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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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22
23<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
24<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
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27
28
29<center><h1>
30EXPGUI Utilities (2), EXCLEDT
31</h1></center>
32This page documents the EXCLEDT utility program
33in the EXPGUI package. The purpose of this tool is to select graphically
34regions of data that will not be included in the refinement.
35The EXCLEDT program is called from the Powder/excledt
36menu item or from the "Data Limits/Exclude" button on the Histogram pane.
37<P>
38A common use for this is
39to adjust the lower 2theta/Q limit (maximum d-space/TOF) so that
40data where no reflections occur can be ignored. It
41is also common to start refinements with
42a somewhat limited range of data, raising the upper 2theta/Q limit
43(minimum d-space/TOF) later. (The ideal is to include all data where
44any peaks can be resolved in the final stages of refinement.)
45Note that there is a disadvantage to changing the data range,
46if one is using the Chebyschev polynomial
47(type 1 background function) to fit the background, as this function
48is scaled over the range of data. If the data range is changed, the
49background function will shift and thus must be refit each time the
50data range is changed.
51<P>
52A second purpose of EXCLEDT is to set and change excluded regions within the
53pattern. When a region is set as excluded, the data within that region
54are ignored with respect to the Rietveld refinement. Note that data should
55be removed only where there is a good explanation why the region cannot be
56accurately modeled. This is sometimes needed to deal with
57scattering from a sample
58container (although this can frequently be modeled as an additional
59phase, using Le Bail extraction for that phase when
60the container is badly textured). Excluded regions are also used occasionally
61when an impurity manifests itself with only a few minor peaks, although it is
62usually much better to model the impurity intensity as an additional phase
63(again using Le Bail extraction for that phase when the structure is unknown or
64the material has severe preferred orientation). Excluded regions are sometime
65needed when a section of pattern is affected by stacking faults. Another
66occasional appropriate use is to eliminate spurious intensity that is due
67instrumental malfunctions.
68It is important not to exclude peaks simply because they cannot be indexed.
69Such peaks may indicate a difference in symmetry or unit cell from the
70structural model, or some other error.
71It is also important that excluded regions be documented in the paper
72which describes the study.
73<P>
74<img SRC="exc1.gif" align=RIGHT alt="EXCLEDT Screen snapshot">
75The EXCLEDT program displays the data in a graph, (see the example to right)
76with the observed data as data points (black X's by default)
77and the computed values as a line (red by default). Any excluded data points
78are shown in a different color (orange, by default).
79Lines (again orange, by default) at the
80bottom of the plot show the allowed data range as well as any excluded regions.
81Note that if POWPREF has been run more recently then GENLES, the calculated
82values are zero.
83The EXCLEDT program can plot data in the native units (2-theta, TOF, energy),
84converted to d-space units, or in the most ideal unit for
85diffraction analysis, Q (2 pi/d).
86<P>
87<br clear=all>
88
89<H3>Mouse use</H3>
90The mouse can be used in three ways depending on the button pressed
91in the lower portion of the window.
92<P>
93<img SRC="exc2.gif" BORDER=3 align=right alt="EXCLEDT Screen snapshot">
94In <B>Zoom mode</B>,
95the cursor appears as
96cross hairs, and the mouse is used to select a region to be magnified by
97clicking on diagonal points in the region with the left mouse button
98(see below) or "zoomed out" with the right mouse button.
99<br clear=all>
100<P>
101<a name="AddRegion"></a>
102<img SRC="exc3.gif" align=RIGHT alt="EXCLEDT Screen snapshot">
103In <B>Add Region mode</B>, the mouse is used to map out a region which that
104will be excluded from the refinement. When this button is selected, the
105mouse cursor changes to an arrow. After the left mouse is pressed once,
106a yellow background is shown for the excluded region and when the left mouse
107button is pressed a second time, the region is selected.
108If the right mouse button is pressed instead, it resets the region selection.
109<br clear=all>
110<img SRC="exc3a.gif" align=RIGHT alt="EXCLEDT Screen snapshot">
111Before the region is added to the excluded list, a message is
112displayed to confirm this. This
113confirmation message can optionally be eliminated (See
114<a href="#prompt">Options/Prompt on add/del</a>.)
115<br clear=all>
116<P>
117In <B>Delete Region mode</B>, the mouse is used to select a region to be
118deleted, causing the data in that region to be included in the refinement.
119The cursor appears as a circle in the graph section of the window. After
120a region has been selected to delete,  a message is
121displayed to confirm the region to be deleted from the exclusion list.
122This confirmation message can optionally be eliminated (See
123<a href="#prompt">Options/Prompt on add/del</a>.)<br clear=all>
124<P>
125<img SRC="exc4.gif" BORDER=3 align=right alt="EXCLEDT excluded regions snapshot">
126<H3>Excluded Region Buttons</H3>
127At the bottom of the window is a set of buttons with the minimum and maximum
128limit on the data as well as a button for every excluded region. Pressing
129a button causes a window to be opened to edit that region by manually entering
130values.
131<P>
132<br clear=all>
133<img SRC="exc5.gif" align=right alt="EXCLEDT informational message">
134If the upper data limit is raised (or d-min ls lowered) this message is
135displayed. The reason is that EXCLEDT cannot display data above the
136upper data limit until the changed limit has been processed in POWPREF.
137If you also want to see the computed intensities in this region,
138you will need to run GENLES as well, so this is also offered as an option.
139<br clear=all>
140<P>
141<a name="LimitTooHigh"></a>
142<img SRC="exc7.gif" align=right alt="EXCLEDT informational message">
143Note that it is possible to set the upper data limit (lower d-min limit)
144well outside the range of data. If this is done, POWPREF will run slower
145because many unneeded reflections are being included in the computation.
146If this occurs and POWPREF is run inside EXCLEDT, a message such as
147that to the right is shown. Unless there is some specific reason
148(I do not know of one) it is probably best to accept this suggestion.
149<br clear=all>
150<P>
151<H3>Exiting EXCLEDT</H3>
152<img SRC="exc6.gif" align=right alt="EXCLEDT informational message">
153EXCLEDT can be exited using the File/Exit menu item or by pressing the
154"Save & Exit" button, or by pressing Control-C. If the excluded regions or
155data limits are changed, a message to reminding you to run POWPREF is
156shown. Note that you <I>must</I> run POWPREF before GENLES, if these
157items are changed.
158<br clear=all>
159<P>
160<H3>File Menu Commands</H3>
161<img SRC="excm1.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot">
162<DL><DL>
163<DT>Tickmarks<DD>Invokes a submenu where tickmarks can be displayed or removed
164for each phase present in the histogram.
165See the Options/"Configure Tickmarks"menu item for information
166on tickmarks
167<DT>Histogram
168<DD>This allows a different histogram to be displayed.
169<DT>Set Min/Max Range
170<DD>This opens a window where the usable data range may be changed.
171<DT>Update Plot
172<DD>The causes EXCLEDT to read read the current histogram again from
173the datafile. If excluded region or data range
174changes have been made, POWPREF & GENLES may be run first.
175<DT>Make PostScript
176<DD>Creates a low quality PostScript file containing the LIVEPLOT
177output. See the Options/"Set PS output" button for where the file is created.
178<DT>Exit<DD>Saves any changes to the excluded regions or data range.
179If changes have been made, POWPREF & GENLES may be run.
180</DL></DL>
181
182<br clear=all>
183<img SRC="excm2.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot">
184<H3>Options Menu</H3>
185<DL><DL>
186<DT>Configure Tickmarks
187<DD>Tickmarks can be placed automatically, similar to their
188 placement in POWPLOT or can be drawn one height to another. The default
189is for lines to be draw from "-Inf" to "Inf", which creates lines from the
190bottom 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
191the vertical placement of the tickmarks can be specified. The "show" flag,
192set in the File/Tickmarks menu can also be changed here.
193<DT>Symbol Type
194<DD>This brings up a menu where the symbol type and size for the
195observed and excluded data points can be selected.
196<DT>Symbol Color
197<DD>The colors for all the displayed lines and symbols can be changed here.
198<DT>X units
199<DD>The x units can be selected here. The choices are
200"as collected" (2Theta/TOF/KeV), d-space (A) or Q (A<sup>-1</sup>)
201<DT>Include Legend
202<DD>The legend is the optional box in the upper left that defines the
203plot entries
204<a name="prompt"></a><DT>Prompt on add/del
205<DD>If this option is set, a prompt will be generated when excluded regions
206are added or deleted.
207<DT>Set PS output
208<DD>For UNIX this allows the file to be sent directly to a printer
209or can be saved in a file. For Windows, a file must be written.
210<DT>Set screen font
211<DD>This option is used to control the font used for menus, graphics and
212other aspects of windows.
213<DT>Save options
214<DD>Causes many of the options set in this menu to be saved in the <TT>.gsas_config</TT> file.
215</DL></DL>
216
217
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219
220<hr>
221<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
222<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
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224</TH></TR></TABLE><BR CLEAR=ALL>
225
226<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
227<br>
228$Revision: 437 $ $Date: 2009-12-04 23:06:09 +0000 (Fri, 04 Dec 2009) $
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