source: trunk/doc/excledt.html @ 498

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# on 2001/10/31 20:12:15, toby did:
major revision for in-line routine

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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">
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22
23<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
24<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
25</TH><TH><A Href="liveplot.html">Previous page</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" alt="EXCLEDT Screen snapshot">
75<br clear=all>
76The EXCLEDT program displays the data in a graph, (see the example above)
77with the observed data as data points (black X's by default)
78and the computed values as a line (red by default). Any excluded data points
79are shown in a different color (orange, by default).
80Lines (again orange, by default) at the
81bottom of the plot show the allowed data range as well as any excluded regions.
82Note that if POWPREF has been run more recently then GENLES, the calculated
83values are zero.
84The EXCLEDT program can plot data in the native units (2-theta, TOF, energy),
85converted to d-space units, or in the most ideal unit for
86diffraction analysis, Q (2 pi/d).
87<P>
88<br clear=all>
89
90<H3>Mouse use</H3>
91The mouse can be used in three ways depending on the button pressed
92in the lower portion of the window.
93<P>
94<img SRC="exc2.gif" BORDER=3 align=right alt="EXCLEDT Screen snapshot">
95In <B>Zoom mode</B>,
96the cursor appears as
97cross hairs, and the mouse is used to select a region to be magnified by
98clicking on diagonal points in the region with the left mouse button
99(see below) or "zoomed out" with the right mouse button.
100Note that is is also possible to set the range manually,
101<a href="#manualzoom">see below.</a>
102<P>
103<a name="AddRegion"></a>
104In <B>Add Region mode</B>, the mouse is used to map out a region which that
105will be excluded from the refinement. When this button is selected, the
106mouse cursor changes to an arrow. After the left mouse is pressed once,
107a yellow background is shown for the excluded region, as is seen below.
108When the left mouse
109button is pressed a second time, the region is selected.
110If the right mouse button is pressed instead, it resets the region selection.
111<br clear=all>
112<img SRC="exc3.gif" alt="EXCLEDT Screen snapshot">
113<br clear=all>
114<img SRC="exc3a.gif" align=RIGHT alt="EXCLEDT Screen snapshot">
115Before the region is added to the excluded list, a message is
116displayed to confirm this. This
117confirmation message can optionally be eliminated (See
118<a href="#prompt">Options/Prompt on add/del</a>.)
119<br clear=all>
120<P>
121In <B>Delete Region mode</B>, the mouse is used to select a region to be
122deleted, causing the data in that region to be included in the refinement.
123The cursor appears as a circle in the graph section of the window. After
124a region has been selected to delete,  a message is
125displayed to confirm the region to be deleted from the exclusion list.
126This confirmation message can optionally be eliminated (See
127<a href="#prompt">Options/Prompt on add/del</a>.)<br clear=all>
128<P>
129<br clear=all>
130<H3>Keypad Shortcuts</H3>
131<a name="manualzoom"></a>
132<img SRC="mzoom.gif" align=RIGHT alt="EXCLEDT manual zoom">
133<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
134Zoom settings can also be entered manually by pressing the "Z" key. This
135opens a dialog, as is shown to the right, where the x- or y-axis range
136can be specified. Any value that is not specified is set to the maximum
137or minimum for the entire dataset. It is possible to zoom further in using
138the mouse, but to zoom out beyond the manual zoom limits, the "reset" button
139on the manual zoom menu must be used.
140<P>
141<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
142If more than one histogram is available to plot, it is possible to cycle
143between the histograms by pressing the "n" or "N" (for next) key.
144<P>
145<br clear=all>
146<P>
147<H3>Excluded Region/Simulation Range Buttons</H3>
148<img SRC="exc4.gif" BORDER=3 align=right alt="EXCLEDT excluded regions snapshot">
149At the bottom of the window is a set of buttons with the minimum and maximum
150limit on the data as well as a button for every excluded region. Pressing
151a button causes a window to be opened to edit that region by manually entering
152values.
153<P>where the data range can be set
154<br clear=all>
155<img SRC="exc4a.gif" BORDER=3 align=right alt="EXCLEDT excluded regions snapshot">
156In the case where a dummy histogram will be edited, the information presented
157in this box is formatted slightly differently (as shown to the right).
158Pressing the set button creates a dialog box where the data range can be set,
159see <a href="#editdummy">Editing Dummy Range</a>.
160
161<br clear=all>
162<P>
163<img SRC="exc5.gif" align=right alt="EXCLEDT informational message">
164If the upper data limit is raised (or d-min is lowered) this message is
165displayed. The reason is that EXCLEDT cannot display data above the
166upper data limit until the changed limit has been processed in POWPREF.
167If you also want to see the computed intensities in this region,
168you will need to run GENLES as well, so this is also offered as an option.
169<br clear=all>
170<P>
171<a name="LimitTooHigh"></a>
172<img SRC="exc7.gif" align=right alt="EXCLEDT informational message">
173Note that it is possible to set the upper data limit (lower d-min limit)
174well outside the range of data. If this is done, POWPREF will run slower
175because many unneeded reflections are being included in the computation.
176If this occurs and POWPREF is run inside EXCLEDT, a message such as
177that to the right is shown. Unless there is some specific reason
178(I do not know of one) it is probably best to accept this suggestion.
179<br clear=all>
180<P>
181<a name="editdummy"></a>
182<H3>Editing Dummy Range</H3>
183<img SRC="exc8.gif" align=right alt="EXCLEDT informational message">
184When the data range is edited, a box such as the one to the right will appear
185to set the data limits and step size. Note that these values are always
186displayed in the native units for the histogram (degrees, microseconds or Kev)
187regardless of the setting for the x-axis units, since the step size is constant
188in these native units. The data range is also shown in d-space and Q.
189<P>
190Note that it is not possible to edit the data range for
191histograms with varying steps. At this time, this only affects
192dummy TOF histograms simulated with logarithmic steps. The range can be
193changed in the EXPEDT program.
194<br clear=all>
195<P>
196<H3>Exiting EXCLEDT</H3>
197<img SRC="exc6.gif" align=right alt="EXCLEDT informational message">
198EXCLEDT can be exited using the File/Exit menu item or by pressing the
199"Save & Exit" button, or by pressing Control-C. If the excluded regions or
200data limits are changed, a message to reminding you to run POWPREF is
201shown. Note that you <I>must</I> run POWPREF before GENLES, if these
202items are changed.
203<br clear=all>
204<P>
205<H3>File Menu Commands</H3>
206<img SRC="excm1.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot">
207<DL><DL>
208<DT>Tickmarks<DD>Invokes a submenu where tickmarks can be displayed or removed
209for each phase present in the histogram.
210See the Options/"Configure Tickmarks"menu item for information
211on tickmarks
212<DT>Histogram
213<DD>This allows a different histogram to be displayed.
214<DT>Set Min/Max Range
215<DD>This opens a window where the usable data range may be changed.
216<DT>Update Plot
217<DD>The causes EXCLEDT to read read the current histogram again from
218the datafile. If excluded region or data range
219changes have been made, POWPREF & GENLES may be run first.
220<DT>Make PostScript
221<DD>Creates a low quality PostScript file containing the LIVEPLOT
222output. See the Options/"Set PS output" button for where the file is created.
223<DT>Exit<DD>Saves any changes to the excluded regions or data range.
224If changes have been made, POWPREF & GENLES may be run.
225</DL></DL>
226
227<br clear=all>
228<img SRC="excm2.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot">
229<H3>Options Menu</H3>
230<DL><DL>
231<DT>Configure Tickmarks
232<DD>Tickmarks can be placed automatically, similar to their
233 placement in POWPLOT or can be drawn one height to another. The default
234is for lines to be draw from "-Inf" to "Inf", which creates lines from the
235bottom 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
236the vertical placement of the tickmarks can be specified. The "show" flag,
237set in the File/Tickmarks menu can also be changed here.
238<DT>Symbol Type
239<DD>This brings up a menu where the symbol type and size for the
240observed and excluded data points can be selected.
241<DT>Symbol Color
242<DD>The colors for all the displayed lines and symbols can be changed here.
243<DT>X units
244<DD>The x units can be selected here. The choices are
245"as collected" (2Theta/TOF/KeV), d-space (A) or Q (A<sup>-1</sup>)
246<DT>Include Legend
247<DD>The legend is the optional box in the upper left that defines the
248plot entries
249<a name="prompt"></a><DT>Prompt on add/del
250<DD>If this option is set, a prompt will be generated when excluded regions
251are added or deleted.
252<DT>Set PS output
253<DD>For UNIX this allows the file to be sent directly to a printer
254or can be saved in a file. For Windows, a file must be written.
255</DL></DL>
256
257
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259
260<hr>
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262<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
263</TH><TH><A Href="liveplot.html">Previous page</A>
264</TH></TR></TABLE><BR CLEAR=ALL>
265
266<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
267<br>
268$Revision: 481 $ $Date: 2009-12-04 23:06:53 +0000 (Fri, 04 Dec 2009) $
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