source: Tutorials/SAimages/Small Angle Image Processing.htm @ 1741

Last change on this file since 1741 was 1741, checked in by vondreele, 9 years ago

SA image processing revised
  • Property svn:mime-type set to text/html
File size: 116.8 KB
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414  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
415  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
416  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
417  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
418  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
419  <w:LsdException Locked="false" Priority="34" QFormat="true"
420   Name="List Paragraph"/>
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423   Name="Intense Quote"/>
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426  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
427  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
428  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
429  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
430  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
431  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
432  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
433  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
434  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
435  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
436  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
437  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
438  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
439  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
440  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
441  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
442  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
443  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
444  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
445  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
446  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
447  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
448  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
449  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
450  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
451  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
452  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
453  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
454  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
455  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
456  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
457  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
458  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
459  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
460  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
461  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
462  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
463  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
464  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
465  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
466  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
467  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
468  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
469  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
470  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
471  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
472  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
473  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
474  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
475  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
476  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
477  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
478  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
479  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
480  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
481  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
482  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
483  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
484  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
485  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
486  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
487  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
488  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
489  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
490  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
491  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
492  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
493  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
494  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
495  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
496  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
497  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
498  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
499  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
500  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
501  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
502  <w:LsdException Locked="false" Priority="19" QFormat="true"
503   Name="Subtle Emphasis"/>
504  <w:LsdException Locked="false" Priority="21" QFormat="true"
505   Name="Intense Emphasis"/>
506  <w:LsdException Locked="false" Priority="31" QFormat="true"
507   Name="Subtle Reference"/>
508  <w:LsdException Locked="false" Priority="32" QFormat="true"
509   Name="Intense Reference"/>
510  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
511  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
512   UnhideWhenUsed="true" Name="Bibliography"/>
513  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
514   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
515  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
516  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
517  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
518  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
519  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
520  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
521  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
522  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
523  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
524  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
525  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
526  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
527  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
528  <w:LsdException Locked="false" Priority="46"
529   Name="Grid Table 1 Light Accent 1"/>
530  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
531  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
532  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
533  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
534  <w:LsdException Locked="false" Priority="51"
535   Name="Grid Table 6 Colorful Accent 1"/>
536  <w:LsdException Locked="false" Priority="52"
537   Name="Grid Table 7 Colorful Accent 1"/>
538  <w:LsdException Locked="false" Priority="46"
539   Name="Grid Table 1 Light Accent 2"/>
540  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
541  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
542  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
543  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
544  <w:LsdException Locked="false" Priority="51"
545   Name="Grid Table 6 Colorful Accent 2"/>
546  <w:LsdException Locked="false" Priority="52"
547   Name="Grid Table 7 Colorful Accent 2"/>
548  <w:LsdException Locked="false" Priority="46"
549   Name="Grid Table 1 Light Accent 3"/>
550  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
551  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
552  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
553  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
554  <w:LsdException Locked="false" Priority="51"
555   Name="Grid Table 6 Colorful Accent 3"/>
556  <w:LsdException Locked="false" Priority="52"
557   Name="Grid Table 7 Colorful Accent 3"/>
558  <w:LsdException Locked="false" Priority="46"
559   Name="Grid Table 1 Light Accent 4"/>
560  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
561  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
562  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
563  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
564  <w:LsdException Locked="false" Priority="51"
565   Name="Grid Table 6 Colorful Accent 4"/>
566  <w:LsdException Locked="false" Priority="52"
567   Name="Grid Table 7 Colorful Accent 4"/>
568  <w:LsdException Locked="false" Priority="46"
569   Name="Grid Table 1 Light Accent 5"/>
570  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
571  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
572  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
573  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
574  <w:LsdException Locked="false" Priority="51"
575   Name="Grid Table 6 Colorful Accent 5"/>
576  <w:LsdException Locked="false" Priority="52"
577   Name="Grid Table 7 Colorful Accent 5"/>
578  <w:LsdException Locked="false" Priority="46"
579   Name="Grid Table 1 Light Accent 6"/>
580  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
581  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
582  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
583  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
584  <w:LsdException Locked="false" Priority="51"
585   Name="Grid Table 6 Colorful Accent 6"/>
586  <w:LsdException Locked="false" Priority="52"
587   Name="Grid Table 7 Colorful Accent 6"/>
588  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
589  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
590  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
591  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
592  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
593  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
594  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
595  <w:LsdException Locked="false" Priority="46"
596   Name="List Table 1 Light Accent 1"/>
597  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
598  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
599  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
600  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
601  <w:LsdException Locked="false" Priority="51"
602   Name="List Table 6 Colorful Accent 1"/>
603  <w:LsdException Locked="false" Priority="52"
604   Name="List Table 7 Colorful Accent 1"/>
605  <w:LsdException Locked="false" Priority="46"
606   Name="List Table 1 Light Accent 2"/>
607  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
608  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
609  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
610  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
611  <w:LsdException Locked="false" Priority="51"
612   Name="List Table 6 Colorful Accent 2"/>
613  <w:LsdException Locked="false" Priority="52"
614   Name="List Table 7 Colorful Accent 2"/>
615  <w:LsdException Locked="false" Priority="46"
616   Name="List Table 1 Light Accent 3"/>
617  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
618  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
619  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
620  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
621  <w:LsdException Locked="false" Priority="51"
622   Name="List Table 6 Colorful Accent 3"/>
623  <w:LsdException Locked="false" Priority="52"
624   Name="List Table 7 Colorful Accent 3"/>
625  <w:LsdException Locked="false" Priority="46"
626   Name="List Table 1 Light Accent 4"/>
627  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
628  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
629  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
630  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
631  <w:LsdException Locked="false" Priority="51"
632   Name="List Table 6 Colorful Accent 4"/>
633  <w:LsdException Locked="false" Priority="52"
634   Name="List Table 7 Colorful Accent 4"/>
635  <w:LsdException Locked="false" Priority="46"
636   Name="List Table 1 Light Accent 5"/>
637  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
638  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
639  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
640  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
641  <w:LsdException Locked="false" Priority="51"
642   Name="List Table 6 Colorful Accent 5"/>
643  <w:LsdException Locked="false" Priority="52"
644   Name="List Table 7 Colorful Accent 5"/>
645  <w:LsdException Locked="false" Priority="46"
646   Name="List Table 1 Light Accent 6"/>
647  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
648  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
649  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
650  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
651  <w:LsdException Locked="false" Priority="51"
652   Name="List Table 6 Colorful Accent 6"/>
653  <w:LsdException Locked="false" Priority="52"
654   Name="List Table 7 Colorful Accent 6"/>
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1153<div class=WordSection1>
1154
1155<h1><strong>Small Angle X-Ray Data – Image Processing<o:p></o:p></strong></h1>
1156
1157<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
1158this tutorial you will reduce 2D SAXS data to create 1D absolute scaled data.
1159The data were collected at APS on beam line 15ID on some polymer base materials
1160to be used for liquid crystal displays. The processing has several steps
1161including detector calibration (i.e. determine sample-detector distance &amp;
1162tilt), integration and scaling to an absolute scaled glassy carbon measurement.
1163The data were collected at a wavelength of 1.0332Å with a <span class=SpellE>MarCCD</span>
1164detector placed ~570mm from the sample. Note that menu entries are listed in
1165bold face below as <b style='mso-bidi-font-weight:normal'><span
1166style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1167mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1168minor-latin'>Help/About GSAS-II</span></b>, which lists first the name of the
1169menu (here <b style='mso-bidi-font-weight:normal'><span style='font-family:
1170"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1171minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Help</span></b>)
1172and second the name of the entry in the menu (here <b style='mso-bidi-font-weight:
1173normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1174minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1175mso-bidi-theme-font:minor-latin'>About GSAS-II</span></b>).<span
1176style='mso-spacerun:yes'>  </span><span style='mso-fareast-font-family:Calibri;
1177mso-fareast-theme-font:minor-latin;mso-bidi-font-weight:bold;mso-bidi-font-style:
1178italic'><o:p></o:p></span></p>
1179
1180<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1181
1182<h2>Step 1: Detector calibration</h2>
1183
1184<p class=MsoNormal>The detector position is determined by using an image
1185collected from silver <span class=SpellE>behenate</span>; do <b
1186style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1187mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data/Read
1188Image data…</span></b> and a file selection dialog box will appear. Go to <b
1189style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1190mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>exercises/<span
1191class=SpellE>SAimages</span></span></b> and select <b style='mso-bidi-font-weight:
1192normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1193minor-latin;mso-hansi-theme-font:minor-latin'>AgBehenate_003.tif</span></b>
1194with either a mouse button double click or <b style='mso-bidi-font-weight:normal'><span
1195style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1196mso-hansi-theme-font:minor-latin'>Open</span></b>; the image will appear</p>
1197
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1205  <v:f eqn="sum 0 0 @1"/>
1206  <v:f eqn="prod @2 1 2"/>
1207  <v:f eqn="prod @3 21600 pixelWidth"/>
1208  <v:f eqn="prod @3 21600 pixelHeight"/>
1209  <v:f eqn="sum @0 0 1"/>
1210  <v:f eqn="prod @6 1 2"/>
1211  <v:f eqn="prod @7 21600 pixelWidth"/>
1212  <v:f eqn="sum @8 21600 0"/>
1213  <v:f eqn="prod @7 21600 pixelHeight"/>
1214  <v:f eqn="sum @10 21600 0"/>
1215 </v:formulas>
1216 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1217 <o:lock v:ext="edit" aspectratio="t"/>
1218</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1062" type="#_x0000_t75"
1219 style='width:525pt;height:450pt;visibility:visible;mso-wrap-style:square'>
1220 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image001.png"
1221  o:title=""/>
1222</v:shape><![endif]--><![if !vml]><img width=700 height=600
1223src="Small%20Angle%20Image%20Processing_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
1224
1225<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1226
1227<p class=MsoNormal>And the <b style='mso-bidi-font-weight:normal'><span
1228style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1229mso-hansi-theme-font:minor-latin'>Image controls</span></b> window will show</p>
1230
1231<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1232 id="Picture_x0020_2" o:spid="_x0000_i1061" type="#_x0000_t75" style='width:472.5pt;
1233 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1234 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image002.png"
1235  o:title=""/>
1236</v:shape><![endif]--><![if !vml]><img width=630 height=518
1237src="Small%20Angle%20Image%20Processing_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1238
1239<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1240
1241<p class=MsoNormal>Note the default <b style='mso-bidi-font-weight:normal'><span
1242style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1243mso-hansi-theme-font:minor-latin'>Type of image data</span></b> is <b
1244style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1245mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR -
1246powder diffraction data</span></b>; you will change that <span
1247style='mso-no-proof:yes'>now.</span> Select <b style='mso-bidi-font-weight:
1248normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1249minor-latin;mso-hansi-theme-font:minor-latin'>SASD – small angle scattering
1250data</span></b> (the window will change). Enter the <b style='mso-bidi-font-weight:
1251normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1252minor-latin;mso-hansi-theme-font:minor-latin'>wavelength</span></b> (<b
1253style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1254mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.0332</span></b>),
1255and select the <span class=SpellE><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'>Calibrant</span></b></span> (near bottom of
1258window) as <b style='mso-bidi-font-weight:normal'><span style='font-family:
1259"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1260minor-latin'>Ag <span class=SpellE>behenate</span></span></b>. Note that the
1261calibration info for Ag <span class=SpellE>behenate</span> was read from a
1262python file – <b style='mso-bidi-font-weight:normal'><span style='font-family:
1263"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1264minor-latin'>GSASII/ImageCalibrants.py</span></b>. If you have a <span
1265class=SpellE>calibrant</span> that isn’t in this file you should enter it in
1266the file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1267mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UserCalibrants.py</span></b>;
1268just follow the format of the examples within <b style='mso-bidi-font-weight:
1269normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1270minor-latin;mso-hansi-theme-font:minor-latin'>ImageCalibrants.py</span></b>.
1271You should move the <b style='mso-bidi-font-weight:normal'><span
1272style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1273mso-hansi-theme-font:minor-latin'>Max intensity</span></b> slider to near the
1274middle of the range – that will improve the image. When done the <b
1275style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1276mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1277controls</span></b> window should look like</p>
1278
1279<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1280 id="Picture_x0020_3" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:472.5pt;
1281 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1282 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image003.png"
1283  o:title=""/>
1284</v:shape><![endif]--><![if !vml]><img width=630 height=518
1285src="Small%20Angle%20Image%20Processing_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
1286
1287<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1288
1289<p class=MsoNormal>And the image will be</p>
1290
1291<p class=MsoNormal><!--[if gte vml 1]><v:shapetype id="_x0000_t32" coordsize="21600,21600"
1292 o:spt="32" o:oned="t" path="m,l21600,21600e" filled="f">
1293 <v:path arrowok="t" fillok="f" o:connecttype="none"/>
1294 <o:lock v:ext="edit" shapetype="t"/>
1295</v:shapetype><v:shape id="Straight_x0020_Arrow_x0020_Connector_x0020_21"
1296 o:spid="_x0000_s1026" type="#_x0000_t32" style='position:absolute;
1297 margin-left:177pt;margin-top:214.5pt;width:48pt;height:15.75pt;flip:y;
1298 z-index:251659264;visibility:visible;mso-wrap-style:square;
1299 mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:9pt;
1300 mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
1301 mso-wrap-distance-bottom:0;mso-position-horizontal:absolute;
1302 mso-position-horizontal-relative:text;mso-position-vertical:absolute;
1303 mso-position-vertical-relative:text;mso-width-percent:0;mso-height-percent:0;
1304 mso-width-relative:page;mso-height-relative:page' o:gfxdata="UEsDBBQABgAIAAAAIQC2gziS/gAAAOEBAAATAAAAW0NvbnRlbnRfVHlwZXNdLnhtbJSRQU7DMBBF
130590jcwfIWJU67QAgl6YK0S0CoHGBkTxKLZGx5TGhvj5O2G0SRWNoz/78nu9wcxkFMGNg6quQqL6RA
13060s5Y6ir5vt9lD1JwBDIwOMJKHpHlpr69KfdHjyxSmriSfYz+USnWPY7AufNIadK6MEJMx9ApD/oD
1307OlTrorhX2lFEilmcO2RdNtjC5xDF9pCuTyYBB5bi6bQ4syoJ3g9WQ0ymaiLzg5KdCXlKLjvcW893
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1318Igr2Dc0fVL2RCAF0XEnoC9DaSJU1kJp1+ZuaYye8ylrInOAXm8L/o5Ufzgdkpm34i4ozJ3qa0TGi
1319MKcusjeIMLA9OEc+ArJqnfwafKgJtncHTIrl6I7+DuTXQLnil2Q6BD89GzX2TFvjv9CaZKtIPBvz
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13255rMEFHHlbcu1gdf95uYOVIjIFjvPZOCbAqzKy4sCc+tH3tJ5F2slIRxyNNDE2Odah6ohh2Hme2K5
1326ffjBYRQ51NoOOEq46/QiSZbaYcvyocGeHhuqvnYnZ6B9Gt/senw/7A/Ovnxuts/zYNGY66tp/QAq
13270hT/zPBbX6pDKZ2O/sQ2qM7AbZbKlmggXdwLiCPNEoGjwDLJQJeF/r+h/AEAAP//AwBQSwECLQAU
1328AAYACAAAACEAtoM4kv4AAADhAQAAEwAAAAAAAAAAAAAAAAAAAAAAW0NvbnRlbnRfVHlwZXNdLnht
1329bFBLAQItABQABgAIAAAAIQA4/SH/1gAAAJQBAAALAAAAAAAAAAAAAAAAAC8BAABfcmVscy8ucmVs
1330c1BLAQItABQABgAIAAAAIQB9d1Df6wEAACkEAAAOAAAAAAAAAAAAAAAAAC4CAABkcnMvZTJvRG9j
1331LnhtbFBLAQItABQABgAIAAAAIQCB0qld3wAAAAsBAAAPAAAAAAAAAAAAAAAAAEUEAABkcnMvZG93
1332bnJldi54bWxQSwUGAAAAAAQABADzAAAAUQUAAAAA
1333" strokecolor="#c0504d [3205]" strokeweight="3pt">
1334 <v:stroke endarrow="open"/>
1335 <v:shadow on="t" color="black" opacity="22937f" origin=",.5" offset="0,.63889mm"/>
1336 <o:lock v:ext="edit" shapetype="f"/>
1337</v:shape><![endif]--><![if !vml]><span style='mso-ignore:vglayout;position:
1338absolute;z-index:251659264;margin-left:234px;margin-top:274px;width:73px;
1339height:38px'><img width=73 height=38
1340src="Small%20Angle%20Image%20Processing_files/image004.png" v:shapes="Straight_x0020_Arrow_x0020_Connector_x0020_21"></span><![endif]><span
1341style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_4"
1342 o:spid="_x0000_i1059" type="#_x0000_t75" style='width:525pt;height:450pt;
1343 visibility:visible;mso-wrap-style:square'>
1344 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image005.png"
1345  o:title=""/>
1346</v:shape><![endif]--><![if !vml]><img width=700 height=600
1347src="Small%20Angle%20Image%20Processing_files/image005.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
1348
1349<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1350
1351<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
1352style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1353mso-hansi-theme-font:minor-latin'>Operations/Calibrate</span></b> from the <b
1354style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1355mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1356Controls</span></b> menu; a bit of instruction will appear on the status line
1357of this window. Select 5 points on the innermost ring (arrowed above); a small
1358red cross will appear at each selection point. Press the right mouse button to
1359finish; calibration will proceed. A sequence of concentric red rings will
1360appear; they will switch to blue when calibration is finished. Select <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'>Show ring
1363picks</span></b> (near bottom right of <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'>Image Controls</span></b> window). The <b
1366style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1367mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1368Controls</span></b> window will show the results of the calibration</p>
1369
1370<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1371 id="Picture_x0020_5" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:472.5pt;
1372 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1373 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image006.png"
1374  o:title=""/>
1375</v:shape><![endif]--><![if !vml]><img width=630 height=518
1376src="Small%20Angle%20Image%20Processing_files/image006.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
1377
1378<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1379
1380<p class=MsoNormal>And the plot will show the points (very sparse!) used in the
1381calibration calculations.</p>
1382
1383<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1384 id="Picture_x0020_6" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:525pt;
1385 height:450pt;visibility:visible;mso-wrap-style:square'>
1386 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image007.png"
1387  o:title=""/>
1388</v:shape><![endif]--><![if !vml]><img width=700 height=600
1389src="Small%20Angle%20Image%20Processing_files/image007.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
1390
1391<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1392
1393<p class=MsoNormal>You would like to use more points from just the visible
1394rings. I suggest you change <b style='mso-bidi-font-weight:normal'><span
1395style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1396mso-hansi-theme-font:minor-latin'>Min ring I/<span class=SpellE><span
1397class=GramE>Ib</span></span></span></b> to <b style='mso-bidi-font-weight:normal'><span
1398style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1399mso-hansi-theme-font:minor-latin'>0.5</span></b> and <b style='mso-bidi-font-weight:
1400normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1401minor-latin;mso-hansi-theme-font:minor-latin'>Min <span class=SpellE>calib</span>
1402d-spacing</span></b> to <b style='mso-bidi-font-weight:normal'><span
1403style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1404mso-hansi-theme-font:minor-latin'>10.0</span></b>. Do <b style='mso-bidi-font-weight:
1405normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1406minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Recalibrate</span></b>;
1407more points will be used and they will be limited to the 5 visible rings in the
1408pattern.</p>
1409
1410<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1411 id="Picture_x0020_7" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:525pt;
1412 height:450pt;visibility:visible;mso-wrap-style:square'>
1413 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image008.png"
1414  o:title=""/>
1415</v:shape><![endif]--><![if !vml]><img width=700 height=600
1416src="Small%20Angle%20Image%20Processing_files/image008.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
1417
1418<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1419
1420<p class=MsoNormal>And give the calibration result as</p>
1421
1422<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1423 id="Picture_x0020_8" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:472.5pt;
1424 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1425 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image009.png"
1426  o:title=""/>
1427</v:shape><![endif]--><![if !vml]><img width=630 height=518
1428src="Small%20Angle%20Image%20Processing_files/image009.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
1429
1430<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1431
1432<p class=MsoNormal>You will need this calibration information to process the
1433other images in this tutorial. To save it for future use do <b
1434style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1435mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Save
1436controls</span></b>; a file dialog will appear. Makeup a file name (no
1437extension needed) for this; I chose <b style='mso-bidi-font-weight:normal'><span
1438style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1439mso-hansi-theme-font:minor-latin'>SASD</span></b>. Press <b style='mso-bidi-font-weight:
1440normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1441minor-latin;mso-hansi-theme-font:minor-latin'>Save</span></b> and the file <span
1442class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1443"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1444minor-latin'>SASD.imctrl</span></b></span> will be written to the local
1445directory. If you are continuing on to the next step do <b style='mso-bidi-font-weight:
1446normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1447minor-latin;mso-hansi-theme-font:minor-latin'>File/New Project</span></b>
1448(don’t bother saving the project file unless you want it; we will not need it
1449here); otherwise you can exit GSAS-II.</p>
1450
1451<h2>Step 2: Data image integration</h2>
1452
1453<p class=MsoNormal>The objective here is to read in the four polymer sample
1454images, a glassy carbon image, an empty container image and a dark image. The
1455images will be integrated after creating masks to remove the beam stop and
1456other objectionable parts of the images. If you have not done so already, start
1457GSAS-II. </p>
1458
1459<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1460
1461<p class=MsoNormal>First do <b style='mso-bidi-font-weight:normal'><span
1462style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1463mso-hansi-theme-font:minor-latin'>Data/Read image data…</span></b>, go to <b
1464style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1465mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>exercises/<span
1466class=SpellE>SAimages</span></span></b> and select all images except <b
1467style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1468mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>AgBehenate_003.tif</span></b>;
1469then press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1470"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1471minor-latin'>Open</span></b> to read all of them. The GSAS-II data tree window
1472will show entries for 7 images and will expand the last one</p>
1473
1474<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1475 id="_x0000_i1054" type="#_x0000_t75" style='width:300pt;height:310.5pt;
1476 visibility:visible;mso-wrap-style:square'>
1477 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image010.png"
1478  o:title=""/>
1479</v:shape><![endif]--><![if !vml]><img width=400 height=414
1480src="Small%20Angle%20Image%20Processing_files/image010.png" v:shapes="_x0000_i1054"><![endif]></span></p>
1481
1482<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1483
1484<p class=MsoNormal>Notice that the Dark, Empty and GC (glassy carbon) are all
14855s images and the Sa1-4 ones are 40s images; this time information is needed
1486later to obtain correct scaling. First select the <b style='mso-bidi-font-weight:
1487normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1488minor-latin;mso-hansi-theme-font:minor-latin'>IMG GC_5s_200.tif</span></b>
1489entry from the tree and expand it (press the <b style='mso-bidi-font-weight:
1490normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1491minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b> box); then select <b
1492style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1493mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1494controls</span></b>. The data window (<b style='mso-bidi-font-weight:normal'><span
1495style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1496mso-hansi-theme-font:minor-latin'>Image Controls</span></b>) will show the
1497default settings.</p>
1498
1499<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1500 id="_x0000_i1053" type="#_x0000_t75" style='width:472.5pt;height:388.5pt;
1501 visibility:visible;mso-wrap-style:square'>
1502 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image011.png"
1503  o:title=""/>
1504</v:shape><![endif]--><![if !vml]><img width=630 height=518
1505src="Small%20Angle%20Image%20Processing_files/image011.png" v:shapes="_x0000_i1053"><![endif]></span></p>
1506
1507<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1508
1509<p class=MsoNormal>Do <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'>Operations/Load controls</span></b> from the
1512menu; a file selection dialog will appear showing the available *.<span
1513class=SpellE>imctrl</span> files (the one you made in Step 1 should be seen).
1514Select it and press <b style='mso-bidi-font-weight:normal'><span
1515style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1516mso-hansi-theme-font:minor-latin'>Open</span></b>; the <b style='mso-bidi-font-weight:
1517normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1518minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> window
1519will be redrawn with the settings obtained in <b style='mso-bidi-font-weight:
1520normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1521minor-latin;mso-hansi-theme-font:minor-latin'>Step 1: Detector calibration</span></b></p>
1522
1523<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1524 id="_x0000_i1052" type="#_x0000_t75" style='width:472.5pt;height:388.5pt;
1525 visibility:visible;mso-wrap-style:square'>
1526 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image012.png"
1527  o:title=""/>
1528</v:shape><![endif]--><![if !vml]><img width=630 height=518
1529src="Small%20Angle%20Image%20Processing_files/image012.png" v:shapes="_x0000_i1052"><![endif]></span></p>
1530
1531<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1532
1533<p class=MsoNormal><span class=GramE>and</span> the image will be that of
1534glassy carbon. Changing the <b style='mso-bidi-font-weight:normal'><span
1535style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1536mso-hansi-theme-font:minor-latin'>Max intensity</span></b> slider on the <b
1537style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1538mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1539Controls</span></b> window will show that the image from the <span
1540class=SpellE>MarCCD</span> is circular and slightly offset from the beam
1541center. A beam stop shadow is evident as well as an arc-like fault in the image
1542(toward the upper left corner of the image). We will sort those out later.</p>
1543
1544<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1545 id="Picture_x0020_55" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:525pt;
1546 height:450pt;visibility:visible;mso-wrap-style:square'>
1547 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image013.png"
1548  o:title=""/>
1549</v:shape><![endif]--><![if !vml]><img width=700 height=600
1550src="Small%20Angle%20Image%20Processing_files/image013.png" v:shapes="Picture_x0020_55"><![endif]></span></p>
1551
1552<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1553
1554<p class=MsoNormal>The next step we will be doing is to set up the integration
1555controls. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
1556"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1557minor-latin'>Dark image</span></b> is <b style='mso-bidi-font-weight:normal'><span
1558style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1559mso-hansi-theme-font:minor-latin'>IMG Dark_5s_003.tif</span></b>, the <b
1560style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1561mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background
1562image</span></b> is <b style='mso-bidi-font-weight:normal'><span
1563style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1564mso-hansi-theme-font:minor-latin'>IMG Empty_5s_014.tif</span></b>; select these
1565two. The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1566mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1567for each are <b style='mso-bidi-font-weight:normal'><span style='font-family:
1568"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1569minor-latin'>-1.0</span></b> because their exposures were the same as this
1570glassy carbon image (5s). Next check the boxes for <b style='mso-bidi-font-weight:
1571normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1572minor-latin;mso-hansi-theme-font:minor-latin'>Show integration limits?</span></b>
1573<span class=GramE>and</span> <b style='mso-bidi-font-weight:normal'><span
1574style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1575mso-hansi-theme-font:minor-latin'>Do full integration?</span></b> A pair of
1576circles with a connecting diagonal line will appear on the plot. Set the <b
1577style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1578mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Inner/Outer
1579q</span></b> values to <b style='mso-bidi-font-weight:normal'><span
1580style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1581mso-hansi-theme-font:minor-latin'>0.05</span></b> and <b style='mso-bidi-font-weight:
1582normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1583minor-latin;mso-hansi-theme-font:minor-latin'>0.9</span></b>, respectively, and
1584set the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1585mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Start
1586azimuth</span></b> to <b style='mso-bidi-font-weight:normal'><span
1587style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1588mso-hansi-theme-font:minor-latin'>0</span></b>. Set the <b style='mso-bidi-font-weight:
1589normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1590minor-latin;mso-hansi-theme-font:minor-latin'>No. 2-theta bins</span></b> to <b
1591style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1592mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>250</span></b>,
1593which is more appropriate for small angle scattering, and set the <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'>Bin style:
1596Constant step bins in</span></b> to <span class=GramE><b style='mso-bidi-font-weight:
1597normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1598minor-latin;mso-hansi-theme-font:minor-latin'>log(</span></b></span><b
1599style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1600mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>q)</span></b>.
1601You should also check the <b style='mso-bidi-font-weight:normal'><span
1602style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1603mso-hansi-theme-font:minor-latin'>Apply sample absorption?</span></b> <span
1604class=GramE>and</span> <b style='mso-bidi-font-weight:normal'><span
1605style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1606mso-hansi-theme-font:minor-latin'>Apply polarization?</span></b> <span
1607class=GramE>boxes</span>; enter the measured <b style='mso-bidi-font-weight:
1608normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1609minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> (<b
1610style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1611mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.818</span></b>)
1612for the glassy carbon sample. When done the <b style='mso-bidi-font-weight:
1613normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1614minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> data
1615window should look like</p>
1616
1617<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1618 id="Picture_x0020_40" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:472.5pt;
1619 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1620 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image014.png"
1621  o:title=""/>
1622</v:shape><![endif]--><![if !vml]><img width=630 height=518
1623src="Small%20Angle%20Image%20Processing_files/image014.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
1624
1625<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1626
1627<p class=MsoNormal>And the plot should look like</p>
1628
1629<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1630 id="Picture_x0020_41" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:525pt;
1631 height:450pt;visibility:visible;mso-wrap-style:square'>
1632 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image015.png"
1633  o:title=""/>
1634</v:shape><![endif]--><![if !vml]><img width=700 height=600
1635src="Small%20Angle%20Image%20Processing_files/image015.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
1636
1637<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1638
1639<p class=MsoNormal>Now copy these controls to the other images. Do <b
1640style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1641mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Copy
1642controls</span></b> and select just the <b style='mso-bidi-font-weight:normal'><span
1643style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1644mso-hansi-theme-font:minor-latin'>Sa1-4</span></b> data names. </p>
1645
1646<p class=MsoNormal>We now need to go to the <b style='mso-bidi-font-weight:
1647normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1648minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> for
1649each of <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1650mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b>
1651to enter the correct transmission for each and change the Dark &amp; Background
1652<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1653mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1654to account for the different exposure times. Start with <b style='mso-bidi-font-weight:
1655normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1656minor-latin;mso-hansi-theme-font:minor-latin'>IMG Sa1_40s_067.tif</span></b>
1657and change <b style='mso-bidi-font-weight:normal'><span style='font-family:
1658"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1659minor-latin'>transmission</span></b> to <b style='mso-bidi-font-weight:normal'><span
1660style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1661mso-hansi-theme-font:minor-latin'>0.943</span></b> and the two <b
1662style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1663mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1664to <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'>-8.0</span></b>.
1666Then go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1667"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1668minor-latin'>IMG Sa2_40s_069.tif</span></b> and change <b style='mso-bidi-font-weight:
1669normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1670minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1671style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1672mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.979</span></b>;
1673<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1674mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1675to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1676mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1677Next go <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1678mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>to IMG
1679Sa3_40s_059.tif</span></b> and change <b style='mso-bidi-font-weight:normal'><span
1680style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1681mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1682style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1683mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.960</span></b>;
1684<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1685mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1686to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1687mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1688Finally, go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1689"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1690minor-latin'>IMG Sa4_40s_061.tif</span></b> and change <b style='mso-bidi-font-weight:
1691normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1692minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1693style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1694mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.968</span></b>;
1695<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1696mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1697to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1698mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1699The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1700mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1701Controls</span></b> data window for this should look like</p>
1702
1703<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1704 id="Picture_x0020_43" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:472.5pt;
1705 height:388.5pt;visibility:visible;mso-wrap-style:square'>
1706 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image016.png"
1707  o:title=""/>
1708</v:shape><![endif]--><![if !vml]><img width=630 height=518
1709src="Small%20Angle%20Image%20Processing_files/image016.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
1710
1711<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1712
1713<p class=MsoNormal>This is a reasonable time to save the project; do <b
1714style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1715mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>File/Save
1716project as…</span></b> from the main GSAS-II data tree menu. Choose a file name
1717(I assumed <b style='mso-bidi-font-weight:normal'><span style='font-family:
1718"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1719minor-latin'>image</span></b>) and it will be written on the local file
1720directory. </p>
1721
1722<p class=MsoNormal>As noted earlier, the images contain some unwanted features;
1723so let’s create masks to remove them. Select <b style='mso-bidi-font-weight:
1724normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1725minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b> from the GSAS-II
1726data tree under <b style='mso-bidi-font-weight:normal'><span style='font-family:
1727"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1728minor-latin'>IMG GC_5s_200.tif</span></b>; the data window will show</p>
1729
1730<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1731 id="Picture_x0020_17" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:337.5pt;
1732 height:99.75pt;visibility:visible;mso-wrap-style:square'>
1733 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image017.png"
1734  o:title=""/>
1735</v:shape><![endif]--><![if !vml]><img width=450 height=133
1736src="Small%20Angle%20Image%20Processing_files/image017.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1737
1738<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1739
1740<p class=MsoNormal>To mask out the regions beyond the circular <span
1741class=SpellE>MarCCD</span> image change the <span class=GramE><b
1742style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1743mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Lower<span
1744style='mso-spacerun:yes'>  </span><span class=SpellE>threshhold</span></span></b></span>
1745from <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1746mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0</span></b>
1747to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1748mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>;
1749the image will be redrawn with these regions in red</p>
1750
1751<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1752 id="Picture_x0020_45" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
1753 height:450pt;visibility:visible;mso-wrap-style:square'>
1754 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image018.png"
1755  o:title=""/>
1756</v:shape><![endif]--><![if !vml]><img width=700 height=600
1757src="Small%20Angle%20Image%20Processing_files/image018.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
1758
1759<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1760
1761<p class=MsoNormal>These are now excluded. The status line for the <b
1762style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1763mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b>
1764data window gives the directions for adding additional masks. You can make arcs
1765(we’ll use that here), rings, spots (this too) and polygons (this as well) as
1766masks. These enclose areas to be excluded. The frame works in the opposite
1767sense in that everything outside the frame is excluded (NB: only one frame is
1768allowed). So let’s first mask the bad arc in the upper left – zoom in on that
1769part of the image</p>
1770
1771<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1772 id="Picture_x0020_62" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt;
1773 height:450pt;visibility:visible;mso-wrap-style:square'>
1774 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image019.png"
1775  o:title=""/>
1776</v:shape><![endif]--><![if !vml]><img width=700 height=600
1777src="Small%20Angle%20Image%20Processing_files/image019.png" v:shapes="Picture_x0020_62"><![endif]></span></p>
1778
1779<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1780
1781<p class=MsoNormal>To add the mask 1: be sure the focus is on the image and the
1782zoom buttons are off, 2: type <span class=GramE><b style='mso-bidi-font-weight:
1783normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1784minor-latin;mso-hansi-theme-font:minor-latin'>a</span></b> to</span> activate
1785the arc mask entry 3: press the left mouse button (<b style='mso-bidi-font-weight:
1786normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1787minor-latin;mso-hansi-theme-font:minor-latin'>LB</span></b>) with the cursor
1788centered on the bad arc. The <b style='mso-bidi-font-weight:normal'><span
1789style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1790mso-hansi-theme-font:minor-latin'>Masks</span></b> window will show a new entry
1791</p>
1792
1793<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1794 id="Picture_x0020_63" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:342pt;
1795 height:136.5pt;visibility:visible;mso-wrap-style:square'>
1796 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image020.png"
1797  o:title=""/>
1798</v:shape><![endif]--><![if !vml]><img width=456 height=182
1799src="Small%20Angle%20Image%20Processing_files/image020.png" v:shapes="Picture_x0020_63"><![endif]></span><span
1800style='mso-spacerun:yes'> </span></p>
1801
1802<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1803
1804<p class=MsoNormal><span class=GramE>and</span> an arc mask will be drawn on
1805the plot.</p>
1806
1807<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1808 id="Picture_x0020_64" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
1809 height:450pt;visibility:visible;mso-wrap-style:square'>
1810 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image021.png"
1811  o:title=""/>
1812</v:shape><![endif]--><![if !vml]><img width=700 height=600
1813src="Small%20Angle%20Image%20Processing_files/image021.png" v:shapes="Picture_x0020_64"><![endif]></span></p>
1814
1815<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1816
1817<p class=MsoNormal>You can change the angular width of the arc by changing <b
1818style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1819mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>thickness</span></b>
1820in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1821mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b>
1822data window, you can change the angular range of the arc by dragging either end
1823of the arc (NB: increments only in whole degrees), and you can move the
1824arc<span style='mso-spacerun:yes'>  </span>along a constant 2&#920; angle by
1825dragging on any point inside the mask. The curvature is centered on the beam
1826center position and follows a constant 2&#920; curve established by the
1827detector calibration.<span style='mso-no-proof:yes'> </span></p>
1828
1829<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1830 id="Picture_x0020_65" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
1831 height:450pt;visibility:visible;mso-wrap-style:square'>
1832 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image022.png"
1833  o:title=""/>
1834</v:shape><![endif]--><![if !vml]><img width=700 height=600
1835src="Small%20Angle%20Image%20Processing_files/image022.png" v:shapes="Picture_x0020_65"><![endif]></span></p>
1836
1837<p class=MsoNormal>Next let’s deal with the beam stop. I’m going to use both a
1838polygon and a spot to cover it. Move the zoom area to be around the center, make
1839sure the zoom buttons are off, enter ‘<b style='mso-bidi-font-weight:normal'><span
1840style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1841mso-hansi-theme-font:minor-latin'>s</span></b>’ on the plot and press mouse <b
1842style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1843mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>LB</span></b>
1844with the cursor positioned where you want the spot. A 1mm diameter red circle
1845will appear on the plot</p>
1846
1847<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1848 id="Picture_x0020_66" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;
1849 height:450pt;visibility:visible;mso-wrap-style:square'>
1850 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image023.png"
1851  o:title=""/>
1852</v:shape><![endif]--><![if !vml]><img width=700 height=600
1853src="Small%20Angle%20Image%20Processing_files/image023.png" v:shapes="Picture_x0020_66"><![endif]></span></p>
1854
1855<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1856
1857<p class=MsoNormal>And the <b style='mso-bidi-font-weight:normal'><span
1858style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1859mso-hansi-theme-font:minor-latin'>Masks</span></b> window will have new
1860information</p>
1861
1862<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1863 id="Picture_x0020_24" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:337.5pt;
1864 height:170.25pt;visibility:visible;mso-wrap-style:square'>
1865 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image024.png"
1866  o:title=""/>
1867</v:shape><![endif]--><![if !vml]><img width=450 height=227
1868src="Small%20Angle%20Image%20Processing_files/image024.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
1869
1870<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1871
1872<p class=MsoNormal>You can change the diameter of the spot, I used <b
1873style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1874mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>7.0</span></b>;
1875the plot now shows a ring that just covers the beam stop. You may have to drag
1876it a bit (Hint: drag the center of the spot) to get it well centered.</p>
1877
1878<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1879 id="Picture_x0020_67" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
1880 height:450pt;visibility:visible;mso-wrap-style:square'>
1881 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image025.png"
1882  o:title=""/>
1883</v:shape><![endif]--><![if !vml]><img width=700 height=600
1884src="Small%20Angle%20Image%20Processing_files/image025.png" v:shapes="Picture_x0020_67"><![endif]></span></p>
1885
1886<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1887
1888<p class=MsoNormal>Next we need to mask the stick holding the beam stop; we’ll
1889use a 4 sided polygon for this. Adjust the zoom &amp; position so you can see
1890the entire beam stop stick. Make sure all zoom buttons are off, press ‘<b
1891style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1892mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>p</span></b>’
1893on the plot, then press the mouse <b style='mso-bidi-font-weight:normal'><span
1894style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1895mso-hansi-theme-font:minor-latin'>LB</span></b> at four points in succession
1896around the beam stop stick. A line segment for the polygon will be drawn
1897following your mouse clicks. Finally press the mouse <b style='mso-bidi-font-weight:
1898normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1899minor-latin;mso-hansi-theme-font:minor-latin'>RB</span></b> to close the
1900polygon. You should see something like</p>
1901
1902<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1903 id="Picture_x0020_68" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
1904 height:450pt;visibility:visible;mso-wrap-style:square'>
1905 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image026.png"
1906  o:title=""/>
1907</v:shape><![endif]--><![if !vml]><img width=700 height=600
1908src="Small%20Angle%20Image%20Processing_files/image026.png" v:shapes="Picture_x0020_68"><![endif]></span></p>
1909
1910<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1911
1912<p class=MsoNormal>You can adjust the position of the polygon vertices by
1913closely dragging it with mouse <b style='mso-bidi-font-weight:normal'><span
1914style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1915mso-hansi-theme-font:minor-latin'>LB</span></b> pressed; a new vertex can be added
1916by dragging an existing vertex with the mouse <b style='mso-bidi-font-weight:
1917normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1918minor-latin;mso-hansi-theme-font:minor-latin'>RB</span></b> pressed. If you
1919drag one vertex onto another, they are merged and cannot be separated.</p>
1920
1921<p class=MsoNormal>We want to use these masks for all the Sa1-4 images. Do <b
1922style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1923mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Copy
1924mask</span></b>; a <b style='mso-bidi-font-weight:normal'><span
1925style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1926mso-hansi-theme-font:minor-latin'>Copy mask information</span></b> dialog box will
1927appear. Select the <b style='mso-bidi-font-weight:normal'><span
1928style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1929mso-hansi-theme-font:minor-latin'>Sa1-4</span></b> items and press <b
1930style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1931mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.
1932Here is a useful place to save your project; do <b style='mso-bidi-font-weight:
1933normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1934minor-latin;mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from
1935the main GSAS-II data tree menu.</p>
1936
1937<h2>Step 3: Integration of images</h2>
1938
1939<p class=MsoNormal>We are now ready to integrate the glassy carbon and the four
1940<span class=GramE>Sa</span> images. Select any <b style='mso-bidi-font-weight:
1941normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1942minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> and
1943then do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1944mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Integrate
1945all</span></b>. A selection dialog will appear; select only the <b
1946style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1947mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>GC</span></b>
1948and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1949mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b>
1950data sets and press <b style='mso-bidi-font-weight:normal'><span
1951style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1952mso-hansi-theme-font:minor-latin'>Ok</span></b>. The image integration will
1953proceed; a progress bar shows as each one is done. Five SASD data items will appear
1954on the GSAS-II data tree; the last one (<b style='mso-bidi-font-weight:normal'><span
1955style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1956mso-hansi-theme-font:minor-latin'>SASD Sa4_40s_061.tif <span class=SpellE>Azm</span>=45.00</span></b>)
1957will be expanded and plotted (you may have to select the <b style='mso-bidi-font-weight:
1958normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1959minor-latin;mso-hansi-theme-font:minor-latin'>Powder Patterns</span></b> tab to
1960see it).</p>
1961
1962<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1963 id="_x0000_i1037" type="#_x0000_t75" style='width:525pt;height:450pt;
1964 visibility:visible;mso-wrap-style:square'>
1965 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image027.png"
1966  o:title=""/>
1967</v:shape><![endif]--><![if !vml]><img width=700 height=600
1968src="Small%20Angle%20Image%20Processing_files/image027.png" v:shapes="_x0000_i1037"><![endif]></span></p>
1969
1970<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1971
1972<p class=MsoNormal>Pretty obviously the SASD pattern is down to background at
1973Q~0.25Å<sup>-1</sup>; the other Sa1-Sa4 patterns are similar. The glassy carbon
1974pattern extends nicely to the highest Q (~1.0Å<sup>-1</sup>) measured.</p>
1975
1976<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1977 id="Picture_x0020_48" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:525pt;
1978 height:450pt;visibility:visible;mso-wrap-style:square'>
1979 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image028.png"
1980  o:title=""/>
1981</v:shape><![endif]--><![if !vml]><img width=700 height=600
1982src="Small%20Angle%20Image%20Processing_files/image028.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
1983
1984<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1985
1986<h2>Step 4: Scaling of SASD patterns</h2>
1987
1988<p class=MsoNormal>To set this data on an absolute scale, we compare it to an
1989absolute scaled glassy carbon scan. One of these is in the same directory as
1990the image data; do <b style='mso-bidi-font-weight:normal'><span
1991style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1992mso-hansi-theme-font:minor-latin'>Import/Small Angle Data/ from <span
1993class=GramE>q(</span>A-1) step X-ray QIE data file</span></b> and select <b
1994style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1995mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>GC
1996calibrated data.txt</span></b> from the file selection dialog. You will need to
1997select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1998mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>any <span
1999class=GramE>file(</span>*.*)</span></b> to see it. A <b style='mso-bidi-font-weight:
2000normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2001minor-latin;mso-hansi-theme-font:minor-latin'>Is this the file you want</span></b>
2002dialog will appear – respond <b style='mso-bidi-font-weight:normal'><span
2003style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2004mso-hansi-theme-font:minor-latin'>Yes</span></b> to read the file; it will be
2005plotted.</p>
2006
2007<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2008 id="Picture_x0020_49" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
2009 height:450pt;visibility:visible;mso-wrap-style:square'>
2010 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image029.png"
2011  o:title=""/>
2012</v:shape><![endif]--><![if !vml]><img width=700 height=600
2013src="Small%20Angle%20Image%20Processing_files/image029.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
2014
2015<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2016
2017<p class=MsoNormal>If you enter ‘<b style='mso-bidi-font-weight:normal'><span
2018style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2019mso-hansi-theme-font:minor-latin'>m</span></b>’ on the plot window, all of the
2020SASD patterns will be plotted together (I’ve adjusted the zoom to see them
2021all).</p>
2022
2023<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2024 id="Picture_x0020_50" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
2025 height:450pt;visibility:visible;mso-wrap-style:square'>
2026 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image030.png"
2027  o:title=""/>
2028</v:shape><![endif]--><![if !vml]><img width=700 height=600
2029src="Small%20Angle%20Image%20Processing_files/image030.png" v:shapes="Picture_x0020_50"><![endif]></span></p>
2030
2031<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2032
2033<p class=MsoNormal>Clearly the measured image data need to be scaled down to
2034have them on absolute scale. First is to discover the scaling between the two
2035glassy carbon patterns. Go to the measured one (<b style='mso-bidi-font-weight:
2036normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2037minor-latin;mso-hansi-theme-font:minor-latin'>SASD GC_5s_200.tif</span></b>)
2038and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2039"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2040minor-latin'>Sample Parameters</span></b>.</p>
2041
2042<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2043 id="Picture_x0020_51" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:291.75pt;
2044 height:408pt;visibility:visible;mso-wrap-style:square'>
2045 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image031.png"
2046  o:title=""/>
2047</v:shape><![endif]--><![if !vml]><img width=389 height=544
2048src="Small%20Angle%20Image%20Processing_files/image031.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
2049
2050<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2051
2052<p class=MsoNormal>We will change <b style='mso-bidi-font-weight:normal'><span
2053style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2054mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> by
2055comparison with the absolute glassy carbon scan. Do <b style='mso-bidi-font-weight:
2056normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2057minor-latin;mso-hansi-theme-font:minor-latin'>Command/Set scale</span></b> from
2058the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2059mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
2060Parameters</span></b> menu; a <b style='mso-bidi-font-weight:normal'><span
2061style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2062mso-hansi-theme-font:minor-latin'>Reference histogram</span></b> dialog will
2063appear.</p>
2064
2065<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2066 id="Picture_x0020_44" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:259.5pt;
2067 height:252pt;visibility:visible;mso-wrap-style:square'>
2068 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image032.png"
2069  o:title=""/>
2070</v:shape><![endif]--><![if !vml]><img width=346 height=336
2071src="Small%20Angle%20Image%20Processing_files/image032.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
2072
2073<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2074
2075<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2076style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2077mso-hansi-theme-font:minor-latin'>SASD GC calibrated data.txt</span></b> (shown
2078in blue above) and press <b style='mso-bidi-font-weight:normal'><span
2079style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2080mso-hansi-theme-font:minor-latin'>Ok</span></b>; the <b style='mso-bidi-font-weight:
2081normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2082minor-latin;mso-hansi-theme-font:minor-latin'>GC_5s_200.tif</span></b> data
2083will be rescaled to the <b style='mso-bidi-font-weight:normal'><span
2084style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2085mso-hansi-theme-font:minor-latin'>GC calibrated data</span></b> and the <b
2086style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2087mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
2088scale factor</span></b> will be changed to the new scaling factor (<b
2089style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2090mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.0008536</span></b>).
2091The plot will be redrawn with the scaled data.</p>
2092
2093<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2094 id="Picture_x0020_52" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:525pt;
2095 height:450pt;visibility:visible;mso-wrap-style:square'>
2096 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image033.png"
2097  o:title=""/>
2098</v:shape><![endif]--><![if !vml]><img width=700 height=600
2099src="Small%20Angle%20Image%20Processing_files/image033.png" v:shapes="Picture_x0020_52"><![endif]></span></p>
2100
2101<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2102
2103<p class=MsoNormal>The divergence at high Q is probably from a background
2104contribution to the standard that is not present in our measured one. Next we
2105have to apply this scale factor to the Sa1-Sa4 data sets. Do <b
2106style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2107mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Command/Copy
2108selected…</span></b> from the <b style='mso-bidi-font-weight:normal'><span
2109style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2110mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> menu; a <b
2111style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2112mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select
2113sample parameters</span></b> dialog will appear</p>
2114
2115<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2116 id="Picture_x0020_46" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:240pt;
2117 height:232.5pt;visibility:visible;mso-wrap-style:square'>
2118 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image034.png"
2119  o:title=""/>
2120</v:shape><![endif]--><![if !vml]><img width=320 height=310
2121src="Small%20Angle%20Image%20Processing_files/image034.png" v:shapes="Picture_x0020_46"><![endif]></span></p>
2122
2123<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2124
2125<p class=MsoNormal>Select only <b style='mso-bidi-font-weight:normal'><span
2126style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2127mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> and press <b
2128style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2129mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>;
2130a <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2131mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Copy sample
2132parameters</span></b> dialog will appear</p>
2133
2134<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2135 id="Picture_x0020_47" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:240pt;
2136 height:232.5pt;visibility:visible;mso-wrap-style:square'>
2137 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image035.png"
2138  o:title=""/>
2139</v:shape><![endif]--><![if !vml]><img width=320 height=310
2140src="Small%20Angle%20Image%20Processing_files/image035.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
2141
2142<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2143
2144<p class=MsoNormal>Select only the <b style='mso-bidi-font-weight:normal'><span
2145style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2146mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b> data sets and press <b
2147style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2148mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.
2149The copy will occur and the plot redrawn</p>
2150
2151<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2152 id="Picture_x0020_53" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
2153 height:450pt;visibility:visible;mso-wrap-style:square'>
2154 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image036.png"
2155  o:title=""/>
2156</v:shape><![endif]--><![if !vml]><img width=700 height=600
2157src="Small%20Angle%20Image%20Processing_files/image036.png" v:shapes="Picture_x0020_53"><![endif]></span></p>
2158
2159<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2160
2161<p class=MsoNormal>I’ve changed the zoom to show all the data. We are not quite
2162done; the scales for the Sa1-Sa4 data sets have to be further reduced by a
2163factor of 8 to account for the longer exposure time. Select <b
2164style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2165mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>SASD
2166Sa1_40s_067.tif</span></b> from the GSAS-II data tree, expand it and choose <b
2167style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2168mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
2169Parameters</span></b></p>
2170
2171<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2172 id="Picture_x0020_54" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:291.75pt;
2173 height:408pt;visibility:visible;mso-wrap-style:square'>
2174 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image037.png"
2175  o:title=""/>
2176</v:shape><![endif]--><![if !vml]><img width=389 height=544
2177src="Small%20Angle%20Image%20Processing_files/image037.png" v:shapes="Picture_x0020_54"><![endif]></span></p>
2178
2179<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2180
2181<p class=MsoNormal>The data items here can take simple mathematical expressions
2182so change <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2183mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
2184scale factor</span></b> to <b style='mso-bidi-font-weight:normal'><span
2185style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2186mso-hansi-theme-font:minor-latin'>0.0008536/8</span></b> and press <b
2187style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2188mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>.
2189The value will change to <b style='mso-bidi-font-weight:normal'><span
2190style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2191mso-hansi-theme-font:minor-latin'>0.0001067</span></b> and the plot redrawn.</p>
2192
2193<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2194 id="Picture_x0020_56" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
2195 height:450pt;visibility:visible;mso-wrap-style:square'>
2196 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image038.png"
2197  o:title=""/>
2198</v:shape><![endif]--><![if !vml]><img width=700 height=600
2199src="Small%20Angle%20Image%20Processing_files/image038.png" v:shapes="Picture_x0020_56"><![endif]></span></p>
2200
2201<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2202
2203<p class=MsoNormal>Next do <b style='mso-bidi-font-weight:normal'><span
2204style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2205mso-hansi-theme-font:minor-latin'>Command/Copy selected</span></b> as before to
2206copy this new scale factor to the other <span class=GramE>Sa</span> data sets.
2207The plot will again be redrawn</p>
2208
2209<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2210 id="Picture_x0020_57" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
2211 height:450pt;visibility:visible;mso-wrap-style:square'>
2212 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image039.png"
2213  o:title=""/>
2214</v:shape><![endif]--><![if !vml]><img width=700 height=600
2215src="Small%20Angle%20Image%20Processing_files/image039.png" v:shapes="Picture_x0020_57"><![endif]></span></p>
2216
2217<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2218
2219<p class=MsoNormal>Everything is now on absolute scale and these polymer
2220samples are quite weak small angle <span class=SpellE>scatterers</span>. This
2221is a good point to do a <b style='mso-bidi-font-weight:normal'><span
2222style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2223mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from the main
2224GSAS-II data tree menu. You can try to fit unified &amp; <span class=SpellE>Porod</span>
2225models to them following the procedures demonstrated in the <strong><span
2226style='font-weight:normal'>Fitting Small Angle X-Ray Data</span></strong><strong><span
2227style='font-weight:normal;mso-bidi-font-weight:bold'> tutorial. I’d set the
2228high Q limit to about 0.25Å<sup>-1</sup> as above that is only noisy
2229background.</span></strong></p>
2230
2231</div>
2232
2233</body>
2234
2235</html>
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