Changeset 2563

Timestamp:

Dec 7, 2016 11:53:18 AM (7 years ago)

Author:

vondreele

Message:

Speed up image integration on Mac by reducing ProgressBar? calls from 3*nBlk*nBlk+3 to Nblk+3
Allow PDF setup to include chemical formula from tif macrofile
fix contour bug for G(R), etc.
fix copy error for masks

Location:

trunk

Files:

• GSASII.py (modified) (5 diffs)
• GSASIIElem.py (modified) (2 diffs)
• GSASIIIO.py (modified) (1 diff)
• GSASIIimage.py (modified) (3 diffs)
• GSASIIimgGUI.py (modified) (1 diff)
• GSASIIplot.py (modified) (3 diffs)
• GSASIIpwdGUI.py (modified) (2 diffs)

trunk/GSASII.py

@@ -73 +73 @@
 GSASIIpath.SetVersionNumber("$Revision$")
 import GSASIIIO as G2IO
+import GSASIIElem as G2elem
 import GSASIIgrid as G2gd
 import GSASIIctrls as G2G
@@ -3425 +3426 @@
         
     def OnMakePDFs(self,event):
-        '''Calculates PDFs
-        '''
+        '''Sets up PDF data structure filled with defaults; if found chemical formula is inserted
+        so a default PDF can be made.
+        '''
+        sind = lambda x: math.sin(x*math.pi/180.)
+        tth2q = lambda t,w:4.0*math.pi*sind(t/2.0)/w
+        tof2q = lambda t,C:2.0*math.pi*C/t
         TextList = []
-        PDFlist = []
+        ElLists = []
+        Qlimits = []
         Names = []
         if self.PatternTree.GetCount():
@@ -3437 +3443 @@
                 if 'PWDR' in name:
                     TextList.append(name)
+                    Comments = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,id,'Comments'))
+                    Parms = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,id,'Instrument Parameters'))[0]
+                    fullLimits = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,id,'Limits'))[0]
+                    if 'C' in Parms['Type'][0]:
+                        wave = G2mth.getWave(Parms)
+                        qMax = tth2q(fullLimits[1],wave)
+                    else:   #'T'of
+                        qMax = tof2q(fullLimits[0],Parms['difC'][1])
+                    Qlimits.append([0.9*qMax,qMax])
+                    ElList = {}
+                    for item in Comments:           #grab chemical formula from Comments
+                        if 'formula' in item:
+                            formula = item.split('=')[1].split()
+                            elems = formula[::2]
+                            nums = formula[1::2]
+                            formula = zip(elems,nums)
+                            for [elem,num] in formula:
+                                ElData = G2elem.GetElInfo(elem,Parms)
+                                ElData['FormulaNo'] = float(num)
+                                ElList[elem] = ElData
+                    ElLists.append(ElList)
                 id, cookie = self.PatternTree.GetNextChild(self.root, cookie)
             if len(TextList) < 1:
@@ -3444 +3471 @@
             try:
                 if dlg.ShowModal() == wx.ID_OK:
-                    PDFlist = [TextList[i] for i in dlg.GetSelections()]
-                    for item in PDFlist:
+                    for i in dlg.GetSelections():
+                        item = TextList[i]
+                        ElList = ElLists[i]
                         PWDRname = item[4:]
                         Id = self.PatternTree.AppendItem(parent=self.root,text='PDF '+PWDRname)
@@ -3452 +3480 @@
                             'Sample Bkg.':{'Name':'','Mult':-1.0,'Add':0.0},
                             'Container':{'Name':'','Mult':-1.0,'Add':0.0},
-                            'Container Bkg.':{'Name':'','Mult':-1.0,'Add':0.0},'ElList':{},
+                            'Container Bkg.':{'Name':'','Mult':-1.0,'Add':0.0},'ElList':ElList,
                             'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0,
-                            'DetType':'Image plate','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':[0,100],
-                            'Lorch':True,'BackRatio':0.0,'Rmax':100.}
+                            'DetType':'Image plate','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':Qlimits[i],
+                            'Lorch':True,'BackRatio':0.0,'Rmax':100.,'noRing':True}
                         self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='PDF Controls'),Data)
                         self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='I(Q)'+PWDRname),[])        

trunk/GSASIIElem.py

@@ -21 +21 @@
 import numpy as np
 import atmdata
+import GSASIImath as G2mth
 
 getElSym = lambda sym: sym.split('+')[0].split('-')[0].capitalize()
@@ -216 +217 @@
     AtomInfo['Lande g'] = 2.0
     return AtomInfo
+    
+def GetElInfo(El,inst):
+    ElemSym = El.strip().capitalize()
+    if 'X' in inst['Type'][0]: 
+        keV = 12.397639/G2mth.getWave(inst)               
+        FpMu = FPcalc(GetXsectionCoeff(ElemSym), keV)
+        ElData = GetFormFactorCoeff(ElemSym)[0]
+        ElData['FormulaNo'] = 0.0
+        ElData.update(GetAtomInfo(ElemSym))
+        ElData.update(dict(zip(['fp','fpp','mu'],FpMu)))
+        ElData.update(GetFFC5(El))
+    else: #'N'eutron
+        ElData = {}
+        ElData.update(GetAtomInfo(ElemSym))
+        ElData['FormulaNo'] = 0.0
+        ElData.update({'mu':0.0,'fp':0.0,'fpp':0.0})
+    return ElData
         
 def GetXsectionCoeff(El):

trunk/GSASIIIO.py

@@ -897 +897 @@
         Sample['Phi'] = data['GonioAngles'][2]
         Sample['Azimuth'] = (azm+dazm)%360.    #put here as bin center 
+        polariz = 0.99    #set default polarization for synchrotron radiation!
+        for item in Comments:
+            if 'polariz' in item:
+                try:
+                    polariz = float(item.split('=')[1])
+                except:
+                    polariz = 0.99
         if 'PWDR' in Aname:
-            parms = ['PXC',data['wavelength'],0.0,0.99,1.0,-0.10,0.4,0.30,1.0,0.0001,Azms[i]]    #set polarization for synchrotron radiation!
+            parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0001,Azms[i]]
         elif 'SASD' in Aname:
             Sample['Trans'] = data['SampleAbs'][0]

trunk/GSASIIimage.py

@@ -900 +900 @@
             TA,tam = Make2ThetaAzimuthMap(data,masks,(iBeg,iFin),(jBeg,jFin),times)           #2-theta & azimuth arrays & create position mask
             Nup += 1
-            if dlg:
-                pause = dlg.Update(Nup)
-                if not pause[0]: CancelPressed = True
+#            if dlg and jBlk == 0:                    #update progress bar on each row
+#                pause = dlg.Update(Nup)
+#                if not pause[0]: CancelPressed = True
             Block = image[iBeg:iFin,jBeg:jFin]
             t0 = time.time()
@@ -909 +909 @@
             times[2] += time.time()-t0
             Nup += 1
-            if dlg:
-                pause = dlg.Update(Nup)
-                if not pause[0]: CancelPressed = True
+#            if dlg and jBlk == 0:                    #update progress bar on each row
+#                pause = dlg.Update(Nup)
+#                if not pause[0]: CancelPressed = True
             tax = np.where(tax > LRazm[1],tax-360.,tax)                 #put azm inside limits if possible
             tax = np.where(tax < LRazm[0],tax+360.,tax)
@@ -932 +932 @@
             Nup += 1
             del tax; del tay; del taz; del tad; del tabs
-            if dlg:
+            if dlg and jBlk == 0:                    #update progress bar on each row
                 pause = dlg.Update(Nup)
                 if not pause[0]: CancelPressed = True

trunk/GSASIIimgGUI.py

@@ -1329 +1329 @@
                     Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,name)
                     MId = G2gd.GetPatternTreeItemId(G2frame,Id,'Masks')
-                    Mask = copy.deepcopy(G2frame.PatternTree.GetItemPyData(MId))
-                    Mask.update(Data)
+                    Mask = G2frame.PatternTree.GetItemPyData(MId)
+                    Mask.update(copy.deepcopy(Data))
                     Mask['Thresholds'][1][0] = Thresh[1][0]  #copy only lower threshold 
                     G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Masks'),Mask)

trunk/GSASIIplot.py

@@ -2357 +2357 @@
             if G2frame.Contour:
                 G2frame.SinglePlot = False
-                Pattern[0]['Offset'] = [0.,0.]
+                Page.Offset = [0.,0.]
         elif event.key == 's':
             if G2frame.Contour:
@@ -2453 +2453 @@
     PDFdata = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'PDF Controls'))
     numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
-    Xb = [0.,10.]
-    Yb = [0.,-40.*np.pi*numbDen]
     Ymax = 0.01
     lenX = 0
@@ -2488 +2486 @@
                 Plot.plot(X,Y,colors[N%6],picker=False)
             if type == 'G(R)':
+                Xb = [0.,10.]
+                Yb = [0.,-40.*np.pi*numbDen]
                 Plot.plot(Xb,Yb,color='k',dashes=(5,5))
             elif type == 'F(Q)':

trunk/GSASIIpwdGUI.py

@@ -4747 +4747 @@
     inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,powId, 'Instrument Parameters'))[0]
     if 'C' in inst['Type'][0]:
-        if 'Lam' in inst:
-            keV = 12.397639/inst['Lam'][1]
-        else:
-            keV = 12.397639/inst['Lam1'][0]
-        wave = 12.397639/keV
+        wave = G2mth.getWave(inst)
+        keV = 12.397639/wave
         qLimits = [tth2q(fullLimits[0],wave),tth2q(fullLimits[1],wave)]
         polariz = inst['Polariz.'][1]
@@ -5124 +5121 @@
             El = PE.Elem
             if El not in ElList and El != 'None':
-                ElemSym = El.strip().capitalize()
-                if 'X' in inst['Type'][0]:                
-                    FpMu = G2elem.FPcalc(G2elem.GetXsectionCoeff(ElemSym), keV)
-                    ElData = G2elem.GetFormFactorCoeff(ElemSym)[0]
-                    ElData['FormulaNo'] = 0.0
-                    ElData.update(G2elem.GetAtomInfo(ElemSym))
-                    ElData.update(dict(zip(['fp','fpp','mu'],FpMu)))
-                    ElData.update(G2elem.GetFFC5(El))
-                else: #'N'eutron
-                    ElData = {}
-                    ElData.update(G2elem.GetAtomInfo(ElemSym))
-                    ElData['FormulaNo'] = 0.0
-                    ElData.update({'mu':0.0,'fp':0.0,'fpp':0.0})
-                data['ElList'][El] = ElData
+                data['ElList'][El] = G2elem.GetElInfo(El)
             data['Form Vol'] = max(10.0,SumElementVolumes())
         PE.Destroy()