Add grouping of histograms #275

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briantoby wants to merge 57 commits into main from TOFgroup

GSASII/GSASIIdataGUI.py

Large diffs are not rendered by default.

GSASII/GSASIIfiles.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -1467,7 +1467,11 @@ def FormatValue(val,maxdigits=None): @@
             digits.append('f')
         if not val:
             digits[2] = 'f'
-        fmt="{:"+str(digits[0])+"."+str(digits[1])+digits[2]+"}"
+        if digits[2] == 'g':
+            fmt="{:#"+str(digits[0])+"."+str(digits[1])+digits[2]+"}"
+            # the # above forces inclusion of a decimal place: 10.000 rather than 10 for 9.999999999
+        else:
+            fmt="{:"+str(digits[0])+"."+str(digits[1])+digits[2]+"}"
         string = fmt.format(float(val)).strip() # will standard .f formatting work?
         if len(string) <= digits[0]:
             if ':' in string: # deal with weird bug where a colon pops up in a number when formatting (EPD 7.3.2!)
@@ Expand Down @@

GSASII/GSASIIgroupGUI.py

Large diffs are not rendered by default.

GSASII/GSASIImiscGUI.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -8,8 +8,6 @@ @@
     '''
-    from __future__ import division, print_function
     # # Allow this to be imported without wx present.
     # try:
     #     import wx
@@ Expand Down Expand Up / @@ -554,6 +552,8 @@ def ProjFileOpen(G2frame,showProvenance=True): @@
             finally:
                 dlg.Destroy()
         wx.BeginBusyCursor()
+        groupDict = {}
+        groupInserted = False   # only need to do this once
         try:
             if GSASIIpath.GetConfigValue('show_gpxSize'):
                 posPrev = 0
@@ Expand All / @@ -575,13 +575,23 @@ def ProjFileOpen(G2frame,showProvenance=True): @@
                     #if unexpectedObject:
                     #    print(datum[0])
                     #    GSASIIpath.IPyBreak()
+                # insert groups before any individual PDWR items
+                if datum[0].startswith('PWDR') and groupDict and not groupInserted:
+                    Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Groups/Powder')
+                    G2frame.GPXtree.SetItemPyData(Id,{})
+                    for nam in groupDict:
+                        sub = G2frame.GPXtree.AppendItem(parent=Id,text=nam)
+                        G2frame.GPXtree.SetItemPyData(sub,{})
+                    groupInserted = True
                 Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0])
                 if datum[0] == 'Phases' and GSASIIpath.GetConfigValue('SeparateHistPhaseTreeItem',False):
                     G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Hist/Phase')
                 if updateFromSeq and datum[0] == 'Phases':
                     for pdata in data[1:]:
                         if pdata[0] in Phases:
                             pdata[1].update(Phases[pdata[0]])
+                elif datum[0] == 'Controls':
+                    groupDict = datum[1].get('Groups',{}).get('groupDict',{})
                 elif updateFromSeq and datum[0] == 'Covariance':
                     data[0][1] = CovData
                 elif updateFromSeq and datum[0] == 'Rigid bodies':
@@ Expand Down Expand Up / @@ -720,7 +730,7 @@ def ProjFileSave(G2frame): @@
                 while item:
                     data = []
                     name = G2frame.GPXtree.GetItemText(item)
-                    if name.startswith('Hist/Phase'):  # skip over this
+                    if name.startswith('Hist/Phase') or name.startswith('Groups'):  # skip over this
                         item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
                         continue
                     data.append([name,G2frame.GPXtree.GetItemPyData(item)])
@@ Expand Down @@

GSASII/GSASIIobj.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -611,9 +611,9 @@ def CompileVarDesc():
  
        for key,value in {

            # derived or other sequential vars

            '([abc])$' : 'Lattice parameter, \\1, from Ai and Djk', # N.B. '$' prevents match if any characters follow

            u'\u03B1' : u'Lattice parameter, \u03B1, computed from both Ai and Djk',

            u'\u03B2' : u'Lattice parameter, \u03B2, computed from both Ai and Djk',

            u'\u03B3' : u'Lattice parameter, \u03B3, computed from both Ai and Djk',

            '\u03B1' : 'Lattice parameter, \u03B1, computed from both Ai and Djk',

            '\u03B2' : 'Lattice parameter, \u03B2, computed from both Ai and Djk',

            '\u03B3' : 'Lattice parameter, \u03B3, computed from both Ai and Djk',

            # ambiguous, alas:

            'Scale' : 'Phase fraction (as p:h:Scale) or Histogram scale factor (as :h:Scale)',

            # Phase vars (p::<var>)

    @@ -647,8 +647,8 @@ def CompileVarDesc():
  
            'D([123][123])' : 'Anisotropic strain coef. \\1',

            'Extinction' : 'Extinction coef.',

            'MD' : 'March-Dollase coef.',

            'Mustrain;.*' : 'Microstrain coefficient (delta Q/Q x 10**6)',

            'Size;.*' : 'Crystallite size value (in microns)',

            'Mustrain;(.*)' : 'Microstrain coefficient (delta Q/Q x 10**6, \\1: i=iso/eq, a=axial, general:0-5, mx=LGmix)',

            'Size;(.*)' : 'Crystallite size value (in microns, \\1: i=iso/eq, a=axial, general:0-5, mx=LGmix)',

            'eA$' : 'Cubic mustrain value',

            'Ep$' : 'Primary extinction',

            'Es$' : 'Secondary type II extinction',

    @@ -669,14 +669,14 @@ def CompileVarDesc():
  
            'SH/L' : ('FCJ peak asymmetry correction',1e-4),

            '([UVW])$' : ('Gaussian instrument broadening \\1',1e-5),

            '([XYZ])$' : ('Cauchy instrument broadening \\1',1e-5),

            'Zero' : 'Debye-Scherrer zero correction',

            'Zero' : 'Debye-Scherrer/TOF zero correction',

            'Shift' : 'Bragg-Brentano sample displ.',

            'SurfRoughA' : 'Bragg-Brentano surface roughness A',

            'SurfRoughB' : 'Bragg-Brentano surface roughness B',

            'Transparency' : 'Bragg-Brentano sample tranparency',

            'DebyeA' : 'Debye model amplitude',

            'DebyeR' : 'Debye model radius',

            'DebyeU' : 'Debye model Uiso',

            'Transparency' : 'Bragg-Brentano sample transparency',

            'DebyeA;(.*)' : 'Debye model peak #\\1 amplitude',

            'DebyeR;(.*)' : 'Debye model peak #\\1 radius',

            'DebyeU;(.*)' : 'Debye model peak #\\1 Uiso',

            'RBV.*' : 'Vector rigid body parameter',

            'RBVO([aijk])' : 'Vector rigid body orientation parameter \\1',

            'RBVP([xyz])' : 'Vector rigid body \\1 position parameter',

    @@ -2271,14 +2271,14 @@ def showEQ(calcobj):
  
        obj.expression = "A*np.exp(B)"

        obj.assgnVars =  {'B': '0::Afrac:1'}

        obj.freeVars =  {'A': [u'A', 0.5, True]}

        obj.freeVars =  {'A': ['A', 0.5, True]}

        #obj.CheckVars()

        calcobj = ExpressionCalcObj(obj)

        obj1 = ExpressionObj()

        obj1.expression = "A*np.exp(B)"

        obj1.assgnVars =  {'B': '0::Afrac:*'}

        obj1.freeVars =  {'A': [u'Free Prm A', 0.5, True]}

        obj1.freeVars =  {'A': ['Free Prm A', 0.5, True]}

        #obj.CheckVars()

        calcobj1 = ExpressionCalcObj(obj1)

GSASII/GSASIIplot.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -213,14 +213,14 @@ def __init__(self,parent,id=-1,dpi=None,**kwargs):
  
    class G2PlotMpl(_tabPlotWin):

        'Creates a Matplotlib 2-D plot in the GSAS-II graphics window'

        def __init__(self,parent,id=-1,dpi=None,publish=None,**kwargs):

        def __init__(self,parent,id=-1,dpi=None,**kwargs):

            _tabPlotWin.__init__(self,parent,id=id,**kwargs)

            mpl.rcParams['legend.fontsize'] = 10

            mpl.rcParams['axes.grid'] = False

            #TODO: set dpi here via config var: this changes the size of the labeling font 72-100 is normal

            self.figure = mplfig.Figure(dpi=dpi,figsize=(5,6))

            self.canvas = Canvas(self,-1,self.figure)

            self.toolbar = GSASIItoolbar(self.canvas,publish=publish)

            self.toolbar = GSASIItoolbar(self.canvas)

            self.toolbar.Realize()

            self.plotStyle = {'qPlot':False,'dPlot':False,'sqrtPlot':False,'sqPlot':False,

                'logPlot':False,'exclude':False,'partials':True,'chanPlot':False}

    @@ -324,6 +324,7 @@ def __init__(self,parent,id=-1,G2frame=None):
  
            self.allowZoomReset = True # this indicates plot should be updated not initialized

                                       # (BHT: should this be in tabbed panel rather than here?)

            self.lastRaisedPlotTab = None

            self.savedPlotLims = None

        def OnNotebookKey(self,event):

            '''Called when a keystroke event gets picked up by the notebook window

    @@ -394,7 +395,7 @@ def GetTabIndex(self,label):
  
        #     if plotNum is not None:

        #         wx.CallAfter(self.SetSelectionNoRefresh,plotNum)

        def FindPlotTab(self,label,Type,newImage=True,publish=None):

        def FindPlotTab(self,label,Type,newImage=True,saveLimits=False):

            '''Open a plot tab for initial plotting, or raise the tab if it already exists

            Set a flag (Page.plotInvalid) that it has been redrawn

            Record the name of the this plot in self.lastRaisedPlotTab

    @@ -408,9 +409,8 @@ def FindPlotTab(self,label,Type,newImage=True,publish=None):
  
            :param bool newImage: forces creation of a new graph for matplotlib

              plots only (defaults as True)

            :param function publish: reference to routine used to create a

              publication version of the current mpl plot (default is None,

              which prevents use of this).

            :param bool saveLimits: When True, limits for all MPL axes (plots)

              are saved in self.savedPlotLims.

            :returns: new,plotNum,Page,Plot,limits where

              * new: will be True if the tab was just created

    @@ -419,15 +419,17 @@ def FindPlotTab(self,label,Type,newImage=True,publish=None):
  
                the plot appears

              * Plot: the mpl.Axes object for the graphic (mpl) or the figure for

                openGL.

              * limits: for mpl plots, when a plot already exists, this will be a tuple

                with plot scaling. None otherwise.

              * limits: for mpl plots, when a plot already exists, this 

                will be a tuple with plot scaling. None otherwise. Only appropriate

                for plots with one set of axes. 

            '''

            limits = None

            Plot = None

            try:

                new = False

                plotNum,Page = self.GetTabIndex(label)

                if Type == 'mpl' or Type == '3d':

                    if saveLimits: self.savePlotLims(Page)

                    Axes = Page.figure.get_axes()

                    Plot = Page.figure.gca()          #get previous plot

                    limits = [Plot.get_xlim(),Plot.get_ylim()] # save previous limits

    @@ -443,7 +445,7 @@ def FindPlotTab(self,label,Type,newImage=True,publish=None):
  
            except (ValueError,AttributeError):

                new = True

                if Type == 'mpl':

                    Plot = self.addMpl(label,publish=publish).gca()

                    Plot = self.addMpl(label).gca()

                elif Type == 'ogl':

                    Plot = self.addOgl(label)

                elif Type == '3d':

    @@ -468,8 +470,63 @@ def FindPlotTab(self,label,Type,newImage=True,publish=None):
  
                Page.helpKey = self.G2frame.dataWindow.helpKey

            except AttributeError:

                Page.helpKey = 'HelpIntro'

            try:

                Page.toolbar.enableArrows() # Disable Arrow keys if present

            except AttributeError:

                pass

            return new,plotNum,Page,Plot,limits

        def savePlotLims(self,Page=None,debug=False,label=None):

            '''Make a copy of all the current axes in the notebook object

            '''

            if label and Page:

                print('Warning: label and Page defined in savePlotLims')

            elif label:

                try:

                    plotNum,Page = self.GetTabIndex(label)

                except ValueError:

                    print(f'Warning: plot {label} not found in savePlotLims')

                    return

            elif not Page:

                print('Error: neither label nor Page defined in savePlotLims')

                return

            self.savedPlotLims = [

                [i.get_xlim() for i in Page.figure.get_axes()],

                [i.get_ylim() for i in Page.figure.get_axes()]]

            if debug:

                print(f'saved {len(self.savedPlotLims[1])} axes limits')

                #print( self.savedPlotLims)

        def restoreSavedPlotLims(self,Page):

            '''Restore the plot limits, when previously saved, and when 

            ``G2frame.restorePlotLimits`` is set to True, which 

            is done when ``GSASIIpwdplot.refPlotUpdate`` is called with

            ``restore=True``, which indicates that "live plotting" is 

            finished. This is also set for certain plot key-press

            combinations.

            The restore operation can only be done once, as the limits

            are deleted after use in this method.

            '''

            if self.savedPlotLims is None:

                #print('---- nothing to restore')

                return

            if not getattr(self.G2frame,'restorePlotLimits',False):

                #print('---- restorePlotLimits not set')

                return

            savedPlotLims = self.savedPlotLims

            axesList = Page.figure.get_axes()

            if len(axesList) != len(savedPlotLims[0]):

                #print('saved lengths differ',len(axesList),len(savedPlotLims[0]))

                return

            for i,ax in enumerate(axesList):

                ax.set_xlim(savedPlotLims[0][i])

                ax.set_ylim(savedPlotLims[1][i])

                #print(i,

                #            savedPlotLims[0][i][0],savedPlotLims[0][i][1],

                #            savedPlotLims[1][i][0],savedPlotLims[1][i][1])

            self.savedPlotLims = None

            self.G2frame.restorePlotLimits = False

            Page.canvas.draw()

        def _addPage(self,name,page):

            '''Add the newly created page to the notebook and associated lists.

    @@ -492,9 +549,9 @@ def _addPage(self,name,page):
  
            #page.replotKWargs = {}

            #self.skipPageChange = False

        def addMpl(self,name="",publish=None):

        def addMpl(self,name=""):

            'Add a tabbed page with a matplotlib plot'

            page = G2PlotMpl(self.nb,publish=publish)

            page = G2PlotMpl(self.nb)

            self._addPage(name,page)

            return page.figure

    @@ -605,7 +662,7 @@ def InvokeTreeItem(self,pid):
  
    class GSASIItoolbar(Toolbar):

        'Override the matplotlib toolbar so we can add more icons'

        def __init__(self,plotCanvas,publish=None,Arrows=True):

        def __init__(self,plotCanvas,Arrows=True):

            '''Adds additional icons to toolbar'''

            self.arrows = {}

            # try to remove a button from the bar

    @@ -630,16 +687,25 @@ def __init__(self,plotCanvas,publish=None,Arrows=True):
  
                        prfx = 'Shift plot '

                    fil = ''.join([i[0].lower() for i in direc.split()]+['arrow.ico'])

                    self.arrows[direc] = self.AddToolBarTool(sprfx+direc,prfx+direc,fil,self.OnArrow)

            if publish:

                self.AddToolBarTool('Publish plot','Create publishable version of plot','publish.ico',publish)

            self.publishId = self.AddToolBarTool('Publish plot','Create publishable version of plot','publish.ico',self.Publish)

            self.publishRoutine = None

            self.EnableTool(self.publishId,False)

            self.Realize()

        def setPublish(self,publish=None):

            'Set the routine to be used to publsh the plot'

            self.publishRoutine = publish

            self.EnableTool(self.publishId,bool(publish))

        def Publish(self,*args,**kwargs):

            'Called to publish the current plot'

            if not self.publishRoutine: return

            self.publishRoutine(*args,**kwargs)

        def set_message(self,s):

            ''' this removes spurious text messages from the tool bar

            '''

            pass

    # TODO: perhaps someday we could pull out the bitmaps and rescale there here    

    # TODO: perhaps someday we could pull out the bitmaps and rescale them here    

    #    def AddTool(self,*args,**kwargs):

    #        print('AddTool',args,kwargs)

    #        return Toolbar.AddTool(self,*args,**kwargs)

    @@ -663,6 +729,27 @@ def _update_view(self):
  
                wx.CallAfter(*self.updateActions)

            Toolbar._update_view(self)

        def home(self, *args):

            '''Override home button to clear saved GROUP plot limits and trigger replot.

            This ensures that pressing home resets to full data range while retaining x-units.

            For GROUP plots, we need to replot rather than use matplotlib's home because

            matplotlib's home would restore the original shared limits, not per-histogram limits.

            (based on MG/Cl Sonnet code)

            '''

            G2frame = wx.GetApp().GetMainTopWindow()

            # Check if we're in GROUP plot mode - if so, clear saved GROUP

            # plot x-limits and trigger a replot

            if self.arrows.get('_groupMode'):

                # PlotPatterns will use full data range

                if hasattr(G2frame, 'groupXlim'):

                    del G2frame.groupXlim

                # Trigger a full replot for GROUP plots

                if self.updateActions:

                    wx.CallAfter(*self.updateActions)

                return

            # For non-GROUP plots, call the parent's home method

            Toolbar.home(self, *args)

        def AnyActive(self):

            for Itool in range(self.GetToolsCount()):

                if self.GetToolState(self.GetToolByPos(Itool).GetId()):

    @@ -678,6 +765,22 @@ def GetActive(self):
  
        def OnArrow(self,event):

            'reposition limits to scan or zoom by button press'

            if self.arrows.get('_groupMode'):

                Page = self.arrows['_groupMode']

                if event.Id == self.arrows['right']:

                    Page.groupOff += 1

                elif event.Id == self.arrows['left']:

                    Page.groupOff -= 1

                elif event.Id == self.arrows['Expand X']:

                    Page.groupMax += 1

                elif event.Id == self.arrows['Shrink X']:

                    if Page.groupMax == 2: return

                    Page.groupMax -= 1

                else:

                    return

                if self.updateActions:

                    wx.CallLater(100,*self.updateActions)

                return

            axlist = self.plotCanvas.figure.get_axes()

            if len(axlist) == 1:

                 ax = axlist[0]

    @@ -735,6 +838,21 @@ def OnArrow(self,event):
  
    #        self.parent.toolbar.push_current()

            if self.updateActions:

                wx.CallAfter(*self.updateActions)

        def enableArrows(self,mode='',updateActions=None):

            '''Disable/Enable arrow keys.

            Disables when updateActions is None.

            mode='group' turns on 'x' buttons only

            '''

            if not self.arrows: return

            self.updateActions = updateActions

            if mode == 'group':

                # assumes that all arrows previously disabled

                for lbl in ('left', 'right', 'Expand X', 'Shrink X'):

                    self.EnableTool(self.arrows[lbl],True)

            else:

                for lbl in ('left','right','up','down', 'Expand X',

                                    'Shrink X','Expand Y','Shrink Y'):

                    self.EnableTool(self.arrows[lbl],bool(updateActions))

        def OnHelp(self,event):

            'Respond to press of help button on plot toolbar'

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