Merge remote-tracking branch 'origin/master' into develop

Author: briantoby

GSASII/GSASIIconstrGUI.py

@@ -26,7 +26,7 @@
 from . import GSASIIlattice as G2lat
 from . import GSASIIdataGUI as G2gd
 from . import GSASIIctrlGUI as G2G
-from . import GSASIIfiles as G2fl
+from . import GSASIIfiles as G2fil
 from . import GSASIIplot as G2plt
 from . import GSASIIobj as G2obj
 from . import GSASIIspc as G2spc
@@ -2756,7 +2756,7 @@ def MakeVectorBody(name=''):
             rd.ReInitialize()
             rd.errors = ""
             if not rd.ContentsValidator(filename):   # Report error
-                G2fl.G2Print("Warning: File {} has a validation error".format(filename))
+                G2fil.G2Print("Warning: File {} has a validation error".format(filename))
                 return
             if len(rd.selections) > 1:
                 print("File {} has {} phases. This is unexpected."
@@ -2767,7 +2767,7 @@ def MakeVectorBody(name=''):
             try:
                 rd.Reader(filename)
             except Exception as msg:
-                G2fl.G2Print("Warning: read of file {} failed\n{}".format(
+                G2fil.G2Print("Warning: read of file {} failed\n{}".format(
                     filename,rd.errors))
                 if GSASIIpath.GetConfigValue('debug'):
                     print(msg)
@@ -4141,14 +4141,14 @@ def _onClose(event):
                 subSizer2.Add((-1,-1))
             subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl)))
             try:
-                value = G2fl.FormatSigFigs(delocc)
+                value = G2fil.FormatSigFigs(delocc)
             except TypeError:
                 value = str(delocc)
             subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
             #subSizer.Add((10,-1))
             subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var)))
             try:
-                value = G2fl.FormatSigFigs(val/norm)
+                value = G2fil.FormatSigFigs(val/norm)
                 if 'varyList' in covdata:
                     if str(G2mode) in covdata['varyList']:
                         sig = covdata['sig'][covdata['varyList'].index(str(G2mode))]

GSASII/GSASIIctrlGUI.py

@@ -9518,7 +9518,144 @@ def gitSelectBranch(event):
     G2fil.openInNewTerm(project)
     print ('exiting GSAS-II')
     sys.exit()
+    
+def gitSwitch2DevBranch(event):
+    '''This is "patch" code to switch from the master branch
+    to the develop (eventually to be renamed main) branch. 
+    Complication here is that the GSASII.py file gets renamed 
+    to G2.py so "shortcuts" need to be re-created to reference that. 
+
+    This is not yet "plumbed" into the current code, but it has been
+    tested with Windows and Mac. At some point this will be made part of the
+    update process in the master branch, but this routine is not needed in 
+    the develop (or eventially main) branch.
+    '''
+    G2frame = wx.App.GetMainTopWindow()
+    gitInst = GSASIIpath.HowIsG2Installed()
+    if not gitInst.startswith('github-rev'):
+        G2MessageBox(G2frame,
+            'Unable to switch branches unless GSAS-II has been installed from GitHub; installed as: '+gitInst,
+            'Not a git install')
+        return
+    if not os.path.exists(GSASIIpath.path2GSAS2): 
+        print(f'Warning: Directory {GSASIIpath.path2GSAS2} not found')
+        return
+    if os.path.exists(os.path.join(GSASIIpath.path2GSAS2,'..','.git')):
+        path2repo = os.path.join(path2GSAS2,'..')  # expected location
+    elif os.path.exists(os.path.join(GSASIIpath.path2GSAS2,'.git')):
+        path2repo = GSASIIpath.path2GSAS2
+    else:
+        print(f'Warning: Repository {path2GSAS2} not found')
+        return
+    try:
+        g2repo = GSASIIpath.openGitRepo(path2repo)
+    except Exception as msg:
+        print(f'Warning: Failed to open repository. Error: {msg}')
+        return
+    if g2repo.is_dirty() or g2repo.index.diff("HEAD"): # changed or staged files
+        G2MessageBox(G2frame,
+            'You have local changes. They must be reset, committed or stashed before switching branches',
+            'Local changes')
+        return
+    if g2repo.head.is_detached:
+        G2MessageBox(G2frame,
+            'You have a old previous version loaded; you must be on a branch head to switching branches',
+            'Detached head')
+        return
+    if g2repo.active_branch.name != "master":
+        G2MessageBox(G2frame,
+            f'You are on the {g2repo.active_branch.name} branch. This can only be run from master.',
+            'Not on master')
+        return
+        
+    # make sure that branches are accessible & get updates
+    print('getting updates...',end='')
+    g2repo.git.remote('set-branches','origin','*')
+    print('..',end='')
+    g2repo.git.fetch()
+    print('.done')
+    branchlist = [i.strip() for i in g2repo.git.branch('-r').split('\n') if '->' not in i]
+    choices = [i for i in  [os.path.split(i)[1] for i in branchlist] if i != g2repo.active_branch.name]
+    b = "develop"
+    if b not in choices: 
+        G2MessageBox(G2frame,
+            f'You are on the {g2repo.active_branch.name!r} branch, but branch {b!r} was not found.',
+            f'No {b} branch')
+        return
+    msg = f'''Confirm switching from git branch {g2repo.active_branch.name!r} to {b!r}.
+
+If confirmed here, GSAS-II will restart. 
+
+Do you want to save your project before restarting?
+Select "Yes" to save, "No" to skip the save, or "Cancel"
+to discontinue the restart process.
+
+If "Yes", GSAS-II will reopen the project after the update.
+
+The switch will be made unless Cancel is pressed.'''
+    dlg = wx.MessageDialog(G2frame, msg, 'Confirm branch switch?',
+                wx.YES_NO|wx.CANCEL|wx.YES_DEFAULT|wx.CENTRE|wx.ICON_QUESTION)
+    ans = dlg.ShowModal()
+    dlg.Destroy()
+    if ans == wx.ID_CANCEL:
+        return
+    elif ans == wx.ID_YES:
+        ans = G2frame.OnFileSave(None)
+        if not ans: return
+        project = os.path.abspath(G2frame.GSASprojectfile)
+        print(f"Restarting GSAS-II with project file {project!r}")
+    else:
+        print("Restarting GSAS-II without a project file ")
+        project = None
+    # I hope that it is possible to do a checkout on Windows
+    # (source files are not locked). If this is not the case
+    # then another approach will be needed, where a .bat file is used
+    # or GSASIIpath is used, as is the case for updates
+    a = g2repo.git.checkout(b)
+    if 'Your branch is behind' in a:
+        print('updating local copy of branch')
+        print(g2repo.git.pull())
+    # post-install stuff (following gitstrap.py)
+    print(f'Byte-compiling all .py files in {GSASIIpath.path2GSAS2!r}... ',end='')
+    import compileall
+    compileall.compile_dir(GSASIIpath.path2GSAS2,quiet=True)
+    print('done')
+    #
+    print('start system-specific install')
+    for k,s in {'win':"makeBat.py", 'darwin':"makeMacApp.py",
+                    'linux':"makeLinux.py"}.items():
+        if sys.platform.startswith(k):
+            script = os.path.join(GSASIIpath.path2GSAS2,'install',s)
+            if not os.path.exists(script):
+                print(f'Platform-specific script {script!r} not found')
+                script = ''
+            break
+    else:
+        print(f'Unknown platform {sys.platform}')
+    # on a Mac, make an applescript
+    if script and sys.platform.startswith('darwin'):
+        print(f'running {script}')
+        import subprocess
+        out = 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)
+    # On linux, make a desktop icon with hard-coded paths to Python and GSAS-II
+    elif script:
+        sys.argv = [script]
+        print(f'running {sys.argv[0]}')
+        with open(sys.argv[0]) as source_file:
+            exec(source_file.read())
+
+    print('system-specific install done')
 
+    G2fil.openInNewTerm(project)
+    print ('exiting GSAS-II')
+    sys.exit()
+    
 #===========================================================================
 # Importer GUI stuff
 def ImportMsg(parent,msgs):
@@ -9577,25 +9714,34 @@ def SelectPkgInstall(event):
     if sel is None: return
     if not any(sel): return
     pkgs = [choices[i][0] for i,f in enumerate(sel) if f]
+    wx.BeginBusyCursor()
+    pdlg = wx.ProgressDialog('Updating','Installing Python packages; this can take a while',
+                    parent=G2frame)
     if GSASIIpath.condaTest():
         patch_condarc()
         if not GSASIIpath.condaTest(True):
             GSASIIpath.addCondaPkg()
         err = GSASIIpath.condaInstall(pkgs)
         if err:
             print(f'Error from conda: {err}')
+            wx.EndBusyCursor()
+            pdlg.Destroy()
             return
     else:
         err = GSASIIpath.pipInstall(pkgs)
         if err:
             print(f'Error from pip: {err}')
+            wx.EndBusyCursor()
+            pdlg.Destroy()
             return
-    msg = '''You must restart GSAS-II to access the importer(s)
-requiring the installed package(s).
-
-Select "Yes" to save, "No" to skip the save, or "Cancel"
-to discontinue the restart process and continue GSAS-II
-without the importer(s).
+    wx.EndBusyCursor()
+    pdlg.Destroy()
+    msg = '''You must restart GSAS-II to access the importer(s) 
+requiring the package(s) just installed.
+
+Select "Yes" to save and restart, "No" to restart without
+the save, or "Cancel" to discontinue the restart process 
+and continue use of GSAS-II without the importer(s).
 
 If "Yes", GSAS-II will reopen the project after the update.
 '''

GSASII/GSASIIdataGUI.py

@@ -3006,10 +3006,7 @@ def __init__(self, parent):
                       GSASIIpath.GetConfigValue('Starting_directory'))
         arg = sys.argv
         if len(arg) > 1 and arg[1]:
-            try:
-                self.GSASprojectfile = os.path.splitext(arg[1])[0]+u'.gpx'
-            except:
-                self.GSASprojectfile = os.path.splitext(arg[1])[0]+'.gpx'
+            self.GSASprojectfile = os.path.splitext(arg[1])[0]+'.gpx'
             self.dirname = os.path.abspath(os.path.dirname(arg[1]))
             if self.dirname:
                 self.GSASprojectfile = os.path.split(self.GSASprojectfile)[1]
@@ -5473,6 +5470,7 @@ def OnRefine(self,event):
             try:
                 if dlg2.ShowModal() == wx.ID_OK:
                     self.reloadFromGPX(rtext,Rvals)
+                    G2IO.LogCellChanges(self)
                 if refPlotUpdate:
                     refPlotUpdate({},restore=True)
                     refPlotUpdate = None
@@ -6964,7 +6962,7 @@ def _makemenu():     # routine to create menu when first used
         # IMG / Masks
         G2G.Define_wxId('wxID_MASKCOPY', 'wxID_MASKSAVE', 'wxID_MASKLOAD', 'wxID_NEWMASKSPOT', 'wxID_NEWMASKARC', 'wxID_NEWMASKRING',
             'wxID_NEWMASKFRAME', 'wxID_NEWMASKPOLY','wxID_NEWMASKXLINE','wxID_NEWMASKYLINE','wxID_MASKLOADNOT',
-            'wxID_FINDSPOTS', 'wxID_AUTOFINDSPOTS', 'wxID_DELETESPOTS',)
+            'wxID_FINDSPOTS', 'wxID_AUTOFINDSPOTS', 'wxID_DELETESPOTS','wxID_MASKCOPYSELECTED')
         def _makemenu():     # routine to create menu when first used
             self.MaskMenu = wx.MenuBar()
             self.PrefillDataMenu(self.MaskMenu)
@@ -6973,6 +6971,7 @@ def _makemenu():     # routine to create menu when first used
             submenu = wx.Menu()
             self.MaskEdit.AppendSubMenu( submenu,'Create new','')
             self.MaskEdit.Append(G2G.wxID_MASKCOPY,'Copy mask','Copy mask to other images')
+            self.MaskEdit.Append(G2G.wxID_MASKCOPYSELECTED,'Copy Selected','Copy selected masks to other images')
             self.MaskEdit.Append(G2G.wxID_MASKSAVE,'Save mask','Save mask to file')
             self.MaskEdit.Append(G2G.wxID_MASKLOADNOT,'Load mask','Load mask from file; ignoring threshold')
             self.MaskEdit.Append(G2G.wxID_MASKLOAD,'Load mask w/threshold','Load mask from file keeping the threshold value')
@@ -7408,6 +7407,11 @@ def OnAddNotebook(event):
             data.append(f'[CM] {dlg.GetValue().strip()}')
         dlg.Destroy()
         wx.CallAfter(UpdateNotebook,G2frame,data)
+    def OnSaveNotebook(event):
+        filename = os.path.splitext(G2frame.GSASprojectfile)[0]+'_notebook.txt'
+        filename = os.path.join(G2frame.dirname,filename)
+        open(filename,'w').write(textBox.GetText())
+        print(f'Notebook contents written into {filename}')
     def onPlotNotebook():
         'Locate R values from the Notebook and plot them'
         NBinfo['plotLbl']
@@ -7439,11 +7443,11 @@ def onPlotNotebook():
     filterLbls = ['all',
                       'Timestamps','Refinement results','Variables',
                       'Comments','Charge flip','Fourier','Peak fit',
-                      'Constraints','Restraints','Rigid Bodies']
+                      'Constraints','Restraints','Rigid Bodies','Cell params']
     filterPrefix = ['',
                         'TS', 'REF','VARS',
                         'CM', 'CF', 'FM', 'PF',
-                        'CNSTR','RSTR','RB']
+                        'CNSTR','RSTR','RB','CEL']
     cId = GetGPXtreeItemId(G2frame,G2frame.root, 'Controls')
     if cId:
         controls = G2frame.GPXtree.GetItemPyData(cId)
@@ -7469,7 +7473,7 @@ def onPlotNotebook():
     botSizer.Clear(True)
     parent = G2frame.dataWindow.bottomPanel
     botSizer.Add((20,-1))
-    controls['Notebook']['order'] = controls['Notebook'].get('order',False)
+    controls['Notebook']['order'] = controls['Notebook'].get('order',True)
     botSizer.Add(wx.StaticText(parent,wx.ID_ANY,'  order: '),0,WACV)
     botSizer.Add(G2G.EnumSelector(parent,controls['Notebook'],
                          'order',['oldest-1st','newest-1st'],[False,True],
@@ -7489,9 +7493,12 @@ def onPlotNotebook():
     botSizer.Add((20,-1))
     botSizer.Add(fBtn,0,WACV)
     botSizer.Add((20,-1),1,wx.EXPAND,1)
+    Btn = wx.Button(parent,label='Save')
+    botSizer.Add(Btn,0,WACV)
+    Btn.Bind(wx.EVT_BUTTON,OnSaveNotebook)
     import wx.stc as stc
-    text = stc.StyledTextCtrl(G2frame.dataWindow,wx.ID_ANY)
-    text.SetScrollWidthTracking(True)    # does not seem to do anything
+    textBox = stc.StyledTextCtrl(G2frame.dataWindow,wx.ID_ANY)
+    textBox.SetScrollWidthTracking(True)    # does not seem to do anything
     if controls['Notebook']['order']:
         # reverse entries in blocks, so that lines stay after their timestamp
         order = []
@@ -7525,22 +7532,22 @@ def onPlotNotebook():
             show = True
         if show:
             if prefix == 'TS':
-                if not first: text.AppendText("\n")
-                text.AppendText(line.strip())
+                if not first: textBox.AppendText("\n")
+                textBox.AppendText(line.strip())
             elif prefix and (controls['Notebook']['filterSel'][0]
                                 or controls['Notebook']['filterSel'][1]):
                 # indent all but timestamps
                 for l in line.strip().split('\n'):
-                    if not first: text.AppendText("\n")
-                    text.AppendText('    '+l.strip())
+                    if not first: textBox.AppendText("\n")
+                    textBox.AppendText('    '+l.strip())
                     first = False
             else:
-                if not first: text.AppendText("\n")
-                text.AppendText(line.strip())
+                if not first: textBox.AppendText("\n")
+                textBox.AppendText(line.strip())
         first = False
     bigSizer = wx.BoxSizer(wx.VERTICAL)
-    bigSizer.Add(text,1,wx.EXPAND)
-    text.SetReadOnly(True)
+    bigSizer.Add(textBox,1,wx.EXPAND)
+    textBox.SetReadOnly(True)
     bigSizer.Layout()
     bigSizer.FitInside(G2frame.dataWindow)
     G2frame.dataWindow.SetSizer(bigSizer)

GSASII/GSASIIimage.py

@@ -8,7 +8,6 @@
 import math
 import time
 import copy
-import sys
 import numpy as np
 import numpy.linalg as nl
 import numpy.ma as ma
@@ -1472,7 +1471,6 @@ def MakeUseMask(data,masks,blkSize=128):
     return useMask
 
 def MakeGainMap(image,Ix,Iy,data,blkSize=128):
-    import scipy.ndimage.filters as sdif
     Iy /= npcosd(Ix[:-1])       #undo parallax
     Iy *= (1000./data['distance'])**2    #undo r^2 effect
     Iy /= np.array(G2pwd.Polarization(data['PolaVal'][0],Ix[:-1],0.)[0])    #undo polarization
@@ -1493,8 +1491,7 @@ def MakeGainMap(image,Ix,Iy,data,blkSize=128):
             TA = Make2ThetaAzimuthMap(data,(iBeg,iFin),(jBeg,jFin))           #2-theta & azimuth arrays & create position mask
             Ipix = IyInt(TA[0])
             GainMap[iBeg:iFin,jBeg:jFin] = image[iBeg:iFin,jBeg:jFin]/(Ipix*TA[3])
-    GainMap = np.nan_to_num(GainMap,1.0)
-    GainMap = sdif.gaussian_filter(GainMap,3.,order=0)
+    GainMap /= np.nanmedian(GainMap)
     return 1./GainMap
 
 def AzimuthIntegrate(image,data,masks,ringId,blkSize=1024):