source: trunk/doc/liveplot.html @ 402

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# on 2001/05/11 04:15:34, toby did:
LIVEPLOT documentation

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1<html>
2<head>
3   <META NAME="Author" CONTENT="Brian H. Toby">
4   <title>EXPGUI -- LIVEPLOT</title>
5</head>
6<BODY BGCOLOR="#FFFFFF">
7
8<A HREF=http://www.ncnr.nist.gov>
9<IMG SRC="http://www.ncnr.nist.gov/images/ncnrtrans.gif" 
10alt="Link to NIST Center for Neutron Research home page"
11ALIGN=RIGHT></A>
12<A HREF=http://www.nist.gov>
13<IMG SRC="http://www.ncnr.nist.gov/images/webidblue_2lineright.gif" 
14alt="Link to National Institute of Standards & Technology home page"
15ALIGN=LEFT></A>
16<CENTER>
17<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
18<IMG SRC="tcltklogo100.gif" 
19alt="Link to Tcl/Tk information">
20</CENTER></A>
21<br clear=all><hr>
22
23<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
24<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
25</TH></TR></TABLE><BR CLEAR=ALL>
26
27<center><h1>
28LIVEPLOT
29</h1></center>
30This page documents the LIVEPLOT utility in the EXPGUI package.
31<P>
32LIVEPLOT gets the current diffraction information by running the TCLDUMP program, if installed, or
33HSTDUMP otherwise. The TCLDUMP program has been optimized for use
34with LIVEPLOT and offers a number of extra
35options that are not available when HSTDUMP is used. Since TCLDUMP has been
36included in GSAS since April of 2000, it is assumed that this is now the case.
37
38Some of the features available in LIVEPLOT are:
39<UL>
40<LI>The plot is updated automatically after each refinement run
41<LI>The plot can be zoomed, by clicking on the corners of the
42area to be magnified.
43<LI>
44The units used for plotting histograms can be selected. Choices are:
45native units (2Theta/TOF/KeV); d-space (A) or Q (A<sup>-1</sup>)
46<LI>
47The background (fixed plus fitted) can be plotted or can be subracted.
48<LI>
49Reflection tickmarks can be displayed in a variety of formats
50<LI>
51LIVEPLOT can be coupled to the LOGIC or CMPR programs, so that
52peak positions from an ICDD entry or for an arbitrary unit cell and
53spacegroup can be shown superimposed on the "Rietveld plot."
54<LI>
55<IMG SRC="note.gif" alt="Note!">
56Reflection indices (<I>hkl</I> values) can be shown for tickmarks
57<LI>
58<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
59The cumulative chi<sup>2</sup> function can be plotted.
60</UL>
61
62<hr><h2>LIVEPLOT Menu Contents</h2>
63<DL><DL>
64<H3>File Menu</H3>
65<DT>Tickmarks
66<DD>Checkbuttons are provided for each phase to determine if tick marks
67are shown. See the Options/"Configure Tickmarks"menu item for information
68on tickmarks
69<DT>Histogram
70<DD>This allows a histogram to be selected to be loaded
71<DT>Update Plot
72<DD>The causes LIVEPLOT to read read the current histogram again from
73the datafile
74<DT>Make PostScript
75<DD>Creates a low quality PostScript file containing the LIVEPLOT
76output. See the Options/"Set PS output" button for where the file is created.
77<DT>Quit
78</DL></DL>
79<DL><DL>
80<H3>File Menu</H3>
81<DT>Configure Tickmarks
82<DD>Tickmarks can be placed automatically, similar to their
83 placement in POWPLOT or can be drawn one height to another. The default
84is for lines to be draw from "-Inf" to "Inf", which creates lines from the
85bottom to the top of the plot. The options for each phase allow the line to be changed between solid and dashed, color of the line can be specified and
86the vertical placement of the tickmarks can be specified. The "show" flag,
87set in the File/Tickmarks menu can also be changed here.
88<DT>Obs symbol
89<DD>This brings up a menu where the symbol type and size for the
90observed data points can be selected.
91<DT>X units
92<DD>The x units can be selected here. The choices are
93"as collected" (2Theta/TOF/KeV), d-space (A) or Q (A<sup>-1</sup>)
94<DT>Y units
95<DD>The intensity values can be normalized by the incident spectrum
96(for energy dispersive methods).
97<DT>HKL labeling
98<DD>This brings up a menu that selects how long <I>hkl</I> values are shown
99before they are erased (0 means that they are not erased), the size of the
100labels and the width around the mouse that is searched for matching
101reflections. If requested using the "Separate window for <I>hkl</I> labels"
102option, labels are also show in a separate window.
103<DT>Subtract background
104<DD>The background is always shown, even when subtracted
105<DT>Include legend
106<DD>The legend is the optional box in the upper left that defines the
107plot entries
108<DT>Set PS output
109<DD>For UNIX this allows the file to be sent directly to a printer
110or can be saved in a file. For Windows, a file must be written.
111<DT>Raise on update
112<DD>This causes the plot to be placed on top of other windows, if partially
113obscured, when the plot is updated. At this time, this option does not
114work in Windows-NT and -2000.
115<DT>Cumulative Chi2
116<DD>The causes the Cumulative chi<sup>2</sup> function to be defined
117(see below).
118<DT>Save Options
119<DD>Causes many of the options set in this menu to be saved in the <TT>.gsas_config</TT> file.
120</DL></DL>
121
122<P>
123<hr><h2>LIVEPLOT Features</h2>
124<B>Plot zooming</B>
125When the left (usual) mouse button is pressed, this defines one corner
126of a region to be magnified. If the mouse is then moved, the diagonal
127corner of this magnification region is defined. When the left mouse button
128is pressed a second time, the selected section of the plot is magnified to
129fill the entire plot.
130<P>
131Zoom settings are saved.
132If the right mouse button is pressed, the previous zoom setting is used,
133so that the left mouse button is used to "zoom in" and the right mouse
134button is used to "zoom out."
135
136<P>
137<B>Reflection indices</B>
138are be displayed by pressing "H" or "h" while the
139mouse is near a reflection (holding the shift key while
140pressing the left mouse button also works).
141<P>
142<B>The cumulative chi<sup>2</sup></B>
143function was first suggested by
144Bill (W.I.F.) David [Accuracy in Powder Diffraction-III, 2001]
145as a way to see which reflections have the greatest influence on
146chi<sup>2</sup>. It is defined for point j as
147<IMG SRC="cchi2.gif" alt="equation for cumulative chi2 function" ALIGN=TOP>.
148
149
150<hr><H2>Customization of LIVEPLOT</H2><A NAME="customize"></A>
151The <TT>localconfig</TT> and <TT>.gsas_config</TT> files are read, if present.
152Note that some of these options are relevant only if the tcldump program is
153present.
154<P>
155The following variables control how LIVEPLOT functions and can be
156customized by changing their values in the
157<TT>localconfig</TT> and <TT>.gsas_config</TT> files:
158<DL><DL>
159<DT><TT>peakinfo(flag<i>n</i>)</TT><DD>
160These variables define if peak positions will be shown
161for reflections in phase "<i>n</i>". Reflections will be shown if
162the value is non-zero.
163
164<DT><TT>peakinfo(color<i>n</i>)</TT><DD>
165These variables define the default colors for
166reflections in phase "<i>n</i>"
167
168<DT><TT>peakinfo(dashes<i>n</i>)</TT><DD>
169These variables define if peaks will be dashed for
170reflections in phase "<i>n</i>" (UNIX only). Lines will be dashed if
171the value is non-zero.
172
173<DT><TT>peakinfo(min<i>n</i>) and peakinfo(max<i>n</i>)</TT><DD>
174These variables dictate the placement vertical position for reflection
175markers, when manually placed (see expgui(autotick), below). To draw
176to the edge of the screen, use -Inf and Inf.
177</DL></DL>
178
179The following variables are written to <tt>.gsas_config</tt> when
180"Save Options" is used. These variables are all set from the GUI and therefore
181do not need to be edited manually.
182
183<DL><DL>
184<DT><TT>graph(printout)</TT><DD>
185This is set to 1 if PostScript files
186will be printed and 0 if they will be written to disk (for Windows all
187files should be written to disk).
188
189<DT><TT>graph(outname)</TT><DD>
190This is the default for the file name used
191when PostScript files will be written to disk.
192
193<DT><TT>graph(outcmd)</TT><DD>
194This is the default for the command used
195to print PostScript files (Unix only).
196
197<DT><TT>graph(legend)</TT><DD>
198Sets the default value for display of the legend in liveplot and widplt.
199
200<DT><TT>graph(autoraise)</TT><DD>
201This option shows up in the options menu item as "Raise on update."
202When set to non-zero, the liveplot window is raised
203(placed on top of any other overlapping) windows
204each time it is updated.
205This option does not seem to work in Windows-NT, but this may depend on
206the version of Tcl/Tk.
207
208<DT><TT>peakinfo(obssym)</TT><DD>
209Symbol for observed data points. Valid choices are square, circle, diamond,
210plus, cross, splus and scross.
211
212<DT><TT>peakinfo(obssize)</TT><DD>
213Size for the symbol for observed data points. A value of 1 corresponds to about 1/8 inch
214(about 3 mm).
215
216<DT><TT>expgui(pixelregion)</TT><DD>
217When hkl values are loaded (using tcldump) and reflections are labeled, reflections
218can be labeled using a Shift-Left-Mouse click. All labeled reflections within expgui(pixelregion)
219pixels of the mouse position are assumed to be overlapped and are labeled.
220
221<DT><TT>expgui(fadetime)</TT><DD>
222The time in seconds before reflection labels are removed. A value of zero means that reflections
223must be deleted manually (Shift-Right-Mouse).
224
225<DT><TT>expgui(lblfontsize)</TT><DD>
226A size for reflections labels in pixels.
227
228<DT><TT>expgui(hklbox)</TT><DD>
229If this variable is non-zero, reflection indices are shown in a box.
230
231<DT><TT>expgui(autotick)</TT><DD>
232If this variable is non-zero, reflection markers positions are
233set automatically.
234</DL></DL>
235<P>
236<hr><H2>Installation details/External Programs</H2>
237<B>Using TCLDUMP with LIVEPLOT.</B>
238LIVEPLOT works with the standard GSAS program HSTDMP, but it works faster and is more
239powerful when used with the TCLDUMP program.
240Note that as of the April 2000 releases, GSAS is now distributed with TCLDUMP
241included. For older versions of GSAS, note the
242instructions for downloading this file can in the installation notes for
243<A HREF="expgui_Win_readme.html">
244Windows</A> and
245<A HREF="expgui_Unix_readme.html">
246UNIX</A>.
247<P>
248
249<B>Combining CMPR and LIVEPLOT.</B>
250If you have <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr.html">CMPR</A>
251installed on your computer, you can use superimpose on the GSAS results
252the peaks for an arbitrary unit cell. If desired, space group extinctions
253can even be shown.
254This is pretty neat! To enable this feature, you must have a version
255of CMPR downloaded after 4 May 1998
256<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr.html">
257(see the CMPR installation instructions.)</A>
258<UL><LI>
259For UNIX, create a link from in the expgui
260directory to file cellgen.tcl in the CMPR directory. For example:
261<PRE>
262   ln -s /usr/local/cmpr/cellgen.tcl /usr/local/gsas/expgui/cellgen.tcl
263</PRE>
264<LI>For Windows, copy all the .tcl and .exe files from the CMPR directory
265into the expgui directory.
266</UL>
267<P>
268
269<B>Combining LOGIC and LIVEPLOT.</B>
270If you have <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/logic.html">LOGIC</A>
271installed on your computer, you can superimpose peaks
272for a entry from the ICDD/JCPDS database on a pattern in LIVEPLOT.
273This is also pretty neat!
274To enable this feature, you must have
275a version of LOGIC downloaded after 4 May 1998
276<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/logic.html">
277(see the LOGIC installation instructions.)</A>
278<UL><LI>
279For UNIX, create a link from in the GSAS GUI
280directory to file icddcmd.tcl in the LOGIC directory. For example:
281<PRE>
282   ln -s /usr/local/powdersuite/icddcmd.tcl /usr/local/gsas/expgui/icddcmd.tcl
283</PRE>
284<LI>For Windows, copy all the LOGIC files into the expgui directory.
285</UL>
286<hr>
287<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
288<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
289</TH></TR></TABLE>
290
291<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
292<br>
293$Revision: 386 $ $Date: 2009-12-04 23:05:18 +0000 (Fri, 04 Dec 2009) $
294</body>
295</html>
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