def test_2d_normalize_to_slope_error(self,combination="FF"):
mirrorLength = 200.1 # cm
Step = 1.0
RandomSeed = 8788
RMS = 0.2e-6 # 2.0e-6 # rad
mirrorWidth = 40.0
StepW = 1.0
RandomSeedW = 8788
RMSW = 0.5e-6 # 1.0e-6
if combination == "EE": # TODO: not yet tested
input_file = package_dirname("srxraylib.metrology") + "/mirror_1d.txt"
values = numpy.loadtxt(input_file)
x_l = values[:, 0]
y_l = values[:, 1]
x_w = values[:, 0]
y_w = values[:, 1]
print("File loaded: %s, Length:%f, StDev: %g"%(input_file,x_l[-1]-x_l[0],y_l.std()))
x,y,z = simulate_profile_2D(random_seed_l=RandomSeed, error_type_l=SLOPE_ERROR, rms_l=RMS,
correlation_length_l=30.0,power_law_exponent_beta_l=1.5,
random_seed_w=RandomSeedW, error_type_w=SLOPE_ERROR, rms_w=RMSW,
correlation_length_w=30.0,power_law_exponent_beta_w=1.5,
x_l=x_l,y_l=y_l,x_w=x_w,y_w=y_w,
combination=combination)
else:
x,y,z = simulate_profile_2D(mirror_length=mirrorLength, step_l=Step, random_seed_l=RandomSeed, error_type_l=SLOPE_ERROR, rms_l=RMS,
correlation_length_l=30.0,power_law_exponent_beta_l=1.5,
mirror_width=mirrorWidth, step_w=StepW, random_seed_w=RandomSeedW, error_type_w=SLOPE_ERROR, rms_w=RMSW,
correlation_length_w=30.0,power_law_exponent_beta_w=1.5,
combination=combination)
tmp1 = slopes(z.T,x,y,return_only_rms=1)
print(" target SLOPE error in WIDTH: %g rad"%(RMSW))
print(" target SLOPE error in LENGTH: %g rad"%(RMS))
print(" obtained HEIGHT error (in LENGTH and WIDTH): %g"%(z.std()))
print(" obtained SLOPE error in WIDTH: %g"%(tmp1[0]))
print(" obtained SLOPE error in LENGTH: %g"%(tmp1[1]))
print(" shape x,y,z:",x.shape,y.shape,z.shape)
# the LENGTH direction must match!!
assert numpy.abs( RMS - tmp1[1] ) < 0.01 * numpy.abs(RMS)
if do_plot:
from srxraylib.plot.gol import plot_surface
plot_surface(z.T*1e7,x,y,xtitle="X [cm]",ytitle="Y [cm",ztitle="Z [nm]",title="test_2d_normalize_to_slope_error")
def calculate_heigth_profile(self, not_interactive_mode=False):
try:
if self.server.y is None: raise Exception("No Profile Selected")
sys.stdout = EmittingStream(textWritten=self.writeStdOut)
self.check_fields()
combination = "EF"
if self.modify_y == 2:
profile_1D_y_x_temp = self.si_to_user_units * self.server.y
if self.use_undetrended == 0: profile_1D_y_y_temp = self.si_to_user_units * self.server.zHeights
else: profile_1D_y_y_temp = self.si_to_user_units * self.server.zHeightsUndetrended
first_coord = profile_1D_y_x_temp[0]
second_coord = profile_1D_y_x_temp[1]
last_coord = profile_1D_y_x_temp[-1]
step = numpy.abs(second_coord - first_coord)
length = numpy.abs(last_coord - first_coord)
n_points_old = len(profile_1D_y_x_temp)
if self.new_length > length:
difference = self.new_length - length
n_added_points = int(difference/step)
if difference % step == 0:
n_added_points += 1
if n_added_points % 2 != 0:
n_added_points += 1
profile_1D_y_x = numpy.arange(n_added_points + n_points_old) * step
profile_1D_y_y = numpy.ones(n_added_points + n_points_old) * self.filler_value * 1e-9 * self.si_to_user_units
profile_1D_y_y[int(n_added_points/2) : n_points_old + int(n_added_points/2)] = profile_1D_y_y_temp
elif self.new_length < length:
difference = length - self.new_length
n_removed_points = int(difference/step)
if difference % step == 0:
n_removed_points -= 1
if n_removed_points % 2 != 0:
n_removed_points -= 1
if n_removed_points >= 2:
profile_1D_y_x = profile_1D_y_x_temp[0 : (n_points_old - n_removed_points)]
profile_1D_y_y = profile_1D_y_y_temp[(int(n_removed_points/2) - 1) : (n_points_old - int(n_removed_points/2) - 1)]
else:
profile_1D_y_x = profile_1D_y_x_temp
profile_1D_y_y = profile_1D_y_y_temp
else:
profile_1D_y_x = profile_1D_y_x_temp
profile_1D_y_y = profile_1D_y_y_temp
else:
if self.modify_y == 0:
profile_1D_y_x = self.si_to_user_units * self.server.y
elif self.modify_y == 1:
profile_1D_y_x = self.si_to_user_units * self.server.y * self.scale_factor_y
if self.use_undetrended == 0: profile_1D_y_y = self.si_to_user_units * self.server.zHeights
else: profile_1D_y_y = self.si_to_user_units * self.server.zHeightsUndetrended
if self.center_y:
first_coord = profile_1D_y_x[0]
last_coord = profile_1D_y_x[-1]
length = numpy.abs(last_coord - first_coord)
profile_1D_y_x_temp = numpy.linspace(-length/2, length/2, len(profile_1D_y_x))
profile_1D_y_x = profile_1D_y_x_temp
if self.renormalize_y == 0:
rms_y = None
else:
if self.error_type_y == profiles_simulation.FIGURE_ERROR:
rms_y = self.si_to_user_units * self.rms_y * 1e-9 # from nm to user units
else:
rms_y = self.rms_y * 1e-6 # from urad to rad
xx, yy, zz = profiles_simulation.simulate_profile_2D(combination = combination,
error_type_l = self.error_type_y,
rms_l = rms_y,
x_l = profile_1D_y_x,
y_l = profile_1D_y_y,
mirror_width = self.dimension_x,
step_w = self.step_x,
rms_w = 0.0)
self.xx = xx
self.yy = yy
self.zz = zz # in user units
self.axis.clear()
x_to_plot, y_to_plot = numpy.meshgrid(xx, yy)
z_to_plot = zz * 1e9 / self.si_to_user_units #nm
self.axis.plot_surface(x_to_plot, y_to_plot, z_to_plot,
rstride=1, cstride=1, cmap=cm.autumn, linewidth=0.5, antialiased=True)
sloperms = profiles_simulation.slopes(zz.T, xx, yy, return_only_rms=1)
title = ' Slope error rms in X direction: %f $\mu$rad' % (sloperms[0]*1e6) + '\n' + \
' Slope error rms in Y direction: %f $\mu$rad' % (sloperms[1]*1e6)
self.axis.set_xlabel("X [" + self.workspace_units_label + "]")
self.axis.set_ylabel("Y [" + self.workspace_units_label + "]")
self.axis.set_zlabel("Z [nm]")
self.axis.set_title(title)
self.axis.mouse_init()
if not not_interactive_mode:
try:
self.plot_canvas[5].draw()
except:
pass
self.tabs.setCurrentIndex(6)
QMessageBox.information(self, "QMessageBox.information()",
"Height Profile calculated: if the result is satisfactory,\nclick \'Generate Height Profile File\' to complete the operation ",
QMessageBox.Ok)
except Exception as exception:
QMessageBox.critical(self, "Error",
exception.args[0],
QMessageBox.Ok)
def test_2d_normalize_to_slope_error(self, combination="FF"):
mirrorLength = 200.1 # cm
Step = 1.0
RandomSeed = 8788
RMS = 0.2e-6 # 2.0e-6 # rad
mirrorWidth = 40.0
StepW = 1.0
RandomSeedW = 8788
RMSW = 0.5e-6 # 1.0e-6
if combination == "EE": # TODO: not yet tested
input_file = package_dirname(
"srxraylib.metrology") + "/mirror_1d.txt"
values = numpy.loadtxt(input_file)
x_l = values[:, 0]
y_l = values[:, 1]
x_w = values[:, 0]
y_w = values[:, 1]
print("File loaded: %s, Length:%f, StDev: %g" %
(input_file, x_l[-1] - x_l[0], y_l.std()))
x, y, z = simulate_profile_2D(random_seed_l=RandomSeed,
error_type_l=SLOPE_ERROR,
rms_l=RMS,
correlation_length_l=30.0,
power_law_exponent_beta_l=1.5,
random_seed_w=RandomSeedW,
error_type_w=SLOPE_ERROR,
rms_w=RMSW,
correlation_length_w=30.0,
power_law_exponent_beta_w=1.5,
x_l=x_l,
y_l=y_l,
x_w=x_w,
y_w=y_w,
combination=combination)
else:
x, y, z = simulate_profile_2D(mirror_length=mirrorLength,
step_l=Step,
random_seed_l=RandomSeed,
error_type_l=SLOPE_ERROR,
rms_l=RMS,
correlation_length_l=30.0,
power_law_exponent_beta_l=1.5,
mirror_width=mirrorWidth,
step_w=StepW,
random_seed_w=RandomSeedW,
error_type_w=SLOPE_ERROR,
rms_w=RMSW,
correlation_length_w=30.0,
power_law_exponent_beta_w=1.5,
combination=combination)
tmp1 = slopes(z.T, x, y, return_only_rms=1)
print(" target SLOPE error in WIDTH: %g rad" % (RMSW))
print(" target SLOPE error in LENGTH: %g rad" % (RMS))
print(" obtained HEIGHT error (in LENGTH and WIDTH): %g" % (z.std()))
print(" obtained SLOPE error in WIDTH: %g" % (tmp1[0]))
print(" obtained SLOPE error in LENGTH: %g" % (tmp1[1]))
print(" shape x,y,z:", x.shape, y.shape, z.shape)
# the LENGTH direction must match!!
assert numpy.abs(RMS - tmp1[1]) < 0.01 * numpy.abs(RMS)
if do_plot:
from srxraylib.plot.gol import plot_surface
plot_surface(z.T * 1e7,
x,
y,
xtitle="X [cm]",
ytitle="Y [cm",
ztitle="Z [nm]",
title="test_2d_normalize_to_slope_error")
def calculate_heigth_profile(self, not_interactive_mode=False):
try:
sys.stdout = EmittingStream(textWritten=self.writeStdOut)
self.check_fields()
#### LENGTH
if self.kind_of_profile_y == 2:
combination = "E"
if self.delimiter_y == 1:
profile_1D_y_x, profile_1D_y_y = numpy.loadtxt(self.heigth_profile_1D_file_name_y, delimiter='\t', unpack=True)
else:
profile_1D_y_x, profile_1D_y_y = numpy.loadtxt(self.heigth_profile_1D_file_name_y, unpack=True)
profile_1D_y_x *= self.conversion_factor_y_x * self.workspace_units_to_cm # to cm
profile_1D_y_y *= self.conversion_factor_y_y * self.workspace_units_to_cm # to cm
if self.modify_y == 2:
profile_1D_y_x_temp = profile_1D_y_x
profile_1D_y_y_temp = profile_1D_y_y
first_coord = profile_1D_y_x_temp[0]
second_coord = profile_1D_y_x_temp[1]
last_coord = profile_1D_y_x_temp[-1]
step = numpy.abs(second_coord - first_coord)
length = numpy.abs(last_coord - first_coord)
n_points_old = len(profile_1D_y_x_temp)
if self.new_length > length:
difference = self.new_length - length
n_added_points = int(difference/step)
if difference % step == 0:
n_added_points += 1
if n_added_points % 2 != 0:
n_added_points += 1
profile_1D_y_x = numpy.arange(n_added_points + n_points_old) * step
profile_1D_y_y = numpy.ones(n_added_points + n_points_old) * self.filler_value * 1e-9 * self.si_to_user_units
profile_1D_y_y[int(n_added_points/2) : n_points_old + int(n_added_points/2)] = profile_1D_y_y_temp
elif self.new_length < length:
difference = length - self.new_length
n_removed_points = int(difference/step)
if difference % step == 0:
n_removed_points -= 1
if n_removed_points % 2 != 0:
n_removed_points -= 1
if n_removed_points >= 2:
profile_1D_y_x = profile_1D_y_x_temp[0 : (n_points_old - n_removed_points)]
profile_1D_y_y = profile_1D_y_y_temp[(int(n_removed_points/2) - 1) : (n_points_old - int(n_removed_points/2) - 1)]
else:
profile_1D_y_x = profile_1D_y_x_temp
profile_1D_y_y = profile_1D_y_y_temp
else:
profile_1D_y_x = profile_1D_y_x_temp
profile_1D_y_y = profile_1D_y_y_temp
elif self.modify_y == 1:
profile_1D_y_x *= self.scale_factor_y
if self.center_y:
first_coord = profile_1D_y_x[0]
last_coord = profile_1D_y_x[-1]
length = numpy.abs(last_coord - first_coord)
profile_1D_y_x_temp = numpy.linspace(-length/2, length/2, len(profile_1D_y_x))
profile_1D_y_x = profile_1D_y_x_temp
if self.renormalize_y == 0:
rms_y = None
else:
if self.error_type_y == profiles_simulation.FIGURE_ERROR:
rms_y = self.rms_y * 1e-7 # from nm to cm
else:
rms_y = self.rms_y * 1e-6 # from urad to rad
else:
if self.kind_of_profile_y == 0: combination = "F"
else: combination = "G"
profile_1D_y_x = None
profile_1D_y_y = None
if self.error_type_y == profiles_simulation.FIGURE_ERROR:
rms_y = self.rms_y * 1e-7 # from nm to cm
else:
rms_y = self.rms_y * 1e-6 # from urad to rad
#### WIDTH
if self.kind_of_profile_x == 2:
combination += "E"
if self.delimiter_x == 1:
profile_1D_x_x, profile_1D_x_y = numpy.loadtxt(self.heigth_profile_1D_file_name_x, delimiter='\t', unpack=True)
else:
profile_1D_x_x, profile_1D_x_y = numpy.loadtxt(self.heigth_profile_1D_file_name_x, unpack=True)
profile_1D_x_x *= self.conversion_factor_x_x * self.workspace_units_to_cm
profile_1D_x_y *= self.conversion_factor_x_y * self.workspace_units_to_cm
if self.modify_x == 2:
profile_1D_x_x_temp = profile_1D_x_x
profile_1D_x_y_temp = profile_1D_x_y
first_coord = profile_1D_x_x_temp[0]
second_coord = profile_1D_x_x_temp[1]
last_coord = profile_1D_x_x_temp[-1]
step = numpy.abs(second_coord - first_coord)
length = numpy.abs(last_coord - first_coord)
n_points_old = len(profile_1D_x_x_temp)
if self.new_length > length:
difference = self.new_length - length
n_added_points = int(difference/step)
if difference % step == 0:
n_added_points += 1
if n_added_points % 2 != 0:
n_added_points += 1
profile_1D_x_x = numpy.arange(n_added_points + n_points_old) * step
profile_1D_x_y = numpy.ones(n_added_points + n_points_old) * self.filler_value * 1e-9 * self.si_to_user_units
profile_1D_x_y[int(n_added_points/2) : n_points_old + int(n_added_points/2)] = profile_1D_x_y_temp
elif self.new_length < length:
difference = length - self.new_length
n_removed_points = int(difference/step)
if difference % step == 0:
n_removed_points -= 1
if n_removed_points % 2 != 0:
n_removed_points -= 1
if n_removed_points >= 2:
profile_1D_x_x = profile_1D_x_x_temp[0 : (n_points_old - n_removed_points)]
profile_1D_x_y = profile_1D_x_y_temp[(int(n_removed_points/2) - 1) : (n_points_old - int(n_removed_points/2) - 1)]
else:
profile_1D_x_x = profile_1D_x_x_temp
profile_1D_x_y = profile_1D_x_y_temp
else:
profile_1D_x_x = profile_1D_x_x_temp
profile_1D_x_y = profile_1D_x_y_temp
elif self.modify_x == 1:
profile_1D_x_x *= self.scale_factor_x
if self.center_x:
first_coord = profile_1D_x_x[0]
last_coord = profile_1D_x_x[-1]
length = numpy.abs(last_coord - first_coord)
profile_1D_x_x_temp = numpy.linspace(-length/2, length/2, len(profile_1D_x_x))
profile_1D_x_x = profile_1D_x_x_temp
if self.renormalize_x == 0:
rms_x = None
else:
if self.error_type_x == profiles_simulation.FIGURE_ERROR:
rms_x = self.rms_x * 1e-7 # from nm to cm
else:
rms_x = self.rms_x * 1e-6 # from urad to rad
else:
profile_1D_x_x = None
profile_1D_x_y = None
if self.kind_of_profile_x == 0: combination += "F"
else: combination += "G"
if self.error_type_x == profiles_simulation.FIGURE_ERROR:
rms_x = self.rms_x * 1e-7 # from nm to cm
else:
rms_x = self.rms_x * 1e-6 # from urad to rad
xx, yy, zz = profiles_simulation.simulate_profile_2D(combination = combination,
mirror_length = self.dimension_y * self.workspace_units_to_cm, # to cm
step_l = self.step_y * self.workspace_units_to_cm, # to cm
random_seed_l = self.montecarlo_seed_y,
error_type_l = self.error_type_y,
rms_l = rms_y,
power_law_exponent_beta_l = self.power_law_exponent_beta_y,
correlation_length_l = self.correlation_length_y * self.workspace_units_to_cm, # to cm
x_l = profile_1D_y_x,
y_l = profile_1D_y_y,
mirror_width = self.dimension_x * self.workspace_units_to_cm, # to cm
step_w = self.step_x * self.workspace_units_to_cm,
random_seed_w = self.montecarlo_seed_x,
error_type_w = self.error_type_x,
rms_w = rms_x,
power_law_exponent_beta_w = self.power_law_exponent_beta_x,
correlation_length_w = self.correlation_length_x * self.workspace_units_to_cm, # to cm
x_w = profile_1D_x_x,
y_w = profile_1D_x_y)
self.xx = xx / self.workspace_units_to_cm # to user units
self.yy = yy / self.workspace_units_to_cm # to user units
self.zz = zz / self.workspace_units_to_cm # to user units
self.axis.clear()
x_to_plot, y_to_plot = numpy.meshgrid(self.xx, self.yy)
z_to_plot = zz * 1e7
self.axis.plot_surface(x_to_plot, y_to_plot, z_to_plot,
rstride=1, cstride=1, cmap=cm.autumn, linewidth=0.5, antialiased=True)
sloperms = profiles_simulation.slopes(zz.T, xx, yy, return_only_rms=1)
title = ' Slope error rms in X direction: %f $\mu$rad' % (sloperms[0]*1e6) + '\n' + \
' Slope error rms in Y direction: %f $\mu$rad' % (sloperms[1]*1e6)
self.axis.set_xlabel("X [" + self.workspace_units_label + "]")
self.axis.set_ylabel("Y [" + self.workspace_units_label + "]")
self.axis.set_zlabel("Z [nm]")
self.axis.set_title(title)
self.axis.mouse_init()
if not not_interactive_mode:
self.figure_canvas.draw()
QMessageBox.information(self, "QMessageBox.information()",
"Height Profile calculated: if the result is satisfactory,\nclick \'Generate Height Profile File\' to complete the operation ",
QMessageBox.Ok)
except Exception as exception:
QMessageBox.critical(self, "Error",
exception.args[0],
QMessageBox.Ok)
def gen_figure_error(L=400e-3,
W=40e-3,
stepL=1e-3,
stepW=1e-3,
rmsL=1e-9,
rmsW=1e-9,
betaL=2.0,
betaW=2.0,
typeL='h',
typeW='h',
seedL=8787,
seedW=8454,
filename='',
plot=False,
print_out=False):
from srxraylib.metrology import profiles_simulation
# ==== Main Parameters ============================== #
if (typeL == 'h'):
typeL = 0 # (0) Normalize by Height RMS, (1) Normalize by Slope RMS
elif (typeL == 's'):
typeL = 1
if (typeW == 'h'):
typeW = 0 # (0) Normalize by Height RMS, (1) Normalize by Slope RMS
elif (typeW == 's'):
typeW = 1
if (seedL == 0):
fct = 1e4 if np.random.random() <= 0.5 else 1e3
seedL = int(np.random.random() * fct)
if (seedW == 0):
fct = 1e4 if np.random.random() <= 0.5 else 1e3
seedW = int(np.random.random() * fct)
# ==== Creates 2D matrix ============================ #
x, y, z = profiles_simulation.simulate_profile_2D(
combination='FF',
mirror_length=L,
step_l=stepL,
random_seed_l=seedL,
error_type_l=typeL,
rms_l=rmsL,
power_law_exponent_beta_l=betaL,
mirror_width=W,
step_w=stepW,
random_seed_w=seedW,
error_type_w=typeW,
rms_w=rmsW,
power_law_exponent_beta_w=betaW)
# ==== Formats matrix to the required by function === #
mtx_fmt = np.zeros((len(x) + 1, len(y) + 1))
mtx_fmt[0, 1:] = y
mtx_fmt[1:, 0] = x
mtx_fmt[1:, 1:] = np.transpose(z)
if (print_out):
print(filename)
print('RMS = {0:.3f} nm'.format(np.std(z[:, 0] * 1e9)))
print('PV = {0:.3f} nm\n'.format(
np.max(z[:, 0] * 1e9) - np.min(z[:, 0] * 1e9)))
# # ==== Writes files for shadow input ================ #
if (filename != ''):
write_shadow_height_error(mtx_fmt, filename, 1e3, ' ') # [mm]
# # ==== Preview Plots ================================ #
if (plot):
plt.figure(figsize=(6, 1))
plt.pcolormesh(y, x, np.transpose(z))
plt.autoscale(enable=True, tight=True)
plt.figure()
plt.plot(y, z[:, 0] * 1e9)
plt.xlabel('L')
plt.ylabel('height error')
plt.show()
return mtx_fmt
