Changeset 526

Timestamp:

Apr 2, 2012 2:30:28 PM (11 years ago)

Author:

vondreele

Message:

make SetNewPhase? routine in GSASIIIO.py to initialize phase info
begin Fourier map search routine
fix atom plotting if no map

Location:

trunk

Files:

• GSASII.py (modified) (1 diff)
• GSASIIIO.py (modified) (4 diffs)
• GSASIIphsGUI.py (modified) (1 diff)
• GSASIIplot.py (modified) (3 diffs)
• GSASIIpwdGUI.py (modified) (2 diffs)
• binwin2.7/histogram2d.pyd (modified) (previous)
• binwin2.7/pack_f.pyd (modified) (previous)
• binwin2.7/polymask.pyd (modified) (previous)

trunk/GSASII.py

@@ -1064 +1064 @@
         sub = self.PatternTree.AppendItem(parent=sub,text=PhaseName)
         E,SGData = G2spc.SpcGroup('P 1')
-        self.PatternTree.SetItemPyData(sub, {
-            'General':{
-                'Name':PhaseName,
-                'Type':'nuclear',
-                'SGData':SGData,
-                'Cell':[False,10.,10.,10.,90.,90.,90,1000.],
-                'Pawley dmin':1.0,
-                'Data plot type':'Mustrain',
-                'SH Texture':{
-                    'Order':0,
-                    'Model':'cylindrical',
-                    'Sample omega':[False,0.0],
-                    'Sample chi':[False,0.0],
-                    'Sample phi':[False,0.0],
-                    'SH Coeff':[False,{}],
-                    'SHShow':False,
-                    'PFhkl':[0,0,1],
-                    'PFxyz':[0,0,1],
-                    'PlotType':'Pole figure'}},
-            'Atoms':[],
-            'Drawing':{},
-            'Histograms':{},
-            'Pawley ref':[],
-            'Models':{},
-            })
+        self.PatternTree.SetItemPyData(sub,G2IO.SetNewPhase(Name=PhaseName,SGData=SGData))
         
     def OnDeletePhase(self,event):

trunk/GSASIIIO.py

@@ -1035 +1035 @@
     print 'index peak list saved'
     
+def SetNewPhase(Name='New Phase',SGData=G2spc.SpcGroup('P 1')[1],cell=[1.0,1.0,1.0,90.,90,90.,1.]):
+    phaseData = {
+        'General':{
+            'Name':Name,
+            'Type':'nuclear',
+            'SGData':SGData,
+            'Cell':[False,]+cell,
+            'Pawley dmin':1.0,
+            'Data plot type':'Mustrain',
+            'SH Texture':{
+                'Order':0,
+                'Model':'cylindrical',
+                'Sample omega':[False,0.0],
+                'Sample chi':[False,0.0],
+                'Sample phi':[False,0.0],
+                'SH Coeff':[False,{}],
+                'SHShow':False,
+                'PFhkl':[0,0,1],
+                'PFxyz':[0,0,1],
+                'PlotType':'Pole figure'}},
+        'Atoms':[],
+        'Drawing':{},
+        'Histograms':{},
+        'Pawley ref':[],
+        'Models':{},
+        }
+    return phaseData
+    
 def ReadEXPPhase(G2frame,filename):
     shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
@@ -1150 +1178 @@
         textureData['SH Coeff'] = [False,shCoef]
         
-    Phase = {
-            'General':{
-                'Name':PhaseName,
-                'Type':Ptype,
-                'SGData':SGData,
-                'Cell':[False,]+abc+angles+[Volume,],
-                'Pawley dmin':1.0,
-                'SH Texture':textureData},
-            'Atoms':Atoms,
-            'Drawing':{},
-            'Histograms':{},
-            'Pawley ref':[],
-            'Models':{},
-            }
+    Phase = SetNewPhase(Name=PhaseName,SGData=SGData,cell=abc+angles+[Volume,])
+    general = Phase['General']
+    general['Type'] = Ptype
+    general['SH Texture'] = textureData
+    Phase['Atoms'] = Atoms
     return Phase
        
@@ -1241 +1260 @@
     else:
         PhaseName = 'None'
-    Phase['General'] = {'Name':PhaseName,'Type':'macromolecular','SGData':SGData,
-        'Cell':[False,]+cell+[Volume,]}
+    Phase = SetNewPhase(Name=PhaseName,SGData=SGData,cell=cell+[Volume,])
+    Phase['General']['Type'] = 'macromolecular'
     Phase['Atoms'] = Atoms
-    Phase['Drawing'] = {}
-    Phase['Histograms'] = {}
     
     return Phase
@@ -1277 +1294 @@
         self.strictExtension = strictExtension
         # define a default Phase structure
-        self.Phase = {}
-        for i in 'General', 'Atoms', 'Drawing', 'Histograms':
-            self.Phase[i] = {}
-        self.Phase['General']['Name'] = 'default'
-        self.Phase['General']['Type'] = 'nuclear'
-        self.Phase['General']['SGData'] = SGData
-        self.Phase['General']['Cell'] = [
-            False, # refinement flag
-            1.,1.,1.,    # a,b,c
-            90.,90.,90., # alpha, beta, gamma
-            1.           # volume
-            ]
+        self.Phase = SetNewPhase(Name='new phase',SGData=SGData)
         self.warnings = ''
         self.errors = ''

trunk/GSASIIphsGUI.py

@@ -3469 +3469 @@
         try:
             mapData = generalData['Map']
-            contLevel = drawingData['contourLevel']*mapData['rhoMax']
-            rho = ma.array(mapData['rho'],mask=(mapData['rho']<contLevel))
+            contLevel = mapData['cutOff']*mapData['rhoMax']/100.
+            rho = copy.copy(mapData['rho'])     #don't mess up original
         except KeyError:
             print '**** ERROR - Fourier map not defined'
             return
-        indx = np.array(ma.nonzero(rho)).T
-        steps = 1./np.array(rho.shape)
-        rhoXYZ = indx*steps
-        print rhoXYZ
+        peaks = []
+        while True:
+            rhoMask = ma.array(rho,mask=(mapData['rho']<contLevel))
+            indx = np.array(ma.nonzero(rhoMask)).T
+            rhoList = np.array([rho[i,j,k] for i,j,k in indx])
+            rhoMax = np.max(rhoList)
+            rMI = indx[np.argmax(rhoList)]
+            print rMI,rhoMax
+            break
+#            steps = 1./np.array(rho.shape)
+#            rhoXYZ = indx*steps
         print 'search Fourier map'
         

trunk/GSASIIplot.py

@@ -753 +753 @@
                 else:
                     Plot.plot(peak.T[1],pos,colors[pId%6]+'|',mew=1,ms=8,picker=3.,label=phase)
-            handles,legends = Plot.get_legend_handles_labels()  #got double entries in the legends for some reason
-            Plot.legend(handles[::2],legends[::2],title='Phases',loc='best')    #skip every other one
+            if len(Phases):
+                handles,legends = Plot.get_legend_handles_labels()  #got double entries in the legends for some reason
+                Plot.legend(handles[::2],legends[::2],title='Phases',loc='best')    #skip every other one
             
     if G2frame.Contour:
@@ -2731 +2732 @@
                             
     def Draw():
-        if 'Map' in generalData:
+        mapData = generalData['Map']
+        rhoXYZ = []
+        if len(mapData['rho']):
             VP = np.array(drawingData['viewPoint'][0])-np.array([.5,.5,.5])
-            mapData = generalData['Map']
             contLevel = drawingData['contourLevel']*mapData['rhoMax']
             if 'delt-F' in mapData['MapType']:
@@ -2739 +2741 @@
             else:
                 rho = ma.array(mapData['rho'],mask=(mapData['rho']<contLevel))
-            if rho.size > 0: 
-                steps = 1./np.array(rho.shape)
-                incre = np.where(VP>0,VP%steps,VP%steps-steps)
-                Vsteps = -np.array(VP/steps,dtype='i')
-                rho = np.roll(np.roll(np.roll(rho,Vsteps[0],axis=0),Vsteps[1],axis=1),Vsteps[2],axis=2)
-                indx = np.array(ma.nonzero(rho)).T
-                rhoXYZ = indx*steps+VP-incre
-                Nc = len(rhoXYZ)
-                rcube = 2000.*Vol/(ForthirdPI*Nc)
-                rmax = math.exp(math.log(rcube)/3.)**2
-                radius = min(drawingData['mapSize']**2,rmax)
-                view = np.array(drawingData['viewPoint'][0])
-                Rok = np.sum(np.inner(Amat,rhoXYZ-view).T**2,axis=1)>radius
-            else:
-                rhoXYZ = []
+            steps = 1./np.array(rho.shape)
+            incre = np.where(VP>0,VP%steps,VP%steps-steps)
+            Vsteps = -np.array(VP/steps,dtype='i')
+            rho = np.roll(np.roll(np.roll(rho,Vsteps[0],axis=0),Vsteps[1],axis=1),Vsteps[2],axis=2)
+            indx = np.array(ma.nonzero(rho)).T
+            rhoXYZ = indx*steps+VP-incre
+            Nc = len(rhoXYZ)
+            rcube = 2000.*Vol/(ForthirdPI*Nc)
+            rmax = math.exp(math.log(rcube)/3.)**2
+            radius = min(drawingData['mapSize']**2,rmax)
+            view = np.array(drawingData['viewPoint'][0])
+            Rok = np.sum(np.inner(Amat,rhoXYZ-view).T**2,axis=1)>radius
         Ind = GetSelectedAtoms()
         VS = np.array(Page.canvas.GetSize())

trunk/GSASIIpwdGUI.py

@@ -16 +16 @@
 import GSASIIpath
 import GSASIIpwd as G2pwd
+import GSASIIIO as G2IO
 import GSASIIlattice as G2lat
 import GSASIIspc as G2spc
@@ -1495 +1496 @@
                 E,SGData = G2spc.SpcGroup(spaceGroups[cell[0]])
                 G2frame.PatternTree.SetItemPyData(sub, \
-                    {'General':{'Name':PhaseName,'Type':'nuclear','SGData':SGData,
-                    'Cell':[False,]+cell[1:],
-                    'Pawley dmin':1.00},'Atoms':[],'Drawing':{},'Histograms':{}})
+                    G2IO.SetNewPhase(Name=PhaseName,SGData=SGData,cell=cell[1:]))
                 Status.SetStatusText('Change space group if needed')
         finally: