Changeset 4895 for trunk

Timestamp:

Apr 27, 2021 10:14:41 PM (4 years ago)

Author:

toby

Message:

allow w to be on before publish; update powder plot help

Location:

trunk

Files:

• GSASIIplot.py (modified) (6 diffs)
• help/gsasII.html (modified) (9 diffs)

trunk/GSASIIplot.py ¶

@@ -1986 +1986 @@
             if msg: msg += '\n'
             msg += " * only when the intensity scale is linear/sqrt (not log)"
-        if G2frame.Weight:
-            if msg: msg += '\n'
-            msg += " * only when weight plot is set to no weight plot"
         if msg:
             msg = 'Publication export is only available under limited plot settings\n'+msg
             G2G.G2MessageBox(G2frame,msg,'Wrong plot settings')
             print(msg)
+        elif G2frame.Weight:
+            G2frame.Weight = False
+            PlotPatterns(G2frame,newPlot=newPlot,plotType=plottype,extraKeys=extraKeys)
+            PublishRietveldPlot(G2frame,Pattern,Plot,Page)
+            G2frame.Weight = True
+            PlotPatterns(G2frame,newPlot=newPlot,plotType=plottype,extraKeys=extraKeys)
+            return
         else:
             PublishRietveldPlot(G2frame,Pattern,Plot,Page)
@@ -2256 +2260 @@
                 q = xpos
                 if q <= 0:
-                    G2frame.G2plotNB.status.SetStatusText('q = %9.5f'%q)
+                    G2frame.G2plotNB.status.SetStatusText('Q = %9.5f'%q)
                     return
                 try:
@@ -2262 +2266 @@
                     xpos = G2lat.Dsp2pos(Parms,2.0*np.pi/q)
                 except ValueError:      #avoid bad value in asin beyond upper limit
-                    G2frame.G2plotNB.status.SetStatusText('q = %9.5f'%q)
+                    G2frame.G2plotNB.status.SetStatusText('Q = %9.5f'%q)
                     return
                 if 'T' in Parms['Type'][0]: # TOF
@@ -2272 +2276 @@
                 q = xpos
                 if q <= 0:
-                    G2frame.G2plotNB.status.SetStatusText('q = %9.5f'%q)
+                    G2frame.G2plotNB.status.SetStatusText('Q = %9.5f'%q)
                     return
                 dsp = 2.*np.pi/q
@@ -2296 +2300 @@
             if G2frame.Contour: #PWDR only
                 if 'T' in Parms['Type'][0]:
-                    G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
+                    G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d=%9.5f Q=%9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
                 else:
-                    G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
+                    G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d=%9.5f Q= %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
             else:
                 if 'T' in Parms['Type'][0]:
                     if Page.plotStyle['sqrtPlot']:
-                        G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
+                        G2frame.G2plotNB.status.SetStatusText('TOF = %9.3f d=%9.5f Q=%9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
                     else:
-                        G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
+                        G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d=%9.5f Q=%9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
                 else:
                     if 'PWDR' in plottype:
                         if Page.plotStyle['sqrtPlot']:
-                            G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
+                            G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d=%9.5f Q=%9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
                         else:
-                            G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
+                            G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d=%9.5f Q=%9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
                     elif plottype == 'SASD':
                         G2frame.G2plotNB.status.SetStatusText('q =%12.5g Intensity =%12.5g d =%9.1f'%(q,ypos,dsp),1)
@@ -5944 +5948 @@
         if xpos:                                        #avoid out of frame mouse position
             ypos = event.ydata
-            G2frame.G2plotNB.status.SetStatusText('q =%.3f%s %sq/q =%.4f'%(xpos,Angstr+Pwrm1,GkDelta,ypos),1)                   
+            G2frame.G2plotNB.status.SetStatusText('Q =%.3f%s %sQ/Q =%.4f'%(xpos,Angstr+Pwrm1,GkDelta,ypos),1)                   
             
     def OnKeyPress(event):

trunk/help/gsasII.html ¶

@@ -4387 +4387 @@
 part of your project are shown on this page. They can be displayed as a stack
 of powder patterns, just a single pattern or as a contour image of the peak
-intensities. What can be done here will depend on which is displayed.
-</P><p class=MsoNormal style='margin-left:1.0in'>
-The difference curve position can be moved
-vertically by clicking on it and then "dragging" it up or down.
-Reflection positions 
-can also be repositioned vertically by dragging them.
-The indicies (hkl values) for reflections can be displayed by
-selecting the "Reflection Lists" entry and then if needed the
-appropriate phase. Letting
-the mouse rest at the position of a reflection in 2-theta, Q,
-etc. (the vertical position does not matter). After a short delay a
-"tool tip" will be displayed for any reflections close to the lateral
-mouse position. 
+intensities. What can be done here will depend on home many patterns
+  are shown as well as what mode is selected.
+Note that when the tick marks and difference curve positions can be
+  customized, as <a href="#PWDR_dragticks">discussed below</a>.
+</P><p class=MsoNormal style='margin-left:1.0in'> 
+  Similar plots to the one here are displayed when different
+  subtree items are selected and on those plots it is possible to
+  view and in some cases edit information associated with the
+  histogram. As examples:
+  <UL style='margin-left:1.0in'>
+    <a name="otherPWDR"></a>
+    <LI>By selecting
+      the <a href="#PWDR_Limits">Limits</a> entry, range of data used,
+    as well as possible excluded regions, can be set.
+    <LI>Selecting <a href="#PWDR_Reflection_Lists">Reflection Lists</a>
+      allows display of reflection indicies (hkl values) for a
+    selected phase.
+    Letting the mouse rest unmoved at the position of a reflection
+    in 2-theta, Q, etc. (the vertical position does not matter) will
+    cause these to be displayed. After a short delay a
+    "tool tip" will appear with indicies for any reflections close
+    to the lateral mouse position. 
+    <LI>Selecting <a href="#PWDR_Background">Background</a> allows
+    a mouse to be used to define
+    fixed points where a background curve
+    can be fitted to those points. 
+    <LI>Selecting <a href="#PWDR_Instrument_Parameters">Instrument
+    Parameters</a>displays plot of peak widths as a function of 2theta
+    or Q.
+    <LI>Selecting <a href="#PWDR_Peak_List">Peak List</a> allows
+    postions of peaks to be defined for use in direct peak fitting.
+    <LI>Selecting <a href="#PWDR_Unit_Cells_List">Unit Cells List</a>
+    can show the positions of reflections for an arbitrary set of
+    unit cell parameters, optionally with space group extinctions
+    applied. 
 </P>
 
+</UL>
 <h5 style='margin-left:.5in'><span
 style='mso-fareast-font-family:"Times New Roman"'>
@@ -4407 +4430 @@
 
 <DL style='margin-left:0.5in'>
-<DT>Move mouse
+  <DT>Move mouse
   <DD>As the mouse cursor is moved across the plot, the plot status line
 will show the cursor position as 2Theta, d-spacing and the
-    intensity. For a Q-plot, Q is shown instead of 2Theta. 
+    intensity. For a Q-plot, Q is shown instead of 2Theta.
+
+  <DT>Press keyboard keys
+  <DD><a href="#PWDR_keylist">See below</a>. The "s" and "w" modes are commonly used. 
+    
+  <a name="PWDR_dragticks"></a>
+  <DT>Drag tickmarks
+  <DD>Click on any tick mark and while holding the left mouse button
+  down move them to where you want them to
+  be displayed (press the s key for Sqrt(I) mode to reset to the
+  defaults). With multiple phases, clicking on the 2nd phase,
+  etc. changes the vertical spacing between tickmarks.
+
+  <DT>Drag the difference curve
+  <DD>When the "normal" obs-calc plot is shown (as opposed to the
+  preferred "w" mode plot where (obs-calc)/sigma is displayed, click
+  on any point in the difference curve and while holding the left mouse button
+  down move the curve to where you want it to
+  be displayed (press the s key for Sqrt(I) mode to reset it to the
+    default).
+    
+  <DT>Display/edit histogram information
+  <DD>By selecting different tree items within the current
+    histogram, it is possible to display and in some cases edit
+    information associated with the histogram.
+    <a href="#otherPWDR">See above.</a>
+    
+  <DT>Create a Publication-ready plot
+  <DD>Press the green "P" button to generate a customizable version
+    of the displayed plot that can be exported at high resolution. 
 </DL>
-<P style='margin-left:.5in'>
+<a name="PWDR_keylist"></a><P style='margin-left:.5in'>
 The following key press characters are defined (not for all plot
 modes). These actions can also be initiated from the <B>Key Press</B>
@@ -4419 +4471 @@
 <I>For line plots:</I></H4>
 <DL style='margin-left:0.75in'>
+<DT><B>    s: Sqrt(I) on/off</b><dd>changes the y-axis to be the
+  square-root of the intensity. The tick mark and the
+  difference curve location is reset. 
+<DT><B> w: toggle diff plot mode</b><dd>for the pattern selected from the
+  data tree, this will replace the difference (obs-calc) curve with
+  the differences divided by their standard uncertainty (esd) values
+  [(obs-calc)/sigma], which shows the significance of the deviations
+  in the fit of the pattern. <i>(Recommended)</I>. 
 <DT><B>    b: subtract background</b><dd>Subtracts the fitted
   background from the powder pattern. Pressing this again turns the
@@ -4434 +4494 @@
     x-axis scale. May not be very useful with data over a wide range. 
 
-<DT><B> w: toggle diff plot</b><dd>for the pattern selected from the
-  data tree, this will replace the difference (obs-calc) curve with
-  the differences divided by their standard uncertainty (esd) values,
-  which shows the significance of the deviations. 
+<DT><B>    e: set excluded region</b>
+<dd>Defines a new excluded region: press the "e" key with the mouse on
+  one side of the region. Move the mouse to the other side and and
+  press "e" again. The region markers (magenta dashed lines) can be
+  dragged to new positions. Available only when 
+  the <a href="#PWDR_Limits">Limits</a> tree entry is selected.
+<DT><B>    x: show excluded region</b>
+<dd>Normally all observed data is plotted. When the "x" key is
+  pressed, data inside excluded regions are not shown.
+<DT><B>    .: scaling diagnostic</b>
+<dd>When the '.' key is pressed, data are plotted where the intensity
+  scale shows the equivalent number of counts so that uncertainty on
+  each point is the sqrt(I).
+<DT><B>    g: grid lines</b>
+<dd>Draws vertical and horizontal grid lines at all axis label
+  positions.
+<DT><B>    a: add magnification region</b>
+<dd>Adds a magnification region to the plot and sets the magnification
+  amount to x2. This can be edited (or deleted) in the table that is
+  shown when the main PWDR tree entry is selected. 
+  
+
 </DL>
 
-<P style='margin-left:.5in'>
-For line plots with more than one powder pattern:</p>
+<H4 style='margin-left:.5in'><I> 
+For line plots with more than one powder pattern:
+</I></H4>
 <DL style='margin-left:0.75in'>
 <DT><B>    c: contour on/off</b><dd>if multiple powder profiles, then a contour plot is shown
 of the observed intensities. All data sets must be the same length as the first
 one to be included in the contour plot.
+<DT><B>    S: set color Scheme</b>
+<dd>Select the color map used for contour plots
+
 <DT><B> m: toggle single/multiple plot</b><dd>for multiple powder profiles, this will show only the one
-selected from the data tree. The offset options are not active.
+selected from the data tree. The offset options (below) are not active.
 <DT><B>f: select data</b><dd>Allows only some powder patterns to be
     plotted, rather than all. 
-<DT><B> +: no selection</b><dd>for multiple powder profiles, only the observed curve is shown.</span></p>
+<DT><B> +,=: no selection</b><dd>for multiple powder profiles, only
+  the observed curve is shown when this mode is turned on ('+' and '='
+  do exactly the same thing).</span></p>
+<DT><B> /: normalize</b><dd>for multiple powder profiles, all
+  diffraction datasets are normalized so that the maximum intensity is 1.
+  </span></p>
 </DL>
   
-<P style='margin-left:.5in'>For line plots in waterfall mode (multiple
-patterns are shown) these key press items are defined:</p>
+<H4 style='margin-left:.5in'><I>
+Offset modes for line plots in waterfall mode (multiple patterns only):
+</I></H4>
 <DL style='margin-left:0.75in'>
 <DT><B>l: offset left</b><dd>
@@ -4465 +4553 @@
 offset to the right (or decrease the left offset.)
 
-<DT><B>    d: offset down</b><dd>for a waterfall plot of multiple
-  powder profiles, increase the offset down. 
-
-<DT><B>    u: offset up</b><dd>for a waterfall plot of multiple powder
+<DT><B>    d,D: offset down</b><dd>for a waterfall plot of multiple
+  powder profiles, increase the offset down.
+  (D does the same as d but to a much larger amount) 
+
+<DT><B>    u,U: offset up</b><dd>for a waterfall plot of multiple powder
   profiles, increase the offset up. 
+  (U does the same as u but to a much larger amount) 
 
 <DT><B>    o: reset offset</b><dd>for a waterfall plot of multiple powder
@@ -4501 +4591 @@
 </DL>
 
+<H4 style='margin-left:.5in'><I>
+For display of reflections from magnetic unit space groups 
+</I></H4>
+<DL style='margin-left:0.75in'>
+  <DT><B>j: show next; reset use flag</b><dd>
+    Show the next magnetic space group in the list, clearing the "Use"
+    flag for the currently displayed space group.
+    (available from Index Unit Cells only).
+  <DT><B>k: show next</b><dd>
+    Show the next magnetic space group in the list. The "Use"
+    flag for the currently displayed space group is unchanged.
+    (available from Index Unit Cells only).
+    </DL>
 <h4 style='margin-left:0.25in'><a name="PWDR_Comments"><u>Comments</u></a></h4>
 
@@ -4575 +4678 @@
 
 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
-"Times New Roman"'>1). A continuous empirical function (‘<span class=SpellE>chebyschev</span>’,
+"Times New Roman"'>1). A continuous empirical function (‘chebyschev’,
+‘chebyschev-1’,
 ‘cosine’, ‘<span class=SpellE>lin</span> interpolate’, ‘inv interpolate’ &amp;
 ‘log interpolate’). The latter three select fixed points with spacing that is
 equal, inversely equal or equal on a log scale of the x-coordinate. The set of
 magnitudes at each point then comprise the background variables. All are
-refined when refine is selected.<o:p></o:p></span></p>
+refined when refine is selected.
+Note that ‘chebyschev-1' is a better choice than ‘chebyschev’. 
+<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in;tab-stops:0in'><span
@@ -4624 +4730 @@
 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
 "Times New Roman"'>where <span class=GramE>A,R</span> &amp; U are the possible
-variables and can be individually selected as desired; Q = 2</span><span
-style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>p</span><span
-style='mso-fareast-font-family:"Times New Roman"'>/d.<o:p></o:p></span></p>
+variables and can be individually selected as desired; Q = 2π/d.</p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
@@ -7560 +7664 @@
 using Sphinx. </span></p>
 
-<P>&nbsp;</P>
+<A name="fullrmc">
+<h3><strong>Access to fullrmc</strong></h3>
+</a>
+<p class=MsoNormal>
+The fullrmc program is a large-box pair distribution function modeling
+library developed by Bachir Aoun ["Fullrmc, a Rigid Body Reverse Monte
+Carlo Modeling Package Enabled with Machine Learning and Artificial
+Intelligence", B. Aoun, <I>Jour. Comp. Chem.</I> <B>(2016)</B>, 37,
+1102-1111.
+DOI: <a href="https://doi.org/10.1002/jcc.24304">10.1002/jcc.24304</a>].
+
+Extensive information about fullrmc is found, including a number of
+explanatory videos, along with the source code on GitHub:
+<A href="https://bachiraoun.github.io/fullrmc/">
+https://bachiraoun.github.io/fullrmc/</A>. 
+
+Use of fullrmc requires a set of Python packages that can be installed along
+with the packages needed for GSAS-II, but Windows and MacOS users will
+likely find it easier to install a pre-compiled version of fullrmc by
+downloading it <A
+href="https://drive.google.com/drive/folders/10hxmQviKoMaW9R4MxsaiDyPSretxr_P7">
+from here</A>.
+
+To locate a version of Python containing fullrmc, the following
+locations are checked (in the order specified):
+<OL>
+  <LI>The GSAS-II <a href=#Preferences>configuration variable</a>
+  <tt>fullrmc_exec</tt> can point to a Python image.
+  <LI>The Python interpreter running GSAS-II is checked if fullrmc can
+  be imported
+  <LI>The location where GSAS-II is installed, the location where
+  Python is installed, the location where the GSAS-II binaries are
+  found, the current default location and all directories in the
+  system path are all checked for a file named
+  <tt>"fullrmc*macOS*i386-64bit"</tt> (MacOS), <tt>"fullrmc*.exe"</tt> (Windows) or
+  <tt>"fullrmc*"</tt> (Linux).
+</OL>
+</p>
+
 
 <hr size=2 width="100%" align=center>
 <hr size=2 width="100%" align=center>
 
-<!-- hhmts start -->Last modified: Sun Feb 28 12:09:25 CST 2021 <!-- hhmts end -->
+<!-- hhmts start -->Last modified: Tue Apr 27 22:09:18 CDT 2021 <!-- hhmts end -->
 
 </div>