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
harmonicPeriod=harmPeriod,
plotFlag=True,
unwrapFlag=True,
verbose=True)
# the spatial resolution is the grating period, what we call the virtual pixel size
virtual_pixelsize = [pixelsize[0]*img.shape[0]/int00.shape[0],
pixelsize[1]*img.shape[1]/int00.shape[1]]
# covert phaseFFT to physical quantities, ie, differential phase
diffPhase01 = -alpha_x*virtual_pixelsize[1]/distDet2sample/wavelength
diffPhase10 = -alpha_y*virtual_pixelsize[0]/distDet2sample/wavelength
phase = wps.frankotchellappa(diffPhase01*pixelsize[1],
diffPhase10*pixelsize[0])
phase = np.real(phase)
# %% Plots
saveFigFlag = True
saveFileSuf = 'results'
wgi.plot_intensities_harms(int00, int01, int10,
virtual_pixelsize, saveFigFlag=saveFigFlag,
titleStr='Intensity',
saveFileSuf=saveFileSuf)
wgi.plot_dark_field(darkField01, darkField10,
virtual_pixelsize, saveFigFlag=saveFigFlag,
# ============================================================================= size = np.shape(dpc_x) pixelsize = .650*1e-6 xx, yy = wpu.realcoordmatrix(size[1], pixelsize, size[0], pixelsize) #============================================================================== # %% Integration #============================================================================== from wavepy.surface_from_grad import frankotchellappa, error_integration result = frankotchellappa(dpc_x, dpc_y, reflec_pad=True) result = np.real(result) result *= -1 result -= np.min(result) np.savetxt(fname_dpc_h5[:-3] + 'FC_integration.dat', result) #============================================================================== # %% Plot integrated 2d #============================================================================== wpu.plot_profile(xx[::5, ::5]*1e6, yy[::5, ::5]*1e6, result[::-5, ::-5])
totalS = np.sqrt(sx**2 + sy**2)
# Differenctial Phase
dpx = kwave * np.arctan2(sx * pixelsizeDetector, distDet2sample)
dpy = kwave * np.arctan2(sy * pixelsizeDetector, distDet2sample)
# Differenctial Thickness
dTx = 1.0 / delta * np.arctan2(sx * pixelsizeDetector, distDet2sample)
dTy = 1.0 / delta * np.arctan2(sy * pixelsizeDetector, distDet2sample)
#==============================================================================
# %% 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)
#==============================================================================
if noise is True:
del_func_2d_x += .01*(2*np.random.rand(size[0],size[1]) -1)
del_func_2d_y += .01*(2*np.random.rand(size[0],size[1]) -1)
#==============================================================================
# %% Integration
#==============================================================================
from wavepy.surface_from_grad import frankotchellappa, error_integration
result = frankotchellappa(del_func_2d_x, del_func_2d_y,
reflec_pad=True)
integrated_2d_mod = np.abs(result)
integrated_2d_r = np.real(result)
integrated_2d_i = np.imag(result)
integrated_2d = integrated_2d_r
xx, yy = wpu.realcoordmatrix(func.shape[1], pixelsize, func.shape[0], pixelsize)
#==============================================================================
# %% Plot derivatives
#==============================================================================
harmonicPeriod=harmPeriod,
plotFlag=True,
unwrapFlag=True,
verbose=True)
# the spatial resolution is the grating period, what we call the virtual pixel size
virtual_pixelsize = [
pixelsize[0] * img.shape[0] / int00.shape[0],
pixelsize[1] * img.shape[1] / int00.shape[1]
]
# covert phaseFFT to physical quantities, ie, differential phase
diffPhase01 = -alpha_x * virtual_pixelsize[1] / distDet2sample / wavelength
diffPhase10 = -alpha_y * virtual_pixelsize[0] / distDet2sample / wavelength
phase = wps.frankotchellappa(diffPhase01 * pixelsize[1],
diffPhase10 * pixelsize[0])
phase = np.real(phase)
# %% Plots
saveFigFlag = True
saveFileSuf = 'results'
wgi.plot_intensities_harms(int00,
int01,
int10,
virtual_pixelsize,
saveFigFlag=saveFigFlag,
titleStr='Intensity',
saveFileSuf=saveFileSuf)
#plt.xlabel('[um]')
#plt.ylabel('[um]')
#
#plt.show()
#wpu.save_figs_with_idx(foutname)
#
#==============================================================================
# %% 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
#==============================================================================