Changeset 3995

Timestamp:

May 24, 2019 2:11:36 PM (4 years ago)

Author:

vondreele

Message:

Add save of indexed peaks to csv file
fix neutron bugs in MEM Dysnomia code

Location:

trunk

Files:

• GSASIIdataGUI.py (modified) (1 diff)
• GSASIIphsGUI.py (modified) (4 diffs)
• GSASIIpwd.py (modified) (4 diffs)
• GSASIIpwdGUI.py (modified) (2 diffs)

trunk/GSASIIdataGUI.py

@@ -5273 +5273 @@
         
         # PDR / Index Peak List
-        G2G.Define_wxId('wxID_INDXRELOAD',)
+        G2G.Define_wxId('wxID_INDXRELOAD','wxID_INDEXSAVE',)
         self.IndPeaksMenu = wx.MenuBar()
         self.PrefillDataMenu(self.IndPeaksMenu)
         self.IndPeaksEdit = wx.Menu(title='')
         self.IndPeaksMenu.Append(menu=self.IndPeaksEdit,title='Operations')
-        self.IndPeaksEdit.Append(G2G.wxID_INDXRELOAD,'Load/Reload','Load/Reload index peaks from peak list') 
+        self.IndPeaksEdit.Append(G2G.wxID_INDXRELOAD,'Load/Reload','Load/Reload index peaks from peak list')
+        self.IndPeaksEdit.Append(G2G.wxID_INDEXSAVE,'Save','Save index peaks to CSV file')
         self.PostfillDataMenu()
         

trunk/GSASIIphsGUI.py

@@ -4213 +4213 @@
     def OnRunDysnomia(event):
         
+        path2GSAS2 = os.path.dirname(os.path.abspath(os.path.expanduser(__file__)))
+        DYSNOMIA = os.path.join(path2GSAS2,'Dysnomia','Dysnomia64.exe')
+        
+        if not os.path.exists(DYSNOMIA):
+            wx.MessageBox(''' Dysnomia is not installed. Please download it from 
+    https://jp-minerals.org/dysnomia/en/ 
+    and install it at.'''+DYSNOMIA,
+                caption='Dysnomia not installed',style=wx.ICON_ERROR)
+            return
+
         generalData = data['General']
         Map = generalData['Map']
@@ -4232 +4242 @@
             for el in generalData['Isotope']:
                 isotope = generalData['Isotope'][el]
+                if el not in generalData['Isotopes']:
+                    continue
                 if generalData['Isotopes'][el][isotope]['SL'][0] < 0.:
                     MEMtype = 1
         prfName = str(G2pwd.makePRFfile(data,MEMtype))
-        if not G2pwd.makeMEMfile(data,reflData,MEMtype):
+        if not G2pwd.makeMEMfile(data,reflData,MEMtype,DYSNOMIA):
             SpGrp = generalData['SGData']['SpGrp']
             wx.MessageBox('Non standard space group '+SpGrp+' not permitted in Dysnomia','Dysnomia Error',
@@ -4241 +4253 @@
             return
 
-        path2GSAS2 = os.path.dirname(os.path.abspath(os.path.expanduser(__file__)))
-        DYSNOMIA = os.path.join(path2GSAS2,'Dysnomia','Dysnomia64.exe')
-        
-        if not os.path.exists(DYSNOMIA):
-            wx.MessageBox(''' Dysnomia is not installed. Please download it from 
-    https://jp-minerals.org/dysnomia/en/ 
-    and install it at.'''+DYSNOMIA,
-                caption='Dysnomia not installed',style=wx.ICON_ERROR)
-            return
 
         wx.MessageBox(''' For use of Dysnomia, please cite:
@@ -4258 +4261 @@
         
         print('Run '+DYSNOMIA)        
-        subp.run([DYSNOMIA,prfName],startupinfo=subp.CREATE_NEW_PROCESS_GROUP)
+        subp.call([DYSNOMIA,prfName],startupinfo=subp.CREATE_NEW_PROCESS_GROUP)
         
         if G2pwd.MEMupdateReflData(prfName,reflData):

trunk/GSASIIpwd.py

@@ -2864 +2864 @@
     return prfName
 
-def makeMEMfile(data,reflData,MEMtype):
+def makeMEMfile(data,reflData,MEMtype,DYSNOMIA):
     ''' make Dysnomia .mem file of reflection data, etc.
     ;param dict data: GSAS-II phase data
@@ -2870 +2870 @@
     :param int MEMtype: 1 for neutron data with negative scattering lengths
                         0 otherwise
+    :param str:DYSNOMIA path to dysnomia.exe
     '''
     
@@ -2912 +2913 @@
         mem.write('%10.3f%10.3f 0.001\n'%(sumpos,sumneg))
     else:
-        mem.write('%10.3 0.001\n'%sumpos)
+        mem.write('%10.3f 0.001\n'%sumpos)
         
     refs = []
@@ -2962 +2963 @@
         Fobs = np.sqrt(ref[6])
         mem.write('%5d%5d%5d%10.3f%10.3f%10.3f\n'%(h,k,l,Fobs*npcosd(ref[7]),Fobs*npsind(ref[7]),max(0.01*Fobs,0.1)))
+    while True:
+        if not len(refs2[-1]):
+            del refs2[-1]
+        else:
+            break
     mem.write('%5d\n'%len(refs2))
-    for ref2 in refs2:
-        if not len(ref2):
-            break
+    for iref2,ref2 in enumerate(refs2):
+        mem.write('#%5d\n'%iref2)
         mem.write('%5d\n'%len(ref2))
         Gsum = 0.

trunk/GSASIIpwdGUI.py

@@ -2902 +2902 @@
         UpdateIndexPeaksGrid(G2frame,data)
         
+    def OnSave(event):
+        pth = G2G.GetExportPath(G2frame)
+        dlg = wx.FileDialog(G2frame, 'Choose Index peaks csv file', pth, '', 
+            'indexing peaks file (*.csv)|*.csv',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
+        try:
+            if dlg.ShowModal() == wx.ID_OK:
+                filename = dlg.GetPath()
+                filename = os.path.splitext(filename)[0]+'.csv'
+                File = open(filename,'w')
+                names = 'h,k,l,position,intensity,d-Obs,d-calc\n'
+                File.write(names)
+                fmt = '%d,%d,%d,%.4f,%.1f,%.5f,%.5f\n'
+                for refl in data[0]:
+                    if refl[3]:
+                        File.write(fmt%(refl[4],refl[5],refl[6],refl[0],refl[1],refl[7],refl[8]))
+                File.close()
+        finally:
+            dlg.Destroy()
+        
     def KeyEditPickGrid(event):
         colList = G2frame.indxPeaks.GetSelectedCols()
@@ -2926 +2945 @@
         G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.IndPeaksMenu)
         G2frame.Bind(wx.EVT_MENU, OnReload, id=G2G.wxID_INDXRELOAD)
+        G2frame.Bind(wx.EVT_MENU, OnSave, id=G2G.wxID_INDEXSAVE)
     G2frame.dataWindow.IndexPeaks.Enable(False)
     G2frame.IndexPeaksTable = []