Exemplo n.º 1
0
    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()))
Exemplo n.º 2
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    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
Exemplo n.º 3
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    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
Exemplo n.º 4
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    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
Exemplo n.º 5
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    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
Exemplo n.º 6
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    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
Exemplo n.º 7
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    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
Exemplo n.º 8
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    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
Exemplo n.º 10
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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()
Exemplo n.º 11
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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()
Exemplo n.º 12
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    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
Exemplo n.º 13
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    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
Exemplo n.º 14
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    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
Exemplo n.º 15
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    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
Exemplo n.º 16
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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()
Exemplo n.º 17
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    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
Exemplo n.º 18
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    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)))
Exemplo n.º 19
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    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
Exemplo n.º 20
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    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
Exemplo n.º 21
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    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
Exemplo n.º 22
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    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
Exemplo n.º 23
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    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)
Exemplo n.º 24
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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()
Exemplo n.º 25
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    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
Exemplo n.º 26
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    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
Exemplo n.º 27
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    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()
Exemplo n.º 28
0

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,
Exemplo n.º 29
0
    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
Exemplo n.º 30
0
    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
Exemplo n.º 31
0
    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()
Exemplo n.º 32
0
    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
Exemplo n.º 33
0
    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
Exemplo n.º 34
0
    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()
Exemplo n.º 35
0
    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()
Exemplo n.º 36
0
    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
Exemplo n.º 37
0
    # 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()
Exemplo n.º 38
0
    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()
Exemplo n.º 39
0
    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
Exemplo n.º 40
0
    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
Exemplo n.º 41
0
    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
Exemplo n.º 42
0
    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
Exemplo n.º 43
0
    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
Exemplo n.º 44
0
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()
Exemplo n.º 45
0
    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()
Exemplo n.º 46
0
    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
Exemplo n.º 47
0

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,
Exemplo n.º 48
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    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
Exemplo n.º 49
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    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
Exemplo n.º 50
0
    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
Exemplo n.º 51
0
    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
Exemplo n.º 52
0
    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
Exemplo n.º 53
0
    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
Exemplo n.º 54
0
    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()