Changeset 3571

Timestamp:

Aug 26, 2018 7:43:05 PM (5 years ago)

Author:

toby

Message:

Add FPA peak fitting

Location:

trunk

Files:

• GSASIIctrlGUI.py (modified) (3 diffs)
• GSASIIdataGUI.py (modified) (6 diffs)
• GSASIIfpaGUI.py (added)
• GSASIIplot.py (modified) (2 diffs)
• GSASIIpwdGUI.py (modified) (1 diff)
• NIST_profile (added)
• NIST_profile/__init__.py (added)
• NIST_profile/profile_functions_class.py (added)
• docs/source/GSASIIGUI.rst (modified) (1 diff)

trunk/GSASIIctrlGUI.py

@@ -3020 +3020 @@
         
 ################################################################################
-def GetImportFile(G2frame, message, defaultDir="", defaultFile="", style=wx.FD_OPEN,
-                  *args, **kwargs):
+def GetImportFile(G2frame, message, defaultDir="", defaultFile="",
+                      style=wx.FD_OPEN, parent=None,
+                      *args, **kwargs):
     '''Uses a customized dialog that gets files from the appropriate import directory. 
     Arguments are used the same as in :func:`wx.FileDialog`. Selection of
@@ -3035 +3036 @@
     :returns: a list of files or an empty list
     '''
-    dlg = wx.FileDialog(G2frame, message, defaultDir, defaultFile, *args,
+    if not parent: parent = G2frame
+    dlg = wx.FileDialog(parent, message, defaultDir, defaultFile, *args,
                         style=style, **kwargs)
     pth = GetImportPath(G2frame)
@@ -3965 +3967 @@
 #####  Get an output file or directory
 ################################################################################           
-def askSaveFile(G2frame,defnam,extension,longFormatName):
+def askSaveFile(G2frame,defnam,extension,longFormatName,parent=None):
     '''Ask the user to supply a file name
+
+    :param wx.Frame G2frame: The main GSAS-II window
+    :param str defnam: a default file name
+    :param str extension: the default file extension beginning with a '.'
+    :param str longFormatName: a description of the type of file
+    :param wx.Frame parent: the parent window for the dialog. Defaults
+      to G2frame.
 
     :returns: a file name (str) or None if Cancel is pressed
     '''
 
+    if not parent: parent = G2frame
     pth = GetExportPath(G2frame)
     dlg = wx.FileDialog(
-        G2frame, 'Input name for file to write', pth, defnam,
+        parent, 'Input name for file to write', pth, defnam,
         longFormatName+' (*'+extension+')|*'+extension,
         wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)

trunk/GSASIIdataGUI.py

@@ -70 +70 @@
 import GSASIIpwd as G2pwd
 import GSASIIstrMain as G2stMn
+import defaultIparms as dI
+import GSASIIfpaGUI as G2fpa
 
 # trig functions in degrees
@@ -1200 +1202 @@
         item = submenu.Append(wx.ID_ANY,'Simulate a dataset','Create a powder data set entry that will be simulated')
         self.Bind(wx.EVT_MENU, self.OnDummyPowder, id=item.GetId())
+        item = submenu.Append(wx.ID_ANY,'Fit instr. profile from fundamental parms...','')
+        self.Bind(wx.EVT_MENU, self.OnPowderFPA, id=item.GetId())
         
     def OpenPowderInstprm(self,instfile):
@@ -1386 +1390 @@
             sind = lambda x: math.sin(x*math.pi/180.)
             tand = lambda x: math.tan(x*math.pi/180.)
-            import defaultIparms as dI
             while True: # loop until we get a choice
                 choices = []
@@ -1949 +1952 @@
         self.EnableRefineCommand()
         return # success
-        
+
+    def AddSimulatedPowder(self,ttArr,intArr,HistName,Lam1,Lam2):
+        '''Create a PDWR entry for a computed powder pattern
+        '''
+        # get a list of existing histograms
+        PWDRlist = []
+        if self.GPXtree.GetCount():
+            item, cookie = self.GPXtree.GetFirstChild(self.root)
+            while item:
+                name = self.GPXtree.GetItemText(item)
+                if name.startswith('PWDR ') and name not in PWDRlist:
+                    PWDRlist.append(name)
+                item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
+        # Initialize a base class reader
+        rd = G2obj.ImportPowderData(
+            extensionlist=tuple(),
+            strictExtension=False,
+            formatName = 'FPA Simulated dataset',
+            longFormatName = 'Fundamental Parameters simulated pattern')
+        rd.powderentry[0] = '' # no filename
+        # #self.powderentry[1] = pos # bank offset (N/A here)
+        rd.powderentry[2] = 1 # only one bank
+        rd.comments.append('This is a powder pattern simulated with Fundamental Parameters')
+        self.CheckNotebook()
+        #self.zipfile = None
+        # get instrument parameters for it
+        rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False],
+            'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]})
+        Iparm1, Iparm2 = G2fil.ReadPowderInstprm(dI.defaultIparms[0],1,1,rd)
+        rd.idstring = ' CW'
+        simType = 'CW'
+        # set wavelength
+        if Lam2:
+            Iparm1['Lam1'][0] = Lam1
+            Iparm1['Lam2'][0] = Lam2
+            Iparm1['Lam1'][1] = Lam1
+            Iparm1['Lam2'][1] = Lam2
+        else:
+            Iparm1['Lam'] = Iparm1['Lam1']
+            del Iparm1['Lam1'],Iparm1['Lam2']
+            Iparm1['Lam'][0] = Lam1
+            Iparm1['Lam'][1] = Lam1
+
+        rd.powderdata = [
+            np.array(ttArr), # x-axis values
+            np.array(intArr), # powder pattern intensities
+            np.ones_like(ttArr), # 1/sig(intensity)^2 values (weights)
+            np.zeros_like(intArr), # calc. intensities (zero)
+            np.zeros_like(ttArr), # calc. background (zero)
+            np.zeros_like(ttArr), # obs-calc profiles
+            ]
+        Tmin = rd.powderdata[0][0]
+        Tmax = rd.powderdata[0][-1]
+        # data are read, now store them in the tree
+        HistName = 'PWDR '+HistName
+        HistName = G2obj.MakeUniqueLabel(HistName,PWDRlist)  # make new histogram names unique
+        Id = self.GPXtree.AppendItem(parent=self.root,text=HistName)
+        Ymin = np.min(rd.powderdata[1])
+        Ymax = np.max(rd.powderdata[1])
+        valuesdict = {
+            'wtFactor':1.0,
+            'Dummy':True,'simType':simType,
+            'ranId':ran.randint(0,sys.maxsize),
+            'Offset':[0.0,0.0],'delOffset':0.02*Ymax,'refOffset':-.1*Ymax,'refDelt':0.1*Ymax,
+            'Yminmax':[Ymin,Ymax]
+            }
+        self.GPXtree.SetItemPyData(Id,[valuesdict,rd.powderdata])
+        self.GPXtree.SetItemPyData(
+            self.GPXtree.AppendItem(Id,text='Comments'),
+            rd.comments)
+        self.GPXtree.SetItemPyData(
+            self.GPXtree.AppendItem(Id,text='Limits'),
+            [(Tmin,Tmax),[Tmin,Tmax]])
+        self.PatternId = GetGPXtreeItemId(self,Id,'Limits')
+        self.GPXtree.SetItemPyData(
+            self.GPXtree.AppendItem(Id,text='Background'),
+            [['chebyschev',True,3,1.0,0.0,0.0],
+             {'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
+        self.GPXtree.SetItemPyData(
+            self.GPXtree.AppendItem(Id,text='Instrument Parameters'),
+            [Iparm1,Iparm2])
+        self.GPXtree.SetItemPyData(
+            self.GPXtree.AppendItem(Id,text='Sample Parameters'),
+            rd.Sample)
+        self.GPXtree.SetItemPyData(
+            self.GPXtree.AppendItem(Id,text='Peak List')
+            ,{'peaks':[],'sigDict':{}})
+        self.GPXtree.SetItemPyData(
+            self.GPXtree.AppendItem(Id,text='Index Peak List'),
+            [[],[]])
+        self.GPXtree.SetItemPyData(
+            self.GPXtree.AppendItem(Id,text='Unit Cells List'),
+            [])
+        self.GPXtree.SetItemPyData(
+            self.GPXtree.AppendItem(Id,text='Reflection Lists'),
+            {})
+        self.GPXtree.Expand(Id)
+        self.GPXtree.SelectItem(Id)
+        print(u'Added simulation powder data {}'.format(HistName))
+        return Id
+    
     def OnPreferences(self,event):
         'Edit the GSAS-II configuration variables'
@@ -2905 +3008 @@
         G2IO.testColumnMetadata(self)
                 
+    def OnPowderFPA(self,event):
+        'Perform FPA simulation/peak fitting'
+        G2fpa.GetFPAInput(self)
+        
     def OnReadPowderPeaks(self,event):
         'Bound to menu Data/Read Powder Peaks'
@@ -3716 +3823 @@
                 self.SetTitleByGPX()
                 self.EnableRefineCommand()
+                self.init_vars()
         finally:
             dlg.Destroy()

trunk/GSASIIplot.py

@@ -48 +48 @@
 :func:`PlotRigidBody`         show rigid body structures as balls & sticks
 :func:`PlotLayers`            show layer structures as balls & sticks
+:func:`PlotFPAconvolutors`    plots the convolutors from Fundamental Parameters
 ============================  ===========================================================================
 
@@ -8704 +8705 @@
     Page.canvas.SetCurrent(Page.context)
     wx.CallAfter(Draw,'main')
+
+def PlotFPAconvolutors(G2frame,NISTpk):
+    '''Plot the convolutions used for the current peak computed with
+    :func:`GSASIIfpaGUI.doFPAcalc`
+    '''
+    import NIST_profile as FP
+    def clearHighlight(event):
+        l,lm,lms = Page.timer.lineinfo
+        l.set_marker(lm)
+        l.set_markersize(lms)
+        Page.canvas.draw()
+        Page.timer = None
+        
+    def onPick(event):
+        '''When a line in the legend is selected, find the matching line
+        in the plot and then highlight it by adding/enlarging markers.
+        Set up a timer to make a reset after 2.5 seconds
+        '''
+        plot = event.artist.get_figure().get_axes()[0]
+        if event.artist not in plot.get_legend().get_lines():  # is this an item in the legend?
+            return
+        if Page.timer: # clear previous highlight
+            Page.timer.Stop()
+            clearHighlight(None)
+            return   # if this is removed, the selected item is automatically highlighted
+        lbl = event.artist.get_label()
+        for l in plot.get_lines():
+            if lbl == l.get_label():
+                Page.timer = wx.Timer()
+                Page.timer.Bind(wx.EVT_TIMER, clearHighlight)
+                Page.timer.lineinfo = (l,l.get_marker(),l.get_markersize())
+                # highlight the selected item
+                if l.get_marker() == 'None':
+                    l.set_marker('o')
+                else:
+                    l.set_markersize(2*l.get_markersize())
+                Page.canvas.draw()
+                Page.timer.Start(5000,oneShot=True)
+                break
+        else:
+            print('Warning: artist matching ',lbl,' not found')
+                    
+    new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('FPA convolutors','mpl')
+    if new:
+        Page.canvas.mpl_connect('pick_event',onPick)
+    Page.timer = None
+    Page.SetToolTipString('')
+    cntr = NISTpk.twotheta_window_center_deg
+    Plot.set_title('Peak convolution functions @ 2theta={:.3f}'.format(cntr))
+    Plot.set_xlabel(r'$\Delta 2\theta, deg$',fontsize=14)
+    Plot.set_ylabel(r'Intensity (arbitrary)',fontsize=14)
+    refColors=['b','r','c','g','m','k']
+    ttmin = ttmax = 0
+    for i,conv in enumerate(NISTpk.convolvers):
+        f = NISTpk.convolver_funcs[conv]()
+        if f is None: continue
+        FFT = FP.best_irfft(f)
+        if f[1].real > 0: FFT = np.roll(FFT,int(len(FFT)/2.))
+        FFT /= FFT.max()
+        ttArr = np.linspace(-NISTpk.twotheta_window_fullwidth_deg/2,
+                             NISTpk.twotheta_window_fullwidth_deg/2,len(FFT))
+        ttmin = min(ttmin,ttArr[np.argmax(FFT>.005)])
+        ttmax = max(ttmax,ttArr[::-1][np.argmax(FFT[::-1]>.005)])
+        color = refColors[i%len(refColors)]
+        Plot.plot(ttArr,FFT,color,label=conv[5:])
+    legend = Plot.legend(loc='best')
+    for line in legend.get_lines():
+        line.set_picker(4)
+    Page.toolbar.push_current()
+    Plot.set_xlim((ttmin,ttmax))
+    Page.toolbar.push_current()
+    Page.toolbar.draw()
+    Page.canvas.draw()

trunk/GSASIIpwdGUI.py

@@ -1607 +1607 @@
         '''
         pth = G2G.GetExportPath(G2frame)
-        dlg = wx.FileDialog(G2frame, 'Choose GSAS-II instrument parameters file', pth, '', 
+        dlg = wx.FileDialog(G2frame, 'Set name to save GSAS-II instrument parameters file', pth, '', 
             'instrument parameter files (*.instprm)|*.instprm',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
         try:

trunk/docs/source/GSASIIGUI.rst

@@ -28 +28 @@
 .. automodule:: GSASIIexprGUI
     :members: 
+
+.. automodule:: GSASIIfpaGUI
+    :members: