Changeset 3825

Timestamp:

Feb 15, 2019 10:43:35 AM (6 years ago)

Author:

vondreele

Message:

create csv exporter for small angle data - includes size distribution histogram if any.
fix formatting issue with size distribution axis label
a bit different incomm. mag str fctr. math - still wrong

Location:

trunk

Files:

• GSASIIIO.py (modified) (6 diffs)
• GSASIIdataGUI.py (modified) (3 diffs)
• GSASIIplot.py (modified) (1 diff)
• GSASIIpy3.py (modified) (1 diff)
• GSASIIstrMath.py (modified) (1 diff)
• exports/G2export_csv.py (modified) (1 diff)

trunk/GSASIIIO.py ¶

@@ -1343 +1343 @@
         self.Histograms = {}
         self.powderDict = {}
+        self.sasdDict = {}
         self.xtalDict = {}
         self.parmDict = {}
@@ -1478 +1479 @@
             else:
                 choices = sorted(self.powderDict.values())
+                hnum = G2G.ItemSelector(choices,self.G2frame)
+                if hnum is None: return True
+                self.histnam = [choices[hnum]]
+                numselected = len(self.histnam)
+        elif self.currentExportType == 'sasd':
+            if len(self.sasdDict) == 0:
+                self.G2frame.ErrorDialog(
+                    'Empty project',
+                    'Project does not contain any small angle data.')
+                return True
+            elif len(self.sasdDict) == 1:
+                self.histnam = self.sasdDict.values()
+            elif self.multiple:
+                choices = sorted(self.sasdDict.values())
+                hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
+                if not hnum: return True
+                self.histnam = [choices[i] for i in hnum]
+                numselected = len(self.histnam)
+            else:
+                choices = sorted(self.sasdDict.values())
                 hnum = G2G.ItemSelector(choices,self.G2frame)
                 if hnum is None: return True
@@ -1655 +1676 @@
         self.OverallParms = {}
         self.powderDict = {}
+        self.sasdDict = {}
         self.xtalDict = {}
         self.Phases = {}
@@ -1680 +1702 @@
         elif self.currentExportType == 'image':
             histType = 'IMG'
+        elif self.currentExportType == 'sasd':
+            histType = 'SASD'
 
         if histType: # Loading just one kind of tree entry
@@ -1712 +1736 @@
                 elif hist.startswith("HKLF"): 
                     d = self.xtalDict
+                elif hist.startswith("SASD"):
+                    d = self.sasdDict
                 else:
                     return                    
@@ -1737 +1763 @@
             elif hist.startswith("HKLF"): 
                 self.xtalDict[i] = hist
+            elif hist.startswith("SASD"):
+                self.sasdDict[i] = hist
 
     def dumpTree(self,mode='type'):

trunk/GSASIIdataGUI.py ¶

@@ -2551 +2551 @@
         mapmenu = wx.Menu()
         item = menu.AppendSubMenu(mapmenu,'Maps as','Export density map(s)')
+        
+        sasdmenu = wx.Menu()
+        item = menu.AppendSubMenu(sasdmenu,'Small angle data as','Export small angle histogram(s)')
 
         # sequential exports are handled differently; N.B. enabled in testSeqRefineMode
@@ -2580 +2583 @@
                 elif typ == "map":
                     submenu = mapmenu
+                elif typ == "sasd":
+                    submenu = sasdmenu
                 # elif typ == "pdf":
                 #     submenu = pdfmenu
@@ -5044 +5049 @@
         for lbl,txt in (('Phase','Export selected phase(s)'),
                         ('Project','Export entire sequential fit'),
-                        ('Powder','Export selected powder histogram(s)')
+                        ('Powder','Export selected powder histogram(s)'),
+                        ('sasd','Export selected small angle histogram(s)')
                         ):
             objlist = []

trunk/GSASIIplot.py ¶

@@ -4982 +4982 @@
     Plot.set_title('Size Distribution')
     Plot.set_xlabel(r'$D, \AA$',fontsize=14)
-    Plot.set_ylabel(r'$Volume distribution f(D)$',fontsize=14)
+    Plot.set_ylabel(r'$Volume\ distribution,\ f(D)$',fontsize=14)
     if data['Size']['logBins']:
         Plot.set_xscale("log",nonposx='mask')

trunk/GSASIIpy3.py ¶

@@ -111 +111 @@
     else: # in range where g formatting should do what I want
         # used? 
-        decimals = digits[0] - 1
+        decimals = digits[0] - 6
         fmt = "{" + (":{:d}.{:d}g".format(digits[0],decimals))+"}"
     try:

trunk/GSASIIstrMath.py ¶

@@ -1609 +1609 @@
             fbm = (Q*TMcorr[nxs,:,nxs,nxs,:]*sinm[nxs,:,nxs,:,:]*SMag[nxs,nxs,:,:,:])
             
-            fas = np.sum(np.sum(fam,axis=-1)**2,axis=-1)      #xyz,Nref,ntau; sum ops & atoms
-            fbs = np.sum(np.sum(fbm,axis=-1)**2,axis=-1)      #ditto
+            fas = np.sum(np.sum(fam,axis=-1),axis=-1)/ngl      #xyz,Nref,ntau; sum ops & atoms
+            fbs = np.sum(np.sum(fbm,axis=-1),axis=-1)/ngl      #ditto
             
-            refl.T[10] = np.sum(np.sum(fas,axis=0)/ngl,axis=-1)+np.sum(np.sum(fbs,axis=0)/ngl,axis=-1)    #square of sums
+            refl.T[10] = np.sum(np.sum(fas,axis=-1),axis=0)**2+np.sum(np.sum(fbs,axis=-1),axis=0)**2    #square of sums
 #            refl.T[11] = mphase[:,0,0]  #ignore f' & f"
             

trunk/exports/G2export_csv.py ¶

@@ -354 +354 @@
         print(hist+' reflections written to file '+self.fullpath)
 
+class ExportSASDCSV(G2IO.ExportBaseclass):
+    '''Used to create a csv file for a small angle data set
+
+    :param wx.Frame G2frame: reference to main GSAS-II frame
+    '''
+    def __init__(self,G2frame):
+        super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__
+            G2frame=G2frame,
+            formatName = 'CSV file',
+            extension='.csv',
+            longFormatName = 'Export small angle data as comma-separated (csv) file'
+            )
+        self.exporttype = ['sasd']
+        #self.multiple = False # only allow one histogram to be selected
+        self.multiple = True
+
+    def Writer(self,TreeName,filename=None):
+        self.OpenFile(filename)
+        histblk = self.Histograms[TreeName]
+        if len(self.Histograms[TreeName]['Models']['Size']['Distribution']):
+            self.Write('"Size Distribution"')
+            Distr = np.array(self.Histograms[TreeName]['Models']['Size']['Distribution'])
+            WriteList(self,("bin_pos","bin_width","bin_value"))
+            digitList = 2*((13,3),)+((13,4,'g'),)
+            for bindata in Distr.T:
+                line = ""
+                for val,digits in zip(bindata,digitList):
+                    if line: line += ','
+                    line += G2py3.FormatValue(val,digits)
+                self.Write(line)            
+        self.Write('"Small angle data"')
+        Parms = self.Histograms[TreeName]['Instrument Parameters'][0]
+        for parm in Parms:
+            if parm in ['Type','Source',]:
+                line = '"Instparm: %s","%s"'%(parm,Parms[parm][0])
+            elif parm in ['Lam',]:
+                line = '"Instparm: %s",%10.6f'%(parm,Parms[parm][1])
+            else:
+                line = '"Instparm: %s",%10.2f'%(parm,Parms[parm][1])
+            self.Write(line)
+        WriteList(self,("q","y_obs","y_sig","y_calc","y_bkg"))
+        digitList = 5*((13,5,'g'),)
+        for vallist in zip(histblk['Data'][0],
+                       histblk['Data'][1],
+                       1./np.sqrt(histblk['Data'][2]),
+                       histblk['Data'][3],
+                       histblk['Data'][4],
+                       ):
+            line = ""
+            for val,digits in zip(vallist,digitList):
+                if line: line += ','
+                line += G2py3.FormatValue(val,digits)
+            self.Write(line)
+        self.CloseFile()
+        
+    def Exporter(self,event=None):
+        '''Export a set of small angle data as a csv file
+        '''
+        # the export process starts here
+        self.InitExport(event)
+        # load all of the tree into a set of dicts
+        self.loadTree()
+        if self.ExportSelect( # set export parameters
+            AskFile='single' # get a file name/directory to save in
+            ): return
+        filenamelist = []
+        for hist in self.histnam:
+            if len(self.histnam) == 1:
+                name = self.filename
+            else:    # multiple files: create a unique name from the histogram
+                name = self.MakePWDRfilename(hist)
+            fileroot = os.path.splitext(G2obj.MakeUniqueLabel(name,filenamelist))[0]
+            # create the file
+            self.filename = os.path.join(self.dirname,fileroot + self.extension)
+            self.Writer(hist)
+            print('Histogram '+hist+' written to file '+self.fullpath)
+
 class ExportSingleCSV(G2IO.ExportBaseclass):
     '''Used to create a csv file with single crystal reflection data