Ignore:
Timestamp:
Jul 26, 2011 12:47:57 PM (10 years ago)
Author:
toby
Message:

liveplot: export to gnuplot; plot I/sigma(I); change title & size of labels; improve tick location; make autoticks standard; expgui: new menu item to create InstParm? file; InstEdit?: bug fixes; remove fprime since not in GSAS anymore; fix 2Theta max bug for CW instruments; updates to doc files

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  • branches/sandbox/doc/liveplot.html

    r1150 r1157  
    4040<P>
    4141Both LIVEPLOT and BKGEDIT get the current diffraction information
    42 by running the GSAS TCLDUMP program, if installed, or
    43 the GSAS HSTDUMP otherwise. The TCLDUMP program has been optimized for use
    44 with LIVEPLOT and allows LIVEPLOT to offer a number of extra
    45 options that are not available when HSTDUMP is used. Since TCLDUMP has been
    46 included in GSAS since April of 2000, the following documentation assumes
    47 that TCLDUMP is installed.
     42by running the GSAS TCLDUMP program. (In GSAS/EXPGUI before 2001, the
     43GSAS HSTDUMP program was used, which was less powerful. This code has
     44not been removed, but will not be used if TCLDUMP is present.)
    4845
    4946<a name="liveplot"></a>
     
    5451Some of the features available in LIVEPLOT are:
    5552<UL>
    56 <LI>The plot is updated automatically after each refinement run
     53<LI><IMG SRC="new.gif" alt="New!">
     54Regions of the plot can be magnified to show more detail, for example
     55  in regions at high Q.
     56<LI><IMG SRC="new.gif" alt="New!">
     57Plots can be <a href="#export">exported to obtain publication-quality
     58graphics </a> -- <B><I>now on all platforms</I></B>.
     59<LI><IMG SRC="new.gif" alt="New!"> Intensity can be displayed as I/sigma(I)
     60 <LI>The plot is updated automatically after each refinement run
    5761<LI>The plot can be "zoomed-in", by clicking on the corners of the
    5862area to be magnified and "zoomed-out" using the
     
    6165The units used for plotting histograms can be selected. Choices are:
    6266native units (2Theta/TOF/KeV); d-space (A) or Q (A<sup>-1</sup>)
    63 <LI><IMG SRC="new.gif" alt="New!">
    64 Regions of the plot can be magnified to show more detail, for example
    65   in regions at high Q.
    66   <LI>
    67 The background (fixed plus fitted) can be plotted or can be subtracted.
     67 <LI>
     68  The background (fixed plus fitted) can be plotted or can be subtracted.
    6869<LI>
    6970Reflection tickmarks can be displayed in a variety of formats
     
    7980<LI>
    8081The cursor position can be displayed
    81 <LI>
    82 Plots can be <a href="#export">exported to obtain publication-quality
    83 graphics.</a>
    8482</UL>
    8583
     
    393391<B>Export plot options</B>
    394392<UL><LI>
    395 The plot can be exported to
     393<IMG SRC="new.gif" alt="New!">
     394The LIVEPLOT program can export plots to to a <I>high quality</I> PDF
     395  file for presentations or publications using <A
     396  HREF="http://www.gnuplot.info/">gnuplot</A>.
     397  The PDF will match what is is shown on fairly
     398  closely with respect to colors, <A href="#plotfont">font sizes</a>
     399  and <a href="#zoom">zoom</a>. The new <A href="#magnification">plot magnification</a> to show detail in
     400  the fit and for publication increase the
     401  <A href="#plotfont">plot font</a> so that the figure size can be
     402  reduced to the standard Rietveld postage stamp, required by so many
     403  Journals -- allowing the text to be discerned, even if the problems in the
     404  fit cannot.
     405  <P>Starting August
     406  2011, windows and Mac versions of gnuplot are included with the GSAS
     407  binaries; gnuplot is easily
     408  installed on Linux with standard tools such as yum (Redhat),
     409  apt-get (ubuntu) or zypper (openSuse).
     410
     411<P><LI>  The plot can be exported to
    396412<A HREF="http://plasma-gate.weizmann.ac.il/Grace/">Grace</A>, WYSIWYG 2D plotting tool for X-Windows
    397 that produces publication-quality graphics. Many UNIX users know
    398 this program under a previous name, xmgr.
    399 The export is implemented
    400 by producing an ASCII file with instructions that
    401 creates a plot with similar formatting to what appears on the
    402 screen in LIVEPLOT/BKGEDIT. However, the output quality from
    403 Grace is much higher quality. Further, Grace
    404 can be used to enhanced and annotate the plot further.
    405 <LI>
     413that produces publication-quality graphics that appear very similar to
     414  what is seen in LIVEPLOT/BKGEDIT. Further, Grace
     415  can be used to enhance the plot, for example by editing captions,
     416  figure display options and even annotate the plot.
     417  Grace runs well on Linux and Mac computers; Many UNIX users know
     418  this program under a previous name, xmgr.
     419  For Windows,
     420  installation of <A HREF="http://cygwin.com/">Cygwin</A> is required.
     421  <P><LI>
    406422For use in many other graphics programs, LIVEPLOT will produce a
    407423"comma separated variable" data file with the data displayed on the screen.
     
    409425set line styles and scaling, etc., but this does provide an option for
    410426generating high-quality graphics for presentations and publications.
    411 <LI>LIVEPLOT will produce PostScript versions of the plot on the screen,
     427<P><LI>LIVEPLOT will produce PostScript versions of the plot on the screen,
    412428but the quality is rather low (this is a limitation of the BLT graphics
    413429package).
     430  <P><LI>LIVEPLOT/BKGFIT can also be used to prepare input for FOX (Free
     431  Objects for Xtallography).
     432 
    414433</UL>
    415434
     
    468487<DT>Export Plot
    469488<DD>This offers options for exporting the plot in multiple formats.
    470 I am hoping to add more export formats eventually.
    471 <DL><DL>
     489<DL><DL>
     490<DT>to PDF
     491 <IMG SRC="new.gif" alt="New!">
     492<DD>Creates a <I>high quality</I> PDF file that may be useful for
     493  presentations or publications. Note that you may wish to use
     494  <A href="#magnification">plot magnification</a> to show detail in
     495  the fit and for publication increase the
     496  <A href="#plotfont">plot font</a> so that the figure size can be
     497  reduced.
     498
    472499<DT>to PostScript
    473500<DD>Creates a <I>low quality</I> PostScript file containing the LIVEPLOT
     
    476503On Windows, a program such ghostview may be needed to translate the
    477504PostScript to a format that can be viewed or printed.
    478 <A name="grace">
     505
     506  <A name="grace">
    479507<DT>to Grace
    480508<IMG SRC="note.gif" alt="Note!">
     
    484512After the plot is exported, it can be further
    485513enhanced and annotated in grace.
     514
     515<DT>to .csv file
     516  <DD>Creates a "comma separated variable" file. This contains all the
     517  diffraction data shown in the plot. It can be used to produce a plot
     518  in some other graphics program.
     519  <DT>Fox XML
     520  <DD>The Fox program provides structure solution capabilities. This
     521  option can be used to write data in the XML format that Fox uses.
    486522</DL></DL>
    487523<DT>Quit
     
    535571<DT>Y units
    536572<DD>The intensity values can be normalized by the incident spectrum
    537 (for energy dispersive methods).
     573(for energy dispersive methods) or
     574  <IMG SRC="new.gif" alt="New!"> can be displayed as a ratio with the
     575  experimental uncertainty [I<sub>obs</sub>/sigma(I<sub>obs</sub>),
     576  I<sub>calc</sub>/sigma(I<sub>obs</sub>) and their difference].
    538577</DL></DL>
    539578<br clear=all>
     
    565604<DT>Set screen font
    566605<DD>This option is used to control the font used for menus, graphics and
    567 other aspects of windows.
     606other aspects of windows. This value can be saved as a default value.
     607<A name="plotfont">
     608  <DT>Set plot font
     609<DD>This option is used to change the font used in the plot
     610  window. This has a similar effect to changing the screen font, but
     611  can be changed over a wider range and only affects the
     612  graph. Changing the font size either way will change the font used
     613  in the exported .PDF.
    568614<DT>Raise on update
    569615<DD>This causes the plot to be placed on top of other windows, if partially
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