source: trunk/help/Calibration of an area detector in GSAS.htm @ 1112

Last change on this file since 1112 was 1112, checked in by toby, 9 years ago

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825<body lang=EN-US link="#000000" vlink=purple style='tab-interval:.5in'>
826
827<div class=WordSection1>
828
829<p class=MsoNormal><span class=Heading1Char><span style='font-size:24.0pt'>Calibration
830of an area detector in GSAS-II</span></span><b><span style='font-size:14.0pt;
831color:#365F91;mso-themecolor:accent1;mso-themeshade:191'><o:p></o:p></span></b></p>
832
833<p class=MsoNormal>In this tutorial, data collected with a Perkin-Elmer area
834detector at APS 11-ID-C with a wavelength 0.10798 A, where the detector was
835intentionally tilted at 45 degrees, are used. Note that menu entries are listed
836in bold face below as <b style='mso-bidi-font-weight:normal'><span
837style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
838minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin'>Help/About
839GSAS-II</span></b>, which lists first the name of the menu (here <b
840style='mso-bidi-font-weight:normal'><span style='font-family:Cambria;
841mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
842Cambria;mso-bidi-theme-font:minor-latin'>Help</span></b>) and second the name
843of the entry in the menu (here <b style='mso-bidi-font-weight:normal'><span
844style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
845minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin'>About
846GSAS-II</span></b>).</p>
847
848<p class=MsoNormal>If you have not done so already, <u><span style='color:#0070C0'><a
849href="Starting%2520GSAS.htm"><span style='color:windowtext;text-decoration:
850none;text-underline:none'>start GSAS-II</span></a></span></u>.</p>
851
852<h1>Step 1: read in the data file</h1>
853
854<p class=MsoNormal><span style="mso-spacerun:yes"> </span>Use the <b
855style='mso-bidi-font-weight:normal'>Data/Read image data</b> menu item to read
856the data file into the current GSAS-II project. </p>
857
858<p class=MsoNormal><span style="mso-spacerun:yes"> </span></p>
859
860<p class=MsoNormal>A file selection dialog will be shown; its appearance will
861depend on your OS. Change the search directory to <b style='mso-bidi-font-weight:
862normal'><span style='font-family:Cambria;mso-ascii-theme-font:minor-latin;
863mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:
864minor-latin'>/Exercises/images</span></b> and then select the file </p>
865
866<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
867style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
868minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin'>La_hex_+45deg-00015.tif</span></b>
869and press <b style='mso-bidi-font-weight:normal'><span style='font-family:Cambria;
870mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
871Cambria;mso-bidi-theme-font:minor-latin'>Open</span></b>.<span
872style='mso-no-proof:yes'> <o:p></o:p></span></p>
873
874<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
875 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
876 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
877 <v:stroke joinstyle="miter"/>
878 <v:formulas>
879  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
880  <v:f eqn="sum @0 1 0"/>
881  <v:f eqn="sum 0 0 @1"/>
882  <v:f eqn="prod @2 1 2"/>
883  <v:f eqn="prod @3 21600 pixelWidth"/>
884  <v:f eqn="prod @3 21600 pixelHeight"/>
885  <v:f eqn="sum @0 0 1"/>
886  <v:f eqn="prod @6 1 2"/>
887  <v:f eqn="prod @7 21600 pixelWidth"/>
888  <v:f eqn="sum @8 21600 0"/>
889  <v:f eqn="prod @7 21600 pixelHeight"/>
890  <v:f eqn="sum @10 21600 0"/>
891 </v:formulas>
892 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
893 <o:lock v:ext="edit" aspectratio="t"/>
894</v:shapetype><v:shape id="_x0000_i1025" type="#_x0000_t75" style='width:300pt;
895 height:188pt;visibility:visible;mso-wrap-style:square'>
896 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image001.png"
897  o:title=""/>
898</v:shape><![endif]--><![if !vml]><img border=0 width=302 height=190
899src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image002.png"
900v:shapes="_x0000_i1025"><![endif]></span></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:Cambria;
905mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
906Cambria;mso-bidi-theme-font:minor-latin'>Image Controls</span><o:p></o:p></b></p>
907
908<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
909 id="Picture_x0020_10" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:473pt;
910 height:342pt;visibility:visible;mso-wrap-style:square'>
911 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image003.png"
912  o:title=""/>
913</v:shape><![endif]--><![if !vml]><img border=0 width=475 height=344
914src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image004.png"
915v:shapes="Picture_x0020_10"><![endif]></span></p>
916
917<p class=MsoNormal><span style="mso-spacerun:yes"> </span>The plot window shows
918the image; notice the elliptical shape of the powder diffraction rings due to
919the 45 degree detector tilt. The blue <b style='mso-bidi-font-weight:normal'><span
920style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
921minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin;
922color:#4F81BD;mso-themecolor:accent1'>X</span></b> marks the beam location
923(which defaults to the image center); the calibration you will perform here
924will find the correct placement for it. Also note that as the mouse is moved
925across the plot the plot window status bar (at bottom of plot window) shows the
926cursor position, as computed from the default (incorrect) calibration values.
927These constants will be correctly determined after you finish the calibration.</p>
928
929<p class=MsoNormal><span style="mso-spacerun:yes"> </span><span
930style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_11"
931 o:spid="_x0000_i1027" type="#_x0000_t75" style='width:525pt;height:450pt;
932 visibility:visible;mso-wrap-style:square'>
933 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image005.png"
934  o:title=""/>
935</v:shape><![endif]--><![if !vml]><img border=0 width=527 height=452
936src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
937v:shapes="Picture_x0020_11"><![endif]></span></p>
938
939<h1><span style="mso-spacerun:yes"> </span>Step 2: Edit image parameters</h1>
940
941<p class=MsoNormal><span style="mso-spacerun:yes"> </span>Note that, alas, very
942few image formats contain all of the important metadata about the image, so it
943needs to be added manually. In this case set the <b style='mso-bidi-font-weight:
944normal'><span style='font-family:Cambria;mso-ascii-theme-font:minor-latin;
945mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:
946minor-latin'>wavelength</span></b> to <b style='mso-bidi-font-weight:normal'><span
947style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
948minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin'>0.10798</span></b>.
949It is also helpful to change the display of the image so that it is easier to
950see the diffraction rings. Lowering the maximum intensity to 10,000 to 20,000
951counts will help (note that this can be done by moving the slider, or by typing
952a value in the box and then clicking on another control or pressing the <b
953style='mso-bidi-font-weight:normal'><span style='font-family:Cambria;
954mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
955Cambria;mso-bidi-theme-font:minor-latin'>Enter</span></b> or <b
956style='mso-bidi-font-weight:normal'><span style='font-family:Cambria;
957mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
958Cambria;mso-bidi-theme-font:minor-latin'>Tab</span></b> key). You may also wish
959to select another color scheme using the <b style='mso-bidi-font-weight:normal'><span
960style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
961minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin'>Color
962bar</span></b> selector. </p>
963
964<h1><span style="mso-spacerun:yes"> </span>Step 3: Calibrate</h1>
965
966<h3><span style="mso-spacerun:yes"> </span>First: </h3>
967
968<p class=MsoNormal><span style="mso-spacerun:yes">   </span>Set the material
969used as a sample in the box labeled <span class=SpellE><b style='mso-bidi-font-weight:
970normal'><span style='font-family:Cambria;mso-ascii-theme-font:minor-latin;
971mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:
972minor-latin'>Calibrant</span></b></span>; select <b style='mso-bidi-font-weight:
973normal'><span style='font-family:Cambria;mso-ascii-theme-font:minor-latin;
974mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:
975minor-latin'>LaB6 SRM660a</span></b></p>
976
977<h3><span style="mso-spacerun:yes"> </span>Second: </h3>
978
979<p class=MsoNormal><span style="mso-spacerun:yes">   </span>Use the <b
980style='mso-bidi-font-weight:normal'><span style='font-family:Cambria;
981mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
982Cambria;mso-bidi-theme-font:minor-latin'>Operations/Calibrate</span></b> menu
983item (note this menu is on the <b style='mso-bidi-font-weight:normal'><span
984style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
985minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin'>Image
986Controls</span></b> window or for the Mac, when the <span class=GramE><b
987style='mso-bidi-font-weight:normal'><span style='font-family:Cambria;
988mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
989Cambria;mso-bidi-theme-font:minor-latin'>Image<span style="mso-spacerun:yes"> 
990</span>Controls</span></b></span> window is made active this menu is added to the
991system menu bar). At this point the status line on the bottom of the <b
992style='mso-bidi-font-weight:normal'><span style='font-family:Cambria;
993mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
994Cambria;mso-bidi-theme-font:minor-latin'>Image Controls</span></b> window
995changes with a prompt to select points for calibration.</p>
996
997<h3>Third: </h3>
998
999<p class=MsoNormal><span style="mso-spacerun:yes">  </span>Use the left mouse
1000button to click on at least five locations on the innermost ring. As each point
1001is defined, a red &quot;<b style='mso-bidi-font-weight:normal'><span
1002style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1003minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin;
1004color:red'>+</span></b>&quot; is added to the plot. You need not hit the ring
1005exactly as the code will search for the locally highest point. (On the Mac with
1006a two or three button mouse, use the left mouse button, or with a standard Mac
1007mouse, use the regular mouse button.)</p>
1008
1009<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1010 id="Picture_x0020_8" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
1011 height:450pt;visibility:visible;mso-wrap-style:square'>
1012 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
1013  o:title=""/>
1014</v:shape><![endif]--><![if !vml]><img border=0 width=527 height=452
1015src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
1016v:shapes="Picture_x0020_8"><![endif]></span></p>
1017
1018<p class=MsoNormal><span style="mso-spacerun:yes">  </span>To remove a point
1019added in error click on that point with the right mouse button (on the Mac, if
1020you have a single-button mouse, hold the control key down and click with the
1021mouse). </p>
1022
1023<h3><span style="mso-spacerun:yes"> </span>Fourth:</h3>
1024
1025<p class=MsoNormal><span style="mso-spacerun:yes">  </span>When done, press the
1026right mouse button well away from any points that have been added (on the Mac,
1027if you have a single-button mouse, hold the control key down and click). </p>
1028
1029<p class=MsoNormal>The calibration is then performed. First the rings are
1030located and an ellipse is optimized for each ring. The indexed rings are first
1031shown in red as the calibration proceeds and center of each ellipse is noted
1032with a blue &quot;<b style='mso-bidi-font-weight:normal'><span
1033style='color:#4F81BD;mso-themecolor:accent1'>+</span></b>&quot;. When all rings
1034have been fitted, the entire ensemble of rings is refitted to the detector
1035parameters and the rings are then shown in blue. The beam position (blue “<span
1036style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1037minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin;
1038color:#4F81BD;mso-themecolor:accent1'>X</span>”) is now correctly positioned.</p>
1039
1040<p class=MsoNormal><span style="mso-spacerun:yes"> </span><span
1041style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_9"
1042 o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;height:450pt;
1043 visibility:visible;mso-wrap-style:square'>
1044 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image009.png"
1045  o:title=""/>
1046</v:shape><![endif]--><![if !vml]><img border=0 width=527 height=452
1047src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image010.png"
1048v:shapes="Picture_x0020_9"><![endif]></span><span
1049style="mso-spacerun:yes"> </span></p>
1050
1051<p class=MsoNormal>The derived calibration results are shown in the <b
1052style='mso-bidi-font-weight:normal'><span style='font-family:Cambria;
1053mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1054Cambria;mso-bidi-theme-font:minor-latin'>Image Controls</span></b> window.</p>
1055
1056<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1057 id="Picture_x0020_13" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:473pt;
1058 height:342pt;visibility:visible;mso-wrap-style:square'>
1059 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image011.png"
1060  o:title=""/>
1061</v:shape><![endif]--><![if !vml]><img border=0 width=475 height=344
1062src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image012.png"
1063v:shapes="Picture_x0020_13"><![endif]></span><span
1064style="mso-spacerun:yes"> </span></p>
1065
1066<p class=MsoNormal><span class=GramE>and</span> the console window shows
1067details of the fit.</p>
1068
1069<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1070 id="Picture_x0020_14" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:397pt;
1071 height:134pt;visibility:visible;mso-wrap-style:square'>
1072 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image013.png"
1073  o:title=""/>
1074</v:shape><![endif]--><![if !vml]><img border=0 width=399 height=136
1075src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image014.png"
1076v:shapes="Picture_x0020_14"><![endif]></span></p>
1077
1078<p class=MsoNormal><span style="mso-spacerun:yes"> </span>To see the actual points
1079selected by the program, click on the <b style='mso-bidi-font-weight:normal'><span
1080style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1081minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin'>show
1082ring picks?</span></b> <span class=GramE>check</span> box </p>
1083
1084<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1085 id="Picture_x0020_15" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
1086 height:450pt;visibility:visible;mso-wrap-style:square'>
1087 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image015.png"
1088  o:title=""/>
1089</v:shape><![endif]--><![if !vml]><img border=0 width=527 height=452
1090src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image016.png"
1091v:shapes="Picture_x0020_15"><![endif]></span><span
1092style="mso-spacerun:yes"> </span><span style='color:#1F497D;mso-themecolor:
1093text2'><o:p></o:p></span></p>
1094
1095<p class=MsoNormal>When this is done, it sometimes occurs that the points
1096selected for the outermost rings are scattered between that and the next ring.
1097This can be repaired by changing the pixel search range to 10 and using the <b
1098style='mso-bidi-font-weight:normal'><span style='font-family:Cambria;
1099mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1100Cambria;mso-bidi-theme-font:minor-latin'>Operations/Recalibrate</span></b> menu
1101item.</p>
1102
1103<p class=MsoNormal>Assuming that these calibration results will be applied to
1104other images in the same GSAS-II project, click on <b style='mso-bidi-font-weight:
1105normal'><span style='font-family:Cambria;mso-ascii-theme-font:minor-latin;
1106mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:
1107minor-latin'>Use as default for all images</span></b>. You may also save a copy
1108of the calibration values to a file <span style='font-family:Cambria;
1109mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1110Cambria;mso-bidi-theme-font:minor-latin'>(<span class=SpellE><i
1111style='mso-bidi-font-style:normal'>name</i><b style='mso-bidi-font-weight:normal'>.imctrl</b></span></span>)
1112with the <b style='mso-bidi-font-weight:normal'><span style='font-family:Cambria;
1113mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1114Cambria;mso-bidi-theme-font:minor-latin'>Operations/Save Controls</span></b>
1115menu item. To save the project, including the now-derived calibration
1116information, use the <b style='mso-bidi-font-weight:normal'><span
1117style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1118minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin'>File/Save</span>
1119</b><b style='mso-bidi-font-weight:normal'><span style='font-family:Cambria;
1120mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1121Cambria;mso-bidi-theme-font:minor-latin'>Project</span></b><span
1122style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1123minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin'> </span>menu
1124item associated with the data tree window; as this project has not been saved
1125before the file save dialog will need a file name. Don’t enter the extension;
1126it will be set to “<b style='mso-bidi-font-weight:normal'><span
1127style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1128minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin'>.<span
1129class=SpellE>gpx</span></span></b>”.</p>
1130
1131<h2>Next step: <span class=MsoHyperlink><span style='color:#0070C0'><a
1132href="Integration%2520of%2520area%2520detector%2520data%2520in%2520GSAS.htm"><u><span
1133style='color:black'>Integrate the Data</span></u></a></span></span></h2>
1134
1135</div>
1136
1137</body>
1138
1139</html>
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