source: trunk/help/Small Angle Image Processing.htm @ 1349

Last change on this file since 1349 was 1349, checked in by vondreele, 9 years ago

small fixes to SASD plotting & GUI & tutorials

File size: 102.0 KB
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838
839<h1><strong>Small Angle X-Ray Data – Image Processing<o:p></o:p></strong></h1>
840
841<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
842this tutorial you will reduce 2D SAXS data to create 1D absolute scaled data.
843The data were collected at APS on beam line 15ID on some polymer base materials
844to be used for liquid crystal displays. The processing has several steps
845including detector calibration (i.e. determine sample-detector distance &amp;
846tilt), integration and scaling to an absolute scaled glassy carbon measurement.
847The data were collected at a wavelength of 1.0332Å with a <span class=SpellE>MarCCD</span>
848detector placed ~570mm from the sample. Note that menu entries are listed in
849bold face below as <b style='mso-bidi-font-weight:normal'><span
850style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
851mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
852minor-latin'>Help/About GSAS-II</span></b>, which lists first the name of the
853menu (here <b style='mso-bidi-font-weight:normal'><span style='font-family:
854"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
855minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Help</span></b>)
856and second the name of the entry in the menu (here <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'>About GSAS-II</span></b>).<span
860style='mso-spacerun:yes'>  </span><span style='mso-fareast-font-family:Calibri;
861mso-fareast-theme-font:minor-latin;mso-bidi-font-weight:bold;mso-bidi-font-style:
862italic'><o:p></o:p></span></p>
863
864<p class=MsoNormal>If you have not done so already, <a
865href="Starting%20GSAS.htm">start GSAS-II</a>.</p>
866
867<h2>Step 1: Detector calibration</h2>
868
869<p class=MsoNormal>The detector position is determined by using an image
870collected from silver <span class=SpellE>behenate</span>; do <b
871style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
872mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data/Read
873Image data…</span></b> and a file selection dialog box will appear</p>
874
875<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
876 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
877 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
878 <v:stroke joinstyle="miter"/>
879 <v:formulas>
880  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
881  <v:f eqn="sum @0 1 0"/>
882  <v:f eqn="sum 0 0 @1"/>
883  <v:f eqn="prod @2 1 2"/>
884  <v:f eqn="prod @3 21600 pixelWidth"/>
885  <v:f eqn="prod @3 21600 pixelHeight"/>
886  <v:f eqn="sum @0 0 1"/>
887  <v:f eqn="prod @6 1 2"/>
888  <v:f eqn="prod @7 21600 pixelWidth"/>
889  <v:f eqn="sum @8 21600 0"/>
890  <v:f eqn="prod @7 21600 pixelHeight"/>
891  <v:f eqn="sum @10 21600 0"/>
892 </v:formulas>
893 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
894 <o:lock v:ext="edit" aspectratio="t"/>
895</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1065" type="#_x0000_t75"
896 style='width:537pt;height:397.5pt;visibility:visible;mso-wrap-style:square'>
897 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image001.png"
898  o:title=""/>
899</v:shape><![endif]--><![if !vml]><img border=0 width=716 height=530
900src="Small%20Angle%20Image%20Processing_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
901
902<p class=MsoNormal><o:p>&nbsp;</o:p></p>
903
904<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
905style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
906mso-hansi-theme-font:minor-latin'>Exercises/Small angle/Image reduction</span></b>
907and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
908"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
909minor-latin'>AgBehenate_003.tif</span></b> with either a mouse button double
910click or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
911mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>;
912the image will appear</p>
913
914<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
915 id="Picture_x0020_16" o:spid="_x0000_i1064" type="#_x0000_t75" style='width:525pt;
916 height:450pt;visibility:visible;mso-wrap-style:square'>
917 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image002.png"
918  o:title=""/>
919</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
920src="Small%20Angle%20Image%20Processing_files/image002.png" v:shapes="Picture_x0020_16"><![endif]></span></p>
921
922<p class=MsoNormal><o:p>&nbsp;</o:p></p>
923
924<p class=MsoNormal>And the <b style='mso-bidi-font-weight:normal'><span
925style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
926mso-hansi-theme-font:minor-latin'>Image controls</span></b> window will show</p>
927
928<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
929 id="Picture_x0020_3" o:spid="_x0000_i1063" type="#_x0000_t75" style='width:472.5pt;
930 height:388.5pt;visibility:visible;mso-wrap-style:square'>
931 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image003.png"
932  o:title=""/>
933</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
934src="Small%20Angle%20Image%20Processing_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
935
936<p class=MsoNormal><o:p>&nbsp;</o:p></p>
937
938<p class=MsoNormal>Note the default <b style='mso-bidi-font-weight:normal'><span
939style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
940mso-hansi-theme-font:minor-latin'>Type of image data</span></b> is <b
941style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
942mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR -
943powder diffraction data</span></b>; you will change that <span
944style='mso-no-proof:yes'>now.</span> Select <b style='mso-bidi-font-weight:
945normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
946minor-latin;mso-hansi-theme-font:minor-latin'>SASD – small angle scattering
947data</span></b> (the window will change). Enter the <b style='mso-bidi-font-weight:
948normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
949minor-latin;mso-hansi-theme-font:minor-latin'>wavelength</span></b> (<b
950style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
951mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.0332</span></b>),
952and select the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
953style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
954mso-hansi-theme-font:minor-latin'>Calibrant</span></b></span> (near bottom of
955window) as <b style='mso-bidi-font-weight:normal'><span style='font-family:
956"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
957minor-latin'>Ag <span class=SpellE>behenate</span></span></b>. Note that the
958calibration info for Ag <span class=SpellE>behenate</span> was read from a
959python file – <b style='mso-bidi-font-weight:normal'><span style='font-family:
960"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
961minor-latin'>GSASII/ImageCalibrants.py</span></b>. If you have a <span
962class=SpellE>calibrant</span> that isn’t in this file you should enter it in
963the file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
964mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UserCalibrants.py</span></b>;
965just follow the format of the examples within <b style='mso-bidi-font-weight:
966normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
967minor-latin;mso-hansi-theme-font:minor-latin'>ImageCalibrants.py</span></b>.
968You should move the <b style='mso-bidi-font-weight:normal'><span
969style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
970mso-hansi-theme-font:minor-latin'>Max intensity</span></b> slider to near the middle
971of the range – that will improve the image. When done the <b style='mso-bidi-font-weight:
972normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
973minor-latin;mso-hansi-theme-font:minor-latin'>Image controls</span></b> window
974should look like</p>
975
976<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
977 id="Picture_x0020_4" o:spid="_x0000_i1062" type="#_x0000_t75" style='width:472.5pt;
978 height:388.5pt;visibility:visible;mso-wrap-style:square'>
979 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image004.png"
980  o:title=""/>
981</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
982src="Small%20Angle%20Image%20Processing_files/image004.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
983
984<p class=MsoNormal><o:p>&nbsp;</o:p></p>
985
986<p class=MsoNormal>And the image will be</p>
987
988<p class=MsoNormal><!--[if gte vml 1]><v:shapetype id="_x0000_t32" coordsize="21600,21600"
989 o:spt="32" o:oned="t" path="m,l21600,21600e" filled="f">
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992</v:shapetype><v:shape id="Straight_x0020_Arrow_x0020_Connector_x0020_21"
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994 margin-left:177pt;margin-top:214.5pt;width:48pt;height:15.75pt;flip:y;
995 z-index:251659264;visibility:visible;mso-wrap-style:square;
996 mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:9pt;
997 mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
998 mso-wrap-distance-bottom:0;mso-position-horizontal:absolute;
999 mso-position-horizontal-relative:text;mso-position-vertical:absolute;
1000 mso-position-vertical-relative:text;mso-width-percent:0;mso-height-percent:0;
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1030" strokecolor="#c0504d [3205]" strokeweight="3pt">
1031 <v:stroke endarrow="open"/>
1032 <v:shadow on="t" color="black" opacity="22937f" origin=",.5" offset="0,.63889mm"/>
1033 <o:lock v:ext="edit" shapetype="f"/>
1034</v:shape><![endif]--><![if !vml]><span style='mso-ignore:vglayout;position:
1035absolute;z-index:251659264;margin-left:234px;margin-top:274px;width:73px;
1036height:38px'><img width=73 height=38
1037src="Small%20Angle%20Image%20Processing_files/image012.png" v:shapes="Straight_x0020_Arrow_x0020_Connector_x0020_21"></span><![endif]><span
1038style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5"
1039 o:spid="_x0000_i1061" type="#_x0000_t75" style='width:525pt;height:450pt;
1040 visibility:visible;mso-wrap-style:square'>
1041 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image006.png"
1042  o:title=""/>
1043</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1044src="Small%20Angle%20Image%20Processing_files/image006.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
1045
1046<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1047
1048<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
1049style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1050mso-hansi-theme-font:minor-latin'>Operations/Calibrate</span></b> from the <b
1051style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1052mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1053Controls</span></b> menu; a bit of instruction will appear on the status line
1054of this window. Select 5 points on the innermost ring (arrowed above); a small
1055red cross will appear at each selection point. Press the right mouse button to
1056finish; calibration will proceed. A sequence of concentric red rings will
1057appear; they will switch to blue when calibration is finished. Select <b
1058style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1059mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show ring
1060picks</span></b> (near bottom right of <b style='mso-bidi-font-weight:normal'><span
1061style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1062mso-hansi-theme-font:minor-latin'>Image Controls</span></b> window). The <b
1063style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1064mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b>
1065window will show the results of the calibration</p>
1066
1067<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1068 id="Picture_x0020_6" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:472.5pt;
1069 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1070 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image007.png"
1071  o:title=""/>
1072</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
1073src="Small%20Angle%20Image%20Processing_files/image007.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
1074
1075<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1076
1077<p class=MsoNormal>And the plot will show the points (very sparse!) used in the
1078calibration calculations.</p>
1079
1080<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1081 id="Picture_x0020_23" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:525pt;
1082 height:450pt;visibility:visible;mso-wrap-style:square'>
1083 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image008.png"
1084  o:title=""/>
1085</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1086src="Small%20Angle%20Image%20Processing_files/image008.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
1087
1088<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1089
1090<p class=MsoNormal>You would like to use more points from just the visible
1091rings. I suggest you change <b style='mso-bidi-font-weight:normal'><span
1092style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1093mso-hansi-theme-font:minor-latin'>Min ring I/<span class=SpellE><span
1094class=GramE>Ib</span></span></span></b> to <b style='mso-bidi-font-weight:normal'><span
1095style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1096mso-hansi-theme-font:minor-latin'>0.5</span></b> and <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'>Min <span class=SpellE>calib</span>
1099d-spacing</span></b> to <b style='mso-bidi-font-weight:normal'><span
1100style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1101mso-hansi-theme-font:minor-latin'>10.0</span></b>. Do <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'>Operations/Recalibrate</span></b>;
1104more points will be used and they will be limited to the 5 visible rings in the
1105pattern.</p>
1106
1107<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1108 id="Picture_x0020_8" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:525pt;
1109 height:450pt;visibility:visible;mso-wrap-style:square'>
1110 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image009.png"
1111  o:title=""/>
1112</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1113src="Small%20Angle%20Image%20Processing_files/image009.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
1114
1115<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1116
1117<p class=MsoNormal>And give the calibration result as</p>
1118
1119<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1120 id="Picture_x0020_25" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:472.5pt;
1121 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1122 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image010.png"
1123  o:title=""/>
1124</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
1125src="Small%20Angle%20Image%20Processing_files/image010.png" v:shapes="Picture_x0020_25"><![endif]></span></p>
1126
1127<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1128
1129<p class=MsoNormal>You will need this calibration information to process the
1130other images in this tutorial. To save it for future use do <b
1131style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1132mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Save
1133controls</span></b>; a file dialog will appear</p>
1134
1135<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1136 id="Picture_x0020_26" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:537pt;
1137 height:397.5pt;visibility:visible;mso-wrap-style:square'>
1138 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image011.png"
1139  o:title=""/>
1140</v:shape><![endif]--><![if !vml]><img border=0 width=716 height=530
1141src="Small%20Angle%20Image%20Processing_files/image011.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
1142
1143<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1144
1145<p class=MsoNormal>Makeup a file name (no extension needed) for this; I chose <b
1146style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1147mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>SASD</span></b>.
1148Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1149mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Save</span></b>
1150and the file <span class=SpellE><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'>SASD.imctrl</span></b></span> will be written
1153to the local directory.</p>
1154
1155<p class=MsoNormal>If you are continuing on to the next step do <b
1156style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1157mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>File/New
1158Project</span></b> (don’t bother saving the project file unless you want it; we
1159will not need it here); otherwise you can exit GSAS-II.</p>
1160
1161<h2>Step 2: Data image integration</h2>
1162
1163<p class=MsoNormal>The objective here is to read in the four polymer sample
1164images, a glassy carbon image, an empty container image and a dark image. The
1165images will be integrated after creating masks to remove the beam stop and
1166other objectionable parts of the images. If you have not done so already, <a
1167href="Starting%20GSAS.htm">start GSAS-II</a>. </p>
1168
1169<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1170
1171<p class=MsoNormal>First do <b style='mso-bidi-font-weight:normal'><span
1172style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1173mso-hansi-theme-font:minor-latin'>Data/Read image data…</span></b>, go to <b
1174style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1175mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Exercises/Small
1176angle/Image reduction</span></b> and select all images except <b
1177style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1178mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>AgBehenate_003.tif</span></b>;
1179then press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1180"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1181minor-latin'>Open</span></b> to read all of them. The GSAS-II data tree window
1182will show entries for 7 images and will expand the last one</p>
1183
1184<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1185 id="Picture_x0020_11" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:300pt;
1186 height:308.25pt;visibility:visible;mso-wrap-style:square'>
1187 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image013.png"
1188  o:title=""/>
1189</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=411
1190src="Small%20Angle%20Image%20Processing_files/image013.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
1191
1192<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1193
1194<p class=MsoNormal>Notice that the Dark, Empty and GC (glassy carbon) are all
11955s images and the Sa1-4 ones are 40s images; this time information is needed
1196later to obtain correct scaling. First select the <b style='mso-bidi-font-weight:
1197normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1198minor-latin;mso-hansi-theme-font:minor-latin'>IMG GC_5s_200.tif</span></b>
1199entry from the tree and expand it (press the <b style='mso-bidi-font-weight:
1200normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1201minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b> box); then select <b
1202style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1203mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1204controls</span></b>. The data window (<b style='mso-bidi-font-weight:normal'><span
1205style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1206mso-hansi-theme-font:minor-latin'>Image Controls</span></b>) will show the
1207default settings.</p>
1208
1209<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1210 id="Picture_x0020_12" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:472.5pt;
1211 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1212 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image014.png"
1213  o:title=""/>
1214</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
1215src="Small%20Angle%20Image%20Processing_files/image014.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
1216
1217<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1218
1219<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
1220style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1221mso-hansi-theme-font:minor-latin'>Operations/Load controls</span></b> from the
1222menu; a file selection dialog will appear showing the available *.<span
1223class=SpellE>imctrl</span> files (the one you made in Step 1 should be seen).</p>
1224
1225<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1226 id="Picture_x0020_13" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:537pt;
1227 height:397.5pt;visibility:visible;mso-wrap-style:square'>
1228 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image015.png"
1229  o:title=""/>
1230</v:shape><![endif]--><![if !vml]><img border=0 width=716 height=530
1231src="Small%20Angle%20Image%20Processing_files/image015.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1232
1233<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1234
1235<p class=MsoNormal>Select it and press <b style='mso-bidi-font-weight:normal'><span
1236style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1237mso-hansi-theme-font:minor-latin'>Open</span></b>; the <b style='mso-bidi-font-weight:
1238normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1239minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> window
1240will be redrawn with the settings obtained in <b style='mso-bidi-font-weight:
1241normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1242minor-latin;mso-hansi-theme-font:minor-latin'>Step 1: Detector calibration</span></b></p>
1243
1244<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1245 id="Picture_x0020_14" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:472.5pt;
1246 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1247 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image016.png"
1248  o:title=""/>
1249</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
1250src="Small%20Angle%20Image%20Processing_files/image016.png" v:shapes="Picture_x0020_14"><![endif]></span></p>
1251
1252<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1253
1254<p class=MsoNormal><span class=GramE>and</span> the image will be that of
1255glassy carbon. Changing the <b style='mso-bidi-font-weight:normal'><span
1256style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1257mso-hansi-theme-font:minor-latin'>Max intensity</span></b> slider on the <b
1258style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1259mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1260Controls</span></b> window will show that the image from the <span
1261class=SpellE>MarCCD</span> is circular and slightly offset from the beam
1262center. A beam stop shadow is evident as well as an arc-like fault in the image
1263(toward the upper left corner of the image). We will sort those out later.</p>
1264
1265<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1266 id="Picture_x0020_15" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:525pt;
1267 height:450pt;visibility:visible;mso-wrap-style:square'>
1268 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image017.png"
1269  o:title=""/>
1270</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1271src="Small%20Angle%20Image%20Processing_files/image017.png" v:shapes="Picture_x0020_15"><![endif]></span></p>
1272
1273<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1274
1275<p class=MsoNormal>The next step we will be doing is to set up the integration
1276controls. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
1277"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1278minor-latin'>Dark image</span></b> is <b style='mso-bidi-font-weight:normal'><span
1279style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1280mso-hansi-theme-font:minor-latin'>IMG Dark_5s_003.tif</span></b>, the <b
1281style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1282mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background
1283image</span></b> is <b style='mso-bidi-font-weight:normal'><span
1284style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1285mso-hansi-theme-font:minor-latin'>IMG Empty_5s_014.tif</span></b>; select these
1286two. The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1287mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1288for each are <b style='mso-bidi-font-weight:normal'><span style='font-family:
1289"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1290minor-latin'>-1.0</span></b> because their exposures were the same as this
1291glassy carbon image (5s). Next check the boxes for <b style='mso-bidi-font-weight:
1292normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1293minor-latin;mso-hansi-theme-font:minor-latin'>Show integration limits?</span></b>
1294<span class=GramE>and</span> <b style='mso-bidi-font-weight:normal'><span
1295style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1296mso-hansi-theme-font:minor-latin'>Do full integration?</span></b> A pair of
1297circles with a connecting diagonal line will appear on the plot. Set the <b
1298style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1299mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Inner/Outer
13002-theta</span></b> values to <b style='mso-bidi-font-weight:normal'><span
1301style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1302mso-hansi-theme-font:minor-latin'>0.5</span></b> and <b style='mso-bidi-font-weight:
1303normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1304minor-latin;mso-hansi-theme-font:minor-latin'>9.0</span></b>, respectively, and
1305set the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1306mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Start
1307azimuth</span></b> to <b style='mso-bidi-font-weight:normal'><span
1308style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1309mso-hansi-theme-font:minor-latin'>0</span></b>. Set the <b style='mso-bidi-font-weight:
1310normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1311minor-latin;mso-hansi-theme-font:minor-latin'>No. 2-theta bins</span></b> to <b
1312style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1313mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>250</span></b>,
1314which is more appropriate for small angle scattering, and set the <b
1315style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1316mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bin style:
1317Constant step bins in</span></b> to <span class=GramE><b style='mso-bidi-font-weight:
1318normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1319minor-latin;mso-hansi-theme-font:minor-latin'>log(</span></b></span><b
1320style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1321mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>q)</span></b>.
1322You should also check the <b style='mso-bidi-font-weight:normal'><span
1323style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1324mso-hansi-theme-font:minor-latin'>Apply sample transmission?</span></b> <span
1325class=GramE>and</span> <b style='mso-bidi-font-weight:normal'><span
1326style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1327mso-hansi-theme-font:minor-latin'>Apply polarization?</span></b> <span
1328class=GramE>boxes</span>; enter the measured <b style='mso-bidi-font-weight:
1329normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1330minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> (<b
1331style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1332mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.818</span></b>)
1333for the glassy carbon sample. When done the <b style='mso-bidi-font-weight:
1334normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1335minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> data
1336window should look like</p>
1337
1338<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1339 id="Picture_x0020_29" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:472.5pt;
1340 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1341 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image018.png"
1342  o:title=""/>
1343</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
1344src="Small%20Angle%20Image%20Processing_files/image018.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
1345
1346<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1347
1348<p class=MsoNormal>And the plot should look like</p>
1349
1350<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1351 id="Picture_x0020_28" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:525pt;
1352 height:450pt;visibility:visible;mso-wrap-style:square'>
1353 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image019.png"
1354  o:title=""/>
1355</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1356src="Small%20Angle%20Image%20Processing_files/image019.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1357
1358<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1359
1360<p class=MsoNormal>Now copy these controls to the other images. Do <b
1361style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1362mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Copy
1363controls</span></b> and select just the <b style='mso-bidi-font-weight:normal'><span
1364style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1365mso-hansi-theme-font:minor-latin'>Sa1-4</span></b> data names. </p>
1366
1367<p class=MsoNormal>We now need to go to the <b style='mso-bidi-font-weight:
1368normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1369minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> for
1370each of <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1371mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b>
1372to enter the correct transmission for each and change the Dark &amp; Background
1373<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1374mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1375to account for the different exposure times. Start with <b style='mso-bidi-font-weight:
1376normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1377minor-latin;mso-hansi-theme-font:minor-latin'>IMG Sa1_40s_067.tif</span></b>
1378and change <b style='mso-bidi-font-weight:normal'><span style='font-family:
1379"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1380minor-latin'>transmission</span></b> to <b style='mso-bidi-font-weight:normal'><span
1381style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1382mso-hansi-theme-font:minor-latin'>0.943</span></b> and the two <b
1383style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1384mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1385to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1386mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1387Then go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1388"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1389minor-latin'>IMG Sa2_40s_069.tif</span></b> and change <b style='mso-bidi-font-weight:
1390normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1391minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1392style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1393mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.979</span></b>;
1394<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1395mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1396to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1397mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1398Next go <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1399mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>to IMG
1400Sa3_40s_059.tif</span></b> and change <b style='mso-bidi-font-weight:normal'><span
1401style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1402mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1403style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1404mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.960</span></b>;
1405<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1406mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1407to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1408mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1409Finally, go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1410"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1411minor-latin'>IMG Sa4_40s_061.tif</span></b> and change <b style='mso-bidi-font-weight:
1412normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1413minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1414style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1415mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.968</span></b>;
1416<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1417mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1418to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1419mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1420The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1421mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1422Controls</span></b> data window for this should look like</p>
1423
1424<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1425 id="Picture_x0020_38" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:472.5pt;
1426 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1427 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image020.png"
1428  o:title=""/>
1429</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
1430src="Small%20Angle%20Image%20Processing_files/image020.png" v:shapes="Picture_x0020_38"><![endif]></span></p>
1431
1432<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1433
1434<p class=MsoNormal>This is a reasonable time to save the project; do <b
1435style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1436mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>File/Save
1437project as…</span></b> from the main GSAS-II data tree menu. Choose a file name
1438(I assumed <b style='mso-bidi-font-weight:normal'><span style='font-family:
1439"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1440minor-latin'>image</span></b>) and it will be written on the local file
1441directory. </p>
1442
1443<p class=MsoNormal>As noted earlier, the images contain some unwanted features;
1444so let’s create masks to remove them. Select <b style='mso-bidi-font-weight:
1445normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1446minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b> from the GSAS-II
1447data tree under <b style='mso-bidi-font-weight:normal'><span style='font-family:
1448"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1449minor-latin'>IMG GC_5s_200.tif</span></b>; the data window will show</p>
1450
1451<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1452 id="Picture_x0020_17" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:337.5pt;
1453 height:99.75pt;visibility:visible;mso-wrap-style:square'>
1454 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image021.png"
1455  o:title=""/>
1456</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=133
1457src="Small%20Angle%20Image%20Processing_files/image021.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1458
1459<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1460
1461<p class=MsoNormal>To mask out the regions beyond the circular <span
1462class=SpellE>MarCCD</span> image change the <span class=GramE><b
1463style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1464mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Lower<span
1465style='mso-spacerun:yes'>  </span><span class=SpellE>threshhold</span></span></b></span>
1466from <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1467mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0</span></b>
1468to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1469mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>;
1470the image will be redrawn with these regions in red</p>
1471
1472<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1473 id="Picture_x0020_30" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
1474 height:450pt;visibility:visible;mso-wrap-style:square'>
1475 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image022.png"
1476  o:title=""/>
1477</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1478src="Small%20Angle%20Image%20Processing_files/image022.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1479
1480<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1481
1482<p class=MsoNormal>These are now excluded. The status line for the <b
1483style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1484mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b>
1485data window gives the directions for adding additional masks. You can make arcs
1486(we’ll use that here), rings, spots (this too) and polygons (this as well) as
1487masks. These enclose areas to be excluded. The frame works in the opposite
1488sense in that everything outside the frame is excluded (NB: only one frame is
1489allowed). So let’s first mask the bad arc in the upper left – zoom in on that
1490part of the image</p>
1491
1492<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1493 id="Picture_x0020_19" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt;
1494 height:450pt;visibility:visible;mso-wrap-style:square'>
1495 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image023.png"
1496  o:title=""/>
1497</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1498src="Small%20Angle%20Image%20Processing_files/image023.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
1499
1500<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1501
1502<p class=MsoNormal>To add the mask 1: be sure the focus is on the image and the
1503zoom buttons are off, 2: type <span class=GramE><b style='mso-bidi-font-weight:
1504normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1505minor-latin;mso-hansi-theme-font:minor-latin'>a</span></b> to</span> activate
1506the arc mask entry 3: press the left mouse button (<b style='mso-bidi-font-weight:
1507normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1508minor-latin;mso-hansi-theme-font:minor-latin'>LB</span></b>) with the cursor
1509centered on the bad arc. The <b style='mso-bidi-font-weight:normal'><span
1510style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1511mso-hansi-theme-font:minor-latin'>Masks</span></b> window will show a new entry
1512</p>
1513
1514<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1515 id="Picture_x0020_20" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:337.5pt;
1516 height:135pt;visibility:visible;mso-wrap-style:square'>
1517 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image024.png"
1518  o:title=""/>
1519</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=180
1520src="Small%20Angle%20Image%20Processing_files/image024.png" v:shapes="Picture_x0020_20"><![endif]></span><span
1521style='mso-spacerun:yes'> </span></p>
1522
1523<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1524
1525<p class=MsoNormal><span class=GramE>and</span> an arc mask will be drawn on
1526the plot.</p>
1527
1528<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1529 id="Picture_x0020_22" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
1530 height:450pt;visibility:visible;mso-wrap-style:square'>
1531 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image025.png"
1532  o:title=""/>
1533</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1534src="Small%20Angle%20Image%20Processing_files/image025.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
1535
1536<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1537
1538<p class=MsoNormal>You can change the angular width of the arc by changing <b
1539style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1540mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>thickness</span></b>
1541in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1542mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b>
1543data window, you can change the angular range of the arc by dragging either end
1544of the arc, and you can move the arc<span style='mso-spacerun:yes'> 
1545</span>along a constant 2&#920; angle by dragging on any point inside the mask.
1546The curvature is centered on the beam center position and follows a constant
15472&#920; curve established by the detector calibration.<span style='mso-no-proof:
1548yes'> <!--[if gte vml 1]><v:shape id="Picture_x0020_34" o:spid="_x0000_i1042"
1549 type="#_x0000_t75" style='width:525pt;height:450pt;visibility:visible;
1550 mso-wrap-style:square'>
1551 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image026.png"
1552  o:title=""/>
1553</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1554src="Small%20Angle%20Image%20Processing_files/image026.png" v:shapes="Picture_x0020_34"><![endif]></span></p>
1555
1556<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1557
1558<p class=MsoNormal>Next let’s deal with the beam stop. I’m going to use both a
1559polygon and a spot to cover it. Move the zoom area to be around the center,
1560make sure the zoom buttons are off, enter ‘<b style='mso-bidi-font-weight:normal'><span
1561style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1562mso-hansi-theme-font:minor-latin'>s</span></b>’ on the plot and press mouse <b
1563style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1564mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>LB</span></b>
1565with the cursor positioned where you want the spot. A 1mm diameter red circle
1566will appear on the plot</p>
1567
1568<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1569 id="Picture_x0020_35" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;
1570 height:450pt;visibility:visible;mso-wrap-style:square'>
1571 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image027.png"
1572  o:title=""/>
1573</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1574src="Small%20Angle%20Image%20Processing_files/image027.png" v:shapes="Picture_x0020_35"><![endif]></span></p>
1575
1576<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1577
1578<p class=MsoNormal>And the <b style='mso-bidi-font-weight:normal'><span
1579style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1580mso-hansi-theme-font:minor-latin'>Masks</span></b> window will have new
1581information</p>
1582
1583<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1584 id="Picture_x0020_24" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:337.5pt;
1585 height:170.25pt;visibility:visible;mso-wrap-style:square'>
1586 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image028.png"
1587  o:title=""/>
1588</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=227
1589src="Small%20Angle%20Image%20Processing_files/image028.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
1590
1591<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1592
1593<p class=MsoNormal>You can change the diameter of the spot, I used <b
1594style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1595mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>7.0</span></b>;
1596the plot now shows a ring that just covers the beam stop. You may have to drag
1597it a bit (Hint: drag the center of the spot) to get it well centered.</p>
1598
1599<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1600 id="Picture_x0020_36" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
1601 height:450pt;visibility:visible;mso-wrap-style:square'>
1602 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image029.png"
1603  o:title=""/>
1604</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1605src="Small%20Angle%20Image%20Processing_files/image029.png" v:shapes="Picture_x0020_36"><![endif]></span></p>
1606
1607<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1608
1609<p class=MsoNormal>Next we need to mask the stick holding the beam stop; we’ll
1610use a 4 sided polygon for this. Adjust the zoom &amp; position so you can see
1611the entire beam stop stick. Make sure all zoom buttons are off, press ‘<b
1612style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1613mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>p</span></b>’
1614on the plot, then press the mouse <b style='mso-bidi-font-weight:normal'><span
1615style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1616mso-hansi-theme-font:minor-latin'>LB</span></b> at four points in succession
1617around the beam stop stick. A line segment for the polygon will be drawn
1618following your mouse clicks. Finally press the mouse <b style='mso-bidi-font-weight:
1619normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1620minor-latin;mso-hansi-theme-font:minor-latin'>RB</span></b> to close the
1621polygon. You should see something like</p>
1622
1623<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1624 id="Picture_x0020_37" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
1625 height:450pt;visibility:visible;mso-wrap-style:square'>
1626 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image030.png"
1627  o:title=""/>
1628</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1629src="Small%20Angle%20Image%20Processing_files/image030.png" v:shapes="Picture_x0020_37"><![endif]></span></p>
1630
1631<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1632
1633<p class=MsoNormal>You can adjust the position of the polygon vertices by
1634closely dragging it with mouse <b style='mso-bidi-font-weight:normal'><span
1635style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1636mso-hansi-theme-font:minor-latin'>LB</span></b> pressed; a new vertex can be
1637added by dragging an existing vertex with the mouse <b style='mso-bidi-font-weight:
1638normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1639minor-latin;mso-hansi-theme-font:minor-latin'>RB</span></b> pressed. If you
1640drag one vertex onto another, they are merged and cannot be separated.</p>
1641
1642<p class=MsoNormal>We want to use these masks for all the Sa1-4 images. <span
1643class=GramE>Do</span> <b style='mso-bidi-font-weight:normal'><span
1644style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1645mso-hansi-theme-font:minor-latin'>Operations/Copy mask</span></b>; a <b
1646style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1647mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Copy mask
1648information</span></b> dialog box will appear. Select the <b style='mso-bidi-font-weight:
1649normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1650minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-4</span></b> items and press <b
1651style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1652mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.
1653Here is a useful place to save your project; do <b style='mso-bidi-font-weight:
1654normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1655minor-latin;mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from
1656the main GSAS-II data tree menu.</p>
1657
1658<h2>Step 3: Integration of images</h2>
1659
1660<p class=MsoNormal>We are now ready to integrate the glassy carbon and the four
1661<span class=GramE>Sa</span> images. Select any <b style='mso-bidi-font-weight:
1662normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1663minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> and
1664then do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1665mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Integrate
1666all</span></b>. A selection dialog will appear; select only the GC and Sa1-Sa4
1667data sets and press Ok. The image integration will proceed; a progress bar
1668shows as each one is done. Five SASD data items will appear on the GSAS-II data
1669tree; the last one (<b style='mso-bidi-font-weight:normal'><span
1670style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1671mso-hansi-theme-font:minor-latin'>SASD Sa4_40s_061.tif <span class=SpellE>Azm</span>=45.00</span></b>)
1672will be expanded and plotted (you may have to select the <b style='mso-bidi-font-weight:
1673normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1674minor-latin;mso-hansi-theme-font:minor-latin'>Powder Patterns</span></b> tab to
1675see it).</p>
1676
1677<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1678 id="Picture_x0020_39" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
1679 height:450pt;visibility:visible;mso-wrap-style:square'>
1680 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image031.png"
1681  o:title=""/>
1682</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1683src="Small%20Angle%20Image%20Processing_files/image031.png" v:shapes="Picture_x0020_39"><![endif]></span></p>
1684
1685<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1686
1687<p class=MsoNormal>Pretty obviously the SASD pattern is down to background at
1688Q~0.25Å<sup>-1</sup>; the other Sa1-Sa4 patterns are similar. The glassy carbon
1689pattern extends nicely to the highest Q (~1.0Å<sup>-1</sup>) measured.</p>
1690
1691<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1692 id="Picture_x0020_40" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:525pt;
1693 height:450pt;visibility:visible;mso-wrap-style:square'>
1694 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image032.png"
1695  o:title=""/>
1696</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1697src="Small%20Angle%20Image%20Processing_files/image032.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
1698
1699<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1700
1701<h2>Step 4: Scaling of SASD patterns</h2>
1702
1703<p class=MsoNormal>To set this data on an absolute scale, we compare it to an
1704absolute scaled glassy carbon scan. One of these is in the same directory as
1705the image data; do <b style='mso-bidi-font-weight:normal'><span
1706style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1707mso-hansi-theme-font:minor-latin'>Import/Small Angle Data/ from <span
1708class=GramE>q(</span>A-1) step X-ray QIE data file</span></b> and select <b
1709style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1710mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>GC
1711calibrated data.txt</span></b> from the file selection dialog. You will need to
1712select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1713mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>any <span
1714class=GramE>file(</span>*.*)</span></b> to see it. A <b style='mso-bidi-font-weight:
1715normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1716minor-latin;mso-hansi-theme-font:minor-latin'>Is <span class=GramE>this the</span>
1717file you want</span></b> dialog will appear – respond <b style='mso-bidi-font-weight:
1718normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1719minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b> to read the file;
1720it will be plotted.</p>
1721
1722<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1723 id="Picture_x0020_41" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
1724 height:450pt;visibility:visible;mso-wrap-style:square'>
1725 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image033.png"
1726  o:title=""/>
1727</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1728src="Small%20Angle%20Image%20Processing_files/image033.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
1729
1730<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1731
1732<p class=MsoNormal>If you <span class=GramE>enter ‘<b style='mso-bidi-font-weight:
1733normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1734minor-latin;mso-hansi-theme-font:minor-latin'>s</span></b>’</span> on the plot
1735window, all of the SASD patterns will be plotted together (I’ve adjusted the
1736zoom to see them all).</p>
1737
1738<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1739 id="Picture_x0020_42" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
1740 height:450pt;visibility:visible;mso-wrap-style:square'>
1741 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image034.png"
1742  o:title=""/>
1743</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1744src="Small%20Angle%20Image%20Processing_files/image034.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
1745
1746<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1747
1748<p class=MsoNormal>Clearly the measured image data need to be scaled down to
1749have them on absolute scale. First is to discover the scaling between the two
1750glassy carbon patterns. Go to the measured one (<b style='mso-bidi-font-weight:
1751normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1752minor-latin;mso-hansi-theme-font:minor-latin'>SASD GC_5s_200.tif</span></b>)
1753and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1754"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1755minor-latin'>Sample Parameters</span></b>.</p>
1756
1757<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1758 id="Picture_x0020_43" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:291.75pt;
1759 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1760 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image035.png"
1761  o:title=""/>
1762</v:shape><![endif]--><![if !vml]><img border=0 width=389 height=518
1763src="Small%20Angle%20Image%20Processing_files/image035.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
1764
1765<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1766
1767<p class=MsoNormal>We will change <b style='mso-bidi-font-weight:normal'><span
1768style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1769mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> by
1770comparison with the absolute glassy carbon scan. Do <b style='mso-bidi-font-weight:
1771normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1772minor-latin;mso-hansi-theme-font:minor-latin'>Command/Set scale</span></b> from
1773the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1774mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1775Parameters</span></b> menu; a <b style='mso-bidi-font-weight:normal'><span
1776style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1777mso-hansi-theme-font:minor-latin'>Reference histogram</span></b> dialog will
1778appear.</p>
1779
1780<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1781 id="Picture_x0020_44" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:259.5pt;
1782 height:252pt;visibility:visible;mso-wrap-style:square'>
1783 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image036.png"
1784  o:title=""/>
1785</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
1786src="Small%20Angle%20Image%20Processing_files/image036.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
1787
1788<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1789
1790<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1791style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1792mso-hansi-theme-font:minor-latin'>SASD GC calibrated data.txt</span></b> (shown
1793in blue above) and press <b style='mso-bidi-font-weight:normal'><span
1794style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1795mso-hansi-theme-font:minor-latin'>Ok</span></b>; the <b style='mso-bidi-font-weight:
1796normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1797minor-latin;mso-hansi-theme-font:minor-latin'>GC_5s_200.tif</span></b> data will
1798be rescaled to the <b style='mso-bidi-font-weight:normal'><span
1799style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1800mso-hansi-theme-font:minor-latin'>GC calibrated data</span></b> and the <b
1801style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1802mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
1803scale factor</span></b> will be changed to the new scaling factor (<b
1804style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1805mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.0008536</span></b>).
1806The plot will be redrawn with the scaled data.</p>
1807
1808<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1809 id="Picture_x0020_45" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:525pt;
1810 height:450pt;visibility:visible;mso-wrap-style:square'>
1811 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image037.png"
1812  o:title=""/>
1813</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1814src="Small%20Angle%20Image%20Processing_files/image037.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
1815
1816<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1817
1818<p class=MsoNormal>The divergence at high Q is probably from a background
1819contribution to the standard that is not present in our measured one. Next we
1820have to apply this scale factor to the Sa1-Sa4 data sets. Do <b
1821style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1822mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Command/Copy
1823selected…</span></b> from the <b style='mso-bidi-font-weight:normal'><span
1824style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1825mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> menu; a <b
1826style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1827mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select sample
1828parameters</span></b> dialog will appear</p>
1829
1830<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1831 id="Picture_x0020_46" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:240pt;
1832 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1833 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image038.png"
1834  o:title=""/>
1835</v:shape><![endif]--><![if !vml]><img border=0 width=320 height=310
1836src="Small%20Angle%20Image%20Processing_files/image038.png" v:shapes="Picture_x0020_46"><![endif]></span></p>
1837
1838<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1839
1840<p class=MsoNormal>Select only <b style='mso-bidi-font-weight:normal'><span
1841style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1842mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> and press <b
1843style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1844mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>;
1845a <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1846mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Copy sample
1847parameters</span></b> dialog will appear</p>
1848
1849<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1850 id="Picture_x0020_47" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:240pt;
1851 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1852 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image039.png"
1853  o:title=""/>
1854</v:shape><![endif]--><![if !vml]><img border=0 width=320 height=310
1855src="Small%20Angle%20Image%20Processing_files/image039.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
1856
1857<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1858
1859<p class=MsoNormal>Select only the <b style='mso-bidi-font-weight:normal'><span
1860style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1861mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b> data sets and press <b
1862style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1863mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.
1864The copy will occur and the plot redrawn</p>
1865
1866<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1867 id="Picture_x0020_48" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
1868 height:450pt;visibility:visible;mso-wrap-style:square'>
1869 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image040.png"
1870  o:title=""/>
1871</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1872src="Small%20Angle%20Image%20Processing_files/image040.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
1873
1874<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1875
1876<p class=MsoNormal>I’ve changed the zoom to show all the data. We are not quite
1877done; the scales for the Sa1-Sa4 data sets have to be further reduced by a
1878factor of 8 to account for the longer exposure time. Select <b
1879style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1880mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>SASD
1881Sa1_40s_067.tif</span></b> from the GSAS-II data tree, expand it and choose <b
1882style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1883mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1884Parameters</span></b></p>
1885
1886<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1887 id="Picture_x0020_49" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:291.75pt;
1888 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1889 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image041.png"
1890  o:title=""/>
1891</v:shape><![endif]--><![if !vml]><img border=0 width=389 height=518
1892src="Small%20Angle%20Image%20Processing_files/image041.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
1893
1894<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1895
1896<p class=MsoNormal>The data items here can take simple mathematical expressions
1897so change <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1898mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
1899scale factor</span></b> to <b style='mso-bidi-font-weight:normal'><span
1900style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1901mso-hansi-theme-font:minor-latin'>0.0008536/8</span></b> and press <b
1902style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1903mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>.
1904The value will change to <b style='mso-bidi-font-weight:normal'><span
1905style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1906mso-hansi-theme-font:minor-latin'>0.0001067</span></b> and the plot redrawn.</p>
1907
1908<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1909 id="Picture_x0020_50" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
1910 height:450pt;visibility:visible;mso-wrap-style:square'>
1911 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image042.png"
1912  o:title=""/>
1913</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1914src="Small%20Angle%20Image%20Processing_files/image042.png" v:shapes="Picture_x0020_50"><![endif]></span></p>
1915
1916<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1917
1918<p class=MsoNormal>Next do <b style='mso-bidi-font-weight:normal'><span
1919style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1920mso-hansi-theme-font:minor-latin'>Command/Copy selected</span></b> as before to
1921copy this new scale factor to the other <span class=GramE>Sa</span> data sets.
1922The plot will again be redrawn</p>
1923
1924<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1925 id="Picture_x0020_51" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
1926 height:450pt;visibility:visible;mso-wrap-style:square'>
1927 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image043.png"
1928  o:title=""/>
1929</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1930src="Small%20Angle%20Image%20Processing_files/image043.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
1931
1932<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1933
1934<p class=MsoNormal>Everything is now on absolute scale and these polymer
1935samples are quite weak small angle <span class=SpellE>scatterers</span>. This
1936is a good point to do a <b style='mso-bidi-font-weight:normal'><span
1937style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1938mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from the main
1939GSAS-II data tree menu. You can try to fit unified &amp; <span class=SpellE>Porod</span>
1940models to them following the procedures demonstrated in the <strong><span
1941style='font-weight:normal;mso-bidi-font-weight:bold'><a
1942href="Fitting%20Small%20Angle%20Scattering%20Data.htm"><span style='mso-bidi-font-weight:
1943normal'>Fitting Small Angle X-Ray Data</span></a> tutorial. I’d set the high Q
1944limit to about 0.25Å<sup>-1</sup> as above that is only noisy background.</span></strong></p>
1945
1946</div>
1947
1948</body>
1949
1950</html>
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