Changeset 4499

Timestamp:

Jun 19, 2020 4:19:13 PM (3 years ago)

Author:

toby

Message:

Add sphere of atoms arround view point; show distances to peaks and atoms around view point

Location:

trunk

Files:

• GSASIIctrlGUI.py (modified) (3 diffs)
• GSASIIphsGUI.py (modified) (14 diffs)
• GSASIIplot.py (modified) (3 diffs)

trunk/GSASIIctrlGUI.py

@@ -1057 +1057 @@
         return  # Returning without calling event.Skip, which eats the keystroke
 
-def G2SliderWidget(parent,loc,key,label,xmin,xmax,iscale):
+def G2SliderWidget(parent,loc,key,label,xmin,xmax,iscale,
+                       onChange=None,onChangeArgs=[]):
     '''A customized combination of a wx.Slider and a validated 
     wx.TextCtrl (see :class:`ValidatedTxtCtrl`) that allows either
@@ -1081 +1082 @@
     :param float iscale: number to scale values to integers which is what the 
        Scale widget uses. If the xmin=1 and xmax=4 and iscale=1 then values
-       only the values 1,2,3 and 4 can be set with the slider. If 
+       only the values 1,2,3 and 4 can be set with the slider.
+
+    :param callable onChange: function to call when value is changed.
+       Default is None where nothing will be called. 
        
+    :param list onChangeArgs: arguments to be passed to onChange function 
+       when called.
     :returns: returns a wx.BoxSizer containing the widgets
     '''
@@ -1089 +1095 @@
         loc[key] = vScale.GetValue()/float(iscale)
         wx.TextCtrl.SetValue(vEntry,str(loc[key])) # will not trigger onValSet
+        if onChange: onChange(*onChangeArgs)
     def onValSet(*args,**kwargs):
         vScale.SetValue(int(0.5+iscale*loc[key]))        
+        if onChange: onChange(*onChangeArgs)
     loc[key] = min(xmax,max(xmin,loc[key]))
     hSizer = wx.BoxSizer(wx.HORIZONTAL)

trunk/GSASIIphsGUI.py

@@ -233 +233 @@
             cx,ct,cs = self.Drawing['atomPtrs'][:3]
             for Id in self.indx:
-                atom = self.Drawing['Atoms'][Id]
-                self.centers.append(atom[cx:cx+3])
-                atoms.append('%s(%s)'%(atom[ct-1],atom[cs-1]))
+                if Id < len(self.Drawing['Atoms']):
+                    atom = self.Drawing['Atoms'][Id]
+                    self.centers.append(atom[cx:cx+3])
+                    atoms.append('%s(%s)'%(atom[ct-1],atom[cs-1]))
+                else:
+                    self.centers.append(list(self.Drawing['viewPoint'][0]))
+                    atoms.append('View point')
             topSizer.Add(wx.ComboBox(self.panel,choices=atoms,value=atoms[0],
                 style=wx.CB_READONLY|wx.CB_DROPDOWN),0,WACV)
@@ -1095 +1099 @@
 #### Phase editing routines
 ################################################################################
-def getAtomSelections(AtmTbl,cn=0,action='action'):
+def getAtomSelections(AtmTbl,cn=0,action='action',includeView=False):
     '''get selected atoms from table or ask user if none are selected
     
-        param: AtmTbl list atom or draw atom table
-        param: int cn atom name position
-        action: str description
-        returns: list indx selected atoms fr tom indices in table
+        :param list AtmTbl: atom or draw atom table
+        :param int cn: atom name position
+        :param str action: description for prompt, when needed
+        :param bool includeView: if True, the viewpoint is included 
+          as an option in the selection dialog
+        :returns: indx (list) selected atoms from indices in table. 
+          If includeView is True, indx can contain index n (where there 
+          are n atoms in table). This is indicates the viewpoint. 
     '''
     indx = AtmTbl.GetSelectedRows()
@@ -1117 +1125 @@
         choices.append(val)
     if not choices: return
+    if includeView:
+        choices.append('View point')
     dlg = G2G.G2MultiChoiceDialog(AtmTbl.GetTopLevelParent(),
         'Select atoms','Select atoms for '+action,choices)
@@ -1469 +1479 @@
             'peakMoveView':True,'PeakDistRadius':0.0,'showVoids':False,'showMap':False,
             'atomsExpandRadius':5.,'atomsDistRadius':2.5,'Voids':[],
+            'VPPeakDistRad':0.,'VPatomsExpandRad':0.,'VPatomsDistRad':0.,
         }
     for key in defaultDrawing:
@@ -7855 +7866 @@
     def AddSphere(event):
         cx,ct,cs,ci = getAtomPtrs(data,draw=True)      
-        indx = getAtomSelections(drawAtoms,ct-1)
+        indx = getAtomSelections(drawAtoms,ct-1,'as center of sphere addition',
+                                     includeView=True)
         if not indx: return
         generalData = data['General']
@@ -8344 +8356 @@
     def OnDrawDistVP(event):
         # distance to view point
-        indx = getAtomSelections(drawAtoms,'distance calc')
+        indx = getAtomSelections(drawAtoms,action='distance calc')
         if not indx: return
         generalData = data['General']
@@ -8505 +8517 @@
                 G2plt.PlotStructure(G2frame,data)
                 
-            def OnContourLevel(event):
-                drawingData['contourLevel'] = contourLevel.GetValue()/100.
-                contourLevelTxt.SetLabel(' Rho maximum: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
-                G2plt.PlotStructure(G2frame,data)
-
-            def OnMapSize(event):
-                drawingData['mapSize'] = mapSize.GetValue()/10.
-                mapSizeTxt.SetLabel(' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
-                G2plt.PlotStructure(G2frame,data)
-
-            
             slopSizer = wx.BoxSizer(wx.HORIZONTAL)
             slideSizer = wx.FlexGridSizer(0,2,0,0)
@@ -8584 +8585 @@
                 magMult.Bind(wx.EVT_SLIDER, OnMagMult)
                 slideSizer.Add(magMult,1,wx.EXPAND|wx.RIGHT)
-            
-            if generalData['Map']['rhoMax'] and not generalData.get('4DmapData',{}):
-                contourLevelTxt = wx.StaticText(drawOptions,-1,' Rho maximum: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
-                slideSizer.Add(contourLevelTxt,0,WACV)
-                contourLevel = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['contourLevel']))
-                contourLevel.SetRange(1,100)
-                contourLevel.Bind(wx.EVT_SLIDER, OnContourLevel)
-                slideSizer.Add(contourLevel,1,wx.EXPAND|wx.RIGHT)
-                mapSizeTxt = wx.StaticText(drawOptions,-1,' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
-                slideSizer.Add(mapSizeTxt,0,WACV)
-                mapSize = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(10*drawingData['mapSize']))
-                mapSize.SetRange(1,100)
-                mapSize.Bind(wx.EVT_SLIDER, OnMapSize)
-                slideSizer.Add(mapSize,1,wx.EXPAND|wx.RIGHT)
-            
+                        
             slopSizer.Add(slideSizer,1,wx.EXPAND|wx.RIGHT)
             slopSizer.Add((10,5),0)
@@ -8631 +8618 @@
             def OnSymFade(event):
                 drawingData['SymFade'] = symFade.GetValue()
-                G2plt.PlotStructure(G2frame,data)
-                
-            def OnShowMap(event):
-                drawingData['showMap'] = showMap.GetValue()
                 G2plt.PlotStructure(G2frame,data)
                 
@@ -8749 +8732 @@
             lineSizer.Add(viewPoint,0,WACV)
             showSizer.Add(lineSizer)
+            mapSizer = DistanceSettingSizer(drawingData,
+                        'VPPeakDistRad','VPatomsExpandRad','VPatomsDistRad')
+            showSizer.Add(mapSizer,0,wx.LEFT,20)
             showSizer.Add((0,5),0)
             
@@ -8775 +8761 @@
             symFade.SetValue(drawingData['SymFade'])
             line3Sizer.Add(symFade,0,WACV)
-            showMap = wx.CheckBox(drawOptions,-1,label=' Show density map?')
-            showMap.Bind(wx.EVT_CHECKBOX, OnShowMap)
-            showMap.SetValue(drawingData['showMap'])
-            line3Sizer.Add(showMap,0,WACV)
             showVoids = wx.CheckBox(drawOptions,-1,label=' Show void map?')
             showVoids.Bind(wx.EVT_CHECKBOX, OnShowVoids)
@@ -8882 +8864 @@
             planeSizer.Add(planeSizer2)
             return planeSizer
+        
+        def DistanceSettingSizer(var,key1,key2,key3):
+            '''Sizer to get distances to show'''
+            def onLeave(*args,**kwargs):
+                print('On leave')
+                G2plt.PlotStructure(G2frame,data)
+                #wx.CallAfter(G2plt.PlotStructure,G2frame,data)
+            for key in key1,key2,key3:
+                if key not in var: var[key] = 0
+            mapSizer = wx.FlexGridSizer(0,3,5,5)
+            mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,'Show Map points within:'),0,WACV)
+            mapSizer.Add(G2G.ValidatedTxtCtrl(drawOptions,var,key1,
+                xmin=0.0,xmax=5.0,nDig=(10,1),size=(50,-1),
+                OnLeave=onLeave))
+            mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,u"\u212B"),0,WACV)
+            mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,'Show atoms within:'),0,WACV)
+            mapSizer.Add(G2G.ValidatedTxtCtrl(drawOptions,var,key2,
+                xmin=0.0,xmax=15.0,nDig=(10,1),size=(50,-1),
+                OnLeave=onLeave))
+            mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,u"\u212B"),0,WACV)
+            mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,'Label distance to atoms within:'),0,WACV)
+            mapSizer.Add(G2G.ValidatedTxtCtrl(drawOptions,var,key3,
+                xmin=0.0,xmax=15.0,nDig=(10,1),size=(50,-1),
+                OnLeave=onLeave))
+            mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,u"\u212B"),0,WACV)
+            return mapSizer
             
 
@@ -8905 +8913 @@
         G2G.HorizontalLine(mainSizer,drawOptions)
         mainSizer.Add(PlaneSizer(),0,)
-        G2G.HorizontalLine(mainSizer,drawOptions)
-        mainSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,'On map peak selection:'),0,WACV)
-        mainSizer.Add(G2G.G2CheckBox(drawOptions,'Move view point',drawingData,'peakMoveView'))
-        mapSizer = wx.FlexGridSizer(0,3,5,5)
-        mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,'Show Map points within:'),0,WACV)
-        mapSizer.Add(G2G.ValidatedTxtCtrl(drawOptions,drawingData,'PeakDistRadius',
-            xmin=0.0,xmax=5.0,nDig=(10,1),size=(50,-1)))
-        mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,u"\u212B"),0,WACV)
-        mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,'Show atoms within:'),0,WACV)
-        mapSizer.Add(G2G.ValidatedTxtCtrl(drawOptions,drawingData,'atomsExpandRadius',
-            xmin=0.0,xmax=15.0,nDig=(10,1),size=(50,-1)))
-        mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,u"\u212B"),0,WACV)
-        mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,'Label distance to atoms within:'),0,WACV)
-        mapSizer.Add(G2G.ValidatedTxtCtrl(drawOptions,drawingData,'atomsDistRadius',
-            xmin=0.0,xmax=15.0,nDig=(10,1),size=(50,-1)))
-        mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,u"\u212B"),0,WACV)
-        mainSizer.Add(mapSizer)
+        if generalData['Map']['rhoMax'] and not generalData.get('4DmapData',{}):
+            G2G.HorizontalLine(mainSizer,drawOptions)
+            def OnShowMap(event):
+                drawingData['showMap'] = showMap.GetValue()
+                G2plt.PlotStructure(G2frame,data)
+            showMap = wx.CheckBox(drawOptions,-1,label=' Show density map?')
+            showMap.Bind(wx.EVT_CHECKBOX, OnShowMap)
+            showMap.SetValue(drawingData['showMap'])
+            mainSizer.Add(showMap,0,WACV)
+            mainSizer.Add(G2G.G2SliderWidget(drawOptions,
+                        drawingData,'contourLevel',
+                        'Max relative to rho max ({:.2f}): '
+                                        .format(generalData['Map']['rhoMax']),
+                        0.01,1.0,100,
+                        onChange=G2plt.PlotStructure,onChangeArgs=(G2frame,data)
+                        ))
+            mainSizer.Add(G2G.G2SliderWidget(drawOptions,
+                        drawingData,'mapSize',
+                        'Range of map surrounding view point: ',0.1,10.,10.,
+                        onChange=G2plt.PlotStructure,onChangeArgs=(G2frame,data)
+                        ))
+            mapSizer = wx.BoxSizer(wx.HORIZONTAL)
+            mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,'On map peak selection:  '),0,WACV)
+            mapSizer.Add(G2G.G2CheckBox(drawOptions,'Move view point',drawingData,'peakMoveView'))
+            mainSizer.Add(mapSizer)
+            mapSizer = DistanceSettingSizer(drawingData,
+                        'PeakDistRadius','atomsExpandRadius','atomsDistRadius')
+            mainSizer.Add(mapSizer,0,wx.LEFT,20)
+
         SetPhaseWindow(drawOptions,mainSizer)
 
@@ -12178 +12198 @@
             FillRigidBodyGrid()
         elif text == 'Map peaks':
+            #print('reimport GSASIIplot')
+            #import imp
+            #imp.reload(G2plt)
             G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.MapPeaksMenu)
             G2plt.PlotStructure(G2frame,data,firstCall=True)

trunk/GSASIIplot.py

@@ -8911 +8911 @@
         GL.glShadeModel(GL.GL_SMOOTH)
                             
+    def distances2Peaks(x,y,z,PeakDistRadius,mapPeaks,peakMax,radius,Amat,matRot):
+        ''' show distances to other peaks within PeakDistRadius A
+        '''
+        XYZ = mapPeaks.T[1:4].T
+        Dx = XYZ-(x,y,z)
+        dist = np.sqrt(np.sum(np.inner(Dx,Amat)**2,axis=1))
+        for i in ma.nonzero(ma.masked_greater(dist,PeakDistRadius))[0]:
+            lbl = '{:.2f}'.format(dist[i])
+            RenderLines(x,y,z,[Dx[i]],Gr)
+            lx,ly,lz = (x,y,z)+(Dx[i]/2)
+            RenderLabel(lx,ly,lz,lbl,radius,wxGreen,matRot)
+            [mag,x1,y1,z1] = mapPeaks[:,:4][i]
+            lbl = '{:.2f}'.format(mag)
+            if mag > 0.:
+                RenderMapPeak(x1,y1,z1,Wt,mag/peakMax)
+                RenderLabel(x1,y1,z1,lbl,radius,wx.Colour(Wt),matRot)
+            else:
+                RenderMapPeak(x1,y1,z1,Or,-2*mag/peakMax)
+                RenderLabel(x1,y1,z1,lbl,radius,wx.Colour(Or),matRot)
+
+    def distances2Atoms(x,y,z,atomsExpandRadius,atomsdistRadius,Amat,matRot):
+        # find and display atoms within atomsExpandRadius A
+        vdwScale = drawingData['vdwScale']
+        ballScale = drawingData['ballScale']
+        xyzA = np.array((x,y,z))
+        cx,ct,cs,ci = G2phG.getAtomPtrs(data)      
+        cellArray = G2lat.CellBlock(1)
+        radDict = dict(zip(*G2phG.getAtomRadii(data)))
+        Names = []
+        Atoms = []
+        Radii = []
+        Color = []
+        for atomB in data['Atoms']:
+            atNum = generalData['AtomTypes'].index(atomB[ct])
+            if 'vdW' in atomB[cs]:
+                radius = vdwScale*vdWRadii[atNum]
+            elif 'H' == atomB[ct]:
+                radius = ballScale*drawingData['sizeH']
+            else:
+                radius = ballScale*BondRadii[atNum]
+            xyzB = np.array(atomB[cx:cx+3])
+            color = np.array(generalData['Color'][generalData['AtomTypes'].index(atomB[ct])])/255.
+            result = G2spc.GenAtom(xyzB,SGData,False,6*[0.],True)
+            for item in result:
+                for xyz in cellArray+np.array(item[0]):
+                    dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2))
+                    if 0 < dist <= max(atomsdistRadius,atomsExpandRadius):
+                        ax,ay,az = xyz
+                        RenderSphere(ax,ay,az,radius,color)
+                        Atoms.append(xyz)
+                        Radii.append(radDict[atomB[ct]])
+                        Names.append(atomB[0])
+                        Color.append(color)
+                    if dist < atomsdistRadius:
+                        RenderLines(x,y,z,[xyz-xyzA],Gr)
+                        lx,ly,lz = (xyzA+xyz)/2
+                        lbl = '{:.2f}'.format(dist)
+                        RenderLabel(lx,ly,lz,lbl,radius,wxGreen,matRot)
+                        ax,ay,az = xyz
+                        RenderLabel(ax,ay,az,'  '+atomB[0],radius,wxGreen,matRot)
+        # find bonds
+        bondData = [[] for i in range(len(Atoms))]
+        Atoms = np.array(Atoms)
+        Radii = np.array(Radii)
+        for i,atom in enumerate(Atoms):
+            Dx = Atoms-atom
+            sumR = Radii + Radii[i]
+            dist = ma.masked_less(np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0)),0.5)
+            IndB = ma.nonzero(ma.masked_greater(dist-data['Drawing']['radiusFactor']*sumR,0.))                 #get indices of bonded atoms
+            for j in IndB[0]:
+                bondData[i].append(Dx[j]*Radii[i]/sumR[j])
+                bondData[j].append(-Dx[j]*Radii[j]/sumR[j])
+        # draw bonds
+        bondR = drawingData['bondRadius']
+        for i,xyz in enumerate(Atoms):
+            ax,ay,az = xyz
+            RenderBonds(ax,ay,az,bondData[i],bondR,Color[i])
+                
     def Draw(caller='',Fade=[]):
         vdWRadii = generalData['vdWRadii']
@@ -9114 +9192 @@
         if not FourD and len(rhoXYZ) and drawingData['showMap']:       #no green dot map for 4D - it's wrong!
             RenderMap(rho,rhoXYZ,indx,Rok)
-        if len(Ind) == 1 and pageName == 'Map peaks':
+        if (pageName == 'Draw Atoms' or pageName == 'Draw Options') and (
+                drawingData['VPPeakDistRad'] + drawingData['VPatomsExpandRad']
+                 + drawingData['VPatomsDistRad']
+                ) > 0:
+            PeakDistRadius = drawingData['VPPeakDistRad']
+            atomsExpandRadius = drawingData['VPatomsExpandRad']
+            atomsdistRadius = drawingData['VPatomsDistRad']
+            x,y,z = drawingData['viewPoint'][0]
+            # distances to other peaks within PeakDistRadius A
+            if PeakDistRadius > 0:
+                distances2Peaks(x,y,z,PeakDistRadius,mapPeaks,radius,peakMax,Amat,matRot)
+            # find and display atoms within atomsExpandRadius A
+            if atomsExpandRadius > 0:
+                distances2Atoms(x,y,z,atomsExpandRadius,atomsdistRadius,Amat,matRot)
+        elif len(Ind) == 1 and (pageName == 'Map peaks' or
+                                    pageName == 'Draw Options'):
             # one peak has been selected, show as selected by draw options
             PeakDistRadius = drawingData['PeakDistRadius']
@@ -9122 +9215 @@
             mag,x,y,z = mapPeaks[:,:4][ind]
             RenderMapPeak(x,y,z,Gr,1.0)
-            # distances to other peaks within PeakDistRadius A
             if PeakDistRadius > 0:
-                XYZ = mapPeaks.T[1:4].T
-                Dx = XYZ-(x,y,z)
-                dist = np.sqrt(np.sum(np.inner(Dx,Amat)**2,axis=1))
-                for i in ma.nonzero(ma.masked_greater(dist,PeakDistRadius))[0]:
-                    lbl = '{:.2f}'.format(dist[i])
-                    RenderLines(x,y,z,[Dx[i]],Gr)
-                    lx,ly,lz = (x,y,z)+(Dx[i]/2)
-                    RenderLabel(lx,ly,lz,lbl,radius,wxGreen,matRot)
-                    [mag,x1,y1,z1] = mapPeaks[:,:4][i]
-                    if mag > 0.:
-                        RenderMapPeak(x1,y1,z1,Wt,mag/peakMax)
-                    else:
-                        RenderMapPeak(x1,y1,z1,Or,-2*mag/peakMax)
+                distances2Peaks(x,y,z,PeakDistRadius,mapPeaks,radius,peakMax,Amat,matRot)
             # find and display atoms within atomsExpandRadius A
             if atomsExpandRadius > 0:
-                xyzA = np.array((x,y,z))
-                cx,ct,cs,ci = G2phG.getAtomPtrs(data)      
-                cellArray = G2lat.CellBlock(1)
-                radDict = dict(zip(*G2phG.getAtomRadii(data)))
-                Names = []
-                Atoms = []
-                Radii = []
-                Color = []
-                for atomB in data['Atoms']:
-                    xyzB = np.array(atomB[cx:cx+3])
-                    color = np.array(generalData['Color'][generalData['AtomTypes'].index(atomB[ct])])/255.
-                    result = G2spc.GenAtom(xyzB,SGData,False,6*[0.],True)
-                    for item in result:
-                        for xyz in cellArray+np.array(item[0]):
-                            dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2))
-                            if 0 < dist <= max(atomsdistRadius,atomsExpandRadius):
-                                ax,ay,az = xyz
-                                RenderSphere(ax,ay,az,radius,color)
-                                Atoms.append(xyz)
-                                Radii.append(radDict[atomB[ct]])
-                                Names.append(atomB[0])
-                                Color.append(color)
-                            if dist < atomsdistRadius:
-                                RenderLines(x,y,z,[xyz-xyzA],Gr)
-                                lx,ly,lz = (xyzA+xyz)/2
-                                lbl = '{:.2f}'.format(dist)
-                                RenderLabel(lx,ly,lz,lbl,radius,wxGreen,matRot)
-                                ax,ay,az = xyz
-                                RenderLabel(ax,ay,az,'  '+atomB[0],radius,wxGreen,matRot)
-                # find bonds
-                bondData = [[] for i in range(len(Atoms))]
-                Atoms = np.array(Atoms)
-                Radii = np.array(Radii)
-                for i,atom in enumerate(Atoms):
-                    Dx = Atoms-atom
-                    sumR = Radii + Radii[i]
-                    dist = ma.masked_less(np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0)),0.5)
-                    IndB = ma.nonzero(ma.masked_greater(dist-data['Drawing']['radiusFactor']*sumR,0.))                 #get indices of bonded atoms
-                    for j in IndB[0]:
-                        bondData[i].append(Dx[j]*Radii[i]/sumR[j])
-                        bondData[j].append(-Dx[j]*Radii[j]/sumR[j])
-                # draw bonds
-                bondR = drawingData['bondRadius']
-                for i,xyz in enumerate(Atoms):
-                    ax,ay,az = xyz
-                    RenderBonds(ax,ay,az,bondData[i],bondR,Color[i])
+                distances2Atoms(x,y,z,atomsExpandRadius,atomsdistRadius,Amat,matRot)
         elif len(mapPeaks):
             XYZ = mapPeaks.T[1:4].T