Merge remote-tracking branch 'origin/main' into kvec_isodistort_zyp

so that it is ready to merge into main as a FF

Author: briantoby

GSASII/GSASIIctrlGUI.py

@@ -31,7 +31,7 @@
 import random as ran
 import numpy as np
 
-import matplotlib as mpl
+#import matplotlib as mpl
 try:
     from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
 except ImportError:
@@ -47,7 +47,7 @@
 from . import GSASIIpwd as G2pwd
 from . import GSASIIlattice as G2lat
 from . import GSASIImath as G2mth
-from . import GSASIIstrMain as G2stMn
+#from . import GSASIIstrMain as G2stMn
 from . import GSASIImiscGUI as G2IO
 from .tutorialIndex import tutorialIndex
 if sys.version_info[0] >= 3:
@@ -5042,7 +5042,7 @@ def SetContents(self,parent):
                 if parent.hisNum != '*' and name.split(':')[1] != parent.hisNum: continue
             if (parent.varName != ' ') and (parent.varName not in name): continue
             self.varList.append(name)
-        oldlen = self.GetItemCount()
+        #oldlen = self.GetItemCount()
         self.SetItemCount(len(self.varList))
 
     def OnRowSelected(self, event, row=None):
@@ -6025,7 +6025,7 @@ def copy2clip(event):
         msg += f"\n\n * For {key} use cite:\n"
         msg += GetCite(key,wrap=95,indent=6)
     msg += '\n\nNote that your citations are one of the strongest ways you can say thank you to the\nscientists who make their software available to you.'
-    res = ShowScrolledInfo(parent,msg,header='Please Cite',
+    ShowScrolledInfo(parent,msg,header='Please Cite',
                            buttonlist=[
         ('Close', lambda event: event.GetEventObject().GetParent().EndModal(wx.ID_OK)),
         ('Copy to clipboard', copy2clip),
@@ -6283,7 +6283,7 @@ def copyURL(event):
     # place HTML title into window title
     dlg.wv.Bind(wx.EVT_UPDATE_UI, lambda event:
                     dlg.SetTitle(dlg.wv.GetCurrentTitle()))
-    lastWebView = dlg.wv
+    #lastWebView = dlg.wv
     sizer.Add(dlg.wv,1,wx.EXPAND)
     # row of buttons & URL label on bottom of window
     bsizer=wx.BoxSizer(wx.HORIZONTAL)
@@ -7349,7 +7349,7 @@ class gitVersionSelector(wx.Dialog):
     from a git repository
     '''
     def __init__(self,parent=None):
-        import git
+        #import git
         self.g2repo = GSASIIpath.openGitRepo(path2GSAS2)
         self.githistory = GSASIIpath.gitHistory('hash',self.g2repo)
         # patch Feb 2024: don't allow access to versions that are too old
@@ -7492,7 +7492,7 @@ def docCommit(self,commit):
 
         :returns: a multi-line string
         '''
-        import datetime
+        #import datetime
         fmtdate = lambda c:"{:%d-%b-%Y %H:%M}".format(c.committed_datetime)
         commit = self.g2repo.commit(commit)  # converts a hash, if supplied
         msg = f'git {commit.hexsha[:10]} from {fmtdate(commit)}'
@@ -9397,6 +9397,15 @@ def askQuestion(parent,question,title):
         dlg.Destroy()
     return ans
 
+def haveGUI():
+    '''Test if there is a GUI that can be accessed
+    :returns: True if a GUI is available
+    '''
+    try:
+        return wx.App.IsMainLoopRunning()
+    except:
+        return False
+
 #===========================================================================
 def gitFetch(G2frame):
     wx.BeginBusyCursor()
@@ -9832,7 +9841,7 @@ def gitSwitchMaster2Main():
 
 See web page GSASII.github.io for information on how to install GSAS-II. 
 '''
-        res = ShowScrolledInfo(G2frame,msg,header='Please Note',
+        ShowScrolledInfo(G2frame,msg,header='Please Note',
                                 height=250)
         return
 
@@ -9941,13 +9950,13 @@ def gitSwitchMaster2Main():
     if script and sys.platform.startswith('darwin'):
         print(f'running {script}')
         import subprocess
-        out = subprocess.run([sys.executable,script],cwd=GSASIIpath.path2GSAS2)
+        subprocess.run([sys.executable,script],cwd=GSASIIpath.path2GSAS2)
     # On windows make a batch file with hard-coded paths to Python and GSAS-II
     elif script and sys.platform.startswith('win'):
         script = os.path.normpath(os.path.join(GSASIIpath.path2GSAS2,'install',s))
         print(f'running {script!r}')
         import subprocess
-        out = subprocess.run([sys.executable,script],cwd=GSASIIpath.path2GSAS2)
+        subprocess.run([sys.executable,script],cwd=GSASIIpath.path2GSAS2)
     # On linux, make a desktop icon with hard-coded paths to Python and GSAS-II
     elif script:
         sys.argv = [script]

GSASII/GSASIIdataGUI.py

@@ -551,7 +551,7 @@ def TestOldVersions():
     warnmsg = ''
     errmsg = ''
     for s,m in [('Python',None), ('wx',wx), ('matplotlib', mpl), ('numpy',np),
-                    ('scipy',sp), ('OpenGL',ogl)]:
+            ('scipy',sp), ('OpenGL',ogl)]:
         if s == 'Python':
             pkgver = platform.python_version()
             prefix = ''
@@ -7158,8 +7158,8 @@ def _makemenu():     # routine to create menu when first used
             G2G.Define_wxId('wxID_ATOMSEDITADD', 'wxID_ATOMSEDITINSERT', 'wxID_ATOMSEDITDELETE',
                 'wxID_ATOMSMODIFY', 'wxID_ATOMSTRANSFORM', 'wxID_ATOMSVIEWADD', 'wxID_ATOMVIEWINSERT',
                 'wxID_RELOADDRAWATOMS', 'wxID_ATOMSDISAGL', 'wxID_ATOMMOVE', 'wxID_MAKEMOLECULE',
-                'wxID_ATOMSPDISAGL', 'wxID_ISODISP', 'wxID_ADDHATOM', 'wxID_UPDATEHATOM',
-                'wxID_ATOMSROTATE', 'wxID_ATOMSDENSITY','wxID_ATOMSBNDANGLHIST',
+                'wxID_ATOMSPDISAGL', 'wxID_ISODISP', 'wxID_ADDHATOM', 'wxID_UPDATEHATOM','wxID_ATOMSCLEARHIST',
+                'wxID_ATOMSROTATE', 'wxID_ATOMSDENSITY','wxID_ATOMSBNDANGLHIST','wxID_ATOMSSAVEHIST',
                 'wxID_ATOMSSETALL', 'wxID_ATOMSSETSEL','wxID_ATOMFRACSPLIT','wxID_COLLECTATOMS',
                 'wxID_ATOMSSETVP', 'wxID_ATOMSSETLST')
             self.AtomsMenu = wx.MenuBar()
@@ -7201,6 +7201,8 @@ def _makemenu():     # routine to create menu when first used
             self.AtomCompute.Append(G2G.wxID_ATOMSDISAGL,'Show Distances && Angles','Compute distances & angles for selected atoms')
             self.AtomCompute.Append(G2G.wxID_ATOMSPDISAGL,'Save Distances && Angles','Compute distances & angles for selected atoms')
             self.AtomCompute.Append(G2G.wxID_ATOMSBNDANGLHIST,'Histogram Bonds && Angles','Histogram bonds & angles for selected atoms')
+            self.AtomCompute.Append(G2G.wxID_ATOMSSAVEHIST,'Save all B&&A histograms','Save all bond & angle histograms')
+            self.AtomCompute.Append(G2G.wxID_ATOMSCLEARHIST,'Clear all B&&A histograms','Clear all bond & angle histograms')
             self.AtomCompute.Append(G2G.wxID_ATOMFRACSPLIT,'Apportion atom frac','2 atom type site fraction apportion')
             self.AtomCompute.Append(G2G.wxID_ATOMSDENSITY,'Density','Compute density for current phase')
             self.AtomCompute.ISOcalc = self.AtomCompute.Append(G2G.wxID_ISODISP,'ISODISTORT mode values',

GSASII/GSASIIimage.py

@@ -1239,10 +1239,9 @@ def polymask(data,Poly,Spots=[]):
     ax0 = figure.add_subplot()
     ax0.axis("off")
     figure.subplots_adjust(bottom=0.,top=1.,left=0.,right=1.,wspace=0.,hspace=0.)
-    for poly in Poly:
-        px = np.array(poly).T[0]/scalex
-        py = np.array(poly).T[1]/scaley
-        ax0.fill(px,py,inmask)
+    px = np.array(Poly).T[0]/scalex
+    py = np.array(Poly).T[1]/scaley
+    ax0.fill(px,py,inmask)
     for spot in Spots:
         px = np.array(spot).T[0]/scalex
         py = np.array(spot).T[1]/scaley
@@ -1271,21 +1270,14 @@ def MakeMaskMap(data,masks,iLim,jLim):
     pixelSize = data['pixelSize']
     scalex = pixelSize[0]/1000.
     scaley = pixelSize[1]/1000.
-    frame = []
-    poly = []
+    frame = np.zeros(data['size'],dtype='uint8')
+    poly = np.zeros(data['size'],dtype='uint8')
     if iLim[0] == jLim[0] == 0:
         if masks['Frames']:
             frame = np.abs(polymask(data,masks['Frames'])-255) #turn inner to outer mask
         if masks['Polygons'] or masks['Points']:
             poly = polymask(data,masks['Polygons'],masks['Points'])
-        if len(frame):
-            masks['Pmask'] =  frame
-            if len(poly):
-                masks['Pmask'] = masks['Pmask']+poly
-        if len(poly):
-            masks['Pmask'] =  poly
-        else:
-            masks['Pmask'] =  []
+        masks['Pmask'] =  frame+poly
     tay,tax = np.mgrid[iLim[0]+0.5:iLim[1]+.5,jLim[0]+.5:jLim[1]+.5]         #bin centers not corners
     tax = np.asarray(tax*scalex,dtype=np.float32).flatten()
     tay = np.asarray(tay*scaley,dtype=np.float32).flatten()
@@ -1426,8 +1418,7 @@ def MakeUseMask(data,masks,blkSize=128):
     return useMask
 
 def MakeGainMap(image,Ix,Iy,data,mask,blkSize=128):
-    Iy /= npcosd(Ix[:-1])       #undo parallax
-    Iy *= (1000./data['distance'])**2    #undo r^2 effect
+    Iy *= npcosd(Ix[:-1])**2       #undo parallax
     Iy /= np.array(G2pwd.Polarization(data['PolaVal'][0],Ix[:-1],0.)[0])    #undo polarization
     if data['Oblique'][1]:
         Iy *= G2pwd.Oblique(data['Oblique'][0],Ix[:-1])     #undo penetration
@@ -1645,8 +1636,7 @@ def ImageIntegrate(image,data,masks,blkSize=128,returnN=False,useTA=None,useMask
     if 'SASD' not in data['type']:
         H0 *= np.array(G2pwd.Polarization(data['PolaVal'][0],H2[:-1],0.)[0])
     if np.abs(data['det2theta']) < 1.0:         #small angle approx only; not appropriate for detectors at large 2-theta
-        H0 /= np.abs(npcosd(H2[:-1]-np.abs(data['det2theta'])))           #parallax correction
-    # H0 *= (data['distance']/1000.)**2    #remove r^2 effect - done earlier
+        H0 /= np.abs(npcosd(H2[:-1]-np.abs(data['det2theta'])))**4           #parallax correction (why **4?)
     if 'SASD' in data['type']:
         H0 /= npcosd(H2[:-1])           #one more for small angle scattering data?
     if data['Oblique'][1]:

GSASII/GSASIIimgGUI.py

@@ -1854,7 +1854,7 @@ def CleanupMasks(data):
     and before saving them or after reading them in. This should also probably be done
     before they are used for integration.
     '''
-    for key in ['Points','Rings','Arcs','Polygons',]:
+    for key in ['Points','Rings','Arcs','Polygons','Frames',]:
         data[key] = data.get(key,[])
         l1 = len(data[key])
         data[key] = [i for i in data[key] if len(i)]

GSASII/GSASIImiscGUI.py

@@ -978,7 +978,8 @@ def ExportSequentialFullCIF(G2frame,seqData,Controls):
     '''Handles access to CIF exporter a bit differently for sequential fits, as this is
     not accessed via the usual export menus
     '''
-    from exports import G2export_CIF
+    from . import exports
+    from GSASII.exports import G2export_CIF
     ##################### debug code to reload exporter before each use ####
     #import importlib as imp
     #imp.reload(G2export_CIF)

GSASII/GSASIIpath.py

@@ -210,22 +210,22 @@ def HowIsG2Installed():
 def getSavedVersionInfo():
     '''Get version number information from a file written by install
     routines. This is faster than getting the information from git. Also,
-    when GSAS-II is installed into Python, the files are no longer in 
-    a git repository so querying git is not possible.
+    when GSAS-II is installed into Python, files are no longer in 
+    a git repository, so querying git is not possible.
 
-    The saved_version.py file is written by install/save_versions.py.
-    The git_verinfo.py file is written by install/tag-version.py or
-    by install/incr-mini-version.py. If both are present, use the 
-    saved_version.py file preferentially. 
+    The git_verinfo.py file is written by install/incr-version.py or 
+    by install/save_versions.py
+    The saved_version.py file was previousl written by 
+    install/save_versions.py but this file is no longer in use.
 
     :returns: a reference to the version variables or None if no 
       version info file is found.
     '''
-    try:
-        from . import saved_version as gv
-        return gv
-    except:
-        pass
+#    try:
+#        from . import saved_version as gv
+#        return gv
+#    except:
+#        pass
     try:
         from . import git_verinfo as gv
         return gv