Merge updates in master into develop branch

.readthedocs.yaml

@@ -15,3 +15,7 @@ conda:
 formats:
   - epub
   - pdf
+
+sphinx:
+  # Path to Sphinx configuration file.
+  configuration: docs/source/conf.py

GSASII/GSASIIfiles.py

@@ -1097,7 +1097,7 @@ def readMasks(filename,masks,ignoreThreshold):
             S = File.readline()
             continue
         [key,val] = S.strip().split(':',1)
-        if key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
+        if key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds','Xlines','Ylines']:
             if ignoreThreshold and key == 'Thresholds':
                 S = File.readline()
                 continue

GSASII/GSASIIimgGUI.py

@@ -74,7 +74,7 @@ def GetImageZ(G2frame,data,newRange=False):
     Npix,imagefile,imagetag = G2IO.GetCheckImageFile(G2frame,G2frame.Image)
     if imagefile is None: return []
     formatName = data.get('formatName','')
-    sumImg = np.array(G2fil.GetImageData(G2frame,imagefile,True,ImageTag=imagetag,FormatName=formatName),dtype='float32')
+    sumImg = np.array(G2fil.GetImageData(G2frame,imagefile,True,ImageTag=imagetag,FormatName=formatName),dtype=np.float32)
     if sumImg is None:
         return []
     darkImg = False
@@ -87,9 +87,9 @@ def GetImageZ(G2frame,data,newRange=False):
                 dformatName = Ddata.get('formatName','')
                 Npix,darkfile,imagetag = G2IO.GetCheckImageFile(G2frame,Did)
 #                darkImage = G2fil.GetImageData(G2frame,darkfile,True,ImageTag=imagetag,FormatName=dformatName)
-                darkImage = np.array(G2fil.GetImageData(G2frame,darkfile,True,ImageTag=imagetag,FormatName=dformatName),dtype='float32')
-                if darkImg is not None:
-                    sumImg += np.array(darkImage*darkScale,dtype='float32')
+                darkImage = np.array(G2fil.GetImageData(G2frame,darkfile,True,ImageTag=imagetag,FormatName=dformatName),dtype=np.float32)
+                if darkImg is not None:                
+                    sumImg += np.array(darkImage*darkScale,dtype=np.float32)
             else:
                 print('Warning: resetting dark image (not found: {})'.format(
                     darkImg))
@@ -102,11 +102,11 @@ def GetImageZ(G2frame,data,newRange=False):
                 Npix,backfile,imagetag = G2IO.GetCheckImageFile(G2frame,Bid)
                 Bdata = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Bid,'Image Controls'))
                 bformatName = Bdata.get('formatName','')
-                backImage = np.array(G2fil.GetImageData(G2frame,backfile,True,ImageTag=imagetag,FormatName=bformatName),dtype='float32')
+                backImage = np.array(G2fil.GetImageData(G2frame,backfile,True,ImageTag=imagetag,FormatName=bformatName),dtype=np.float32)
                 if darkImg and backImage is not None:
-                    backImage += np.array(darkImage*darkScale/backScale,dtype='float32')
+                    backImage += np.array(darkImage*darkScale/backScale,dtype=np.float32)
                 if backImage is not None:
-                    sumImg += np.array(backImage*backScale,dtype='float32')
+                    sumImg += np.array(backImage*backScale,dtype=np.float32)
     if 'Gain map' in data:
         gainMap = data['Gain map']
         if gainMap:
@@ -122,7 +122,8 @@ def GetImageZ(G2frame,data,newRange=False):
     Imin = np.min(sumImg)
     if 'range' not in data or newRange:
         data['range'] = [(Imin,Imax),[Imin,Imax]]
-    return np.asarray(np.rint(sumImg),dtype='int32')
+    #return np.asarray(np.rint(sumImg),dtype=np.int32)
+    return np.array(np.array(np.rint(sumImg),dtype=int),dtype=np.int32)  # double-cast removes warning. Why?
 
 def UpdateImageData(G2frame,data):
 
@@ -1789,7 +1790,7 @@ def newReplot(*args,**kwargs):
     def onDeleteMask(event):
         Obj = event.GetEventObject()
         typ = Obj.locationcode.split('+')[0]
-        num = int(Obj.locationcode.split('+')[1])
+        num = int(Obj.locationcode.split('+')[1])-1 #off by one?
         del(data[typ][num])
         wx.CallAfter(UpdateMasks,G2frame,data)
         G2plt.PlotExposedImage(G2frame,event=event)
@@ -2013,7 +2014,6 @@ def OnNewRingMask(event):
 
     def OnNewXlineMask(event):
         'Start a new x-line mask'
-        print('x')
         G2frame.MaskKey = 'x'
         G2plt.OnStartMask(G2frame)
 
@@ -2194,7 +2194,7 @@ def OnDelPixMask(event):
     def OnAzimuthPlot(event):
         GkTheta = chr(0x03f4)
         Obj = event.GetEventObject()
-        ringId = int(Obj.locationcode.split('+')[1])
+        ringId = int(Obj.locationcode.split('+')[1])-1
         Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Image Controls'))
         image = GetImageZ(G2frame,Controls)
         RingInt = G2img.AzimuthIntegrate(image,Controls,data,ringId)

GSASII/GSASIIindex.py

@@ -344,6 +344,8 @@ def IndexPeaks(peaks,HKL):
         if peak[2]:
             if peak[-1] > 0.:
                 peak[3] = True
+    if len(peaks) < 7:
+        return False,peaks  #nothing indexed!
     if np.any(peaks[4])*np.any(peaks[5])*np.any(peaks[6]):
         return True,peaks
     else:

GSASII/GSASIImath.py

@@ -4655,7 +4655,7 @@ def peakHess(parms,rX,rY,rZ,rho,res,SGLaue):
         res = mapData['GridStep']*2.
         incre = np.array(rho.shape,dtype=float)
         step = max(1.0,1./res)+1
-        steps = np.array((3*[step,]),dtype='int32')
+        steps = np.array((3*[step,]),dtype=np.int32)
     except KeyError:
         G2fil.G2Print ('**** ERROR - Fourier map not defined')
         return peaks,mags

GSASII/GSASIIpwdGUI.py

@@ -9586,7 +9586,7 @@ def OnNoRing(event):
         sqBox.Add((1,1),1,wx.EXPAND,1)
         sqBox.Add(wx.StaticText(G2frame.dataWindow,label='Rmin: '),0,WACV)
         rmin = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'Rmin',nDig=(5,1),
-                typeHint=float,size=wx.Size(50,20))
+                xmin=0.01,typeHint=float,size=wx.Size(50,20))
         sqBox.Add(rmin,0,WACV)
         sfgSizer.Add(sqBox,0,wx.EXPAND)
 

GSASII/GSASIIscriptable.py

@@ -684,7 +684,7 @@ def _getCorrImage(ImageReaderlist,proj,imageRef):
     sumImg = G2fil.RereadImageData(ImageReaderlist,imagefile,ImageTag=ImageTag,FormatName=formatName)
     if sumImg is None:
         return []
-    sumImg = np.array(sumImg,dtype='int32')
+    sumImg = np.array(sumImg,dtype=np.int32)
     darkImg = False
     if 'dark image' in Controls:
         darkImg,darkScale = Controls['dark image']
@@ -697,7 +697,7 @@ def _getCorrImage(ImageReaderlist,proj,imageRef):
             darkImage = G2fil.RereadImageData(ImageReaderlist,imagefile,ImageTag=ImageTag,FormatName=formatName)
             if darkImg is None:
                 raise Exception('Error reading dark image {}'.format(imagefile))
-            sumImg += np.array(darkImage*darkScale,dtype='int32')
+            sumImg += np.array(darkImage*darkScale,dtype=np.int32)
     if 'background image' in Controls:
         backImg,backScale = Controls['background image']
         if backImg:     #ignores any transmission effect in the background image
@@ -709,9 +709,9 @@ def _getCorrImage(ImageReaderlist,proj,imageRef):
             if backImage is None:
                 raise Exception('Error reading background image {}'.format(imagefile))
             if darkImg:
-                backImage += np.array(darkImage*darkScale/backScale,dtype='int32')
+                backImage += np.array(darkImage*darkScale/backScale,dtype=np.int32)
             else:
-                sumImg += np.array(backImage*backScale,dtype='int32')
+                sumImg += np.array(backImage*backScale,dtype=np.int32)
     if 'Gain map' in Controls:
         gainMap = Controls['Gain map']
         if gainMap:
@@ -726,7 +726,7 @@ def _getCorrImage(ImageReaderlist,proj,imageRef):
     sumImg -= int(Controls.get('Flat Bkg',0))
     Imax = np.max(sumImg)
     Controls['range'] = [(0,Imax),[0,Imax]]
-    return np.asarray(sumImg,dtype='int32')
+    return np.asarray(sumImg,dtype=np.int32)
 
 def _constr_type(var):
     '''returns the constraint type based on phase/histogram use

GSASII/GSASIItestplot.py

@@ -4,7 +4,6 @@
 '''
 import wx
 import wx.aui
-import matplotlib as mpl
 import matplotlib.figure as mplfig
 try:
     from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas

GSASII/fprime.py

@@ -208,12 +208,20 @@ def OnChoice2(event):
             else:
                 self.FFxaxis = 'T'
             self.UpDateFPlot(self.Wave,rePlot=False)
-
+
+        def OnChoice3(event):
+            self.Norm = not self.Norm
+            self.UpDateFPlot(self.Wave,rePlot=False)
+
         self.choice2 = wx.ComboBox(id=wxID_FPRIMECHOICE2, value=' sin('+Gktheta+')/'+Gklambda,
             choices=[' sin('+Gktheta+')/'+Gklambda,' 2'+Gktheta,' Q'],
             parent=panel, style=wx.CB_READONLY|wx.CB_DROPDOWN)
         choiceSizer.Add(self.choice2,0)
         self.choice2.Bind(wx.EVT_COMBOBOX, OnChoice2, id=wxID_FPRIMECHOICE2)
+        self.choice3 = wx.CheckBox(panel,label='Normalize ff by Z')
+        self.choice3.Bind(wx.EVT_CHECKBOX,OnChoice3)
+        choiceSizer.Add((10,10),0)
+        choiceSizer.Add(self.choice3,0)
         mainSizer.Add(choiceSizer,0)
         mainSizer.Add((10,10),0)
         panel.SetSizer(mainSizer)
@@ -224,7 +232,8 @@ def __init__(self, parent):
         self.Lines = []
         self.Elems = []
         self.linePicked = None
-
+        self.Norm = False
+
     def OnFPRIMEExitMenu(self, event):
         self.parent.G2plotNB.Delete('Fprime')
         self.Close()
@@ -379,7 +388,10 @@ def UpDateFPlot(self,Wave,rePlot=True):
             self.ax.legend(loc='best')
         self.Page.figure.subplots_adjust(hspace=0.25)
         if self.ifWave:
-            self.bx.set_title('%s%s%6.4f%s'%('Form factors (',r'$\lambda=$',self.Wave,r'$\AA)$'),x=0,ha='left')
+            if self.Norm:
+                self.bx.set_title('%s%s%6.4f%s'%('Normalized form factors (',r'$\lambda=$',self.Wave,r'$\AA)$'),x=0,ha='left')
+            else:
+                self.bx.set_title('%s%s%6.4f%s'%('Form factors (',r'$\lambda=$',self.Wave,r'$\AA)$'),x=0,ha='left')
         else:
             self.bx.set_title('%s%6.2f%s'%('Form factors  (E =',self.Energy,'keV)'),x=0,ha='left')
         if self.FFxaxis == 'S':
@@ -391,7 +403,10 @@ def UpDateFPlot(self,Wave,rePlot=True):
         else:
             self.bxlabel = 'Q, '+Angstr+Pwrm1
             self.bx.set_xlabel(r'$Q, \AA$',fontsize=14)
-        self.bx.set_ylabel("f+f ', e-",fontsize=14)
+        if self.Norm:
+            self.bx.set_ylabel("(f+f ')/Z",fontsize=14)
+        else:
+            self.bx.set_ylabel("f+f ', e-",fontsize=14)
         E = self.Energy
         DE = E*self.Eres                         #smear by defined source resolution
         StlMax = min(2.0,math.sin(80.0*math.pi/180.)/Wave)
@@ -400,7 +415,10 @@ def UpDateFPlot(self,Wave,rePlot=True):
         for i,Elem in enumerate(self.Elems):
             Els = Elem[0]
             Els = Els = Els.ljust(2).lower().capitalize()
-            Ymax = max(Ymax,Elem[1])
+            if self.Norm:
+                Ymax = 0.2
+            else:
+                Ymax = max(Ymax,Elem[1])
             res1 = G2elem.FPcalc(Elem[3],E+DE)
             res2 = G2elem.FPcalc(Elem[3],E-DE)
             res = (res1[0]+res2[0])/2.0
@@ -420,6 +438,9 @@ def UpDateFPlot(self,Wave,rePlot=True):
                     X.append(360.0*math.asin(S*self.Wave)/math.pi)
                 else:
                     X.append(4.0*S*math.pi)
+            if self.Norm:
+                ff = [f/Elem[1] for f in ff]
+                ffo = [f/Elem[1] for f in ffo]
             Color = colors[i%6]
             Xp = np.array(X)
             ffop = np.array(ffo)

GSASII/imports/G2img_HDF5.py

@@ -72,7 +72,7 @@ def Reader(self, filename, ParentFrame=None, **kwarg):
                     fp.close()
                     return False
                 nsel = GSASIIpath.GetConfigValue('HDF5selection',getDefault=True)
-                self.buffer['selectedImages'] = []
+                self.buffer['selectedImages'] = list(range(len(self.buffer['imagemap'])))
                 if ParentFrame and len(self.buffer['imagemap']) > nsel and nsel >= 0:
                     import wx
                     from .. import GSASIIctrlGUI as G2G

GSASII/tutorialIndex.py

@@ -94,6 +94,14 @@
 
     ['Magnetic-V', 'Magnetic-V.htm',"Magnetic Structure Analysis-V",
      '''Analysis of a complex Type IV antiferromagnet with two propagation vectorse using Bilbao k-SUBGROUPSMAG from TOF neutron powder data'''],
+
+    ['k_vec_tutorial', 'k_vec_tutorial.html', 'k-vector searching in GSAS-II #1',
+    '''Search neutron diffraction data of Er2Ge2O7 for a all-zero magnetic k-vector'''],
+
+    ['k_vec_tutorial_non_zero', 'k_vec_tutorial_non_zero.html', 'k-vector searching in GSAS-II #2',
+    '''Search neutron diffraction data used in Magnetic Structure Analysis-III for a non-zero magnetic k-vector'''],
+
+    #['ExampleDir', 'ExamplePage.html', 'Example Tutorial Title', '''Example descriptive text'''],
 
 ['Parametric sequential fitting'], #######################################################
     ['SeqRefine', 'SequentialTutorial.htm', 'Sequential refinement of multiple datasets',
@@ -245,6 +253,10 @@
     ['ClusterAnalysis','Cluster and Outlier Analysis.htm', 'Cluster and Outlier Analysis',
      '''This gives an example of using Cluster and Outlier Analysis with PWDR data.'''],
 
-    #['ExampleDir', 'ExamplePage.html', 'Example Tutorial Title', '''Exam'ple descriptive text'''],
+    ['FontSize', 'FontSize.html', 'Changing the GSAS-II Font Size',
+    '''Configuration variables allow GSAS-II to be customized. In this example the configuration variable that changes the font size 
+    used in the GUI is changed.'''],
+
+    #['ExampleDir', 'ExamplePage.html', 'Example Tutorial Title', '''Example descriptive text'''],
     )