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3   <title>EXPGUI -- EXCLEDT</title>
4   <meta name="keywords" content="crystallography, Rietveld, diffraction,
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23<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
24</TH><TH><A Href="liveplot.html">Previous page</A>
29<HR noshade width="75%" size="2" align="center">
30EXPGUI Utilities (2), EXCLEDT
31<HR noshade width="75%" size="2" align="center">
33This page documents the EXCLEDT utility program
34in the EXPGUI package. The purpose of this tool is to select graphically
35regions of data that will not be included in the refinement.
36The EXCLEDT program is called from the Powder/excledt
37menu item or from the "Data Limits/Exclude" button on the Histogram pane.
39A common use for this is
40to adjust the lower 2theta/Q limit (maximum d-space/TOF) so that
41data where no reflections occur can be ignored. It
42is also common to start refinements with
43a somewhat limited range of data, raising the upper 2theta/Q limit
44(minimum d-space/TOF) later. (The ideal is to include all data where
45any peaks can be resolved in the final stages of refinement.)
46Note that there is a disadvantage to changing the data range,
47if one is using the Chebyschev polynomial
48(type 1 background function) to fit the background, as this function
49is scaled over the range of data. If the data range is changed, the
50background function will shift and thus must be refit each time the
51data range is changed.
53A second purpose of EXCLEDT is to set and change excluded regions within the
54pattern. When a region is set as excluded, the data within that region
55are ignored with respect to the Rietveld refinement. Note that data should
56be removed only where there is a good explanation why the region cannot be
57accurately modeled. This is sometimes needed to deal with
58scattering from a sample
59container (although this can frequently be modeled as an additional
60phase, using Le Bail extraction for that phase when
61the container is badly textured). Excluded regions are also used occasionally
62when an impurity manifests itself with only a few minor peaks, although it is
63usually much better to model the impurity intensity as an additional phase
64(again using Le Bail extraction for that phase when the structure is unknown or
65the material has severe preferred orientation). Excluded regions are sometime
66needed when a section of pattern is affected by stacking faults. Another
67occasional appropriate use is to eliminate spurious intensity that is due
68instrumental malfunctions.
69It is important not to exclude peaks simply because they cannot be indexed.
70Such peaks may indicate a difference in symmetry or unit cell from the
71structural model, or some other error.
72It is also important that excluded regions be documented in the paper
73which describes the study.
75<img SRC="exc1.gif" alt="EXCLEDT Screen snapshot">
76<br clear=all>
77The EXCLEDT program displays the data in a graph, (see the example above)
78with the observed data as data points (black X's by default)
79and the computed values as a line (red by default). Any excluded data points
80are shown in a different color (orange, by default).
81Lines (again orange, by default) at the
82bottom of the plot show the allowed data range as well as any excluded regions.
83Note that if POWPREF has been run more recently then GENLES, the calculated
84values are zero.
85The EXCLEDT program can plot data in the native units (2-theta, TOF, energy),
86converted to d-space units, or in the most ideal unit for
87diffraction analysis, Q (2 pi/d).
89<br clear=all>
91<H3>Mouse use</H3>
92The mouse can be used in three ways depending on the button pressed
93in the lower portion of the window.
95<img SRC="exc2.gif" BORDER=3 align=right alt="EXCLEDT Screen snapshot">
96In <B>Zoom mode</B>,
97the cursor appears as
98cross hairs, and the mouse is used to select a region to be magnified by
99clicking on diagonal points in the region with the left mouse button
100(see below) or "zoomed out" with the right mouse button.
101Note that is is also possible to set the range manually,
102<a href="#manualzoom">see below.</a>
104<a name="AddRegion"></a>
105In <B>Add Region mode</B>, the mouse is used to map out a region which that
106will be excluded from the refinement. When this button is selected, the
107mouse cursor changes to an arrow. After the left mouse is pressed once,
108a yellow background is shown for the excluded region, as is seen below.
109When the left mouse
110button is pressed a second time, the region is selected.
111If the right mouse button is pressed instead, it resets the region selection.
112<br clear=all>
113<img SRC="exc3.gif" alt="EXCLEDT Screen snapshot">
114<br clear=all>
115<img SRC="exc3a.gif" align=RIGHT alt="EXCLEDT Screen snapshot">
116Before the region is added to the excluded list, a message is
117displayed to confirm this. This
118confirmation message can optionally be eliminated (See
119<a href="#prompt">Options/Prompt on add/del</a>.)
120<br clear=all>
122In <B>Delete Region mode</B>, the mouse is used to select a region to be
123deleted, causing the data in that region to be included in the refinement.
124The cursor appears as a circle in the graph section of the window. After
125a region has been selected to delete,  a message is
126displayed to confirm the region to be deleted from the exclusion list.
127This confirmation message can optionally be eliminated (See
128<a href="#prompt">Options/Prompt on add/del</a>.)<br clear=all>
130<br clear=all>
131<H3>Keypad Shortcuts</H3>
132<a name="manualzoom"></a>
133<img SRC="mzoom.gif" align=RIGHT alt="EXCLEDT manual zoom">
134<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
135Zoom settings can also be entered manually by pressing the "Z" key. This
136opens a dialog, as is shown to the right, where the x- or y-axis range
137can be specified. Any value that is not specified is set to the maximum
138or minimum for the entire dataset. It is possible to zoom further in using
139the mouse, but to zoom out beyond the manual zoom limits, the "reset" button
140on the manual zoom menu must be used.
142<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
143If more than one histogram is available to plot, it is possible to cycle
144between the histograms by pressing the "n" or "N" (for next) key.
146<br clear=all>
148<H3>Excluded Region/Simulation Range Buttons</H3>
149<img SRC="exc4.gif" BORDER=3 align=right alt="EXCLEDT excluded regions snapshot">
150At the bottom of the window is a set of buttons with the minimum and maximum
151limit on the data as well as a button for every excluded region. Pressing
152a button causes a window to be opened to edit that region by manually entering
154<P>where the data range can be set
155<br clear=all>
156<img SRC="exc4a.gif" BORDER=3 align=right alt="EXCLEDT excluded regions snapshot">
157In the case where a dummy histogram will be edited, the information presented
158in this box is formatted slightly differently (as shown to the right).
159Pressing the set button creates a dialog box where the data range can be set,
160see <a href="#editdummy">Editing Dummy Range</a>.
162<br clear=all>
164<img SRC="exc5.gif" align=right alt="EXCLEDT informational message">
165If the upper data limit is raised (or d-min is lowered) this message is
166displayed. The reason is that EXCLEDT cannot display data above the
167upper data limit until the changed limit has been processed in POWPREF.
168If you also want to see the computed intensities in this region,
169you will need to run GENLES as well, so this is also offered as an option.
170<br clear=all>
172<a name="LimitTooHigh"></a>
173<img SRC="exc7.gif" align=right alt="EXCLEDT informational message">
174Note that it is possible to set the upper data limit (lower d-min limit)
175well outside the range of data. If this is done, POWPREF will run slower
176because many unneeded reflections are being included in the computation.
177If this occurs and POWPREF is run inside EXCLEDT, a message such as
178that to the right is shown. Unless there is some specific reason
179(I do not know of one) it is probably best to accept this suggestion.
180<br clear=all>
182<a name="editdummy"></a>
183<H3>Editing Dummy Range</H3>
184<img SRC="exc8.gif" align=right alt="EXCLEDT informational message">
185When the data range is edited, a box such as the one to the right will appear
186to set the data limits and step size. Note that these values are always
187displayed in the native units for the histogram (degrees, microseconds or Kev)
188regardless of the setting for the x-axis units, since the step size is constant
189in these native units. The data range is also shown in d-space and Q.
191Note that it is not possible to edit the data range for
192histograms with varying steps. At this time, this only affects
193dummy TOF histograms simulated with logarithmic steps. The range can be
194changed in the EXPEDT program.
195<br clear=all>
197<H3>Exiting EXCLEDT</H3>
198<img SRC="exc6.gif" align=right alt="EXCLEDT informational message">
199EXCLEDT can be exited using the File/Exit menu item or by pressing the
200"Save & Exit" button, or by pressing Control-C. If the excluded regions or
201data limits are changed, a message to reminding you to run POWPREF is
202shown. Note that you <I>must</I> run POWPREF before GENLES, if these
203items are changed.
204<br clear=all>
206<H3>File Menu Commands</H3>
207<img SRC="excm1.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot">
209<DT>Tickmarks<DD>Invokes a submenu where tickmarks can be displayed or removed
210for each phase present in the histogram.
211See the Options/"Configure Tickmarks"menu item for information
212on tickmarks
214<DD>This allows a different histogram to be displayed.
215<DT>Set Min/Max Range
216<DD>This opens a window where the usable data range may be changed.
217<DT>Update Plot
218<DD>The causes EXCLEDT to read read the current histogram again from
219the datafile. If excluded region or data range
220changes have been made, POWPREF & GENLES may be run first.
221<DT>Make PostScript
222<DD>Creates a low quality PostScript file containing the LIVEPLOT
223output. See the Options/"Set PS output" button for where the file is created.
224<DT>Exit<DD>Saves any changes to the excluded regions or data range.
225If changes have been made, POWPREF & GENLES may be run.
228<br clear=all>
229<img SRC="excm2.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot">
230<H3>Options Menu</H3>
232<DT>Configure Tickmarks
233<DD>Tickmarks can be placed automatically, similar to their
234 placement in POWPLOT or can be drawn one height to another. The default
235is for lines to be draw from "-Inf" to "Inf", which creates lines from the
236bottom 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
237the vertical placement of the tickmarks can be specified. The "show" flag,
238set in the File/Tickmarks menu can also be changed here.
239<DT>Symbol Type
240<DD>This brings up a menu where the symbol type and size for the
241observed and excluded data points can be selected.
242<DT>Symbol Color
243<DD>The colors for all the displayed lines and symbols can be changed here.
244<DT>X units
245<DD>The x units can be selected here. The choices are
246"as collected" (2Theta/TOF/KeV), d-space (A) or Q (A<sup>-1</sup>)
247<DT>Include Legend
248<DD>The legend is the optional box in the upper left that defines the
249plot entries
250<a name="prompt"></a><DT>Prompt on add/del
251<DD>If this option is set, a prompt will be generated when excluded regions
252are added or deleted.
253<DT>Set PS output
254<DD>For UNIX this allows the file to be sent directly to a printer
255or can be saved in a file. For Windows, a file must be written.
259<br clear=all>
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267<P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
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269<br>$Revision: 564 $ $Date: 2009-12-04 23:08:17 +0000 (Fri, 04 Dec 2009) $
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