Changeset 1127

Timestamp:

Oct 29, 2013 11:42:23 AM (10 years ago)

Author:

toby

Message:

more export changes to catch up to data structure updates; update docs; change RF^{2 to use superscript since} 2 is not working -- at least on Mac

Location:

trunk

Files:

• GSASIIIO.py (modified) (1 diff)
• GSASIIgrid.py (modified) (1 diff)
• GSASIIobj.py (modified) (7 diffs)
• exports/G2export_CIF.py (modified) (4 diffs)
• exports/G2export_csv.py (modified) (2 diffs)
• exports/G2export_examples.py (modified) (2 diffs)

trunk/GSASIIIO.py

@@ -2034 +2034 @@
                             name += '-1'
                     self.Histograms[name] = {}
+                    # the main info goes into Data, but the 0th
+                    # element contains refinement results, carry
+                    # that over too now. 
                     self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
+                    self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
                     item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
                     while item2: 

trunk/GSASIIgrid.py

@@ -3253 +3253 @@
                 mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' For phase '+name+':'))
                 mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
-                    ' Unweighted phase residuals RF^2: %.3f%%, RF: %.3f%% on %d reflections  '% \
+                    u' Unweighted phase residuals RF\u00b2: %.3f%%, RF: %.3f%% on %d reflections  '% \
                     (data[0][pfx+'Rf^2'],data[0][pfx+'Rf'],data[0][value])))
     mainSizer.Add((5,5),)

trunk/GSASIIobj.py

@@ -353 +353 @@
 Reflection Lists              \           A dict with an entry for each phase in the
                                           histogram. The contents of each dict item
-                                          is a list of reflections as described in the
-                                          :ref:`Powder Reflections <PowderRefl_table>`
+                                          is a dict containing reflections, as described in
+                                          the :ref:`Powder Reflections <PowderRefl_table>`
                                           description.
 Instrument Parameters         \           A list containing two dicts where the possible
@@ -457 +457 @@
    single: Data object descriptions; Powder Reflections
    
-For every phase in a histogram, the ``Reflection Lists`` value is a list of
-reflections. The items in that list are documented below.
+For every phase in a histogram, the ``Reflection Lists`` value is a dict
+one element of which is `'RefList'`, which is a np.array containing
+reflections. The columns in that array are documented below.
 
 ==========  ====================================================
@@ -472 +473 @@
  9           :math:`F_{calc}^2`
  10          reflection phase, in degrees
- 11          the equivalent reflections as a (m x 3) 
-             np.array, where m is 0.5 * multiplicity. Note
-             that Freidel pairs, (-h,-k-,l), are not
-             included. 
- 12          phase shift for each of the equivalent
-             reflections as a length (m) array
- 13          intensity correction for reflection, this times
+ 11          intensity correction for reflection, this times
              :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc 
- 14          dict with the form factor (f or b) by atom type
-             symbol at the reflection position.
 ==========  ====================================================
 
@@ -490 +483 @@
 
 .. index::
-   single: Single Crytsal data object description
+   single: Single Crystal data object description
    single: Data object descriptions; Single crystal data
 
@@ -508 +501 @@
 ======================  ===============  ====================================================
 Data
-                                          A list of lists, where each inner item
-                                          is an individual reflection
+                                          A dict that contains the 
+                                          reflection table,
                                           as described in the
                                           :ref:`Single Crystal Reflections
@@ -549 +542 @@
    single: Data object descriptions; Single Crystal Reflections
    
-For every phase in a histogram, the ``Reflection Lists`` value is a list of
-reflections. The items in that list are documented below.
+For every simgle crystal a histogram, the ``'Data'`` item contains
+the structure factors as an np.array in item `'RefList'`.
+The columns in that array are documented below.
 
 ==========  ====================================================
@@ -564 +558 @@
  9           :math:`F_{calc}^2T`
  10          reflection phase, in degrees
- 11          the equivalent reflections as a (m x 3) 
-             np.array.
- 12          phase shift for each of the equivalent
-             reflections as a length (m) array
- 13          intensity correction for reflection, this times
+ 11          intensity correction for reflection, this times
              :math:`F_{obs}^2` or :math:`F_{calc}^2`
              gives Iobs or Icalc
-             (not used in single crystals?)
- 14          dict with the form factor (f or b) by atom type
-             symbol at the reflection position.
 ==========  ====================================================
 

trunk/exports/G2export_CIF.py

@@ -1156 +1156 @@
             'Write out the selected single crystal histogram info'
             histblk = self.Histograms[histlbl]
+
             #refprx = '_refln.' # mm
             refprx = '_refln_' # normal
@@ -1200 +1201 @@
                 dmin = min(dmin,ref[4])
                 WriteCIFitem(s)
-            WriteReflStat(refcount,hklmin,hklmax,dmin,dmax)
-            hId = histblk['hId']
-            pfx = '0:'+str(hId)+':'
-            WriteCIFitem('_reflns_wR_factor_obs    ','%.4f'%(histblk['wR']/100.))
-            WriteCIFitem('_reflns_R_F_factor_obs   ','%.4f'%(histblk[pfx+'Rf']/100.))
-            WriteCIFitem('_reflns_R_Fsqd_factor_obs','%.4f'%(histblk[pfx+'Rf^2']/100.))
+            if not self.quickmode: # statistics only in a full CIF
+                WriteReflStat(refcount,hklmin,hklmax,dmin,dmax)
+                hId = histblk[0]['hId']
+                pfx = '0:'+str(hId)+':'
+                WriteCIFitem('_reflns_wR_factor_obs    ','%.4f'%(histblk[0]['wR']/100.))
+                WriteCIFitem('_reflns_R_F_factor_obs   ','%.4f'%(histblk[0][pfx+'Rf']/100.))
+                WriteCIFitem('_reflns_R_Fsqd_factor_obs','%.4f'%(histblk[0][pfx+'Rf^2']/100.))
         def EditAuthor(event=None):
             'dialog to edit the CIF author info'
@@ -1565 +1567 @@
         self.quickmode = False
         phasenam = None # include all phases
-        if self.mode != "full" or len(self.powderDict) + len(self.xtalDict) == 0:
-            self.quickmode = True
-            oneblock = True
-            if len(self.Phases) == 0:
+        if self.mode == "simple" and self.currentExportType == 'phase':
+            if len(self.Phases) == 0: # this check is probably not needed
                 self.G2frame.ErrorDialog(
                     'No phase present',
                     'Cannot create a coordinates CIF with no phases')
                 return
-            elif len(self.Phases) > 1: # quick mode: get selected phase
+            self.quickmode = True
+            oneblock = True
+            if len(self.Phases) > 1: # quick mode: get selected phase
                 phasenam = self.phasenam[0]
-        # will this require a multiblock CIF?
+        elif self.mode == "simple": # powder/single xtal data export
+            self.quickmode = True
+            oneblock = True
+        # Project export: will this require a multiblock CIF?
         elif len(self.Phases) > 1:
             oneblock = False
@@ -1583 +1588 @@
             oneblock = True
 
-        # make sure needed infomation is present
+        # make sure required information is present
         # get CIF author name -- required for full CIFs
         try:

trunk/exports/G2export_csv.py

@@ -192 +192 @@
         for i,phasenam in enumerate(sorted(histblk['Reflection Lists'])):
             for (
-                h,k,l,mult,dsp,pos,sig,gam,Fobs,Fcalc,phase,eqlist,phaselist,Icorr,FFdict
-                ) in histblk['Reflection Lists'][phasenam]:
+                h,k,l,mult,dsp,pos,sig,gam,Fobs,Fcalc,phase,Icorr
+                ) in histblk['Reflection Lists'][phasenam]['RefList']:
                 self.Write(fmt.format(h,k,l,pos,Fobs,Fcalc,phase,mult,i))
         self.CloseFile()
@@ -229 +229 @@
         fmt = "{:.0f},{:.0f},{:.0f},{:.3f},{:.2f},{:.4f},{:.2f},{:.2f},{:.0f}"
         for (
-            h,k,l,mult,dsp,Fobs,sigFobs,Fcalc,FobsT,FcalcT,phase,eqlist,phaselist,Icorr,FFdict
-            ) in histblk['Data']:
+            h,k,l,mult,dsp,Fobs,sigFobs,Fcalc,FobsT,FcalcT,phase,Icorr
+            ) in histblk['Data']['RefList']:
             self.Write(fmt.format(h,k,l,dsp,Fobs,sigFobs,Fcalc,phase,mult))
         self.CloseFile()

trunk/exports/G2export_examples.py

@@ -195 +195 @@
             self.Write(80*'=')
             for (
-                h,k,l,mult,dsp,pos,sig,gam,Fobs,Fcalc,phase,eqlist,phaselist,Icorr,FFdict
-                ) in histblk['Reflection Lists'][phasenam]:
+                h,k,l,mult,dsp,pos,sig,gam,Fobs,Fcalc,phase,Icorr
+                ) in histblk['Reflection Lists'][phasenam]['RefList']:
                 self.Write(fmt.format(hklfmt.format(h,k,l),pos,Fobs,Fcalc,phase,mult))
         self.CloseFile()
@@ -237 +237 @@
         self.Write(80*'=')
         for (
-            h,k,l,mult,dsp,Fobs,sigFobs,Fcalc,FobsT,FcalcT,phase,eqlist,phaselist,Icorr,FFdict
-            ) in histblk['Data']:
+            h,k,l,mult,dsp,Fobs,sigFobs,Fcalc,FobsT,FcalcT,phase,Icorr
+            ) in histblk['Data']['RefList']:
             self.Write(fmt.format(hklfmt.format(h,k,l),dsp,Fobs,sigFobs,Fcalc,phase,mult))
         self.CloseFile()