source: trunk/doc/excledt.html @ 434

Last change on this file since 434 was 434, checked in by toby, 12 years ago

# on 2001/09/04 23:05:49, toby did:
Describes EXCLEDT

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1<html>
2<head>
3   <META NAME="Author" CONTENT="Brian H. Toby">
4   <title>EXPGUI -- EXCLEDT</title>
5</head>
6<BODY BGCOLOR="#FFFFFF">
7
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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>
28EXCLEDT
29</h1></center>
30This page documents the EXCLEDT utility program
31in the EXPGUI package. The purpose of this tool is to select graphically
32regions of data that will not be included in the refinement.
33The EXCLEDT program is called from the Powder/excledt
34menu item or from the "Data Limits/Exclude" button on the Histogram pane.
35<P>
36A common use for this is
37to adjust the lower 2theta/Q limit (maximum d-space/TOF) so that
38data where no reflections occur can be ignored. It
39is also common to start refinements with
40a somewhat limited range of data, raising the upper 2theta/Q limit
41(minimum d-space/TOF) later. (The ideal is to include all data where
42any peaks can be resolved in the final stages of refinement.)
43Note that there is a disadvantage to changing the data range,
44if one is using the Chebyschev polynomial
45(type 1 background function) to fit the background, as this function
46is scaled over the range of data. If the data range is changed, the
47background function will shift and thus must be refit each time the
48data range is changed.
49<P>
50A second purpose of EXCLEDT is to set and change excluded regions within the
51pattern. When a region is set as excluded, the data within that region
52are ignored with respect to the Rietveld refinement. Note that data should
53be removed only where there is a good explanation why the region cannot be
54accurately modeled. This is sometimes needed to deal with
55scattering from a sample
56container (although this can frequently be modeled as an additional
57phase, using Le Bail extraction for that phase when
58the container is badly textured). Excluded regions are also used occasionally
59when an impurity manifests itself with only a few minor peaks, although it is
60usually much better to model the impurity intensity as an additional phase
61(again using Le Bail extraction for that phase when the structure is unknown or
62the material has severe preferred orientation). Excluded regions are sometime
63needed when a section of pattern is affected by stacking faults. Another
64occasional appropriate use is to eliminate spurious intensity that is due
65instrumental malfunctions.
66It is important not to exclude peaks simply because they cannot be indexed.
67Such peaks may indicate a difference in symmetry or unit cell from the
68structural model, or some other error.
69It is also important that excluded regions be documented in the paper
70which describes the study.
71<P>
72<img SRC="exc1.gif" align=RIGHT alt="EXCLEDT Screen snapshot">
73The EXCLEDT program displays the data in a graph, (see the example to right)
74with the observed data as data points (black X's by default)
75and the computed values as a line (red by default). Any excluded data points
76are shown in a different color (orange, by default).
77Lines (again orange, by default) at the
78bottom of the plot show the allowed data range as well as any excluded regions.
79Note that if POWPREF has been run more recently then GENLES, the calculated
80values are zero.
81The EXCLEDT program can plot data in the native units (2-theta, TOF, energy),
82converted to d-space units, or in the most ideal unit for
83diffraction analysis, Q (2 pi/d).
84<P>
85<br clear=all>
86
87<H3>Mouse use</H3>
88The mouse can be used in three ways depending on the button pressed
89in the lower portion of the window.
90<P>
91<img SRC="exc2.gif" BORDER=3 align=LEFT alt="EXCLEDT Screen snapshot">
92In <B>Zoom mode</B>,
93the cursor appears as
94cross hairs, and the mouse is used to select a region to be magnified by
95clicking on diagonal points in the region with the left mouse button
96(see below) or "zoomed out" with the right mouse button.
97<br clear=all>
98<P>
99<img SRC="exc3.gif" align=RIGHT alt="EXCLEDT Screen snapshot">
100In <B>Add Region mode</B>, the mouse is used to map out a region which that
101will be excluded from the refinement. When this button is selected, the
102mouse cursor changes to an arrow. After the left mouse is pressed once,
103a yellow background is shown for the excluded region and when the left mouse
104button is pressed a second time, the region is selected.
105If the right mouse button is pressed instead, it resets the region selection.
106<br clear=all>
107<img SRC="exc3a.gif" align=RIGHT alt="EXCLEDT Screen snapshot">
108Before the region is added to the excluded list, a message is
109displayed to confirm this. This
110confirmation message can optionally be eliminated (See
111<a href="#prompt">Options/Prompt on add/del</a>.)
112<br clear=all>
113<P>
114In <B>Delete Region mode</B>, the mouse is used to select a region to be
115deleted, causing the data in that region to be included in the refinement.
116The cursor appears as a circle in the graph section of the window. After
117a region has been selected to delete,  a message is
118displayed to confirm the region to be deleted from the exclusion list.
119This confirmation message can optionally be eliminated (See
120<a href="#prompt">Options/Prompt on add/del</a>.)<br clear=all>
121<P>
122<img SRC="exc4.gif" BORDER=3 align=right alt="EXCLEDT excluded regions snapshot">
123<H3>Excluded Region Buttons</H3>
124At the bottom of the window is a set of buttons with the minimum and maximum
125limit on the data as well as a button for every excluded region. Pressing
126a button causes a window to be opened to edit that region by manually entering
127values.
128<br clear=all>
129<H3>File Menu Commands</H3>
130<img SRC="excm1.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot">
131<DL><DL>
132<DT>Tickmarks<DD>Invokes a submenu where tickmarks can be displayed or removed
133for each phase present in the histogram.
134See the Options/"Configure Tickmarks"menu item for information
135on tickmarks
136<DT>Histogram
137<DD>This allows a different histogram to be displayed.
138<DT>Set Min/Max Range
139<DD>This opens a window where the usable data range may be changed.
140<DT>Update Plot
141<DD>The causes EXCLEDT to read read the current histogram again from
142the datafile. If excluded region or data range
143changes have been made, POWPREF & GENLES may be run first.
144<DT>Make PostScript
145<DD>Creates a low quality PostScript file containing the LIVEPLOT
146output. See the Options/"Set PS output" button for where the file is created.
147<DT>Exit<DD>Saves any changes to the excluded regions or data range.
148If changes have been made, POWPREF & GENLES may be run.
149</DL></DL>
150
151<br clear=all>
152<img SRC="excm2.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot">
153<H3>Options Menu</H3>
154<DL><DL>
155<DT>Configure Tickmarks
156<DD>Tickmarks can be placed automatically, similar to their
157 placement in POWPLOT or can be drawn one height to another. The default
158is for lines to be draw from "-Inf" to "Inf", which creates lines from the
159bottom 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
160the vertical placement of the tickmarks can be specified. The "show" flag,
161set in the File/Tickmarks menu can also be changed here.
162<DT>Symbol Type
163<DD>This brings up a menu where the symbol type and size for the
164observed and excluded data points can be selected.
165<DT>Symbol Color
166<DD>The colors for all the displayed lines and symbols can be changed here.
167<DT>X units
168<DD>The x units can be selected here. The choices are
169"as collected" (2Theta/TOF/KeV), d-space (A) or Q (A<sup>-1</sup>)
170<DT>Include Legend
171<DD>The legend is the optional box in the upper left that defines the
172plot entries
173<a name="prompt"></a><DT>Prompt on add/del
174<DD>If this option is set, a prompt will be generated when excluded regions
175are added or deleted.
176<DT>Set PS output
177<DD>For UNIX this allows the file to be sent directly to a printer
178or can be saved in a file. For Windows, a file must be written.
179<DT>Set screen font
180<DD>This option is used to control the font used for menus, graphics and
181other aspects of windows.
182<DT>Save options
183<DD>Causes many of the options set in this menu to be saved in the <TT>.gsas_config</TT> file.
184</DL></DL>
185
186
187<br clear=all>
188
189<hr>
190<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
191<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
192</TH></TR></TABLE>
193
194<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
195<br>
196$Revision: 434 $ $Date: 2009-12-04 23:06:06 +0000 (Fri, 04 Dec 2009) $
197</body>
198</html>
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