Changeset 1141

Timestamp:

Nov 7, 2013 2:46:36 PM (9 years ago)

Author:

toby

Message:

minor tweaks: move indexing of Ids to histogram load, remove Type from HAP var list

Location:

trunk

Files:

• GSASII.py (modified) (2 diffs)
• GSASIIconstrGUI.py (modified) (3 diffs)
• GSASIIobj.py (modified) (6 diffs)
• GSASIIstrIO.py (modified) (3 diffs)
• GSASIIstrMain.py (modified) (1 diff)

trunk/GSASII.py

@@ -72 +72 @@
 import GSASIIstrIO as G2stIO
 import GSASIImapvars as G2mv
+import GSASIIobj as G2obj
 
 #wx inspector - use as needed
@@ -2537 +2538 @@
                             print('For phase "'+str(phase)+
                                   '" unresolved reference to histogram "'+str(hist)+'"')
+        G2obj.IndexAllIds(Histograms=Histograms,Phases=Phases)
         return Histograms,Phases
         

trunk/GSASIIconstrGUI.py

@@ -204 +204 @@
     #reload(G2gd)
     ###################################################
-    Histograms,Phases = G2obj.IndexAllIds(G2frame)
+    Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
     ##################################################################################
     # patch: convert old-style (str) variables in constraints to G2VarObj objects
@@ -216 +216 @@
                     j += 1
         if j:
-            print str(key) + ': '+str(j)+' variable(s) strings converted to objects'
+            print str(key) + ': '+str(j)+' variable(s) as strings converted to objects'
     ##################################################################################
     rigidbodyDict = G2frame.PatternTree.GetItemPyData(
@@ -252 +252 @@
             
     hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,Histograms,Print=False)
-    hapList = hapDict.keys()
+    hapList = [i for i in hapDict.keys() if i.split(':')[2] not in ('Type',)]
     hapList.sort()
     histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)

trunk/GSASIIobj.py

@@ -438 +438 @@
 diffraction data for that information are directly associated with
 that tree item and there are a series of children to that item. The
-routine :func:`~GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree` will
+routines :func:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`
+and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
 load this information into a dictionary where the child tree name is
 used as a key, and the information in the main entry is assigned
@@ -592 +593 @@
 diffraction data for that information are directly associated with
 that tree item and there are a series of children to that item. The
-routine :func:`~GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree` will
+routines :func:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`
+and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
 load this information into a dictionary where the child tree name is
 used as a key, and the information in the main entry is assigned
@@ -723 +725 @@
 '''
 
-def IndexAllIds(G2frame=None,Histograms=None,Phases=None):
+def IndexAllIds(Histograms,Phases):
     '''Scan through the used phases & histograms and create an index
     to the random numbers of phases, histograms and atoms. While doing this,
@@ -732 +734 @@
     element each atom record.
 
+    This is called in two places (only) :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`
+    (which loads the histograms and phases from a GPX file) and
+    :meth:`GSASII.GSASII.GetUsedHistogramsAndPhases`
+    (which loads the histograms and phases from the data tree.)
+
     TODO: do we need a lookup for rigid body variables?
     '''
-    if G2frame:
-        Histograms,phaseDict = G2frame.GetUsedHistogramsAndPhasesfromTree()
-    else:
-        Histograms,phaseDict = Histograms,Phases
     # process phases and atoms
     PhaseIdLookup.clear()
@@ -744 +747 @@
     AtomRanIdLookup.clear()
     ShortPhaseNames.clear()
-    for Phase in phaseDict:
-        cx,ct,cs,cia = phaseDict[Phase]['General']['AtomPtrs']
-        ranId = phaseDict[Phase]['ranId'] 
+    for ph in Phases:
+        cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
+        ranId = Phases[ph]['ranId'] 
         while ranId in PhaseRanIdLookup:
             # Found duplicate random Id! note and reassign
-            print ("\n\n*** Phase "+str(Phase)+" has repeated ranId. Fixing.\n")
-            phaseDict[Phase]['ranId'] = ranId = ran.randint(0,sys.maxint)
-        pId = str(phaseDict[Phase]['pId'])
-        PhaseIdLookup[pId] = (Phase,ranId)
+            print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
+            Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxint)
+        pId = str(Phases[ph]['pId'])
+        PhaseIdLookup[pId] = (ph,ranId)
         PhaseRanIdLookup[ranId] = pId
-        shortname = Phase[:10]
+        shortname = ph[:10]
         while shortname in ShortPhaseNames.values():
-            shortname = Phase[:8] + ' ('+ pId + ')'
+            shortname = ph[:8] + ' ('+ pId + ')'
         ShortPhaseNames[pId] = shortname
         AtomIdLookup[pId] = {}
         AtomRanIdLookup[pId] = {}
-        for iatm,at in enumerate(phaseDict[Phase]['Atoms']):
+        for iatm,at in enumerate(Phases[ph]['Atoms']):
             ranId = at[-1]
             while ranId in AtomRanIdLookup[pId]: # check for dups
-                print ("\n\n*** Phase "+str(Phase)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
+                print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
                 at[-1] = ranId = ran.randint(0,sys.maxint)
             AtomRanIdLookup[pId][ranId] = str(iatm)
-            if phaseDict[Phase]['General']['Type'] == 'macromolecular':
+            if Phases[ph]['General']['Type'] == 'macromolecular':
                 label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
             else:
@@ -788 +791 @@
             shortname = hist[:11] + ' ('+ hId + ')'
         ShortHistNames[hId] = shortname
-
-    return Histograms,phaseDict
 
 def LookupAtomId(pId,ranId):

trunk/GSASIIstrIO.py

@@ -64 +64 @@
 def GetConstraints(GPXfile):
     '''Read the constraints from the GPX file and interpret them
+
+    called in :func:`CheckConstraints`, :func:`GSASIIstrMain.Refine`
+    and :func:`GSASIIstrMain.SeqRefine`. 
     '''
     constList = []
@@ -177 +180 @@
     if not Histograms:
         return 'Error: no diffraction data',''
-    G2obj.IndexAllIds(Histograms=Histograms,Phases=Phases)
     rigidbodyDict = GetRigidBodies(GPXfile)
     rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
@@ -395 +397 @@
                         print('For phase "'+str(phase)+
                               '" unresolved reference to histogram "'+str(hist)+'"')
+    G2obj.IndexAllIds(Histograms=Histograms,Phases=Phases)
     return Histograms,Phases
     

trunk/GSASIIstrMain.py

@@ -59 +59 @@
     calcControls = {}
     calcControls.update(Controls)            
-    constrDict,fixedList = G2stIO.GetConstraints(GPXfile) # better to pass in Histograms,Phases
+    constrDict,fixedList = G2stIO.GetConstraints(GPXfile)
     restraintDict = G2stIO.GetRestraints(GPXfile)
     Histograms,Phases = G2stIO.GetUsedHistogramsAndPhases(GPXfile)
-    G2obj.IndexAllIds(Histograms=Histograms,Phases=Phases)
     if not Phases:
         print ' *** ERROR - you have no phases! ***'