Changeset 2187


Ignore:
Timestamp:
Mar 31, 2016 3:17:43 PM (7 years ago)
Author:
vondreele
Message:

Modify the Cite please banners to add small angle & DIFFaX references
remov
e 'axial' from DIFFaX choices (for now) as it leads to a streak calculation not supported in GSAS-II
replace pylab stuff with use of PlotXYZ which has been improved
fix character Greek 'mu' in Layers GUI
new GSAS-II function for calculating selected area diffraction (still testing)

Location:
trunk
Files:
6 edited

Legend:

Unmodified
Added
Removed

  • trunk/GSASIIctrls.py

    r2151 r2187  
    30853085
    30863086Please cite as:
    3087 B.H. Toby & R.B. Von Dreele, J. Appl. Cryst. 46, 544-549 (2013) '''
     3087B.H. Toby & R.B. Von Dreele, J. Appl. Cryst. 46, 544-549 (2013)
     3088For small angle use cite:
     3089R.B. Von Dreele, J. Appl. Cryst. 47, 1748-9 (2014)
     3090For DIFFaX use cite:
     3091M.M.J. Treacy, J.M. Newsam & M.W. Deem,
     3092       Proc. Roy. Soc. Lond. A 433, 499-520 (1991)
     3093'''
    30883094
    30893095        info.WebSite = ("https://subversion.xray.aps.anl.gov/trac/pyGSAS","GSAS-II home page")

  • trunk/GSASIIgrid.py

    r2183 r2187  
    621621            return '0\n0\n4\n1\n%d\n%d\n16\n1\n%d\n0\nend\n'%    \
    622622                (self.planeChoice.index(self.plane)+1,self.lmaxChoice.index(self.lmax)+1,   \
    623                 self.multChoice.index(self.mult)+1),self.plane,self.lmax,       \
     623                self.multChoice.index(self.mult)+1),self.plane,self.lmax,self.mult,       \
    624624                self.Parm,self.parmRange,self.parmStep
    625625

  • trunk/GSASIIphsGUI.py

    r2184 r2187  
    24022402       
    24032403        laueChoice = ['-1','2/m(ab)','2/m(c)','mmm','-3','-3m','4/m','4/mmm',
    2404             '6/m','6/mmm','axial','unknown']
     2404            '6/m','6/mmm','unknown']
    24052405        colLabels = ['Name','Type','x','y','z','frac','Uiso']
    24062406        transLabels = ['Prob','Dx','Dy','Dz','refine','plot']
    … …  
    24282428        def OnSadpPlot(event):
    24292429            sadpPlot.SetValue(False)
    2430             import pylab as pl
    24312430            labels = Layers['Sadp']['Plane']
    24322431            lmax = float(Layers['Sadp']['Lmax'])
    2433             pl.imshow(Layers['Sadp']['Img'],aspect='auto',extent=[-lmax,lmax,-lmax,lmax])
    2434             pl.ylabel(labels[-1])
    2435             pl.xlabel(labels[:-1])
    2436             pl.title(Layers['Sadp']['Plane'])
    2437             pl.show()
     2432            XY = 2*lmax*np.mgrid[0:256:256j,0:256:256j]/256.-lmax
     2433            G2plt.PlotXYZ(G2frame,XY,Layers['Sadp']['Img'].T,labelX=labels[:-1],
     2434                labelY=labels[-1],newPlot=False,Title=Layers['Sadp']['Plane'])
    24382435           
    24392436        def CellSizer():
    … …  
    25292526            widthSizer = wx.BoxSizer(wx.HORIZONTAL)
    25302527            for i in range(2):
    2531                 widthSizer.Add(wx.StaticText(layerData,label=' layer width(%s) (<= 1\xb5m): '%(Labels[i])),0,WACV)
     2528                widthSizer.Add(wx.StaticText(layerData,label=u' layer width(%s) (<= 1\xb5m): '%(Labels[i])),0,WACV)
    25322529                widthVal = wx.TextCtrl(layerData,value='%.3f'%(widths[i]),style=wx.TE_PROCESS_ENTER)
    25332530                widthVal.Bind(wx.EVT_TEXT_ENTER,OnWidthChange)       
    … …  
    29282925        dlg = G2gd.DIFFaXcontrols(G2frame,ctrls)
    29292926        if dlg.ShowModal() == wx.ID_OK:
    2930             ctrls,plane,lmax,x,x,x = dlg.GetSelection()
     2927            ctrls,plane,lmax,mult,x,x,x = dlg.GetSelection()
    29312928            data['Layers']['Sadp'] = {}
    29322929            data['Layers']['Sadp']['Plane'] = plane
    29332930            data['Layers']['Sadp']['Lmax'] = lmax
     2931            data['Layers']['Sadp']['Mult'] = mult
    29342932        else:
    29352933            return
    … …  
    29692967        else:   #selected area
    29702968            G2pwd.StackSim(data['Layers'],ctrls)
    2971 #            if GSASIIpath.GetConfigValue('debug'):
    2972 #                G2pwd.CalcStackingSADP(data['Layers'])
     2969#            G2pwd.CalcStackingSADP(data['Layers'])
    29732970        wx.CallAfter(UpdateLayerData)
    29742971       
    … …  
    29792976        dlg = G2gd.DIFFaXcontrols(G2frame,ctrls,Parms)
    29802977        if dlg.ShowModal() == wx.ID_OK:
    2981             ctrls,plane,lmax,parm,parmRange,parmStep = dlg.GetSelection()
     2978            ctrls,plane,lmax,mult,parm,parmRange,parmStep = dlg.GetSelection()
    29822979            data['Layers']['Sadp'] = {}
    29832980            data['Layers']['Sadp']['Plane'] = plane
    29842981            data['Layers']['Sadp']['Lmax'] = lmax
     2982            data['Layers']['Sadp']['Mult'] = mult
    29852983            data['Layers']['Multi'] = [parm,parmRange,parmStep]
    29862984        else:

  • trunk/GSASIIplot.py

    r2183 r2187  
    23972397    '''simple contour plot of xyz data, used for diagnostic purposes
    23982398    '''
     2399    def OnKeyPress(event):
     2400        if event.key == 'u':
     2401            G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
     2402        elif event.key == 'd':
     2403            G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
     2404        elif event.key == 'o':
     2405            G2frame.Cmax = 1.0
     2406           
     2407        elif event.key == 'i':
     2408            choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
     2409               'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
     2410               'mitchell','sinc','lanczos']
     2411            dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
     2412            if dlg.ShowModal() == wx.ID_OK:
     2413                sel = dlg.GetSelection()
     2414                G2frame.Interpolate = choice[sel]
     2415            else:
     2416                G2frame.Interpolate = 'nearest'
     2417            dlg.Destroy()
     2418           
     2419        elif event.key == 's':
     2420            choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
     2421            choice.sort()
     2422            dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
     2423            if dlg.ShowModal() == wx.ID_OK:
     2424                sel = dlg.GetSelection()
     2425                G2frame.ContourColor = choice[sel]
     2426            else:
     2427                G2frame.ContourColor = 'Paired'
     2428            dlg.Destroy()
     2429        wx.CallAfter(PlotXYZ,G2frame,XY,Z,labelX,labelY,False,Title)
     2430   
    23992431    def OnMotion(event):
    24002432        xpos = event.xdata
    2401         if xpos:                                        #avoid out of frame mouse position
     2433        if Xmin<xpos<Xmax:                                        #avoid out of frame mouse position
    24022434            ypos = event.ydata
    2403             Page.canvas.SetCursor(wx.CROSS_CURSOR)
    2404             ix = int(Nxy[0]*(xpos-Xmin)+0.5)
    2405             iy = int(Nxy[1]*(ypos-Ymin)+0.5)
    2406             try:
    2407                 G2frame.G2plotNB.status.SetStatusText('%s =%9.3f %s =%9.3f val =%9.3f'% \
    2408                     (labelX,xpos,labelY,ypos,Z[ix,iy]),1)                   
    2409             except TypeError:
    2410                 G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1)
    2411 
     2435            if Ymin<ypos<Ymax:
     2436                Xwd = Xmax-Xmin
     2437                Ywd = Ymax-Ymin
     2438                Page.canvas.SetCursor(wx.CROSS_CURSOR)
     2439                ix = int(Nxy[0]*(xpos-Xmin)/Xwd)
     2440                iy = int(Nxy[1]*(ypos-Ymin)/Ywd)
     2441                try:
     2442                    G2frame.G2plotNB.status.SetStatusText('%s =%9.3f %s =%9.3f val =%9.3f'% \
     2443                        (labelX,xpos,labelY,ypos,Z[ix,iy]),1)                   
     2444                except TypeError:
     2445                    G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1)
     2446                   
    24122447    try:
    24132448        plotNum = G2frame.G2plotNB.plotList.index(Title)
    … …  
    24242459        Page = G2frame.G2plotNB.nb.GetPage(plotNum)
    24252460        Page.canvas.mpl_connect('motion_notify_event', OnMotion)
     2461        Page.canvas.mpl_connect('key_press_event', OnKeyPress)
    24262462   
    2427     Page.Choice = None
     2463    Page.Choice = (' key press','d: lower contour max','u: raise contour max','o: reset contour max',
     2464        'i: interpolation method','s: color scheme')
    24282465    Page.SetFocus()
    24292466    G2frame.G2plotNB.status.DestroyChildren()
    24302467    Nxy = Z.shape
     2468    Zmax = np.max(Z)
    24312469    Xmin = np.min(XY[0])
    24322470    Xmax = np.max(XY[0])
    … …  
    24422480    else:
    24432481        Plot.set_ylabel(r'Y',fontsize=14)
    2444     Img = Plot.imshow(Z.T,cmap='Paired',interpolation='nearest',origin='lower', \
    2445         aspect='auto',extent=[Xmin,Xmax,Ymin,Ymax])
     2482    acolor = mpl.cm.get_cmap(G2frame.ContourColor)
     2483    Img = Plot.imshow(Z.T,cmap=acolor,interpolation=G2frame.Interpolate,origin='lower', \
     2484        aspect='auto',extent=[Xmin,Xmax,Ymin,Ymax],vmin=0,vmax=Zmax*G2frame.Cmax)
    24462485    Page.figure.colorbar(Img)
    24472486    if not newPlot:

  • trunk/GSASIIpwd.py

    r2184 r2187  
    2222import scipy as sp
    2323import numpy.linalg as nl
     24import random as rand
    2425from numpy.fft import ifft, fft, fftshift
    2526import scipy.interpolate as si
    … …  
    3637import GSASIImath as G2mth
    3738import pypowder as pyd
     39import pydiffax as pyx
    3840
    3941# trig functions in degrees
    … …  
    19121914        bakType,backDict,backVary = SetBackgroundParms(background)
    19131915        backDict['Lam1'] = G2mth.getWave(inst)
    1914     #    GSASIIpath.IPyBreak()
    19151916        profile[4][iBeg:iFin] = getBackground('',backDict,bakType,inst['Type'][0],profile[0][iBeg:iFin])[0]   
    19161917        profile[3][iBeg:iFin] = Xpat[2]*scale+profile[4][iBeg:iFin]
    … …  
    19361937def CalcStackingSADP(Layers):
    19371938   
     1939    rand.seed()
     1940    ranSeed = rand.randint(1,2**16-1)
     1941# Scattering factors
     1942    import atmdata
    19381943    atTypes = Layers['AtInfo'].keys()
    1939     Adat = []
     1944    aTypes = []
     1945    for atype in atTypes:
     1946        aTypes.append('%4s'%(atype.ljust(4)))
     1947    SFdat = []
    19401948    for atType in atTypes:
    19411949        if atType == 'H':
    … …  
    19431951        else:
    19441952            blen = Layers['AtInfo'][atType]['Isotopes']['Nat. Abund.']['SL'][0]
    1945         Adat.append([[Adat['fa'][i],Adat['fb'][i]] for i in range(4)]+[Adat['fc'],])
    1946     Adat = np.array(Adat).flatten()
     1953        Adat = atmdata.XrayFF[atType]
     1954        SF = np.zeros(9)
     1955        SF[:8:2] = Adat['fa']
     1956        SF[1:8:2] = Adat['fb']
     1957        SF[8] = Adat['fc']
     1958        SFdat.append(SF)
     1959    SFdat = np.array(SFdat)
     1960    pyx.pyloadscf(len(atTypes),aTypes,SFdat.T)
     1961# Controls
     1962    try:   
     1963        laueId = ['-1','2/m(ab)','2/m(c)','mmm','-3','-3m','4/m','4/mmm',
     1964            '6/m','6/mmm'].index(Layers['Laue'])+1
     1965    except ValueError:
     1966        laueId = -1
     1967    planeId = ['h0l','0kl','hhl','h-hl'].index(Layers['Sadp']['Plane'])+1
     1968    lmax = int(Layers['Sadp']['Lmax'])
     1969    mult = int(Layers['Sadp']['Mult'])
     1970# Sequences
     1971    StkType = ['recursive','explicit'].index(Layers['Stacking'][0])
     1972    try:
     1973        StkParm = ['infinite','random','list'].index(Layers['Stacking'][1])
     1974    except ValueError:
     1975        StkParm = -1
     1976    if StkParm == 2:    #list
     1977        StkSeq = [int(val) for val in Layers['Stacking'][2].split()]
     1978        Nstk = len(StkSeq)
     1979    else:
     1980        Nstk = 1
     1981        StkSeq = [0,]
     1982    if StkParm == -1:
     1983        StkParm = int(Layers['Stacking'][1])
     1984    Wdth = Layers['Width'][0]
     1985    controls = [laueId,planeId,lmax,mult,StkType,StkParm,ranSeed]
     1986    LaueSym = Layers['Laue'].ljust(12)
     1987    pyx.pygetclay(controls,LaueSym,Wdth,Nstk,StkSeq)
     1988   
     1989    Cell = Layers['Cell'][1:4]+Layers['Cell'][6:7]
     1990# atoms in layers
    19471991    AtomXOU = []
    19481992    AtomTp = []
    1949     AtomNL = []
    19501993    LayerSymm = []
    19511994    LayerNum = []
    19521995    layerNames = []
    1953     Natm = 1
     1996    Natm = 0
    19541997    Nuniq = 0
    19551998    for layer in Layers['Layers']:
    … …  
    19602003            continue
    19612004        else:
    1962             LayerNum.append(il)
     2005            LayerNum.append(il+1)
    19632006            Nuniq += 1
    19642007        if '-1' in layer['Symm']:
    … …  
    19662009        else:
    19672010            LayerSymm.append(0)
    1968         AtomNL.append(Natm)
    19692011        for ia,atom in enumerate(layer['Atoms']):
    19702012            [name,atype,x,y,z,frac,Uiso] = atom
    19712013            Natm += 1
    1972             AtomTp.append(atype)
    1973             AtomXOU.append([x,y,z,frac,Uiso*78.9568])
     2014            AtomTp.append('%4s'%(atype.ljust(4)))
     2015            Ta = atTypes.index(atype)+1
     2016            AtomXOU.append([float(Nuniq),float(ia+1),float(Ta),x,y,z,frac,Uiso*78.9568])
     2017    AtomXOU = np.array(AtomXOU)
     2018    Nlayers = len(layerNames)
     2019    pyx.pycellayer(Cell,Natm,AtomTp,AtomXOU.T,Nuniq,LayerSymm,Nlayers,LayerNum)
     2020# Transitions
    19742021    TransX = []
    19752022    TransP = []
    … …  
    19772024        TransP.append([trans[0] for trans in Ytrans])   #get just the numbers
    19782025        TransX.append([trans[1:4] for trans in Ytrans])   #get just the numbers
    1979     TransP = np.array(Trans,dtype='float')
    1980     TransX = np.array(Trans,dtype='float')
    1981     Nlayers = np.sqrt(TransP.shape[0])
    1982     Cell = Layers['Cell'][1:4]+Layers['Cell'][6:7]
    1983        
    1984     laueId = ['-1','2/m(ab)','2/m(c)','mmm','-3','-3m','4/m','4/mmm',
    1985         '6/m','6/mmm','axial','unknown'].index(Layers['Laue'])
    1986     planeId = ['h0l','0kl','hhl','h-hl'],index(Layers['Sadp']['Plane'])+1
    1987     lmax = float(Layers['Sadp']['Lmax'])
    1988     controls = [laueId,planeId,lmax,Nuniq,]
    1989        
    1990     Sadp = np.array(256**2)   
    1991     Sadp = pygetsadp(controls,len(AtTypes),AtTypes,Adat,Cell,Natm,AtomTp,AtomXOU,Nlayers,TransP,TransX,stackseq,Sadp)
    1992    
     2026    TransP = np.array(TransP,dtype='float')
     2027    TransX = np.array(TransX,dtype='float')
     2028    pyx.pygettrans(Nlayers,TransP,TransX)
     2029# result as Sadp
     2030    mirror = laueId in [2,3,4,7,8,9,10]
     2031    Nspec = 20001       
     2032    spec = np.zeros(Nspec,dtype='double')   
     2033    time0 = time.time()
     2034    hkLim,Incr = pyx.pygetsadp(controls,Nspec,spec)
     2035#    GSASIIpath.IPyBreak()
     2036    Sapd = np.zeros((256,256))
     2037    maxInt = np.max(spec[1:])
     2038    Scale = mult*32767./maxInt
     2039    iB = 0
     2040    for i in range(hkLim):
     2041        iF = iB+128
     2042        p1 = 128+int(i*Incr)
     2043        Sapd[:128,p1] = spec[iB:iF]
     2044        Sapd[128:,p1] = spec[iF:iB:-1]
     2045        if mirror:
     2046            p2 = 128-int(i*Incr)
     2047            Sapd[:128,p2] = spec[iB:iF]
     2048            Sapd[128:,p2] = spec[iF:iB:-1]
     2049        iB += 128
     2050    Sapd *= Scale
     2051    Sapd = np.where(Sapd<32767.,Sapd,32767.)
     2052    Layers['Sadp']['Img'] = Sapd
     2053    print 'GETSAD time = %.2fs'%(time.time()-time0)
    19932054   
    19942055#testing data

  • trunk/makeBat.py

    r2133 r2187  
    2020@echo                   for small angle use also cite:
    2121@echo      R.B. Von Dreele, J. Appl. Cryst. 47, 1784-9 (2014)
     22@echo                   for DIFFaX use also cite:
     23@echo      M.M.J. Treacy, J.M. Newsam and M.W. Deem,
     24@echo                   Proc. Roy. Soc. Lond. 433A, 499-520 (1991)
    2225@echo ========================================================================
    2326@
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