| 1 | <html> |
|---|
| 2 | <head> |
|---|
| 3 | <title>EXPGUI -- LIVEPLOT/BKGEDIT</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="excledt.html">Next page<BR>(EXCLEDT)</A> |
|---|
| 25 | </TH><TH><A Href="expguic.html">Previous page</A> |
|---|
| 26 | </TH></TR></TABLE><BR CLEAR=ALL> |
|---|
| 27 | |
|---|
| 28 | <center><h1> |
|---|
| 29 | <HR noshade width="75%" size="2" align="center"> |
|---|
| 30 | EXPGUI Utilities (1),<BR>LIVEPLOT and BKGEDIT |
|---|
| 31 | <HR noshade width="75%" size="2" align="center"> |
|---|
| 32 | </h1></center> |
|---|
| 33 | This page documents the LIVEPLOT and BKGEDIT utility programs |
|---|
| 34 | in the EXPGUI package. |
|---|
| 35 | LIVEPLOT and BKGEDIT are actually the same program, but perform |
|---|
| 36 | different functions, depending on how they are invoked. |
|---|
| 37 | LIVEPLOT is used to display the quality of the diffraction fit, while |
|---|
| 38 | BKGEDIT is used to fit a background function to fixed background points |
|---|
| 39 | that have been input by the user. |
|---|
| 40 | <P> |
|---|
| 41 | Both LIVEPLOT and BKGEDIT get the current diffraction information |
|---|
| 42 | by running the TCLDUMP program, if installed, or |
|---|
| 43 | HSTDUMP otherwise. The TCLDUMP program has been optimized for use |
|---|
| 44 | with LIVEPLOT and offers a number of extra |
|---|
| 45 | options that are not available when HSTDUMP is used. Since TCLDUMP has been |
|---|
| 46 | included in GSAS since April of 2000, it is assumed that this is now the case. |
|---|
| 47 | |
|---|
| 48 | <a name="liveplot"></a> |
|---|
| 49 | <H3>LIVEPLOT</H3> |
|---|
| 50 | LIVEPLOT is started by pressing the LIVEPLOT button on the toolbar |
|---|
| 51 | or via the Graphs/liveplot menu item. |
|---|
| 52 | <P> |
|---|
| 53 | Some of the features available in LIVEPLOT are: |
|---|
| 54 | <UL> |
|---|
| 55 | <LI>The plot is updated automatically after each refinement run |
|---|
| 56 | <LI>The plot can be zoomed, by clicking on the corners of the |
|---|
| 57 | area to be magnified. |
|---|
| 58 | <LI> |
|---|
| 59 | The units used for plotting histograms can be selected. Choices are: |
|---|
| 60 | native units (2Theta/TOF/KeV); d-space (A) or Q (A<sup>-1</sup>) |
|---|
| 61 | <LI> |
|---|
| 62 | The background (fixed plus fitted) can be plotted or can be subtracted. |
|---|
| 63 | <LI> |
|---|
| 64 | Reflection tickmarks can be displayed in a variety of formats |
|---|
| 65 | <LI> |
|---|
| 66 | LIVEPLOT can be coupled to the LOGIC or CMPR programs, so that |
|---|
| 67 | peak positions from an ICDD entry or for an arbitrary unit cell and |
|---|
| 68 | spacegroup can be shown superimposed on the "Rietveld plot." |
|---|
| 69 | <LI> |
|---|
| 70 | <IMG SRC="note.gif" alt="Note!"> |
|---|
| 71 | Reflection indices (<I>hkl</I> values) can be shown for tickmarks |
|---|
| 72 | <LI> |
|---|
| 73 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 74 | The cumulative chi<sup>2</sup> function can be plotted. |
|---|
| 75 | <LI> |
|---|
| 76 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 77 | The cursor position can be displayed |
|---|
| 78 | <LI> |
|---|
| 79 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 80 | Plots can be <a href="#export">exported to obtain publication-quality |
|---|
| 81 | graphics.</a> |
|---|
| 82 | </UL> |
|---|
| 83 | |
|---|
| 84 | <a name="bkgedit"></a> |
|---|
| 85 | <H3>BKGEDIT</H3> |
|---|
| 86 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 87 | BKGEDIT is used to fit a background function to a set of points |
|---|
| 88 | selected by the user. |
|---|
| 89 | For most refinements, this is not needed, |
|---|
| 90 | as it is possible to simply select a background |
|---|
| 91 | function (I find that the type 1 function, |
|---|
| 92 | shifted Chebyschev polynomials, works well) |
|---|
| 93 | and then refine, adding terms until a good fit is obtained. |
|---|
| 94 | On occasion, poor initial fits are obtained in this manner. This is |
|---|
| 95 | most common in cases where large numbers of peaks are poorly fit. Since |
|---|
| 96 | significant sections of the data are not well fit, the refinement results in |
|---|
| 97 | an unreasonable background function, because this yields better agreement |
|---|
| 98 | with the observed data. |
|---|
| 99 | In these cases, |
|---|
| 100 | it may be best to fix the background to follow a "reasonable" curve in the |
|---|
| 101 | initial stages and then refine the background in the final stages of |
|---|
| 102 | refinement, when a good model has been obtained. |
|---|
| 103 | <P> |
|---|
| 104 | The BKGEDIT program, as shown below, is used to input a set a background |
|---|
| 105 | points via the mouse. The points are then used to determine a type 1 |
|---|
| 106 | (Chebyschev) background function that fits the input background points. These |
|---|
| 107 | terms can then be saved in the experiment file creating a background that |
|---|
| 108 | is good enough for the initial stages of refinement and that can be |
|---|
| 109 | refined once the model is adequate for the task. |
|---|
| 110 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 111 | BKGEDIT can be used to fit GSAS background functions 1-6 (though |
|---|
| 112 | for most purposes only type 1 is needed.) |
|---|
| 113 | <P> |
|---|
| 114 | <IMG SRC="b1.gif" align=TEXTOP alt="BKGEDIT screen image"> |
|---|
| 115 | <H4>Steps in fitting a background function</H4> |
|---|
| 116 | The BKGEDIT program is started from |
|---|
| 117 | via the Powder/bkgedit menu item or by pressing the |
|---|
| 118 | "Fit Background Graphically" button on the |
|---|
| 119 | <A href="expgui3.html#EditBackground">"Edit Background"</A> |
|---|
| 120 | dialog box (invoked from the "Edit Background" button on the |
|---|
| 121 | <A href="expgui3.html">Histogram pane</A>.) |
|---|
| 122 | toolbar |
|---|
| 123 | or |
|---|
| 124 | <OL> |
|---|
| 125 | <LI><a href="#zoom">Zoom in</a> on the lower intensity section of the |
|---|
| 126 | plot, so that the background is clearly discernible. In some cases, the |
|---|
| 127 | data will need to be handled in sections. |
|---|
| 128 | <LI>Press the "Add" button to add background points. |
|---|
| 129 | Note the cursor changes from cross-hairs to an arrow, |
|---|
| 130 | when the "Add" button is pressed. |
|---|
| 131 | <LI>Move the mouse to the first location |
|---|
| 132 | where a background point will be added and click with the left |
|---|
| 133 | mouse button. A magenta triangle will appear at the location. |
|---|
| 134 | Points can be added in any order. It is best to make sure that the fixed points |
|---|
| 135 | are placed over the entire range of the data, e.g. near the maximum and minimum |
|---|
| 136 | data points in TOF, 2theta, etc. |
|---|
| 137 | <DL><DL> |
|---|
| 138 | Note that it is advisable to place many background points in areas where |
|---|
| 139 | the background is changing rapidly (where the background is most bumpy). |
|---|
| 140 | </DL></DL> |
|---|
| 141 | As background points are entered, they are saved in a file named |
|---|
| 142 | <I>EXPNAM</I><font face="courier">.bkg</font><I>N</I>, where |
|---|
| 143 | <I>EXPNAM</I> is the experiment name and <I>N</I> is the histogram number. |
|---|
| 144 | If BKGEDIT is restarted at some later time, these points are reread. |
|---|
| 145 | <LI>If any points are placed in incorrect positions, they can be deleted by |
|---|
| 146 | pressing the "Delete" button. The mouse cursor changes to a circle. When |
|---|
| 147 | the mouse left clicked, the fixed background point closest to the mouse |
|---|
| 148 | position (which may be outside the zoom range) is deleted. |
|---|
| 149 | <LI>Background points can also be edited by entering numbers into the |
|---|
| 150 | "Background points" area. |
|---|
| 151 | <LI>After enough background points have been entered, the |
|---|
| 152 | "Fit" button turns from gray to black. When pressed, the selected |
|---|
| 153 | background function is fitted |
|---|
| 154 | and the resulting curve is shown as a blue dashed line. |
|---|
| 155 | <DL><DL> |
|---|
| 156 | <LI>It is suggested that you start with relatively few |
|---|
| 157 | terms and add terms and background points as needed. |
|---|
| 158 | Note that the maximum number of increases as |
|---|
| 159 | more background points are entered. |
|---|
| 160 | <LI>Editing the terms manually is possible. The curve is reevaluated as |
|---|
| 161 | changes are made. |
|---|
| 162 | <LI>For the type 3 background function (radial distribution function), |
|---|
| 163 | the R terms are listed separately from the other |
|---|
| 164 | background terms. These R (radii) values must be entered manually and |
|---|
| 165 | are not refined. |
|---|
| 166 | </DL></DL> |
|---|
| 167 | <LI>Once a good background function is determined, it can be saved in the |
|---|
| 168 | experiment file by pressing the "Save in EXP file & Exit" button. This will |
|---|
| 169 | set the background type, and save the terms. |
|---|
| 170 | It will also turn off |
|---|
| 171 | the background refinement flag for the appropriate histogram so that the |
|---|
| 172 | terms are not refined inadvertently. |
|---|
| 173 | </OL> |
|---|
| 174 | |
|---|
| 175 | <P> |
|---|
| 176 | Note that POWPREF must be run at least once before BKGEDIT can be used, |
|---|
| 177 | however, use of |
|---|
| 178 | GENLES before BKGEDIT is optional. If the data range is changed, for example |
|---|
| 179 | by excluding a section of the data at the lower end, or changing tmax (dmin), |
|---|
| 180 | the Chebyschev polynomial terms must change to generate the same |
|---|
| 181 | background values, so both POWPREF and BKGEDIT should be rerun to |
|---|
| 182 | regenerate the Chebyschev terms. |
|---|
| 183 | |
|---|
| 184 | <H4>Why not use fixed background points?</H4> |
|---|
| 185 | I personally feel that |
|---|
| 186 | a refined background function is preferrable to use of a fixed model, |
|---|
| 187 | if at all possible. |
|---|
| 188 | One reason for this is that Rietveld refinements usually achieve better fits |
|---|
| 189 | when the background is optimized. A second reason refining the background |
|---|
| 190 | provides a |
|---|
| 191 | feel for the interaction between background values and displacement |
|---|
| 192 | (thermal) parameters. |
|---|
| 193 | Usually, background and displacement parameters are fairly independent, but |
|---|
| 194 | for some materials, where the high Q (high 2theta) portion of the pattern |
|---|
| 195 | has many completely overlapped peaks, it is impossible to uniquely |
|---|
| 196 | determine where the |
|---|
| 197 | background should be placed, either by refinement or by manual placement. |
|---|
| 198 | Under these circumstances, the background should be refined with the |
|---|
| 199 | displacement parameters fixed at an appropriate value for the material. The |
|---|
| 200 | background should then be fixed for all future refinements |
|---|
| 201 | and the displacement parameters can then be refined. <I>Of course this |
|---|
| 202 | means you have predjudiced the refinement to result in the expected |
|---|
| 203 | average displacement parameter and this </I><B>must</B><I> be noted |
|---|
| 204 | any publication. However, if this is necessary, the data simply do not |
|---|
| 205 | contain sufficient information to independently determine |
|---|
| 206 | background and displacement parameters. Use of fixed background points |
|---|
| 207 | would not demonstrate this and would lead the researcher to a false |
|---|
| 208 | sense of security (or fear, if the values are unreasonable) |
|---|
| 209 | that the displacement parameters actually mean something.</I> |
|---|
| 210 | <P> |
|---|
| 211 | If you still want to use fixed background points, despite this tirade, |
|---|
| 212 | be sure to set the estimated |
|---|
| 213 | error on those points to be 0.0. Use of non-zero estimated errors, can |
|---|
| 214 | result in artificially lowered R-factors and chi-squared values. |
|---|
| 215 | In one test, I was able to lower the R<sub>wp</sub> and |
|---|
| 216 | reduced chi<sup>2</sup> values, |
|---|
| 217 | from the correct values of 0.042 and 3.0, respectively, to misleading |
|---|
| 218 | values of 0.036 and 0.8, |
|---|
| 219 | respectively. [As expected, the R(F<sup>2</sup>) stayed constant at 0.045 |
|---|
| 220 | with the different fixed background errors; |
|---|
| 221 | FYI, refining the background caused R(F<sup>2</sup>) to drop to 0.036, |
|---|
| 222 | so I would consider the refined background to be better.] |
|---|
| 223 | <P> |
|---|
| 224 | If the background is so truly irregular that only use of fixed background |
|---|
| 225 | points will do, |
|---|
| 226 | BKGEDIT can be used to generate these fixed background points. |
|---|
| 227 | The file used by BKGEDIT to save these points, |
|---|
| 228 | <I>EXPNAM</I><font face="courier">.bkg</font><I>N</I>, |
|---|
| 229 | will define the background points if read directly into EXPEDT |
|---|
| 230 | by typing "@R" at the initial prompt in EXPEDT: |
|---|
| 231 | <FONT FACE="COURIER"><PRE> |
|---|
| 232 | Is this the file you wish to use? (?,D,K,Q,R,Y) ><u>@r</u> |
|---|
| 233 | </PRE></FONT> |
|---|
| 234 | prompt and then supplying the name of the file, in response to the next prompt: |
|---|
| 235 | <FONT FACE="COURIER"><PRE> |
|---|
| 236 | Enter the name of your macro file: <u>GARNET.bkg1</u> |
|---|
| 237 | </PRE></FONT> |
|---|
| 238 | Doing this will cause the background points you entered into BKGEDIT to |
|---|
| 239 | be used in GSAS |
|---|
| 240 | fixed background points. If you do this you do not want to save the |
|---|
| 241 | fitted background function as well, as this would effectively subtract |
|---|
| 242 | double the desired background. |
|---|
| 243 | Note that GSAS allows simultaneous use of |
|---|
| 244 | both fixed and a refined background; |
|---|
| 245 | this is seldom done. |
|---|
| 246 | |
|---|
| 247 | <hr><h2>LIVEPLOT/BKGEDIT Features</h2> |
|---|
| 248 | <B>Plot contents:</B> |
|---|
| 249 | Reflection markers can be placed using the File/Tickmarks menu item |
|---|
| 250 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">or by pressing the |
|---|
| 251 | "1" key for phase 1, "2" for phase 2,... Note that many attributes |
|---|
| 252 | for reflection markers can be edited using |
|---|
| 253 | Options/<a href="#configTick">Configure Tickmarks</a> |
|---|
| 254 | |
|---|
| 255 | <P> |
|---|
| 256 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 257 | If more than one histogram is available to plot, it is possible to cycle |
|---|
| 258 | between the histograms by pressing the "n" or "N" (for next) key. |
|---|
| 259 | <P> |
|---|
| 260 | <a name="zoom"></a> |
|---|
| 261 | <B>Plot zooming:</B> |
|---|
| 262 | When the left (usual) mouse button is pressed, this defines one corner |
|---|
| 263 | of a region to be magnified, as is shown to the right. |
|---|
| 264 | If the mouse is then moved, the diagonal |
|---|
| 265 | corner of this magnification region is defined. When the left mouse button |
|---|
| 266 | is pressed a second time, the selected section of the plot is magnified to |
|---|
| 267 | fill the entire plot. |
|---|
| 268 | <P> |
|---|
| 269 | <img SRC="mzoom.gif" align=RIGHT alt="LIVEPLOT manual zoom"> |
|---|
| 270 | Zoom settings are saved. |
|---|
| 271 | If the right mouse button is pressed, the previous zoom setting is used, |
|---|
| 272 | so that the left mouse button is used to "zoom in" and the right mouse |
|---|
| 273 | button is used to "zoom out." |
|---|
| 274 | <P> |
|---|
| 275 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 276 | Zoom settings can also be entered manually by pressing the "Z" key. This |
|---|
| 277 | opens a dialog, as is shown to the right, where the x- or y-axis range |
|---|
| 278 | can be specified. Any value that is not specified is set to the maximum |
|---|
| 279 | or minimum for the entire dataset. It is possible to zoom further in using |
|---|
| 280 | the mouse, but to zoom out beyond the manual zoom limits, the "reset" button |
|---|
| 281 | on the manual zoom menu must be used. |
|---|
| 282 | <P> |
|---|
| 283 | <a name="LiveCursor"></a> |
|---|
| 284 | <img SRC="cursor.gif" align=RIGHT alt="LIVEPLOT live cursor"> |
|---|
| 285 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 286 | <B>Cursor Display:</B> |
|---|
| 287 | Pressing the "L" (or "l") key, or using the Option/Show Cursor Position |
|---|
| 288 | menu button causes the position of the cursor (mouse position) |
|---|
| 289 | in plot to be shown. The coordinates are listing in a small area below |
|---|
| 290 | the plot. The position display is updated as the mouse is moved. The |
|---|
| 291 | same key, menu button, or the button labeled "Close cursor display" can be |
|---|
| 292 | used to remove the display. |
|---|
| 293 | <P> |
|---|
| 294 | <br clear=all> |
|---|
| 295 | <h2>Features in LIVEPLOT only</h2> |
|---|
| 296 | <img SRC="lz.gif" BORDER=3 align=RIGHT alt="LIVEPLOT Screen snapshot"> |
|---|
| 297 | <a name="Cchi2"></a> |
|---|
| 298 | <B>The cumulative chi<sup>2</sup></B> |
|---|
| 299 | function was first suggested by |
|---|
| 300 | Bill David as a way to see which reflections have the greatest influence on |
|---|
| 301 | chi<sup>2</sup> [W.I.F. David, <I>Accuracy in Powder Diffraction-III</I>, 2001]. |
|---|
| 302 | It is defined for point j as |
|---|
| 303 | <IMG SRC="cchi2.gif" alt="equation for cumulative chi2 function" ALIGN=TOP> |
|---|
| 304 | where y<sub>obs,i</sub> and y<sub>calc,i</sub> are the observed and computed |
|---|
| 305 | data points and sigma<sub>i</sub> is the expected error. Thus, the statistically |
|---|
| 306 | expected value for |
|---|
| 307 | [(y<sub>obs,i</sub>-y<sub>calc,i</sub>)/sigma<sub>i</sub>]<sup>2</sup> is 1 |
|---|
| 308 | and this function should rise in a smooth line if all points are fitted as |
|---|
| 309 | statistically expected. |
|---|
| 310 | <P> |
|---|
| 311 | In the plot to the right, the cumulative chi<sup>2</sup> function is shown in |
|---|
| 312 | purple. Note that first peak is not well fit, but the low angle "shoulder" is |
|---|
| 313 | as important as the peak misfitting, with respect to the chi<sup>2</sup>. |
|---|
| 314 | <br clear=all> |
|---|
| 315 | <P> |
|---|
| 316 | <img SRC="lind.gif" BORDER=3 align=RIGHT alt="LIVEPLOT Screen snapshot"> |
|---|
| 317 | <B>Reflection indices</B> |
|---|
| 318 | are be displayed by pressing "H" or "h" while the |
|---|
| 319 | mouse is near a reflection (holding the shift key while |
|---|
| 320 | pressing the left mouse button also works, but sometimes interferes with the |
|---|
| 321 | zoom feature). |
|---|
| 322 | Pressing "A" or "a" shows all reflections in the displayed region. |
|---|
| 323 | The indices are shown |
|---|
| 324 | on the screen for phases with tickmarks (as shown to the right). |
|---|
| 325 | Indices are listed in the "Separate window for <I>hkl</I> labels" |
|---|
| 326 | (as seen below) for all phases, regardless of the tickmark settings. |
|---|
| 327 | Displayed indices will remain on the screen for a preset time and |
|---|
| 328 | then will be deleted; alternately, pressing "D" or "d" deletes the hkl labels. |
|---|
| 329 | Several aspects of reflection labeling can be customized, |
|---|
| 330 | see the <a href="#hklOpts">HKL labeling options</a> for further information. |
|---|
| 331 | |
|---|
| 332 | <img SRC="lind1.gif" align=LEFT alt="LIVEPLOT Screen snapshot"> |
|---|
| 333 | |
|---|
| 334 | <br clear=all> |
|---|
| 335 | <P> |
|---|
| 336 | <a name="export"></a> |
|---|
| 337 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36> |
|---|
| 338 | <B>Export plot options</B> |
|---|
| 339 | <UL><LI> |
|---|
| 340 | The plot can be exported to |
|---|
| 341 | <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://plasma-gate.weizmann.ac.il/Grace/">Grace</A>, WYSIWYG 2D plotting tool for X-Windows |
|---|
| 342 | that produces publication-quality graphics. Many UNIX users know |
|---|
| 343 | this program under a previous name, xmgr. |
|---|
| 344 | The export is implemented |
|---|
| 345 | by producing an ASCII file with instructions that |
|---|
| 346 | creates a plot with similar formatting to what appears on the |
|---|
| 347 | screen in LIVEPLOT/BKGEDIT. However, the output quality from |
|---|
| 348 | Grace is much higher quality. Further, Grace |
|---|
| 349 | can be used to enhanced and annotate the plot further. |
|---|
| 350 | <LI> |
|---|
| 351 | For use in many other graphics programs, LIVEPLOT will produce a |
|---|
| 352 | "comma separated variable" data file with the data displayed on the screen. |
|---|
| 353 | The user will need to read this in, |
|---|
| 354 | set line styles and scaling, etc., but this does provide an option for |
|---|
| 355 | generating high-quality graphics for presentations and publications. |
|---|
| 356 | <LI>LIVEPLOT will produce PostScript versions of the plot on the screen, |
|---|
| 357 | but the quality is rather low (this is a limitation of the BLT graphics |
|---|
| 358 | package). |
|---|
| 359 | </UL> |
|---|
| 360 | |
|---|
| 361 | <hr><h2>LIVEPLOT/BKGEDIT Menu Contents</h2> |
|---|
| 362 | A few of these options are omitted from BKGEDIT. |
|---|
| 363 | <img SRC="lm1.gif" align=RIGHT alt="LIVEPLOT Menu"> |
|---|
| 364 | <H3>File Menu</H3> |
|---|
| 365 | <DL><DL> |
|---|
| 366 | <DT>Tickmarks |
|---|
| 367 | <DD>Checkbuttons are provided for each phase to determine if tick marks |
|---|
| 368 | will be shown. |
|---|
| 369 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">Tickmarks can also be |
|---|
| 370 | toggled by pressing the |
|---|
| 371 | "1" key for phase 1, "2" for phase 2,... |
|---|
| 372 | Also see the Options/<a href="#configTick">Configure Tickmarks</a> |
|---|
| 373 | menu item for information |
|---|
| 374 | on tickmarks. |
|---|
| 375 | <DT>Histogram |
|---|
| 376 | <DD>This allows a histogram to be selected to be loaded |
|---|
| 377 | <DL><DL> |
|---|
| 378 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 379 | It is also possible to advance |
|---|
| 380 | between the histograms by pressing the "n" or "N" (for next) key. |
|---|
| 381 | </DL></DL> |
|---|
| 382 | <DT>Update Plot |
|---|
| 383 | <DD>The causes LIVEPLOT to read read the current histogram again from |
|---|
| 384 | the datafile |
|---|
| 385 | <DT>Export Plot |
|---|
| 386 | <DD>This offers options for exporting the plot in multiple formats. |
|---|
| 387 | I am hoping to add more export formats eventually. |
|---|
| 388 | <DL><DL> |
|---|
| 389 | <DT>to PostScript |
|---|
| 390 | <DD>Creates a <I>low quality</I> PostScript file containing the LIVEPLOT |
|---|
| 391 | output. See the Options/"Set PS output" button for where the file is created. |
|---|
| 392 | Most unix systems are capable or printing PostScript files. |
|---|
| 393 | On Windows, a program such ghostview may be needed to translate the |
|---|
| 394 | PostScript to a format that can be viewed or printed. |
|---|
| 395 | <A name="grace"> |
|---|
| 396 | <DT>to Grace |
|---|
| 397 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36> |
|---|
| 398 | <DD>Plots can be exported to |
|---|
| 399 | <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://plasma-gate.weizmann.ac.il/Grace/">Grace</A>, WYSIWYG 2D plotting tool for X-Windows |
|---|
| 400 | that produces publication-quality graphics. |
|---|
| 401 | After the plot is exported, it can be further |
|---|
| 402 | enhanced and annotated in grace. |
|---|
| 403 | </DL></DL> |
|---|
| 404 | <DT>Quit |
|---|
| 405 | <DD>Exits BKGEDIT/LIVEPLOT. |
|---|
| 406 | </DL></DL> |
|---|
| 407 | <br clear=all> |
|---|
| 408 | <img SRC="lm2.gif" align=RIGHT alt="LIVEPLOT Menu"> |
|---|
| 409 | <H3>Options Menu</H3> |
|---|
| 410 | <DL><DL> |
|---|
| 411 | <a name="configTick"></a> |
|---|
| 412 | <DT>Configure Tickmarks<DD> |
|---|
| 413 | This submenu provides options that controls how tickmarks are displayed. |
|---|
| 414 | <DL><DL> |
|---|
| 415 | <DT>Auto locate<DD> |
|---|
| 416 | When this option is selected, tickmarks are placed in different positions |
|---|
| 417 | for each phase, automatically, similar to how tickmarks are shown in POWPLOT. |
|---|
| 418 | <DT>Manual Placement<DD> |
|---|
| 419 | Tickmarks are drawn at specific heights that can be set for each phase |
|---|
| 420 | (see below). The default |
|---|
| 421 | is for lines to be draw from "-Inf" to "Inf", which creates lines from the |
|---|
| 422 | bottom to the top of the plot. |
|---|
| 423 | <DT>Label by name |
|---|
| 424 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 425 | <DD> |
|---|
| 426 | By default, a label "Phase1",... is displayed in the legend when tickmarks |
|---|
| 427 | for that phase are displayed. When this button is pressed, the first |
|---|
| 428 | 20 characters of each phase name (phase title) are used instead. This |
|---|
| 429 | label can be edited, as described in the next paragraph. |
|---|
| 430 | <DT>Phase <I>n</I> opts<DD> |
|---|
| 431 | The options for each phase allow the line to be changed between |
|---|
| 432 | solid and dashed, color of the line can be specified and |
|---|
| 433 | the vertical placement of the tickmarks can be specified. The |
|---|
| 434 | "Show Reflections" flag, |
|---|
| 435 | set in the File/Tickmarks menu, |
|---|
| 436 | as well as the label used for the phase can also be changed here. |
|---|
| 437 | |
|---|
| 438 | </DL></DL> |
|---|
| 439 | <DT>Obs Symbol (Symbol Type) |
|---|
| 440 | <DD>This brings up a menu where the symbol type and size for the |
|---|
| 441 | observed data points (and for BKGEDIT, the fixed background points) |
|---|
| 442 | can be selected. |
|---|
| 443 | <DT>Symbol Color |
|---|
| 444 | <DD>The colors for all the displayed lines and symbols can be changed here. |
|---|
| 445 | <DT>X units |
|---|
| 446 | <DD>The x units can be selected here. The choices are |
|---|
| 447 | "as collected" (2Theta/TOF/KeV), d-space (A) or Q (A<sup>-1</sup>) |
|---|
| 448 | <DT>Y units |
|---|
| 449 | <DD>The intensity values can be normalized by the incident spectrum |
|---|
| 450 | (for energy dispersive methods). |
|---|
| 451 | </DL></DL> |
|---|
| 452 | <br clear=all> |
|---|
| 453 | <img SRC="lm3.gif" align=RIGHT alt="LIVEPLOT menu"> |
|---|
| 454 | <a name="hklOpts"></a> |
|---|
| 455 | <DL><DL> |
|---|
| 456 | <DT>HKL labeling |
|---|
| 457 | <DD>This brings up a menu that selects |
|---|
| 458 | <UL><LI>Erase time: |
|---|
| 459 | how long in seconds that <I>hkl</I> values are shown |
|---|
| 460 | before they are erased (0 means that they are not erased), |
|---|
| 461 | <LI>Label size: the size of the |
|---|
| 462 | labels in pixels, |
|---|
| 463 | <LI>Search Region: only reflections within this number of pixels of the mouse, |
|---|
| 464 | when the "h" key is pressed (if any) are labeled, |
|---|
| 465 | <LI>Separate window: when this |
|---|
| 466 | option is selected, reflection labels are shown in a text window |
|---|
| 467 | </UL> |
|---|
| 468 | <DT>Subtract background |
|---|
| 469 | <DD>The background is always shown, even when subtracted |
|---|
| 470 | <DT>Include legend |
|---|
| 471 | <DD>The legend is the optional box in the upper left that defines the |
|---|
| 472 | plot entries |
|---|
| 473 | <DT>Show [Hide] Cursor Position |
|---|
| 474 | <DD>This turns <a href="#LiveCursor">Cursor position display</a> on and off. |
|---|
| 475 | <DT>Set PS output |
|---|
| 476 | <DD>For UNIX this allows the file to be sent directly to a printer |
|---|
| 477 | or can be saved in a file. For Windows, a file must be written. |
|---|
| 478 | <DT>Set screen font |
|---|
| 479 | <DD>This option is used to control the font used for menus, graphics and |
|---|
| 480 | other aspects of windows. |
|---|
| 481 | <DT>Raise on update |
|---|
| 482 | <DD>This causes the plot to be placed on top of other windows, if partially |
|---|
| 483 | obscured, when the plot is updated. At this time, this option does not |
|---|
| 484 | work in Windows-NT and -2000. |
|---|
| 485 | <DT>Cumulative Chi2 |
|---|
| 486 | <DD>The causes the Cumulative chi<sup>2</sup> function to be displayed |
|---|
| 487 | (as <a href="#Cchi2">presented above</a>). |
|---|
| 488 | <DT>Save Options |
|---|
| 489 | <DD>Causes many of the options set in this menu to be saved in the <FONT FACE="COURIER">.gsas_config</FONT> file. |
|---|
| 490 | </DL></DL> |
|---|
| 491 | <br clear=all> |
|---|
| 492 | |
|---|
| 493 | <P> |
|---|
| 494 | <hr><H2>Customization of LIVEPLOT & BKGEDIT</H2><A NAME="customize"></A> |
|---|
| 495 | The <FONT FACE="COURIER">localconfig</FONT> and <FONT FACE="COURIER">.gsas_config</FONT> files are read, if present. |
|---|
| 496 | The following variables control how LIVEPLOT, and in most cases BKGEDIT, |
|---|
| 497 | function and can be |
|---|
| 498 | customized by changing their values in the |
|---|
| 499 | <FONT FACE="COURIER">localconfig</FONT> and <FONT FACE="COURIER">.gsas_config</FONT> files. |
|---|
| 500 | Note that some of these options are relevant only if the tcldump program is |
|---|
| 501 | present. |
|---|
| 502 | <DL><DL> |
|---|
| 503 | <DT><FONT FACE="COURIER">peakinfo(flag<i>n</i>)</FONT><DD> |
|---|
| 504 | These variables define if peak positions will be shown |
|---|
| 505 | for reflections in phase "<i>n</i>". Reflections will be shown if |
|---|
| 506 | the value is non-zero. |
|---|
| 507 | |
|---|
| 508 | <DT><FONT FACE="COURIER">peakinfo(color<i>n</i>)</FONT><DD> |
|---|
| 509 | These variables define the default colors for |
|---|
| 510 | reflections in phase "<i>n</i>" |
|---|
| 511 | |
|---|
| 512 | <DT><FONT FACE="COURIER">peakinfo(dashes<i>n</i>)</FONT><DD> |
|---|
| 513 | These variables define if peaks will be dashed for |
|---|
| 514 | reflections in phase "<i>n</i>" (UNIX only). Lines will be dashed if |
|---|
| 515 | the value is non-zero. |
|---|
| 516 | |
|---|
| 517 | <DT><FONT FACE="COURIER">peakinfo(min<i>n</i>) and peakinfo(max<i>n</i>)</FONT><DD> |
|---|
| 518 | These variables dictate the placement vertical position for reflection |
|---|
| 519 | markers, when manually placed (see expgui(autotick), below). To draw |
|---|
| 520 | to the edge of the screen, use -Inf and Inf. |
|---|
| 521 | </DL></DL> |
|---|
| 522 | |
|---|
| 523 | The following variables are written to <font face="courier">.gsas_config</font> when |
|---|
| 524 | "Save Options" is used. These variables are all set from the GUI and therefore |
|---|
| 525 | do not need to be edited manually. |
|---|
| 526 | |
|---|
| 527 | <DL><DL> |
|---|
| 528 | <DT><FONT FACE="COURIER">graph(printout)</FONT><DD> |
|---|
| 529 | This is set to 1 if PostScript files |
|---|
| 530 | will be printed and 0 if they will be written to disk (for Windows all |
|---|
| 531 | files should be written to disk). |
|---|
| 532 | |
|---|
| 533 | <DT><FONT FACE="COURIER">graph(outname)</FONT><DD> |
|---|
| 534 | This is the default for the file name used |
|---|
| 535 | when PostScript files will be written to disk. |
|---|
| 536 | |
|---|
| 537 | <DT><FONT FACE="COURIER">graph(outcmd)</FONT><DD> |
|---|
| 538 | This is the default for the command used |
|---|
| 539 | to print PostScript files (Unix only). |
|---|
| 540 | |
|---|
| 541 | <DT><FONT FACE="COURIER">graph(legend)</FONT><DD> |
|---|
| 542 | Sets the default value for display of the legend in LIVEPLOT and WIDPLT. |
|---|
| 543 | |
|---|
| 544 | <DT><FONT FACE="COURIER">graph(autoraise)</FONT><DD> |
|---|
| 545 | This option shows up in the options menu item as "Raise on update." |
|---|
| 546 | When set to non-zero, the LIVEPLOT window is raised |
|---|
| 547 | (placed on top of any other overlapping) windows |
|---|
| 548 | each time it is updated. |
|---|
| 549 | This option does not seem to work in Windows-NT, but this may depend on |
|---|
| 550 | the version of Tcl/Tk. |
|---|
| 551 | |
|---|
| 552 | <DT><FONT FACE="COURIER">peakinfo(obssym)</FONT><DD> |
|---|
| 553 | Symbol for observed data points. Valid choices are square, circle, diamond, |
|---|
| 554 | plus, cross, splus and scross. |
|---|
| 555 | |
|---|
| 556 | <DT><FONT FACE="COURIER">peakinfo(obssize)</FONT><DD> |
|---|
| 557 | Size for the symbol for observed data points. A value of 1 corresponds to about 1/8 inch |
|---|
| 558 | (about 3 mm). |
|---|
| 559 | |
|---|
| 560 | <DT><FONT FACE="COURIER">expgui(pixelregion)</FONT><DD> |
|---|
| 561 | When hkl values are loaded (using tcldump) and reflections are labeled, reflections |
|---|
| 562 | can be labeled using a Shift-Left-Mouse click. All labeled reflections within expgui(pixelregion) |
|---|
| 563 | pixels of the mouse position are assumed to be overlapped and are labeled. |
|---|
| 564 | |
|---|
| 565 | <DT><FONT FACE="COURIER">expgui(fadetime)</FONT><DD> |
|---|
| 566 | The time in seconds before reflection labels are removed. A value of zero means that reflections |
|---|
| 567 | must be deleted manually (Shift-Right-Mouse). |
|---|
| 568 | |
|---|
| 569 | <DT><FONT FACE="COURIER">expgui(lblfontsize)</FONT><DD> |
|---|
| 570 | A size for reflections labels in pixels. |
|---|
| 571 | |
|---|
| 572 | <DT><FONT FACE="COURIER">expgui(hklbox)</FONT><DD> |
|---|
| 573 | If this variable is non-zero, reflection indices are shown in a box. |
|---|
| 574 | |
|---|
| 575 | <DT><FONT FACE="COURIER">expgui(autotick)</FONT><DD> |
|---|
| 576 | If this variable is non-zero, reflection markers positions are |
|---|
| 577 | set automatically. |
|---|
| 578 | </DL></DL> |
|---|
| 579 | <P> |
|---|
| 580 | <hr><H2>Installation details/External Programs</H2> |
|---|
| 581 | <B>Using TCLDUMP with LIVEPLOT.</B> |
|---|
| 582 | LIVEPLOT works with the standard GSAS program HSTDMP, but it works faster and is more |
|---|
| 583 | powerful when used with the TCLDUMP program. |
|---|
| 584 | Note that as of the April 2000 releases, GSAS is now distributed with TCLDUMP |
|---|
| 585 | included. For older versions of GSAS, note the |
|---|
| 586 | instructions for downloading this file can in the installation notes for |
|---|
| 587 | <A HREF="expgui_Win_readme.html"> |
|---|
| 588 | Windows</A> and |
|---|
| 589 | <A HREF="expgui_Unix_readme.html"> |
|---|
| 590 | UNIX</A>. |
|---|
| 591 | <P> |
|---|
| 592 | |
|---|
| 593 | <B>Combining CMPR and LIVEPLOT.</B> |
|---|
| 594 | If you have <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr">CMPR</A> |
|---|
| 595 | installed on your computer, you can use superimpose on the GSAS results |
|---|
| 596 | the peaks for an arbitrary unit cell. If desired, space group extinctions |
|---|
| 597 | can even be shown. |
|---|
| 598 | This is pretty neat! To enable this feature, you must have a version |
|---|
| 599 | of CMPR downloaded after 4 May 1998 |
|---|
| 600 | <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr"> |
|---|
| 601 | (see link for CMPR installation instructions.)</A> |
|---|
| 602 | <UL><LI> |
|---|
| 603 | For UNIX, create a link from in the EXPGUI |
|---|
| 604 | directory to file cellgen.tcl in the CMPR directory. For example: |
|---|
| 605 | <FONT FACE="COURIER"><PRE> |
|---|
| 606 | ln -s /usr/local/cmpr/cellgen.tcl /usr/local/gsas/expgui/cellgen.tcl |
|---|
| 607 | </PRE></FONT> |
|---|
| 608 | <LI>For Windows, copy all the .tcl and .exe files from the CMPR directory |
|---|
| 609 | into the EXPGUI directory. |
|---|
| 610 | </UL> |
|---|
| 611 | <P> |
|---|
| 612 | |
|---|
| 613 | <B>Combining LOGIC and LIVEPLOT.</B> |
|---|
| 614 | If you have <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/logic.html">LOGIC</A> |
|---|
| 615 | installed on your computer, you can superimpose peaks |
|---|
| 616 | for a entry from the ICDD/JCPDS database on a pattern in LIVEPLOT. |
|---|
| 617 | This is also pretty neat! |
|---|
| 618 | To enable this feature, you must have |
|---|
| 619 | a version of LOGIC downloaded after 4 May 1998 |
|---|
| 620 | <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/logic.html"> |
|---|
| 621 | (see the LOGIC installation instructions.)</A> |
|---|
| 622 | <UL><LI> |
|---|
| 623 | For UNIX, create a link from in the GSAS GUI |
|---|
| 624 | directory to file icddcmd.tcl in the LOGIC directory. For example: |
|---|
| 625 | <FONT FACE="COURIER"><PRE> |
|---|
| 626 | ln -s /usr/local/powdersuite/icddcmd.tcl /usr/local/gsas/expgui/icddcmd.tcl |
|---|
| 627 | </PRE></FONT> |
|---|
| 628 | <LI>For Windows, copy all the LOGIC files into the EXPGUI directory. |
|---|
| 629 | </UL> |
|---|
| 630 | <hr> |
|---|
| 631 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
|---|
| 632 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
|---|
| 633 | </TH><TH><A Href="excledt.html">Next page<BR>(EXCLEDT)</A> |
|---|
| 634 | </TH><TH><A Href="expguic.html">Previous page</A> |
|---|
| 635 | </TH></TR></TABLE> |
|---|
| 636 | |
|---|
| 637 | <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> |
|---|
| 638 | <font size=-1><? lastmod(); ?> </font> |
|---|
| 639 | <br> |
|---|
| 640 | $Revision: 656 $ $Date: 2009-12-04 23:09:49 +0000 (Fri, 04 Dec 2009) $ |
|---|
| 641 | </blockquote> |
|---|
| 642 | </body> |
|---|
| 643 | </html> |
|---|
