Source code for pySAXS.guisaxs.LSAbsorptionXRL

#!/usr/bin/python

import wx
import numpy
import sys
from pySAXS.LS import absorptionXRL
import xraylib
from pySAXS.tools import isNumeric
'''
29/08/2012 OT : rename file and class LSAbsDlg to LSAbsorptionDlg

15/06/2009 OT : change from Dialog to Frame
    Add Label for NIST
    Change size of Frame

initial work by Antoine Thill

'''

[docs]class AbsorptionForm(wx.Frame): def __init__(self, parent, set_dir = None,printout=None): wx.Frame.__init__(self, parent, -1, "X-Ray absorption tool using Xraylib", \ size=wx.Size(580,650),\ pos=wx.DefaultPosition,style = wx.DEFAULT_DIALOG_STYLE) if dir(parent).__contains__('favicon'): wx.Frame.SetIcon(self,parent.favicon) self.printout=printout self.energy=8.03 self.SetBackgroundColour(wx.LIGHT_GREY) self.res=numpy.array([0.,0.,0.]) self.Z=0 self.ActiveFormula="" self.ActiveAtomes=numpy.zeros(120) self.ChampText = wx.StaticText(self, 101, "click to select atoms", wx.Point(200, 100)) #energy slider and buttons # the current NRJ is obtained with NRJslider.GetValue() in eV self.NRJlabel = wx.StaticText(self, -1, "Energy (keV)", wx.Point(20, 20)) self.NRJTextCtrl=wx.TextCtrl(self,104,"",wx.Point(100,20),wx.Size(100,20)) self.NRJTextCtrl.SetValue(str(self.energy)) #self.Bind(wx.EVT_TEXT, self.NRJUpdate) if self.energy!=0: lambdaValue=xraylib.KEV2ANGST/self.energy self.LambdaLabel= wx.StaticText(self, -1, "Lambda (Angstrom) = "+str(lambdaValue), wx.Point(250, 20)) ''' self.NRJslider=wx.Slider(self,104,8030,1000,50000,\ wx.Point(20,20),\ wx.Size(200,15),\ wx.SL_HORIZONTAL|wx.SL_AUTOTICKS) self.NRJslider.SetTickFreq(5000,1) self.Bind(wx.EVT_SLIDER, self.sliderUpdate) self.NRJText = wx.StaticText(self, 105, "8.03 keV", wx.Point(250, 15))''' self.CommonsourceText = wx.StaticText(self, -1, "Common x-ray source :", wx.Point(50, 52)) for i in range(len(absorptionXRL.COMMON_XRAY_SOURCE_MATERIALS)): Beg=1 # H button self.buttonSource =wx.Button(self, 1000+i, absorptionXRL.COMMON_XRAY_SOURCE_MATERIALS[i], wx.Point(200+i*35,47),wx.Size(30,30)) self.Bind(wx.EVT_BUTTON, self.OnClickSource, self.buttonSource) self.ResetButton =wx.Button(self, 106, "Reset", wx.Point(520,12),wx.Size(50,30)) wx.EVT_BUTTON(self, 106, self.OnResetClick) ''' #Check box for musrho or musrhoen self.MuenBox=wx.CheckBox(self,107,"Mu_en ",(450,15)) self.Bind(wx.EVT_CHECKBOX, self.CheckBoxUpdate) self.MuenBox.SetValue(1) ''' self.button=[] ################# #Definition des bouttons de chaque atome pris en charge dans le module ################# Bcol=20 Blig=100 Bsiz=30 Znb=1 # H button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+17*Bsiz # He button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=20 Blig=Blig+Bsiz # Li button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # Be button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+11*Bsiz # B button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # C button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # N button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # O button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # F button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # Ne button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=20 Blig=Blig+Bsiz # Na button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # Mg button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+11*Bsiz # Al button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # Si button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # P button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # S button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # Cl button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # Ar button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=20 Blig=Blig+Bsiz #ligne 4 for n in numpy.arange(18): # next button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz Bcol=20 Blig=Blig+Bsiz #ligne 5 for n in numpy.arange(18): # next button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz Bcol=20 Blig=Blig+Bsiz # Cs button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # Ba button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # La button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 #Lanthanides line Bcol=20 Blig=Blig+3*Bsiz for n in numpy.arange(14): # next button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz #fin de la ligne 6 Bcol=20+3*Bsiz Blig=Blig-3*Bsiz for n in numpy.arange(15): # next button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz Bcol=20 Blig=Blig+Bsiz # Fr button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # Ra button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz # Ac button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 #Acthinides line Bcol=20 Blig=Blig+3*Bsiz for n in numpy.arange(3): # next button self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz)) self.Bind(wx.EVT_BUTTON, self.OnClick, self.button) Znb=Znb+1 Bcol=Bcol+Bsiz decal=50 self.SymboleText = wx.StaticText(self, 101, "Symbole = ", wx.Point(20, 365+decal)) self.NameText = wx.StaticText(self, 101, "Name = ", wx.Point(20, 380+decal)) self.ZText = wx.StaticText(self, 101, "Atomic number = ", wx.Point(20, 395+decal)) self.MasseText = wx.StaticText(self, 101, "Atomic weight = ", wx.Point(20, 410+decal)) self.MuText = wx.StaticText(self, 101, "Mu_en/rho = ", wx.Point(20, 425+decal)) # Add button self.AtomsNumberLabel=wx.StaticText(self,1092,"Number of atoms = ",wx.Point(20,455+decal)) self.AtomsNumber=wx.TextCtrl(self,1091,"",wx.Point(130,453+decal),wx.Size(50,20)) self.AtomsNumber.SetValue("1.0") #self.Bind(wx.EVT_TEXT, self.ThicknessUpdate) self.Addbutton=wx.Button(self, 108, "Add", wx.Point(20,475+decal),wx.Size(50,30)) wx.EVT_BUTTON(self, 108, self.OnAddClick) # Remove button self.RemoveButton =wx.Button(self, 109, "Remove", wx.Point(70,475+decal),wx.Size(60,30)) wx.EVT_BUTTON(self, 109, self.OnRemoveClick) # Remove all button self.RemoveButton =wx.Button(self, 1090, "Remove All", wx.Point(130,475+decal),wx.Size(80,30)) wx.EVT_BUTTON(self, 1090, self.OnRemoveAllClick) self.FormulaLabel=wx.StaticText(self,110,"Active Formula = ",wx.Point(250,350+decal)) self.CompoundMuLabel=wx.StaticText(self,112,"Compound Mu_en/rho = ",wx.Point(250,370+decal)) self.DensityLabel=wx.StaticText(self,113,"Density = ",wx.Point(250,390+decal)) self.DensityText=wx.TextCtrl(self,114,"",wx.Point(375,390+decal),wx.Size(75,20)) self.DensityText.SetValue("1.00") #self.Bind(wx.EVT_TEXT, self.DensityUpdate) self.DensityUnitLabel=wx.StaticText(self,115,"(g/cm3)",wx.Point(500,390+decal)) self.CompoundEDLabel=wx.StaticText(self,116,"Electronic density = ",wx.Point(250,410+decal)) self.CompoundSLLabel=wx.StaticText(self,117,"Scattering length density = ",wx.Point(250,430+decal)) self.ThicknessLabel=wx.StaticText(self,118,"Thickness = ",wx.Point(250,450+decal)) self.ThicknessText=wx.TextCtrl(self,119,"",wx.Point(375,450+decal),wx.Size(75,20)) self.ThicknessText.SetValue("0.1") self.Bind(wx.EVT_TEXT, self.UpdateFormula) self.ThicknessUnitLabel=wx.StaticText(self,120,"(cm)",wx.Point(500,450+decal)) self.TransLabel=wx.StaticText(self,121,"X-ray trans = ",wx.Point(250,470+decal)) self.QuitButton=wx.Button(self,wx.ID_EXIT,"QUIT",wx.Point(275,500+decal),wx.Size(75,30)) wx.EVT_BUTTON(self, wx.ID_EXIT, self.OnExitClick) self.Bind(wx.EVT_CLOSE, self.OnExitClick) #XRAY LIB self.NISTLabel=wx.StaticText(self,129,"Datas from xraylib libraries",wx.Point(100,550+decal)) self.NISTLabel.SetForegroundColour('blue')
[docs] def OnResetClick(self,event): self.Z=0 '''self.NRJslider.SetValue(8028) self.NRJText.SetLabel(str(self.NRJslider.GetValue()/1000.0) +" keV")''' self.energy=8.03 self.NRJTextCtrl.SetValue(str(self.energy)) self.ChampText.SetLabel("click to select an atom") self.SymboleText.SetLabel("Symbole = ") self.NameText.SetLabel("Name = " ) self.ZText.SetLabel("Atomic number = ") self.MasseText.SetLabel("Atomic weight = ") self.UpdateFormula() #### #On clique sur l'un des bouttons du tableau ####
[docs] def OnClick(self,event): #self.DensityText.SetValue(absorptionXRL.ATOMS[event.GetId()-1]) Z=event.GetId() self.SymboleText.SetLabel("Symbol = " + xraylib.AtomicNumberToSymbol(Z)) self.NameText.SetLabel("Name = " + absorptionXRL.getNameZ(Z)) self.ZText.SetLabel("Atomic number : " + str(Z)) self.Z=Z self.MasseText.SetLabel("Atomic weight : "+ str(xraylib.AtomicWeight(Z))) self.MuText.SetLabel("Mu/rho = " + str(absorptionXRL.getMuZ(Z,self.energy)))
[docs] def UpdateFormula(self,verbose=False): Tr=-1 ED=-1 SLD=-1 #print "Fupdate" energy=self.NRJTextCtrl.GetValue() if isNumeric.isNumeric(energy): self.energy=float(energy) if self.energy!=0: lambdaValue=xraylib.KEV2ANGST/self.energy self.LambdaLabel.SetLabel("Lambda (Angstrom) = "+str(lambdaValue)) self.ActiveFormula="" #If at least one atome exist if sum(self.ActiveAtomes)!=0: N=self.ActiveAtomes.take(numpy.where(self.ActiveAtomes!=0)[0]) ind=numpy.where(self.ActiveAtomes!=0)[0] j=0 for i in ind: #self.ActiveFormula=self.ActiveFormula + str(absorptionXRL.ATOMS[int(i)]) + ' ' + str(int(N[int(j)])) + ' ' self.ActiveFormula=self.ActiveFormula + xraylib.AtomicNumberToSymbol(int(i)+1) + ' ' + str(N[int(j)]) + ' ' j=j+1 self.FormulaLabel.SetLabel("Active Formula = "+self.ActiveFormula.strip()) MuRho=absorptionXRL.getMuFormula(self.ActiveFormula,self.energy) self.CompoundMuLabel.SetLabel("Compound Mu/rho = %1.5f (cm2/g)" % MuRho) density=self.DensityText.GetValue() if isNumeric.isNumeric(density): density=float(density) ED=absorptionXRL.getElectronDensity(self.ActiveFormula,density)[0] self.CompoundEDLabel.SetLabel("Electronic density = %1.5e (1/cm3)" % ED) SLD=absorptionXRL.getElectronDensity(self.ActiveFormula,density)[1] self.CompoundSLLabel.SetLabel("Scattering length density = %1.5e (1/cm2)" % SLD) if isNumeric.isNumeric(self.ThicknessText.GetValue()): thickness=float(self.ThicknessText.GetValue()) Tr=absorptionXRL.getTransmission(self.ActiveFormula,\ thickness,\ density,\ self.energy) #self.TransLabel.SetLabel("X-ray transmission = %1.5e" % numpy.exp(-float(self.DensityText.GetValue())*absorptionXRL.getMuFormula(self.ActiveFormula,self.NRJslider.GetValue()/1000.,self.MuenBox.GetValue())*float(self.ThicknessText.GetValue()))) self.TransLabel.SetLabel("X-ray transmission = %1.5e" % Tr) if verbose: self.printTXT("------ Absorption tools using xraylib -----") self.printTXT("Energy : (keV) ", self.energy) self.printTXT("Compound formula: ", self.ActiveFormula) self.printTXT("Compound Mu_en/rho = (cm2/g) ",MuRho) self.printTXT("Electronic density = (1/cm3) ",ED) self.printTXT("Scattering length density = (1/cm2) ",SLD) self.printTXT("X-ray transmission = ",Tr) else: try: self.FormulaLabel.SetLabel("Active Formula = ") self.CompoundMuLabel.SetLabel("Compound Mu_en/rho = (cm2/g)") self.CompoundEDLabel.SetLabel("Electronic density = (1/cm3)") self.CompoundSLLabel.SetLabel("Scattering length density = (1/cm2)") self.TransLabel.SetLabel("X-ray transmission = ") except: pass
[docs] def OnAddClick(self,event): an=self.AtomsNumber.GetValue() if isNumeric.isNumeric(an): an=float(an) an=abs(an) else: an=1.0 if self.Z!= 0: if self.ActiveAtomes[self.Z-1] != 0 : #The new Atome is already present self.ActiveAtomes[self.Z-1]=self.ActiveAtomes[self.Z-1]+an else : #its a brend new atome self.ActiveAtomes[self.Z-1]=an self.UpdateFormula()
[docs] def OnRemoveClick(self,event): if self.Z != 0: if self.ActiveAtomes[self.Z-1] != 0: if self.ActiveAtomes[self.Z-1]<=1: #It has to be removed self.ActiveAtomes[self.Z-1]=0 else: #One atome has to be removed self.ActiveAtomes[self.Z-1]=self.ActiveAtomes[self.Z-1]-1 self.UpdateFormula()
[docs] def OnRemoveAllClick(self,event): self.ActiveAtomes=numpy.zeros(120) self.UpdateFormula()
[docs] def OnClickSource(self,event): sourceID=1000-event.GetId() source=absorptionXRL.COMMON_XRAY_SOURCE_MATERIALS[sourceID] energy=absorptionXRL.getEnergyFromSource(source) self.NRJTextCtrl.SetValue(str(energy))
[docs] def OnExitClick(self,event): self.UpdateFormula(verbose=True) self.Destroy()
[docs] def printTXT(self,txt="",par=""): ''' for printing messages ''' if self.printout==None: print(str(txt)+str(par)) else: self.printout(txt,par) #######
if __name__== '__main__': app = wx.PySimpleApp() frame=AbsorptionForm(None, -1) frame.Show() app.MainLoop()