def _plot_profile(data, pixelsize, title, arg4main={'cmap': 'viridis'}):
xxGrid, yyGrid = wpu.grid_coord(data, pixelsize)
wpu.plot_profile(xxGrid*1e6, yyGrid*1e6, data[::-1, :],
xlabel=r'$x [\mu m]$', ylabel=r'$y [\mu m]$',
title=title,
xunit='\mu m', yunit='\mu m',
arg4main=arg4main)
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])
# %%
fig = plt.figure(figsize=(10, 7))
ax = fig.add_subplot(111, projection='3d')
surf = ax.plot_surface(xx[::5, ::5]*1e6, yy[::5, ::5],
-result[::-5, ::-5],
rstride=result.shape[0] // 501 + 1,
cstride=result.shape[1] // 501 + 1,
cmap='viridis', linewidth=0.1)
plt.xlabel(r'$x$ [$\mu m$]')
plt.ylabel(r'$y$ [$\mu m$]')
plt.colorbar(surf, shrink=.8, aspect=20)
def plot_integration(integrated,
pixelsize,
titleStr='Title',
ctitle=' ',
max3d_grid_points=101,
plotProfile=True,
plot3dFlag=True,
saveFigFlag=False,
saveFileSuf='graph',
**kwarg4surf):
'''
TODO: Write Docstring
'''
xxGrid, yyGrid = wpu.grid_coord(integrated, pixelsize)
factor_x, unit_x = wpu.choose_unit(xxGrid)
factor_y, unit_y = wpu.choose_unit(yyGrid)
# Plot Integration 2
if plot3dFlag:
fig = plt.figure(figsize=(10, 8))
ax = fig.add_subplot(111, projection='3d')
rstride = integrated.shape[0] // max3d_grid_points + 1
cstride = integrated.shape[1] // max3d_grid_points + 1
surf = ax.plot_surface(xxGrid * factor_x,
yyGrid * factor_y,
integrated[::-1, :],
rstride=rstride,
cstride=cstride,
cmap='viridis',
linewidth=0.1,
**kwarg4surf)
ax_lim = np.max([np.abs(xxGrid * factor_x), np.abs(yyGrid * factor_y)])
ax.set_xlim3d(-ax_lim, ax_lim)
ax.set_ylim3d(-ax_lim, ax_lim)
if 'vmin' in kwarg4surf:
ax.set_zlim3d(bottom=kwarg4surf['vmin'])
if 'vmax' in kwarg4surf:
ax.set_zlim3d(top=kwarg4surf['vmax'])
plt.xlabel(r'$x [' + unit_x + ' m]$', fontsize=24)
plt.ylabel(r'$y [' + unit_y + ' m]$', fontsize=24)
plt.title(titleStr, fontsize=24, weight='bold')
cbar = plt.colorbar(surf, shrink=.8, aspect=20)
cbar.ax.set_title(ctitle, y=1.01)
plt.tight_layout(rect=[0, 0, 1, 1])
ax.text2D(0.05,
0.9,
'strides = {}, {}'.format(rstride, cstride),
transform=ax.transAxes)
if saveFigFlag:
ax.view_init(elev=30, azim=60)
wpu.save_figs_with_idx(saveFileSuf)
ax.view_init(elev=30, azim=-120)
wpu.save_figs_with_idx(saveFileSuf)
plt.pause(.5)
plt.show(block=False)
if plotProfile:
wpu.plot_profile(xxGrid * factor_x,
yyGrid * factor_y,
integrated[::-1, :],
xlabel=r'$x [' + unit_x + ' m]$',
ylabel=r'$y [' + unit_y + ' m]$',
title=titleStr,
xunit='\mu m',
yunit='\mu m',
arg4main={
'cmap': 'viridis',
'lw': 3
})
if saveFigFlag:
plt.ioff()
plt.figure(figsize=(10, 8))
plt.imshow(integrated[::-1, :],
cmap='viridis',
extent=wpu.extent_func(integrated, pixelsize) * factor_x,
**kwarg4surf)
plt.xlabel(r'$x [' + unit_x + ' m]$', fontsize=24)
plt.ylabel(r'$y [' + unit_x + ' m]$', fontsize=24)
plt.title(titleStr, fontsize=18, weight='bold')
cbar = plt.colorbar()
cbar.ax.set_title(ctitle, y=1.01)
wpu.save_figs_with_idx(saveFileSuf)
plt.close()
plt.ion()
##=========================================================#
# %% Plot u1
##=========================================================#
factorX, unitStrX = wpu.choose_unit(X)
factorY, unitStrY = wpu.choose_unit(Y)
unitStrX = unitStrX + ' m'
unitStrY = unitStrY + ' m'
#
## U1
wpu.plot_profile(X * factorX,
Y * factorY,
np.abs(u1_xy**2),
r'$x [' + unitStrX + ']$',
r'$y [' + unitStrY + ']$',
r'Intensity [a.u.]',
xo=0.0,
yo=0.0,
xunit=unitStrX,
yunit=unitStrY)
plt.show(block=True)
##=========================================================#
# %% Propagation
##=========================================================#
print('WG: Propagation...')
#u2_xy = propTForIR(u1_xy, Lx, Ly, wavelength, zz)
#titleStr = str(r'propTForIR, zz=%.3fmm, Intensity [a.u.]'
# % (zz*1e3))
# %% DPC
dpc_1d = unwrap_phase(dpc_1d)
wpu.plot_slide_colorbar(dpc_1d / np.pi / 2.0,
title=r'DPC [$\pi rad$]',
xlabel=r'x [$\mu m$]',
ylabel=r'y [$\mu m$]',
extent=wpu.extent_func(dpc_1d, pixelSize) * 1e6)
# %%
xx, yy = wpu.realcoordmatrix(dpc_1d.shape[1], pixelSize, dpc_1d.shape[0],
pixelSize)
wpu.plot_profile(xx * 1e3,
yy * 1e3,
dpc_1d / np.pi / 2.0,
xlabel='[mm]',
ylabel='[mm]')
# %% chi2
plt.figure()
hist = plt.hist(chi2[np.where(chi2 < 10 * np.std(chi2))], 100, log=False)
plt.title(r'$\chi^2$', fontsize=14, weight='bold')
plt.show(block=False)
chi2_copy = np.copy(chi2)
wpu.plot_slide_colorbar(chi2_copy,
title=r'$\chi^2$ sample',
xlabel=r'x [$\mu m$ ]',
def plot_residual_parabolic_lens_2d(thickness,
pixelsize,
fitted,
fitParameters,
saveFigFlag=False,
savePickle=False,
str4title='',
saveSdfData=False,
vlimErrSigma=1,
plotProfileFlag=True,
plot3dFlag=True,
makeAnimation=False):
xmatrix, ymatrix = wpu.grid_coord(thickness, pixelsize)
errorThickness = thickness - fitted
argNotNAN = np.isfinite(errorThickness)
factorx, unitx = wpu.choose_unit(xmatrix)
factory, unity = wpu.choose_unit(ymatrix)
factorz, unitz = wpu.choose_unit(errorThickness[argNotNAN])
ptp = np.ptp(errorThickness[argNotNAN].flatten() * factorz)
wpu.print_red('PV: {0:4.3g} '.format(ptp) + unitz[-1] + 'm')
sigmaError = np.std(errorThickness[argNotNAN].flatten() * factorz)
wpu.print_red('SDV: {0:4.3g} '.format(sigmaError) + unitz[-1] + 'm')
str4title += r'Residual, ' + \
r'R $= {:.4g} \mu m$,'.format(fitParameters[0]*1e6) + '\n' + \
r'PV $= {0:.2f}$ '.format(ptp) + '$' + unitz + ' m$, '\
'SDV $= {0:.2f}$ '.format(sigmaError) + '$' + unitz + ' m$'
# Plot Histogram
plt.figure(figsize=(7, 8))
plt.hist(errorThickness[argNotNAN] * factorz,
100,
color='r',
histtype='step')
plt.xlabel(r'Residual [$' + unitz + ' m$ ]')
plt.title(str4title)
if saveFigFlag:
wpu.save_figs_with_idx(fname2save, extension='png')
plt.show(block=False)
# Plot Profiles
vlimErr = wpu.mean_plus_n_sigma(errorThickness[argNotNAN] * factorz,
vlimErrSigma / 2)
cmap4graph = plt.cm.Spectral_r
cmap4graph.set_over('m')
cmap4graph.set_under('c')
if plotProfileFlag:
wpu.plot_profile(xmatrix * factorx,
ymatrix * factory,
errorThickness * factorz,
title=str4title,
xlabel=r'[$' + unitx + ' m$ ]',
ylabel=r'[$' + unity + ' m$ ]',
zlabel=r'[$' + unitz + ' m$ ]',
arg4main={
'cmap': 'Spectral_r',
'vmin': -vlimErr,
'vmax': vlimErr,
'extend': 'both'
})
if savePickle or saveFigFlag:
fig = plt.figure(figsize=(10, 7))
cf = plt.contourf(xmatrix * factorx,
ymatrix * factory,
errorThickness * factorz,
256,
cmap=cmap4graph,
extend='both')
plt.clim(-vlimErr, vlimErr)
plt.contour(cf, levels=cf.levels[::32], colors='gray')
plt.xlabel(r'[$' + unitx + ' m$ ]', fontsize=22)
plt.ylabel(r'[$' + unity + ' m$ ]', fontsize=22)
plt.title(str4title, fontsize=22)
cbar = plt.colorbar(cf, shrink=.8, aspect=20)
# cbar.set_clim(-vlimErr, vlimErr)
cbar.ax.set_title(r'[$' + unitz + ' m$ ]', y=1.01)
plt.gca().set_aspect('equal', adjustable='box')
plt.grid(color='grey')
if saveFigFlag:
wpu.save_figs_with_idx(fname2save, extension='png')
if savePickle:
wpu.save_figs_with_idx_pickle(fig, fname2save)
plt.show(block=True)
# Plot 3D
if plot3dFlag:
wpu.print_red('MESSAGE: Ploting 3d in the background')
fig = plt.figure(figsize=(10, 7), facecolor="white")
ax = fig.gca(projection='3d')
plt.tight_layout(pad=2.5)
surf = ax.plot_trisurf(xmatrix[argNotNAN].flatten() * factorx,
ymatrix[argNotNAN].flatten() * factory,
errorThickness[argNotNAN].flatten() * factorz,
vmin=-vlimErr,
vmax=vlimErr,
cmap=cmap4graph,
linewidth=0.1,
shade=False)
ax.view_init(azim=-120, elev=40)
plt.xlabel(r'$x$ [$' + unitx + ' m$ ]')
plt.ylabel(r'$y$ [$' + unity + ' m$ ]')
plt.title(str4title)
cbar = plt.colorbar(surf, shrink=.8, aspect=20, extend='both')
cbar.ax.set_title(r'[$' + unitz + ' m$ ]', y=1.01)
plt.tight_layout()
if saveFigFlag:
wpu.save_figs_with_idx(fname2save, extension='png')
ax.view_init(azim=690, elev=40)
wpu.save_figs_with_idx(fname2save, extension='png')
if makeAnimation:
# plt.show(block=False)
plt.pause(1.0)
wpu.rocking_3d_figure(ax,
wpu.get_unique_filename(fname2save, 'gif'),
elevOffset=45,
azimOffset=60,
elevAmp=0,
azimAmpl=-1,
dpi=80,
npoints=5)
plt.pause(1.0)
plt.close('all')
# plt.show(block=True)
if saveSdfData:
mask_for_sdf = errorThickness * 0.0
mask_for_sdf[~argNotNAN] = 1.0
errorThickness[~argNotNAN] = 00000000
wpu.save_sdf_file(
errorThickness, pixelsize,
wpu.get_unique_filename(fname2save + '_residual', 'sdf'))
wpu.save_sdf_file(
mask_for_sdf, pixelsize,
wpu.get_unique_filename(fname2save + '_residual_mask', 'sdf'))
return sigmaError / factorz, ptp / factorz
idx4crop = wpu.graphical_roi_idx(thickness_temp * 1e6, verbose=True)
thickness = wpu.crop_matrix_at_indexes(thickness, idx4crop)
xx = wpu.crop_matrix_at_indexes(xx, idx4crop)
yy = wpu.crop_matrix_at_indexes(yy, idx4crop)
stride = thickness.shape[0] // 125
if gui_mode:
wpu.plot_profile(xx[::stride, ::stride] * 1e6,
yy[::stride, ::stride] * 1e6,
thickness[::stride, ::stride] * 1e6,
xlabel=r'$x$ [$\mu m$ ]',
ylabel=r'$y$ [$\mu m$ ]',
zlabel=r'$z$ [$\mu m$ ]',
arg4main={'cmap': 'Spectral_r'})
# %% Center image
radius4centering = np.min(thickness.shape) * np.min(pixelSize) * .75
# thickness = -1*thickness + np.max(thickness)
thickness = center_lens_array_max_fit(thickness, pixelSize,
radius4centering)
wpu.log_this('Array cropped to have the max at the center of the array',
preffname=fname2save)
# thickness = center_lens_array_max_fit(thickness, pixelSize, radius4centering)
rho_x, rho_y = wpu.reciprocalcoordmatrix(qx.shape[1], qy[1, 0] - qy[0, 0],
qy.shape[0], qx[0, 1] - qx[0, 0])
rho_x *= 2 * np.pi
rho_y *= 2 * np.pi
# %%
#plotThis = norm_abs_fftimg # *wpu.nan_mask_threshold(norm_abs_fftimg,1e-2*1j)
#plotThis = scipy.ndimage.uniform_filter(norm_abs_fftimg, size=(1,1))
plotThis = scipy.ndimage.uniform_filter(norm_abs_fftimg, size=(1, 1))
plotThis[plotThis >= .01] = 0.0
wpu.plot_profile(rho_x, rho_y, plotThis, arg4main={'vmax': 1e-2})
plt.show(block=True)
# %%
def create_mask_peaks2D(array2D, threshold=None, order=3):
if threshold is not None:
mask_threshold = wpu.nan_mask_threshold(array2D, threshold=threshold)
else:
mask_threshold = array2D * 0.0 + 1.0
idx_x_axis_0, idx_y_axis_0 = scipy.signal.argrelmax(array2D *
mask_threshold,
thickness_croped = center_max_2darray(thickness_croped)
xVec_croped1 = wpu.realcoordvec(thickness_croped.shape[1], pixelsizeImg)
yVec_croped1 = wpu.realcoordvec(thickness_croped.shape[0], pixelsizeImg)
xmatrix_croped1, ymatrix_croped1 = np.meshgrid(xVec_croped1, yVec_croped1)
# %%
lim = 1
wpu.plot_profile(xmatrix_croped1[lim:-lim, lim:-lim] * 1e6,
ymatrix_croped1[lim:-lim, lim:-lim] * 1e6,
thickness_croped[lim:-lim, lim:-lim] * 1e6,
title='Thickness centered [um]',
xlabel='[um]',
ylabel='[um]',
arg4main={'cmap': 'Spectral_r'}) #, xo=0.0, yo=0.0)
plt.show(block=True)
# %%
#
fig = plt.figure(figsize=(10, 7))
ax = fig.add_subplot(111, projection='3d')
stride = thickness_croped.shape[0] // 100
if stride == 0: stride = 1
ylabel=r'y [$\mu m$]',
extent=wpu.extent_func(dpc_1d, pixelSize)*1e6)
# %% DPC
dpc_1d = unwrap_phase(dpc_1d)
wpu.plot_slide_colorbar(dpc_1d/np.pi/2.0,
title=r'DPC [$\pi rad$]',
xlabel=r'x [$\mu m$]',
ylabel=r'y [$\mu m$]',
extent=wpu.extent_func(dpc_1d, pixelSize)*1e6)
# %%
xx, yy = wpu.realcoordmatrix(dpc_1d.shape[1], pixelSize,
dpc_1d.shape[0], pixelSize)
wpu.plot_profile(xx*1e3, yy*1e3, dpc_1d/np.pi/2.0,
xlabel='[mm]', ylabel='[mm]')
# %% chi2
plt.figure()
hist = plt.hist(chi2[np.where(chi2 < 10*np.std(chi2))], 100, log=False)
plt.title(r'$\chi^2$', fontsize=14, weight='bold')
plt.show(block=False)
chi2_copy = np.copy(chi2)
wpu.plot_slide_colorbar(chi2_copy, title=r'$\chi^2$ sample',
xlabel=r'x [$\mu m$ ]',
ylabel=r'y [$\mu m$ ]',
extent=wpu.extent_func(chi2, pixelSize)*1e6)
import numpy as np
import wavepy.utils as wpu
if len(sys.argv) != 1:
fname = sys.argv[1]
else:
fname = easyqt.get_file_names("Data File to Plot")[0]
data = dxchange.read_tiff(fname)
data = wpu.crop_graphic_image(data, kargs4graph={'cmap': 'rainbow'})[0]
# %%
nx, ny = np.shape(data)
stride = 1
if nx > 200 or ny > 200:
stride = easyqt.get_int(
'Number of points: {} x {}.'.format(nx, ny) +
' Enter value for stride:', 'Enter Value', 2, 1, 101)
yyGrid, xxGrid = np.mgrid[0:nx:stride, 0:ny:stride]
# %%
wpu.plot_profile(xxGrid, yyGrid, data[::stride, ::stride], title=fname)
# %%
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)
#==============================================================================
# %% Plot
#==============================================================================
def plotsidebyside(array1, array2, title1='', title2='', maintitle=''):
fig = plt.figure(figsize=(14, 5))
def plot_integration(integrated, pixelsize,
titleStr='Title', ctitle=' ',
max3d_grid_points=101,
plotProfile=True,
plot3dFlag=True,
saveFigFlag=False,
saveFileSuf='graph',
**kwarg4surf):
'''
TODO: Write Docstring
'''
xxGrid, yyGrid = wpu.grid_coord(integrated, pixelsize)
factor_x, unit_x = wpu.choose_unit(xxGrid)
factor_y, unit_y = wpu.choose_unit(yyGrid)
# Plot Integration 2
if plot3dFlag:
fig = plt.figure(figsize=(10, 8))
ax = fig.add_subplot(111, projection='3d')
rstride = integrated.shape[0] // max3d_grid_points + 1
cstride = integrated.shape[1] // max3d_grid_points + 1
surf = ax.plot_surface(xxGrid*factor_x, yyGrid*factor_y,
integrated[::-1, :],
rstride=rstride,
cstride=cstride,
cmap='viridis', linewidth=0.1, **kwarg4surf)
ax_lim = np.max([np.abs(xxGrid*factor_x), np.abs(yyGrid*factor_y)])
ax.set_xlim3d(-ax_lim, ax_lim)
ax.set_ylim3d(-ax_lim, ax_lim)
if 'vmin' in kwarg4surf:
ax.set_zlim3d(bottom=kwarg4surf['vmin'])
if 'vmax' in kwarg4surf:
ax.set_zlim3d(top=kwarg4surf['vmax'])
plt.xlabel(r'$x [' + unit_x + ' m]$', fontsize=24)
plt.ylabel(r'$y [' + unit_y + ' m]$', fontsize=24)
plt.title(titleStr, fontsize=24, weight='bold')
cbar = plt.colorbar(surf, shrink=.8, aspect=20)
cbar.ax.set_title(ctitle, y=1.01)
plt.tight_layout(rect=[0, 0, 1, 1])
ax.text2D(0.05, 0.9, 'strides = {}, {}'.format(rstride, cstride),
transform=ax.transAxes)
if saveFigFlag:
ax.view_init(elev=30, azim=60)
wpu.save_figs_with_idx(saveFileSuf)
ax.view_init(elev=30, azim=-120)
wpu.save_figs_with_idx(saveFileSuf)
plt.pause(.5)
plt.show(block=False)
if plotProfile:
wpu.plot_profile(xxGrid*factor_x, yyGrid*factor_y,
integrated[::-1, :],
xlabel=r'$x [' + unit_x + ' m]$',
ylabel=r'$y [' + unit_y + ' m]$',
title=titleStr,
xunit='\mu m', yunit='\mu m',
arg4main={'cmap': 'viridis', 'lw': 3})
if saveFigFlag:
plt.ioff()
plt.figure(figsize=(10, 8))
plt.imshow(integrated[::-1, :], cmap='viridis',
extent=wpu.extent_func(integrated, pixelsize)*factor_x,
**kwarg4surf)
plt.xlabel(r'$x [' + unit_x + ' m]$', fontsize=24)
plt.ylabel(r'$y [' + unit_x + ' m]$', fontsize=24)
plt.title(titleStr, fontsize=18, weight='bold')
cbar = plt.colorbar()
cbar.ax.set_title(ctitle, y=1.01)
wpu.save_figs_with_idx(saveFileSuf)
plt.close()
plt.ion()
def plot_integration(integrated, pixelsize,
titleStr='Title', ctitle=' ', saveFigFlag=False,
saveFileSuf='graph'):
'''
TODO: Write Docstring
'''
xxGrid, yyGrid = wpu.grid_coord(integrated, pixelsize)
factor_x, unit_x = wpu.choose_unit(xxGrid)
factor_y, unit_y = wpu.choose_unit(yyGrid)
wpu.plot_profile(xxGrid*factor_x, yyGrid*factor_y, integrated[::-1, :],
xlabel=r'$x [' + unit_x + ' m]$',
ylabel=r'$y [' + unit_y + ' m]$',
title=titleStr,
xunit='\mu m', yunit='\mu m',
arg4main={'cmap': 'viridis', 'lw': 3})
if saveFigFlag:
plt.ioff()
plt.figure(figsize=(10, 8))
plt.imshow(integrated[::-1, :], cmap='viridis',
extent=wpu.extent_func(integrated, pixelsize)*factor_x)
plt.xlabel(r'$x [' + unit_x + ' m]$', fontsize=24)
plt.ylabel(r'$y [' + unit_x + ' m]$', fontsize=24)
plt.title(titleStr, fontsize=18, weight='bold')
cbar = plt.colorbar()
cbar.ax.set_title(ctitle, y=1.01)
wpu.save_figs_with_idx(saveFileSuf)
# plt.show(block=False)
plt.close(plt.gcf())
plt.ion()
# Plot Integration 2
fig = plt.figure(figsize=(10, 8))
ax = fig.add_subplot(111, projection='3d')
rstride = integrated.shape[0] // 101 + 1
cstride = integrated.shape[1] // 101 + 1
surf = ax.plot_surface(xxGrid*factor_x, yyGrid*factor_y,
integrated[::-1, :],
rstride=rstride,
cstride=cstride,
cmap='viridis', linewidth=0.1)
ax_lim = np.max([np.abs(xxGrid*factor_x), np.abs(yyGrid*factor_y)])
ax.set_xlim3d(-ax_lim, ax_lim)
ax.set_ylim3d(-ax_lim, ax_lim)
plt.xlabel(r'$x [' + unit_x + ' m]$', fontsize=24)
plt.ylabel(r'$y [' + unit_y + ' m]$', fontsize=24)
plt.title(titleStr, fontsize=24, weight='bold')
cbar = plt.colorbar(surf, shrink=.8, aspect=20)
cbar.ax.set_title(ctitle, y=1.01)
fig.tight_layout()
plt.tight_layout()
if saveFigFlag:
wpu.save_figs_with_idx(saveFileSuf)
ax.text2D(0.05, 0.9, 'strides = {}, {}'.format(rstride, cstride),
transform=ax.transAxes)
plt.show(block=False)
return ax