source: trunk/help/Small Angle Image Processing.htm @ 1346

Last change on this file since 1346 was 1346, checked in by vondreele, 9 years ago

new Small Angle Image Processing tutorial

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835
836<h1><strong>Small Angle X-Ray Data – Image Processing<o:p></o:p></strong></h1>
837
838<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
839this tutorial you will reduce 2D SAXS data to create 1D absolute scaled data.
840The data were collected at APS on beam line 15ID on some polymer base materials
841to be used for liquid crystal displays. The processing has several steps including
842detector calibration (i.e. determine sample-detector distance &amp; tilt),
843integration and scaling to an absolute scaled glassy carbon measurement. The
844data were collected at a wavelength of 1.0332Å with a <span class=SpellE>MarCCD</span>
845detector placed ~570mm from the sample. Note that menu entries are listed in
846bold face below as <b style='mso-bidi-font-weight:normal'><span
847style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
848mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
849minor-latin'>Help/About GSAS-II</span></b>, which lists first the name of the
850menu (here <b style='mso-bidi-font-weight:normal'><span style='font-family:
851"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
852minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Help</span></b>)
853and second the name of the entry in the menu (here <b style='mso-bidi-font-weight:
854normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
855minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
856mso-bidi-theme-font:minor-latin'>About GSAS-II</span></b>).<span
857style='mso-spacerun:yes'>  </span><span style='mso-fareast-font-family:Calibri;
858mso-fareast-theme-font:minor-latin;mso-bidi-font-weight:bold;mso-bidi-font-style:
859italic'><o:p></o:p></span></p>
860
861<p class=MsoNormal>If you have not done so already, <a
862href="Starting%20GSAS.htm">start GSAS-II</a>.</p>
863
864<h2>Step 1: Detector calibration</h2>
865
866<p class=MsoNormal>The detector position is determined by using an image
867collected from silver <span class=SpellE>behenate</span>; do <b
868style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
869mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data/Read
870Image data…</span></b> and a file selection dialog box will appear</p>
871
872<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
873 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
874 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
875 <v:stroke joinstyle="miter"/>
876 <v:formulas>
877  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
878  <v:f eqn="sum @0 1 0"/>
879  <v:f eqn="sum 0 0 @1"/>
880  <v:f eqn="prod @2 1 2"/>
881  <v:f eqn="prod @3 21600 pixelWidth"/>
882  <v:f eqn="prod @3 21600 pixelHeight"/>
883  <v:f eqn="sum @0 0 1"/>
884  <v:f eqn="prod @6 1 2"/>
885  <v:f eqn="prod @7 21600 pixelWidth"/>
886  <v:f eqn="sum @8 21600 0"/>
887  <v:f eqn="prod @7 21600 pixelHeight"/>
888  <v:f eqn="sum @10 21600 0"/>
889 </v:formulas>
890 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
891 <o:lock v:ext="edit" aspectratio="t"/>
892</v:shapetype><v:shape id="_x0000_i1065" type="#_x0000_t75" style='width:537pt;
893 height:397.5pt;visibility:visible;mso-wrap-style:square'>
894 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image001.png"
895  o:title=""/>
896</v:shape><![endif]--><![if !vml]><img border=0 width=716 height=530
897src="Small%20Angle%20Image%20Processing_files/image001.png" v:shapes="_x0000_i1065"><![endif]></span></p>
898
899<p class=MsoNormal><o:p>&nbsp;</o:p></p>
900
901<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
902style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
903mso-hansi-theme-font:minor-latin'>Exercises/Small angle/Image reduction</span></b>
904and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
905"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
906minor-latin'>AgBehenate_003.tif</span></b> with either a mouse button double click
907or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
908mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>;
909the image will appear</p>
910
911<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
912 id="Picture_x0020_16" o:spid="_x0000_i1064" type="#_x0000_t75" style='width:525pt;
913 height:450pt;visibility:visible;mso-wrap-style:square'>
914 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image002.png"
915  o:title=""/>
916</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
917src="Small%20Angle%20Image%20Processing_files/image002.png" v:shapes="Picture_x0020_16"><![endif]></span></p>
918
919<p class=MsoNormal><o:p>&nbsp;</o:p></p>
920
921<p class=MsoNormal>And the <b style='mso-bidi-font-weight:normal'><span
922style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
923mso-hansi-theme-font:minor-latin'>Image controls</span></b> window will show</p>
924
925<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
926 id="_x0000_i1063" type="#_x0000_t75" style='width:472.5pt;height:388.5pt;
927 visibility:visible;mso-wrap-style:square'>
928 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image003.png"
929  o:title=""/>
930</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
931src="Small%20Angle%20Image%20Processing_files/image003.png" v:shapes="_x0000_i1063"><![endif]></span></p>
932
933<p class=MsoNormal><o:p>&nbsp;</o:p></p>
934
935<p class=MsoNormal>Note the default <b style='mso-bidi-font-weight:normal'><span
936style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
937mso-hansi-theme-font:minor-latin'>Type of image data</span></b> is <b
938style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
939mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR -
940powder diffraction data</span></b>; you will change that <span
941style='mso-no-proof:yes'>now.</span> Select <b style='mso-bidi-font-weight:
942normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
943minor-latin;mso-hansi-theme-font:minor-latin'>SASD – small angle scattering
944data</span></b> (the window will change). Enter the <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'>wavelength</span></b> (<b
947style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
948mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.0332</span></b>),
949and select the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
950style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
951mso-hansi-theme-font:minor-latin'>Calibrant</span></b></span> (near bottom of
952window) as <b style='mso-bidi-font-weight:normal'><span style='font-family:
953"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
954minor-latin'>Ag <span class=SpellE>behenate</span></span></b>. Note that the
955calibration info for Ag <span class=SpellE>behenate</span> was read from a
956python file – <b style='mso-bidi-font-weight:normal'><span style='font-family:
957"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
958minor-latin'>GSASII/ImageCalibrants.py</span></b>. If you have a <span
959class=SpellE>calibrant</span> that isn’t in this file you should enter it in
960the file <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'>UserCalibrants.py</span></b>;
962just follow the format of the examples within <b style='mso-bidi-font-weight:
963normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
964minor-latin;mso-hansi-theme-font:minor-latin'>ImageCalibrants.py</span></b>.
965You should move the <b style='mso-bidi-font-weight:normal'><span
966style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
967mso-hansi-theme-font:minor-latin'>Max intensity</span></b> slider to near the
968middle of the range – that will improve the image. When done the <b
969style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
970mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
971controls</span></b> window should look like</p>
972
973<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
974 id="_x0000_i1062" type="#_x0000_t75" style='width:472.5pt;height:388.5pt;
975 visibility:visible;mso-wrap-style:square'>
976 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image004.png"
977  o:title=""/>
978</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
979src="Small%20Angle%20Image%20Processing_files/image004.png" v:shapes="_x0000_i1062"><![endif]></span></p>
980
981<p class=MsoNormal><o:p>&nbsp;</o:p></p>
982
983<p class=MsoNormal>And the image will be</p>
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986 o:spt="32" o:oned="t" path="m,l21600,21600e" filled="f">
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992 z-index:251659264;visibility:visible;mso-wrap-style:square;
993 mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:9pt;
994 mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
995 mso-wrap-distance-bottom:0;mso-position-horizontal:absolute;
996 mso-position-horizontal-relative:text;mso-position-vertical:absolute;
997 mso-position-vertical-relative:text;mso-width-percent:0;mso-height-percent:0;
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1027" strokecolor="#c0504d [3205]" strokeweight="3pt">
1028 <v:stroke endarrow="open"/>
1029 <v:shadow on="t" color="black" opacity="22937f" origin=",.5" offset="0,.63889mm"/>
1030 <o:lock v:ext="edit" shapetype="f"/>
1031</v:shape><![endif]--><![if !vml]><span style='mso-ignore:vglayout;position:
1032absolute;z-index:251659264;margin-left:234px;margin-top:274px;width:73px;
1033height:38px'><img width=73 height=38
1034src="Small%20Angle%20Image%20Processing_files/image005.png" v:shapes="Straight_x0020_Arrow_x0020_Connector_x0020_21"></span><![endif]><span
1035style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1061" type="#_x0000_t75"
1036 style='width:525pt;height:450pt;visibility:visible;mso-wrap-style:square'>
1037 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image006.png"
1038  o:title=""/>
1039</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1040src="Small%20Angle%20Image%20Processing_files/image006.png" v:shapes="_x0000_i1061"><![endif]></span></p>
1041
1042<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1043
1044<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
1045style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1046mso-hansi-theme-font:minor-latin'>Operations/Calibrate</span></b> from the <b
1047style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1048mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1049Controls</span></b> menu; a bit of instruction will appear on the status line
1050of this window. Select 5 points on the innermost ring (arrowed above); a small
1051red cross will appear at each selection point. Press the right mouse button to
1052finish; calibration will proceed. A sequence of concentric red rings will
1053appear; they will switch to blue when calibration is finished. Select <b
1054style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1055mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show ring
1056picks</span></b> (near bottom right of <b style='mso-bidi-font-weight:normal'><span
1057style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1058mso-hansi-theme-font:minor-latin'>Image Controls</span></b> window). The <b
1059style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1060mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1061Controls</span></b> window will show the results of the calibration</p>
1062
1063<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1064 id="_x0000_i1060" type="#_x0000_t75" style='width:472.5pt;height:388.5pt;
1065 visibility:visible;mso-wrap-style:square'>
1066 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image007.png"
1067  o:title=""/>
1068</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
1069src="Small%20Angle%20Image%20Processing_files/image007.png" v:shapes="_x0000_i1060"><![endif]></span></p>
1070
1071<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1072
1073<p class=MsoNormal>And the plot will show the points (very sparse!) used in the
1074calibration calculations.</p>
1075
1076<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1077 id="Picture_x0020_23" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:525pt;
1078 height:450pt;visibility:visible;mso-wrap-style:square'>
1079 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image008.png"
1080  o:title=""/>
1081</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1082src="Small%20Angle%20Image%20Processing_files/image008.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
1083
1084<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1085
1086<p class=MsoNormal>You would like to use more points from just the visible rings.
1087I suggest you change <b style='mso-bidi-font-weight:normal'><span
1088style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1089mso-hansi-theme-font:minor-latin'>Min ring I/<span class=SpellE><span
1090class=GramE>Ib</span></span></span></b> to <b style='mso-bidi-font-weight:normal'><span
1091style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1092mso-hansi-theme-font:minor-latin'>0.5</span></b> and <b style='mso-bidi-font-weight:
1093normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1094minor-latin;mso-hansi-theme-font:minor-latin'>Min <span class=SpellE>calib</span>
1095d-spacing</span></b> to <b style='mso-bidi-font-weight:normal'><span
1096style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1097mso-hansi-theme-font:minor-latin'>10.0</span></b>. Do <b style='mso-bidi-font-weight:
1098normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1099minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Recalibrate</span></b>;
1100more points will be used and they will be limited to the 5 visible rings in the
1101pattern.</p>
1102
1103<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1104 id="_x0000_i1058" type="#_x0000_t75" style='width:525pt;height:450pt;
1105 visibility:visible;mso-wrap-style:square'>
1106 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image009.png"
1107  o:title=""/>
1108</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1109src="Small%20Angle%20Image%20Processing_files/image009.png" v:shapes="_x0000_i1058"><![endif]></span></p>
1110
1111<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1112
1113<p class=MsoNormal>And give the calibration result as</p>
1114
1115<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1116 id="Picture_x0020_25" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:472.5pt;
1117 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1118 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image010.png"
1119  o:title=""/>
1120</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
1121src="Small%20Angle%20Image%20Processing_files/image010.png" v:shapes="Picture_x0020_25"><![endif]></span></p>
1122
1123<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1124
1125<p class=MsoNormal>You will need this calibration information to process the
1126other images in this tutorial. To save it for future use do <b
1127style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1128mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Save
1129controls</span></b>; a file dialog will appear</p>
1130
1131<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1132 id="Picture_x0020_26" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:537pt;
1133 height:397.5pt;visibility:visible;mso-wrap-style:square'>
1134 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image011.png"
1135  o:title=""/>
1136</v:shape><![endif]--><![if !vml]><img border=0 width=716 height=530
1137src="Small%20Angle%20Image%20Processing_files/image011.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
1138
1139<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1140
1141<p class=MsoNormal>Makeup a file name (no extension needed) for this; I chose <b
1142style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1143mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>SASD</span></b>.
1144Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1145mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Save</span></b>
1146and the file <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1147style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1148mso-hansi-theme-font:minor-latin'>SASD.imctrl</span></b></span> will be written
1149to the local directory.</p>
1150
1151<p class=MsoNormal>If you are continuing on to the next step do <b
1152style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1153mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>File/New
1154Project</span></b> (don’t bother saving the project file unless you want it; we
1155will not need it here); otherwise you can exit GSAS-II.</p>
1156
1157<h2>Step 2: Data image integration</h2>
1158
1159<p class=MsoNormal>The objective here is to read in the four polymer sample
1160images, a glassy carbon image, an empty container image and a dark image. The
1161images will be integrated after creating masks to remove the beam stop and
1162other objectionable parts of the images. If you have not done so already, <a
1163href="Starting%20GSAS.htm">start GSAS-II</a>. </p>
1164
1165<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1166
1167<p class=MsoNormal>First do <b style='mso-bidi-font-weight:normal'><span
1168style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1169mso-hansi-theme-font:minor-latin'>Data/Read image data…</span></b>, go to <b
1170style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1171mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Exercises/Small
1172angle/Image reduction</span></b> and select all images except <b
1173style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1174mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>AgBehenate_003.tif</span></b>;
1175then press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1176"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1177minor-latin'>Open</span></b> to read all of them. The GSAS-II data tree window
1178will show entries for 7 images and will expand the last one</p>
1179
1180<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1181 id="Picture_x0020_11" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:300pt;
1182 height:308.25pt;visibility:visible;mso-wrap-style:square'>
1183 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image013.png"
1184  o:title=""/>
1185</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=411
1186src="Small%20Angle%20Image%20Processing_files/image013.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
1187
1188<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1189
1190<p class=MsoNormal>Notice that the Dark, Empty and GC (glassy carbon) are all
11915s images and the Sa1-4 ones are 40s images; this time information is needed
1192later to obtain correct scaling. First select the <b style='mso-bidi-font-weight:
1193normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1194minor-latin;mso-hansi-theme-font:minor-latin'>IMG GC_5s_200.tif</span></b>
1195entry from the tree and expand it (press the <b style='mso-bidi-font-weight:
1196normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1197minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b> box); then select <b
1198style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1199mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1200controls</span></b>. The data window (<b style='mso-bidi-font-weight:normal'><span
1201style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1202mso-hansi-theme-font:minor-latin'>Image Controls</span></b>) will show the
1203default settings.</p>
1204
1205<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1206 id="Picture_x0020_12" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:472.5pt;
1207 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1208 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image014.png"
1209  o:title=""/>
1210</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
1211src="Small%20Angle%20Image%20Processing_files/image014.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
1212
1213<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1214
1215<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
1216style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1217mso-hansi-theme-font:minor-latin'>Operations/Load controls</span></b> from the
1218menu; a file selection dialog will appear showing the available *.<span
1219class=SpellE>imctrl</span> files (the one you made in Step 1 should be seen).</p>
1220
1221<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1222 id="Picture_x0020_13" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:537pt;
1223 height:397.5pt;visibility:visible;mso-wrap-style:square'>
1224 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image015.png"
1225  o:title=""/>
1226</v:shape><![endif]--><![if !vml]><img border=0 width=716 height=530
1227src="Small%20Angle%20Image%20Processing_files/image015.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1228
1229<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1230
1231<p class=MsoNormal>Select it and press <b style='mso-bidi-font-weight:normal'><span
1232style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1233mso-hansi-theme-font:minor-latin'>Open</span></b>; the <b style='mso-bidi-font-weight:
1234normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1235minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> window
1236will be redrawn with the settings obtained in <b style='mso-bidi-font-weight:
1237normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1238minor-latin;mso-hansi-theme-font:minor-latin'>Step 1: Detector calibration</span></b></p>
1239
1240<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1241 id="Picture_x0020_14" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:472.5pt;
1242 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1243 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image016.png"
1244  o:title=""/>
1245</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
1246src="Small%20Angle%20Image%20Processing_files/image016.png" v:shapes="Picture_x0020_14"><![endif]></span></p>
1247
1248<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1249
1250<p class=MsoNormal><span class=GramE>and</span> the image will be that of
1251glassy carbon. Changing the <b style='mso-bidi-font-weight:normal'><span
1252style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1253mso-hansi-theme-font:minor-latin'>Max intensity</span></b> slider on the <b
1254style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1255mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1256Controls</span></b> window will show that the image from the <span
1257class=SpellE>MarCCD</span> is circular and slightly offset from the beam
1258center. A beam stop shadow is evident as well as an arc-like fault in the image
1259(toward the upper left corner of the image). We will sort those out later.</p>
1260
1261<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1262 id="Picture_x0020_15" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:525pt;
1263 height:450pt;visibility:visible;mso-wrap-style:square'>
1264 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image017.png"
1265  o:title=""/>
1266</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1267src="Small%20Angle%20Image%20Processing_files/image017.png" v:shapes="Picture_x0020_15"><![endif]></span></p>
1268
1269<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1270
1271<p class=MsoNormal>The next step we will be doing is to set up the integration
1272controls. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
1273"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1274minor-latin'>Dark image</span></b> is <b style='mso-bidi-font-weight:normal'><span
1275style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1276mso-hansi-theme-font:minor-latin'>IMG Dark_5s_003.tif</span></b>, the <b
1277style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1278mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background
1279image</span></b> is <b style='mso-bidi-font-weight:normal'><span
1280style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1281mso-hansi-theme-font:minor-latin'>IMG Empty_5s_014.tif</span></b>; select these
1282two. The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1283mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1284for each are <b style='mso-bidi-font-weight:normal'><span style='font-family:
1285"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1286minor-latin'>-1.0</span></b> because their exposures were the same as this
1287glassy carbon image (5s). Next check the boxes for <b style='mso-bidi-font-weight:
1288normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1289minor-latin;mso-hansi-theme-font:minor-latin'>Show integration limits?</span></b>
1290<span class=GramE>and</span> <b style='mso-bidi-font-weight:normal'><span
1291style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1292mso-hansi-theme-font:minor-latin'>Do full integration?</span></b> A pair of
1293circles with a connecting diagonal line will appear on the plot. Set the <b
1294style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1295mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Inner/Outer
12962-theta</span></b> values to <b style='mso-bidi-font-weight:normal'><span
1297style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1298mso-hansi-theme-font:minor-latin'>0.5</span></b> and <b style='mso-bidi-font-weight:
1299normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1300minor-latin;mso-hansi-theme-font:minor-latin'>9.0</span></b>, respectively, and
1301set the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1302mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Start
1303azimuth</span></b> to <b style='mso-bidi-font-weight:normal'><span
1304style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1305mso-hansi-theme-font:minor-latin'>0</span></b>. Set the <b style='mso-bidi-font-weight:
1306normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1307minor-latin;mso-hansi-theme-font:minor-latin'>No. 2-theta bins</span></b> to <b
1308style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1309mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>250</span></b>,
1310which is more appropriate for small angle scattering, and set the <b
1311style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1312mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bin style:
1313Constant step bins in</span></b> to <span class=GramE><b style='mso-bidi-font-weight:
1314normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1315minor-latin;mso-hansi-theme-font:minor-latin'>log(</span></b></span><b
1316style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1317mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>q)</span></b>.
1318You should also check the <b style='mso-bidi-font-weight:normal'><span
1319style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1320mso-hansi-theme-font:minor-latin'>Apply sample transmission?</span></b> <span
1321class=GramE>and</span> <b style='mso-bidi-font-weight:normal'><span
1322style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1323mso-hansi-theme-font:minor-latin'>Apply polarization?</span></b> <span
1324class=GramE>boxes</span>; enter the measured <b style='mso-bidi-font-weight:
1325normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1326minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> (<b
1327style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1328mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.818</span></b>)
1329for the glassy carbon sample. When done the <b style='mso-bidi-font-weight:
1330normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1331minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> data
1332window should look like</p>
1333
1334<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1335 id="Picture_x0020_29" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:472.5pt;
1336 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1337 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image018.png"
1338  o:title=""/>
1339</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
1340src="Small%20Angle%20Image%20Processing_files/image018.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
1341
1342<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1343
1344<p class=MsoNormal>And the plot should look like</p>
1345
1346<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1347 id="Picture_x0020_28" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:525pt;
1348 height:450pt;visibility:visible;mso-wrap-style:square'>
1349 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image019.png"
1350  o:title=""/>
1351</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1352src="Small%20Angle%20Image%20Processing_files/image019.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1353
1354<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1355
1356<p class=MsoNormal>Now copy these controls to the other images. Do <b
1357style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1358mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Copy
1359controls</span></b> and select just the <b style='mso-bidi-font-weight:normal'><span
1360style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1361mso-hansi-theme-font:minor-latin'>Sa1-4</span></b> data names. </p>
1362
1363<p class=MsoNormal>We now need to go to the <b style='mso-bidi-font-weight:
1364normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1365minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> for
1366each of <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1367mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b>
1368to enter the correct transmission for each and change the Dark &amp; Background
1369<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1370mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1371to account for the different exposure times. Start with <b style='mso-bidi-font-weight:
1372normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1373minor-latin;mso-hansi-theme-font:minor-latin'>IMG Sa1_40s_067.tif</span></b>
1374and change <b style='mso-bidi-font-weight:normal'><span style='font-family:
1375"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1376minor-latin'>transmission</span></b> to <b style='mso-bidi-font-weight:normal'><span
1377style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1378mso-hansi-theme-font:minor-latin'>0.943</span></b> and the two <b
1379style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1380mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1381to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1382mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1383Then go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1384"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1385minor-latin'>IMG Sa2_40s_069.tif</span></b> and change <b style='mso-bidi-font-weight:
1386normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1387minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1388style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1389mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.979</span></b>;
1390<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1391mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1392to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1393mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1394Next go <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'>to IMG Sa3_40s_059.tif</span></b>
1396and change <b style='mso-bidi-font-weight:normal'><span style='font-family:
1397"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1398minor-latin'>transmission</span></b> to <b style='mso-bidi-font-weight:normal'><span
1399style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1400mso-hansi-theme-font:minor-latin'>0.960</span></b>; <b style='mso-bidi-font-weight:
1401normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1402minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</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'>-8.0</span></b>.
1405Finally, go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1406"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1407minor-latin'>IMG Sa4_40s_061.tif</span></b> and change <b style='mso-bidi-font-weight:
1408normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1409minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1410style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1411mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.968</span></b>;
1412<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1413mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1414to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1415mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1416The <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'>Image
1418Controls</span></b> data window for this should look like<o:p></o:p></p>
1419
1420<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1421 id="Picture_x0020_38" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:472.5pt;
1422 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1423 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image020.png"
1424  o:title=""/>
1425</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=518
1426src="Small%20Angle%20Image%20Processing_files/image020.png" v:shapes="Picture_x0020_38"><![endif]></span><o:p></o:p></p>
1427
1428<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1429
1430<p class=MsoNormal>This is a reasonable time to save the project; do <b
1431style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1432mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>File/Save
1433project as…</span></b> from the main GSAS-II data tree menu. Choose a file name
1434(I assumed <b style='mso-bidi-font-weight:normal'><span style='font-family:
1435"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1436minor-latin'>image</span></b>) and it will be written on the local file
1437directory. </p>
1438
1439<p class=MsoNormal>As noted earlier, this image contains some unwanted features;
1440so let’s create masks to remove them. Select <b style='mso-bidi-font-weight:
1441normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1442minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b> from the GSAS-II
1443data tree under <b style='mso-bidi-font-weight:normal'><span style='font-family:
1444"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1445minor-latin'>IMG GC_5s_200.tif</span></b>; the data window will show</p>
1446
1447<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1448 id="Picture_x0020_17" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:337.5pt;
1449 height:99.75pt;visibility:visible;mso-wrap-style:square'>
1450 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image021.png"
1451  o:title=""/>
1452</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=133
1453src="Small%20Angle%20Image%20Processing_files/image021.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1454
1455<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1456
1457<p class=MsoNormal>To mask out the regions beyond the circular <span
1458class=SpellE>MarCCD</span> image change the <span class=GramE><b
1459style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1460mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Lower<span
1461style='mso-spacerun:yes'>  </span><span class=SpellE>threshhold</span></span></b></span>
1462from <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1463mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0</span></b>
1464to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1465mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>;
1466the image will be redrawn with these regions in red</p>
1467
1468<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1469 id="Picture_x0020_30" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
1470 height:450pt;visibility:visible;mso-wrap-style:square'>
1471 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image022.png"
1472  o:title=""/>
1473</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1474src="Small%20Angle%20Image%20Processing_files/image022.png" v:shapes="Picture_x0020_30"><![endif]></span><o:p></o:p></p>
1475
1476<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1477
1478<p class=MsoNormal>These are now excluded. The status line for the <b
1479style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1480mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b>
1481data window gives the directions for adding additional masks. You can make arcs
1482(we’ll use that here), rings, spots (this too) and polygons (this as well) as
1483masks. These enclose areas to be excluded. The frame works in the opposite
1484sense in that everything outside the frame is excluded (NB: only one frame is
1485allowed). So let’s first mask the bad arc in the upper left – zoom in on that
1486part of the image</p>
1487
1488<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1489 id="Picture_x0020_19" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt;
1490 height:450pt;visibility:visible;mso-wrap-style:square'>
1491 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image023.png"
1492  o:title=""/>
1493</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1494src="Small%20Angle%20Image%20Processing_files/image023.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
1495
1496<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1497
1498<p class=MsoNormal>To add the mask 1: be sure the focus is on the image and the
1499zoom buttons are off, 2: type <span class=GramE><b style='mso-bidi-font-weight:
1500normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1501minor-latin;mso-hansi-theme-font:minor-latin'>a</span></b> to</span> activate
1502the arc mask entry 3: press the left mouse button (<b style='mso-bidi-font-weight:
1503normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1504minor-latin;mso-hansi-theme-font:minor-latin'>LB</span></b>) with the cursor
1505centered on the bad arc. The <b style='mso-bidi-font-weight:normal'><span
1506style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1507mso-hansi-theme-font:minor-latin'>Masks</span></b> window will show a new entry
1508</p>
1509
1510<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1511 id="Picture_x0020_20" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:337.5pt;
1512 height:135pt;visibility:visible;mso-wrap-style:square'>
1513 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image024.png"
1514  o:title=""/>
1515</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=180
1516src="Small%20Angle%20Image%20Processing_files/image024.png" v:shapes="Picture_x0020_20"><![endif]></span><span
1517style='mso-spacerun:yes'> </span></p>
1518
1519<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1520
1521<p class=MsoNormal><span class=GramE>and</span> an arc mask will be drawn on
1522the plot.</p>
1523
1524<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1525 id="Picture_x0020_22" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
1526 height:450pt;visibility:visible;mso-wrap-style:square'>
1527 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image025.png"
1528  o:title=""/>
1529</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1530src="Small%20Angle%20Image%20Processing_files/image025.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
1531
1532<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1533
1534<p class=MsoNormal>You can change the angular width of the arc by changing <b
1535style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1536mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>thickness</span></b>
1537in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1538mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b>
1539data window, you can change the angular range of the arc by dragging either end
1540of the arc, and you can move the arc <span
1541style='mso-spacerun:yes'> </span>along a constant 2&#920; angle by dragging on any
1542point inside the mask. The curvature is centered on the beam center position and
1543follows a constant 2&#920; curve established by the detector calibration.<span
1544style='mso-no-proof:yes'> <!--[if gte vml 1]><v:shape id="Picture_x0020_34"
1545 o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;height:450pt;
1546 visibility:visible;mso-wrap-style:square'>
1547 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image026.png"
1548  o:title=""/>
1549</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1550src="Small%20Angle%20Image%20Processing_files/image026.png" v:shapes="Picture_x0020_34"><![endif]></span></p>
1551
1552<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1553
1554<p class=MsoNormal>Next let’s deal with the beam stop. I’m going to use both a
1555polygon and a spot to cover it. Move the zoom area to be around the center, make
1556sure the zoom buttons are off, enter ‘<b style='mso-bidi-font-weight:normal'><span
1557style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1558mso-hansi-theme-font:minor-latin'>s</span></b>’ on the plot and press mouse <b
1559style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1560mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>LB</span></b>
1561with the cursor positioned where you want the spot. A 1mm diameter red circle
1562will appear on the plot</p>
1563
1564<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1565 id="Picture_x0020_35" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;
1566 height:450pt;visibility:visible;mso-wrap-style:square'>
1567 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image027.png"
1568  o:title=""/>
1569</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1570src="Small%20Angle%20Image%20Processing_files/image027.png" v:shapes="Picture_x0020_35"><![endif]></span></p>
1571
1572<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1573
1574<p class=MsoNormal>And the <b style='mso-bidi-font-weight:normal'><span
1575style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1576mso-hansi-theme-font:minor-latin'>Masks</span></b> window will have new
1577information</p>
1578
1579<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1580 id="Picture_x0020_24" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:337.5pt;
1581 height:170.25pt;visibility:visible;mso-wrap-style:square'>
1582 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image028.png"
1583  o:title=""/>
1584</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=227
1585src="Small%20Angle%20Image%20Processing_files/image028.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
1586
1587<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1588
1589<p class=MsoNormal>You can change the diameter of the spot, I used <b
1590style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1591mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>7.0</span></b>;
1592the plot now shows a ring that just covers the beam stop. You may have to drag
1593it a bit (Hint: drag the center of the spot) to get it well centered.</p>
1594
1595<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1596 id="Picture_x0020_36" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
1597 height:450pt;visibility:visible;mso-wrap-style:square'>
1598 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image029.png"
1599  o:title=""/>
1600</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1601src="Small%20Angle%20Image%20Processing_files/image029.png" v:shapes="Picture_x0020_36"><![endif]></span></p>
1602
1603<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1604
1605<p class=MsoNormal>Next we need to mask the stick holding the beam stop; we’ll
1606use a 4 sided polygon for this. Adjust the zoom &amp; position so you can see
1607the entire beam stop stick. Make sure all zoom buttons are off, press ‘<b
1608style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1609mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>p</span></b>’
1610on the plot, then press the mouse <b style='mso-bidi-font-weight:normal'><span
1611style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1612mso-hansi-theme-font:minor-latin'>LB</span></b> at four points in succession
1613around the beam stop stick. A line segment for the polygon will be drawn
1614following your mouse clicks. Finally press the mouse <b style='mso-bidi-font-weight:
1615normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1616minor-latin;mso-hansi-theme-font:minor-latin'>RB</span></b> to close the
1617polygon. You should see something like</p>
1618
1619<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1620 id="Picture_x0020_37" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
1621 height:450pt;visibility:visible;mso-wrap-style:square'>
1622 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image030.png"
1623  o:title=""/>
1624</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1625src="Small%20Angle%20Image%20Processing_files/image030.png" v:shapes="Picture_x0020_37"><![endif]></span></p>
1626
1627<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1628
1629<p class=MsoNormal>You can adjust the position of the polygon vertices by
1630closely dragging it with mouse <b style='mso-bidi-font-weight:normal'><span
1631style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1632mso-hansi-theme-font:minor-latin'>LB</span></b> pressed; a new vertex can be
1633added by dragging an existing vertex with the mouse <b style='mso-bidi-font-weight:
1634normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1635minor-latin;mso-hansi-theme-font:minor-latin'>RB</span></b> pressed. If you
1636drag one vertex onto another, they are merged and cannot be separated.</p>
1637
1638<p class=MsoNormal>We want to use these masks for all the Sa1-4 images. <span
1639class=GramE>Do</span> <b style='mso-bidi-font-weight:normal'><span
1640style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1641mso-hansi-theme-font:minor-latin'>Operations/Copy mask</span></b>; a <b
1642style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1643mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Copy mask
1644information</span></b> dialog box will appear. Select the <b style='mso-bidi-font-weight:
1645normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1646minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-4</span></b> items and press <b
1647style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1648mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.
1649Here is a useful place to save your project; do <b style='mso-bidi-font-weight:
1650normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1651minor-latin;mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from
1652the main GSAS-II data tree menu.</p>
1653
1654<h2>Step 3: Integration of images</h2>
1655
1656<p class=MsoNormal>We are now ready to integrate the glassy carbon and the four
1657<span class=GramE>Sa</span> images. Select any Image Controls and then do
1658Operations/Integrate all. A selection dialog will appear; select only the GC
1659and Sa1-Sa4 data sets and press Ok. The image integration will proceed; a
1660progress bar shows as each one is done. Five SASD data items will appear on the
1661GSAS-II data tree; the last one (<b style='mso-bidi-font-weight:normal'><span
1662style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1663mso-hansi-theme-font:minor-latin'>SASD Sa4_40s_061.tif <span class=SpellE>Azm</span>=45.00</span></b>)
1664will be expanded and plotted.</p>
1665
1666<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1667 id="Picture_x0020_39" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
1668 height:450pt;visibility:visible;mso-wrap-style:square'>
1669 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image031.png"
1670  o:title=""/>
1671</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1672src="Small%20Angle%20Image%20Processing_files/image031.png" v:shapes="Picture_x0020_39"><![endif]></span></p>
1673
1674<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1675
1676<p class=MsoNormal>Pretty obviously the SASD pattern is down to background at Q~0.25Å<sup>-1</sup>;
1677the other Sa1-Sa4 patterns are similar. The glassy carbon pattern extends
1678nicely to the highest Q (~1.0Å<sup>-1</sup>) measured.</p>
1679
1680<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1681 id="Picture_x0020_40" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:525pt;
1682 height:450pt;visibility:visible;mso-wrap-style:square'>
1683 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image032.png"
1684  o:title=""/>
1685</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1686src="Small%20Angle%20Image%20Processing_files/image032.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
1687
1688<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1689
1690<h2>Step 4: Scaling of SASD patterns</h2>
1691
1692<p class=MsoNormal>To set this data on an absolute scale, we compare it to an
1693absolute scaled glassy carbon scan. One of these is in the same directory as
1694the image data; do <b style='mso-bidi-font-weight:normal'><span
1695style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1696mso-hansi-theme-font:minor-latin'>Import/Small Angle Data/ from <span
1697class=GramE>q(</span>A-1) step X-ray QIE data file</span></b> and select <b
1698style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1699mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>GC
1700calibrated data.txt</span></b> from the file selection dialog. You will need to
1701select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1702mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>any <span
1703class=GramE>file(</span>*.*)</span></b> to see it. A <b style='mso-bidi-font-weight:
1704normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1705minor-latin;mso-hansi-theme-font:minor-latin'>Is <span class=GramE>this the</span>
1706file you want</span></b> dialog will appear – respond <b style='mso-bidi-font-weight:
1707normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1708minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b> to read the file;
1709it will be plotted.</p>
1710
1711<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1712 id="Picture_x0020_41" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
1713 height:450pt;visibility:visible;mso-wrap-style:square'>
1714 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image033.png"
1715  o:title=""/>
1716</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1717src="Small%20Angle%20Image%20Processing_files/image033.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
1718
1719<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1720
1721<p class=MsoNormal>If you <span class=GramE>enter ‘<b style='mso-bidi-font-weight:
1722normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1723minor-latin;mso-hansi-theme-font:minor-latin'>s</span></b>’</span> on the plot
1724window, all of the SASD patterns will be plotted together (I’ve adjusted the
1725zoom to see them all).</p>
1726
1727<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1728 id="Picture_x0020_42" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
1729 height:450pt;visibility:visible;mso-wrap-style:square'>
1730 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image034.png"
1731  o:title=""/>
1732</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1733src="Small%20Angle%20Image%20Processing_files/image034.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
1734
1735<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1736
1737<p class=MsoNormal>Clearly the measured image data need to be scaled down to
1738have them on absolute scale. First is to discover the scaling between the two
1739glassy carbon patterns. Go to the measured one (<b style='mso-bidi-font-weight:
1740normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1741minor-latin;mso-hansi-theme-font:minor-latin'>SASD GC_5s_200.tif</span></b>)
1742and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1743"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1744minor-latin'>Sample Parameters</span></b>.</p>
1745
1746<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1747 id="Picture_x0020_43" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:291.75pt;
1748 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1749 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image035.png"
1750  o:title=""/>
1751</v:shape><![endif]--><![if !vml]><img border=0 width=389 height=518
1752src="Small%20Angle%20Image%20Processing_files/image035.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
1753
1754<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1755
1756<p class=MsoNormal>We will change <b style='mso-bidi-font-weight:normal'><span
1757style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1758mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> by
1759comparison with the absolute glassy carbon scan. Do <b style='mso-bidi-font-weight:
1760normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1761minor-latin;mso-hansi-theme-font:minor-latin'>Command/Set scale</span></b> from
1762the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1763mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1764Parameters</span></b> menu; a <b style='mso-bidi-font-weight:normal'><span
1765style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1766mso-hansi-theme-font:minor-latin'>Reference histogram</span></b> dialog will
1767appear.</p>
1768
1769<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1770 id="Picture_x0020_44" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:259.5pt;
1771 height:252pt;visibility:visible;mso-wrap-style:square'>
1772 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image036.png"
1773  o:title=""/>
1774</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
1775src="Small%20Angle%20Image%20Processing_files/image036.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
1776
1777<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1778
1779<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1780style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1781mso-hansi-theme-font:minor-latin'>SASD GC calibrated data.txt</span></b> (shown
1782in blue above) and press <b style='mso-bidi-font-weight:normal'><span
1783style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1784mso-hansi-theme-font:minor-latin'>Ok</span></b>; the <b style='mso-bidi-font-weight:
1785normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1786minor-latin;mso-hansi-theme-font:minor-latin'>GC_5s_200.tif</span></b> data
1787will be rescaled to the <b style='mso-bidi-font-weight:normal'><span
1788style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1789mso-hansi-theme-font:minor-latin'>GC calibrated data</span></b> and the <b
1790style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1791mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
1792scale factor</span></b> will be changed to the new scaling factor (<b
1793style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1794mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.0008536</span></b>).
1795The plot will be redrawn with the scaled data.</p>
1796
1797<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1798 id="Picture_x0020_45" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:525pt;
1799 height:450pt;visibility:visible;mso-wrap-style:square'>
1800 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image037.png"
1801  o:title=""/>
1802</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1803src="Small%20Angle%20Image%20Processing_files/image037.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
1804
1805<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1806
1807<p class=MsoNormal>The divergence at high Q is probably from a background
1808contribution to the standard that is not present in our measured one. Next we
1809have to apply this scale factor to the Sa1-Sa4 data sets. Do <b
1810style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1811mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Command/Copy
1812selected…</span></b> from the <b style='mso-bidi-font-weight:normal'><span
1813style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1814mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> menu; a <b
1815style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1816mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select
1817sample parameters</span></b> dialog will appear</p>
1818
1819<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1820 id="Picture_x0020_46" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:240pt;
1821 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1822 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image038.png"
1823  o:title=""/>
1824</v:shape><![endif]--><![if !vml]><img border=0 width=320 height=310
1825src="Small%20Angle%20Image%20Processing_files/image038.png" v:shapes="Picture_x0020_46"><![endif]></span></p>
1826
1827<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1828
1829<p class=MsoNormal>Select only <b style='mso-bidi-font-weight:normal'><span
1830style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1831mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> and press <b
1832style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1833mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>;
1834a <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1835mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Copy sample
1836parameters</span></b> dialog will appear</p>
1837
1838<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1839 id="Picture_x0020_47" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:240pt;
1840 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1841 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image039.png"
1842  o:title=""/>
1843</v:shape><![endif]--><![if !vml]><img border=0 width=320 height=310
1844src="Small%20Angle%20Image%20Processing_files/image039.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
1845
1846<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1847
1848<p class=MsoNormal>Select only the <b style='mso-bidi-font-weight:normal'><span
1849style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1850mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b> data sets and press <b
1851style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1852mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.
1853The copy will occur and the plot redrawn</p>
1854
1855<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1856 id="Picture_x0020_48" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
1857 height:450pt;visibility:visible;mso-wrap-style:square'>
1858 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image040.png"
1859  o:title=""/>
1860</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1861src="Small%20Angle%20Image%20Processing_files/image040.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
1862
1863<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1864
1865<p class=MsoNormal>I’ve changed the zoom to show all the data. We are not quite
1866done; the scales for the Sa1-Sa4 data sets have to be further reduced by a
1867factor of 8 to account for the longer exposure time. Select SASD
1868Sa1_40s_067.tif from the GSAS-II data tree, expand it and choose Sample
1869Parameters</p>
1870
1871<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1872 id="Picture_x0020_49" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:291.75pt;
1873 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1874 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image041.png"
1875  o:title=""/>
1876</v:shape><![endif]--><![if !vml]><img border=0 width=389 height=518
1877src="Small%20Angle%20Image%20Processing_files/image041.png" v:shapes="Picture_x0020_49"><![endif]></span><o:p></o:p></p>
1878
1879<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1880
1881<p class=MsoNormal>The data items here can take simple mathematical expressions
1882so change Histogram scale factor to 0.0008536/8 and press Enter. The value will
1883change to 0.0001067 and the plot redrawn.</p>
1884
1885<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1886 id="Picture_x0020_50" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
1887 height:450pt;visibility:visible;mso-wrap-style:square'>
1888 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image042.png"
1889  o:title=""/>
1890</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1891src="Small%20Angle%20Image%20Processing_files/image042.png" v:shapes="Picture_x0020_50"><![endif]></span></p>
1892
1893<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1894
1895<p class=MsoNormal>Next do Command/Copy selected as before to copy this new
1896scale factor to the other <span class=GramE>Sa</span> data sets. The plot will
1897again be redrawn</p>
1898
1899<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1900 id="Picture_x0020_51" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
1901 height:450pt;visibility:visible;mso-wrap-style:square'>
1902 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image043.png"
1903  o:title=""/>
1904</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1905src="Small%20Angle%20Image%20Processing_files/image043.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
1906
1907<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1908
1909<p class=MsoNormal>Everything is now on absolute scale and these polymer
1910samples are quite weak small angle <span class=SpellE>scatterers</span>. This
1911is a good point to do a <b style='mso-bidi-font-weight:normal'><span
1912style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1913mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from the main
1914GSAS-II data tree menu. You can try to fit unified &amp; <span class=SpellE>Porod</span>
1915models to them following the procedures demonstrated in the <strong><span
1916style='font-weight:normal;mso-bidi-font-weight:bold'><a
1917href="Fitting%20Small%20Angle%20Scattering%20Data.htm"><span style='mso-bidi-font-weight:
1918normal'>Fitting Small Angle X-Ray Data</span></a> tutorial. I’d set the high Q
1919limit to about 0.25Å<sup>-1</sup> as above that is only noisy background.</span></strong></p>
1920
1921</div>
1922
1923</body>
1924
1925</html>
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