def test_save_load_h5_file(self):
wfr = GenericWavefront2D.initialize_wavefront_from_range(
-0.004, 0.004, -0.001, 0.001, (500, 200))
wfr.set_gaussian(0.002 / 6, 0.001 / 12)
wfr.save_h5_file("tmp_wofry.h5",
subgroupname="wfr",
intensity=True,
phase=True,
overwrite=True)
wfr.set_gaussian(0.002 / 6 / 2, 0.001 / 12 / 2)
print("Writing file: tmp_wofry.h5")
wfr.save_h5_file("tmp_wofry.h5",
subgroupname="wfr2",
intensity=True,
phase=False,
overwrite=False)
# test same amplitudes:
print("Accessing file, path: ", "tmp_wofry.h5", "wfr2")
wfr2 = GenericWavefront2D.load_h5_file("tmp_wofry.h5", "wfr2")
print("Cleaning file tmp_wofry.h5")
os.remove("tmp_wofry.h5")
assert (wfr2.is_identical(wfr))
if __name__ == "__main__":
from json_tools import load_from_json_file
from wofry.propagator.wavefront2D.generic_wavefront import GenericWavefront2D
from srxraylib.plot.gol import plot_image
from wofry.propagator.propagator import PropagationManager, PropagationElements, PropagationParameters
from wofryimpl.propagator.propagators2D.fresnel_zoom_xy import FresnelZoomXY2D
wfr = GenericWavefront2D.load_h5_file("source.h5", "wfr")
plot_image(wfr.get_intensity(),
1e6 * wfr.get_coordinate_x(),
1e6 * wfr.get_coordinate_y(),
title="Source",
xtitle="X [um]",
ytitle="Y [um]")
bl = load_from_json_file("beamline.json")
#
# propagate elements using Fresnel Zoom propagator
#
magnification_x = [1, 1, 0.01, 440, 1, 1, 1, 0.00007]
magnification_y = [1, 1, 1, 5, 1, 0.5, 1, 0.00009]
# define propagator to be used
propagator = PropagationManager.Instance()
try:
propagator.add_propagator(FresnelZoomXY2D())
except:
wfr.get_coordinate_y(),
title="PHI in rads")
wfr2 = wfr.duplicate()
wfr2.add_phase_shifts(PHI, polarization=Polarization.SIGMA)
wfr2.add_phase_shifts(PHI, polarization=Polarization.PI)
return wfr2
if __name__ == "__main__":
from srxraylib.plot.gol import plot, plot_image, set_qt
#
file_name = "/home/manuel/Oasys/tmp.h5"
wfr = GenericWavefront2D.load_h5_file(file_name, "wfr")
phase = wfr.get_phase(polarization=Polarization.SIGMA)
plot_image(phase,
wfr.get_coordinate_x(),
wfr.get_coordinate_y(),
title="before",
show=False)
wfr2 = generic_wfr_add_grating_error(wfr, "LEG_300 l_mm.txt", do_plot=True)
phase2 = wfr2.get_phase(polarization=Polarization.SIGMA)
plot_image(phase2,
wfr2.get_coordinate_x(),
wfr2.get_coordinate_y(),
title="after")
def run_wofry():
#
# create/import your input_wavefront (THIS IS A PLACEHOLDER - REPLACE WITH YOUR SOURCE)
#
#
from wofry.propagator.wavefront2D.generic_wavefront import GenericWavefront2D
input_wavefront = GenericWavefront2D.load_h5_file(
"/users/srio/Working/paper-hierarchical/WORKSPACES/tmp.h5", "wfr")
# initialize_wavefront_from_range(-10e-6,10e-6,-100e-6,100e-6,(200,100),1e-10)
#
# info on current oe
#
#
# -------WOScreen---------
# -------BoundaryShape---------
#
#
# define current oe
#
from wofry.beamline.optical_elements.ideal_elements.screen import WOScreen
optical_element = WOScreen()
#
# propagating (*** ONLY THE ZOOM PROPAGATOR IS IMPLEMENTED ***)
#
#
propagation_elements = PropagationElements()
beamline_element = BeamlineElement(
optical_element=optical_element,
coordinates=ElementCoordinates(
p=0.000000,
q=28.300000,
angle_radial=numpy.radians(0.000000),
angle_azimuthal=numpy.radians(0.000000)))
propagation_elements.add_beamline_element(beamline_element)
propagation_parameters = PropagationParameters(
wavefront=input_wavefront.duplicate(),
propagation_elements=propagation_elements)
#self.set_additional_parameters(propagation_parameters)
#
propagation_parameters.set_additional_parameters('shift_half_pixel', 1)
propagation_parameters.set_additional_parameters('magnification_x',
8.000000)
propagation_parameters.set_additional_parameters('magnification_y',
10.000000)
#
propagator = PropagationManager.Instance()
try:
propagator.add_propagator(FresnelZoomXY2D())
except:
pass
output_wavefront = propagator.do_propagation(
propagation_parameters=propagation_parameters,
handler_name='FRESNEL_ZOOM_XY_2D')
input_wavefront = output_wavefront
#
# info on current oe
#
#
# -------WOSlit---------
# -------Rectangle---------
# x_left: -0.0018849 m # x (width) minimum (signed)
# x_right: 0.0018849 m # x (width) maximum (signed)
# y_bottom: -0.0018849 m # y (length) minimum (signed)
# y_top: 0.0018849 m # y (length) maximum (signed)
#
#
# define current oe
#
from syned.beamline.shape import Rectangle
boundary_shape = Rectangle(x_left=-0.0018849,
x_right=0.0018849,
y_bottom=-0.0018849,
y_top=0.0018849)
from wofry.beamline.optical_elements.absorbers.slit import WOSlit
optical_element = WOSlit(boundary_shape=boundary_shape)
#
# propagating (*** ONLY THE ZOOM PROPAGATOR IS IMPLEMENTED ***)
#
#
propagation_elements = PropagationElements()
beamline_element = BeamlineElement(
optical_element=optical_element,
coordinates=ElementCoordinates(
p=0.000000,
q=0.000000,
angle_radial=numpy.radians(0.000000),
angle_azimuthal=numpy.radians(0.000000)))
propagation_elements.add_beamline_element(beamline_element)
propagation_parameters = PropagationParameters(
wavefront=input_wavefront.duplicate(),
propagation_elements=propagation_elements)
#self.set_additional_parameters(propagation_parameters)
#
propagation_parameters.set_additional_parameters('shift_half_pixel', 1)
propagation_parameters.set_additional_parameters('magnification_x',
1.000000)
propagation_parameters.set_additional_parameters('magnification_y',
1.000000)
#
propagator = PropagationManager.Instance()
try:
propagator.add_propagator(FresnelZoomXY2D())
except:
pass
output_wavefront = propagator.do_propagation(
propagation_parameters=propagation_parameters,
handler_name='FRESNEL_ZOOM_XY_2D')
input_wavefront = output_wavefront
#
# info on current oe
#
#
# -------WOIdealLens---------
# focal_x: 8.319 m # Focal length in x [horizontal]
# focal_y: 99999999999999.0 m # Focal length in y [vertical]
#
#
# define current oe
#
from wofry.beamline.optical_elements.ideal_elements.lens import WOIdealLens
optical_element = WOIdealLens(name='',
focal_x=8.319000,
focal_y=99999999999999.000000)
#
# propagating (*** ONLY THE ZOOM PROPAGATOR IS IMPLEMENTED ***)
#
#
propagation_elements = PropagationElements()
beamline_element = BeamlineElement(
optical_element=optical_element,
coordinates=ElementCoordinates(
p=0.000000,
q=0.000000,
angle_radial=numpy.radians(0.000000),
angle_azimuthal=numpy.radians(0.000000)))
propagation_elements.add_beamline_element(beamline_element)
propagation_parameters = PropagationParameters(
wavefront=input_wavefront.duplicate(),
propagation_elements=propagation_elements)
#self.set_additional_parameters(propagation_parameters)
#
propagation_parameters.set_additional_parameters('shift_half_pixel', 1)
propagation_parameters.set_additional_parameters('magnification_x',
1.000000)
propagation_parameters.set_additional_parameters('magnification_y',
1.000000)
#
propagator = PropagationManager.Instance()
try:
propagator.add_propagator(FresnelZoomXY2D())
except:
pass
output_wavefront = propagator.do_propagation(
propagation_parameters=propagation_parameters,
handler_name='FRESNEL_ZOOM_XY_2D')
input_wavefront = output_wavefront
#
# info on current oe
#
#
# -------WOSlit---------
# -------Rectangle---------
# x_left: -2.5e-05 m # x (width) minimum (signed)
# x_right: 2.5e-05 m # x (width) maximum (signed)
# y_bottom: -0.5 m # y (length) minimum (signed)
# y_top: 0.5 m # y (length) maximum (signed)
#
#
# define current oe
#
from syned.beamline.shape import Rectangle
boundary_shape = Rectangle(x_left=-2.5e-05,
x_right=2.5e-05,
y_bottom=-0.5,
y_top=0.5)
from wofry.beamline.optical_elements.absorbers.slit import WOSlit
optical_element = WOSlit(boundary_shape=boundary_shape)
#
# propagating (*** ONLY THE ZOOM PROPAGATOR IS IMPLEMENTED ***)
#
#
propagation_elements = PropagationElements()
beamline_element = BeamlineElement(
optical_element=optical_element,
coordinates=ElementCoordinates(
p=11.700000,
q=0.000000,
angle_radial=numpy.radians(0.000000),
angle_azimuthal=numpy.radians(0.000000)))
propagation_elements.add_beamline_element(beamline_element)
propagation_parameters = PropagationParameters(
wavefront=input_wavefront.duplicate(),
propagation_elements=propagation_elements)
#self.set_additional_parameters(propagation_parameters)
#
propagation_parameters.set_additional_parameters('shift_half_pixel', 1)
propagation_parameters.set_additional_parameters('magnification_x',
0.010000)
propagation_parameters.set_additional_parameters('magnification_y',
1.000000)
#
propagator = PropagationManager.Instance()
try:
propagator.add_propagator(FresnelZoomXY2D())
except:
pass
output_wavefront = propagator.do_propagation(
propagation_parameters=propagation_parameters,
handler_name='FRESNEL_ZOOM_XY_2D')
input_wavefront = output_wavefront
#
#
# ######################### KB #########################################
#
#
#
# info on current oe
#
#
# -------WOSlit---------
# -------Rectangle---------
# x_left: -0.025 m # x (width) minimum (signed)
# x_right: 0.025 m # x (width) maximum (signed)
# y_bottom: -0.00045 m # y (length) minimum (signed)
# y_top: 0.00045 m # y (length) maximum (signed)
#
#
# define current oe
#
from syned.beamline.shape import Rectangle
boundary_shape = Rectangle(x_left=-0.025,
x_right=0.025,
y_bottom=-0.00045,
y_top=0.00045)
from wofry.beamline.optical_elements.absorbers.slit import WOSlit
optical_element = WOSlit(boundary_shape=boundary_shape)
#
# propagating (*** ONLY THE ZOOM PROPAGATOR IS IMPLEMENTED ***)
#
#
propagation_elements = PropagationElements()
beamline_element = BeamlineElement(
optical_element=optical_element,
coordinates=ElementCoordinates(
p=144.900000,
q=0.000000,
angle_radial=numpy.radians(0.000000),
angle_azimuthal=numpy.radians(0.000000)))
propagation_elements.add_beamline_element(beamline_element)
propagation_parameters = PropagationParameters(
wavefront=input_wavefront.duplicate(),
propagation_elements=propagation_elements)
# self.set_additional_parameters(propagation_parameters)
#
propagation_parameters.set_additional_parameters('shift_half_pixel', 1)
propagation_parameters.set_additional_parameters('magnification_x',
440.000000)
propagation_parameters.set_additional_parameters('magnification_y',
5.000000)
#
propagator = PropagationManager.Instance()
try:
propagator.add_propagator(FresnelZoomXY2D())
except:
pass
output_wavefront = propagator.do_propagation(
propagation_parameters=propagation_parameters,
handler_name='FRESNEL_ZOOM_XY_2D')
input_wavefront = output_wavefront
#
# info on current oe
#
#
# -------WOIdealLens---------
# focal_x: 100000000.0 m # Focal length in x [horizontal]
# focal_y: 0.09994594594594594 m # Focal length in y [vertical]
#
#
# define current oe
#
from wofry.beamline.optical_elements.ideal_elements.lens import WOIdealLens
optical_element = WOIdealLens(name='',
focal_x=100000000.000000,
focal_y=0.099946)
#
# propagating (*** ONLY THE ZOOM PROPAGATOR IS IMPLEMENTED ***)
#
#
propagation_elements = PropagationElements()
beamline_element = BeamlineElement(
optical_element=optical_element,
coordinates=ElementCoordinates(
p=0.000000,
q=0.000000,
angle_radial=numpy.radians(0.000000),
angle_azimuthal=numpy.radians(0.000000)))
propagation_elements.add_beamline_element(beamline_element)
propagation_parameters = PropagationParameters(
wavefront=input_wavefront.duplicate(),
propagation_elements=propagation_elements)
# self.set_additional_parameters(propagation_parameters)
#
propagation_parameters.set_additional_parameters('shift_half_pixel', 1)
propagation_parameters.set_additional_parameters('magnification_x',
1.000000)
propagation_parameters.set_additional_parameters('magnification_y',
1.000000)
#
propagator = PropagationManager.Instance()
try:
propagator.add_propagator(FresnelZoomXY2D())
except:
pass
output_wavefront = propagator.do_propagation(
propagation_parameters=propagation_parameters,
handler_name='FRESNEL_ZOOM_XY_2D')
input_wavefront = output_wavefront
#
# info on current oe
#
#
# -------WOSlit---------
# -------Rectangle---------
# x_left: -0.000195 m # x (width) minimum (signed)
# x_right: 0.000195 m # x (width) maximum (signed)
# y_bottom: -0.0065 m # y (length) minimum (signed)
# y_top: 0.0065 m # y (length) maximum (signed)
#
#
# define current oe
#
from syned.beamline.shape import Rectangle
boundary_shape = Rectangle(x_left=-0.000195,
x_right=0.000195,
y_bottom=-0.0065,
y_top=0.0065)
from wofry.beamline.optical_elements.absorbers.slit import WOSlit
optical_element = WOSlit(boundary_shape=boundary_shape)
#
# propagating (*** ONLY THE ZOOM PROPAGATOR IS IMPLEMENTED ***)
#
#
propagation_elements = PropagationElements()
beamline_element = BeamlineElement(
optical_element=optical_element,
coordinates=ElementCoordinates(
p=0.050000,
q=0.000000,
angle_radial=numpy.radians(0.000000),
angle_azimuthal=numpy.radians(0.000000)))
propagation_elements.add_beamline_element(beamline_element)
propagation_parameters = PropagationParameters(
wavefront=input_wavefront.duplicate(),
propagation_elements=propagation_elements)
# self.set_additional_parameters(propagation_parameters)
#
propagation_parameters.set_additional_parameters('shift_half_pixel', 1)
propagation_parameters.set_additional_parameters('magnification_x',
1.000000)
propagation_parameters.set_additional_parameters('magnification_y',
0.500000)
#
propagator = PropagationManager.Instance()
try:
propagator.add_propagator(FresnelZoomXY2D())
except:
pass
output_wavefront = propagator.do_propagation(
propagation_parameters=propagation_parameters,
handler_name='FRESNEL_ZOOM_XY_2D')
input_wavefront = output_wavefront
#
# info on current oe
#
#
# -------WOIdealLens---------
# focal_x: 0.049982758620701014 m # Focal length in x [horizontal]
# focal_y: 100000000.0 m # Focal length in y [vertical]
#
#
# define current oe
#
from wofry.beamline.optical_elements.ideal_elements.lens import WOIdealLens
optical_element = WOIdealLens(name='',
focal_x=0.049983,
focal_y=100000000.000000)
#
# propagating (*** ONLY THE ZOOM PROPAGATOR IS IMPLEMENTED ***)
#
#
propagation_elements = PropagationElements()
beamline_element = BeamlineElement(
optical_element=optical_element,
coordinates=ElementCoordinates(
p=0.000000,
q=0.000000,
angle_radial=numpy.radians(0.000000),
angle_azimuthal=numpy.radians(0.000000)))
propagation_elements.add_beamline_element(beamline_element)
propagation_parameters = PropagationParameters(
wavefront=input_wavefront.duplicate(),
propagation_elements=propagation_elements)
# self.set_additional_parameters(propagation_parameters)
#
propagation_parameters.set_additional_parameters('shift_half_pixel', 1)
propagation_parameters.set_additional_parameters('magnification_x',
1.000000)
propagation_parameters.set_additional_parameters('magnification_y',
1.000000)
#
propagator = PropagationManager.Instance()
try:
propagator.add_propagator(FresnelZoomXY2D())
except:
pass
output_wavefront = propagator.do_propagation(
propagation_parameters=propagation_parameters,
handler_name='FRESNEL_ZOOM_XY_2D')
input_wavefront = output_wavefront
#
# info on current oe
#
#
# -------WOSlit---------
# -------Rectangle---------
# x_left: -0.5 m # x (width) minimum (signed)
# x_right: 0.5 m # x (width) maximum (signed)
# y_bottom: -0.5 m # y (length) minimum (signed)
# y_top: 0.5 m # y (length) maximum (signed)
#
#
# define current oe
#
from syned.beamline.shape import Rectangle
boundary_shape = Rectangle(x_left=-0.5,
x_right=0.5,
y_bottom=-0.5,
y_top=0.5)
from wofry.beamline.optical_elements.absorbers.slit import WOSlit
optical_element = WOSlit(boundary_shape=boundary_shape)
#
# propagating (*** ONLY THE ZOOM PROPAGATOR IS IMPLEMENTED ***)
#
#
propagation_elements = PropagationElements()
beamline_element = BeamlineElement(
optical_element=optical_element,
coordinates=ElementCoordinates(
p=0.050000,
q=0.000000,
angle_radial=numpy.radians(0.000000),
angle_azimuthal=numpy.radians(0.000000)))
propagation_elements.add_beamline_element(beamline_element)
propagation_parameters = PropagationParameters(
wavefront=input_wavefront.duplicate(),
propagation_elements=propagation_elements)
# self.set_additional_parameters(propagation_parameters)
#
propagation_parameters.set_additional_parameters('shift_half_pixel', 1)
propagation_parameters.set_additional_parameters('magnification_x',
0.000070)
propagation_parameters.set_additional_parameters('magnification_y',
0.000090)
#
propagator = PropagationManager.Instance()
try:
propagator.add_propagator(FresnelZoomXY2D())
except:
pass
output_wavefront = propagator.do_propagation(
propagation_parameters=propagation_parameters,
handler_name='FRESNEL_ZOOM_XY_2D')
input_wavefront = output_wavefront
return input_wavefront