def dpc_integration(dpc01,
dpc10,
pixelsize,
idx4crop=[0, -1, 0, -1],
plotErrorIntegration=False,
saveFileSuf=None,
shifthalfpixel=False,
method='FC'):
'''
TODO: Write Docstring
Integration of DPC to obtain phase. Currently only supports
Frankot Chellappa
'''
if idx4crop == '':
vmin = wpu.mean_plus_n_sigma(dpc01**2 + dpc10**2, -3)
vmax = wpu.mean_plus_n_sigma(dpc01**2 + dpc10**2, 3)
_, idx = wpu.crop_graphic_image(dpc01**2 + dpc10**2,
kargs4graph={
'cmap': 'viridis',
'vmin': vmin,
'vmax': vmax
})
else:
idx = idx4crop
dpc01 = wpu.crop_matrix_at_indexes(dpc01, idx)
dpc10 = wpu.crop_matrix_at_indexes(dpc10, idx)
if method == 'FC':
phase = wps.frankotchellappa(dpc01 * pixelsize[1],
dpc10 * pixelsize[0],
reflec_pad=True)
phase = np.real(phase)
else:
wpu.print_red('ERROR: Unknown integration method: ' + method)
if plotErrorIntegration:
wps.error_integration(dpc01 * pixelsize[1],
dpc10 * pixelsize[0],
phase,
pixelsize,
errors=False,
shifthalfpixel=shifthalfpixel,
plot_flag=True)
if saveFileSuf is not None:
wpu.save_figs_with_idx(saveFileSuf)
return phase
def dpc_integration(dpc01, dpc10, pixelsize, idx4crop=[0, -1, 0, -1],
plotErrorIntegration=False,
saveFileSuf=None,
shifthalfpixel=False, method='FC'):
'''
TODO: Write Docstring
Integration of DPC to obtain phase. Currently only supports
Frankot Chellappa
'''
if idx4crop == '':
vmin = wpu.mean_plus_n_sigma(dpc01**2+dpc10**2, -3)
vmax = wpu.mean_plus_n_sigma(dpc01**2+dpc10**2, 3)
_, idx = wpu.crop_graphic_image(dpc01**2+dpc10**2,
kargs4graph={'cmap': 'viridis',
'vmin': vmin,
'vmax': vmax})
else:
idx = idx4crop
dpc01 = wpu.crop_matrix_at_indexes(dpc01, idx)
dpc10 = wpu.crop_matrix_at_indexes(dpc10, idx)
if method == 'FC':
phase = wps.frankotchellappa(dpc01*pixelsize[1],
dpc10*pixelsize[0],
reflec_pad=True)
phase = np.real(phase)
else:
wpu.print_red('ERROR: Unknown integration method: ' + method)
if plotErrorIntegration:
wps.error_integration(dpc01*pixelsize[1],
dpc10*pixelsize[0],
phase, pixelsize, errors=False,
shifthalfpixel=shifthalfpixel, plot_flag=True)
if saveFileSuf is not None:
wpu.save_figs_with_idx(saveFileSuf)
return phase
phase = wgi.dpc_integration(diffPhase01, diffPhase10, virtual_pixelsize)
#phase = np.real(phase)
delta = 5.3276849026895334e-06
wgi.plot_integration(-(phase - np.min(phase))/kwave/delta*1e6,
virtual_pixelsize,
titleStr=r'Thickness Beryllium $[\mu m]$,' +'\n Frankot Chellappa integration',
plot3dFlag=True,
saveFigFlag=True,
saveFileSuf=saveFileSuf)
wps.error_integration(diffPhase01*virtual_pixelsize[1],
diffPhase10*virtual_pixelsize[0],
phase, virtual_pixelsize, errors=False,
plot_flag=True)
wpu.save_figs_with_idx(saveFileSuf)
# %%
def _pad_2_make_square(array, mode='edge'):
diff_shape = array.shape[0] - array.shape[1]
if diff_shape > 1:
return np.pad(array, ((0, 0), (0, diff_shape)), mode=mode)
elif diff_shape < 1:
return np.pad(array, ((0, -diff_shape), (0, 0)), mode=mode)
#==============================================================================
# %% integration frankotchellappa
#==============================================================================
#integration_res = frankotchellappa(dTx,dTy)
integration_res = wpsg.frankotchellappa(dTx * pixelsizeImg, dTy * pixelsizeImg)
thickness = np.real(integration_res)
thickness = thickness - np.min(thickness)
# %%
wpsg.error_integration(dTx * pixelsizeImg,
dTy * pixelsizeImg,
thickness,
pixelsizeImg,
shifthalfpixel=True,
plot_flag=True)
#==============================================================================
# %% Plot
#==============================================================================
def mySaveFig(figname=None):
if figname is None:
figname = str('output/graph_{0:02d}.png'.format(next(figCount)))
plt.savefig(figname)
print(figname + ' SAVED')
plt.plot(yy[:,midleY], func[:,midleY], '-kx', markersize=10, label='f y') shifted = integrated_2d[:,midleY] + np.mean(func[:,midleY]-integrated_2d[:,midleY]) plt.plot(yy[:,midleY]-pixelsize/2, shifted, '-ro', label='intemidleXgrated shifted f y') plt.xlabel(r'$y$') plt.legend() plt.title(r'Profile $y$') plt.show(block=True) # %% Plot Integration Qaulity errorx, errory = error_integration(del_func_2d_x, del_func_2d_y, integrated_2d, pixelsize, plot_flag=True) # %% #exit() # %% foo = del_func_2d_y[midleX,:] plt.figure() plt.plot(xx[midleX,:], foo, '-kx', markersize=10) plt.plot(xx[midleX,:]+pixelsize/2, wpu.shift_subpixel_1d(foo, 2), '-r.', markersize=10) plt.plot(xx[midleX,:]+pixelsize/4, wpu.shift_subpixel_1d(foo, 4), '-b.', markersize=10)
#phase = np.real(phase)
delta, _ = wpu.get_delta(phenergy, choice_idx=1, gui_mode=False)
wgi.plot_integration(-(phase - np.min(phase)) / kwave / delta * 1e6,
virtual_pixelsize,
titleStr=r'Thickness Beryllium $[\mu m]$,' +
'\n Frankot Chellappa integration',
plot3dFlag=True,
saveFigFlag=True,
saveFileSuf=saveFileSuf)
wps.error_integration(diffPhase01 * virtual_pixelsize[1],
diffPhase10 * virtual_pixelsize[0],
phase,
virtual_pixelsize,
errors=False,
plot_flag=True)
wpu.save_figs_with_idx(saveFileSuf)
# %%
def _pad_2_make_square(array, mode='edge'):
diff_shape = array.shape[0] - array.shape[1]
if diff_shape > 1:
return np.pad(array, ((0, 0), (0, diff_shape)), mode=mode)
#==============================================================================
# %% integration frankotchellappa
#==============================================================================
#integration_res = frankotchellappa(dTx,dTy)
integration_res = wpsg.frankotchellappa(dTx*pixelsizeImg, dTy*pixelsizeImg)
thickness = np.real(integration_res)
thickness = thickness - np.min(thickness)
# %%
wpsg.error_integration(dTx*pixelsizeImg, dTy*pixelsizeImg, thickness,
[pixelsizeImg, pixelsizeImg], shifthalfpixel=True, plot_flag=True)
#==============================================================================
# %% Thickness
#==============================================================================
stride = 1
wpu.plot_profile(xmatrix[::stride, ::stride]*1e6,
ymatrix[::stride, ::stride]*1e6,
thickness[::stride, ::stride]*1e6,
title='Thickness', xlabel='[um]', ylabel='[um]',
arg4main={'cmap':'spectral'}) #, xo=0.0, yo=0.0)_1Dparabol_4_fit
plt.show(block=True)