R[2,1]*_ycirc_p) / _R[2,2]
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# Plot 3d Wireframe of source plane and reference plane
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fig = plt.figure(figsize=(8,8))
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ax = plt.axes(projection='3d')
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ax.plot_wireframe(_zs, _xs, _ys, label='source frame', color='blue', alpha=.3)
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ax.plot_wireframe(_zr, _xr, _yr, label='reference frame', color='red', alpha=.3)
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ax.plot3D(_zcirc, _xcirc, _ycirc, 'blue')
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ax.plot3D(_zcirc_r, _xcirc_r, _ycirc_r, 'red', alpha=.2)
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ax.plot3D(_zcirc_p, _xcirc_p, _ycirc_p, 'black')
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ax.set_xlabel('z')
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ax.set_ylabel('x')
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ax.set_zlabel('y')
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ax.set_xlim([-3,3])
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ax.set_ylim([-3,3])
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ax.set_zlim([-3,3])
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ax.grid(True, alpha=0.3)
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ax.legend()
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plt.tight_layout()
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# plt.savefig('./coordinate_rotation_figures/coordinate_rotation_rx{:.0f}_ry{:.0f}.png'.format(np.degrees(Rx), np.degrees(Ry)), bbox_inches='tight')
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# plt.close()
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plt.show(block=False)
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if __name__ == '__main__':
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# Pick a wavelength
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l = 30e-3
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# Initiate Fourier Optics
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fou = FourierOptics(l=l)
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fouOpt_norm = fouOpt.FourierOptics(l=l)
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# Pick sampling parameters
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dpix = 1/15*l
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n, m = 1001, 1001
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print ('Your resolution is {}x{} with a pixel size of {}'.format(n,m,dpix))
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# Initiate the profiles class and pick a profile (tophat, obscured tophat or spider)
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prof = fouOpt.Profiles()
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# Use a Top Hat profile:
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# A = prof.top_hat(4*l, n, m, dpix=dpix, oversample=1)
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# Or use a gaussian:
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x, y = np.meshgrid(np.linspace(-n/2*dpix, n/2*dpix, n), np.linspace(-m/2*dpix, m/2*dpix, m))
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gauss = fouOpt.GaussianBeam(0.06, l)
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A = gauss.fundamental_mode(4*l,n,m,np.max(x))
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# Definition of the rotation angles.
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# Rotation about the x-axis is done first, then about the y-axis.
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theta_x = 45 # Degrees
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theta_y = 45 # Degrees
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# Plane wave propagation to 4*lambda
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# Exyz,x4l,y4l = fouOpt_norm.plane_wave_propagation(A, dz=4*l, dpix=dpix, show=True)
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# Show the input distribution
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_E_rot_extent = [np.min(x), np.max(x), np.min(y), np.max(y)]
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fig = plt.figure(figsize=(8,3))
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ax = fig.add_subplot(121)
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im = ax.imshow(np.abs(A), cmap='hot', extent=_E_rot_extent)
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ax.set_xlabel('x [mm]')
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ax.set_ylabel('y [mm]')
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fig.colorbar(im, ax=ax, label='Normalized intensity')
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ax2 = fig.add_subplot(122)
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im2 = ax2.imshow(np.angle(A), cmap='hot', extent=_E_rot_extent)
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ax2.set_xlabel('x [mm]')
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ax2.set_ylabel('y [mm]')
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fig.colorbar(im2, ax=ax2)
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plt.tight_layout()
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plt.show()
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# Illustration of the rotation and projection for the given rotation angles.
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fou.coordinate_rotation(theta_x,theta_y)
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# Plane wave propagation onto a rotated plane.
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Erot,x,y = fou.plane_wave_propagation_rotation(A, dpix=dpix, Rx=theta_x, Ry=theta_y, show=True)
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'''
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# Compare phase to gaussian analysis.
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z0 = n*dpix * np.tan(np.deg2rad(30))
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z = np.linspace(0, 2*z0, n)
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print(int((3+np.sqrt(3))/3*n))
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datacube = []
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for i in range(len(z)):
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print(i)
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A = gauss.fundamental_mode(z[i],n,m,np.max(x))
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# _f_ip_real = interpolate.interp2d(x, y, A.real, kind='linear')
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# _f_ip_imag = interpolate.interp2d(x, y, A.imag, kind='linear')
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# A_out_ip_real = _f_ip_real(_xi, _yi)
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# A_out_ip_imag = _f_ip_imag(_xi, _yi)
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# A = _E_out_ip_real + _E_out_ip_imag*1j
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datacube.append(A[:,i])
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plt.imshow(np.angle(np.asarray(datacube)));plt.colorbar();plt.show()
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plt.imshow(np.abs(np.asarray(datacube)));plt.colorbar();plt.show()
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'''
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