def runShadowSource(self):
self.setStatusMessage("")
self.progressBarInit()
try:
self.checkFields()
###########################################
# TODO: TO BE ADDED JUST IN CASE OF BROKEN
# ENVIRONMENT: MUST BE FOUND A PROPER WAY
# TO TEST SHADOW
self.fixWeirdShadowBug()
###########################################
shadow_src = ShadowSource.create_bm_src()
self.populateFields(shadow_src)
self.progressBarSet(10)
self.setStatusMessage("Running SHADOW")
sys.stdout = EmittingStream(textWritten=self.writeStdOut)
if self.trace_shadow:
grabber = TTYGrabber()
grabber.start()
self.progressBarSet(50)
write_begin_file, write_start_file, write_end_file = self.get_write_file_options(
)
beam_out = ShadowBeam.traceFromSource(
shadow_src,
write_begin_file=write_begin_file,
write_start_file=write_start_file,
write_end_file=write_end_file,
widget_class_name=self.__class__.name)
if self.trace_shadow:
grabber.stop()
for row in grabber.ttyData:
self.writeStdOut(row)
self.setStatusMessage("Plotting Results")
self.progressBarSet(80)
self.plot_results(beam_out)
self.setStatusMessage("")
self.send("Beam", beam_out)
except Exception as exception:
QtWidgets.QMessageBox.critical(self, "Error", str(exception),
QtWidgets.QMessageBox.Ok)
if self.IS_DEVELOP: raise exception
self.progressBarFinished()
def completeOperations(self, shadow_oe=None):
self.setStatusMessage("Running SHADOW")
if self.trace_shadow:
grabber = TTYGrabber()
grabber.start()
self.progressBarSet(50)
###########################################
# TODO: TO BE ADDED JUST IN CASE OF BROKEN
# ENVIRONMENT: MUST BE FOUND A PROPER WAY
# TO TEST SHADOW
self.fixWeirdShadowBug()
###########################################
beam_out = ShadowBeam.traceFromOE(self.input_beam, shadow_oe)
self.adjust_divergence_and_intensity(beam_out)
if self.trace_shadow:
grabber.stop()
for row in grabber.ttyData:
self.writeStdOut(row)
self.setStatusMessage("Plotting Results")
self.plot_results(beam_out)
self.setStatusMessage("")
self.send("Beam", beam_out)
self.send("Trigger", TriggerIn(new_object=True))
def plot_results(self):
try:
plotted = False
sys.stdout = EmittingStream(textWritten=self.writeStdOut)
if self.trace_shadow:
grabber = TTYGrabber()
grabber.start()
if ShadowCongruence.checkEmptyBeam(self.input_beam):
ShadowPlot.set_conversion_active(self.getConversionActive())
# self.number_of_bins = congruence.checkStrictlyPositiveNumber(self.number_of_bins, "Number of Bins")
x, y, c, auto_x_title, auto_y_title, xum, yum = self.get_titles(
)
self.plot_scatter(x,
y,
c,
title=self.title,
xtitle=auto_x_title,
ytitle=auto_y_title,
xum=xum,
yum=yum)
plotted = True
if self.trace_shadow:
grabber.stop()
for row in grabber.ttyData:
self.writeStdOut(row)
time.sleep(
0.5
) # prevents a misterious dead lock in the Orange cycle when refreshing the histogram
return plotted
except Exception as exception:
QtWidgets.QMessageBox.critical(self, "Error", str(exception),
QtWidgets.QMessageBox.Ok)
if self.IS_DEVELOP: raise exception
return False
def completeOperations(self, shadow_oe=None):
self.setStatusMessage("Running SHADOW")
if self.trace_shadow:
grabber = TTYGrabber()
grabber.start()
self.progressBarSet(50)
###########################################
# TODO: TO BE ADDED JUST IN CASE OF BROKEN
# ENVIRONMENT: MUST BE FOUND A PROPER WAY
# TO TEST SHADOW
self.fixWeirdShadowBug()
###########################################
write_start_files, write_end_files, write_star_files, write_mirr_files = self.get_write_file_options(
)
beam_out = ShadowBeam.traceFromCompoundOE(
self.input_beam,
shadow_oe,
write_start_files=write_start_files,
write_end_files=write_end_files,
write_star_files=write_star_files,
write_mirr_files=write_mirr_files,
widget_class_name=type(self).__name__)
if self.trace_shadow:
grabber.stop()
for row in grabber.ttyData:
self.writeStdOut(row)
self.setStatusMessage("Plotting Results")
self.plot_results(beam_out)
self.setStatusMessage("")
self.send("Beam", beam_out)
self.send("Trigger", TriggerIn(new_object=True))
def traceOpticalElement(self):
try:
self.error(self.error_id)
self.setStatusMessage("")
self.progressBarInit()
if ShadowCongruence.checkEmptyBeam(self.input_beam):
if ShadowCongruence.checkGoodBeam(self.input_beam):
sys.stdout = EmittingStream(textWritten=self.writeStdOut)
self.progressBarSet(10)
self.checkFields()
self.setStatusMessage("Running SHADOW")
if self.trace_shadow:
grabber = TTYGrabber()
grabber.start()
self.progressBarSet(50)
###########################################
# TODO: TO BE ADDED JUST IN CASE OF BROKEN
# ENVIRONMENT: MUST BE FOUND A PROPER WAY
# TO TEST SHADOW
self.fixWeirdShadowBug()
###########################################
shadow_oe_1 = ShadowOpticalElement.create_screen_slit()
self.populateFields_1(shadow_oe_1)
beam_out = ShadowBeam.traceFromOE(self.input_beam, shadow_oe_1)
self.adjust_first_divergence(beam_out)
self.progressBarSet(60)
shadow_oe_2 = ShadowOpticalElement.create_screen_slit()
self.populateFields_2(shadow_oe_2)
beam_out = ShadowBeam.traceFromOE(beam_out, shadow_oe_2)
self.adjust_second_divergence_and_intensity(beam_out)
self.progressBarSet(70)
shadow_oe_3 = ShadowOpticalElement.create_screen_slit()
self.populateFields_3(shadow_oe_3)
beam_out = ShadowBeam.traceFromOE(beam_out, shadow_oe_3)
if self.trace_shadow:
grabber.stop()
for row in grabber.ttyData:
self.writeStdOut(row)
self.setStatusMessage("Plotting Results")
self.plot_results(beam_out)
self.setStatusMessage("")
self.send("Beam", beam_out)
self.send("Trigger", TriggerIn(new_object=True))
else:
raise Exception("Input Beam with no good rays")
else:
raise Exception("Empty Input Beam")
except Exception as exception:
QtWidgets.QMessageBox.critical(self, "QMessageBox.critical()",
str(exception),
QtWidgets.QMessageBox.Ok)
self.error_id = self.error_id + 1
self.error(self.error_id, "Exception occurred: " + str(exception))
self.progressBarFinished()
def runShadowSource(self):
#self.error(self.error_id)
self.setStatusMessage("")
self.progressBarInit()
sys.stdout = EmittingStream(textWritten=self.writeStdOut)
if self.trace_shadow:
grabber = TTYGrabber()
grabber.start()
try:
self.checkFields()
###########################################
# TODO: TO BE ADDED JUST IN CASE OF BROKEN
# ENVIRONMENT: MUST BE FOUND A PROPER WAY
# TO TEST SHADOW
self.fixWeirdShadowBug()
###########################################
wigFile = bytes(congruence.checkFileName("xshwig.sha"), 'utf-8')
if self.type_combo == 0:
inData = ""
elif self.type_combo == 1:
inData = congruence.checkUrl(self.file_with_b_vs_y)
elif self.type_combo == 2:
inData = congruence.checkUrl(self.file_with_harmonics)
self.progressBarSet(10)
#self.information(0, "Calculate electron trajectory")
self.shadow_output.setText("")
self.setStatusMessage("Calculate electron trajectory")
(traj, pars) = srfunc.wiggler_trajectory(b_from=self.type_combo,
inData=inData,
nPer=self.number_of_periods,
nTrajPoints=501,
ener_gev=self.energy,
per=self.id_period,
kValue=self.k_value,
trajFile=congruence.checkFileName("tmp.traj"),
shift_x_flag=self.shift_x_flag,
shift_x_value=self.shift_x_value,
shift_betax_flag=self.shift_betax_flag,
shift_betax_value=self.shift_betax_value)
#
# calculate cdf and write file for Shadow/Source
#
self.progressBarSet(20)
#self.information(0, "Calculate cdf and write file for Shadow/Source")
self.setStatusMessage("Calculate cdf and write file for Shadow/Source")
srfunc.wiggler_cdf(traj,
enerMin=self.e_min,
enerMax=self.e_max,
enerPoints=1001,
outFile=wigFile,
elliptical=False)
#self.information(0, "CDF written to file %s \n"%(wigFile))
self.setStatusMessage("CDF written to file %s \n"%(str(wigFile)))
self.progressBarSet(40)
#self.information(0, "Set the wiggler parameters in the wiggler container")
self.setStatusMessage("Set the wiggler parameters in the wiggler container")
shadow_src = ShadowSource.create_wiggler_src()
self.populateFields(shadow_src)
shadow_src.src.FILE_TRAJ = wigFile
self.progressBarSet(50)
self.setStatusMessage("Running Shadow/Source")
write_begin_file, write_start_file, write_end_file = self.get_write_file_options()
beam_out = ShadowBeam.traceFromSource(shadow_src,
write_begin_file=write_begin_file,
write_start_file=write_start_file,
write_end_file=write_end_file)
if self.trace_shadow:
grabber.stop()
for row in grabber.ttyData:
self.writeStdOut(row)
#self.information(0, "Plotting Results")
self.setStatusMessage("Plotting Results")
self.progressBarSet(80)
self.plot_results(beam_out, progressBarValue=80)
self.setStatusMessage("Plotting Wiggler Data")
self.plot_wiggler_results()
#self.information()
self.setStatusMessage("")
self.send("Beam", beam_out)
#
# create python script for the preprocessors and display in the standard output
#
dict_parameters = {
"b_from" : self.type_combo,
"inData" : inData,
"nPer" : self.number_of_periods,
"nTrajPoints" : 501,
"ener_gev" : self.energy,
"per" : self.id_period,
"kValue" : self.k_value,
"trajFile" : "tmp.traj",
"shift_x_flag" : self.shift_x_flag,
"shift_x_value" : self.shift_x_value,
"shift_betax_flag" : self.shift_betax_flag,
"shift_betax_value" : self.shift_betax_value,
"enerMin" : self.e_min,
"enerMax" : self.e_max,
"enerPoints" : 1001,
"outFile" : wigFile,
"elliptical" : False,
"electron_current_mA" : self.electron_current,
}
# write python script in standard output
print(self.script_template().format_map(dict_parameters))
except Exception as exception:
QtWidgets.QMessageBox.critical(self, "Error",
str(exception),
QtWidgets.QMessageBox.Ok)
#self.error_id = self.error_id + 1
#self.error(self.error_id, "Exception occurred: " + str(exception))
self.progressBarFinished()
def traceOpticalElement(self):
try:
self.setStatusMessage("")
self.progressBarInit()
if ShadowCongruence.checkEmptyBeam(self.input_beam):
if ShadowCongruence.checkGoodBeam(self.input_beam):
self.checkFields()
sys.stdout = EmittingStream(textWritten=self.writeStdOut)
if self.trace_shadow:
grabber = TTYGrabber()
grabber.start()
###########################################
# TODO: TO BE ADDED JUST IN CASE OF BROKEN
# ENVIRONMENT: MUST BE FOUND A PROPER WAY
# TO TEST SHADOW
self.fixWeirdShadowBug()
###########################################
self.progressBarSet(10)
if self.source_distance_flag == 0:
self.source_distance = self.source_plane_distance
zone_plate_beam = self.get_zone_plate_beam()
go = numpy.where(zone_plate_beam._beam.rays[:, 9] == GOOD)
self.avg_wavelength = ShadowPhysics.getWavelengthFromShadowK(numpy.average(zone_plate_beam._beam.rays[go, 10]))*1e-1 #ANGSTROM->nm
self.focal_distance = (self.delta_rn*(self.diameter*1000)/self.avg_wavelength)* (1e-9/self.workspace_units_to_m) # WS Units
self.image_position = self.focal_distance*self.source_distance/(self.source_distance-self.focal_distance) # WS Units
self.magnification = numpy.abs(self.image_position/self.source_distance)
self.avg_wavelength = numpy.round(self.avg_wavelength, 6) # nm
self.focal_distance = numpy.round(self.focal_distance, 6)
self.image_position = numpy.round(self.image_position, 6)
self.magnification = numpy.round(self.magnification, 6)
if self.automatically_set_image_plane == 1:
self.image_plane_distance = self.image_position
self.progressBarSet(30)
if self.type_of_zp == PHASE_ZP:
efficiency, max_efficiency, thickness_max_efficiency = ZonePlate.calculate_efficiency(self.avg_wavelength, # Angstrom
self.zone_plate_material,
self.zone_plate_thickness)
self.efficiency = numpy.round(100*efficiency, 3)
self.max_efficiency = numpy.round(100*max_efficiency, 3)
self.thickness_max_efficiency = thickness_max_efficiency
else:
self.efficiency = numpy.round(100/(numpy.pi**2), 3)
self.max_efficiency = numpy.nan
self.thickness_max_efficiency = numpy.nan
focused_beam, \
self.number_of_zones = ZonePlate.apply_fresnel_zone_plate(zone_plate_beam, # WS Units
self.type_of_zp,
self.diameter, # micron
self.delta_rn, # nm
self.substrate_material,
self.substrate_thickness,
self.zone_plate_material,
self.zone_plate_thickness,
self.source_distance, # WS Units
self.workspace_units_to_m)
self.progressBarSet(60)
beam_out = self.get_output_beam(focused_beam)
self.progressBarSet(80)
if self.trace_shadow:
grabber.stop()
for row in grabber.ttyData:
self.writeStdOut(row)
self.setStatusMessage("Plotting Results")
self.plot_results(beam_out)
self.plot_efficiency()
self.setStatusMessage("")
beam_out.setScanningData(self.input_beam.scanned_variable_data)
self.send("Beam", beam_out)
self.send("Trigger", TriggerIn(new_object=True))
else:
if self.not_interactive: self.sendEmptyBeam()
else: raise Exception("Input Beam with no good rays")
else:
if self.not_interactive: self.sendEmptyBeam()
else: raise Exception("Empty Input Beam")
except Exception as exception:
QMessageBox.critical(self, "Error",
str(exception), QMessageBox.Ok)
if self.IS_DEVELOP: raise exception
self.progressBarFinished()
def xoppy_calc_power3Dcomponent(self):
#
# important: the transmittivity calculated here is referred on axes perp to the beam
# therefore they do not include geometrical corrections for correct integral
#
substance = self.EL1_FOR
thick = self.EL1_THI
angle = self.EL1_ANG
defection = self.EL1_DEF
dens = self.EL1_DEN
roughness = self.EL1_ROU
flags = self.EL1_FLAG
hgap = self.EL1_HGAP
vgap = self.EL1_VGAP
hmag = self.EL1_HMAG
vmag = self.EL1_VMAG
hrot = self.EL1_HROT
vrot = self.EL1_VROT
if self.INPUT_BEAM_FROM == 1:
self.load_input_file()
p0, e0, h0, v0 = self.input_beam.get_content("xoppy_data")
p = p0.copy()
e = e0.copy()
h = h0.copy()
v = v0.copy()
transmittance = numpy.ones_like(p)
E = e.copy()
H = h.copy()
V = v.copy()
# initialize results
#
# get undefined densities
#
if flags <= 1:
try: # apply written value
rho = float(dens)
except: # in case of ?
# grabber = TTYGrabber()
# grabber.start()
rho = density(substance)
# grabber.stop()
# for row in grabber.ttyData:
# self.writeStdOut(row)
print("Density for %s: %g g/cm3"%(substance,rho))
dens = rho
txt = ""
if flags == 0:
txt += ' ***** oe [Filter] *************\n'
txt += ' Material: %s\n'%(substance)
txt += ' Density [g/cm^3]: %f \n'%(dens)
txt += ' thickness [mm] : %f \n'%(thick)
txt += ' H gap [mm]: %f \n'%(hgap)
txt += ' V gap [mm]: %f \n'%(vgap)
txt += ' H rotation angle [deg]: %f \n'%(hrot)
txt += ' V rotation angle [deg]: %f \n'%(vrot)
elif flags == 1:
txt += ' ***** oe [Mirror] *************\n'
txt += ' Material: %s\n'%(substance)
txt += ' Density [g/cm^3]: %f \n'%(dens)
txt += ' grazing angle [mrad]: %f \n'%(angle)
txt += ' roughness [A]: %f \n'%(roughness)
elif flags == 2:
txt += ' ***** oe [Aperture] *************\n'
txt += ' H gap [mm]: %f \n'%(hgap)
txt += ' V gap [mm]: %f \n'%(vgap)
elif flags == 3:
txt += ' ***** oe [Magnifier] *************\n'
txt += ' H magnification: %f \n'%(hmag)
txt += ' V magnification: %f \n'%(vmag)
elif flags == 4:
txt += ' ***** oe [Screen rotated] *************\n'
txt += ' H rotation angle [deg]: %f \n'%(hrot)
txt += ' V rotation angle [deg]: %f \n'%(vrot)
if flags == 0: # filter
grabber = TTYGrabber()
grabber.start()
for j,energy in enumerate(e):
tmp = xraylib.CS_Total_CP(substance,energy/1000.0)
transmittance[j,:,:] = numpy.exp(-tmp*dens*(thick/10.0))
grabber.stop()
for row in grabber.ttyData:
self.writeStdOut(row)
# rotation
H = h / numpy.cos(hrot * numpy.pi / 180)
V = v / numpy.cos(vrot * numpy.pi / 180)
# aperture
h_indices_bad = numpy.where(numpy.abs(H) > 0.5*hgap)
if len(h_indices_bad) > 0:
transmittance[:, h_indices_bad, :] = 0.0
v_indices_bad = numpy.where(numpy.abs(V) > 0.5*vgap)
if len(v_indices_bad) > 0:
transmittance[:, :, v_indices_bad] = 0.0
absorbance = 1.0 - transmittance
elif flags == 1: # mirror
tmp = numpy.zeros(e.size)
for j,energy in enumerate(e):
tmp[j] = xraylib.Refractive_Index_Re(substance,energy/1000.0,dens)
if tmp[0] == 0.0:
raise Exception("Probably the substrance %s is wrong"%substance)
delta = 1.0 - tmp
beta = numpy.zeros(e.size)
for j,energy in enumerate(e):
beta[j] = xraylib.Refractive_Index_Im(substance,energy/1000.0,dens)
try:
(rs,rp,runp) = reflectivity_fresnel(refraction_index_beta=beta,refraction_index_delta=delta,\
grazing_angle_mrad=angle,roughness_rms_A=roughness,\
photon_energy_ev=e)
except:
raise Exception("Failed to run reflectivity_fresnel")
for j,energy in enumerate(e):
transmittance[j,:,:] = rs[j]
# rotation
if defection == 0: # horizontally deflecting
H = h / numpy.sin(self.EL1_ANG * 1e-3)
elif defection == 1: # vertically deflecting
V = v / numpy.sin(self.EL1_ANG * 1e-3)
# size
absorbance = 1.0 - transmittance
h_indices_bad = numpy.where(numpy.abs(H) > 0.5*hgap)
if len(h_indices_bad) > 0:
transmittance[:, h_indices_bad, :] = 0.0
absorbance[:, h_indices_bad, :] = 0.0
v_indices_bad = numpy.where(numpy.abs(V) > 0.5*vgap)
if len(v_indices_bad) > 0:
transmittance[:, :, v_indices_bad] = 0.0
absorbance[:, :, v_indices_bad] = 0.0
elif flags == 2: # aperture
h_indices_bad = numpy.where(numpy.abs(H) > 0.5*hgap)
if len(h_indices_bad) > 0:
transmittance[:, h_indices_bad, :] = 0.0
v_indices_bad = numpy.where(numpy.abs(V) > 0.5*vgap)
if len(v_indices_bad) > 0:
transmittance[:, :, v_indices_bad] = 0.0
absorbance = 1.0 - transmittance
elif flags == 3: # magnifier
H = h * hmag
V = v * vmag
absorbance = 1.0 - transmittance
elif flags == 4: # rotation screen
# transmittance[:, :, :] = numpy.cos(hrot * numpy.pi / 180) * numpy.cos(vrot * numpy.pi / 180)
H = h / numpy.cos(hrot * numpy.pi / 180)
V = v / numpy.cos(vrot * numpy.pi / 180)
absorbance = 1.0 - transmittance
txt += self.info_total_power(p, e, v, h, transmittance, absorbance)
print(txt)
calculated_data = (transmittance, absorbance, E, H, V)
if self.FILE_DUMP == 0:
pass
elif self.FILE_DUMP == 1:
self.xoppy_write_h5file(calculated_data)
elif self.FILE_DUMP == 2:
self.xoppy_write_txt(calculated_data, method="3columns")
elif self.FILE_DUMP == 3:
self.xoppy_write_txt(calculated_data, method="matrix")
return calculated_data