source: trunk/help/Calibration of an area detector in GSAS.htm @ 585

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789<div class=WordSection1>
790
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793
794<p class=MsoTitle><span class=Heading1Char><span style='font-size:14.0pt'>Calibration
795of an area detector in GSAS-II</span></span><b><span style='font-size:14.0pt;
796color:#365F91;mso-themecolor:accent1;mso-themeshade:191'><o:p></o:p></span></b></p>
797
798</div>
799
800<p class=MsoNormal>In this demo, data collected with a Perkin-Elmer area
801detector at APS 11-ID-C with a wavelength 0.10798 A, where the detector was
802intentionally tilted at 45 degrees, are used. Note that menu entries are listed
803in bold face below as <b style='mso-bidi-font-weight:normal'>Help/About GSAS-II</b>,
804which lists first the name of the menu (here <b style='mso-bidi-font-weight:
805normal'>Help</b>) and second the name of the entry in the menu (here <b
806style='mso-bidi-font-weight:normal'>About GSAS-II</b>).<o:p></o:p></p>
807
808<h2><span style='mso-spacerun:yes'> </span>Step 1: Download the data file <o:p></o:p></h2>
809
810<p class=MsoNormal>Download the sample data file from one of these links:</p>
811
812<p class=MsoNormal><a
813href="https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/images/tilt-11ID/La_hex_%2B45deg-00015.tif?format=raw">https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/images/tilt-11ID/La_hex_%2B45deg-00015.tif?format=raw</a><o:p></o:p></p>
814
815<p class=MsoNormal><span style='mso-spacerun:yes'>    </span><span class=GramE>or</span>
816</p>
817
818<p class=MsoNormal><a
819href="https://subversion.xor.aps.anl.gov/pyGSAS/Examples/images/tilt-11ID/La_hex_+45deg-00015.tif">https://subversion.xor.aps.anl.gov/pyGSAS/Examples/images/tilt-11ID/La_hex_+45deg-00015.tif</a><o:p></o:p></p>
820
821<h2>Step 2: Start GSAS-II </h2>
822
823<p class=MsoNormal>This is done in different ways, depending on your OS and how
824GSAS-II is installed. A console window is opened (if necessary) and displays a banner
825and some information about the version of python and the packages used by
826GSAS-II. This console window will display important information as data
827processing by GSAS-II proceeds. You may wish to cut-and-paste parts of this
828window to another place if desired.<o:p></o:p></p>
829
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874 <v:textbox style='mso-fit-shape-to-text:t'>
875  <![if !mso]>
876  <table cellpadding=0 cellspacing=0 width="100%">
877   <tr>
878    <td><![endif]>
879    <div>
880    <p class=MsoNormal>========================================================================<br>
881    <span style='mso-spacerun:yes'>               </span>General Structure
882    Analysis System-II<br>
883    <span style='mso-spacerun:yes'>             </span>by Robert B. Von <span
884    class=SpellE>Dreele</span> and Brian H. Toby<br>
885    <span style='mso-spacerun:yes'>      </span><span
886    style='mso-spacerun:yes'>         </span>Argonne National Laboratory(C),
887    2010<br>
888    <span style='mso-spacerun:yes'> </span>This product includes software
889    developed by the <span class=SpellE>UChicago</span> Argonne, LLC,<br>
890    <span style='mso-spacerun:yes'>            </span>as Operator of Argonne
891    National Laboratory.<br>
892    ========================================================================<br>
893    d:\pyGSAS&gt;python d:\pyGSAS\\GSASII.py<br>
894    Available python module versions for GSASII<span class=GramE>:</span><br>
895    python:<span style='mso-spacerun:yes'>      </span>2.7.1<br>
896    <span class=SpellE>wxpython</span>:<span style='mso-spacerun:yes'>   
897    </span>2.8.10.1<br>
898    <span class=SpellE>matplotlib</span>:<span style='mso-spacerun:yes'> 
899    </span>1.0.1<br>
900    <span class=SpellE>numpy</span>:<span style='mso-spacerun:yes'>      
901    </span>1.5.1<br>
902    <span class=SpellE>scipy</span>:<span style='mso-spacerun:yes'>      
903    </span>0.9.0rc2<br>
904    OpenGL:<span style='mso-spacerun:yes'>      </span>3.0.1<br>
905    Max threads<span style='mso-spacerun:yes'>  </span>2<br>
906    This is GSAS-II version:<span style='mso-spacerun:yes'>      </span>0.1.5<o:p></o:p></p>
907    </div>
908    <![if !mso]></td>
909   </tr>
910  </table>
911  <![endif]></v:textbox>
912 <w:wrap type="none"/>
913 <w:anchorlock/>
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915src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image001.png"
916alt="Text Box: ========================================================================&#13;&#10;               General Structure Analysis System-II&#13;&#10;             by Robert B. Von Dreele and Brian H. Toby&#13;&#10;               Argonne National Laboratory(C), 2010&#13;&#10; This product includes software developed by the UChicago Argonne, LLC,&#13;&#10;            as Operator of Argonne National Laboratory.&#13;&#10;========================================================================&#13;&#10;d:\pyGSAS&gt;python d:\pyGSAS\\GSASII.py&#13;&#10;Available python module versions for GSASII:&#13;&#10;python:      2.7.1&#13;&#10;wxpython:    2.8.10.1&#13;&#10;matplotlib:  1.0.1&#13;&#10;numpy:       1.5.1&#13;&#10;scipy:       0.9.0rc2&#13;&#10;OpenGL:      3.0.1&#13;&#10;Max threads  2&#13;&#10;This is GSAS-II version:      0.1.5&#13;&#10;"
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921 <v:formulas>
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923  <v:f eqn="sum @0 1 0"/>
924  <v:f eqn="sum 0 0 @1"/>
925  <v:f eqn="prod @2 1 2"/>
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927  <v:f eqn="prod @3 21600 pixelHeight"/>
928  <v:f eqn="sum @0 0 1"/>
929  <v:f eqn="prod @6 1 2"/>
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931  <v:f eqn="sum @8 21600 0"/>
932  <v:f eqn="prod @7 21600 pixelHeight"/>
933  <v:f eqn="sum @10 21600 0"/>
934 </v:formulas>
935 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
936 <o:lock v:ext="edit" aspectratio="t"/>
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939 <v:imagedata croptop="-65520f" cropbottom="65520f"/>
940</v:shape><span style='mso-element:field-end'></span><![endif]--></p>
941
942<p class=MsoNormal>The GSAS-II program has now been started and an empty
943project file is created. The project file contains all data and results related
944to the project you are working on. (Exception: image files are not stored in
945the project; to save space only the file name is saved.) <o:p></o:p></p>
946
947<p class=MsoNormal><span style='mso-spacerun:yes'> </span>You should see three
948windows, two of which are empty. One, in the upper right, is labeled GSASII
949data tree, the second, immediately under the first is labeled GSAS-II data
950display and the third on the left is labeled GSAS-II Plots. These windows may
951be moved anywhere on the screen. On Linux and Windows a menu bar appears at the
952top <span class=GramE>of <span style='mso-spacerun:yes'> </span>the</span> data
953tree and data display windows; on a Mac these menus will appear in the system
954menu bar location (usually at the screen top) depending on which GSAS-II window
955has the focus. <o:p></o:p></p>
956
957<h1>Step 3: read in the data file<o:p></o:p></h1>
958
959<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
960style='mso-bidi-font-weight:normal'>Data/Read image data</b> menu item to read
961the data file into the current GSAS-II project. <o:p></o:p></p>
962
963<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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967  o:title="" croptop="9965f" cropbottom="37297f" cropleft="53272f" cropright="5473f"/>
968</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=273
969src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image003.jpg"
970v:shapes="Picture_x0020_1"><![endif]></span><span
971style='mso-spacerun:yes'> </span></p>
972
973<p class=MsoNormal>A file selection dialog will be shown; its appearance will
974depend on your OS. Change the search directory if necessary and then select the
975file </p>
976
977<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><i style='mso-bidi-font-style:
978normal'>La_hex_+45deg-<span class=GramE>00015.tif<span style='font-weight:normal;
979font-style:normal'> <span style='mso-spacerun:yes'> </span>and</span></span></i></b>
980press Open.<span style='mso-no-proof:yes'> </span></p>
981
982<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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986  o:title=""/>
987</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=271
988src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
989v:shapes="Picture_x0020_6"><![endif]></span></p>
990
991<p class=MsoNormal>At this point the data tree window will have several entries;
992the highlighted one specifies the contents of the data window as <b
993style='mso-bidi-font-weight:normal'>Image Controls</b><o:p></o:p></p>
994
995<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
996 id="Picture_x0020_5" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:510.75pt;
997 height:303pt;visibility:visible;mso-wrap-style:square'>
998 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
999  o:title=""/>
1000</v:shape><![endif]--><![if !vml]><img border=0 width=681 height=404
1001src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
1002v:shapes="Picture_x0020_5"><![endif]></span></p>
1003
1004<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>the</span>
1005plot window shows the image; notice the elliptical shape of the powder
1006diffraction rings. The x marks the default beam location (image center); your
1007calibration will correctly place it.<o:p></o:p></p>
1008
1009<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
1010style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_4"
1011 o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;height:450pt;
1012 visibility:visible;mso-wrap-style:square'>
1013 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
1014  o:title=""/>
1015</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1016src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
1017v:shapes="Picture_x0020_4"><![endif]></span><o:p></o:p></p>
1018
1019<h1><span style='mso-spacerun:yes'> </span>Step 4: Edit image parameters<o:p></o:p></h1>
1020
1021<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Note that, alas, very
1022few image formats contain all of the important metadata about the image, so it
1023needs to be added manually. In this case set the <b style='mso-bidi-font-weight:
1024normal'>wavelength</b> to <b style='mso-bidi-font-weight:normal'>0.10798</b>.
1025It is also helpful to change the display of the image so that it is easier to
1026see the diffraction rings. Lowering the maximum intensity to 10,000 to 20,000
1027counts will help (note that this can be done by moving the <span class=GramE>slider,</span>
1028or by typing a value in the box and then clicking on another control or the
1029typing the Enter/return key). You may also wish to select another color scheme
1030using the Color bar selector. <o:p></o:p></p>
1031
1032<h1><span style='mso-spacerun:yes'> </span>Step 5: Calibrate<o:p></o:p></h1>
1033
1034<h3><span style='mso-spacerun:yes'> </span>First: <o:p></o:p></h3>
1035
1036<p class=MsoNormal><span style='mso-spacerun:yes'>   </span>Set the material
1037used as a sample in the box labeled <span class=SpellE><b style='mso-bidi-font-weight:
1038normal'>Calibrant</b></span>; select <b style='mso-bidi-font-weight:normal'>LaB6
1039SRM660a</b><o:p></o:p></p>
1040
1041<h3><span style='mso-spacerun:yes'> </span>Second: <o:p></o:p></h3>
1042
1043<p class=MsoNormal><span style='mso-spacerun:yes'>   </span>Use the <b
1044style='mso-bidi-font-weight:normal'>Operations/Calibrate</b> menu item (note
1045this menu is on the <b style='mso-bidi-font-weight:normal'>Image Controls</b>
1046window or for the Mac, the <span class=GramE><b style='mso-bidi-font-weight:
1047normal'>Image<span style='mso-spacerun:yes'>  </span>Controls</b></span> window
1048must be active to place this into the system menu bar). At this point the
1049status line on the bottom of the <b style='mso-bidi-font-weight:normal'>Image
1050Controls</b> window changes with a prompt to select points for calibration.<o:p></o:p></p>
1051
1052<h3>Third: <o:p></o:p></h3>
1053
1054<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Use the left mouse
1055button to click on at least five locations on the innermost ring. As each point
1056is defined, a red &quot;+&quot; is added to the plot. You need not hit the ring
1057exactly as the code will search for the locally highest point. <o:p></o:p></p>
1058
1059<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1060 id="Picture_x0020_8" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
1061 height:450pt;visibility:visible;mso-wrap-style:square'>
1062 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image009.png"
1063  o:title=""/>
1064</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1065src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image009.png"
1066v:shapes="Picture_x0020_8"><![endif]></span><o:p></o:p></p>
1067
1068<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>To remove a point
1069added in error click on that point with the right mouse button [on the Mac, if
1070you have a single-button mouse, hold the Command (<span style='font-family:
1071"Cambria Math","serif";mso-bidi-font-family:"Cambria Math"'>&#8984;</span>) key
1072down and click]. <o:p></o:p></p>
1073
1074<h3><span style='mso-spacerun:yes'> </span>Fourth:<o:p></o:p></h3>
1075
1076<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>When done, press the
1077right mouse button well away from any points that have been added [on the Mac,
1078if you have a single-button mouse, hold the Command (<span style='font-family:
1079"Cambria Math","serif";mso-bidi-font-family:"Cambria Math"'>&#8984;</span>) key
1080down and click].<o:p></o:p></p>
1081
1082<p class=MsoNormal><span style='mso-spacerun:yes'> </span>The calibration is
1083then performed. First the rings are located and an ellipse is optimized for
1084each ring. The indexed rings are first shown in red as the calibration proceeds
1085and center of each ellipse is noted with a blue &quot;+&quot;. When all rings
1086have been fitted, the entire ensemble of rings is refitted to the detector
1087parameters and the rings are then shown in blue.<o:p></o:p></p>
1088
1089<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
1090style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_9"
1091 o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;height:450pt;
1092 visibility:visible;mso-wrap-style:square'>
1093 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image010.png"
1094  o:title=""/>
1095</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1096src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image010.png"
1097v:shapes="Picture_x0020_9"><![endif]></span><span
1098style='mso-spacerun:yes'> </span></p>
1099
1100<p class=MsoNormal>The derived calibration results are shown in the Image
1101Controls window.<o:p></o:p></p>
1102
1103<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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1108</v:shape><![endif]--><![if !vml]><img border=0 width=681 height=404
1109src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image011.png"
1110v:shapes="Picture_x0020_12"><![endif]></span><span
1111style='mso-spacerun:yes'> </span></p>
1112
1113<p class=MsoNormal><span class=GramE>and</span> the console window shows
1114details of the fit; a trial refinement for the wavelength is also given for you
1115to consider.</p>
1116
1117<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1118 id="Picture_x0020_14" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:396.75pt;
1119 height:134.25pt;visibility:visible;mso-wrap-style:square'>
1120 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image012.png"
1121  o:title=""/>
1122</v:shape><![endif]--><![if !vml]><img border=0 width=529 height=179
1123src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image012.png"
1124v:shapes="Picture_x0020_14"><![endif]></span><o:p></o:p></p>
1125
1126<p class=MsoNormal><span style='mso-spacerun:yes'> </span>To see the actual
1127points selected by the program, click on the &quot;show ring picks?&quot; check
1128button <o:p></o:p></p>
1129
1130<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1131 id="Picture_x0020_15" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
1132 height:450pt;visibility:visible;mso-wrap-style:square'>
1133 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image013.png"
1134  o:title=""/>
1135</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1136src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image013.png"
1137v:shapes="Picture_x0020_15"><![endif]></span><span
1138style='mso-spacerun:yes'> </span></p>
1139
1140<p class=MsoNormal>When this is done, it sometimes occurs that the points selected
1141for the outermost ring are scattered between that and the next ring. This can
1142be repaired by changing the pixel search range to 10 and using the <b
1143style='mso-bidi-font-weight:normal'>Operations/Recalibrate</b> menu item.<o:p></o:p></p>
1144
1145<p class=MsoNormal>Assuming that these calibration results will be applied to
1146other images in the same GSAS-II project, click on <b style='mso-bidi-font-weight:
1147normal'>Use as default for all images</b>. You may also save a copy of the
1148calibration values to a file (<span class=SpellE><i style='mso-bidi-font-style:
1149normal'>name</i><b style='mso-bidi-font-weight:normal'>.imctrl</b></span>) with
1150the <b style='mso-bidi-font-weight:normal'>Operations/Save Controls</b> menu
1151item. To save the project, including the now-derived calibration information,
1152use the <b style='mso-bidi-font-weight:normal'>File/Save Project</b> menu item
1153associated with the data tree window; as this project has not been saved before
1154the file save dialog will need a file name. Don’t enter the extension; it will
1155be set to “.<span class=SpellE>gpx</span>”.<o:p></o:p></p>
1156
1157<h2>Next step: <a href="Integration%20of%20area%20detector%20data%20in%20GSAS.htm">Integrate
1158the Data</a></h2>
1159
1160</div>
1161
1162</body>
1163
1164</html>
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