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812
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814
815<p class=MsoNormal><span class=Heading1Char><span style='font-size:24.0pt'>Calibration
816of an area detector in GSAS-II</span></span><b><span style='font-size:14.0pt;
817color:#365F91;mso-themecolor:accent1;mso-themeshade:191'><o:p></o:p></span></b></p>
818
819<p class=MsoNormal>In this tutorial, data collected with a Perkin-Elmer area
820detector at APS 11-ID-C with a wavelength 0.10798 A, where the detector was
821intentionally tilted at 45 degrees, are used. Note that menu entries are listed
822in bold face below as <b style='mso-bidi-font-weight:normal'><span
823style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
824mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
825minor-latin'>Help/About GSAS-II</span></b>, which lists first the name of the
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830normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
831minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
832mso-bidi-theme-font:minor-latin'>About GSAS-II</span></b>).</p>
833
834<p class=MsoNormal>If you have not done so already, <u><span style='color:#0070C0'><a
835href="Starting%20GSAS.htm"><span style='color:windowtext;text-decoration:none;
836text-underline:none'>start GSAS-II</span></a></span></u>.</p>
837
838<h1>Step 1: read in the data file</h1>
839
840<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
841style='mso-bidi-font-weight:normal'>Data/Read image data</b> menu item to read
842the data file into the current GSAS-II project. </p>
843
844<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
845
846<p class=MsoNormal>A file selection dialog will be shown; its appearance will
847depend on your OS. Change the search directory to <b style='mso-bidi-font-weight:
848normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
849minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
850mso-bidi-theme-font:minor-latin'>/Exercises/images</span></b> and then select
851the file </p>
852
853<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
854style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
855mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
856minor-latin'>La_hex_+45deg-00015.tif</span></b> and press <b style='mso-bidi-font-weight:
857normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
858minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
859mso-bidi-theme-font:minor-latin'>Open</span></b>.<span style='mso-no-proof:
860yes'> <o:p></o:p></span></p>
861
862<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
863 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
864 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
865 <v:stroke joinstyle="miter"/>
866 <v:formulas>
867  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
868  <v:f eqn="sum @0 1 0"/>
869  <v:f eqn="sum 0 0 @1"/>
870  <v:f eqn="prod @2 1 2"/>
871  <v:f eqn="prod @3 21600 pixelWidth"/>
872  <v:f eqn="prod @3 21600 pixelHeight"/>
873  <v:f eqn="sum @0 0 1"/>
874  <v:f eqn="prod @6 1 2"/>
875  <v:f eqn="prod @7 21600 pixelWidth"/>
876  <v:f eqn="sum @8 21600 0"/>
877  <v:f eqn="prod @7 21600 pixelHeight"/>
878  <v:f eqn="sum @10 21600 0"/>
879 </v:formulas>
880 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
881 <o:lock v:ext="edit" aspectratio="t"/>
882</v:shapetype><v:shape id="_x0000_i1032" type="#_x0000_t75" style='width:300pt;
883 height:187.5pt;visibility:visible;mso-wrap-style:square'>
884 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image001.png"
885  o:title=""/>
886</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=250
887src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image001.png"
888v:shapes="_x0000_i1032"><![endif]></span></p>
889
890<p class=MsoNormal>At this point the data tree window will have several
891entries; the highlighted one specifies the contents of the data window as <b
892style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
893mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
894Calibri;mso-bidi-theme-font:minor-latin'>Image Controls</span><o:p></o:p></b></p>
895
896<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
897 id="Picture_x0020_10" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:472.5pt;
898 height:342pt;visibility:visible;mso-wrap-style:square'>
899 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image002.png"
900  o:title=""/>
901</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=456
902src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image002.png"
903v:shapes="Picture_x0020_10"><![endif]></span></p>
904
905<p class=MsoNormal><span style='mso-spacerun:yes'> </span>The plot window shows
906the image; notice the elliptical shape of the powder diffraction rings. The
907blue <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
908mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
909Calibri;mso-bidi-theme-font:minor-latin;color:#4F81BD;mso-themecolor:accent1'>X</span></b>
910marks the default beam location (image center); your calibration will correctly
911place it. Also notice that the values shown in the plot window status bar (at
912bottom of plot window) change as you move the cursor over the plot; these
913values are at present in error as they are computed from the default
914calibration values. They will be correct after you finish the calibration.</p>
915
916<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
917style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_11"
918 o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;height:450pt;
919 visibility:visible;mso-wrap-style:square'>
920 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image003.png"
921  o:title=""/>
922</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
923src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image003.png"
924v:shapes="Picture_x0020_11"><![endif]></span></p>
925
926<h1><span style='mso-spacerun:yes'> </span>Step 2: Edit image parameters</h1>
927
928<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Note that, alas, very
929few image formats contain all of the important metadata about the image, so it
930needs to be added manually. In this case set the <b style='mso-bidi-font-weight:
931normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
932minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
933mso-bidi-theme-font:minor-latin'>wavelength</span></b> to <b style='mso-bidi-font-weight:
934normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
935minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
936mso-bidi-theme-font:minor-latin'>0.10798</span></b>. It is also helpful to
937change the display of the image so that it is easier to see the diffraction
938rings. Lowering the maximum intensity to 10,000 to 20,000 counts will help
939(note that this can be done by moving the <span class=GramE>slider,</span> or
940by typing a value in the box and then clicking on another control or pressing
941the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
942mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
943Calibri;mso-bidi-theme-font:minor-latin'>Enter</span></b> or <b
944style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
945mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
946Calibri;mso-bidi-theme-font:minor-latin'>Tab</span></b> key). You may also wish
947to select another color scheme using the <b style='mso-bidi-font-weight:normal'><span
948style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
949mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
950minor-latin'>Color bar</span></b> selector. </p>
951
952<h1><span style='mso-spacerun:yes'> </span>Step 3: Calibrate</h1>
953
954<h3><span style='mso-spacerun:yes'> </span>First: </h3>
955
956<p class=MsoNormal><span style='mso-spacerun:yes'>   </span>Set the material
957used as a sample in the box labeled <span class=SpellE><b style='mso-bidi-font-weight:
958normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
959minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
960mso-bidi-theme-font:minor-latin'>Calibrant</span></b></span>; select <b
961style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
962mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
963Calibri;mso-bidi-theme-font:minor-latin'>LaB6 SRM660a</span></b></p>
964
965<h3><span style='mso-spacerun:yes'> </span>Second: </h3>
966
967<p class=MsoNormal><span style='mso-spacerun:yes'>   </span>Use the <b
968style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
969mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
970Calibri;mso-bidi-theme-font:minor-latin'>Operations/Calibrate</span></b> menu
971item (note this menu is on the <b style='mso-bidi-font-weight:normal'><span
972style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
973mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
974minor-latin'>Image Controls</span></b> window or for the Mac, the <span
975class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
976"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
977minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Image<span
978style='mso-spacerun:yes'>  </span>Controls</span></b></span> window must be
979active to place this into the system menu bar). At this point the status line
980on the bottom of the <b style='mso-bidi-font-weight:normal'><span
981style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
982mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
983minor-latin'>Image Controls</span></b> window changes with a prompt to select
984points for calibration.</p>
985
986<h3>Third: </h3>
987
988<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Use the left mouse
989button to click on at least five locations on the innermost ring. As each point
990is defined, a red &quot;<b style='mso-bidi-font-weight:normal'><span
991style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
992mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
993minor-latin;color:red'>+</span></b>&quot; is added to the plot. You need not
994hit the ring exactly as the code will search for the locally highest point. </p>
995
996<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
997 id="Picture_x0020_8" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
998 height:450pt;visibility:visible;mso-wrap-style:square'>
999 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image004.png"
1000  o:title=""/>
1001</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1002src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image004.png"
1003v:shapes="Picture_x0020_8"><![endif]></span></p>
1004
1005<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>To remove a point
1006added in error click on that point with the right mouse button [on the Mac, if
1007you have a single-button mouse, hold the Command (<span style='font-family:
1008"Cambria Math","serif";mso-bidi-font-family:"Cambria Math"'>&#8984;</span>) key
1009down and click]. </p>
1010
1011<h3><span style='mso-spacerun:yes'> </span>Fourth:</h3>
1012
1013<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>When done, press the
1014right mouse button well away from any points that have been added [on the Mac,
1015if you have a single-button mouse, hold the Command (<span style='font-family:
1016"Cambria Math","serif";mso-bidi-font-family:"Cambria Math"'>&#8984;</span>) key
1017down and click].</p>
1018
1019<p class=MsoNormal>The calibration is then performed. First the rings are
1020located and an ellipse is optimized for each ring. The indexed rings are first
1021shown in red as the calibration proceeds and center of each ellipse is noted
1022with a blue &quot;<b style='mso-bidi-font-weight:normal'><span
1023style='color:#4F81BD;mso-themecolor:accent1'>+</span></b>&quot;. When all rings
1024have been fitted, the entire ensemble of rings is refitted to the detector
1025parameters and the rings are then shown in blue. The beam position (blue “<span
1026style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1027mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1028minor-latin;color:#4F81BD;mso-themecolor:accent1'>X</span>”) is now correctly
1029positioned.</p>
1030
1031<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
1032style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_9"
1033 o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;height:450pt;
1034 visibility:visible;mso-wrap-style:square'>
1035 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image005.png"
1036  o:title=""/>
1037</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1038src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image005.png"
1039v:shapes="Picture_x0020_9"><![endif]></span><span
1040style='mso-spacerun:yes'> </span></p>
1041
1042<p class=MsoNormal>The derived calibration results are shown in the <b
1043style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1044mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1045Calibri;mso-bidi-theme-font:minor-latin'>Image Controls</span></b> window.</p>
1046
1047<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1048 id="Picture_x0020_13" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:472.5pt;
1049 height:342pt;visibility:visible;mso-wrap-style:square'>
1050 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
1051  o:title=""/>
1052</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=456
1053src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
1054v:shapes="Picture_x0020_13"><![endif]></span><span
1055style='mso-spacerun:yes'> </span></p>
1056
1057<p class=MsoNormal><span class=GramE>and</span> the console window shows
1058details of the fit.</p>
1059
1060<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1061 id="Picture_x0020_14" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:396.75pt;
1062 height:134.25pt;visibility:visible;mso-wrap-style:square'>
1063 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
1064  o:title=""/>
1065</v:shape><![endif]--><![if !vml]><img border=0 width=529 height=179
1066src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
1067v:shapes="Picture_x0020_14"><![endif]></span></p>
1068
1069<p class=MsoNormal><span style='mso-spacerun:yes'> </span>To see the actual
1070points selected by the program, click on the <b style='mso-bidi-font-weight:
1071normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1072minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1073mso-bidi-theme-font:minor-latin'>show ring picks?</span></b> <span class=GramE>check</span>
1074box </p>
1075
1076<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1077 id="Picture_x0020_15" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
1078 height:450pt;visibility:visible;mso-wrap-style:square'>
1079 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
1080  o:title=""/>
1081</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1082src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
1083v:shapes="Picture_x0020_15"><![endif]></span><span
1084style='mso-spacerun:yes'> </span><span style='color:#1F497D;mso-themecolor:
1085text2'><o:p></o:p></span></p>
1086
1087<p class=MsoNormal>When this is done, it sometimes occurs that the points
1088selected for the outermost rings are scattered between that and the next ring.
1089This can be repaired by changing the pixel search range to 10 and using the <b
1090style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1091mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1092Calibri;mso-bidi-theme-font:minor-latin'>Operations/Recalibrate</span></b> menu
1093item.</p>
1094
1095<p class=MsoNormal>Assuming that these calibration results will be applied to
1096other images in the same GSAS-II project, click on <b style='mso-bidi-font-weight:
1097normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1098minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1099mso-bidi-theme-font:minor-latin'>Use as default for all images</span></b>. You
1100may also save a copy of the calibration values to a file <span
1101style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1102mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1103minor-latin'>(<span class=SpellE><i style='mso-bidi-font-style:normal'>name</i><b
1104style='mso-bidi-font-weight:normal'>.imctrl</b></span></span>) with the <b
1105style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1106mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1107Calibri;mso-bidi-theme-font:minor-latin'>Operations/Save Controls</span></b>
1108menu item. To save the project, including the now-derived calibration information,
1109use the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1110mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1111Calibri;mso-bidi-theme-font:minor-latin'>File/Save</span> </b><b
1112style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1113mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1114Calibri;mso-bidi-theme-font:minor-latin'>Project</span></b><span
1115style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1116mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1117minor-latin'> </span>menu item associated with the data tree window; as this
1118project has not been saved before the file save dialog will need a file name.
1119Don’t enter the extension; it will be set to “<b style='mso-bidi-font-weight:
1120normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1121minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1122mso-bidi-theme-font:minor-latin'>.<span class=SpellE>gpx</span></span></b>”.</p>
1123
1124<h2>Next step: <span class=MsoHyperlink><span style='color:#0070C0'><a
1125href="Integration%20of%20area%20detector%20data%20in%20GSAS.htm"><u><span
1126style='color:black'>Integrate the Data</span></u></a></span></span></h2>
1127
1128</div>
1129
1130</body>
1131
1132</html>
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