def slope_error_hist(thickness_cropped,
fitted,
pixelSize,
delta=1,
sourcedistance=1.0,
saveFigFlag=True,
str4title=''):
errorThickness = thickness_cropped - fitted
plt.figure(figsize=(15, 8))
plt.subplot(121)
slope_error_h = np.diff(errorThickness, axis=0) / pixelSize[0] * delta
argNotNAN = np.isfinite(slope_error_h)
factor_seh, unit_seh = wpu.choose_unit(slope_error_h[argNotNAN])
sigma_seh = np.std(slope_error_h[argNotNAN].flatten())
plt.hist(slope_error_h[argNotNAN].flatten() * factor_seh,
100,
histtype='stepfilled')
plt.xlabel(r'Slope Error [$ ' + unit_seh + ' rad$ ]')
plt.title('Horizontal, SDV = ' + '{:.2f}'.format(sigma_seh * factor_seh) +
' $' + unit_seh + ' rad$')
plt.subplot(122)
slope_error_v = np.diff(errorThickness, axis=1) / pixelSize[1] * delta
argNotNAN = np.isfinite(slope_error_v)
factor_sev, unit_sev = wpu.choose_unit(slope_error_v[argNotNAN])
sigma_sev = np.std(slope_error_v[argNotNAN].flatten())
plt.hist(slope_error_v[argNotNAN].flatten() * factor_sev,
100,
histtype='stepfilled')
plt.xlabel(r'Slope Error [$ ' + unit_sev + ' rad$ ]')
plt.title('Vertical, SDV = ' + '{:.2f}'.format(sigma_sev * factor_sev) +
' $' + unit_sev + ' rad$')
if delta != 1:
str4title += ' WF slope error'
else:
str4title += ' Thickness slope error'
plt.suptitle(str4title, fontsize=18, weight='bold')
if saveFigFlag:
wpu.save_figs_with_idx(fname2save, extension='png')
wpu.log_this('Slope Error Hor SDV = ' +
'{:.3f}'.format(sigma_seh * factor_seh) + unit_seh + ' rad')
wpu.log_this('Slope Error Ver SDV = ' +
'{:.3f}'.format(sigma_sev * factor_sev) + unit_sev + ' rad')
plt.show(block=True)
return sigma_seh, sigma_sev
def plot_DPC(dpc01,
dpc10,
pixelsize,
titleStr='',
saveFigFlag=False,
saveFileSuf='graph'):
'''
TODO: Write Docstring
Plot differencial phase signal
'''
if titleStr is not '':
titleStr = ', ' + titleStr
factor, unit_xy = wpu.choose_unit(np.sqrt(dpc01.size) * pixelsize[0])
dpc01_plot = dpc01 * pixelsize[1] / np.pi
dpc10_plot = dpc10 * pixelsize[0] / np.pi
vlim01 = np.max((np.abs(wpu.mean_plus_n_sigma(dpc01_plot, -5)),
np.abs(wpu.mean_plus_n_sigma(dpc01_plot, 5))))
vlim10 = np.max((np.abs(wpu.mean_plus_n_sigma(dpc10_plot, -5)),
np.abs(wpu.mean_plus_n_sigma(dpc10_plot, 5))))
plt.figure(figsize=(12, 6))
plt.subplot(121)
plt.imshow(dpc01_plot,
cmap='RdGy_r',
vmin=-vlim01,
vmax=vlim01,
extent=wpu.extent_func(dpc01_plot, pixelsize) * factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('DPC - Horizontal', fontsize=18, weight='bold') # 01
plt.subplot(122)
plt.imshow(dpc10_plot,
cmap='RdGy_r',
vmin=-vlim10,
vmax=vlim10,
extent=wpu.extent_func(dpc10_plot, pixelsize) * factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('DPC - Vertical', fontsize=18, weight='bold')
plt.suptitle('Differential Phase ' + r'[$\pi$ rad]' + titleStr,
fontsize=18,
weight='bold')
plt.tight_layout(rect=[0, 0, 1, 1])
if saveFigFlag:
wpu.save_figs_with_idx(saveFileSuf)
plt.show(block=False)
def plot_intensities_harms(int00,
int01,
int10,
pixelsize,
titleStr,
saveFigFlag=False,
saveFileSuf='graph'):
# Plot Real image (intensity)
if titleStr is not '':
titleStr = ', ' + titleStr
factor, unit_xy = wpu.choose_unit(np.sqrt(int00.size) * pixelsize[0])
plt.figure(figsize=(14, 6))
plt.subplot(131)
plt.imshow(int00,
cmap='viridis',
vmax=wpu.mean_plus_n_sigma(int00, 4),
extent=wpu.extent_func(int00, pixelsize) * factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('00', fontsize=18, weight='bold')
plt.subplot(132)
plt.imshow(int01,
cmap='viridis',
vmax=wpu.mean_plus_n_sigma(int01, 4),
extent=wpu.extent_func(int01, pixelsize) * factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('01', fontsize=18, weight='bold')
plt.subplot(133)
plt.imshow(int10,
cmap='viridis',
vmax=wpu.mean_plus_n_sigma(int10, 4),
extent=wpu.extent_func(int10, pixelsize) * factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('10', fontsize=18, weight='bold')
plt.suptitle('Absorption obtained from the Harmonics' + titleStr,
fontsize=18,
weight='bold')
plt.tight_layout(rect=[0, 0, 1, 1])
if saveFigFlag:
wpu.save_figs_with_idx(saveFileSuf)
plt.show(block=False)
def plot_DPC(dpc01, dpc10,
pixelsize, titleStr='',
saveFigFlag=False, saveFileSuf='graph'):
'''
TODO: Write Docstring
Plot differencial phase signal
'''
if titleStr is not '':
titleStr = ', ' + titleStr
factor, unit_xy = wpu.choose_unit(np.sqrt(dpc01.size)*pixelsize[0])
dpc01_plot = dpc01*pixelsize[1]/np.pi
dpc10_plot = dpc10*pixelsize[0]/np.pi
vlim01 = np.max((np.abs(wpu.mean_plus_n_sigma(dpc01_plot, -5)),
np.abs(wpu.mean_plus_n_sigma(dpc01_plot, 5))))
vlim10 = np.max((np.abs(wpu.mean_plus_n_sigma(dpc10_plot, -5)),
np.abs(wpu.mean_plus_n_sigma(dpc10_plot, 5))))
plt.figure(figsize=(12, 6))
plt.subplot(121)
plt.imshow(dpc01_plot, cmap='RdGy_r',
vmin=-vlim01, vmax=vlim01,
extent=wpu.extent_func(dpc01_plot, pixelsize)*factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('DPC - Horizontal', fontsize=18, weight='bold') # 01
plt.subplot(122)
plt.imshow(dpc10_plot, cmap='RdGy_r',
vmin=-vlim10, vmax=vlim10,
extent=wpu.extent_func(dpc10_plot, pixelsize)*factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('DPC - Vertical', fontsize=18,
weight='bold')
plt.suptitle('Differential Phase ' + r'[$\pi$ rad]' + titleStr,
fontsize=18, weight='bold')
plt.tight_layout(rect=[0, 0, 1, 1])
if saveFigFlag:
wpu.save_figs_with_idx(saveFileSuf)
plt.show(block=False)
def plot_intensities_harms(int00, int01, int10,
pixelsize, titleStr,
saveFigFlag=False, saveFileSuf='graph'):
# Plot Real image (intensity)
if titleStr is not '':
titleStr = ', ' + titleStr
factor, unit_xy = wpu.choose_unit(np.sqrt(int00.size)*pixelsize[0])
plt.figure(figsize=(14, 6))
plt.subplot(131)
plt.imshow(int00, cmap='viridis',
vmax=wpu.mean_plus_n_sigma(int00, 4),
extent=wpu.extent_func(int00, pixelsize)*factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('00', fontsize=18, weight='bold')
plt.subplot(132)
plt.imshow(int01, cmap='viridis',
vmax=wpu.mean_plus_n_sigma(int01, 4),
extent=wpu.extent_func(int01, pixelsize)*factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('01', fontsize=18, weight='bold')
plt.subplot(133)
plt.imshow(int10, cmap='viridis',
vmax=wpu.mean_plus_n_sigma(int10, 4),
extent=wpu.extent_func(int10, pixelsize)*factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('10', fontsize=18, weight='bold')
plt.suptitle('Absorption obtained from the Harmonics' + titleStr,
fontsize=18, weight='bold')
plt.tight_layout(rect=[0, 0, 1, 1])
if saveFigFlag:
wpu.save_figs_with_idx(saveFileSuf)
plt.show(block=False)
def plot_dark_field(darkField01,
darkField10,
pixelsize,
titleStr='',
saveFigFlag=False,
saveFileSuf='graph'):
'''
TODO: Write Docstring
Plot Dark field
'''
if titleStr is not '':
titleStr = ', ' + titleStr
factor, unit_xy = wpu.choose_unit(np.sqrt(darkField01.size) * pixelsize[0])
plt.figure(figsize=(14, 6))
plt.subplot(121)
plt.imshow(darkField01,
cmap='viridis',
vmax=wpu.mean_plus_n_sigma(darkField01, 4),
extent=wpu.extent_func(darkField01, pixelsize) * factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('Horizontal', fontsize=18, weight='bold') # 01
plt.subplot(122)
plt.imshow(darkField10,
cmap='viridis',
vmax=wpu.mean_plus_n_sigma(darkField01, 4),
extent=wpu.extent_func(darkField10, pixelsize) * factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('Vertical', fontsize=18, weight='bold') # 10
plt.suptitle('Dark Field', fontsize=18, weight='bold')
plt.tight_layout(rect=[0, 0, 1, 1])
if saveFigFlag:
wpu.save_figs_with_idx(saveFileSuf)
plt.show(block=False)
def plot_dark_field(darkField01, darkField10,
pixelsize, titleStr='',
saveFigFlag=False, saveFileSuf='graph'):
'''
TODO: Write Docstring
Plot Dark field
'''
if titleStr is not '':
titleStr = ', ' + titleStr
factor, unit_xy = wpu.choose_unit(np.sqrt(darkField01.size)*pixelsize[0])
plt.figure(figsize=(14, 6))
plt.subplot(121)
plt.imshow(darkField01, cmap='viridis',
vmax=wpu.mean_plus_n_sigma(darkField01, 4),
extent=wpu.extent_func(darkField01, pixelsize)*factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('Horizontal', fontsize=18, weight='bold') # 01
plt.subplot(122)
plt.imshow(darkField10, cmap='viridis',
vmax=wpu.mean_plus_n_sigma(darkField01, 4),
extent=wpu.extent_func(darkField10, pixelsize)*factor)
plt.xlabel(r'$[{0} m]$'.format(unit_xy))
plt.ylabel(r'$[{0} m]$'.format(unit_xy))
plt.colorbar(shrink=0.5)
plt.title('Vertical', fontsize=18, weight='bold') # 10
plt.suptitle('Dark Field', fontsize=18, weight='bold')
plt.tight_layout(rect=[0, 0, 1, 1])
if saveFigFlag:
wpu.save_figs_with_idx(saveFileSuf)
plt.show(block=False)
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()
# u1_xy = circ(X, Y, wx, wy)
# u1_xy = circ(X, Y, wx, wy)*tFuncLens(X, Y, wavelength, fx=(1/5.0+1/zz)**-1)* \
# u1_xy = gaussianBeam(.2e-3, wavelength, z=0.0, L=Ly, npoints=My)
# u1_xy = circ(X, Y, wx, wy)* \
# gaussianBeam(10e-6, wavelength, 5.000, Lx, X.shape[0])
#u1_xy = circ(X, Y, wx, wy, 0, 80e-6) + circ(X, Y, wx, wy, 0,-80e-6) # double slit
##=========================================================#
# %% 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)
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
def plot_residual_1d(xvec,
data,
fitted,
str4title='',
saveFigFlag=False,
saveAsciiFlag=False):
# Plot Horizontal profile
errorThickness = -data + fitted
argNotNAN = np.isfinite(errorThickness)
factorx, unitx = wpu.choose_unit(xvec)
factory1, unity1 = wpu.choose_unit(data)
factory2, unity2 = wpu.choose_unit(errorThickness)
ptp = np.ptp(errorThickness[argNotNAN].flatten() * factory2)
wpu.print_red('PV: {0:4.3g} '.format(ptp) + unity2[-1] + 'm')
sigmaError = np.std(errorThickness[argNotNAN].flatten() * factory2)
wpu.print_red('SDV: {0:4.3g} '.format(sigmaError) + unity2[-1] + 'm')
str4title += '\n' + \
r'PV $= {0:.2f}$ '.format(ptp) + '$' + unity2 + ' m$, '\
'SDV $= {0:.2f}$ '.format(sigmaError) + '$' + unity2 + ' m$'
plt.figure(figsize=(10, 7))
ax1 = plt.gca()
ax1.plot(xvec[argNotNAN] * factorx,
data[argNotNAN] * factory1,
'-ko',
markersize=5,
label='1D data')
ax1.plot(xvec[argNotNAN] * factorx,
fitted[argNotNAN] * factory1,
'-+r',
label='Fit parabolic')
ax2 = ax1.twinx()
# trick to add both axes to legend
ax2.plot(np.nan, '-ko', label='1D data')
ax2.plot(np.nan, '-+r', label='Fit parabolic')
ax2.plot(xvec[argNotNAN] * factorx,
errorThickness[argNotNAN] * factory2,
'-+',
markersize=5,
label='fit residual')
plt.title(str4title)
for tl in ax2.get_yticklabels():
tl.set_color('b')
ax2.legend(loc=1, fontsize='small')
# trick to add both axes to legend
ax1.grid(color='gray')
ax1.set_xlabel(r'[$' + unitx + ' m$]')
ax1.set_ylabel(r'Thickness ' + r'[$' + unity1 + ' m$]')
# ax2.set_ylim([-20, 20])
ax2.set_ylim(-1.1 * np.max(np.abs(errorThickness[argNotNAN]) * factory2),
1.1 * np.max(np.abs(errorThickness[argNotNAN]) * factory2))
ax2.set_ylabel(r'Residual' + r'[$' + unity2 + ' m$]')
ax2.grid(b='off')
plt.xlim(-1.1 * np.max(xvec * factorx), 1.1 * np.max(xvec * factorx))
plt.tight_layout(rect=(0, 0, 1, .98))
if saveFigFlag:
wpu.save_figs_with_idx(fname2save, extension='png')
if saveAsciiFlag:
csv_fname = wpu.get_unique_filename(fname2save, 'csv')
np.savetxt(csv_fname,
np.transpose([xvec, data, fitted, fitted - data]),
delimiter=',\t',
header="xvec, data, fitted, residual, " + str4title,
fmt='%.6g')
plt.show(block=False)
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 integrate_DPC_cumsum(data_DPC,
wavelength,
grazing_angle=0.0,
projectionFromDiv=1.0,
labels=[],
xlabel='x',
ylabel='Height',
titleStr='',
saveFileSuf=''):
ls_cycle, lc_cycle = wpu.line_style_cycle(['-'], ['o', 's', 'd', '^'],
ncurves=data_DPC.shape[1] - 1,
cmap_str='gist_rainbow_r')
if grazing_angle // .00001 > 0:
projection = 1 / np.sin(grazing_angle) * projectionFromDiv
else:
projection = projectionFromDiv
xvec = data_DPC[:, 0] * projection
plt.figure(figsize=(12, 12 * 9 / 16))
list_integrated = [xvec]
header = [xlabel + ' [m]']
for j_line in range(1, data_DPC.shape[1]):
integrated = (
np.cumsum(data_DPC[:, j_line] - np.mean(data_DPC[:, j_line])) *
(xvec[1] - xvec[0]))
integrated *= -1 / 2 / np.pi * wavelength * np.abs(projection)
# TODO: check here!!
if j_line == 1:
factor_x, unit_x = wpu.choose_unit(xvec)
factor_y, unit_y = wpu.choose_unit(integrated)
list_integrated.append(integrated)
header.append(labels[j_line - 1])
plt.plot(xvec * factor_x,
integrated * factor_y,
next(ls_cycle),
c=next(lc_cycle),
label=labels[j_line - 1])
marginx = 0.1 * np.ptp(xvec * factor_x)
plt.xlim(
[np.min(xvec * factor_x) - marginx,
np.max(xvec * factor_x) + marginx])
plt.xlabel(xlabel + r' [$' + unit_x + ' m$]')
plt.ylabel(ylabel + r' [$' + unit_y + ' m$]')
plt.legend(loc=0, fontsize=12)
if grazing_angle // .00001 > 0:
plt.title(titleStr + 'Mirror Height,\n' +
'grazing angle {:.2f} mrad,\n'.format(grazing_angle * 1e3) +
'projection due divergence = ' +
r'$ \times $ {:.2f}'.format(projectionFromDiv))
else:
plt.title(titleStr + 'Integration Cumulative Sum')
plt.tight_layout()
wpu.save_figs_with_idx(saveFileSuf)
plt.show()
data2saveV = np.asarray(list_integrated).T
header.append(ylabel + ' [m]')
if grazing_angle // .00001 > 0:
header.append('grazing_angle = {:.4g}'.format(grazing_angle))
if projectionFromDiv // 1 != 1:
header.append('projection due divergence = ' +
'{:.2f}x'.format(projectionFromDiv))
wpu.save_csv_file(data2saveV,
wpu.get_unique_filename(
saveFileSuf + '_integrated_' + xlabel, 'csv'),
headerList=header)
return np.asarray(list_integrated).T
def curv_from_height(height, virtual_pixelsize,
grazing_angle=0.0, projectionFromDiv=1.0,
labels=[],
xlabel='x', ylabel='Curvature',
titleStr='', saveFileSuf=''):
ls_cycle, lc_cycle = wpu.line_style_cycle(['-'], ['o', 's', 'd', '^'],
ncurves=height.shape[1] - 1,
cmap_str='gist_rainbow_r')
if grazing_angle//.00001 > 0:
projection = 1/np.sin(grazing_angle)*projectionFromDiv
else:
projection = projectionFromDiv
projected_pixel = virtual_pixelsize*projection
xvec = wpu.realcoordvec(height.shape[0]-2, projected_pixel)
print('projected_pixel')
print(projected_pixel)
plt.figure(figsize=(12, 12*9/16))
list_curv = [xvec]
header = [xlabel + ' [m]']
for j_line in range(1, height.shape[1]):
curv = np.diff(np.diff(height[:, j_line]))/projected_pixel**2
if j_line == 1:
factor_x, unit_x = wpu.choose_unit(xvec)
#factor_y, unit_y = wpu.choose_unit(curv)
list_curv.append(curv)
header.append(labels[j_line - 1])
plt.plot(xvec*factor_x, curv,
next(ls_cycle), c=next(lc_cycle),
label=labels[j_line - 1])
marginx = 0.1*np.ptp(xvec*factor_x)
plt.xlim([np.min(xvec*factor_x)-marginx,
np.max(xvec*factor_x)+marginx])
plt.xlabel(xlabel + r' [$' + unit_x + ' m$]')
plt.ylabel(ylabel + r'[$m^{-1}$]')
plt.legend(loc=0, fontsize=12)
if grazing_angle//.00001 > 0:
plt.title(titleStr + 'Mirror Curvature,\n' +
'grazing angle {:.2f} mrad,\n'.format(grazing_angle*1e3) +
'projection due divergence = ' +
r'$ \times $ {:.2f}'.format(projectionFromDiv))
else:
plt.title(titleStr + 'Curvature')
plt.tight_layout()
wpu.save_figs_with_idx(saveFileSuf)
plt.show()
data2saveV = np.asarray(list_curv).T
header.append(ylabel + ' [1/m]')
if grazing_angle//.00001 > 0:
header.append(', grazing_angle = {:.4g}'.format(grazing_angle))
if projectionFromDiv//1 != 1:
header.append('projection due divergence = ' +
'{:.2f}x'.format(projectionFromDiv))
wpu.save_csv_file(data2saveV,
wpu.get_unique_filename(saveFileSuf +
'_curv_' + xlabel, 'csv'),
headerList=header)
return np.asarray(list_curv).T
def integrate_DPC_cumsum(data_DPC, wavelength,
grazing_angle=0.0, projectionFromDiv=1.0,
remove2ndOrder=False,
labels=[],
xlabel='x', ylabel='Height',
titleStr='', saveFileSuf=''):
ls_cycle, lc_cycle = wpu.line_style_cycle(['-'], ['o', 's', 'd', '^'],
ncurves=data_DPC.shape[1] - 1,
cmap_str='gist_rainbow_r')
if grazing_angle//.00001 > 0:
projection = 1/np.sin(grazing_angle)*projectionFromDiv
else:
projection = projectionFromDiv
xvec = data_DPC[:, 0]*projection
plt.figure(figsize=(12, 12*9/16))
list_integrated = [xvec]
header = [xlabel + ' [m]']
for j_line in range(1, data_DPC.shape[1]):
integrated = (np.cumsum(data_DPC[:, j_line] - np.mean(data_DPC[:, j_line]))
* (xvec[1]-xvec[0])) # TODO: removed mean 20181020
# integrated = (np.cumsum(data_DPC[:, j_line])) * (xvec[1]-xvec[0])
integrated *= -1/2/np.pi*wavelength*np.abs(projection)
p02 = np.polyfit(xvec, integrated, 2)
fitted_pol2 = p02[0]*xvec**2 + p02[1]*xvec + p02[2]
if remove2ndOrder:
integrated -= fitted_pol2
titleStr += 'Removed 2nd order, '
# TODO: check here!!
if j_line == 1:
factor_x, unit_x = wpu.choose_unit(xvec)
factor_y, unit_y = wpu.choose_unit(integrated)
list_integrated.append(integrated)
header.append(labels[j_line - 1])
lc = next(lc_cycle)
plt.plot(xvec*factor_x,
integrated*factor_y,
next(ls_cycle), c=lc,
label=labels[j_line - 1])
if not remove2ndOrder:
plt.plot(xvec*1e6, (fitted_pol2)*factor_y,
'--', color=lc, lw=3)
marginx = 0.1*np.ptp(xvec*factor_x)
plt.xlim([np.min(xvec*factor_x)-marginx,
np.max(xvec*factor_x)+marginx])
plt.xlabel(xlabel + r' [$' + unit_x + ' m$]')
plt.ylabel(ylabel + r' [$' + unit_y + ' m$]')
plt.legend(loc=0, fontsize=12)
if grazing_angle//.00001 > 0:
plt.title(titleStr + 'Mirror Height,\n' +
'grazing angle {:.2f} mrad,\n'.format(grazing_angle*1e3) +
'projection due divergence = ' +
r'$ \times $ {:.2f}'.format(projectionFromDiv))
else:
plt.title(titleStr + 'Integration Cumulative Sum')
plt.tight_layout()
wpu.save_figs_with_idx(saveFileSuf)
plt.show()
data2saveV = np.asarray(list_integrated).T
header.append(ylabel + ' [m]')
if grazing_angle//.00001 > 0:
header.append('grazing_angle = {:.4g}'.format(grazing_angle))
if projectionFromDiv//1 != 1:
header.append('projection due divergence = ' +
'{:.2f}x'.format(projectionFromDiv))
wpu.save_csv_file(data2saveV,
wpu.get_unique_filename(saveFileSuf +
'_integrated_' + xlabel, 'csv'),
headerList=header)
return np.asarray(list_integrated).T
def curv_from_height(height,
virtual_pixelsize,
grazing_angle=0.0,
projectionFromDiv=1.0,
labels=[],
xlabel='x',
ylabel='Curvature',
titleStr='',
saveFileSuf=''):
ls_cycle, lc_cycle = wpu.line_style_cycle(['-'], ['o', 's', 'd', '^'],
ncurves=height.shape[1] - 1,
cmap_str='gist_rainbow_r')
if grazing_angle // .00001 > 0:
projection = 1 / np.sin(grazing_angle) * projectionFromDiv
else:
projection = projectionFromDiv
projected_pixel = virtual_pixelsize * projection
xvec = wpu.realcoordvec(height.shape[0] - 2, projected_pixel)
print('projected_pixel')
print(projected_pixel)
plt.figure(figsize=(12, 12 * 9 / 16))
list_curv = [xvec]
header = [xlabel + ' [m]']
for j_line in range(1, height.shape[1]):
curv = np.diff(np.diff(height[:, j_line])) / projected_pixel**2
if j_line == 1:
factor_x, unit_x = wpu.choose_unit(xvec)
#factor_y, unit_y = wpu.choose_unit(curv)
list_curv.append(curv)
header.append(labels[j_line - 1])
plt.plot(xvec * factor_x,
curv,
next(ls_cycle),
c=next(lc_cycle),
label=labels[j_line - 1])
marginx = 0.1 * np.ptp(xvec * factor_x)
plt.xlim(
[np.min(xvec * factor_x) - marginx,
np.max(xvec * factor_x) + marginx])
plt.xlabel(xlabel + r' [$' + unit_x + ' m$]')
plt.ylabel(ylabel + r'[$m^{-1}$]')
plt.legend(loc=0, fontsize=12)
if grazing_angle // .00001 > 0:
plt.title(titleStr + 'Mirror Curvature,\n' +
'grazing angle {:.2f} mrad,\n'.format(grazing_angle * 1e3) +
'projection due divergence = ' +
r'$ \times $ {:.2f}'.format(projectionFromDiv))
else:
plt.title(titleStr + 'Curvature')
plt.tight_layout()
wpu.save_figs_with_idx(saveFileSuf)
plt.show()
data2saveV = np.asarray(list_curv).T
header.append(ylabel + ' [1/m]')
if grazing_angle // .00001 > 0:
header.append(', grazing_angle = {:.4g}'.format(grazing_angle))
if projectionFromDiv // 1 != 1:
header.append('projection due divergence = ' +
'{:.2f}x'.format(projectionFromDiv))
wpu.save_csv_file(data2saveV,
wpu.get_unique_filename(saveFileSuf + '_curv_' + xlabel,
'csv'),
headerList=header)
return np.asarray(list_curv).T
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
