Changeset 3571


Ignore:
Timestamp:
Aug 26, 2018 7:43:05 PM (3 years ago)
Author:
toby
Message:

Add FPA peak fitting

Location:
trunk
Files:
4 added
5 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASIIctrlGUI.py

    r3565 r3571  
    30203020       
    30213021################################################################################
    3022 def GetImportFile(G2frame, message, defaultDir="", defaultFile="", style=wx.FD_OPEN,
    3023                   *args, **kwargs):
     3022def GetImportFile(G2frame, message, defaultDir="", defaultFile="",
     3023                      style=wx.FD_OPEN, parent=None,
     3024                      *args, **kwargs):
    30243025    '''Uses a customized dialog that gets files from the appropriate import directory.
    30253026    Arguments are used the same as in :func:`wx.FileDialog`. Selection of
     
    30353036    :returns: a list of files or an empty list
    30363037    '''
    3037     dlg = wx.FileDialog(G2frame, message, defaultDir, defaultFile, *args,
     3038    if not parent: parent = G2frame
     3039    dlg = wx.FileDialog(parent, message, defaultDir, defaultFile, *args,
    30383040                        style=style, **kwargs)
    30393041    pth = GetImportPath(G2frame)
     
    39653967#####  Get an output file or directory
    39663968################################################################################           
    3967 def askSaveFile(G2frame,defnam,extension,longFormatName):
     3969def askSaveFile(G2frame,defnam,extension,longFormatName,parent=None):
    39683970    '''Ask the user to supply a file name
     3971
     3972    :param wx.Frame G2frame: The main GSAS-II window
     3973    :param str defnam: a default file name
     3974    :param str extension: the default file extension beginning with a '.'
     3975    :param str longFormatName: a description of the type of file
     3976    :param wx.Frame parent: the parent window for the dialog. Defaults
     3977      to G2frame.
    39693978
    39703979    :returns: a file name (str) or None if Cancel is pressed
    39713980    '''
    39723981
     3982    if not parent: parent = G2frame
    39733983    pth = GetExportPath(G2frame)
    39743984    dlg = wx.FileDialog(
    3975         G2frame, 'Input name for file to write', pth, defnam,
     3985        parent, 'Input name for file to write', pth, defnam,
    39763986        longFormatName+' (*'+extension+')|*'+extension,
    39773987        wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
  • trunk/GSASIIdataGUI.py

    r3570 r3571  
    7070import GSASIIpwd as G2pwd
    7171import GSASIIstrMain as G2stMn
     72import defaultIparms as dI
     73import GSASIIfpaGUI as G2fpa
    7274
    7375# trig functions in degrees
     
    12001202        item = submenu.Append(wx.ID_ANY,'Simulate a dataset','Create a powder data set entry that will be simulated')
    12011203        self.Bind(wx.EVT_MENU, self.OnDummyPowder, id=item.GetId())
     1204        item = submenu.Append(wx.ID_ANY,'Fit instr. profile from fundamental parms...','')
     1205        self.Bind(wx.EVT_MENU, self.OnPowderFPA, id=item.GetId())
    12021206       
    12031207    def OpenPowderInstprm(self,instfile):
     
    13861390            sind = lambda x: math.sin(x*math.pi/180.)
    13871391            tand = lambda x: math.tan(x*math.pi/180.)
    1388             import defaultIparms as dI
    13891392            while True: # loop until we get a choice
    13901393                choices = []
     
    19491952        self.EnableRefineCommand()
    19501953        return # success
    1951        
     1954
     1955    def AddSimulatedPowder(self,ttArr,intArr,HistName,Lam1,Lam2):
     1956        '''Create a PDWR entry for a computed powder pattern
     1957        '''
     1958        # get a list of existing histograms
     1959        PWDRlist = []
     1960        if self.GPXtree.GetCount():
     1961            item, cookie = self.GPXtree.GetFirstChild(self.root)
     1962            while item:
     1963                name = self.GPXtree.GetItemText(item)
     1964                if name.startswith('PWDR ') and name not in PWDRlist:
     1965                    PWDRlist.append(name)
     1966                item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
     1967        # Initialize a base class reader
     1968        rd = G2obj.ImportPowderData(
     1969            extensionlist=tuple(),
     1970            strictExtension=False,
     1971            formatName = 'FPA Simulated dataset',
     1972            longFormatName = 'Fundamental Parameters simulated pattern')
     1973        rd.powderentry[0] = '' # no filename
     1974        # #self.powderentry[1] = pos # bank offset (N/A here)
     1975        rd.powderentry[2] = 1 # only one bank
     1976        rd.comments.append('This is a powder pattern simulated with Fundamental Parameters')
     1977        self.CheckNotebook()
     1978        #self.zipfile = None
     1979        # get instrument parameters for it
     1980        rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False],
     1981            'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]})
     1982        Iparm1, Iparm2 = G2fil.ReadPowderInstprm(dI.defaultIparms[0],1,1,rd)
     1983        rd.idstring = ' CW'
     1984        simType = 'CW'
     1985        # set wavelength
     1986        if Lam2:
     1987            Iparm1['Lam1'][0] = Lam1
     1988            Iparm1['Lam2'][0] = Lam2
     1989            Iparm1['Lam1'][1] = Lam1
     1990            Iparm1['Lam2'][1] = Lam2
     1991        else:
     1992            Iparm1['Lam'] = Iparm1['Lam1']
     1993            del Iparm1['Lam1'],Iparm1['Lam2']
     1994            Iparm1['Lam'][0] = Lam1
     1995            Iparm1['Lam'][1] = Lam1
     1996
     1997        rd.powderdata = [
     1998            np.array(ttArr), # x-axis values
     1999            np.array(intArr), # powder pattern intensities
     2000            np.ones_like(ttArr), # 1/sig(intensity)^2 values (weights)
     2001            np.zeros_like(intArr), # calc. intensities (zero)
     2002            np.zeros_like(ttArr), # calc. background (zero)
     2003            np.zeros_like(ttArr), # obs-calc profiles
     2004            ]
     2005        Tmin = rd.powderdata[0][0]
     2006        Tmax = rd.powderdata[0][-1]
     2007        # data are read, now store them in the tree
     2008        HistName = 'PWDR '+HistName
     2009        HistName = G2obj.MakeUniqueLabel(HistName,PWDRlist)  # make new histogram names unique
     2010        Id = self.GPXtree.AppendItem(parent=self.root,text=HistName)
     2011        Ymin = np.min(rd.powderdata[1])
     2012        Ymax = np.max(rd.powderdata[1])
     2013        valuesdict = {
     2014            'wtFactor':1.0,
     2015            'Dummy':True,'simType':simType,
     2016            'ranId':ran.randint(0,sys.maxsize),
     2017            'Offset':[0.0,0.0],'delOffset':0.02*Ymax,'refOffset':-.1*Ymax,'refDelt':0.1*Ymax,
     2018            'Yminmax':[Ymin,Ymax]
     2019            }
     2020        self.GPXtree.SetItemPyData(Id,[valuesdict,rd.powderdata])
     2021        self.GPXtree.SetItemPyData(
     2022            self.GPXtree.AppendItem(Id,text='Comments'),
     2023            rd.comments)
     2024        self.GPXtree.SetItemPyData(
     2025            self.GPXtree.AppendItem(Id,text='Limits'),
     2026            [(Tmin,Tmax),[Tmin,Tmax]])
     2027        self.PatternId = GetGPXtreeItemId(self,Id,'Limits')
     2028        self.GPXtree.SetItemPyData(
     2029            self.GPXtree.AppendItem(Id,text='Background'),
     2030            [['chebyschev',True,3,1.0,0.0,0.0],
     2031             {'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
     2032        self.GPXtree.SetItemPyData(
     2033            self.GPXtree.AppendItem(Id,text='Instrument Parameters'),
     2034            [Iparm1,Iparm2])
     2035        self.GPXtree.SetItemPyData(
     2036            self.GPXtree.AppendItem(Id,text='Sample Parameters'),
     2037            rd.Sample)
     2038        self.GPXtree.SetItemPyData(
     2039            self.GPXtree.AppendItem(Id,text='Peak List')
     2040            ,{'peaks':[],'sigDict':{}})
     2041        self.GPXtree.SetItemPyData(
     2042            self.GPXtree.AppendItem(Id,text='Index Peak List'),
     2043            [[],[]])
     2044        self.GPXtree.SetItemPyData(
     2045            self.GPXtree.AppendItem(Id,text='Unit Cells List'),
     2046            [])
     2047        self.GPXtree.SetItemPyData(
     2048            self.GPXtree.AppendItem(Id,text='Reflection Lists'),
     2049            {})
     2050        self.GPXtree.Expand(Id)
     2051        self.GPXtree.SelectItem(Id)
     2052        print(u'Added simulation powder data {}'.format(HistName))
     2053        return Id
     2054   
    19522055    def OnPreferences(self,event):
    19532056        'Edit the GSAS-II configuration variables'
     
    29053008        G2IO.testColumnMetadata(self)
    29063009               
     3010    def OnPowderFPA(self,event):
     3011        'Perform FPA simulation/peak fitting'
     3012        G2fpa.GetFPAInput(self)
     3013       
    29073014    def OnReadPowderPeaks(self,event):
    29083015        'Bound to menu Data/Read Powder Peaks'
     
    37163823                self.SetTitleByGPX()
    37173824                self.EnableRefineCommand()
     3825                self.init_vars()
    37183826        finally:
    37193827            dlg.Destroy()
  • trunk/GSASIIplot.py

    r3567 r3571  
    4848:func:`PlotRigidBody`         show rigid body structures as balls & sticks
    4949:func:`PlotLayers`            show layer structures as balls & sticks
     50:func:`PlotFPAconvolutors`    plots the convolutors from Fundamental Parameters
    5051============================  ===========================================================================
    5152
     
    87048705    Page.canvas.SetCurrent(Page.context)
    87058706    wx.CallAfter(Draw,'main')
     8707
     8708def PlotFPAconvolutors(G2frame,NISTpk):
     8709    '''Plot the convolutions used for the current peak computed with
     8710    :func:`GSASIIfpaGUI.doFPAcalc`
     8711    '''
     8712    import NIST_profile as FP
     8713    def clearHighlight(event):
     8714        l,lm,lms = Page.timer.lineinfo
     8715        l.set_marker(lm)
     8716        l.set_markersize(lms)
     8717        Page.canvas.draw()
     8718        Page.timer = None
     8719       
     8720    def onPick(event):
     8721        '''When a line in the legend is selected, find the matching line
     8722        in the plot and then highlight it by adding/enlarging markers.
     8723        Set up a timer to make a reset after 2.5 seconds
     8724        '''
     8725        plot = event.artist.get_figure().get_axes()[0]
     8726        if event.artist not in plot.get_legend().get_lines():  # is this an item in the legend?
     8727            return
     8728        if Page.timer: # clear previous highlight
     8729            Page.timer.Stop()
     8730            clearHighlight(None)
     8731            return   # if this is removed, the selected item is automatically highlighted
     8732        lbl = event.artist.get_label()
     8733        for l in plot.get_lines():
     8734            if lbl == l.get_label():
     8735                Page.timer = wx.Timer()
     8736                Page.timer.Bind(wx.EVT_TIMER, clearHighlight)
     8737                Page.timer.lineinfo = (l,l.get_marker(),l.get_markersize())
     8738                # highlight the selected item
     8739                if l.get_marker() == 'None':
     8740                    l.set_marker('o')
     8741                else:
     8742                    l.set_markersize(2*l.get_markersize())
     8743                Page.canvas.draw()
     8744                Page.timer.Start(5000,oneShot=True)
     8745                break
     8746        else:
     8747            print('Warning: artist matching ',lbl,' not found')
     8748                   
     8749    new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('FPA convolutors','mpl')
     8750    if new:
     8751        Page.canvas.mpl_connect('pick_event',onPick)
     8752    Page.timer = None
     8753    Page.SetToolTipString('')
     8754    cntr = NISTpk.twotheta_window_center_deg
     8755    Plot.set_title('Peak convolution functions @ 2theta={:.3f}'.format(cntr))
     8756    Plot.set_xlabel(r'$\Delta 2\theta, deg$',fontsize=14)
     8757    Plot.set_ylabel(r'Intensity (arbitrary)',fontsize=14)
     8758    refColors=['b','r','c','g','m','k']
     8759    ttmin = ttmax = 0
     8760    for i,conv in enumerate(NISTpk.convolvers):
     8761        f = NISTpk.convolver_funcs[conv]()
     8762        if f is None: continue
     8763        FFT = FP.best_irfft(f)
     8764        if f[1].real > 0: FFT = np.roll(FFT,int(len(FFT)/2.))
     8765        FFT /= FFT.max()
     8766        ttArr = np.linspace(-NISTpk.twotheta_window_fullwidth_deg/2,
     8767                             NISTpk.twotheta_window_fullwidth_deg/2,len(FFT))
     8768        ttmin = min(ttmin,ttArr[np.argmax(FFT>.005)])
     8769        ttmax = max(ttmax,ttArr[::-1][np.argmax(FFT[::-1]>.005)])
     8770        color = refColors[i%len(refColors)]
     8771        Plot.plot(ttArr,FFT,color,label=conv[5:])
     8772    legend = Plot.legend(loc='best')
     8773    for line in legend.get_lines():
     8774        line.set_picker(4)
     8775    Page.toolbar.push_current()
     8776    Plot.set_xlim((ttmin,ttmax))
     8777    Page.toolbar.push_current()
     8778    Page.toolbar.draw()
     8779    Page.canvas.draw()
  • trunk/GSASIIpwdGUI.py

    r3570 r3571  
    16071607        '''
    16081608        pth = G2G.GetExportPath(G2frame)
    1609         dlg = wx.FileDialog(G2frame, 'Choose GSAS-II instrument parameters file', pth, '',
     1609        dlg = wx.FileDialog(G2frame, 'Set name to save GSAS-II instrument parameters file', pth, '',
    16101610            'instrument parameter files (*.instprm)|*.instprm',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
    16111611        try:
  • trunk/docs/source/GSASIIGUI.rst

    r3000 r3571  
    2828.. automodule:: GSASIIexprGUI
    2929    :members:
     30
     31.. automodule:: GSASIIfpaGUI
     32    :members:
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