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3   <title>EXPGUI -- EXCLEDT</title>
4   <meta name="keywords" content="crystallography, Rietveld, diffraction,
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17   include("/var/www/include/");
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30<HR noshade width="75%" size="2" align="center">
31EXPGUI Utilities (2), EXCLEDT
32<HR noshade width="75%" size="2" align="center">
34This page documents the EXCLEDT utility program
35in the EXPGUI package. The purpose of this tool is to select graphically
36regions of data that will not be included in the refinement.
37The EXCLEDT program is called from the Powder/excledt
38menu item or from the "Data Limits/Exclude" button on the Histogram pane.
40A common use for this is
41to adjust the lower 2theta/Q limit (maximum d-space/TOF) so that
42data where no reflections occur can be ignored. It
43is also common to start refinements with
44a somewhat limited range of data, raising the upper 2theta/Q limit
45(minimum d-space/TOF) later. (The ideal is to include all data where
46any peaks can be resolved in the final stages of refinement.)
47Note that there is a disadvantage to changing the data range,
48if one is using the Chebyschev polynomial
49(type 1 background function) to fit the background, as this function
50is scaled over the range of data. If the data range is changed, the
51background function will shift and thus must be refit each time the
52data range is changed.
54A second purpose of EXCLEDT is to set and change excluded regions within the
55pattern. When a region is set as excluded, the data within that region
56are ignored with respect to the Rietveld refinement. Note that data should
57be removed only where there is a good explanation why the region cannot be
58accurately modeled. This is sometimes needed to deal with
59scattering from a sample
60container (although this can frequently be modeled as an additional
61phase, using Le Bail extraction for that phase when
62the container is badly textured). Excluded regions are also used occasionally
63when an impurity manifests itself with only a few minor peaks, although it is
64usually much better to model the impurity intensity as an additional phase
65(again using Le Bail extraction for that phase when the structure is unknown or
66the material has severe preferred orientation). Excluded regions are sometime
67needed when a section of pattern is affected by stacking faults. Another
68occasional appropriate use is to eliminate spurious intensity that is due
69instrumental malfunctions.
70It is important not to exclude peaks simply because they cannot be indexed.
71Such peaks may indicate a difference in symmetry or unit cell from the
72structural model, or some other error.
73It is also important that excluded regions be documented in the paper
74which describes the study.
76<img SRC="exc1.gif" alt="EXCLEDT Screen snapshot">
77<br clear=all>
78The EXCLEDT program displays the data in a graph, (see the example above)
79with the observed data as data points (black X's by default)
80and the computed values as a line (red by default). Any excluded data points
81are shown in a different color (orange, by default).
82Lines (again orange, by default) at the
83bottom of the plot show the allowed data range as well as any excluded regions.
84Note that if POWPREF has been run more recently then GENLES, the calculated
85values are zero.
86The EXCLEDT program can plot data in the native units (2-theta, TOF, energy),
87converted to d-space units, or in the most ideal unit for
88diffraction analysis, Q (2 pi/d).
90<br clear=all>
92<H3>Mouse use</H3>
93The mouse can be used in three ways depending on the button pressed
94in the lower portion of the window.
96<img SRC="exc2.gif" BORDER=3 align=right alt="EXCLEDT Screen snapshot">
97In <B>Zoom mode</B>,
98the cursor appears as
99cross hairs, and the mouse is used to select a region to be magnified by
100clicking on diagonal points in the region with the left mouse button
101(see below) or "zoomed out" with the right mouse button.
102Note that is is also possible to set the range manually,
103<a href="#manualzoom">see below.</a>
105<a name="AddRegion"></a>
106In <B>Add Region mode</B>, the mouse is used to map out a region which that
107will be excluded from the refinement. When this button is selected, the
108mouse cursor changes to an arrow. After the left mouse is pressed once,
109a yellow background is shown for the excluded region, as is seen below.
110When the left mouse
111button is pressed a second time, the region is selected.
112If the right mouse button is pressed instead, it resets the region selection.
113<br clear=all>
114<img SRC="exc3.gif" alt="EXCLEDT Screen snapshot">
115<br clear=all>
116<img SRC="exc3a.gif" align=RIGHT alt="EXCLEDT Screen snapshot">
117Before the region is added to the excluded list, a message is
118displayed to confirm this. This
119confirmation message can optionally be eliminated (See
120<a href="#prompt">Options/Prompt on add/del</a>.)
121<br clear=all>
123In <B>Delete Region mode</B>, the mouse is used to select a region to be
124deleted, causing the data in that region to be included in the refinement.
125The cursor appears as a circle in the graph section of the window. After
126a region has been selected to delete,  a message is
127displayed to confirm the region to be deleted from the exclusion list.
128This confirmation message can optionally be eliminated (See
129<a href="#prompt">Options/Prompt on add/del</a>.)<br clear=all>
131<br clear=all>
132<H3>Keypad Shortcuts</H3>
133<a name="manualzoom"></a>
134<img SRC="mzoom.gif" align=RIGHT alt="EXCLEDT manual zoom">
135<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
136Zoom settings can also be entered manually by pressing the "Z" key. This
137opens a dialog, as is shown to the right, where the x- or y-axis range
138can be specified. Any value that is not specified is set to the maximum
139or minimum for the entire dataset. It is possible to zoom further in using
140the mouse, but to zoom out beyond the manual zoom limits, the "reset" button
141on the manual zoom menu must be used.
143<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
144If more than one histogram is available to plot, it is possible to cycle
145between the histograms by pressing the "n" or "N" (for next) key.
147<IMG SRC="new.gif" alt="New!">
148Tickmarks can be toggled on or off by pressing the
149"1" key for phase 1, "2" for phase 2,...
151<br clear=all>
153<H3>Excluded Region/Simulation Range Buttons</H3>
154<img SRC="exc4.gif" BORDER=3 align=right alt="EXCLEDT excluded regions snapshot">
155At the bottom of the window is a set of buttons with the minimum and maximum
156limit on the data as well as a button for every excluded region. Pressing
157a button causes a window to be opened to edit that region by manually entering
159<P>where the data range can be set
160<br clear=all>
161<img SRC="exc4a.gif" BORDER=3 align=right alt="EXCLEDT excluded regions snapshot">
162In the case where a dummy histogram will be edited, the information presented
163in this box is formatted slightly differently (as shown to the right).
164Pressing the set button creates a dialog box where the data range can be set,
165see <a href="#editdummy">Editing Dummy Range</a>.
167<br clear=all>
169<img SRC="exc5.gif" align=right alt="EXCLEDT informational message">
170If the upper data limit is raised (or d-min is lowered) this message is
171displayed. The reason is that EXCLEDT cannot display data above the
172upper data limit until the changed limit has been processed in POWPREF.
173If you also want to see the computed intensities in this region,
174you will need to run GENLES as well, so this is also offered as an option.
175<br clear=all>
177<a name="LimitTooHigh"></a>
178<img SRC="exc7.gif" align=right alt="EXCLEDT informational message">
179Note that it is possible to set the upper data limit (lower d-min limit)
180well outside the range of data. If this is done, POWPREF will run slower
181because many unneeded reflections are being included in the computation.
182If this occurs and POWPREF is run inside EXCLEDT, a message such as
183that to the right is shown. Unless there is some specific reason
184(I do not know of one) it is probably best to accept this suggestion.
185<br clear=all>
187<a name="editdummy"></a>
188<H3>Editing Dummy Range</H3>
189<img SRC="exc8.gif" align=right alt="EXCLEDT informational message">
190When the data range is edited, a box such as the one to the right will appear
191to set the data limits and step size. Note that these values are always
192displayed in the native units for the histogram (degrees, microseconds or Kev)
193regardless of the setting for the x-axis units, since the step size is constant
194in these native units. The data range is also shown in d-space and Q.
196Note that it is not possible to edit the data range for
197histograms with varying steps. At this time, this only affects
198dummy TOF histograms simulated with logarithmic steps. The range can be
199changed in the EXPEDT program.
200<br clear=all>
202<H3>Exiting EXCLEDT</H3>
203<img SRC="exc6.gif" align=right alt="EXCLEDT informational message">
204EXCLEDT can be exited using the File/Exit menu item or by pressing the
205"Save & Exit" button, or by pressing Control-C. If the excluded regions or
206data limits are changed, a message to reminding you to run POWPREF is
207shown. Note that you <I>must</I> run POWPREF before GENLES, if these
208items are changed.
209<br clear=all>
211<H3>File Menu Commands</H3>
212<img SRC="excm1.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot">
214<DT>Tickmarks<DD>Invokes a submenu where tickmarks can be displayed or removed
215for each phase present in the histogram.
216Alternately, tickmarks can be displayed or removed
217<IMG SRC="new.gif" alt="New!">by pressing the
218"1" key for phase 1, "2" for phase 2,...
219See the Options/"Configure Tickmarks"menu item for information
220on tickmarks
222<DD>This allows a different histogram to be displayed.
223<DT>Set Min/Max Range
224<DD>This opens a window where the usable data range may be changed.
225<DT>Update Plot
226<DD>The causes EXCLEDT to read read the current histogram again from
227the datafile. If excluded region or data range
228changes have been made, POWPREF & GENLES may be run first.
229<DT>Make PostScript
230<DD>Creates a low quality PostScript file containing the LIVEPLOT
231output. See the Options/"Set PS output" button for where the file is created.
232<DT>Exit<DD>Saves any changes to the excluded regions or data range.
233If changes have been made, POWPREF & GENLES may be run.
236<br clear=all>
237<img SRC="excm2.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot">
238<H3>Options Menu</H3>
240<DT>Configure Tickmarks
241<DD>Tickmarks can be placed automatically, similar to their
242 placement in POWPLOT or can be drawn one height to another. The default
243is for lines to be draw from "-Inf" to "Inf", which creates lines from the
244bottom 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
245the vertical placement of the tickmarks can be specified. The "show" flag,
246set in the File/Tickmarks menu can also be changed here.
247<DT>Symbol Type
248<DD>This brings up a menu where the symbol type and size for the
249observed and excluded data points can be selected.
250<DT>Symbol Color
251<DD>The colors for all the displayed lines and symbols can be changed here.
252<DT>X units
253<DD>The x units can be selected here. The choices are
254"as collected" (2Theta/TOF/KeV), d-space (A) or Q (A<sup>-1</sup>)
255<DT>Include Legend
256<DD>The legend is the optional box in the upper left that defines the
257plot entries
258<a name="prompt"></a><DT>Prompt on add/del
259<DD>If this option is set, a prompt will be generated when excluded regions
260are added or deleted.
261<DT>Set PS output
262<DD>For UNIX this allows the file to be sent directly to a printer
263or can be saved in a file. For Windows, a file must be written.
267<br clear=all>
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276<P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
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278<br>$Revision: 764 $ $Date: 2009-12-04 23:11:38 +0000 (Fri, 04 Dec 2009) $
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