source: trunk/help/Calibration of an area detector in GSAS.htm @ 588

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810</head>
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812<body lang=EN-US link="#000000" vlink=purple style='tab-interval:.5in'>
813
814<div class=WordSection1>
815
816<p class=MsoNormal><span class=Heading1Char><span style='font-size:24.0pt'>Calibration
817of an area detector in GSAS-II</span></span><b><span style='font-size:14.0pt;
818color:#365F91;mso-themecolor:accent1;mso-themeshade:191'><o:p></o:p></span></b></p>
819
820<p class=MsoNormal>In this tutorial, data collected with a Perkin-Elmer area
821detector at APS 11-ID-C with a wavelength 0.10798 A, where the detector was
822intentionally tilted at 45 degrees, are used. Note that menu entries are listed
823in bold face below as <b style='mso-bidi-font-weight:normal'><span
824style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
825mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Help/About
826GSAS-II</span></b>, which lists first the name of the menu (here <b
827style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
828mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
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830(here <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
831mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
832minor-latin'>About GSAS-II</span></b>).</p>
833
834<p class=MsoNormal><span style='font-size:11.0pt'><o:p>&nbsp;</o:p></span></p>
835
836<p class=MsoNormal>If you have not done so already, <u><span style='color:#0070C0'><a
837href="Starting%20GSAS.htm">start GSAS-II</a></span></u>.<o:p></o:p></p>
838
839<h1>Step 1: read in the data file</h1>
840
841<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
842style='mso-bidi-font-weight:normal'>Data/Read image data</b> menu item to read
843the data file into the current GSAS-II project. </p>
844
845<p class=MsoNormal><o:p>&nbsp;</o:p></p>
846
847<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
848 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
849 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
850 <v:stroke joinstyle="miter"/>
851 <v:formulas>
852  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
853  <v:f eqn="sum @0 1 0"/>
854  <v:f eqn="sum 0 0 @1"/>
855  <v:f eqn="prod @2 1 2"/>
856  <v:f eqn="prod @3 21600 pixelWidth"/>
857  <v:f eqn="prod @3 21600 pixelHeight"/>
858  <v:f eqn="sum @0 0 1"/>
859  <v:f eqn="prod @6 1 2"/>
860  <v:f eqn="prod @7 21600 pixelWidth"/>
861  <v:f eqn="sum @8 21600 0"/>
862  <v:f eqn="prod @7 21600 pixelHeight"/>
863  <v:f eqn="sum @10 21600 0"/>
864 </v:formulas>
865 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
866 <o:lock v:ext="edit" aspectratio="t"/>
867</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1033" type="#_x0000_t75"
868 style='width:225pt;height:204.75pt;visibility:visible;mso-wrap-style:square'>
869 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image001.png"
870  o:title="" croptop="9965f" cropbottom="37297f" cropleft="53272f" cropright="5473f"/>
871</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=273
872src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image002.jpg"
873v:shapes="Picture_x0020_1"><![endif]></span><span
874style='mso-spacerun:yes'> </span></p>
875
876<p class=MsoNormal>A file selection dialog will be shown; its appearance will
877depend on your OS. Change the search directory to <b style='mso-bidi-font-weight:
878normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
879minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>/Exercises/images</span></b>
880and then select the file </p>
881
882<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
883style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
884mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>La_hex_+45deg-00015.tif</span></b>
885and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
886mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
887minor-latin'>Open</span></b>.<span style='mso-no-proof:yes'> <o:p></o:p></span></p>
888
889<p class=MsoNormal><o:p>&nbsp;</o:p></p>
890
891<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
892 id="Picture_x0020_6" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:225pt;
893 height:203.25pt;visibility:visible;mso-wrap-style:square'>
894 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image003.png"
895  o:title=""/>
896</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=271
897src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image003.png"
898v:shapes="Picture_x0020_6"><![endif]></span></p>
899
900<p class=MsoNormal><o:p>&nbsp;</o:p></p>
901
902<p class=MsoNormal>At this point the data tree window will have several
903entries; the highlighted one specifies the contents of the data window as <b
904style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
905mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
906minor-latin'>Image Controls</span><o:p></o:p></b></p>
907
908<p class=MsoNormal><o:p>&nbsp;</o:p></p>
909
910<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
911 id="Picture_x0020_5" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:510.75pt;
912 height:303pt;visibility:visible;mso-wrap-style:square'>
913 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image004.png"
914  o:title=""/>
915</v:shape><![endif]--><![if !vml]><img border=0 width=681 height=404
916src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image004.png"
917v:shapes="Picture_x0020_5"><![endif]></span></p>
918
919<p class=MsoNormal><o:p>&nbsp;</o:p></p>
920
921<p class=MsoNormal><span style='mso-spacerun:yes'> </span>The plot window shows
922the image; notice the elliptical shape of the powder diffraction rings. The
923blue <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
924mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
925minor-latin;color:#4F81BD;mso-themecolor:accent1'>X</span></b> marks the
926default beam location (image center); your calibration will correctly place it.
927Also notice that the values shown in the plot window status bar (at bottom of
928plot window) change as you move the cursor over the plot; these values are at
929present in error as they are computed from the default calibration values. They
930will be correct after you finish the calibration.</p>
931
932<p class=MsoNormal><o:p>&nbsp;</o:p></p>
933
934<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
935style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_4"
936 o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;height:450pt;
937 visibility:visible;mso-wrap-style:square'>
938 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image005.png"
939  o:title=""/>
940</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
941src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image005.png"
942v:shapes="Picture_x0020_4"><![endif]></span></p>
943
944<h1><span style='mso-spacerun:yes'> </span>Step 2: Edit image parameters</h1>
945
946<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Note that, alas, very
947few image formats contain all of the important metadata about the image, so it
948needs to be added manually. In this case set the <b style='mso-bidi-font-weight:
949normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
950minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>wavelength</span></b>
951to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
952mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
953minor-latin'>0.10798</span></b>. It is also helpful to change the display of
954the image so that it is easier to see the diffraction rings. Lowering the
955maximum intensity to 10,000 to 20,000 counts will help (note that this can be
956done by moving the <span class=GramE>slider,</span> or by typing a value in the
957box and then clicking on another control or pressing the <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-theme-font:minor-latin'>Enter</span></b>
960or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
961mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
962minor-latin'>Tab</span></b> key). You may also wish to select another color
963scheme using the <b style='mso-bidi-font-weight:normal'><span style='font-family:
964"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
965minor-latin;mso-bidi-theme-font:minor-latin'>Color bar</span></b> selector. </p>
966
967<h1><span style='mso-spacerun:yes'> </span>Step 3: Calibrate</h1>
968
969<h3><span style='mso-spacerun:yes'> </span>First: </h3>
970
971<p class=MsoNormal><span style='mso-spacerun:yes'>   </span>Set the material
972used as a sample in the box labeled <span class=SpellE><b style='mso-bidi-font-weight:
973normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
974minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calibrant</span></b></span>;
975select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
976mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
977minor-latin'>LaB6 SRM660a</span></b></p>
978
979<h3><span style='mso-spacerun:yes'> </span>Second: </h3>
980
981<p class=MsoNormal><span style='mso-spacerun:yes'>   </span>Use the <b
982style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
983mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
984minor-latin'>Operations/Calibrate</span></b> menu item (note this menu is on
985the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
986mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
987minor-latin'>Image Controls</span></b> window or for the Mac, the <span
988class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
989"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
990minor-latin;mso-bidi-theme-font:minor-latin'>Image<span
991style='mso-spacerun:yes'>  </span>Controls</span></b></span> window must be
992active to place this into the system menu bar). At this point the status line
993on the bottom of the <b style='mso-bidi-font-weight:normal'><span
994style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
995mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Image
996Controls</span></b> window changes with a prompt to select points for
997calibration.</p>
998
999<h3>Third: </h3>
1000
1001<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Use the left mouse
1002button to click on at least five locations on the innermost ring. As each point
1003is defined, a red &quot;<b style='mso-bidi-font-weight:normal'><span
1004style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1005mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin;color:red'>+</span></b>&quot;
1006is added to the plot. You need not hit the ring exactly as the code will search
1007for the locally highest point. </p>
1008
1009<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1010
1011<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1012 id="Picture_x0020_8" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
1013 height:450pt;visibility:visible;mso-wrap-style:square'>
1014 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
1015  o:title=""/>
1016</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1017src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
1018v:shapes="Picture_x0020_8"><![endif]></span></p>
1019
1020<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1021
1022<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>To remove a point
1023added in error click on that point with the right mouse button [on the Mac, if
1024you have a single-button mouse, hold the Command (<span style='font-family:
1025"Cambria Math","serif";mso-bidi-font-family:"Cambria Math"'>&#8984;</span>) key
1026down and click]. </p>
1027
1028<h3><span style='mso-spacerun:yes'> </span>Fourth:</h3>
1029
1030<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>When done, press the
1031right mouse button well away from any points that have been added [on the Mac,
1032if you have a single-button mouse, hold the Command (<span style='font-family:
1033"Cambria Math","serif";mso-bidi-font-family:"Cambria Math"'>&#8984;</span>) key
1034down and click].</p>
1035
1036<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1037
1038<p class=MsoNormal><span style='mso-spacerun:yes'> </span>The calibration is
1039then performed. First the rings are located and an ellipse is optimized for
1040each ring. The indexed rings are first shown in red as the calibration proceeds
1041and center of each ellipse is noted with a blue &quot;<span style='color:#4F81BD;
1042mso-themecolor:accent1'>+</span>&quot;. When all rings have been fitted, the
1043entire ensemble of rings is refitted to the detector parameters and the rings
1044are then shown in blue. The beam position (blue “<span style='font-family:"Calibri","sans-serif";
1045mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1046minor-latin;color:#4F81BD;mso-themecolor:accent1'>X</span>”) is now correctly
1047positioned.</p>
1048
1049<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1050
1051<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
1052style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_9"
1053 o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;height:450pt;
1054 visibility:visible;mso-wrap-style:square'>
1055 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
1056  o:title=""/>
1057</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1058src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
1059v:shapes="Picture_x0020_9"><![endif]></span><span
1060style='mso-spacerun:yes'> </span></p>
1061
1062<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1063
1064<p class=MsoNormal>The derived calibration results are shown in the <b
1065style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1066mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1067minor-latin'>Image Controls</span></b> window.</p>
1068
1069<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1070
1071<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1072 id="Picture_x0020_12" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:510.75pt;
1073 height:303pt;visibility:visible;mso-wrap-style:square'>
1074 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
1075  o:title=""/>
1076</v:shape><![endif]--><![if !vml]><img border=0 width=681 height=404
1077src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
1078v:shapes="Picture_x0020_12"><![endif]></span><span
1079style='mso-spacerun:yes'> </span></p>
1080
1081<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1082
1083<p class=MsoNormal><span class=GramE>and</span> the console window shows
1084details of the fit; a trial refinement for the wavelength is also given for you
1085to consider.</p>
1086
1087<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1088
1089<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1090 id="Picture_x0020_14" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:396.75pt;
1091 height:134.25pt;visibility:visible;mso-wrap-style:square'>
1092 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image009.png"
1093  o:title=""/>
1094</v:shape><![endif]--><![if !vml]><img border=0 width=529 height=179
1095src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image009.png"
1096v:shapes="Picture_x0020_14"><![endif]></span></p>
1097
1098<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1099
1100<p class=MsoNormal><span style='mso-spacerun:yes'> </span>To see the actual
1101points selected by the program, click on the <b style='mso-bidi-font-weight:
1102normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1103minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>show
1104ring picks?</span></b> <span class=GramE>check</span> box </p>
1105
1106<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1107
1108<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1109 id="Picture_x0020_15" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
1110 height:450pt;visibility:visible;mso-wrap-style:square'>
1111 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image010.png"
1112  o:title=""/>
1113</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1114src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image010.png"
1115v:shapes="Picture_x0020_15"><![endif]></span><span
1116style='mso-spacerun:yes'> </span><span style='color:#1F497D;mso-themecolor:
1117text2'><o:p></o:p></span></p>
1118
1119<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1120
1121<p class=MsoNormal>When this is done, it sometimes occurs that the points
1122selected for the outermost rings are scattered between that and the next ring.
1123This can be repaired by changing the pixel search range to 10 and using the <b
1124style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1125mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1126minor-latin'>Operations/Recalibrate</span></b> menu item.</p>
1127
1128<p class=MsoNormal>Assuming that these calibration results will be applied to
1129other images in the same GSAS-II project, click on <b style='mso-bidi-font-weight:
1130normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1131minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Use
1132as default for all images</span></b>. You may also save a copy of the
1133calibration values to a file <span style='font-family:"Calibri","sans-serif";
1134mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1135minor-latin'>(<span class=SpellE><i style='mso-bidi-font-style:normal'>name</i><b
1136style='mso-bidi-font-weight:normal'>.imctrl</b></span></span>) with the <b
1137style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1138mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1139minor-latin'>Operations/Save Controls</span></b> menu item. To save the
1140project, including the now-derived calibration information, use the <b
1141style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1142mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1143minor-latin'>File/Save</span> </b><b style='mso-bidi-font-weight:normal'><span
1144style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1145mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Project</span></b><span
1146style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1147mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> </span>menu
1148item associated with the data tree window; as this project has not been saved
1149before the file save dialog will need a file name. Don’t enter the extension;
1150it will be set to “<b style='mso-bidi-font-weight:normal'><span
1151style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1152mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>.<span
1153class=SpellE>gpx</span></span></b>”.</p>
1154
1155<h2>Next step: <span class=MsoHyperlink><span style='color:#0070C0'><a
1156href="Integration%20of%20area%20detector%20data%20in%20GSAS.htm"><u>Integrate
1157the Data</u></a></span></span></h2>
1158
1159</div>
1160
1161</body>
1162
1163</html>
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