def extract_data_from_xoppy_output(self, calculation_output):
spec_file_name = calculation_output
sf = specfile.Specfile(spec_file_name)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ", spec_file_name)
out = numpy.loadtxt(spec_file_name)
if len(out) == 0 : raise Exception("Calculation gave no results (empty data)")
#get labels
txt = open(spec_file_name).readlines()
tmp = [ line.find("#L") for line in txt]
itmp = numpy.where(numpy.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ","").split(" ")
print("data labels: ", labels)
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
calculated_data.add_content("xoppy_specfile", spec_file_name)
calculated_data.add_content("xoppy_data", out)
return calculated_data
else:
raise Exception("File %s contains %d scans. Cannot send it as xoppy_table" % (spec_file_name, sf.scanno()))
def extract_data_from_xoppy_output(self, calculation_output):
data, fm, a, energy_ev = calculation_output
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
calculated_data.add_content("xoppy_data", data)
calculated_data.add_content("xoppy_data_3D", [fm, a, energy_ev])
return calculated_data
def extract_data_from_xoppy_output(self, calculation_output):
e, h, v, p, code = calculation_output
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
calculated_data.add_content("xoppy_data", [p, e, h, v])
calculated_data.add_content("xoppy_code", code)
return calculated_data
def extract_data_from_xoppy_output(self, calculation_output):
out_dict = calculation_output
if "info" in out_dict.keys():
print(out_dict["info"])
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
calculated_data.add_content("xoppy_data", out_dict["data"])
return calculated_data
def extract_data_from_xoppy_output(self, calculation_output):
out_dict = calculation_output
if "info" in out_dict.keys():
print(out_dict["info"])
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
calculated_data.add_content("xoppy_data", out_dict["data"])
return calculated_data
def extract_data_from_xoppy_output(self, calculation_output):
e, f, sp = calculation_output
data = numpy.zeros((len(e), 3))
data[:, 0] = numpy.array(e)
data[:, 1] = numpy.array(f)
data[:, 2] = numpy.array(sp)
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
calculated_data.add_content("xoppy_data", data)
return calculated_data
def extract_data_from_xoppy_output(self, calculation_output):
e, f, sp = calculation_output
data = numpy.zeros((len(e), 3))
data[:, 0] = numpy.array(e)
data[:, 1] = numpy.array(f)
data[:, 2] = numpy.array(sp)
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
calculated_data.add_content("xoppy_data", data)
return calculated_data
def read_spectrum_and_filters_file(self):
try:
data = numpy.loadtxt("filters.dat", skiprows=1)
calculated_data = DataExchangeObject(program_name="ShadowOui",
widget_name="PowerLoopPoint")
calculated_data.add_content("filters_data", data)
self.acceptFilters(calculated_data)
except Exception:
self.filters = None
self.read_spectrum_file(False)
def read_spectrum_file(self):
try:
data = numpy.loadtxt("autobinning.dat", skiprows=1)
calculated_data = DataExchangeObject(
program_name="SRW", widget_name="UNDULATOR_SPECTRUM")
calculated_data.add_content("srw_data", data)
self.send("ExchangeData", calculated_data)
except Exception as e:
QMessageBox.critical(self, "Error", str(e), QMessageBox.Ok)
if self.IS_DEVELOP: raise e
def example_1d():
app = QtGui.QApplication([])
ow = OWPlotSimpleExchange()
a = DataExchangeObject("TEXT","TEST")
a.add_content("data",numpy.array([
[ 8.47091837e+04, 1.16210756e+12],
[ 8.57285714e+04, 1.10833975e+12],
[ 8.67479592e+04, 1.05700892e+12],
[ 8.77673469e+04, 1.00800805e+12] ]))
ow.do_plot(a)
ow.show()
app.exec_()
ow.saveSettings()
def example_1d():
app = QtWidgets.QApplication([])
ow = OWPlotSimpleExchange()
a = DataExchangeObject("TEXT","TEST")
a.add_content("data",numpy.array([
[ 8.47091837e+04, 1.16210756e+12],
[ 8.57285714e+04, 1.10833975e+12],
[ 8.67479592e+04, 1.05700892e+12],
[ 8.77673469e+04, 1.00800805e+12] ]))
ow.do_plot(a)
ow.show()
app.exec_()
ow.saveSettings()
def extract_data_from_xoppy_output(self, calculation_output):
transmittance, absorbance, E, H, V = calculation_output
p0, e0, h0, v0 = self.input_beam.get_content("xoppy_data")
p = p0.copy()
e = e0.copy()
h = h0.copy()
v = v0.copy()
# coordinates to send: the same as incident beam (perpendicular to the optical axis)
# except for the magnifier
if self.EL1_FLAG == 3: # magnifier <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
h *= self.EL1_HMAG
v *= self.EL1_VMAG
p_transmitted = p * transmittance / (h[0] / h0[0]) / (v[0] / v0[0])
data_to_send = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
data_to_send.add_content("xoppy_data", [p_transmitted, e, h, v])
data_to_send.add_content("xoppy_transmittivity", calculation_output)
data_to_send.add_content("xoppy_code", "power3Dcomponent")
self.output_beam = data_to_send
return data_to_send
def extract_data_from_xoppy_output(self, calculation_output):
K_scan,harmonics,P_scan,energy_values_at_flux_peak,flux_values = calculation_output
harmonics_data = []
for ih,harmonic_number in enumerate(harmonics):
harmonics_data.append([harmonic_number,None])
data = numpy.zeros((K_scan.size, 5))
data[:, 0] = numpy.array(energy_values_at_flux_peak[:,ih])
data[:, 1] = numpy.array(flux_values[:,ih])
data[:, 2] = numpy.array(flux_values[:,ih])*codata.e*1e3
data[:, 3] = numpy.array(K_scan)
data[:, 4] = numpy.array(P_scan)
harmonics_data[ih][1] = data
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data_harmonics", harmonics_data)
calculated_data.add_content("plot_x_col", 1)
calculated_data.add_content("plot_y_col", 2)
except:
pass
try:
calculated_data.add_content("labels",["Photon energy [eV]","Flux [photons/s/0.1%bw]","Ky","Power [W]"])
except:
pass
return calculated_data
def read_spectrum_file(self, reset_filters=True):
try:
if reset_filters:
self.filters = None
self.filter_plot.clear()
data = numpy.loadtxt("autobinning.dat", skiprows=1)
calculated_data = DataExchangeObject(program_name="ShadowOui",
widget_name="PowerLoopPoint")
calculated_data.add_content("spectrum_data", data)
self.acceptEnergySpectrum(calculated_data)
except Exception as e:
QMessageBox.critical(self, "Error", str(e), QMessageBox.Ok)
if self.IS_DEVELOP: raise e
def extract_data_from_xoppy_output(self, calculation_output):
e, h, v, p, traj = calculation_output
calculated_data = DataExchangeObject(
"XOPPY", self.get_data_exchange_widget_name())
calculated_data.add_content("xoppy_data", [p, e, h, v])
calculated_data.add_content("xoppy_trajectory", traj)
calculated_data.add_content("xoppy_code", "srfunc")
return calculated_data
def example_2d():
app = QtGui.QApplication([])
ow = OWPlotSimpleExchange()
a = DataExchangeObject("TEXT","TEST")
x = numpy.linspace(-4, 4, 20)
y = numpy.linspace(-4, 4, 20)
z = numpy.sqrt(x[numpy.newaxis, :]**2 + y[:, numpy.newaxis]**2)
a.add_content("data2D",z)
a.add_content("dataX",x)
a.add_content("dataY",y)
ow.do_plot(a)
ow.show()
app.exec_()
ow.saveSettings()
def create_exchange_data(self, tickets):
ticket = tickets[0]
if isinstance(ticket['histogram'].shape, list):
f = ticket['histogram'][0]
else:
f = ticket['histogram']
e = ticket['bins']
data = numpy.zeros((len(e), 2))
data[:, 0] = numpy.array(e)
data[:, 1] = numpy.array(f)
calculated_data = DataExchangeObject(program_name="SRW",
widget_name="UNDULATOR_SPECTRUM")
calculated_data.add_content("srw_data", data)
return calculated_data
def extract_data_from_xoppy_output(self, calculation_output):
spec_file_name = calculation_output
sf = SpecFile(spec_file_name)
if len(sf) == 1:
#load spec file with one scan, # is comment
print(("Loading file: ", spec_file_name))
out = numpy.loadtxt(spec_file_name)
if len(out) == 0 : raise Exception("Calculation gave no results (empty data)")
#get labels
# txt = open(spec_file_name).readlines()
# tmp = [ line.find("#L") for line in txt]
# itmp = numpy.where(numpy.array(tmp) != (-1))
# labels = txt[int(itmp[0])].replace("#L ","").split(" ")
# print("data labels: ", labels)
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
calculated_data.add_content("xoppy_specfile", spec_file_name)
calculated_data.add_content("xoppy_data", out)
return calculated_data
else:
raise Exception("File %s contains %d scans. Cannot send it as xoppy_table" % (spec_file_name, len(sf)))
def extract_data_from_xoppy_output(self, calculation_output):
data, fm, a, energy_ev = calculation_output
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
calculated_data.add_content("xoppy_data", data)
calculated_data.add_content("xoppy_data_3D", [fm, a, energy_ev])
return calculated_data
def extract_data_from_xoppy_output(self, calculation_output):
[p, e, h, v] = self.input_beam.get_content("xoppy_data")
data_to_send = DataExchangeObject("XOPPY",
self.get_data_exchange_widget_name())
data_to_send.add_content(
"xoppy_data", [p * calculation_output.prod(axis=0), e, h, v])
data_to_send.add_content("xoppy_transmittivity", calculation_output)
data_to_send.add_content("xoppy_code", "power3")
self.output_beam = data_to_send
return data_to_send
def extract_data_from_xoppy_output(self, calculation_output):
h, v, p, code = calculation_output
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
calculated_data.add_content("xoppy_data", [h, v, p])
calculated_data.add_content("xoppy_code", code)
return calculated_data
def extract_data_from_xoppy_output(self, calculation_output):
[p, e, h, v] = self.input_beam.get_content("xoppy_data")
data_to_send = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
data_to_send.add_content("xoppy_data", [p*calculation_output.prod(axis=0), e, h, v])
data_to_send.add_content("xoppy_transmittivity", calculation_output)
data_to_send.add_content("xoppy_code", "power3")
self.output_beam = data_to_send
return data_to_send
def load_input_file(self):
e, h, v, p, code = self.extract_data_from_h5file(self.INPUT_BEAM_FILE, "XOPPY_RADIATION")
received_data = DataExchangeObject("XOPPY", "POWER3DCOMPONENT")
received_data.add_content("xoppy_data", [p, e, h, v])
received_data.add_content("xoppy_code", code)
self.input_beam = received_data
print("Input beam read from file %s \n\n"%self.INPUT_BEAM_FILE)
def example_2d():
app = QtGui.QApplication([])
ow = OWPlotSimpleExchange()
a = DataExchangeObject("TEXT", "TEST")
x = numpy.linspace(-4, 4, 20)
y = numpy.linspace(-4, 4, 20)
z = numpy.sqrt(x[numpy.newaxis, :]**2 + y[:, numpy.newaxis]**2)
a.add_content("data2D", z)
a.add_content("dataX", x)
a.add_content("dataY", y)
ow.do_plot(a)
ow.show()
app.exec_()
ow.saveSettings()
def extract_data_from_xoppy_output(self, calculation_output):
K_scan,harmonics,P_scan,energy_values_at_flux_peak,flux_values = calculation_output
harmonics_data = []
for ih in range(len(harmonics)):
harmonic_number = int(harmonics[ih])
harmonics_data.append([harmonic_number,None])
data = numpy.zeros((K_scan.size, 5))
data[:, 0] = numpy.array(energy_values_at_flux_peak[:,ih])
data[:, 1] = numpy.array(flux_values[:,ih])
data[:, 2] = numpy.array(flux_values[:,ih])*codata.e*1e3
data[:, 3] = numpy.array(K_scan)
data[:, 4] = numpy.array(P_scan)
harmonics_data[ih][1] = data
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data_harmonics", harmonics_data)
calculated_data.add_content("plot_x_col", 1)
calculated_data.add_content("plot_y_col", 2)
except:
pass
try:
calculated_data.add_content("labels",["Photon energy [eV]","Flux [photons/s/0.1%bw]","Ky","Power [W]"])
except:
pass
return calculated_data
def xoppy_calc_xtcap(self):
for file in ["tcap.inp","tcap.out","tcap.log"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
with open("tcap.inp", "wt") as f:
f.write("TCAP called from xoppy\n")
f.write("%10.3f %10.2f %10.6f %s\n"%(self.ENERGY,self.CURRENT,self.ENERGY_SPREAD,"Ring-Energy(GeV) Current(mA) Beam-Energy-Spread"))
f.write("%10.4f %10.4f %10.4f %10.4f %s\n"%(self.SIGX,self.SIGY,self.SIGX1,self.SIGY1,"Sx(mm) Sy(mm) Sx1(mrad) Sy1(mrad)"))
f.write("%10.3f %d %s\n"%(self.PERIOD,self.NP,"Period(cm) N"))
f.write("%10.1f %10.1f %d %s\n"%(self.EMIN,self.EMAX,self.N,"Emin Emax Ne"))
f.write("%10.3f %10.3f %10.3f %10.3f %10.3f %d %d %s\n"%(self.DISTANCE,self.XPC,self.YPC,self.XPS,self.YPS,10,10,"d xpc ypc xps yps nxp nyp"))
f.write("%d %d %d %d %s\n"%(self.HARMONIC_FROM,self.HARMONIC_TO,self.HARMONIC_STEP,self.HRED,"Hmin Hmax Hstep Hreduction"))
f.write("%d %d %d %d %d %s\n"%(self.HELICAL,self.METHOD,1,self.NEKS,self.BSL,"Helical Method Print_K Neks Bsl-Subtr "))
f.write("foreground\n")
if platform.system() == "Windows":
command = "\"" + os.path.join(locations.home_bin(),'tcap.exe') + "\""
else:
command = "'" + os.path.join(locations.home_bin(), 'tcap') + "'"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
# os.system(command)
#
# catch the optut and write the output to a log file as well as print it.
#
retvalue = os.popen(command).read()
print(retvalue)
with open("tcap.log", "wt") as f:
f.write(retvalue)
print("Output file: '%s/tcap.out'"%(os.getcwd()) )
print("\n--------------------------------------------------------\n")
#
# parse result files to exchange object
#
with open("tcap.out","r") as f:
lines = f.readlines()
# print output file
# for line in lines:
# print(line, end="")
# remove returns
lines = [line[:-1] for line in lines]
harmonics_data = []
# separate numerical data from text
floatlist = []
harmoniclist = []
txtlist = []
for line in lines:
try:
tmp = line.strip()
if tmp.startswith("Harmonic"):
# harmonic_number = int(tmp.split("Harmonic")[1].strip())
harmonic_number = int(tmp.split()[1])
if harmonic_number != self.HARMONIC_FROM:
harmonics_data[-1][1] = harmoniclist
harmoniclist = []
harmonics_data.append([harmonic_number, None])
tmp = float(line.strip()[0])
floatlist.append(line)
harmoniclist.append(line)
except:
txtlist.append(line)
harmonics_data[-1][1] = harmoniclist
data = numpy.loadtxt(floatlist)
for index in range(0, len(harmonics_data)):
# print (harmonics_data[index][0], harmonics_data[index][1])
harmonics_data[index][1] = numpy.loadtxt(harmonics_data[index][1])
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", data)
calculated_data.add_content("xoppy_data_harmonics", harmonics_data)
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", 1)
except:
pass
try:
calculated_data.add_content("labels",["Energy(eV)","Flux(ph/s/0.1%bw)","FWHM(eV)","Ky",
"Ptot(W)","Pd(W/mm^2)","IntP(W)"])
except:
pass
try:
calculated_data.add_content("info",txtlist)
except:
pass
return calculated_data
def submit(self):
self.progressBarInit()
self.setStatusMessage("Submitting Request")
self.checkFields()
parameters = {}
parameters.update({"xway" : self.decode_xway()})
parameters.update({"wave" : str(self.wave)})
parameters.update({"line" : self.line})
parameters.update({"ipol" : str(self.ipol + 1)})
parameters.update({"code" : self.code})
parameters.update({"df1df2" : self.decode_df1df2()})
parameters.update({"sigma" : str(self.sigma)})
parameters.update({"w0" : str(self.w0)})
parameters.update({"wh" : str(self.wh)})
parameters.update({"i1" : str(self.i1)})
parameters.update({"i2" : str(self.i2)})
parameters.update({"i3" : str(self.i3)})
parameters.update({"daa" : str(self.daa)})
parameters.update({"igie" : self.decode_igie()})
parameters.update({"fcentre" : str(self.fcentre)})
parameters.update({"unic" : str(self.unic - 1)})
parameters.update({"n1" : str(self.n1)})
parameters.update({"n2" : str(self.n2)})
parameters.update({"n3" : str(self.n3)})
parameters.update({"m1" : str(self.m1)})
parameters.update({"m2" : str(self.m2)})
parameters.update({"m3" : str(self.m3)})
parameters.update({"miscut" : str(self.miscut)})
parameters.update({"unim" : str(self.unim)})
parameters.update({"a1" : str(self.a1)})
parameters.update({"a2" : str(self.a2)})
parameters.update({"a3" : str(self.a3)})
parameters.update({"scanmin" : str(self.scanmin)})
parameters.update({"scanmax" : str(self.scanmax)})
parameters.update({"unis" : str(self.unis)})
parameters.update({"nscan" : str(self.nscan)})
parameters.update({"invert" : str(self.invert)})
parameters.update({"axis" : self.decode_axis()})
parameters.update({"column" : self.decode_column()})
parameters.update({"alphamax" : str(self.alphamax)})
parameters.update({"profile" : self.profile})
try:
self.progressBarSet(10)
response = HttpManager.send_xray_server_request_GET(APPLICATION, parameters)
self.progressBarSet(50)
data = self.extract_plots(response)
exchange_data = DataExchangeObject("XRAYSERVER", "GID_SL")
exchange_data.add_content("x-ray_diffraction_profile", data)
exchange_data.add_content("x-ray_diffraction_profile_units_to_degrees", self.get_units_to_degrees())
self.send("xrayserver_data", exchange_data)
except urllib.error.HTTPError as e:
ShowTextDialog.show_text("Error", 'The server couldn\'t fulfill the request.\nError Code: '
+ str(e.code) + "\n\n" +
server.BaseHTTPRequestHandler.responses[e.code][1], parent=self)
except urllib.error.URLError as e:
ShowTextDialog.show_text("Error", 'We failed to reach a server.\nReason: ' + e.reason, parent=self)
except XrayServerException as e:
ShowHtmlDialog.show_html("X-ray Server Error", e.response, width=750, height=500, parent=self)
except Exception as e:
ShowTextDialog.show_text("Error", 'Error Occurred.\nReason: ' + str(e), parent=self)
self.setStatusMessage("")
self.progressBarFinished()
if __name__ == "__main__":
from oasys.widgets.exchange import DataExchangeObject
input_data_type = "POWER3D"
if input_data_type == "POWER":
# create fake UNDULATOR_FLUX xoppy exchange data
e = numpy.linspace(1000.0, 10000.0, 100)
source = e/10
received_data = DataExchangeObject("XOPPY", "POWER")
received_data.add_content("xoppy_data", numpy.vstack((e,e,source)).T)
received_data.add_content("xoppy_code", "US")
elif input_data_type == "POWER3D":
# create unulator_radiation xoppy exchange data
from orangecontrib.xoppy.util.xoppy_undulators import xoppy_calc_undulator_radiation
e, h, v, p, code = xoppy_calc_undulator_radiation(ELECTRONENERGY=6.04,ELECTRONENERGYSPREAD=0.001,ELECTRONCURRENT=0.2,\
ELECTRONBEAMSIZEH=0.000395,ELECTRONBEAMSIZEV=9.9e-06,\
ELECTRONBEAMDIVERGENCEH=1.05e-05,ELECTRONBEAMDIVERGENCEV=3.9e-06,\
PERIODID=0.018,NPERIODS=222,KV=1.68,DISTANCE=30.0,
SETRESONANCE=0,HARMONICNUMBER=1,
GAPH=0.001,GAPV=0.001,\
HSLITPOINTS=41,VSLITPOINTS=41,METHOD=0,
PHOTONENERGYMIN=7000,PHOTONENERGYMAX=8100,PHOTONENERGYPOINTS=20,
def xoppy_calc_xtc(self):
for file in ["tc.inp","tc.out"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
with open("tc.inp", "wt") as f:
f.write("TS called from xoppy\n")
f.write("%10.3f %10.2f %10.6f %s\n"%(self.ENERGY,self.CURRENT,self.ENERGY_SPREAD,"Ring-Energy(GeV) Current(mA) Beam-Energy-Spread"))
f.write("%10.4f %10.4f %10.4f %10.4f %s\n"%(self.SIGX,self.SIGY,self.SIGX1,self.SIGY1,"Sx(mm) Sy(mm) Sx1(mrad) Sy1(mrad)"))
f.write("%10.3f %d %s\n"%(self.PERIOD,self.NP,"Period(cm) N"))
f.write("%10.1f %10.1f %d %s\n"%(self.EMIN,self.EMAX,self.N,"Emin Emax Ne"))
f.write("%d %d %d %s\n"%(self.HARMONIC_FROM,self.HARMONIC_TO,self.HARMONIC_STEP,"Hmin Hmax Hstep"))
f.write("%d %d %d %d %s\n"%(self.HELICAL,self.METHOD,1,self.NEKS,"Helical Method Print_K Neks"))
f.write("foreground\n")
if platform.system() == "Windows":
command = os.path.join(locations.home_bin(),'tc.exe')
else:
command = "'" + os.path.join(locations.home_bin(), 'tc') + "'"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("Output file: %s"%("tc.out"))
print("\n--------------------------------------------------------\n")
#
# parse result files to exchange object
#
with open("tc.out","r") as f:
lines = f.readlines()
# print output file
# for line in lines:
# print(line, end="")
# remove returns
lines = [line[:-1] for line in lines]
harmonics_data = []
# separate numerical data from text
floatlist = []
harmoniclist = []
txtlist = []
for line in lines:
try:
tmp = line.strip()
if tmp.startswith("Harmonic"):
harmonic_number = int(tmp.split("Harmonic")[1].strip())
if harmonic_number != self.HARMONIC_FROM:
harmonics_data[-1][1] = harmoniclist
harmoniclist = []
harmonics_data.append([harmonic_number, None])
tmp = float(line.strip()[0])
floatlist.append(line)
harmoniclist.append(line)
except:
txtlist.append(line)
harmonics_data[-1][1] = harmoniclist
data = numpy.loadtxt(floatlist)
for index in range(0, len(harmonics_data)):
# print (harmonics_data[index][0], harmonics_data[index][1])
harmonics_data[index][1] = numpy.loadtxt(harmonics_data[index][1])
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", data)
calculated_data.add_content("xoppy_data_harmonics", harmonics_data)
calculated_data.add_content("plot_x_col", 1)
calculated_data.add_content("plot_y_col", 2)
except:
pass
try:
calculated_data.add_content("labels",["Energy (eV) without emittance", "Energy (eV) with emittance",
"Brilliance (ph/s/mrad^2/mm^2/0.1%bw)","Ky","Total Power (W)","Power density (W/mr^2)"])
except:
pass
try:
calculated_data.add_content("info",txtlist)
except:
pass
return calculated_data
def xoppy_calc_mlayer(self):
# copy the variable locally, so no more use of self.
MODE = self.MODE
SCAN = self.SCAN
F12_FLAG = self.F12_FLAG
SUBSTRATE = self.SUBSTRATE
ODD_MATERIAL = self.ODD_MATERIAL
EVEN_MATERIAL = self.EVEN_MATERIAL
ENERGY = self.ENERGY
THETA = self.THETA
SCAN_STEP = self.SCAN_STEP
NPOINTS = self.NPOINTS
ODD_THICKNESS = self.ODD_THICKNESS
EVEN_THICKNESS = self.EVEN_THICKNESS
NLAYERS = self.NLAYERS
FILE=self.FILE
for file in ["mlayer.inp","mlayer.par","mlayer.f12"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
#
# write input file for Fortran mlayer: mlayer.inp
#
f = open('mlayer.inp','w')
if SCAN == 0 and MODE == 0: a0 = 1
if SCAN == 1 and MODE == 0: a0 = 5
if SCAN == 0 and MODE == 1: a0 = 3
if SCAN == 1 and MODE == 1: a0 = 5
f.write("%d \n"%a0)
f.write("N\n")
f.write("%g\n"%( codata.h * codata.c / codata.e * 1e10 / ENERGY))
f.write("%g\n"%THETA)
if SCAN == 0:
f.write("%g\n"%SCAN_STEP)
a2 = codata.h * codata.c / codata.e * 1e10 / ENERGY
a3 = codata.h * codata.c / codata.e * 1e10 / (ENERGY + SCAN_STEP)
a4 = a3 - a2
if SCAN != 0:
f.write("%g\n"%a4)
f.write("%d\n"%NPOINTS)
if MODE == 0:
f.write("%d\n"%NLAYERS)
if MODE == 0:
if a0 != 5:
f.write("%g %g \n"%(ODD_THICKNESS,EVEN_THICKNESS))
else:
for i in range(NLAYERS):
f.write("%g %g \n"%(ODD_THICKNESS,EVEN_THICKNESS))
if MODE != 0:
f1 = open(FILE,'r')
a5 = f1.read()
f1.close()
if MODE != 0:
print("Number of layers in %s file is %d "%(FILE,NLAYERS))
f.write("%d\n"%NLAYERS)
f.write(a5)
f.write("mlayer.par\n")
f.write("mlayer.dat\n")
f.write("6\n")
f.close()
print('File written to disk: mlayer.inp')
#
# create f12 file
#
if F12_FLAG == 0:
energy = numpy.arange(0,500)
elefactor = numpy.log10(10000.0 / 30.0) / 300.0
energy = 10.0 * 10**(energy * elefactor)
f12_s = f1f2_calc(SUBSTRATE,energy)
f12_e = f1f2_calc(EVEN_MATERIAL,energy)
f12_o = f1f2_calc(ODD_MATERIAL,energy)
f = open("mlayer.f12",'w')
f.write('; File created by xoppy for materials [substrate=%s,even=%s,odd=%s]: \n'%(SUBSTRATE,EVEN_MATERIAL,ODD_MATERIAL))
f.write('; Atomic masses: \n')
f.write("%g %g %g \n"%(xraylib.AtomicWeight(xraylib.SymbolToAtomicNumber(SUBSTRATE)),
xraylib.AtomicWeight(xraylib.SymbolToAtomicNumber(EVEN_MATERIAL)),
xraylib.AtomicWeight(xraylib.SymbolToAtomicNumber(ODD_MATERIAL)) ))
f.write('; Densities: \n')
f.write("%g %g %g \n"%(xraylib.ElementDensity(xraylib.SymbolToAtomicNumber(SUBSTRATE)),
xraylib.ElementDensity(xraylib.SymbolToAtomicNumber(EVEN_MATERIAL)),
xraylib.ElementDensity(xraylib.SymbolToAtomicNumber(ODD_MATERIAL)) ))
f.write('; Number of energy points: \n')
f.write("%d\n"%(energy.size))
f.write('; For each energy point, energy[eV], f1[substrate], f2[substrate], f1[even], f2[even], f1[odd], f2[odd]: \n')
for i in range(energy.size):
f.write("%g %g %g %g %g %g %g \n"%(energy[i],f12_s[0,i],f12_s[1,i],f12_e[0,i],f12_e[1,i],f12_o[0,i],f12_o[1,i]))
f.close()
print('File written to disk: mlayer.f12')
#
# run external program mlayer
#
command = os.path.join(locations.home_bin(), 'mlayer') + " < mlayer.inp"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", numpy.loadtxt("mlayer.dat"))
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", 3)
calculated_data.add_content("units_to_degrees", 1.0)
except:
pass
try:
calculated_data.add_content("labels",["Grazing angle Theta [deg]","s-reflectivity","p-reflectivity","averaged reflectivity","s-phase shift","p-phase shift","(s-electric field)^2","(p-electric field)^2"])
except:
pass
try:
info = "ML %s(%3.2f A):%s(%3.2f A) %d pairs; E=%5.3f eV"%(ODD_MATERIAL,ODD_THICKNESS,EVEN_MATERIAL,EVEN_THICKNESS,NLAYERS,ENERGY)
calculated_data.add_content("info",info)
except:
pass
return calculated_data
def submit(self):
self.progressBarInit()
self.setStatusMessage("Submitting Request")
self.checkFields()
parameters = {}
parameters.update({"xway" : str(self.xway + 1)})
parameters.update({"wave" : str(self.wave)})
parameters.update({"line" : self.line})
parameters.update({"coway" : str(self.coway)})
parameters.update({"code" : self.code})
parameters.update({"amor" : self.amor})
parameters.update({"chem" : self.chem})
parameters.update({"rho" : str(self.rho)})
parameters.update({"i1" : str(self.i1)})
parameters.update({"i2" : str(self.i2)})
parameters.update({"i3" : str(self.i3)})
parameters.update({"df1df2" : self.decode_df1df2()})
parameters.update({"modeout" : "0" })
parameters.update({"detail" : str(self.detail)})
try:
response = HttpManager.send_xray_server_request_GET(APPLICATION, parameters)
response = self.clear_response(response)
self.tabs_widget.setCurrentIndex(0)
self.x0h_output.setHtml(response)
data0, data1, data2 = self.extract_plots(response)
try:
exchange_data = DataExchangeObject("XRAYSERVER", "X0H")
if self.coway == 0: # crystals
dictionary = self.extract_structure_data(response)
exchange_data.add_content("structure", dictionary["structure"])
exchange_data.add_content("h", self.i1)
exchange_data.add_content("k", self.i2)
exchange_data.add_content("l", self.i3)
exchange_data.add_content("d_spacing", dictionary["d_spacing"])
exchange_data.add_content("energy", dictionary["energy"])
exchange_data.add_content("bragg_angle", dictionary["bragg_angle"])
exchange_data.add_content("xr0", dictionary["xr0"])
exchange_data.add_content("xi0", dictionary["xi0"])
exchange_data.add_content("xrh_s", dictionary["xrh_s"])
exchange_data.add_content("xih_s", dictionary["xih_s"])
exchange_data.add_content("xrh_p", dictionary["xrh_p"])
exchange_data.add_content("xih_p", dictionary["xih_p"])
exchange_data.add_content("reflectivity", data0)
exchange_data.add_content("reflectivity_units_to_degrees", 1.0)
exchange_data.add_content("x-ray_diffraction_profile_sigma", data1)
exchange_data.add_content("x-ray_diffraction_profile_sigma_units_to_degrees", 0.000277777805)
exchange_data.add_content("x-ray_diffraction_profile_pi", data2)
exchange_data.add_content("x-ray_diffraction_profile_pi_units_to_degrees", 0.000277777805)
self.send("xrayserver_data", exchange_data)
except: #problems with xrayserver, no data found
pass
except urllib.error.HTTPError as e:
self.x0h_output.setHtml('The server couldn\'t fulfill the request.\nError Code: '
+ str(e.code) + "\n\n" +
server.BaseHTTPRequestHandler.responses[e.code][1])
except urllib.error.URLError as e:
self.x0h_output.setHtml('We failed to reach a server.\nReason: ' + e.reason)
except XrayServerException as e:
ShowHtmlDialog.show_html("X-ray Server Error", e.response, width=750, height=500, parent=self)
except Exception as e:
ShowTextDialog.show_text("Error", 'Error Occurred.\nReason: ' + str(e), parent=self)
self.setStatusMessage("")
self.progressBarFinished()
def xoppy_calc_xf1f2(self):
MAT_FLAG = self.MAT_FLAG
DESCRIPTOR = self.DESCRIPTOR
density = self.DENSITY
CALCULATE = self.CALCULATE
GRID = self.GRID
GRIDSTART = self.GRIDSTART
GRIDEND = self.GRIDEND
GRIDN = self.GRIDN
THETAGRID = self.THETAGRID
ROUGH = self.ROUGH
THETA1 = self.THETA1
THETA2 = self.THETA2
THETAN = self.THETAN
if MAT_FLAG == 0: # element
descriptor = DESCRIPTOR
density = xraylib.ElementDensity(
xraylib.SymbolToAtomicNumber(DESCRIPTOR))
elif MAT_FLAG == 1: # formula
descriptor = DESCRIPTOR
if GRID == 0: # standard energy grid
energy = numpy.arange(0, 500)
elefactor = numpy.log10(10000.0 / 30.0) / 300.0
energy = 10.0 * 10**(energy * elefactor)
elif GRID == 1: # user energy grid
if GRIDN == 1:
energy = numpy.array([GRIDSTART])
else:
energy = numpy.linspace(GRIDSTART, GRIDEND, GRIDN)
elif GRID == 2: # single energy point
energy = numpy.array([GRIDSTART])
if THETAGRID == 0:
theta = numpy.array([THETA1])
else:
theta = numpy.linspace(THETA1, THETA2, THETAN)
CALCULATE_items = [
'f1', 'f2', 'delta', 'beta', 'mu [cm^-1]', 'mu [cm^2/g]',
'Cross Section [barn]', 'reflectivity-s', 'reflectivity-p',
'reflectivity-unpol', 'delta/beta '
]
out = numpy.zeros((energy.size, theta.size))
for i, itheta in enumerate(theta):
if MAT_FLAG == 0: # element
tmp = f1f2_calc(descriptor,
energy,
1e-3 * itheta,
F=1 + CALCULATE,
rough=ROUGH,
density=density)
out[:, i] = tmp
else:
tmp = f1f2_calc_mix(descriptor,
energy,
1e-3 * itheta,
F=1 + CALCULATE,
rough=ROUGH,
density=density)
out[:, i] = tmp
if ((energy.size == 1) and (theta.size == 1)):
info = "** Single value calculation E=%g eV, theta=%g mrad, Result(F=%d)=%g " % (
energy[0], theta[0], 1 + CALCULATE, out[0, 0])
labels = ["Energy [eV]", CALCULATE_items[CALCULATE]]
tmp = numpy.vstack((energy, out[:, 0]))
print(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>", energy.shape, out.shape,
tmp.shape)
out_dict = {
"application": "xoppy",
"name": "xf12",
"info": info,
"data": tmp,
"labels": labels
}
elif theta.size == 1:
tmp = numpy.vstack((energy, out[:, 0]))
labels = ["Energy [eV]", CALCULATE_items[CALCULATE]]
out_dict = {
"application": "xoppy",
"name": "xf12",
"data": tmp,
"labels": labels
}
elif energy.size == 1:
tmp = numpy.vstack((theta, out[0, :]))
labels = ["Theta [mrad]", CALCULATE_items[CALCULATE]]
out_dict = {
"application": "xoppy",
"name": "xf12",
"data": tmp,
"labels": labels
}
else:
labels = [r"energy[eV]", r"theta [mrad]"]
out_dict = {
"application": "xoppy",
"name": "xf12",
"data2D": out,
"dataX": energy,
"dataY": theta,
"labels": labels
}
#
#
#
if "info" in out_dict.keys():
print(out_dict["info"])
#send exchange
calculated_data = DataExchangeObject(
"XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", out_dict["data"].T)
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", -1)
except:
pass
try:
calculated_data.add_content("labels", out_dict["labels"])
except:
pass
try:
calculated_data.add_content("info", out_dict["info"])
except:
pass
try:
calculated_data.add_content("data2D", out_dict["data2D"])
calculated_data.add_content("dataX", out_dict["dataX"])
calculated_data.add_content("dataY", out_dict["dataY"])
except:
pass
if self.DUMP_TO_FILE:
with open(self.FILE_NAME, "w") as file:
try:
file.write("#F %s\n" % self.FILE_NAME)
file.write("\n#S 1 xoppy f1f2 results\n")
print("data shape", out_dict["data"].shape)
print("labels: ", out_dict["labels"])
file.write("#N 2\n")
file.write("#L %s %s\n" %
(out_dict["labels"][0], out_dict["labels"][1]))
out = out_dict["data"]
for j in range(out.shape[1]):
file.write(
("%19.12e " * out.shape[0] + "\n") %
tuple(out[i, j] for i in range(out.shape[0])))
file.close()
print("File written to disk: %s \n" % self.FILE_NAME)
except:
raise Exception(
"CrossSec: The data could not be dumped onto the specified file!\n"
)
return calculated_data
def do_xoppy_calculation(self):
out_dict = self.xoppy_calc_xcrosssec()
if "info" in out_dict.keys():
print(out_dict["info"])
#send exchange
calculated_data = DataExchangeObject(
"XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", out_dict["data"].T)
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", -1)
except:
pass
try:
calculated_data.add_content("labels", out_dict["labels"])
except:
pass
try:
calculated_data.add_content("info", out_dict["info"])
except:
pass
return calculated_data
def submit(self):
self.progressBarInit()
self.setStatusMessage("Submitting Request")
self.checkFields()
parameters = {}
parameters.update({"xway" : self.decode_xway()})
parameters.update({"wave" : str(self.wave)})
parameters.update({"line" : self.line})
parameters.update({"ipol" : str(self.ipol + 1)})
parameters.update({"subway" : str(self.subway + 1)})
parameters.update({"code" : self.code})
parameters.update({"df1df2" : self.decode_df1df2()})
parameters.update({"chem" : self.chem})
parameters.update({"rho" : str(self.rho)})
parameters.update({"x0" : str(self.x0)})
parameters.update({"w0" : str(self.w0)})
parameters.update({"sigma" : str(self.sigma)})
parameters.update({"tr" : str(self.tr)})
parameters.update({"scanmin" : str(self.scanmin)})
parameters.update({"scanmax" : str(self.scanmax)})
parameters.update({"unis" : str(self.unis)})
parameters.update({"nscan" : str(self.nscan)})
parameters.update({"swflag" : self.decode_swflag()})
if self.swflag == True or self.swflag == 1:
parameters.update({"swref" : str(self.swref)})
parameters.update({"swmin" : str(self.swmin)})
parameters.update({"swmax" : str(self.swmax)})
parameters.update({"swpts" : str(self.swpts)})
parameters.update({"profile" : self.profile})
try:
self.progressBarSet(10)
response = HttpManager.send_xray_server_request_GET(APPLICATION, parameters)
self.progressBarSet(50)
data = self.extract_plots(response)
exchange_data = DataExchangeObject("XRAYSERVER", "TER_SL")
exchange_data.add_content("ter_sl_result", data)
exchange_data.add_content("ter_sl_result_units_to_degrees", self.get_units_to_degrees())
self.send("xrayserver_data", exchange_data)
except urllib.error.HTTPError as e:
ShowTextDialog.show_text("Error", 'The server couldn\'t fulfill the request.\nError Code: '
+ str(e.code) + "\n\n" +
server.BaseHTTPRequestHandler.responses[e.code][1], parent=self)
except urllib.error.URLError as e:
ShowTextDialog.show_text("Error", 'We failed to reach a server.\nReason: ' + e.reason, parent=self)
except XrayServerException as e:
ShowHtmlDialog.show_html("X-ray Server Error", e.response, width=750, height=500, parent=self)
except Exception as e:
ShowTextDialog.show_text("Error", 'Error Occurred.\nReason: ' + str(e), parent=self)
self.setStatusMessage("")
self.progressBarFinished()
def _callable_2(self, html):
try:
self.x0h_input.loadFinished.disconnect()
self.x0h_input.back()
self.x0h_input.setHidden(False)
response_1 = self.clear_response(html)
response_2 = self.clear_response(html)
self.tabs_widget.setCurrentIndex(0)
self.x0h_output.setHtml(response_1)
data0, data1, data2 = self.extract_plots(response_2)
exchange_data = DataExchangeObject("XRAYSERVER", "X0H")
exchange_data.add_content("reflectivity", data0)
exchange_data.add_content("reflectivity_units_to_degrees", 1.0)
exchange_data.add_content("x-ray_diffraction_profile_sigma", data1)
exchange_data.add_content(
"x-ray_diffraction_profile_sigma_units_to_degrees",
0.000277777805)
exchange_data.add_content("x-ray_diffraction_profile_pi", data2)
exchange_data.add_content(
"x-ray_diffraction_profile_pi_units_to_degrees",
0.000277777805)
self.send("xrayserver_data", exchange_data)
except urllib.error.HTTPError as e:
self.x0h_output.setHtml(
'The server couldn\'t fulfill the request.\nError Code: ' +
str(e.code) + "\n\n" +
server.BaseHTTPRequestHandler.responses[e.code][1])
except urllib.error.URLError as e:
self.x0h_output.setHtml('We failed to reach a server.\nReason: ' +
e.reason)
except XrayServerException as e:
ShowHtmlDialog.show_html("X-ray Server Error",
e.response,
width=750,
height=500,
parent=self)
except Exception as e:
self.x0h_output.setHtml('We failed to reach a server.\nReason: ' +
str(e))
self.tabs_widget.setCurrentIndex(0)
self.setStatusMessage("")
self.progressBarFinished()
def xoppy_calc_xcrystal(self):
CRYSTAL_MATERIAL = self.CRYSTAL_MATERIAL
MILLER_INDEX_H = self.MILLER_INDEX_H
MILLER_INDEX_K = self.MILLER_INDEX_K
MILLER_INDEX_L = self.MILLER_INDEX_L
TEMPER = self.TEMPER
MOSAIC = self.MOSAIC
GEOMETRY = self.GEOMETRY
SCAN = self.SCAN
UNIT = self.UNIT
SCANFROM = self.SCANFROM
SCANTO = self.SCANTO
SCANPOINTS = self.SCANPOINTS
ENERGY = self.ENERGY
ASYMMETRY_ANGLE = self.ASYMMETRY_ANGLE
THICKNESS = self.THICKNESS
MOSAIC_FWHM = self.MOSAIC_FWHM
RSAG = self.RSAG
RMER = self.RMER
ANISOTROPY = self.ANISOTROPY
POISSON = self.POISSON
CUT = self.CUT
FILECOMPLIANCE = self.FILECOMPLIANCE
for file in ["diff_pat.dat","diff_pat.gle","diff_pat.par","diff_pat.xop","xcrystal.bra"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
if (GEOMETRY == 1) or (GEOMETRY == 3):
if ASYMMETRY_ANGLE == 0.0:
print("xoppy_calc_xcrystal: WARNING: In xcrystal the asymmetry angle is the angle between Bragg planes and crystal surface,"+
"in BOTH Bragg and Laue geometries.")
descriptor = Crystal_GetCrystalsList()[CRYSTAL_MATERIAL]
if SCAN == 3: # energy scan
emin = SCANFROM - 1
emax = SCANTO + 1
else:
emin = ENERGY - 100.0
emax = ENERGY + 100.0
print("Using crystal descriptor: ",descriptor)
bragg_dictionary = bragg_calc(descriptor=descriptor,
hh=MILLER_INDEX_H,kk=MILLER_INDEX_K,ll=MILLER_INDEX_L,
temper=float(TEMPER),
emin=emin,emax=emax,estep=5.0,fileout="xcrystal.bra")
with open("xoppy.inp", "wt") as f:
f.write("xcrystal.bra\n")
f.write("%d\n"%MOSAIC)
f.write("%d\n"%GEOMETRY)
if MOSAIC == 1:
f.write("%g\n"%MOSAIC_FWHM)
f.write("%g\n"%THICKNESS)
else:
f.write("%g\n"%THICKNESS)
f.write("%g\n"%ASYMMETRY_ANGLE)
scan_flag = 1 + SCAN
f.write("%d\n"%scan_flag)
f.write("%19.9f\n"%ENERGY)
if scan_flag <= 3:
f.write("%d\n"%UNIT)
f.write("%g\n"%SCANFROM)
f.write("%g\n"%SCANTO)
f.write("%d\n"%SCANPOINTS)
if MOSAIC > 1: # bent
f.write("%g\n"%RSAG)
f.write("%g\n"%RMER)
f.write("0\n")
if ( (descriptor == "Si") or (descriptor == "Si2") or (descriptor == "Si_NIST") or (descriptor == "Ge") or descriptor == "Diamond"):
pass
else: # not Si,Ge,Diamond
if ((ANISOTROPY == 1) or (ANISOTROPY == 2)):
raise Exception("Anisotropy data not available for this crystal. Either use isotropic or use external compliance file. Please change and run again'")
f.write("%d\n"%ANISOTROPY)
if ANISOTROPY == 0:
f.write("%g\n"%POISSON)
elif ANISOTROPY == 1:
f.write("%d\n"%CRYSTAL_MATERIAL)
f.write("%g\n"%ASYMMETRY_ANGLE)
f.write("%d\n"%MILLER_INDEX_H)
f.write("%d\n"%MILLER_INDEX_K)
f.write("%d\n"%MILLER_INDEX_L)
elif ANISOTROPY == 2:
f.write("%d\n"%CRYSTAL_MATERIAL)
f.write("%g\n"%ASYMMETRY_ANGLE)
# TODO: check syntax for CUT: Cut syntax is: valong_X valong_Y valong_Z ; vnorm_X vnorm_Y vnorm_Z ; vperp_x vperp_Y vperp_Z
f.write("%s\n"%CUT.split(";")[0])
f.write("%s\n"%CUT.split(";")[1])
f.write("%s\n"%CUT.split(";")[2])
elif ANISOTROPY == 3:
f.write("%s\n"%FILECOMPLIANCE)
command = os.path.join(locations.home_bin(), 'diff_pat') + " < xoppy.inp"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
#show calculated parameters in standard output
txt_info = open("diff_pat.par").read()
for line in txt_info:
print(line,end="")
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", numpy.loadtxt("diff_pat.dat", skiprows=5))
calculated_data.add_content("plot_x_col",0)
calculated_data.add_content("plot_y_col",-1)
calculated_data.add_content("units_to_degrees", self.get_units_to_degrees())
except Exception as e:
raise Exception("Error loading diff_pat.dat :" + str(e))
try:
calculated_data.add_content("labels",
["Th-ThB{in} [" + self.unit_combo.itemText(self.UNIT) + "]",
"Th-ThB{out} [" + self.unit_combo.itemText(self.UNIT) + "]",
"phase_p[rad]",
"phase_s[rad]","Circ Polariz",
"p-polarized reflectivity",
"s-polarized reflectivity"])
except:
pass
try:
with open("diff_pat.par") as f:
info = f.readlines()
calculated_data.add_content("info",info)
except:
pass
return calculated_data
# create unulator_radiation xoppy exchange data
from orangecontrib.xoppy.util.xoppy_undulators import xoppy_calc_undulator_radiation
from oasys.widgets.exchange import DataExchangeObject
e, h, v, p, code = xoppy_calc_undulator_radiation(ELECTRONENERGY=6.04,ELECTRONENERGYSPREAD=0.001,ELECTRONCURRENT=0.2,\
ELECTRONBEAMSIZEH=0.000395,ELECTRONBEAMSIZEV=9.9e-06,\
ELECTRONBEAMDIVERGENCEH=1.05e-05,ELECTRONBEAMDIVERGENCEV=3.9e-06,\
PERIODID=0.018,NPERIODS=222,KV=1.68,DISTANCE=30.0,
SETRESONANCE=0,HARMONICNUMBER=1,
GAPH=0.001,GAPV=0.001,\
HSLITPOINTS=41,VSLITPOINTS=41,METHOD=2,
PHOTONENERGYMIN=7000,PHOTONENERGYMAX=8100,PHOTONENERGYPOINTS=20,
USEEMITTANCES=1)
# received_data = DataExchangeObject("XOPPY", "UNDULATOR_RADIATION")
received_data = DataExchangeObject("XOPPY", "POWER3D")
received_data.add_content("xoppy_data", [p, e, h, v])
received_data.add_content("xoppy_code", code)
#
app = QApplication(sys.argv)
w = OWpower3D()
w.acceptExchangeData(received_data)
w.show()
app.exec()
w.saveSettings()
def submit(self):
self.progressBarInit()
self.setStatusMessage("Submitting Request")
if platform.system() == 'Darwin':
self.x0h_input.page().toHtml(self._callable_1)
elif platform.system() == 'Linux':
doc = self.x0h_input.page().mainFrame().documentElement()
submit_btn = doc.findFirst("input[id=submit-btn]")
try:
response = ""
#response = HttpManager.send_xray_server_request_POST(APPLICATION, parameters)
response = self.clear_response(response)
self.tabs_widget.setCurrentIndex(0)
self.x0h_output.setHtml(response)
data0, data1, data2 = self.extract_plots(response)
exchange_data = DataExchangeObject("XRAYSERVER", "X0H")
exchange_data.add_content("reflectivity", data0)
exchange_data.add_content("reflectivity_units_to_degrees", 1.0)
exchange_data.add_content("x-ray_diffraction_profile_sigma", data1)
exchange_data.add_content("x-ray_diffraction_profile_sigma_units_to_degrees", 0.000277777805)
exchange_data.add_content("x-ray_diffraction_profile_pi", data2)
exchange_data.add_content("x-ray_diffraction_profile_pi_units_to_degrees", 0.000277777805)
self.send("xrayserver_data", exchange_data)
pass
except urllib.error.HTTPError as e:
self.x0h_output.setHtml('The server couldn\'t fulfill the request.\nError Code: '
+ str(e.code) + "\n\n" +
server.BaseHTTPRequestHandler.responses[e.code][1])
raise e
except urllib.error.URLError as e:
self.x0h_output.setHtml('We failed to reach a server.\nReason: '
+ e.reason)
raise e
except XrayServerException as e:
ShowHtmlDialog.show_html("X-ray Server Error", e.response, width=750, height=500, parent=self)
raise e
except Exception as e:
self.x0h_output.setHtml('We failed to reach a server.\nReason: '
+ str(e))
raise e
self.setStatusMessage("")
self.progressBarFinished()
def xoppy_calc_xpowder_fml(self):
for file in ["xpowder_fml.par", "xpowder_fml.ref", "xpowder_fml.out"]:
try:
os.remove(os.path.join(locations.home_bin_run(), file))
except:
pass
with open("xoppy.inp", "wt") as f:
f.write("%s\n" % (self.FILE))
f.write("%s\n" % (self.TITLE))
f.write("%g\n" % (self.LAMBDA))
f.write("%s\n" % (self.JOB))
f.write("%g\n" % (self.U))
f.write("%g\n" % (self.V))
f.write("%g\n" % (self.W))
f.write("%g\n" % (self.X))
f.write("%g\n" % (self.LS))
f.write("%g\n" % (self.THMIN))
f.write("%g\n" % (self.STEP))
f.write("%s\n" % (self.THMAX))
command = "'" + os.path.join(locations.home_bin(),
'xpowder_fml') + "' < xoppy.inp"
print("Running command '%s' in directory: %s " %
(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
print(
"Files written to disk:\n xpowder_fml.par (text output)\n xpowder_fml.ref (reflections)\n xpowder_fml.out (diffractogram)",
)
#
# data = numpy.loadtxt("xpowder_fml.out",skiprows=3).T
#send exchange
calculated_data = DataExchangeObject(
"XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content(
"xoppy_data", numpy.loadtxt("xpowder_fml.out", skiprows=3))
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", -1)
except:
pass
try:
calculated_data.add_content("labels",
["TwoTheta[Deg]", "Intensity[a.u.]"])
except:
pass
try:
with open("xpowder_fml.par") as f:
info = f.readlines()
info = [line[:-1] for line in info] # remove "\n"
calculated_data.add_content("info", info)
except:
pass
return calculated_data
def xoppy_calc_xf1f2(self):
MAT_FLAG = self.MAT_FLAG
DESCRIPTOR = self.DESCRIPTOR
density = self.DENSITY
CALCULATE = self.CALCULATE
GRID = self.GRID
GRIDSTART = self.GRIDSTART
GRIDEND = self.GRIDEND
GRIDN = self.GRIDN
THETAGRID = self.THETAGRID
ROUGH = self.ROUGH
THETA1 = self.THETA1
THETA2 = self.THETA2
THETAN = self.THETAN
if MAT_FLAG == 0: # element
descriptor = DESCRIPTOR
density = xraylib.ElementDensity(xraylib.SymbolToAtomicNumber(DESCRIPTOR))
elif MAT_FLAG == 1: # formula
descriptor = DESCRIPTOR
if GRID == 0: # standard energy grid
energy = numpy.arange(0,500)
elefactor = numpy.log10(10000.0 / 30.0) / 300.0
energy = 10.0 * 10**(energy * elefactor)
elif GRID == 1: # user energy grid
if GRIDN == 1:
energy = numpy.array([GRIDSTART])
else:
energy = numpy.linspace(GRIDSTART,GRIDEND,GRIDN)
elif GRID == 2: # single energy point
energy = numpy.array([GRIDSTART])
if THETAGRID == 0:
theta = numpy.array([THETA1])
else:
theta = numpy.linspace(THETA1,THETA2,THETAN)
CALCULATE_items=['f1', 'f2', 'delta', 'beta', 'mu [cm^-1]', 'mu [cm^2/g]', 'Cross Section [barn]', 'reflectivity-s', 'reflectivity-p', 'reflectivity-unpol', 'delta/beta ']
out = numpy.zeros((energy.size,theta.size))
for i,itheta in enumerate(theta):
if MAT_FLAG == 0: # element
tmp = f1f2_calc(descriptor,energy,1e-3*itheta,F=1+CALCULATE,rough=ROUGH,density=density)
out[:,i] = tmp
else:
tmp = f1f2_calc_mix(descriptor,energy,1e-3*itheta,F=1+CALCULATE,rough=ROUGH,density=density)
out[:,i] = tmp
if ((energy.size == 1) and (theta.size == 1)):
info = "** Single value calculation E=%g eV, theta=%g mrad, Result(F=%d)=%g "%(energy[0],theta[0],1+CALCULATE,out[0,0])
labels = ["Energy [eV]",CALCULATE_items[CALCULATE]]
tmp = numpy.vstack((energy,out[:,0]))
print(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>",energy.shape,out.shape,tmp.shape)
out_dict = {"application":"xoppy","name":"xf12","info":info, "data":tmp,"labels":labels}
elif theta.size == 1:
tmp = numpy.vstack((energy,out[:,0]))
labels = ["Energy [eV]",CALCULATE_items[CALCULATE]]
out_dict = {"application":"xoppy","name":"xf12","data":tmp,"labels":labels}
elif energy.size == 1:
tmp = numpy.vstack((theta,out[0,:]))
labels = ["Theta [mrad]",CALCULATE_items[CALCULATE]]
out_dict = {"application":"xoppy","name":"xf12","data":tmp,"labels":labels}
else:
labels = [r"energy[eV]",r"theta [mrad]"]
out_dict = {"application":"xoppy","name":"xf12","data2D":out,"dataX":energy,"dataY":theta,"labels":labels}
#
#
#
if "info" in out_dict.keys():
print(out_dict["info"])
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", out_dict["data"].T)
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", -1)
except:
pass
try:
calculated_data.add_content("labels", out_dict["labels"])
except:
pass
try:
calculated_data.add_content("info", out_dict["info"])
except:
pass
try:
calculated_data.add_content("data2D", out_dict["data2D"])
calculated_data.add_content("dataX", out_dict["dataX"])
calculated_data.add_content("dataY", out_dict["dataY"])
except:
pass
return calculated_data
def xoppy_calc_xpower(self):
#
# prepare input for xpower_calc
# Note that the input for xpower_calc accepts any number of elements.
#
substance = [self.EL1_FOR,self.EL2_FOR,self.EL3_FOR,self.EL4_FOR,self.EL5_FOR]
thick = numpy.array( (self.EL1_THI,self.EL2_THI,self.EL3_THI,self.EL4_THI,self.EL5_THI))
angle = numpy.array( (self.EL1_ANG,self.EL2_ANG,self.EL3_ANG,self.EL4_ANG,self.EL5_ANG))
dens = [self.EL1_DEN,self.EL2_DEN,self.EL3_DEN,self.EL4_DEN,self.EL5_DEN]
roughness = numpy.array( (self.EL1_ROU,self.EL2_ROU,self.EL3_ROU,self.EL4_ROU,self.EL5_ROU))
flags = numpy.array( (self.EL1_FLAG,self.EL2_FLAG,self.EL3_FLAG,self.EL4_FLAG,self.EL5_FLAG))
substance = substance[0:self.NELEMENTS+1]
thick = thick[0:self.NELEMENTS+1]
angle = angle[0:self.NELEMENTS+1]
dens = dens[0:self.NELEMENTS+1]
roughness = roughness[0:self.NELEMENTS+1]
flags = flags[0:self.NELEMENTS+1]
if self.SOURCE == 0:
energies = numpy.arange(0,500)
elefactor = numpy.log10(10000.0 / 30.0) / 300.0
energies = 10.0 * 10**(energies * elefactor)
source = numpy.ones(energies.size)
tmp = numpy.vstack( (energies,source))
if self.SOURCE == 1:
energies = numpy.linspace(self.ENER_MIN,self.ENER_MAX,self.ENER_N)
source = numpy.ones(energies.size)
tmp = numpy.vstack( (energies,source))
if self.SOURCE >= 2:
if self.SOURCE == 2: source_file = self.SOURCE_FILE
if self.SOURCE == 3: source_file = "SRCOMPE"
if self.SOURCE == 4: source_file = "SRCOMPF"
try:
tmp = numpy.loadtxt(source_file)
energies = tmp[:,0]
source = tmp[:,1]
except:
print("Error loading file %s "%(source_file))
raise
if self.FILE_DUMP == 0:
output_file = None
else:
output_file = "xpower.spec"
out_dictionary = xpower_calc(energies=energies,source=source,substance=substance,
flags=flags,dens=dens,thick=thick,angle=angle,roughness=roughness,output_file=output_file)
try:
print(out_dictionary["info"])
except:
pass
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", out_dictionary["data"].T)
calculated_data.add_content("plot_x_col",0)
calculated_data.add_content("plot_y_col",-1)
except:
pass
try:
print(out_dictionary["labels"])
calculated_data.add_content("labels", out_dictionary["labels"])
except:
pass
try:
calculated_data.add_content("info",out_dictionary["info"])
except:
pass
return calculated_data
def do_xoppy_calculation(self):
out_dict = self.xoppy_calc_xf0()
if "info" in out_dict.keys():
print(out_dict["info"])
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", out_dict["data"].T)
calculated_data.add_content("plot_x_col",0)
calculated_data.add_content("plot_y_col",-1)
except:
pass
try:
calculated_data.add_content("labels",out_dict["labels"])
except:
pass
try:
calculated_data.add_content("info",out_dict["info"])
except:
pass
return calculated_data
def xoppy_calc_xtc(self):
for file in ["tc.inp", "tc.out"]:
try:
os.remove(os.path.join(locations.home_bin_run(), file))
except:
pass
with open("tc.inp", "wt") as f:
f.write("TS called from xoppy\n")
f.write("%10.3f %10.2f %10.6f %s\n" %
(self.ENERGY, self.CURRENT, self.ENERGY_SPREAD,
"Ring-Energy(GeV) Current(mA) Beam-Energy-Spread"))
f.write("%10.4f %10.4f %10.4f %10.4f %s\n" %
(self.SIGX, self.SIGY, self.SIGX1, self.SIGY1,
"Sx(mm) Sy(mm) Sx1(mrad) Sy1(mrad)"))
f.write("%10.3f %d %s\n" % (self.PERIOD, self.NP, "Period(cm) N"))
f.write("%10.1f %10.1f %d %s\n" %
(self.EMIN, self.EMAX, self.N, "Emin Emax Ne"))
f.write("%d %d %d %s\n" % (self.HARMONIC_FROM, self.HARMONIC_TO,
self.HARMONIC_STEP, "Hmin Hmax Hstep"))
f.write("%d %d %d %d %s\n" %
(self.HELICAL, self.METHOD, 1, self.NEKS,
"Helical Method Print_K Neks"))
f.write("foreground\n")
if platform.system() == "Windows":
command = os.path.join(locations.home_bin(), 'tc.exe')
else:
command = "'" + os.path.join(locations.home_bin(), 'tc') + "'"
print("Running command '%s' in directory: %s " %
(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("Output file: %s" % ("tc.out"))
print("\n--------------------------------------------------------\n")
#
# parse result files to exchange object
#
with open("tc.out", "r") as f:
lines = f.readlines()
# print output file
# for line in lines:
# print(line, end="")
# remove returns
lines = [line[:-1] for line in lines]
harmonics_data = []
# separate numerical data from text
floatlist = []
harmoniclist = []
txtlist = []
for line in lines:
try:
tmp = line.strip()
if tmp.startswith("Harmonic"):
harmonic_number = int(tmp.split("Harmonic")[1].strip())
if harmonic_number != self.HARMONIC_FROM:
harmonics_data[-1][1] = harmoniclist
harmoniclist = []
harmonics_data.append([harmonic_number, None])
tmp = float(line.strip()[0])
floatlist.append(line)
harmoniclist.append(line)
except:
txtlist.append(line)
harmonics_data[-1][1] = harmoniclist
data = numpy.loadtxt(floatlist)
for index in range(0, len(harmonics_data)):
# print (harmonics_data[index][0], harmonics_data[index][1])
harmonics_data[index][1] = numpy.loadtxt(harmonics_data[index][1])
#send exchange
calculated_data = DataExchangeObject(
"XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", data)
calculated_data.add_content("xoppy_data_harmonics", harmonics_data)
calculated_data.add_content("plot_x_col", 1)
calculated_data.add_content("plot_y_col", 2)
except:
pass
try:
calculated_data.add_content("labels", [
"Energy (eV) without emittance", "Energy (eV) with emittance",
"Brilliance (ph/s/mrad^2/mm^2/0.1%bw)", "Ky",
"Total Power (W)", "Power density (W/mr^2)"
])
except:
pass
try:
calculated_data.add_content("info", txtlist)
except:
pass
return calculated_data
if __name__ == "__main__":
# create unulator_radiation xoppy exchange data
from orangecontrib.xoppy.util.xoppy_undulators import xoppy_calc_undulator_radiation
from oasys.widgets.exchange import DataExchangeObject
e, h, v, p, code = xoppy_calc_undulator_radiation(ELECTRONENERGY=6.04,ELECTRONENERGYSPREAD=0.001,ELECTRONCURRENT=0.2,\
ELECTRONBEAMSIZEH=0.000395,ELECTRONBEAMSIZEV=9.9e-06,\
ELECTRONBEAMDIVERGENCEH=1.05e-05,ELECTRONBEAMDIVERGENCEV=3.9e-06,\
PERIODID=0.018,NPERIODS=222,KV=1.68,DISTANCE=30.0,
SETRESONANCE=0,HARMONICNUMBER=1,
GAPH=0.001,GAPV=0.001,\
HSLITPOINTS=41,VSLITPOINTS=41,METHOD=2,
PHOTONENERGYMIN=7000,PHOTONENERGYMAX=8100,PHOTONENERGYPOINTS=20,
USEEMITTANCES=1)
# received_data = DataExchangeObject("XOPPY", "UNDULATOR_RADIATION")
received_data = DataExchangeObject("XOPPY", "POWER3D")
received_data.add_content("xoppy_data", [p, e, h, v])
received_data.add_content("xoppy_code", code)
#
app = QApplication(sys.argv)
w = OWpower3D()
w.acceptExchangeData(received_data)
w.show()
app.exec()
w.saveSettings()
def submit(self):
self.progressBarInit()
self.setStatusMessage("Submitting Request")
if platform.system() == 'Darwin':
self.x0h_input.page().toHtml(self._callable_1)
elif platform.system() == 'Linux':
doc = self.x0h_input.page().mainFrame().documentElement()
submit_btn = doc.findFirst("input[id=submit-btn]")
try:
response = ""
#response = HttpManager.send_xray_server_request_POST(APPLICATION, parameters)
response = self.clear_response(response)
self.tabs_widget.setCurrentIndex(0)
self.x0h_output.setHtml(response)
data0, data1, data2 = self.extract_plots(response)
exchange_data = DataExchangeObject("XRAYSERVER", "X0H")
exchange_data.add_content("reflectivity", data0)
exchange_data.add_content("reflectivity_units_to_degrees", 1.0)
exchange_data.add_content("x-ray_diffraction_profile_sigma",
data1)
exchange_data.add_content(
"x-ray_diffraction_profile_sigma_units_to_degrees",
0.000277777805)
exchange_data.add_content("x-ray_diffraction_profile_pi",
data2)
exchange_data.add_content(
"x-ray_diffraction_profile_pi_units_to_degrees",
0.000277777805)
self.send("xrayserver_data", exchange_data)
pass
except urllib.error.HTTPError as e:
self.x0h_output.setHtml(
'The server couldn\'t fulfill the request.\nError Code: ' +
str(e.code) + "\n\n" +
server.BaseHTTPRequestHandler.responses[e.code][1])
raise e
except urllib.error.URLError as e:
self.x0h_output.setHtml(
'We failed to reach a server.\nReason: ' + e.reason)
raise e
except XrayServerException as e:
ShowHtmlDialog.show_html("X-ray Server Error",
e.response,
width=750,
height=500,
parent=self)
raise e
except Exception as e:
self.x0h_output.setHtml(
'We failed to reach a server.\nReason: ' + str(e))
raise e
self.setStatusMessage("")
self.progressBarFinished()
def xoppy_calc_xfh(self):
#TODO: remove I_ABSORP
ILATTICE = self.ILATTICE
HMILLER = self.HMILLER
KMILLER = self.KMILLER
LMILLER = self.LMILLER
I_PLOT = self.I_PLOT
TEMPER = self.TEMPER
ENERGY = self.ENERGY
ENERGY_END = self.ENERGY_END
NPOINTS = self.NPOINTS
descriptor = Crystal_GetCrystalsList()[ILATTICE]
print("Using crystal descriptor: ",descriptor)
bragg_dictionary = bragg_calc(descriptor=descriptor,hh=HMILLER,kk=KMILLER,ll=LMILLER,temper=TEMPER,
emin=ENERGY,emax=ENERGY_END,estep=50.0,fileout="/dev/null")
energy = numpy.linspace(ENERGY,ENERGY_END,NPOINTS)
out = numpy.zeros((25,NPOINTS))
info = ""
for i,ienergy in enumerate(energy):
dic2 = crystal_fh(bragg_dictionary,ienergy)
print("Energy=%g eV FH=(%g,%g)"%(ienergy,dic2["STRUCT"].real,dic2["STRUCT"].imag))
out[0,i] = ienergy
out[1,i] = dic2["WAVELENGTH"]*1e10
out[2,i] = dic2["THETA"]*180/numpy.pi
out[3,i] = dic2["F_0"].real
out[4,i] = dic2["F_0"].imag
out[5,i] = dic2["FH"].real
out[6,i] = dic2["FH"].imag
out[7,i] = dic2["FH_BAR"].real
out[8,i] = dic2["FH_BAR"].imag
out[9,i] = dic2["psi_0"].real
out[10,i] = dic2["psi_0"].imag
out[11,i] = dic2["psi_h"].real
out[12,i] = dic2["psi_h"].imag
out[13,i] = dic2["psi_hbar"].real
out[14,i] = dic2["psi_hbar"].imag
out[15,i] = dic2["STRUCT"].real
out[16,i] = dic2["STRUCT"].imag
out[17,i] = dic2["DELTA_REF"]
out[18,i] = dic2["REFRAC"].real
out[19,i] = dic2["REFRAC"].imag
out[20,i] = dic2["ABSORP"]
out[21,i] = 1e6 * dic2["ssr"] # in microrads
out[22,i] = 1e6 * dic2["spr"] # in microrads
out[23,i] = dic2["RATIO"]
out[24,i] = dic2["psi_over_f"]
info += "#\n#\n#\n"
info += dic2["info"]
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", out.T)
calculated_data.add_content("plot_x_col",0)
calculated_data.add_content("plot_y_col", I_PLOT)
except:
pass
try:
calculated_data.add_content("labels",self.plotOptionList())
except:
pass
try:
calculated_data.add_content("info",info)
except:
pass
return calculated_data
if __name__ == "__main__":
from oasys.widgets.exchange import DataExchangeObject
input_data_type = "POWER"
if input_data_type == "POWER":
# create fake UNDULATOR_FLUX xoppy exchange data
e = numpy.linspace(1000.0, 10000.0, 100)
source = e/10
received_data = DataExchangeObject("XOPPY", "POWER")
received_data.add_content("xoppy_data", numpy.vstack((e,e,source)).T)
received_data.add_content("xoppy_code", "US")
elif input_data_type == "POWER3D":
# create unulator_radiation xoppy exchange data
from orangecontrib.xoppy.util.xoppy_undulators import xoppy_calc_undulator_radiation
e, h, v, p, code = xoppy_calc_undulator_radiation(ELECTRONENERGY=6.04,ELECTRONENERGYSPREAD=0.001,ELECTRONCURRENT=0.2,\
ELECTRONBEAMSIZEH=0.000395,ELECTRONBEAMSIZEV=9.9e-06,\
ELECTRONBEAMDIVERGENCEH=1.05e-05,ELECTRONBEAMDIVERGENCEV=3.9e-06,\
PERIODID=0.018,NPERIODS=222,KV=1.68,DISTANCE=30.0,
SETRESONANCE=0,HARMONICNUMBER=1,
GAPH=0.001,GAPV=0.001,\
HSLITPOINTS=41,VSLITPOINTS=41,METHOD=0,
PHOTONENERGYMIN=7000,PHOTONENERGYMAX=8100,PHOTONENERGYPOINTS=20,
def xoppy_calc_xpowder_fml(self):
for file in ["xpowder_fml.par","xpowder_fml.ref","xpowder_fml.out"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
with open("xoppy.inp", "wt") as f:
f.write("%s\n"% (self.FILE))
f.write("%s\n"%(self.TITLE))
f.write("%g\n"%(self.LAMBDA))
f.write("%s\n"%(self.JOB))
f.write("%g\n"%(self.U))
f.write("%g\n"%(self.V))
f.write("%g\n"%(self.W))
f.write("%g\n"%(self.X))
f.write("%g\n"%(self.LS))
f.write("%g\n"%(self.THMIN))
f.write("%g\n"%(self.STEP))
f.write("%s\n"%(self.THMAX))
if platform.system() == "Windows":
command = os.path.join(locations.home_bin(),'xpowder_fml.exe < xoppy.inp')
else:
command = "'" + os.path.join(locations.home_bin(), 'xpowder_fml') + "' < xoppy.inp"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
print("Files written to disk:\n xpowder_fml.par (text output)\n xpowder_fml.ref (reflections)\n xpowder_fml.out (diffractogram)",)
#
# data = numpy.loadtxt("xpowder_fml.out",skiprows=3).T
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", numpy.loadtxt("xpowder_fml.out", skiprows=3))
calculated_data.add_content("plot_x_col",0)
calculated_data.add_content("plot_y_col",-1)
except:
pass
try:
calculated_data.add_content("labels",["TwoTheta[Deg]","Intensity[a.u.]"])
except:
pass
try:
with open("xpowder_fml.par") as f:
info = f.readlines()
info = [line[:-1] for line in info] # remove "\n"
calculated_data.add_content("info",info)
except:
pass
return calculated_data
def xoppy_calc_mlayer(self):
# copy the variable locally, so no more use of self.
MODE = self.MODE
SCAN = self.SCAN
F12_FLAG = self.F12_FLAG
SUBSTRATE = self.SUBSTRATE
ODD_MATERIAL = self.ODD_MATERIAL
EVEN_MATERIAL = self.EVEN_MATERIAL
ENERGY = self.ENERGY
THETA = self.THETA
SCAN_STEP = self.SCAN_STEP
NPOINTS = self.NPOINTS
ODD_THICKNESS = self.ODD_THICKNESS
EVEN_THICKNESS = self.EVEN_THICKNESS
NLAYERS = self.NLAYERS
FILE = self.FILE
for file in ["mlayer.inp", "mlayer.par", "mlayer.f12"]:
try:
os.remove(os.path.join(locations.home_bin_run(), file))
except:
pass
#
# write input file for Fortran mlayer: mlayer.inp
#
f = open('mlayer.inp', 'w')
if SCAN == 0 and MODE == 0: a0 = 1
if SCAN == 1 and MODE == 0: a0 = 2
if SCAN == 0 and MODE == 1: a0 = 3
if SCAN == 1 and MODE == 1: a0 = 4
f.write("%d \n" % a0)
f.write("N\n")
f.write("%g\n" % (codata.h * codata.c / codata.e * 1e10 / ENERGY))
f.write("%g\n" % THETA)
#
if SCAN == 0:
f.write("%g\n" % SCAN_STEP)
a2 = codata.h * codata.c / codata.e * 1e10 / ENERGY
a3 = codata.h * codata.c / codata.e * 1e10 / (ENERGY + SCAN_STEP)
a4 = a3 - a2
if SCAN != 0:
f.write("%g\n" % a4)
#
f.write("%d\n" % NPOINTS)
if MODE == 0:
f.write("%d\n" % NLAYERS)
if MODE == 0:
if a0 != 5:
f.write("%g %g \n" % (ODD_THICKNESS, EVEN_THICKNESS))
else:
for i in range(NLAYERS):
f.write("%g %g \n" % (ODD_THICKNESS, EVEN_THICKNESS))
if MODE != 0:
f1 = open(FILE, 'r')
a5 = f1.read()
f1.close()
if MODE != 0:
print("Number of layers in %s file is %d " % (FILE, NLAYERS))
f.write("%d\n" % NLAYERS)
f.write(a5)
f.write("mlayer.par\n")
f.write("mlayer.dat\n")
f.write("6\n")
f.close()
print('File written to disk: mlayer.inp')
#
# create f12 file
#
if F12_FLAG == 0:
energy = numpy.arange(0, 500)
elefactor = numpy.log10(10000.0 / 30.0) / 300.0
energy = 10.0 * 10**(energy * elefactor)
f12_s = f1f2_calc(SUBSTRATE, energy)
f12_e = f1f2_calc(EVEN_MATERIAL, energy)
f12_o = f1f2_calc(ODD_MATERIAL, energy)
f = open("mlayer.f12", 'w')
f.write(
'; File created by xoppy for materials [substrate=%s,even=%s,odd=%s]: \n'
% (SUBSTRATE, EVEN_MATERIAL, ODD_MATERIAL))
f.write('; Atomic masses: \n')
f.write(
"%g %g %g \n" %
(xraylib.AtomicWeight(xraylib.SymbolToAtomicNumber(SUBSTRATE)),
xraylib.AtomicWeight(
xraylib.SymbolToAtomicNumber(EVEN_MATERIAL)),
xraylib.AtomicWeight(
xraylib.SymbolToAtomicNumber(ODD_MATERIAL))))
f.write('; Densities: \n')
f.write("%g %g %g \n" %
(xraylib.ElementDensity(
xraylib.SymbolToAtomicNumber(SUBSTRATE)),
xraylib.ElementDensity(
xraylib.SymbolToAtomicNumber(EVEN_MATERIAL)),
xraylib.ElementDensity(
xraylib.SymbolToAtomicNumber(ODD_MATERIAL))))
f.write('; Number of energy points: \n')
f.write("%d\n" % (energy.size))
f.write(
'; For each energy point, energy[eV], f1[substrate], f2[substrate], f1[even], f2[even], f1[odd], f2[odd]: \n'
)
for i in range(energy.size):
f.write("%g %g %g %g %g %g %g \n" %
(energy[i], f12_s[0, i], f12_s[1, i], f12_e[0, i],
f12_e[1, i], f12_o[0, i], f12_o[1, i]))
f.close()
print('File written to disk: mlayer.f12')
#
# run external program mlayer
#
if platform.system() == "Windows":
command = os.path.join(locations.home_bin(),
'mlayer.exe < mlayer.inp')
else:
command = "'" + os.path.join(locations.home_bin(),
'mlayer') + "' < mlayer.inp"
print("Running command '%s' in directory: %s " %
(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
#send exchange
calculated_data = DataExchangeObject(
"XOPPY", self.get_data_exchange_widget_name())
try:
if SCAN == 0:
calculated_data.add_content("xoppy_data",
numpy.loadtxt("mlayer.dat"))
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", 3)
elif SCAN == 1: # internal scan is in wavelength. Add a column with energy
aa = numpy.loadtxt("mlayer.dat")
photon_energy = (codata.h * codata.c / codata.e * 1e10) / aa[:,
0]
bb = numpy.zeros((aa.shape[0], 1 + aa.shape[1]))
bb[:, 0] = photon_energy
bb[:, 1:] = aa
calculated_data.add_content("xoppy_data", bb)
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", 4)
calculated_data.add_content("units_to_degrees", 1.0)
except:
pass
try:
info = "ML %s(%3.2f A):%s(%3.2f A) %d pairs; E=%5.3f eV" % (
ODD_MATERIAL, ODD_THICKNESS, EVEN_MATERIAL, EVEN_THICKNESS,
NLAYERS, ENERGY)
calculated_data.add_content("info", info)
except:
pass
return calculated_data
def xoppy_calc_xpower(self):
#
# prepare input for xpower_calc
# Note that the input for xpower_calc accepts any number of elements.
#
substance = [self.EL1_FOR,self.EL2_FOR,self.EL3_FOR,self.EL4_FOR,self.EL5_FOR]
thick = numpy.array( (self.EL1_THI,self.EL2_THI,self.EL3_THI,self.EL4_THI,self.EL5_THI))
angle = numpy.array( (self.EL1_ANG,self.EL2_ANG,self.EL3_ANG,self.EL4_ANG,self.EL5_ANG))
dens = [self.EL1_DEN,self.EL2_DEN,self.EL3_DEN,self.EL4_DEN,self.EL5_DEN]
roughness = numpy.array( (self.EL1_ROU,self.EL2_ROU,self.EL3_ROU,self.EL4_ROU,self.EL5_ROU))
flags = numpy.array( (self.EL1_FLAG,self.EL2_FLAG,self.EL3_FLAG,self.EL4_FLAG,self.EL5_FLAG))
substance = substance[0:self.NELEMENTS+1]
thick = thick[0:self.NELEMENTS+1]
angle = angle[0:self.NELEMENTS+1]
dens = dens[0:self.NELEMENTS+1]
roughness = roughness[0:self.NELEMENTS+1]
flags = flags[0:self.NELEMENTS+1]
if self.SOURCE == 0:
# energies = numpy.arange(0,500)
# elefactor = numpy.log10(10000.0 / 30.0) / 300.0
# energies = 10.0 * 10**(energies * elefactor)
# source = numpy.ones(energies.size)
# tmp = numpy.vstack( (energies,source))
if self.input_spectrum is None:
raise Exception("No input beam")
else:
energies = self.input_spectrum[0,:].copy()
source = self.input_spectrum[1,:].copy()
elif self.SOURCE == 1:
energies = numpy.linspace(self.ENER_MIN,self.ENER_MAX,self.ENER_N)
source = numpy.ones(energies.size)
tmp = numpy.vstack( (energies,source))
self.input_spectrum = source
elif self.SOURCE == 2:
if self.SOURCE == 2: source_file = self.SOURCE_FILE
# if self.SOURCE == 3: source_file = "SRCOMPE"
# if self.SOURCE == 4: source_file = "SRCOMPF"
try:
tmp = numpy.loadtxt(source_file)
energies = tmp[:,0]
source = tmp[:,1]
self.input_spectrum = source
except:
print("Error loading file %s "%(source_file))
raise
if self.FILE_DUMP == 0:
output_file = None
else:
output_file = "power.spec"
out_dictionary = xpower_calc(energies=energies,source=source,substance=substance,
flags=flags,dens=dens,thick=thick,angle=angle,roughness=roughness,output_file=output_file)
try:
print(out_dictionary["info"])
except:
pass
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", out_dictionary["data"].T)
calculated_data.add_content("plot_x_col",0)
calculated_data.add_content("plot_y_col",-1)
except:
pass
try:
# print(out_dictionary["labels"])
calculated_data.add_content("labels", out_dictionary["labels"])
except:
pass
try:
calculated_data.add_content("info",out_dictionary["info"])
except:
pass
return calculated_data
def xoppy_calc_xfh(self):
#TODO: remove I_ABSORP
ILATTICE = self.ILATTICE
HMILLER = self.HMILLER
KMILLER = self.KMILLER
LMILLER = self.LMILLER
I_PLOT = self.I_PLOT
TEMPER = self.TEMPER
ENERGY = self.ENERGY
ENERGY_END = self.ENERGY_END
NPOINTS = self.NPOINTS
descriptor = Crystal_GetCrystalsList()[ILATTICE]
print("Using crystal descriptor: ", descriptor)
bragg_dictionary = bragg_calc(descriptor=descriptor,
hh=HMILLER,
kk=KMILLER,
ll=LMILLER,
temper=TEMPER,
emin=ENERGY,
emax=ENERGY_END,
estep=50.0,
fileout=None)
energy = numpy.linspace(ENERGY, ENERGY_END, NPOINTS)
out = numpy.zeros((25, NPOINTS))
info = ""
for i, ienergy in enumerate(energy):
dic2 = crystal_fh(bragg_dictionary, ienergy)
print("Energy=%g eV FH=(%g,%g)" %
(ienergy, dic2["STRUCT"].real, dic2["STRUCT"].imag))
out[0, i] = ienergy
out[1, i] = dic2["WAVELENGTH"] * 1e10
out[2, i] = dic2["THETA"] * 180 / numpy.pi
out[3, i] = dic2["F_0"].real
out[4, i] = dic2["F_0"].imag
out[5, i] = dic2["FH"].real
out[6, i] = dic2["FH"].imag
out[7, i] = dic2["FH_BAR"].real
out[8, i] = dic2["FH_BAR"].imag
out[9, i] = dic2["psi_0"].real
out[10, i] = dic2["psi_0"].imag
out[11, i] = dic2["psi_h"].real
out[12, i] = dic2["psi_h"].imag
out[13, i] = dic2["psi_hbar"].real
out[14, i] = dic2["psi_hbar"].imag
out[15, i] = dic2["STRUCT"].real
out[16, i] = dic2["STRUCT"].imag
out[17, i] = dic2["DELTA_REF"]
out[18, i] = dic2["REFRAC"].real
out[19, i] = dic2["REFRAC"].imag
out[20, i] = dic2["ABSORP"]
out[21, i] = 1e6 * dic2["ssr"] # in microrads
out[22, i] = 1e6 * dic2["spr"] # in microrads
out[23, i] = dic2["RATIO"]
out[24, i] = dic2["psi_over_f"]
info += "#\n#\n#\n"
info += dic2["info"]
#send exchange
calculated_data = DataExchangeObject(
"XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", out.T)
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", I_PLOT)
except:
pass
try:
calculated_data.add_content("labels", self.plotOptionList())
except:
pass
try:
calculated_data.add_content("info", info)
except:
pass
if self.DUMP_TO_FILE:
with open(self.FILE_NAME, "w") as file:
try:
file.write("#F %s\n" % self.FILE_NAME)
file.write("\n#S 1 xoppy CrossSec results\n")
file.write("#N %d\n" % (out.shape[0]))
tmp = "#L"
for item in self.plotOptionList():
tmp += " %s" % (item)
tmp += "\n"
file.write(tmp)
for j in range(out.shape[1]):
file.write(
("%19.12e " * out.shape[0] + "\n") %
tuple(out[i, j] for i in range(out.shape[0])))
file.close()
print("File written to disk: %s \n" % self.FILE_NAME)
except:
raise Exception(
"CrossSec: The data could not be dumped onto the specified file!\n"
)
return calculated_data
def calculate_total_filter(self):
try:
congruence.checkStrictlyPositiveNumber(self.energy_from,
"Energy From")
congruence.checkStrictlyPositiveNumber(self.energy_to, "Energy to")
congruence.checkStrictlyPositiveNumber(self.energy_nr,
"Nr. of energies")
congruence.checkLessThan(self.energy_from, self.energy_to,
"Energy From", "Energy to")
energies = numpy.linspace(self.energy_from, self.energy_to,
self.energy_nr)
total_filter = numpy.ones((self.energy_nr, 2))
total_filter[:, 0] = energies
self.__add_data_to_total_filter(total_filter, self.ref_1,
self.n_ref_1, self.check_ref_1)
self.__add_data_to_total_filter(total_filter, self.ref_2,
self.n_ref_2, self.check_ref_2)
self.__add_data_to_total_filter(total_filter, self.ref_3,
self.n_ref_3, self.check_ref_3)
self.__add_data_to_total_filter(total_filter, self.dif_1,
self.n_dif_1, self.check_dif_1)
self.__add_data_to_total_filter(total_filter, self.dif_2,
self.n_dif_2, self.check_dif_2)
self.__add_data_to_total_filter(total_filter, self.mul_1,
self.n_mul_1, self.check_mul_1)
self.__add_data_to_total_filter(total_filter, self.mul_2,
self.n_mul_2, self.check_mul_2)
self.__add_data_to_total_filter(total_filter,
self.pow_1,
0,
self.check_pow_1,
absorbed=self.abs_tran == 0)
total_filter[numpy.where(numpy.isnan(total_filter))] = 0.0
if not total_filter[:, 1].sum() == total_filter.shape[0]:
self.filter_plot.clear()
self.filter_plot.addCurve(total_filter[:, 0],
total_filter[:, 1],
replace=True,
legend="Total Filter")
self.filter_plot.setGraphXLabel("Energy [eV]")
self.filter_plot.setGraphYLabel("Intensity Factor")
self.filter_plot.setGraphTitle("Total Filter")
calculated_data = DataExchangeObject("ShadowOui_Thermal",
"TOTAL_FILTER")
calculated_data.add_content("total_filter", total_filter)
self.send("Total Filter", calculated_data)
else:
raise ValueError("Calculation not possibile: no input data")
except Exception as e:
QMessageBox.critical(self, "Error", str(e), QMessageBox.Ok)
if self.IS_DEVELOP: raise e
def xoppy_calc_xcrystal(self):
CRYSTAL_MATERIAL = self.CRYSTAL_MATERIAL
MILLER_INDEX_H = self.MILLER_INDEX_H
MILLER_INDEX_K = self.MILLER_INDEX_K
MILLER_INDEX_L = self.MILLER_INDEX_L
TEMPER = self.TEMPER
MOSAIC = self.MOSAIC
GEOMETRY = self.GEOMETRY
SCAN = self.SCAN
UNIT = self.UNIT
SCANFROM = self.SCANFROM
SCANTO = self.SCANTO
SCANPOINTS = self.SCANPOINTS
ENERGY = self.ENERGY
ASYMMETRY_ANGLE = self.ASYMMETRY_ANGLE
THICKNESS = self.THICKNESS
MOSAIC_FWHM = self.MOSAIC_FWHM
RSAG = self.RSAG
RMER = self.RMER
ANISOTROPY = self.ANISOTROPY
POISSON = self.POISSON
CUT = self.CUT
FILECOMPLIANCE = self.FILECOMPLIANCE
for file in ["diff_pat.dat","diff_pat.gle","diff_pat.par","diff_pat.xop","xcrystal.bra"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
if (GEOMETRY == 1) or (GEOMETRY == 3):
if ASYMMETRY_ANGLE == 0.0:
print("xoppy_calc_xcrystal: WARNING: In xcrystal the asymmetry angle is the angle between Bragg planes and crystal surface,"+
"in BOTH Bragg and Laue geometries.")
descriptor = Crystal_GetCrystalsList()[CRYSTAL_MATERIAL]
if SCAN == 3: # energy scan
emin = SCANFROM - 1
emax = SCANTO + 1
else:
emin = ENERGY - 100.0
emax = ENERGY + 100.0
print("Using crystal descriptor: ",descriptor)
bragg_dictionary = bragg_calc(descriptor=descriptor,
hh=MILLER_INDEX_H,kk=MILLER_INDEX_K,ll=MILLER_INDEX_L,
temper=float(TEMPER),
emin=emin,emax=emax,estep=5.0,fileout="xcrystal.bra")
with open("xoppy.inp", "wt") as f:
f.write("xcrystal.bra\n")
f.write("%d\n"%MOSAIC)
f.write("%d\n"%GEOMETRY)
if MOSAIC == 1:
f.write("%g\n"%MOSAIC_FWHM)
f.write("%g\n"%THICKNESS)
else:
f.write("%g\n"%THICKNESS)
f.write("%g\n"%ASYMMETRY_ANGLE)
scan_flag = 1 + SCAN
f.write("%d\n"%scan_flag)
f.write("%19.9f\n"%ENERGY)
if scan_flag <= 3:
f.write("%d\n"%UNIT)
f.write("%g\n"%SCANFROM)
f.write("%g\n"%SCANTO)
f.write("%d\n"%SCANPOINTS)
if MOSAIC > 1: # bent
f.write("%g\n"%RSAG)
f.write("%g\n"%RMER)
f.write("0\n")
if ( (descriptor == "Si") or (descriptor == "Si2") or (descriptor == "Si_NIST") or (descriptor == "Ge") or descriptor == "Diamond"):
pass
else: # not Si,Ge,Diamond
if ((ANISOTROPY == 1) or (ANISOTROPY == 2)):
raise Exception("Anisotropy data not available for this crystal. Either use isotropic or use external compliance file. Please change and run again'")
f.write("%d\n"%ANISOTROPY)
if ANISOTROPY == 0:
f.write("%g\n"%POISSON)
elif ANISOTROPY == 1:
f.write("%d\n"%CRYSTAL_MATERIAL)
f.write("%g\n"%ASYMMETRY_ANGLE)
f.write("%d\n"%MILLER_INDEX_H)
f.write("%d\n"%MILLER_INDEX_K)
f.write("%d\n"%MILLER_INDEX_L)
elif ANISOTROPY == 2:
f.write("%d\n"%CRYSTAL_MATERIAL)
f.write("%g\n"%ASYMMETRY_ANGLE)
# TODO: check syntax for CUT: Cut syntax is: valong_X valong_Y valong_Z ; vnorm_X vnorm_Y vnorm_Z ; vperp_x vperp_Y vperp_Z
f.write("%s\n"%CUT.split(";")[0])
f.write("%s\n"%CUT.split(";")[1])
f.write("%s\n"%CUT.split(";")[2])
elif ANISOTROPY == 3:
f.write("%s\n"%FILECOMPLIANCE)
command = "'" + os.path.join(locations.home_bin(), 'diff_pat') + "' < xoppy.inp"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
#show calculated parameters in standard output
txt_info = open("diff_pat.par").read()
for line in txt_info:
print(line,end="")
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", numpy.loadtxt("diff_pat.dat", skiprows=5))
calculated_data.add_content("plot_x_col",0)
calculated_data.add_content("plot_y_col",-1)
calculated_data.add_content("units_to_degrees", self.get_units_to_degrees())
except Exception as e:
raise Exception("Error loading diff_pat.dat :" + str(e))
try:
calculated_data.add_content("labels",
["Th-ThB{in} [" + self.unit_combo.itemText(self.UNIT) + "]",
"Th-ThB{out} [" + self.unit_combo.itemText(self.UNIT) + "]",
"phase_p[rad]",
"phase_s[rad]","Circ Polariz",
"p-polarized reflectivity",
"s-polarized reflectivity"])
except:
pass
try:
with open("diff_pat.par") as f:
info = f.readlines()
calculated_data.add_content("info",info)
except:
pass
return calculated_data
def _callable_2(self, html):
try:
self.x0h_input.loadFinished.disconnect()
self.x0h_input.back()
self.x0h_input.setHidden(False)
response_1 = self.clear_response(html)
response_2 = self.clear_response(html)
self.tabs_widget.setCurrentIndex(0)
self.x0h_output.setHtml(response_1)
data0, data1, data2 = self.extract_plots(response_2)
exchange_data = DataExchangeObject("XRAYSERVER", "X0H")
exchange_data.add_content("reflectivity", data0)
exchange_data.add_content("reflectivity_units_to_degrees", 1.0)
exchange_data.add_content("x-ray_diffraction_profile_sigma", data1)
exchange_data.add_content("x-ray_diffraction_profile_sigma_units_to_degrees", 0.000277777805)
exchange_data.add_content("x-ray_diffraction_profile_pi", data2)
exchange_data.add_content("x-ray_diffraction_profile_pi_units_to_degrees", 0.000277777805)
self.send("xrayserver_data", exchange_data)
except urllib.error.HTTPError as e:
self.x0h_output.setHtml('The server couldn\'t fulfill the request.\nError Code: '
+ str(e.code) + "\n\n" +
server.BaseHTTPRequestHandler.responses[e.code][1])
except urllib.error.URLError as e:
self.x0h_output.setHtml('We failed to reach a server.\nReason: '
+ e.reason)
except XrayServerException as e:
ShowHtmlDialog.show_html("X-ray Server Error", e.response, width=750, height=500, parent=self)
except Exception as e:
self.x0h_output.setHtml('We failed to reach a server.\nReason: '
+ str(e))
self.tabs_widget.setCurrentIndex(0)
self.setStatusMessage("")
self.progressBarFinished()
