| 1 | <html> |
|---|
| 2 | <head> |
|---|
| 3 | <META NAME="Author" CONTENT="Brian H. Toby"> |
|---|
| 4 | <title>EXPGUI -- EXCLEDT</title> |
|---|
| 5 | </head> |
|---|
| 6 | <BODY BGCOLOR="#FFFFFF"> |
|---|
| 7 | |
|---|
| 8 | <A HREF=http://www.ncnr.nist.gov> |
|---|
| 9 | <IMG SRC="http://www.ncnr.nist.gov/images/ncnrtrans.gif" |
|---|
| 10 | alt="Link to NIST Center for Neutron Research home page" |
|---|
| 11 | ALIGN=RIGHT></A> |
|---|
| 12 | <A HREF=http://www.nist.gov> |
|---|
| 13 | <IMG SRC="http://www.ncnr.nist.gov/images/webidblue_2lineright.gif" |
|---|
| 14 | alt="Link to National Institute of Standards & Technology home page" |
|---|
| 15 | ALIGN=LEFT></A> |
|---|
| 16 | <CENTER> |
|---|
| 17 | <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html"> |
|---|
| 18 | <IMG SRC="tcltklogo100.gif" |
|---|
| 19 | alt="Link to Tcl/Tk information"> |
|---|
| 20 | </CENTER></A> |
|---|
| 21 | <br clear=all><hr> |
|---|
| 22 | |
|---|
| 23 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
|---|
| 24 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
|---|
| 25 | </TH></TR></TABLE><BR CLEAR=ALL> |
|---|
| 26 | |
|---|
| 27 | <center><h1> |
|---|
| 28 | EXCLEDT |
|---|
| 29 | </h1></center> |
|---|
| 30 | This page documents the EXCLEDT utility program |
|---|
| 31 | in the EXPGUI package. The purpose of this tool is to select graphically |
|---|
| 32 | regions of data that will not be included in the refinement. |
|---|
| 33 | The EXCLEDT program is called from the Powder/excledt |
|---|
| 34 | menu item or from the "Data Limits/Exclude" button on the Histogram pane. |
|---|
| 35 | <P> |
|---|
| 36 | A common use for this is |
|---|
| 37 | to adjust the lower 2theta/Q limit (maximum d-space/TOF) so that |
|---|
| 38 | data where no reflections occur can be ignored. It |
|---|
| 39 | is also common to start refinements with |
|---|
| 40 | a somewhat limited range of data, raising the upper 2theta/Q limit |
|---|
| 41 | (minimum d-space/TOF) later. (The ideal is to include all data where |
|---|
| 42 | any peaks can be resolved in the final stages of refinement.) |
|---|
| 43 | Note that there is a disadvantage to changing the data range, |
|---|
| 44 | if one is using the Chebyschev polynomial |
|---|
| 45 | (type 1 background function) to fit the background, as this function |
|---|
| 46 | is scaled over the range of data. If the data range is changed, the |
|---|
| 47 | background function will shift and thus must be refit each time the |
|---|
| 48 | data range is changed. |
|---|
| 49 | <P> |
|---|
| 50 | A second purpose of EXCLEDT is to set and change excluded regions within the |
|---|
| 51 | pattern. When a region is set as excluded, the data within that region |
|---|
| 52 | are ignored with respect to the Rietveld refinement. Note that data should |
|---|
| 53 | be removed only where there is a good explanation why the region cannot be |
|---|
| 54 | accurately modeled. This is sometimes needed to deal with |
|---|
| 55 | scattering from a sample |
|---|
| 56 | container (although this can frequently be modeled as an additional |
|---|
| 57 | phase, using Le Bail extraction for that phase when |
|---|
| 58 | the container is badly textured). Excluded regions are also used occasionally |
|---|
| 59 | when an impurity manifests itself with only a few minor peaks, although it is |
|---|
| 60 | usually much better to model the impurity intensity as an additional phase |
|---|
| 61 | (again using Le Bail extraction for that phase when the structure is unknown or |
|---|
| 62 | the material has severe preferred orientation). Excluded regions are sometime |
|---|
| 63 | needed when a section of pattern is affected by stacking faults. Another |
|---|
| 64 | occasional appropriate use is to eliminate spurious intensity that is due |
|---|
| 65 | instrumental malfunctions. |
|---|
| 66 | It is important not to exclude peaks simply because they cannot be indexed. |
|---|
| 67 | Such peaks may indicate a difference in symmetry or unit cell from the |
|---|
| 68 | structural model, or some other error. |
|---|
| 69 | It is also important that excluded regions be documented in the paper |
|---|
| 70 | which describes the study. |
|---|
| 71 | <P> |
|---|
| 72 | <img SRC="exc1.gif" align=RIGHT alt="EXCLEDT Screen snapshot"> |
|---|
| 73 | The EXCLEDT program displays the data in a graph, (see the example to right) |
|---|
| 74 | with the observed data as data points (black X's by default) |
|---|
| 75 | and the computed values as a line (red by default). Any excluded data points |
|---|
| 76 | are shown in a different color (orange, by default). |
|---|
| 77 | Lines (again orange, by default) at the |
|---|
| 78 | bottom of the plot show the allowed data range as well as any excluded regions. |
|---|
| 79 | Note that if POWPREF has been run more recently then GENLES, the calculated |
|---|
| 80 | values are zero. |
|---|
| 81 | The EXCLEDT program can plot data in the native units (2-theta, TOF, energy), |
|---|
| 82 | converted to d-space units, or in the most ideal unit for |
|---|
| 83 | diffraction analysis, Q (2 pi/d). |
|---|
| 84 | <P> |
|---|
| 85 | <br clear=all> |
|---|
| 86 | |
|---|
| 87 | <H3>Mouse use</H3> |
|---|
| 88 | The mouse can be used in three ways depending on the button pressed |
|---|
| 89 | in the lower portion of the window. |
|---|
| 90 | <P> |
|---|
| 91 | <img SRC="exc2.gif" BORDER=3 align=LEFT alt="EXCLEDT Screen snapshot"> |
|---|
| 92 | In <B>Zoom mode</B>, |
|---|
| 93 | the cursor appears as |
|---|
| 94 | cross hairs, and the mouse is used to select a region to be magnified by |
|---|
| 95 | clicking on diagonal points in the region with the left mouse button |
|---|
| 96 | (see below) or "zoomed out" with the right mouse button. |
|---|
| 97 | <br clear=all> |
|---|
| 98 | <P> |
|---|
| 99 | <img SRC="exc3.gif" align=RIGHT alt="EXCLEDT Screen snapshot"> |
|---|
| 100 | In <B>Add Region mode</B>, the mouse is used to map out a region which that |
|---|
| 101 | will be excluded from the refinement. When this button is selected, the |
|---|
| 102 | mouse cursor changes to an arrow. After the left mouse is pressed once, |
|---|
| 103 | a yellow background is shown for the excluded region and when the left mouse |
|---|
| 104 | button is pressed a second time, the region is selected. |
|---|
| 105 | If the right mouse button is pressed instead, it resets the region selection. |
|---|
| 106 | <br clear=all> |
|---|
| 107 | <img SRC="exc3a.gif" align=RIGHT alt="EXCLEDT Screen snapshot"> |
|---|
| 108 | Before the region is added to the excluded list, a message is |
|---|
| 109 | displayed to confirm this. This |
|---|
| 110 | confirmation message can optionally be eliminated (See |
|---|
| 111 | <a href="#prompt">Options/Prompt on add/del</a>.) |
|---|
| 112 | <br clear=all> |
|---|
| 113 | <P> |
|---|
| 114 | In <B>Delete Region mode</B>, the mouse is used to select a region to be |
|---|
| 115 | deleted, causing the data in that region to be included in the refinement. |
|---|
| 116 | The cursor appears as a circle in the graph section of the window. After |
|---|
| 117 | a region has been selected to delete, a message is |
|---|
| 118 | displayed to confirm the region to be deleted from the exclusion list. |
|---|
| 119 | This confirmation message can optionally be eliminated (See |
|---|
| 120 | <a href="#prompt">Options/Prompt on add/del</a>.)<br clear=all> |
|---|
| 121 | <P> |
|---|
| 122 | <img SRC="exc4.gif" BORDER=3 align=right alt="EXCLEDT excluded regions snapshot"> |
|---|
| 123 | <H3>Excluded Region Buttons</H3> |
|---|
| 124 | At the bottom of the window is a set of buttons with the minimum and maximum |
|---|
| 125 | limit on the data as well as a button for every excluded region. Pressing |
|---|
| 126 | a button causes a window to be opened to edit that region by manually entering |
|---|
| 127 | values. |
|---|
| 128 | <br clear=all> |
|---|
| 129 | <H3>File Menu Commands</H3> |
|---|
| 130 | <img SRC="excm1.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot"> |
|---|
| 131 | <DL><DL> |
|---|
| 132 | <DT>Tickmarks<DD>Invokes a submenu where tickmarks can be displayed or removed |
|---|
| 133 | for each phase present in the histogram. |
|---|
| 134 | See the Options/"Configure Tickmarks"menu item for information |
|---|
| 135 | on tickmarks |
|---|
| 136 | <DT>Histogram |
|---|
| 137 | <DD>This allows a different histogram to be displayed. |
|---|
| 138 | <DT>Set Min/Max Range |
|---|
| 139 | <DD>This opens a window where the usable data range may be changed. |
|---|
| 140 | <DT>Update Plot |
|---|
| 141 | <DD>The causes EXCLEDT to read read the current histogram again from |
|---|
| 142 | the datafile. If excluded region or data range |
|---|
| 143 | changes have been made, POWPREF & GENLES may be run first. |
|---|
| 144 | <DT>Make PostScript |
|---|
| 145 | <DD>Creates a low quality PostScript file containing the LIVEPLOT |
|---|
| 146 | output. See the Options/"Set PS output" button for where the file is created. |
|---|
| 147 | <DT>Exit<DD>Saves any changes to the excluded regions or data range. |
|---|
| 148 | If changes have been made, POWPREF & GENLES may be run. |
|---|
| 149 | </DL></DL> |
|---|
| 150 | |
|---|
| 151 | <br clear=all> |
|---|
| 152 | <img SRC="excm2.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot"> |
|---|
| 153 | <H3>Options Menu</H3> |
|---|
| 154 | <DL><DL> |
|---|
| 155 | <DT>Configure Tickmarks |
|---|
| 156 | <DD>Tickmarks can be placed automatically, similar to their |
|---|
| 157 | placement in POWPLOT or can be drawn one height to another. The default |
|---|
| 158 | is for lines to be draw from "-Inf" to "Inf", which creates lines from the |
|---|
| 159 | 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 |
|---|
| 160 | the vertical placement of the tickmarks can be specified. The "show" flag, |
|---|
| 161 | set in the File/Tickmarks menu can also be changed here. |
|---|
| 162 | <DT>Symbol Type |
|---|
| 163 | <DD>This brings up a menu where the symbol type and size for the |
|---|
| 164 | observed and excluded data points can be selected. |
|---|
| 165 | <DT>Symbol Color |
|---|
| 166 | <DD>The colors for all the displayed lines and symbols can be changed here. |
|---|
| 167 | <DT>X units |
|---|
| 168 | <DD>The x units can be selected here. The choices are |
|---|
| 169 | "as collected" (2Theta/TOF/KeV), d-space (A) or Q (A<sup>-1</sup>) |
|---|
| 170 | <DT>Include Legend |
|---|
| 171 | <DD>The legend is the optional box in the upper left that defines the |
|---|
| 172 | plot entries |
|---|
| 173 | <a name="prompt"></a><DT>Prompt on add/del |
|---|
| 174 | <DD>If this option is set, a prompt will be generated when excluded regions |
|---|
| 175 | are added or deleted. |
|---|
| 176 | <DT>Set PS output |
|---|
| 177 | <DD>For UNIX this allows the file to be sent directly to a printer |
|---|
| 178 | or can be saved in a file. For Windows, a file must be written. |
|---|
| 179 | <DT>Set screen font |
|---|
| 180 | <DD>This option is used to control the font used for menus, graphics and |
|---|
| 181 | other aspects of windows. |
|---|
| 182 | <DT>Save options |
|---|
| 183 | <DD>Causes many of the options set in this menu to be saved in the <TT>.gsas_config</TT> file. |
|---|
| 184 | </DL></DL> |
|---|
| 185 | |
|---|
| 186 | |
|---|
| 187 | <br clear=all> |
|---|
| 188 | |
|---|
| 189 | <hr> |
|---|
| 190 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
|---|
| 191 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
|---|
| 192 | </TH></TR></TABLE> |
|---|
| 193 | |
|---|
| 194 | <a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>) |
|---|
| 195 | <br> |
|---|
| 196 | $Revision: 434 $ $Date: 2009-12-04 23:06:06 +0000 (Fri, 04 Dec 2009) $ |
|---|
| 197 | </body> |
|---|
| 198 | </html> |
|---|
