| 1 | <html> |
|---|
| 2 | <head> |
|---|
| 3 | <title>EXPGUI -- EXCLEDT</title> |
|---|
| 4 | <meta name="keywords" content="crystallography, Rietveld, diffraction, |
|---|
| 5 | GSAS, EXPGUI"> |
|---|
| 6 | </HEAD> |
|---|
| 7 | <style> |
|---|
| 8 | A:link {text-decoration:none} |
|---|
| 9 | A:vlink {text-decoration:none} |
|---|
| 10 | </style> |
|---|
| 11 | |
|---|
| 12 | <BODY BGCOLOR="#FFFFFF" |
|---|
| 13 | topmargin="0" leftmargin="0" marginwidth="0" marginheight="0" |
|---|
| 14 | text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff"> |
|---|
| 15 | |
|---|
| 16 | <? |
|---|
| 17 | include("/var/www/include/navigation.inc"); |
|---|
| 18 | include("/var/www/include/utility.inc"); |
|---|
| 19 | ?> |
|---|
| 20 | <blockquote><font face="arial, helvetica, sans-serif"> |
|---|
| 21 | |
|---|
| 22 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
|---|
| 23 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
|---|
| 24 | </TH><TH><A Href="gsas2cif.html">Next page<BR>(CIF export)</A> |
|---|
| 25 | </TH><TH><A Href="liveplot.html">Previous page</A> |
|---|
| 26 | </TH></TR></TABLE><BR CLEAR=ALL> |
|---|
| 27 | |
|---|
| 28 | |
|---|
| 29 | <center><h1> |
|---|
| 30 | <HR noshade width="75%" size="2" align="center"> |
|---|
| 31 | EXPGUI Utilities (2), EXCLEDT |
|---|
| 32 | <HR noshade width="75%" size="2" align="center"> |
|---|
| 33 | </h1></center> |
|---|
| 34 | This page documents the EXCLEDT utility program |
|---|
| 35 | in the EXPGUI package. The purpose of this tool is to select graphically |
|---|
| 36 | regions of data that will not be included in the refinement. |
|---|
| 37 | The EXCLEDT program is called from the Powder/excledt |
|---|
| 38 | menu item or from the "Data Limits/Exclude" button on the Histogram pane. |
|---|
| 39 | <P> |
|---|
| 40 | A common use for this is |
|---|
| 41 | to adjust the lower 2theta/Q limit (maximum d-space/TOF) so that |
|---|
| 42 | data where no reflections occur can be ignored. It |
|---|
| 43 | is also common to start refinements with |
|---|
| 44 | a 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 |
|---|
| 46 | any peaks can be resolved in the final stages of refinement.) |
|---|
| 47 | Note that there is a disadvantage to changing the data range, |
|---|
| 48 | if one is using the Chebyschev polynomial |
|---|
| 49 | (type 1 background function) to fit the background, as this function |
|---|
| 50 | is scaled over the range of data. If the data range is changed, the |
|---|
| 51 | background function will shift and thus must be refit each time the |
|---|
| 52 | data range is changed. |
|---|
| 53 | <P> |
|---|
| 54 | A second purpose of EXCLEDT is to set and change excluded regions within the |
|---|
| 55 | pattern. When a region is set as excluded, the data within that region |
|---|
| 56 | are ignored with respect to the Rietveld refinement. Note that data should |
|---|
| 57 | be removed only where there is a good explanation why the region cannot be |
|---|
| 58 | accurately modeled. This is sometimes needed to deal with |
|---|
| 59 | scattering from a sample |
|---|
| 60 | container (although this can frequently be modeled as an additional |
|---|
| 61 | phase, using Le Bail extraction for that phase when |
|---|
| 62 | the container is badly textured). Excluded regions are also used occasionally |
|---|
| 63 | when an impurity manifests itself with only a few minor peaks, although it is |
|---|
| 64 | usually 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 |
|---|
| 66 | the material has severe preferred orientation). Excluded regions are sometime |
|---|
| 67 | needed when a section of pattern is affected by stacking faults. Another |
|---|
| 68 | occasional appropriate use is to eliminate spurious intensity that is due |
|---|
| 69 | instrumental malfunctions. |
|---|
| 70 | It is important not to exclude peaks simply because they cannot be indexed. |
|---|
| 71 | Such peaks may indicate a difference in symmetry or unit cell from the |
|---|
| 72 | structural model, or some other error. |
|---|
| 73 | It is also important that excluded regions be documented in the paper |
|---|
| 74 | which describes the study. |
|---|
| 75 | <P> |
|---|
| 76 | <img SRC="exc1.gif" alt="EXCLEDT Screen snapshot"> |
|---|
| 77 | <br clear=all> |
|---|
| 78 | The EXCLEDT program displays the data in a graph, (see the example above) |
|---|
| 79 | with the observed data as data points (black X's by default) |
|---|
| 80 | and the computed values as a line (red by default). Any excluded data points |
|---|
| 81 | are shown in a different color (orange, by default). |
|---|
| 82 | Lines (again orange, by default) at the |
|---|
| 83 | bottom of the plot show the allowed data range as well as any excluded regions. |
|---|
| 84 | Note that if POWPREF has been run more recently then GENLES, the calculated |
|---|
| 85 | values are zero. |
|---|
| 86 | The EXCLEDT program can plot data in the native units (2-theta, TOF, energy), |
|---|
| 87 | converted to d-space units, or in the most ideal unit for |
|---|
| 88 | diffraction analysis, Q (2 pi/d). |
|---|
| 89 | <P> |
|---|
| 90 | <br clear=all> |
|---|
| 91 | |
|---|
| 92 | <H3>Mouse use</H3> |
|---|
| 93 | The mouse can be used in three ways depending on the button pressed |
|---|
| 94 | in the lower portion of the window. |
|---|
| 95 | <P> |
|---|
| 96 | <img SRC="exc2.gif" BORDER=3 align=right alt="EXCLEDT Screen snapshot"> |
|---|
| 97 | In <B>Zoom mode</B>, |
|---|
| 98 | the cursor appears as |
|---|
| 99 | cross hairs, and the mouse is used to select a region to be magnified by |
|---|
| 100 | clicking on diagonal points in the region with the left mouse button |
|---|
| 101 | (see below) or "zoomed out" with the right mouse button. |
|---|
| 102 | Note that is is also possible to set the range manually, |
|---|
| 103 | <a href="#manualzoom">see below.</a> |
|---|
| 104 | <P> |
|---|
| 105 | <a name="AddRegion"></a> |
|---|
| 106 | In <B>Add Region mode</B>, the mouse is used to map out a region which that |
|---|
| 107 | will be excluded from the refinement. When this button is selected, the |
|---|
| 108 | mouse cursor changes to an arrow. After the left mouse is pressed once, |
|---|
| 109 | a yellow background is shown for the excluded region, as is seen below. |
|---|
| 110 | When the left mouse |
|---|
| 111 | button is pressed a second time, the region is selected. |
|---|
| 112 | If 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"> |
|---|
| 117 | Before the region is added to the excluded list, a message is |
|---|
| 118 | displayed to confirm this. This |
|---|
| 119 | confirmation message can optionally be eliminated (See |
|---|
| 120 | <a href="#prompt">Options/Prompt on add/del</a>.) |
|---|
| 121 | <br clear=all> |
|---|
| 122 | <P> |
|---|
| 123 | In <B>Delete Region mode</B>, the mouse is used to select a region to be |
|---|
| 124 | deleted, causing the data in that region to be included in the refinement. |
|---|
| 125 | The cursor appears as a circle in the graph section of the window. After |
|---|
| 126 | a region has been selected to delete, a message is |
|---|
| 127 | displayed to confirm the region to be deleted from the exclusion list. |
|---|
| 128 | This confirmation message can optionally be eliminated (See |
|---|
| 129 | <a href="#prompt">Options/Prompt on add/del</a>.)<br clear=all> |
|---|
| 130 | <P> |
|---|
| 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!"> |
|---|
| 136 | Zoom settings can also be entered manually by pressing the "Z" key. This |
|---|
| 137 | opens a dialog, as is shown to the right, where the x- or y-axis range |
|---|
| 138 | can be specified. Any value that is not specified is set to the maximum |
|---|
| 139 | or minimum for the entire dataset. It is possible to zoom further in using |
|---|
| 140 | the mouse, but to zoom out beyond the manual zoom limits, the "reset" button |
|---|
| 141 | on the manual zoom menu must be used. |
|---|
| 142 | <P> |
|---|
| 143 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 144 | If more than one histogram is available to plot, it is possible to cycle |
|---|
| 145 | between the histograms by pressing the "n" or "N" (for next) key. |
|---|
| 146 | <P> |
|---|
| 147 | <IMG SRC="new.gif" alt="New!"> |
|---|
| 148 | Tickmarks can be toggled on or off by pressing the |
|---|
| 149 | "1" key for phase 1, "2" for phase 2,... |
|---|
| 150 | <P> |
|---|
| 151 | <IMG SRC="new.gif" alt="New!"> |
|---|
| 152 | To shift the zoom region around, |
|---|
| 153 | the right and left arrow keys can be used to shift the |
|---|
| 154 | region 10 % to the left or right. |
|---|
| 155 | Likewise, |
|---|
| 156 | the up and down arrow keys can be used to shift the region up or down by 10 %. |
|---|
| 157 | Holding down the control key down while pressing these keys increases |
|---|
| 158 | the amount of the shift to 100 %. |
|---|
| 159 | <P> |
|---|
| 160 | <br clear=all> |
|---|
| 161 | <P> |
|---|
| 162 | <H3>Excluded Region/Simulation Range Buttons</H3> |
|---|
| 163 | <img SRC="exc4.gif" BORDER=3 align=right alt="EXCLEDT excluded regions snapshot"> |
|---|
| 164 | At the bottom of the window is a set of buttons with the minimum and maximum |
|---|
| 165 | limit on the data as well as a button for every excluded region. Pressing |
|---|
| 166 | a button causes a window to be opened to edit that region by manually entering |
|---|
| 167 | values. |
|---|
| 168 | <P>where the data range can be set |
|---|
| 169 | <br clear=all> |
|---|
| 170 | <img SRC="exc4a.gif" BORDER=3 align=right alt="EXCLEDT excluded regions snapshot"> |
|---|
| 171 | In the case where a dummy histogram will be edited, the information presented |
|---|
| 172 | in this box is formatted slightly differently (as shown to the right). |
|---|
| 173 | Pressing the set button creates a dialog box where the data range can be set, |
|---|
| 174 | see <a href="#editdummy">Editing Dummy Range</a>. |
|---|
| 175 | |
|---|
| 176 | <br clear=all> |
|---|
| 177 | <P> |
|---|
| 178 | <img SRC="exc5.gif" align=right alt="EXCLEDT informational message"> |
|---|
| 179 | If the upper data limit is raised (or d-min is lowered) this message is |
|---|
| 180 | displayed. The reason is that EXCLEDT cannot display data above the |
|---|
| 181 | upper data limit until the changed limit has been processed in POWPREF. |
|---|
| 182 | If you also want to see the computed intensities in this region, |
|---|
| 183 | you will need to run GENLES as well, so this is also offered as an option. |
|---|
| 184 | <br clear=all> |
|---|
| 185 | <P> |
|---|
| 186 | <a name="LimitTooHigh"></a> |
|---|
| 187 | <img SRC="exc7.gif" align=right alt="EXCLEDT informational message"> |
|---|
| 188 | Note that it is possible to set the upper data limit (lower d-min limit) |
|---|
| 189 | well outside the range of data. If this is done, POWPREF will run slower |
|---|
| 190 | because many unneeded reflections are being included in the computation. |
|---|
| 191 | If this occurs and POWPREF is run inside EXCLEDT, a message such as |
|---|
| 192 | that to the right is shown. Unless there is some specific reason |
|---|
| 193 | (I do not know of one) it is probably best to accept this suggestion. |
|---|
| 194 | <br clear=all> |
|---|
| 195 | <P> |
|---|
| 196 | <a name="editdummy"></a> |
|---|
| 197 | <H3>Editing Dummy Range</H3> |
|---|
| 198 | <img SRC="exc8.gif" align=right alt="EXCLEDT informational message"> |
|---|
| 199 | When the data range is edited, a box such as the one to the right will appear |
|---|
| 200 | to set the data limits and step size. Note that these values are always |
|---|
| 201 | displayed in the native units for the histogram (degrees, microseconds or Kev) |
|---|
| 202 | regardless of the setting for the x-axis units, since the step size is constant |
|---|
| 203 | in these native units. The data range is also shown in d-space and Q. |
|---|
| 204 | <P> |
|---|
| 205 | Note that it is not possible to edit the data range for |
|---|
| 206 | histograms with varying steps. At this time, this only affects |
|---|
| 207 | dummy TOF histograms simulated with logarithmic steps. The range can be |
|---|
| 208 | changed in the EXPEDT program. |
|---|
| 209 | <br clear=all> |
|---|
| 210 | <P> |
|---|
| 211 | <H3>Exiting EXCLEDT</H3> |
|---|
| 212 | <img SRC="exc6.gif" align=right alt="EXCLEDT informational message"> |
|---|
| 213 | EXCLEDT can be exited using the File/Exit menu item or by pressing the |
|---|
| 214 | "Save & Exit" button, or by pressing Control-C. If the excluded regions or |
|---|
| 215 | data limits are changed, a message to reminding you to run POWPREF is |
|---|
| 216 | shown. Note that you <I>must</I> run POWPREF before GENLES, if these |
|---|
| 217 | items are changed. |
|---|
| 218 | <br clear=all> |
|---|
| 219 | <P> |
|---|
| 220 | <H3>File Menu Commands</H3> |
|---|
| 221 | <img SRC="excm1.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot"> |
|---|
| 222 | <DL><DL> |
|---|
| 223 | <DT>Tickmarks<DD>Invokes a submenu where tickmarks can be displayed or removed |
|---|
| 224 | for each phase present in the histogram. |
|---|
| 225 | Alternately, tickmarks can be displayed or removed |
|---|
| 226 | <IMG SRC="new.gif" alt="New!">by pressing the |
|---|
| 227 | "1" key for phase 1, "2" for phase 2,... |
|---|
| 228 | See the Options/"Configure Tickmarks"menu item for information |
|---|
| 229 | on tickmarks |
|---|
| 230 | <DT>Histogram |
|---|
| 231 | <DD>This allows a different histogram to be displayed. |
|---|
| 232 | <DT>Set Min/Max Range |
|---|
| 233 | <DD>This opens a window where the usable data range may be changed. |
|---|
| 234 | <DT>Update Plot |
|---|
| 235 | <DD>The causes EXCLEDT to read read the current histogram again from |
|---|
| 236 | the datafile. If excluded region or data range |
|---|
| 237 | changes have been made, POWPREF & GENLES may be run first. |
|---|
| 238 | <DT>Make PostScript |
|---|
| 239 | <DD>Creates a low quality PostScript file containing the LIVEPLOT |
|---|
| 240 | output. See the Options/"Set PS output" button for where the file is created. |
|---|
| 241 | <DT>Exit<DD>Saves any changes to the excluded regions or data range. |
|---|
| 242 | If changes have been made, POWPREF & GENLES may be run. |
|---|
| 243 | </DL></DL> |
|---|
| 244 | |
|---|
| 245 | <br clear=all> |
|---|
| 246 | <img SRC="excm2.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot"> |
|---|
| 247 | <H3>Options Menu</H3> |
|---|
| 248 | <DL><DL> |
|---|
| 249 | <DT>Configure Tickmarks |
|---|
| 250 | <DD>Tickmarks can be placed automatically, similar to their |
|---|
| 251 | placement in POWPLOT or can be drawn one height to another. The default |
|---|
| 252 | is for lines to be draw from "-Inf" to "Inf", which creates lines from the |
|---|
| 253 | bottom 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 |
|---|
| 254 | the vertical placement of the tickmarks can be specified. The "show" flag, |
|---|
| 255 | set in the File/Tickmarks menu can also be changed here. |
|---|
| 256 | <DT>Symbol Type |
|---|
| 257 | <DD>This brings up a menu where the symbol type and size for the |
|---|
| 258 | observed and excluded data points can be selected. |
|---|
| 259 | <DT>Symbol Color |
|---|
| 260 | <DD>The colors for all the displayed lines and symbols can be changed here. |
|---|
| 261 | <DT>X units |
|---|
| 262 | <DD>The x units can be selected here. The choices are |
|---|
| 263 | "as collected" (2Theta/TOF/KeV), d-space (A) or Q (A<sup>-1</sup>) |
|---|
| 264 | <DT>Include Legend |
|---|
| 265 | <DD>The legend is the optional box in the upper left that defines the |
|---|
| 266 | plot entries |
|---|
| 267 | <a name="prompt"></a><DT>Prompt on add/del |
|---|
| 268 | <DD>If this option is set, a prompt will be generated when excluded regions |
|---|
| 269 | are added or deleted. |
|---|
| 270 | <DT>Set PS output |
|---|
| 271 | <DD>For UNIX this allows the file to be sent directly to a printer |
|---|
| 272 | or can be saved in a file. For Windows, a file must be written. |
|---|
| 273 | </DL></DL> |
|---|
| 274 | |
|---|
| 275 | |
|---|
| 276 | <br clear=all> |
|---|
| 277 | |
|---|
| 278 | <hr> |
|---|
| 279 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
|---|
| 280 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
|---|
| 281 | </TH><TH><A Href="gsas2cif.html">Next page<BR>(CIF export)</A> |
|---|
| 282 | </TH><TH><A Href="liveplot.html">Previous page</A> |
|---|
| 283 | </TH></TR></TABLE> |
|---|
| 284 | |
|---|
| 285 | <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR> |
|---|
| 286 | <font size=-1><? lastmod(); ?> </font> |
|---|
| 287 | <br>$Revision: 784 $ $Date: 2009-12-04 23:11:58 +0000 (Fri, 04 Dec 2009) $ |
|---|
| 288 | </blockquote> |
|---|
| 289 | </body> |
|---|
| 290 | </html> |
|---|
