Changeset 2653


Ignore:
Timestamp:
Jan 21, 2017 3:11:39 PM (6 years ago)
Author:
toby
Message:

fix Update bug; Enhancements for Peak List: widen selected peak line; remove peak highlight on cell selection; add double-click on labels; change Tutorial limits fig.

Files:
6 edited

Legend:

Unmodified
Added
Removed

  • Tutorials/FitPeaks/Fit Peaks.htm

    r2389 r2653  
    16111611style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    16121612mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1613 minor-latin'>changed</span></b> row of entry boxes to set <span class=SpellE><b
     1613minor-latin'>new</span></b> column of entry boxes to set <span class=SpellE><b
    16141614style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16151615mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    … …  
    16261626limit lines have moved to these positions; the green lower limit is just below
    16271627the 1<sup>st</sup> peak and the red upper limit is in a wide gap between peaks.
    1628 You may also drag the limit lines to the desired location or place them by a left
     1628You may also drag the limit lines to the desired location. Limits may
     1629also be set by a left
    16291630mouse click on a data point for the lower limit or a right click on a data
    16301631point for the upper limit.</p>
    16311632
    1632 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1633  id="Picture_x0020_3" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:226.5pt;
    1634  height:123.75pt;visibility:visible;mso-wrap-style:square'>
    1635  <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
    1636 </v:shape><![endif]--><![if !vml]><img border=0 width=302 height=165
    1637 src="Fit%20Peaks_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
     1633<p class=MsoNormal><span style='mso-no-proof:yes'>
     1634<img border=0 width=296 height=121
     1635src="Fit%20Peaks_files/image003.png" v:shapes="Picture_x0020_3"></span></p>
    16381636
    16391637<h2>Step 3: Determine Peak Positions</h2>

  • trunk/GSASIIctrls.py

    r2651 r2653  
    32953295        try:
    32963296            self.frame.OnFileSave(event)
     3297            GPX = self.frame.GSASprojectfile
    32973298        except AttributeError:
    32983299            self.frame.G2frame.OnFileSave(event)
    3299         GSASIIpath.svnUpdateProcess(projectfile=self.frame.GSASprojectfile)
     3300            GPX = self.frame.G2frame.GSASprojectfile
     3301        GSASIIpath.svnUpdateProcess(projectfile=GPX)
    33003302        return
    33013303
    … …  
    33543356        dlg.Destroy()
    33553357        print('start regress to '+str(ver))
    3356         GSASIIpath.svnUpdateProcess(
    3357             projectfile=self.frame.GSASprojectfile,
    3358             version=str(ver)
    3359             )
    33603358        try:
    33613359            self.frame.OnFileSave(event)
     3360            GPX = self.frame.GSASprojectfile
    33623361        except AttributeError:
    33633362            self.frame.G2frame.OnFileSave(event)
     3363            GPX = self.frame.G2frame.GSASprojectfile
     3364        GSASIIpath.svnUpdateProcess(projectfile=GPX,version=str(ver))
    33643365        return
    33653366

  • trunk/GSASIIplot.py

    r2647 r2653  
    21542154                            else:
    21552155                                Lines.append(Plot.axvline(item[0],color=colors[Ni%6],picker=2.))
     2156                            if Ni == N+1:
     2157                                Lines[-1].set_lw(Lines[-1].get_lw()+1)
    21562158                    if G2frame.PatternTree.GetItemText(PickId) == 'Limits':
    21572159                        tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'

  • trunk/GSASIIpwdGUI.py

    r2650 r2653  
    498498       
    499499    def OnLSQPeakFit(event):
     500        if G2frame.dataDisplay.IsCellEditControlEnabled(): # complete any grid edits in progress
     501            G2frame.dataDisplay.HideCellEditControl()
     502            G2frame.dataDisplay.DisableCellEditControl()
    500503        if not G2frame.GSASprojectfile:            #force a save of the gpx file so SaveState can write in the same directory
    501504            G2frame.OnFileSaveas(event)
    502         OnPeakFit('LSQ')
     505        wx.CallAfter(OnPeakFit,'LSQ')
    503506       
    504507    def OnOneCycle(event):
    505         OnPeakFit('LSQ',oneCycle=True)
     508        if G2frame.dataDisplay.IsCellEditControlEnabled(): # complete any grid edits in progress
     509            G2frame.dataDisplay.HideCellEditControl()
     510            G2frame.dataDisplay.DisableCellEditControl()
     511        wx.CallAfter(OnPeakFit,'LSQ',oneCycle=True)
    506512       
    507513    def OnSeqPeakFit(event):
    … …  
    636642        finally:
    637643            print 'finished'
    638             dlg.Destroy()   
    639         G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'),copy.copy(peaks))
    640         UpdatePeakGrid(G2frame,copy.copy(peaks))
     644            dlg.Destroy()
     645        newpeaks = copy.copy(peaks)
     646        G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'),newpeaks)
    641647        G2plt.PlotPatterns(G2frame,plotType='PWDR')
     648        wx.CallAfter(UpdatePeakGrid,G2frame,newpeaks)
    642649        return
    643650       
    … …  
    677684                                                 
    678685    def KeyEditPeakGrid(event):
     686        '''Respond to pressing a key to act on selection of a row, column or cell
     687        in the Peak List table
     688        '''
    679689        rowList = G2frame.dataDisplay.GetSelectedRows()
    680690        colList = G2frame.dataDisplay.GetSelectedCols()
    … …  
    687697        elif event.GetKeyCode() == wx.WXK_SHIFT:
    688698            event.Skip(True)
    689         elif rowList:
     699        elif rowList and (event.GetKeyCode() == wx.WXK_DELETE or event.GetKeyCode() == 8):
     700            # pressing the delete key or backspace deletes selected peak(s)
    690701            G2frame.dataDisplay.ClearSelection()
    691             if event.GetKeyCode() == wx.WXK_DELETE:
    692                 G2frame.dataDisplay.ClearGrid()
    693                 rowList.sort()
    694                 rowList.reverse()
    695                 nDel = 0
    696                 for row in rowList:
    697                     G2frame.PeakTable.DeleteRow(row)
    698                     nDel += 1
    699                 if nDel:
    700                     msg = wg.GridTableMessage(G2frame.PeakTable,
    701                         wg.GRIDTABLE_NOTIFY_ROWS_DELETED,0,nDel)
    702                     G2frame.dataDisplay.ProcessTableMessage(msg)
    703                 data['peaks'] = G2frame.PeakTable.GetData()[:-nDel]
    704                 G2frame.PatternTree.SetItemPyData(G2frame.PickId,data)
    705                 G2frame.dataDisplay.ForceRefresh()
    706                 setBackgroundColors()
    707                        
    708         elif colList:
     702            G2frame.dataDisplay.ClearGrid()
     703            rowList.sort()
     704            rowList.reverse()
     705            nDel = 0
     706            for row in rowList:
     707                G2frame.PeakTable.DeleteRow(row)
     708                nDel += 1
     709            if nDel:
     710                msg = wg.GridTableMessage(G2frame.PeakTable,
     711                    wg.GRIDTABLE_NOTIFY_ROWS_DELETED,0,nDel)
     712                G2frame.dataDisplay.ProcessTableMessage(msg)
     713            data['peaks'] = G2frame.PeakTable.GetData()[:-nDel]
     714            G2frame.PatternTree.SetItemPyData(G2frame.PickId,data)
     715            wx.CallAfter(G2frame.dataDisplay.ForceRefresh)
     716            setBackgroundColors()
     717        elif colList and (event.GetKeyCode() == 89 or event.GetKeyCode() == 78):
    709718            G2frame.dataDisplay.ClearSelection()
    710719            key = event.GetKeyCode()
    … …  
    715724                    elif key == 78:  #'N'
    716725                        for row in range(G2frame.PeakTable.GetNumberRows()): data['peaks'][row][col]=False
    717         elif selectList:
     726        elif selectList and (event.GetKeyCode() == 89 or event.GetKeyCode() == 78):
    718727            G2frame.dataDisplay.ClearSelection()
    719728            key = event.GetKeyCode()
    … …  
    724733                    elif key == 78:  #'N'
    725734                        data['peaks'][row][col]=False
     735        else:
     736            event.Skip()
     737            return
    726738        G2plt.PlotPatterns(G2frame,plotType='PWDR')
     739        #wx.CallAfter(G2frame.dataDisplay.ForceRefresh) # did not always work
     740        wx.CallAfter(UpdatePeakGrid,G2frame,data)
    727741           
    728742    def SelectVars(rows):
    … …  
    764778        SelectVars(range(G2frame.dataDisplay.GetNumberRows()))
    765779
    766     def onSelectedRow(event):
     780    def onCellListSClick(event):
    767781        '''Called when a peak is selected so that it can be highlighted in the plot
    768782        '''
    769783        event.Skip()
    770         wx.CallAfter(G2plt.PlotPatterns,G2frame,plotType='PWDR')
    771                            
     784        r,c =  event.GetRow(),event.GetCol()
     785        if c < 0: # replot except whan a column is selected
     786            wx.CallAfter(G2plt.PlotPatterns,G2frame,plotType='PWDR')
     787       
     788    def onCellListDClick(event):
     789        '''Called after a double-click on a cell label'''
     790        r,c =  event.GetRow(),event.GetCol()
     791        grid = G2frame.dataDisplay
     792        if r < 0 and c < 0:
     793            for row in range(grid.GetNumberRows()):
     794                grid.SelectRow(row,True)                   
     795            for col in range(grid.GetNumberCols()):
     796                grid.SelectCol(col,True)                   
     797        elif r > 0:     #row label: select it and replot!
     798            grid.ClearSelection()
     799            grid.SelectRow(r,True)
     800            wx.CallAfter(G2frame.dataDisplay.ForceRefresh)
     801            wx.CallAfter(G2plt.PlotPatterns,G2frame,plotType='PWDR')
     802        elif c > 0:     #column label: just select it (& redisplay)
     803            grid.ClearSelection()
     804            grid.SelectCol(c,True)
     805            if grid.GetColLabelValue(c) != 'refine': return
     806            choice = ['Y - vary all','N - vary none',]
     807            dlg = wx.SingleChoiceDialog(G2frame.dataFrame,
     808                                        'Select refinement option for '+grid.GetColLabelValue(c-1),
     809                                        'Refinement controls',choice)
     810            dlg.CenterOnParent()
     811            if dlg.ShowModal() == wx.ID_OK:
     812                sel = dlg.GetSelection()
     813                if sel == 0:
     814                    for row in range(grid.GetNumberRows()): data['peaks'][row][c]=True
     815                else:
     816                    for row in range(grid.GetNumberRows()): data['peaks'][row][c]=False
     817            wx.CallAfter(UpdatePeakGrid,G2frame,data)
     818                 
    772819    #======================================================================
    773820    # beginning of UpdatePeakGrid init
    … …  
    837884    G2frame.dataDisplay.Bind(wg.EVT_GRID_CELL_CHANGE, RefreshPeakGrid)
    838885    G2frame.dataDisplay.Bind(wx.EVT_KEY_DOWN, KeyEditPeakGrid)
    839     G2frame.dataDisplay.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, onSelectedRow)
    840     G2frame.dataDisplay.Bind(wg.EVT_GRID_CELL_LEFT_CLICK, onSelectedRow)
     886    G2frame.dataDisplay.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, onCellListSClick)
     887#    G2frame.dataDisplay.Bind(wg.EVT_GRID_CELL_LEFT_CLICK, onCellListSClick)
     888    G2frame.dataDisplay.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, onCellListDClick)
     889#    G2frame.dataDisplay.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, onCellListDClick)
    841890    G2frame.dataDisplay.SetMargins(0,0)
    842891    G2frame.dataDisplay.AutoSizeColumns(False)
    843892    G2frame.dataFrame.setSizePosLeft([535,350])
    844     G2frame.dataFrame.SendSizeEvent()
     893    #G2frame.dataFrame.SendSizeEvent()
    845894
    846895################################################################################

  • trunk/help/gsasII.html

    r2611 r2653  
    36193619  <LI>Menu <B><A name="Calculate_menu">Calculate</A></B>
    36203620  <DL style='margin-left:.2in'>
    3621     <DT><b>Make new PDFs</b>
     3621    <DT><b>Setup PDFs</b>
    36223622    <DD>This creates the pair distribution function (PDF) controls for
    3623   each powder pattern selected in the dialog box. See <b><a
    3624   href="#PDF_Controls">PDF Controls</a></b> for further directions.
     3623  each powder pattern selected in the dialog box, but does not compute
     3624  the PDF, which must be done from <b><a
     3625  href="#PDF">PDF tree entries</a></b>. See <b><a
     3626  href="#PDF_Controls">PDF Controls</a></b> for information on the PDF
     3627  input.
    36253628    <DT><b>View LS parms</b>
    36263629    <DD>This shows a dialog box with all the parameters for your
    … …  
    49824985
    49834986<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4984 "Times New Roman"'>This window shows the list of peaks that will be used by the
    4985 peak fitting refinement. It is filled by picking peaks in the powder pattern
    4986 displayed in the GSASII Plots window as a sequence of ‘+’ marks.<span
    4987 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    4988 text-underline:none'><o:p></o:p></span></span></span></p>
     4987"Times New Roman"'>The Peak List data tree entry is used to fit
     4988diffraction peaks at user-supplied positions (not generated from a
     4989unit cell). Peak positions and intensities may be selected for
     4990individual refinement. Gaussian (sigma) and
     4991Lorentzian (gamma) peak widths may be varied individually or the values
     4992may be generated from the U,V & W (sigma) and X & Y (gamma) values in the Instrument
     4993Parameters tree item: If individual values are
     4994refined, then the value in the table is used. If values are not
     4995refined, then those determined by U,V & W and/or X & Y are placed in
     4996the table and are used. Likewise, the background is generated using the parameters in
     4997the Background data tree entry and the range of data used in the fit
     4998is set from the Limits tree item. Note that optionally the parameters on
     4999the Background and in the Instrument
     5000Parameters tree items may be refined as peak settings are fitted.
     5001</p>
    49895002
    49905003<h5 style='margin-left:.5in'>
    49915004What can I do here?</a></h5>
    49925005
    4993 <h5 style='margin-left:81.0pt;text-indent:-.25in;mso-list:l13 level1 lfo22'><span
    4994 style='mso-bookmark:Index_Peaks'><![if !supportLists]><span class=MsoHyperlink><span
    4995 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    4996 normal;mso-bidi-font-weight:bold;text-decoration:none;text-underline:none'><span
    4997 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4998 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    4999 "Times New Roman";color:windowtext;font-weight:normal;mso-bidi-font-weight:
    5000 bold'>Menu ‘</span></span><span style='mso-bookmark:Index_Peaks'><span
    5001 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Peak Fitting</span></span><span
    5002 style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
    5003 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'>’ – <span
    5004 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5005 text-underline:none'><o:p></o:p></span></span></span></span></h5>
    5006 
    5007 <h5 style='margin-left:1.5in;text-indent:-.25in;mso-list:l13 level2 lfo22;
    5008 tab-stops:list 1.0in'><span style='mso-bookmark:Index_Peaks'><![if !supportLists]><span
    5009 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5010 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration:
    5011 none;text-underline:none'><span style='mso-list:Ignore'>a.<span
    5012 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><![endif]><span
    5013 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Auto search</span></span><span
    5014 style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
    5015 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this fills
     5006<P style='margin-left:1.0in'>
     5007There are three ways to interact with Peak List data tree item:
     5008through its menu, labeled <B>Peak Fitting</B>, through interaction
     5009with the peak list table, and through interactions with the plot.
     5010</P>
     5011
     5012<P style='margin-left:1.0in'>
     5013The following interactions are available with the peak table:
     5014      </P>
     5015
     5016<BL>
     5017      <LI style='margin-left:1.25in'>
     5018You can change individual
     5019peak coefficient values. Enter the value then press Enter or Tab or click the
     5020mouse elsewhere in the Peak List window. This will set the new value.
     5021      </LI><P>
     5022      <LI style='margin-left:1.25in'>
     5023      You can change the individual refine flags either by
     5024clicking on the check boxes.
     5025      </LI><P>
     5026      <LI style='margin-left:1.25in'>
     5027      You can change all refine flags in a column by clicking on a single one
     5028      and then click on the column label above. The entire column
     5029      should be highlighted in blue.
     5030      Type ‘y’ to set the refine flags or ‘n’ to clear the flags. This
     5031      can also be done by double-clicking on the column label, which
     5032      brings up a menu.
     5033      </LI><P>
     5034      <LI style='margin-left:1.25in'> 
     5035You can delete peaks in the Peak List by selecting a row by clicking
     5036      on the row label to the left (multiple selection of rows is
     5037      allowed). Selected rows will be highlighted in the plot (see
     5038      below). Then press the Delete or backspace key. (Note that peaks
     5039      can also be deleted from the plot, see below.)
     5040      </LI><P>
     5041      <LI style='margin-left:1.25in'> 
     5042You can highlight a peak by clicking or double-clicking on the row
     5043label (to the left) for a peak. The color of the line will change from
     5044blue to green.</LI>
     5045</BL>
     5046
     5047<P style='margin-left:1.0in'>
     5048The <B>Peak Fitting</B> menu contains the following commands:</P>
     5049
     5050<DL style='margin-left:1.25in'>
     5051  <DT>Set sel. ref flags</DT>
     5052  <DD>If one or more row of peaks are selected by clicking on the peak
     5053  label to the left, this menu item can be used to set the refinement
     5054  flags for the selected reflections.
     5055    </DD>
     5056  <DT>Set all ref flags</DT>
     5057  <DD>This sets refinement flags for all peaks in the table.
     5058    </DD>
     5059  <DT>Auto search</DT>
     5060  <DD>
     5061    This fills
    50165062the table with peak positions. These are selected based on peak tops that are
    50175063substantially above background. Noisy data will give spurious peaks and small
    5018 peaks or shoulders will not be found. Examine results &amp; modify as needed.<span
    5019 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5020 text-underline:none'><o:p></o:p></span></span></span></span></h5>
    5021 
    5022 <h5 style='margin-left:1.5in;text-indent:-.25in;mso-list:l13 level2 lfo22;
    5023 tab-stops:list 1.0in'><span style='mso-bookmark:Index_Peaks'><![if !supportLists]><span
    5024 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5025 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration:
    5026 none;text-underline:none'><span style='mso-list:Ignore'>b.<span
    5027 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><![endif]><span
    5028 class=SpellE><span style='mso-fareast-font-family:"Times New Roman";color:windowtext'>UnDo</span></span></span><span
    5029 style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
    5030 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – resets peak
     5064peaks or shoulders will not be found. Examine results &amp; modify as
     5065  needed.
     5066    </DD>
     5067      <DT>UnDo</DT>
     5068      <DD>Resets peak
    50315069parameters, background and instrument parameter values varied in the last peak
    50325070fitting refinement back to their original values. Use this to recover from a
    5033 failed refinement. Note:<span style='mso-spacerun:yes'>  </span>there is only a
    5034 single level of recovery available.<span class=MsoHyperlink><span
    5035 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>
    5036 
    5037 <h5 style='margin-left:1.5in;text-indent:-.25in;mso-list:l13 level2 lfo22;
    5038 tab-stops:list 1.0in'><span style='mso-bookmark:Index_Peaks'><![if !supportLists]><span
    5039 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5040 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration:
    5041 none;text-underline:none'><span style='mso-list:Ignore'>c.<span
    5042 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><![endif]><span
    5043 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>LSQ <span
    5044 class=SpellE>PeakFit</span></span></span><span style='mso-bookmark:Index_Peaks'><span
    5045 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    5046 normal;mso-bidi-font-weight:bold'> – perform a least squares fit of the peaks
     5071failed refinement. Note: only one previous refinement is saved, so
     5072  this cannot be pressed twice to return to the refinement before the
     5073  previous.
     5074</DD>
     5075      <DT>PeakFit</DT>
     5076      <DD>Performs a least squares fit of the peaks
    50475077in Peak List to the data. Any peak parameters, background parameters and
    50485078instrument parameters with refine checked will be varied in this refinement.
    … …  
    50555085are widely different, their individual sigma and gamma parameters may be
    50565086refined. If the refinement results in negative peak coefficients, these will be
    5057 highlighted in red. If this happens, you should </span></span><span
    5058 style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
    5059 color:windowtext'>UnDo</span></span><span style='mso-bookmark:Index_Peaks'><span
    5060 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    5061 normal;mso-bidi-font-weight:bold'> the refinement and reconsider your choice of
    5062 parameters to be varied.<span class=MsoHyperlink><span style='color:windowtext;
    5063 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>
    5064 
    5065 <h5 style='margin-left:1.5in;text-indent:-.25in;mso-list:l13 level2 lfo22;
    5066 tab-stops:list 1.0in'><span style='mso-bookmark:Index_Peaks'><![if !supportLists]><span
    5067 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5068 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration:
    5069 none;text-underline:none'><span style='mso-list:Ignore'>d.<span
    5070 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><![endif]><span
    5071 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>LSQ one
    5072 cycle </span></span><span style='mso-bookmark:Index_Peaks'><span
    5073 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    5074 normal;mso-bidi-font-weight:bold'>– perform a single cycle of least squares
     5087highlighted in red. If this happens, you should use the <B>UnDo</B>
     5088      menu item (above) to return to the refinement and reconsider your choice of
     5089parameters to be varied.
     5090        </DD>
     5091
     5092      <DT>LSQ one cycle </DT>
     5093      <DD>       
     5094        Perform a single cycle of least squares
    50755095refinement. This can be used in difficult cases to get a refinement started
    5076 toward convergence.<span class=MsoHyperlink><span style='color:windowtext;
    5077 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>
    5078 
    5079 <h5 style='margin-left:1.5in;text-indent:-.25in;mso-list:l13 level2 lfo22;
    5080 tab-stops:list 1.0in'><span style='mso-bookmark:Index_Peaks'><![if !supportLists]><span
    5081 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5082 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration:
    5083 none;text-underline:none'><span style='mso-list:Ignore'>e.<span
    5084 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><![endif]><span
    5085 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Reset sig
    5086 and gam </span></span><span style='mso-bookmark:Index_Peaks'><span
    5087 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    5088 normal;mso-bidi-font-weight:bold'>– this resets the values of sigma and gamma
    5089 to those computed from the instrument parameters U, V, W, X &amp; Y.<span
    5090 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5091 text-underline:none'><o:p></o:p></span></span></span></span></h5>
    5092 
    5093 <h5 style='margin-left:1.5in;text-indent:-.25in;mso-list:l13 level2 lfo22;
    5094 tab-stops:list 1.0in'><span style='mso-bookmark:Index_Peaks'><![if !supportLists]><span
    5095 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5096 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration:
    5097 none;text-underline:none'><span style='mso-list:Ignore'>f.<span
    5098 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5099 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    5100 "Times New Roman";color:windowtext'>Clear peaks </span></span><span
    5101 style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
    5102 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'>– this removes
    5103 all the peaks from the Peak List.<span class=MsoHyperlink><span
    5104 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>
    5105 
    5106 <h5 style='margin-left:81.0pt;text-indent:-.25in;mso-list:l13 level1 lfo22'><span
    5107 style='mso-bookmark:Index_Peaks'><![if !supportLists]><span class=MsoHyperlink><span
    5108 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    5109 normal;mso-bidi-font-weight:bold;text-decoration:none;text-underline:none'><span
    5110 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5111 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    5112 "Times New Roman";color:windowtext;font-weight:normal;mso-bidi-font-weight:
    5113 bold'>You can add peaks to the Peak list using the mouse on the plot by: 1)
    5114 position the pointer near to the top point on a peak, 2) press the left mouse
    5115 button. The selected peak will be added to the Peak List in its correct sorted
    5116 order and a blue vertical line will be plotted on that position. Be sure that
    5117 the Zoom/Pan buttons are not selected on the Plot window. We recommend that you
     5096toward convergence.
     5097        </DD>
     5098       
     5099      <DT>Reset sig and gam </DT>
     5100      <DD>       
     5101        This resets the values of sigma and gamma in the table
     5102to those computed from the instrument parameters U, V, W, X &amp; Y.
     5103        </DD>
     5104
     5105      <DT>Peak copy</DT>
     5106      <DD>Copy the currebt set of peaks to other histogram(s)
     5107        </DD>
     5108
     5109      <DT>Seq PeakFit</DT>
     5110      <DD>Fit peaks for multiple histograms       
     5111        </DD>
     5112       
     5113      <DT>Clear peaks</DT>
     5114      <DD>This removes all the peaks from the Peak List.
     5115        </DD>
     5116       
     5117      <DT>Move selected peak</DT>
     5118      <DD>
     5119        A peak may be moved using the following process: select it
     5120      in the table by clicking on its label (to left), use this menu
     5121      item. The peak line will then follow movement of the mouse in
     5122      the plot window. Click with the left mouse button to set a new
     5123      position. Click with the right mouse button to delete that
     5124      peak. Click outside the axes to abort the move and return to the
     5125      previous position. (Note that peak movement is also possible
     5126      with the plot window, see below.)
     5127        </DD>
     5128      </DL>
     5129
     5130<h5 style='margin-left:.5in'><span
     5131style='mso-fareast-font-family:"Times New Roman"'>
     5132What is plotted here?</span></h5>
     5133<P style='margin-left:1.0in'>
     5134The plot window shows the observed and computed patterns, as well as
     5135the background and peak positions. Observed points are shown as blue
     5136crosses (+) and the fitted pattern is shown as a solid green line. The
     5137background is shown as a red line and the difference curve is shown as
     5138a cyan (turquoise) line, below the observed and computed
     5139pattern. Peak positions are shown as vertical blue lines (or
     5140green when selected). The upper and lower data limits are shown as red
     5141and green dashed vertical lines, respectively.
     5142</P>
     5143
     5144<h5 style='margin-left:.5in'><span
     5145style='mso-fareast-font-family:"Times New Roman"'>
     5146What can I do with the plot?</span></h5>
     5147<BL>
     5148<P style='margin-left:1.0in'>
     5149For all actions involving mouse clicks such as those below, be sure that
     5150the Zoom/Pan buttons are not selected on the Plot window, as the mouse
     5151clicks will be used for zooming or panning, not the desired action.
     5152</P>
     5153<LI style='margin-left:1.25in'>
     5154You can add peaks to the Peak list using the mouse on the plot by:
     5155position the cursor pointer onto a cross for an observed point and
     5156pressing the left mouse
     5157button. The selected peak will be added to the Peak List in the
     5158appropriate position to keep peaks sorted
     5159and a blue vertical line will be plotted on that position. We recommend that you
    51185160begin picking peaks from the right side of the pattern; that way the tool tip
    5119 won’t be in your way as you select peaks.<span class=MsoHyperlink><span
    5120 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>
    5121 
    5122 <h5 style='margin-left:81.0pt;text-indent:-.25in;mso-list:l13 level1 lfo22'><span
    5123 style='mso-bookmark:Index_Peaks'><![if !supportLists]><span class=MsoHyperlink><span
    5124 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    5125 normal;mso-bidi-font-weight:bold;text-decoration:none;text-underline:none'><span
    5126 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5127 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    5128 "Times New Roman";color:windowtext;font-weight:normal;mso-bidi-font-weight:
    5129 bold'>You can move a Peak List item using the mouse on the plot by: 1) position
    5130 the pointer on the blue line for the peak you wish to move, 2) holding the left
    5131 mouse button down, drag to the desired position &amp; then release the button.
    5132 The peak line will be drawn in the new position. Be sure that the Zoom/Pan
    5133 buttons are not selected on the Plot window.<span class=MsoHyperlink><span
    5134 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>
    5135 
    5136 <p class=MsoListParagraphCxSpFirst style='margin-left:81.0pt;mso-add-space:
    5137 auto;text-indent:-.25in;mso-list:l13 level1 lfo22'><span style='mso-bookmark:
    5138 Index_Peaks'><![if !supportLists]><span class=MsoHyperlink><span
    5139 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration:
    5140 none;text-underline:none'><span style='mso-list:Ignore'>4.<span
    5141 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><![endif]><span
    5142 style='mso-fareast-font-family:"Times New Roman"'>You can change individual
    5143 peak coefficient values. Enter the value then press Enter or Tab or click the
    5144 mouse elsewhere in the Peak List window. This will set the new value.<span
    5145 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5146 text-underline:none'><o:p></o:p></span></span></span></span></p>
    5147 
    5148 <p class=MsoListParagraphCxSpLast style='margin-left:81.0pt;mso-add-space:auto;
    5149 text-indent:-.25in;mso-list:l13 level1 lfo22'><span style='mso-bookmark:Index_Peaks'><![if !supportLists]><span
    5150 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5151 color:windowtext;text-decoration:none;text-underline:none'><span
    5152 style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5153 </span></span></span></span><![endif]>You can change the refine flags either by
    5154 clicking on the box or by selecting one and then selecting the column (a single
    5155 click on the column heading; column should show in blue). Then type ‘y’ to set
    5156 the refine flags or ‘n’ to clear the flags. </span><span style='mso-bookmark:
    5157 Index_Peaks'><span class=MsoHyperlink><span style='mso-fareast-font-family:
    5158 "Times New Roman";color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    5159 
    5160 <h5 style='margin-left:81.0pt;text-indent:-.25in;mso-list:l13 level1 lfo22'><span
    5161 style='mso-bookmark:Index_Peaks'><![if !supportLists]><span class=MsoHyperlink><span
    5162 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    5163 normal;mso-bidi-font-weight:bold;text-decoration:none;text-underline:none'><span
    5164 style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5165 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    5166 "Times New Roman";color:windowtext;font-weight:normal;mso-bidi-font-weight:
    5167 bold'>You can delete peaks in the Peak List by selecting rows (should appear in
    5168 blue) and then pressing the Delete key. You can also delete peaks using the
     5161won’t be in your way as you select peaks.
     5162      </LI><P>
     5163<LI style='margin-left:1.25in'>   
     5164You can delete peaks using the
    51695165mouse on the plot by positioning the pointer on the blue line for the peak to
    51705166be deleted and then pressing the right mouse button. The blue line should
    5171 vanish and the corresponding peak will be removed from the Peak List. Be sure
    5172 that the Zoom/Pan buttons are not selected on the Plot window.<span
    5173 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5174 text-underline:none'><o:p></o:p></span></span></span></span></h5>
    5175 
     5167vanish and the corresponding peak will be removed from the Peak
     5168List.
     5169      </LI><P>
     5170<LI style='margin-left:1.25in'> 
     5171You can move a Peak List item using the mouse on the plot by: position
     5172the pointer on the blue line for the peak you wish to move and then hold the left
     5173mouse button down, dragging the line to the desired position. When the
     5174mouse button is released, the peak line will be drawn in the new
     5175position.
     5176      </LI><P>
     5177<LI style='margin-left:1.25in'>
     5178The fit limits can be changed without selecting the Limits item in the
     5179data tree from the plot. Change the upper and lower Tmin values by clicking on the
     5180appropriate vertical line and dragging it to the right or left.
     5181</LI>
     5182</BL>
    51765183<h4 style='margin-left:0.25in'><a name="PWDR_Index_Peak_List"></a><u>
    51775184Index Peak List</u></a></h4>
    … …  
    55365543<p class=MsoNormal style='margin-left:.5in'>
    55375544A PDF entry is created from a <a href="#PWDR">powder histogram (PWDR
    5538 entry)</a> using the <b>Make new PDFs</b> entry in the <A
     5545entry)</a> using the <b>Setup PDFs</b> entry in the <A
    55395546href="#Calculate_menu">Calculate menu</A>. The main PDF data tree item
    5540 has no parameters and provides no new menu items. When this item is
    5541 selected, the <a href="#PDF_I_Q">I(Q) function</a> is plotted, see below.
     5547displays the same window as the PDF Controls, below. When this item is
     5548selected, the <a href="#PDF_S_Q">S(Q) function</a> is plotted, see below.
    55425549
    55435550<h4 style='margin-left:0.25in'><a name="PDF_Controls">PDF Controls</a></h4>
    … …  
    55535560<a href="#PDF_G_R">G(R) functions</a> to be plotted, as described
    55545561below.
     5562</p>
     5563<p class=MsoNormal style='margin-left:.5in'>The Optimize PDF button
     5564can be used to refine the values of the "Flat Bkg", "Background ratio"
     5565and "Ruland width" parameters to best agree with the -4*pi*r line that
     5566is plotted for r < Rmin. Rmin should be set to a distance below the
     5567shortest expected interatomic distance for the material.
    55555568</p>
    55565569
    … …  
    55835596    forced with this menu item.
    55845597  <DT>Compute all PDFs
    5585   <DD>Recomputes the PDFs for all PDF entries. This is usually done
    5586     after Copy Controls is used.
     5598  <DD>Recomputes the PDFs for all selected PDF entries. This is usually done
     5599    after Copy Controls is used. By default PDFs are optimized to
     5600    reduce the low G(r) region, but this can be turned off.
    55875601</DL>
    55885602
    … …  
    72007214<hr size=2 width="100%" align=center>
    72017215
    7202 <!-- hhmts start -->Last modified: Wed Jan  4 16:40:54 CST 2017 <!-- hhmts end -->
     7216<!-- hhmts start -->Last modified: Sat Jan 21 14:53:49 CST 2017 <!-- hhmts end -->
    72037217
    72047218</div>
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