source: Tutorials/SAimages/Small Angle Image Processing.htm @ 2799

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415  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
416  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
417  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
418  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
419  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
420  <w:LsdException Locked="false" Priority="34" QFormat="true"
421   Name="List Paragraph"/>
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423  <w:LsdException Locked="false" Priority="30" QFormat="true"
424   Name="Intense Quote"/>
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427  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
428  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
429  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
430  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
431  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
432  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
433  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
434  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
435  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
436  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
437  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
438  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
439  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
440  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
441  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
442  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
443  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
444  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
445  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
446  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
447  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
448  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
449  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
450  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
451  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
452  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
453  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
454  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
455  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
456  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
457  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
458  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
459  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
460  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
461  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
462  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
463  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
464  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
465  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
466  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
467  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
468  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
469  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
470  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
471  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
472  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
473  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
474  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
475  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
476  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
477  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
478  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
479  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
480  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
481  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
482  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
483  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
484  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
485  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
486  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
487  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
488  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
489  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
490  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
491  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
492  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
493  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
494  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
495  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
496  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
497  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
498  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
499  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
500  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
501  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
502  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
503  <w:LsdException Locked="false" Priority="19" QFormat="true"
504   Name="Subtle Emphasis"/>
505  <w:LsdException Locked="false" Priority="21" QFormat="true"
506   Name="Intense Emphasis"/>
507  <w:LsdException Locked="false" Priority="31" QFormat="true"
508   Name="Subtle Reference"/>
509  <w:LsdException Locked="false" Priority="32" QFormat="true"
510   Name="Intense Reference"/>
511  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
512  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
513   UnhideWhenUsed="true" Name="Bibliography"/>
514  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
515   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
516  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
517  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
518  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
519  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
520  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
521  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
522  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
523  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
524  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
525  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
526  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
527  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
528  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
529  <w:LsdException Locked="false" Priority="46"
530   Name="Grid Table 1 Light Accent 1"/>
531  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
532  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
533  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
534  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
535  <w:LsdException Locked="false" Priority="51"
536   Name="Grid Table 6 Colorful Accent 1"/>
537  <w:LsdException Locked="false" Priority="52"
538   Name="Grid Table 7 Colorful Accent 1"/>
539  <w:LsdException Locked="false" Priority="46"
540   Name="Grid Table 1 Light Accent 2"/>
541  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
542  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
543  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
544  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
545  <w:LsdException Locked="false" Priority="51"
546   Name="Grid Table 6 Colorful Accent 2"/>
547  <w:LsdException Locked="false" Priority="52"
548   Name="Grid Table 7 Colorful Accent 2"/>
549  <w:LsdException Locked="false" Priority="46"
550   Name="Grid Table 1 Light Accent 3"/>
551  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
552  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
553  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
554  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
555  <w:LsdException Locked="false" Priority="51"
556   Name="Grid Table 6 Colorful Accent 3"/>
557  <w:LsdException Locked="false" Priority="52"
558   Name="Grid Table 7 Colorful Accent 3"/>
559  <w:LsdException Locked="false" Priority="46"
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561  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
562  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
563  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
564  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
565  <w:LsdException Locked="false" Priority="51"
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567  <w:LsdException Locked="false" Priority="52"
568   Name="Grid Table 7 Colorful Accent 4"/>
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570   Name="Grid Table 1 Light Accent 5"/>
571  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
572  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
573  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
574  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
575  <w:LsdException Locked="false" Priority="51"
576   Name="Grid Table 6 Colorful Accent 5"/>
577  <w:LsdException Locked="false" Priority="52"
578   Name="Grid Table 7 Colorful Accent 5"/>
579  <w:LsdException Locked="false" Priority="46"
580   Name="Grid Table 1 Light Accent 6"/>
581  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
582  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
583  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
584  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
585  <w:LsdException Locked="false" Priority="51"
586   Name="Grid Table 6 Colorful Accent 6"/>
587  <w:LsdException Locked="false" Priority="52"
588   Name="Grid Table 7 Colorful Accent 6"/>
589  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
590  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
591  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
592  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
593  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
594  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
595  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
596  <w:LsdException Locked="false" Priority="46"
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598  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
599  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
600  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
601  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
602  <w:LsdException Locked="false" Priority="51"
603   Name="List Table 6 Colorful Accent 1"/>
604  <w:LsdException Locked="false" Priority="52"
605   Name="List Table 7 Colorful Accent 1"/>
606  <w:LsdException Locked="false" Priority="46"
607   Name="List Table 1 Light Accent 2"/>
608  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
609  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
610  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
611  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
612  <w:LsdException Locked="false" Priority="51"
613   Name="List Table 6 Colorful Accent 2"/>
614  <w:LsdException Locked="false" Priority="52"
615   Name="List Table 7 Colorful Accent 2"/>
616  <w:LsdException Locked="false" Priority="46"
617   Name="List Table 1 Light Accent 3"/>
618  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
619  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
620  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
621  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
622  <w:LsdException Locked="false" Priority="51"
623   Name="List Table 6 Colorful Accent 3"/>
624  <w:LsdException Locked="false" Priority="52"
625   Name="List Table 7 Colorful Accent 3"/>
626  <w:LsdException Locked="false" Priority="46"
627   Name="List Table 1 Light Accent 4"/>
628  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
629  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
630  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
631  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
632  <w:LsdException Locked="false" Priority="51"
633   Name="List Table 6 Colorful Accent 4"/>
634  <w:LsdException Locked="false" Priority="52"
635   Name="List Table 7 Colorful Accent 4"/>
636  <w:LsdException Locked="false" Priority="46"
637   Name="List Table 1 Light Accent 5"/>
638  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
639  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
640  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
641  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
642  <w:LsdException Locked="false" Priority="51"
643   Name="List Table 6 Colorful Accent 5"/>
644  <w:LsdException Locked="false" Priority="52"
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646  <w:LsdException Locked="false" Priority="46"
647   Name="List Table 1 Light Accent 6"/>
648  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
649  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
650  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
651  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
652  <w:LsdException Locked="false" Priority="51"
653   Name="List Table 6 Colorful Accent 6"/>
654  <w:LsdException Locked="false" Priority="52"
655   Name="List Table 7 Colorful Accent 6"/>
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1167
1168<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
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1170<div class=WordSection1>
1171
1172<h1><strong>Small Angle X-Ray Data – Image Processing<o:p></o:p></strong></h1>
1173
1174<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
1175this tutorial you will reduce 2D SAXS data to create 1D absolute scaled data.
1176The data were collected at APS on beam line 15ID on some polymer base materials
1177to be used for liquid crystal displays. The processing has several steps
1178including detector calibration (i.e. determine sample-detector distance &amp;
1179tilt), integration and scaling to an absolute scaled glassy carbon measurement.
1180The data were collected at a wavelength of 1.0332Å with a <span class=SpellE>MarCCD</span>
1181detector placed ~570mm from the sample. Note that menu entries are listed in
1182bold face below as <b style='mso-bidi-font-weight:normal'><span
1183style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1184mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Help/About
1185GSAS-II</span></b>, which lists first the name of the menu (here <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;mso-bidi-theme-font:
1188minor-latin'>Help</span></b>) and second the name of the entry in the menu
1189(here <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1190mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1191minor-latin'>About GSAS-II</span></b>).<span style='mso-spacerun:yes'>  </span><span
1192style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
1193mso-bidi-font-weight:bold;mso-bidi-font-style:italic'><o:p></o:p></span></p>
1194
1195<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1196
1197<h2>Step 1: Detector calibration</h2>
1198
1199<p class=MsoNormal>The detector position is determined by using an image
1200collected from silver <span class=SpellE>behenate</span>; do <b
1201style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1202mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data/Read
1203Image data…</span></b> and a file selection dialog box will appear. Go to <span
1204class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1205"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
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1207style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1208mso-hansi-theme-font:minor-latin'>/data</span></b> and select <b
1209style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1210mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>AgBehenate_003.tif</span></b>
1211with either a mouse button double click or <b style='mso-bidi-font-weight:normal'><span
1212style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1213mso-hansi-theme-font:minor-latin'>Open</span></b>; the image will appear</p>
1214
1215<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1216 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1217 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1218 <v:stroke joinstyle="miter"/>
1219 <v:formulas>
1220  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1221  <v:f eqn="sum @0 1 0"/>
1222  <v:f eqn="sum 0 0 @1"/>
1223  <v:f eqn="prod @2 1 2"/>
1224  <v:f eqn="prod @3 21600 pixelWidth"/>
1225  <v:f eqn="prod @3 21600 pixelHeight"/>
1226  <v:f eqn="sum @0 0 1"/>
1227  <v:f eqn="prod @6 1 2"/>
1228  <v:f eqn="prod @7 21600 pixelWidth"/>
1229  <v:f eqn="sum @8 21600 0"/>
1230  <v:f eqn="prod @7 21600 pixelHeight"/>
1231  <v:f eqn="sum @10 21600 0"/>
1232 </v:formulas>
1233 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1234 <o:lock v:ext="edit" aspectratio="t"/>
1235</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1062" type="#_x0000_t75"
1236 style='width:525pt;height:450pt;visibility:visible;mso-wrap-style:square'>
1237 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image001.png"
1238  o:title=""/>
1239</v:shape><![endif]--><![if !vml]><img width=700 height=600
1240src="Small%20Angle%20Image%20Processing_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
1241
1242<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1243
1244<p class=MsoNormal>And the <b style='mso-bidi-font-weight:normal'><span
1245style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1246mso-hansi-theme-font:minor-latin'>Image controls</span></b> window will show
1247(you may have to select the <b style='mso-bidi-font-weight:normal'><span
1248style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1249mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>IMG</span></b>
1250tree entry &amp; then it’s <b style='mso-bidi-font-weight:normal'><span
1251style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1252mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Image
1253Controls</span></b>).</p>
1254
1255<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1256 id="_x0000_i1061" type="#_x0000_t75" style='width:468pt;height:402pt;
1257 visibility:visible;mso-wrap-style:square'>
1258 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image002.png"
1259  o:title=""/>
1260</v:shape><![endif]--><![if !vml]><img width=624 height=536
1261src="Small%20Angle%20Image%20Processing_files/image003.png" v:shapes="_x0000_i1061"><![endif]></span></p>
1262
1263<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1264
1265<p class=MsoNormal>Note the default <b style='mso-bidi-font-weight:normal'><span
1266style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1267mso-hansi-theme-font:minor-latin'>Type of image data</span></b> is <b
1268style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1269mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR -
1270powder diffraction data</span></b>; you will change that <span
1271style='mso-no-proof:yes'>now.</span> Select <b style='mso-bidi-font-weight:
1272normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1273minor-latin;mso-hansi-theme-font:minor-latin'>SASD – small angle scattering
1274data</span></b> (the window will change). Enter the <b style='mso-bidi-font-weight:
1275normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1276minor-latin;mso-hansi-theme-font:minor-latin'>wavelength</span></b> (<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'>1.0332</span></b>),
1279and select the <span class=SpellE><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'>Calibrant</span></b></span> (near bottom of
1282window) as <b style='mso-bidi-font-weight:normal'><span style='font-family:
1283"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1284minor-latin'>Ag <span class=SpellE>behenate</span></span></b>. Note that the
1285calibration info for Ag <span class=SpellE>behenate</span> was read from a
1286python file – <b style='mso-bidi-font-weight:normal'><span style='font-family:
1287"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1288minor-latin'>GSASII/ImageCalibrants.py</span></b>. If you have a <span
1289class=SpellE>calibrant</span> that isn’t in this file you should enter it in
1290the file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1291mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UserCalibrants.py</span></b>;
1292just follow the format of the examples within <b style='mso-bidi-font-weight:
1293normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1294minor-latin;mso-hansi-theme-font:minor-latin'>ImageCalibrants.py</span></b>.
1295You should move the <b style='mso-bidi-font-weight:normal'><span
1296style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1297mso-hansi-theme-font:minor-latin'>Max intensity</span></b> slider to near the
1298middle of the range – that will improve the image. When done the <b
1299style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1300mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1301controls</span></b> window should look like</p>
1302
1303<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1304 id="_x0000_i1060" type="#_x0000_t75" style='width:468pt;height:402pt;
1305 visibility:visible;mso-wrap-style:square'>
1306 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image004.png"
1307  o:title=""/>
1308</v:shape><![endif]--><![if !vml]><img width=624 height=536
1309src="Small%20Angle%20Image%20Processing_files/image005.png" v:shapes="_x0000_i1060"><![endif]></span></p>
1310
1311<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1312
1313<p class=MsoNormal>And the image will be</p>
1314
1315<p class=MsoNormal><!--[if gte vml 1]><v:shapetype id="_x0000_t32" coordsize="21600,21600"
1316 o:spt="32" o:oned="t" path="m,l21600,21600e" filled="f">
1317 <v:path arrowok="t" fillok="f" o:connecttype="none"/>
1318 <o:lock v:ext="edit" shapetype="t"/>
1319</v:shapetype><v:shape id="Straight_x0020_Arrow_x0020_Connector_x0020_21"
1320 o:spid="_x0000_s1026" type="#_x0000_t32" style='position:absolute;
1321 margin-left:150pt;margin-top:194.25pt;width:48pt;height:15.75pt;flip:y;
1322 z-index:251659264;visibility:visible;mso-wrap-style:square;
1323 mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:9pt;
1324 mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
1325 mso-wrap-distance-bottom:0;mso-position-horizontal:absolute;
1326 mso-position-horizontal-relative:text;mso-position-vertical:absolute;
1327 mso-position-vertical-relative:text;mso-width-percent:0;mso-height-percent:0;
1328 mso-width-relative:page;mso-height-relative:page' o:gfxdata="UEsDBBQABgAIAAAAIQC2gziS/gAAAOEBAAATAAAAW0NvbnRlbnRfVHlwZXNdLnhtbJSRQU7DMBBF
132990jcwfIWJU67QAgl6YK0S0CoHGBkTxKLZGx5TGhvj5O2G0SRWNoz/78nu9wcxkFMGNg6quQqL6RA
13300s5Y6ir5vt9lD1JwBDIwOMJKHpHlpr69KfdHjyxSmriSfYz+USnWPY7AufNIadK6MEJMx9ApD/oD
1331OlTrorhX2lFEilmcO2RdNtjC5xDF9pCuTyYBB5bi6bQ4syoJ3g9WQ0ymaiLzg5KdCXlKLjvcW893
1332SUOqXwnz5DrgnHtJTxOsQfEKIT7DmDSUCaxw7Rqn8787ZsmRM9e2VmPeBN4uqYvTtW7jvijg9N/y
1333JsXecLq0q+WD6m8AAAD//wMAUEsDBBQABgAIAAAAIQA4/SH/1gAAAJQBAAALAAAAX3JlbHMvLnJl
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1341RVWWm2IAbD2CVCHQ7e2U5LvMr7WS8aPWQUVmG069xRwxx4cUi91W1CcUvjNybkP8Qxe9MI6KLlS3
1342Igr2Dc0fVL2RCAF0XEnoC9DaSJU1kJp1+ZuaYye8ylrInOAXm8L/o5Ufzgdkpm34i4ozJ3qa0TGi
1343MKcusjeIMLA9OEc+ArJqnfwafKgJtncHTIrl6I7+DuTXQLnil2Q6BD89GzX2TFvjv9CaZKtIPBvz
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1347H777DgAA//8DAFBLAwQUAAYACAAAACEAuvjFqd8AAAALAQAADwAAAGRycy9kb3ducmV2LnhtbEyP
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1350T987jLL2lbY9DmLuWn2fJHPtsGFJqLGjp5rK793JGWieh3e7Hj4O+4Ozr1+b7cs0WDTm9mZcL0FF
1351GuNFDH/4gg6FMB39iW1QrYFZkkiXKEOaPoISxWwxl8vRwIMkgy5y/b9D8QsAAP//AwBQSwECLQAU
1352AAYACAAAACEAtoM4kv4AAADhAQAAEwAAAAAAAAAAAAAAAAAAAAAAW0NvbnRlbnRfVHlwZXNdLnht
1353bFBLAQItABQABgAIAAAAIQA4/SH/1gAAAJQBAAALAAAAAAAAAAAAAAAAAC8BAABfcmVscy8ucmVs
1354c1BLAQItABQABgAIAAAAIQB9d1Df6wEAACkEAAAOAAAAAAAAAAAAAAAAAC4CAABkcnMvZTJvRG9j
1355LnhtbFBLAQItABQABgAIAAAAIQC6+MWp3wAAAAsBAAAPAAAAAAAAAAAAAAAAAEUEAABkcnMvZG93
1356bnJldi54bWxQSwUGAAAAAAQABADzAAAAUQUAAAAA
1357" strokecolor="#c0504d [3205]" strokeweight="3pt">
1358 <v:stroke endarrow="open"/>
1359 <v:shadow on="t" color="black" opacity="22937f" origin=",.5" offset="0,.63889mm"/>
1360 <o:lock v:ext="edit" shapetype="f"/>
1361</v:shape><![endif]--><![if !vml]><span style='mso-ignore:vglayout;position:
1362absolute;z-index:251659264;margin-left:198px;margin-top:246px;width:73px;
1363height:39px'><img width=73 height=39
1364src="Small%20Angle%20Image%20Processing_files/image006.png" v:shapes="Straight_x0020_Arrow_x0020_Connector_x0020_21"></span><![endif]><span
1365style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_41"
1366 o:spid="_x0000_i1059" type="#_x0000_t75" style='width:468pt;height:401.25pt;
1367 visibility:visible;mso-wrap-style:square'>
1368 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image007.png"
1369  o:title=""/>
1370</v:shape><![endif]--><![if !vml]><img width=624 height=535
1371src="Small%20Angle%20Image%20Processing_files/image008.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
1372
1373<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1374
1375<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
1376style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1377mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calibration</span></b><b
1378style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1379mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>/Calibrate</span></b>
1380from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1381mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1382Controls</span></b> menu; a bit of instruction will appear on the status line
1383of this window. Select 5 points on the innermost ring (arrowed above); a small
1384red cross will appear at each selection point. Press the right mouse button to
1385finish; calibration will proceed. A sequence of concentric red rings will
1386appear; they will switch to blue when calibration is finished. Select <b
1387style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1388mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show ring
1389picks</span></b> (near bottom right of <b style='mso-bidi-font-weight:normal'><span
1390style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1391mso-hansi-theme-font:minor-latin'>Image Controls</span></b> window). The <b
1392style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1393mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1394Controls</span></b> window will show the results of the calibration</p>
1395
1396<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1397 id="Picture_x0020_5" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:468pt;
1398 height:402pt;visibility:visible;mso-wrap-style:square'>
1399 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image009.png"
1400  o:title=""/>
1401</v:shape><![endif]--><![if !vml]><img width=624 height=536
1402src="Small%20Angle%20Image%20Processing_files/image010.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
1403
1404<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1405
1406<p class=MsoNormal>And the plot will show the points used in the calibration
1407calculations.</p>
1408
1409<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1410 id="Picture_x0020_6" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:468pt;
1411 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1412 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image011.png"
1413  o:title=""/>
1414</v:shape><![endif]--><![if !vml]><img width=624 height=535
1415src="Small%20Angle%20Image%20Processing_files/image012.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
1416
1417<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1418
1419<p class=MsoNormal>You would like to use more points from just the visible
1420rings. I suggest you change <b style='mso-bidi-font-weight:normal'><span
1421style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1422mso-hansi-theme-font:minor-latin'>Min ring I/<span class=SpellE>Ib</span></span></b>
1423to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1424mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.5</span></b>
1425and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1426mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Min <span
1427class=SpellE>calib</span> d-spacing</span></b> to <b style='mso-bidi-font-weight:
1428normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1429minor-latin;mso-hansi-theme-font:minor-latin'>10.0</span></b>. Do <b
1430style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1431mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calibrate/Recalibrate</span></b>;
1432more points will be used and they will be limited to the 5 visible rings in the
1433pattern.</p>
1434
1435<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1436 id="Picture_x0020_7" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:468pt;
1437 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1438 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image013.png"
1439  o:title=""/>
1440</v:shape><![endif]--><![if !vml]><img width=624 height=535
1441src="Small%20Angle%20Image%20Processing_files/image014.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
1442
1443<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1444
1445<p class=MsoNormal>And give the calibration result as</p>
1446
1447<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1448 id="Picture_x0020_8" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:468pt;
1449 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1450 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image013.png"
1451  o:title=""/>
1452</v:shape><![endif]--><![if !vml]><img width=624 height=535
1453src="Small%20Angle%20Image%20Processing_files/image015.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
1454
1455<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1456
1457<p class=MsoNormal>You will need this calibration information to process the
1458other images in this tutorial. To save it for future use do <span class=SpellE><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'>Parms</span></b></span><b
1461style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1462mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>/Save
1463controls</span></b>; a file dialog will appear. Makeup a file name (no
1464extension needed) for this; I chose <b style='mso-bidi-font-weight:normal'><span
1465style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1466mso-hansi-theme-font:minor-latin'>SASD</span></b>. Press <b style='mso-bidi-font-weight:
1467normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1468minor-latin;mso-hansi-theme-font:minor-latin'>Save</span></b> and the file <span
1469class=SpellE><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'>SASD.imctrl</span></b></span> will be written to the local
1472directory. If you are continuing on to the next step do <b style='mso-bidi-font-weight:
1473normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1474minor-latin;mso-hansi-theme-font:minor-latin'>File/New Project</span></b>
1475(don’t bother saving the project file unless you want it; we will not need it
1476here); otherwise you can exit GSAS-II.</p>
1477
1478<h2>Step 2: Data image integration</h2>
1479
1480<p class=MsoNormal>The objective here is to read in the four polymer sample
1481images, a glassy carbon image, an empty container image and a dark image. The
1482images will be integrated after creating masks to remove the beam stop and
1483other objectionable parts of the images. If you have not done so already, start
1484GSAS-II. </p>
1485
1486<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1487
1488<p class=MsoNormal>First do <b style='mso-bidi-font-weight:normal'><span
1489style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1490mso-hansi-theme-font:minor-latin'>Data/Read image data…</span></b>, go to <b
1491style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1492mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>exercises/<span
1493class=SpellE>SAimages</span></span></b> and select all images except <b
1494style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1495mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>AgBehenate_003.tif</span></b>;
1496then press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1497"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1498minor-latin'>Open</span></b> to read all of them. The GSAS-II data tree window
1499will show entries for 7 images and will expand the last one</p>
1500
1501<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1502 id="Picture_x0020_9" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:300pt;
1503 height:310.5pt;visibility:visible;mso-wrap-style:square'>
1504 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image016.png"
1505  o:title=""/>
1506</v:shape><![endif]--><![if !vml]><img width=400 height=414
1507src="Small%20Angle%20Image%20Processing_files/image016.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
1508
1509<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1510
1511<p class=MsoNormal>Notice that the Dark, Empty and GC (glassy carbon) are all
15125s images and the Sa1-4 ones are 40s images; this time information is needed
1513later to obtain correct scaling. First select the <b style='mso-bidi-font-weight:
1514normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1515minor-latin;mso-hansi-theme-font:minor-latin'>IMG GC_5s_200.tif</span></b>
1516entry from the tree and expand it (press 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'>+</span></b> box); then select <b
1519style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1520mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1521controls</span></b>. The data window (<b style='mso-bidi-font-weight:normal'><span
1522style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1523mso-hansi-theme-font:minor-latin'>Image Controls</span></b>) will show the
1524default settings.</p>
1525
1526<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1527 id="Picture_x0020_10" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:468pt;
1528 height:402pt;visibility:visible;mso-wrap-style:square'>
1529 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image017.png"
1530  o:title=""/>
1531</v:shape><![endif]--><![if !vml]><img width=624 height=536
1532src="Small%20Angle%20Image%20Processing_files/image018.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
1533
1534<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1535
1536<p class=MsoNormal>Do <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1537style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1538mso-hansi-theme-font:minor-latin'>Parms</span></b></span><b style='mso-bidi-font-weight:
1539normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1540minor-latin;mso-hansi-theme-font:minor-latin'>/Load controls</span></b> from
1541the menu; a file selection dialog will appear showing the available *.<span
1542class=SpellE>imctrl</span> files (the one you made in Step 1 should be seen).
1543Select it and press <b style='mso-bidi-font-weight:normal'><span
1544style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1545mso-hansi-theme-font:minor-latin'>Open</span></b>; the <b style='mso-bidi-font-weight:
1546normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1547minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> window
1548will be redrawn with the settings obtained in <b style='mso-bidi-font-weight:
1549normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1550minor-latin;mso-hansi-theme-font:minor-latin'>Step 1: Detector calibration</span></b></p>
1551
1552<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1553 id="Picture_x0020_11" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:468pt;
1554 height:402pt;visibility:visible;mso-wrap-style:square'>
1555 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image019.png"
1556  o:title=""/>
1557</v:shape><![endif]--><![if !vml]><img width=624 height=536
1558src="Small%20Angle%20Image%20Processing_files/image020.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
1559
1560<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1561
1562<p class=MsoNormal>and the image will be that of glassy carbon. Changing the <b
1563style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1564mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Max
1565intensity</span></b> slider on the <b style='mso-bidi-font-weight:normal'><span
1566style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1567mso-hansi-theme-font:minor-latin'>Image Controls</span></b> window will show
1568that the image from the <span class=SpellE>MarCCD</span> is circular and
1569slightly offset from the beam center. You can also select from the drop down to
1570the left of the intensity sliders; <b style='mso-bidi-font-weight:normal'><span
1571style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1572mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>90%</span></b>
1573will suffice. A beam stop shadow is evident as well as an arc-like fault in the
1574image (a bit hard to see - toward the upper left corner of the image). We will
1575sort those out later.</p>
1576
1577<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1578 id="Picture_x0020_12" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:468pt;
1579 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1580 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image021.png"
1581  o:title=""/>
1582</v:shape><![endif]--><![if !vml]><img width=624 height=535
1583src="Small%20Angle%20Image%20Processing_files/image022.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
1584
1585<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1586
1587<p class=MsoNormal>The next step we will be doing is to set up the integration
1588controls. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
1589"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1590minor-latin'>Dark image</span></b> is <b style='mso-bidi-font-weight:normal'><span
1591style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1592mso-hansi-theme-font:minor-latin'>IMG Dark_5s_003.tif</span></b>, the <b
1593style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1594mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background
1595image</span></b> is <b style='mso-bidi-font-weight:normal'><span
1596style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1597mso-hansi-theme-font:minor-latin'>IMG Empty_5s_014.tif</span></b>. We will be
1598needing the background image; the dark is not needed as it would be subtracted
1599from both sample and background thus cancelling out. Select just <b
1600style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1601mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>IMG
1602Empty_5s_<span class=GramE>014.tif<span style='font-family:"Times New Roman",serif;
1603font-weight:normal'><span style='mso-spacerun:yes'>  </span>for</span></span></span></b>
1604the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1605mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1606minor-latin'>Background image</span></b>; leave Dark image blank. The <b
1607style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1608mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multiplier</span></b>
1609is <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1610mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-1.0</span></b>
1611because its exposure was the same as this glassy carbon image (5s). Notice that
1612the background is instantly applied to the image. Next check the boxes for <b
1613style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1614mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show
1615integration limits?</span></b> and <b style='mso-bidi-font-weight:normal'><span
1616style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1617mso-hansi-theme-font:minor-latin'>Do full integration?</span></b> A pair of
1618circles with a connecting diagonal line will appear on the plot. Set the <b
1619style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1620mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Inner/Outer
1621q</span></b> values to <b style='mso-bidi-font-weight:normal'><span
1622style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1623mso-hansi-theme-font:minor-latin'>0.05</span></b> and <b style='mso-bidi-font-weight:
1624normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1625minor-latin;mso-hansi-theme-font:minor-latin'>0.9</span></b>, respectively, and
1626set the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1627mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Start
1628azimuth</span></b> to <b style='mso-bidi-font-weight:normal'><span
1629style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1630mso-hansi-theme-font:minor-latin'>0</span></b>. Set the <b style='mso-bidi-font-weight:
1631normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1632minor-latin;mso-hansi-theme-font:minor-latin'>No. 2-theta bins</span></b> to <b
1633style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1634mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>250</span></b>,
1635which is more appropriate for small angle scattering, and set the <b
1636style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1637mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bin style:
1638Constant step bins in</span></b> to <b style='mso-bidi-font-weight:normal'><span
1639style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1640mso-hansi-theme-font:minor-latin'>log(q)</span></b>. You should also check the <b
1641style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1642mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Apply sample
1643absorption?</span></b> and <b style='mso-bidi-font-weight:normal'><span
1644style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1645mso-hansi-theme-font:minor-latin'>Apply polarization?</span></b> <span
1646class=GramE>boxes</span>; set the sample shape to <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;mso-bidi-theme-font:minor-latin'>Fixed
1649flat plate</span></b> and enter the measured <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'>transmission</span></b> (<b
1652style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1653mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.818</span></b>)
1654for the glassy carbon sample. When done the <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'>Image Controls</span></b> data
1657window should look like</p>
1658
1659<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1660 id="Picture_x0020_13" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:468pt;
1661 height:402pt;visibility:visible;mso-wrap-style:square'>
1662 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image023.png"
1663  o:title=""/>
1664</v:shape><![endif]--><![if !vml]><img width=624 height=536
1665src="Small%20Angle%20Image%20Processing_files/image024.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1666
1667<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1668
1669<p class=MsoNormal>And the plot should look like</p>
1670
1671<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1672 id="Picture_x0020_14" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:468pt;
1673 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1674 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image025.png"
1675  o:title=""/>
1676</v:shape><![endif]--><![if !vml]><img width=624 height=535
1677src="Small%20Angle%20Image%20Processing_files/image026.png" v:shapes="Picture_x0020_14"><![endif]></span></p>
1678
1679<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1680
1681<p class=MsoNormal>Now copy these controls to the other images. Do <span
1682class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1683"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1684minor-latin'>Parms</span></b></span><b style='mso-bidi-font-weight:normal'><span
1685style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1686mso-hansi-theme-font:minor-latin'>/Copy controls</span></b> and select just the
1687<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1688mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-4</span></b>
1689data names. </p>
1690
1691<p class=MsoNormal>We now need to go to the <b style='mso-bidi-font-weight:
1692normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1693minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> for
1694each of <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1695mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b>
1696to enter the correct transmission for each and change the Background <b
1697style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1698mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multiplier</span></b>
1699to account for the different exposure times. Start with <b style='mso-bidi-font-weight:
1700normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1701minor-latin;mso-hansi-theme-font:minor-latin'>IMG Sa1_40s_067.tif</span></b>
1702and change <b style='mso-bidi-font-weight:normal'><span style='font-family:
1703"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1704minor-latin'>transmission</span></b> to <b style='mso-bidi-font-weight:normal'><span
1705style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1706mso-hansi-theme-font:minor-latin'>0.943</span></b> and the <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'>multiplier</span></b> to <b
1709style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1710mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1711Then go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1712"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1713minor-latin'>IMG Sa2_40s_069.tif</span></b> and change <b style='mso-bidi-font-weight:
1714normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1715minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1716style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1717mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.979</span></b>;
1718<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1719mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multiplier</span></b>
1720to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1721mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1722Next go <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1723mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>to IMG
1724Sa3_40s_059.tif</span></b> and change <b style='mso-bidi-font-weight:normal'><span
1725style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1726mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1727style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1728mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.960</span></b>;
1729<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1730mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multiplier</span></b>
1731to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1732mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1733Finally, go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1734"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1735minor-latin'>IMG Sa4_40s_061.tif</span></b> and change <b style='mso-bidi-font-weight:
1736normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1737minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1738style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1739mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.968</span></b>;
1740<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1741mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multiplier</span></b>
1742to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1743mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1744The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1745mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1746Controls</span></b> data window for this should look like</p>
1747
1748<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1749 id="Picture_x0020_39" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt;
1750 height:402pt;visibility:visible;mso-wrap-style:square'>
1751 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image027.png"
1752  o:title=""/>
1753</v:shape><![endif]--><![if !vml]><img width=624 height=536
1754src="Small%20Angle%20Image%20Processing_files/image028.png" v:shapes="Picture_x0020_39"><![endif]></span></p>
1755
1756<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1757
1758<p class=MsoNormal>You will notice that the image changes as you change the Background
1759image multiplier; it applies this correction immediately. Pretty clearly much
1760of the Sa1-4 images are largely background (intensities ~0; negative ones shown
1761as red); we’ll see the result of this when we integrate them. </p>
1762
1763<p class=MsoNormal>This is a reasonable time to save the project; do <b
1764style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1765mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>File/Save
1766project as…</span></b> from the main GSAS-II data tree menu. Choose a file name
1767(I assumed <b style='mso-bidi-font-weight:normal'><span style='font-family:
1768"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1769minor-latin'>image</span></b>) and it will be written on the local file
1770directory. </p>
1771
1772<p class=MsoNormal>As noted earlier, the images contain some unwanted features;
1773so let’s create masks to remove them. Select <b style='mso-bidi-font-weight:
1774normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1775minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b> from the GSAS-II
1776data tree under <b style='mso-bidi-font-weight:normal'><span style='font-family:
1777"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1778minor-latin'>IMG GC_5s_200.tif</span></b>; the data window will show</p>
1779
1780<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1781 id="Picture_x0020_40" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:453.75pt;
1782 height:140.25pt;visibility:visible;mso-wrap-style:square'>
1783 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image029.png"
1784  o:title=""/>
1785</v:shape><![endif]--><![if !vml]><img width=605 height=187
1786src="Small%20Angle%20Image%20Processing_files/image029.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
1787
1788<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1789
1790<p class=MsoNormal>To mask out the regions beyond the circular <span
1791class=SpellE>MarCCD</span> image change the <span class=GramE><b
1792style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1793mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Lower<span
1794style='mso-spacerun:yes'>  </span><span class=SpellE>threshhold</span></span></b></span>
1795from <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1796mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0</span></b>
1797to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1798mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>;
1799the image will be redrawn with these regions in red</p>
1800
1801<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1802 id="Picture_x0020_43" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:468pt;
1803 height:430.5pt;visibility:visible;mso-wrap-style:square'>
1804 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image030.png"
1805  o:title=""/>
1806</v:shape><![endif]--><![if !vml]><img width=624 height=574
1807src="Small%20Angle%20Image%20Processing_files/image031.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
1808
1809<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1810
1811<p class=MsoNormal>These are now excluded. The status line for the <b
1812style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1813mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b>
1814data window gives the directions for adding additional masks. You can make arcs
1815(we’ll use that here), rings, spots (this too) and polygons (this as well) as
1816masks. These enclose areas to be excluded. The frame works in the opposite
1817sense in that everything outside the frame is excluded (NB: only one frame is
1818allowed). So let’s first mask the bad arc in the upper left – zoom in on that
1819part of the image</p>
1820
1821<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1822 id="Picture_x0020_44" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:468pt;
1823 height:430.5pt;visibility:visible;mso-wrap-style:square'>
1824 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image032.png"
1825  o:title=""/>
1826</v:shape><![endif]--><![if !vml]><img width=624 height=574
1827src="Small%20Angle%20Image%20Processing_files/image033.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
1828
1829<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1830
1831<p class=MsoNormal>To add the mask 1: be sure the focus is on the image and the
1832zoom buttons are off, 2: type <b style='mso-bidi-font-weight:normal'><span
1833style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1834mso-hansi-theme-font:minor-latin'>a</span></b> to activate the arc mask entry
18353: press the left mouse button (<b style='mso-bidi-font-weight:normal'><span
1836style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1837mso-hansi-theme-font:minor-latin'>LB</span></b>) with the cursor centered on
1838the bad arc. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
1839"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1840minor-latin'>Masks</span></b> window will show a new entry </p>
1841
1842<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1843 id="Picture_x0020_45" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:453.75pt;
1844 height:183.75pt;visibility:visible;mso-wrap-style:square'>
1845 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image034.png"
1846  o:title=""/>
1847</v:shape><![endif]--><![if !vml]><img width=605 height=245
1848src="Small%20Angle%20Image%20Processing_files/image034.png" v:shapes="Picture_x0020_45"><![endif]></span><span
1849style='mso-spacerun:yes'> </span></p>
1850
1851<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1852
1853<p class=MsoNormal>and an arc mask will be drawn on the plot.</p>
1854
1855<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1856 id="Picture_x0020_46" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:468pt;
1857 height:430.5pt;visibility:visible;mso-wrap-style:square'>
1858 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image035.png"
1859  o:title=""/>
1860</v:shape><![endif]--><![if !vml]><img width=624 height=574
1861src="Small%20Angle%20Image%20Processing_files/image036.png" v:shapes="Picture_x0020_46"><![endif]></span></p>
1862
1863<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1864
1865<p class=MsoNormal>You can change the angular width of the arc by changing <b
1866style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1867mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>thickness</span></b>
1868in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1869mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b>
1870data window, you can change the angular range of the arc by RB dragging either
1871end of the arc (NB: increments only in whole degrees), and you can move the
1872arc<span style='mso-spacerun:yes'>  </span>along a constant 2&#920; angle by LB
1873dragging on any edge of the mask. The curvature is centered on the beam center
1874position and follows a constant 2&#920; curve established by the detector
1875calibration.<span style='mso-no-proof:yes'> </span></p>
1876
1877<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1878 id="Picture_x0020_65" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
1879 height:450pt;visibility:visible;mso-wrap-style:square'>
1880 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image037.png"
1881  o:title=""/>
1882</v:shape><![endif]--><![if !vml]><img width=700 height=600
1883src="Small%20Angle%20Image%20Processing_files/image037.png" v:shapes="Picture_x0020_65"><![endif]></span></p>
1884
1885<p class=MsoNormal>Next let’s deal with the beam stop. I’m going to use both a
1886polygon and a spot to cover it. Move the zoom area to be around the center,
1887make sure the zoom buttons are off, enter ‘<b style='mso-bidi-font-weight:normal'><span
1888style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1889mso-hansi-theme-font:minor-latin'>s</span></b>’ on the plot and press mouse <b
1890style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1891mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>LB</span></b>
1892with the cursor positioned where you want the spot (probably on the ‘X’ – beam center
1893position). A 1mm diameter red circle will appear on the plot</p>
1894
1895<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1896 id="Picture_x0020_66" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;
1897 height:450pt;visibility:visible;mso-wrap-style:square'>
1898 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image038.png"
1899  o:title=""/>
1900</v:shape><![endif]--><![if !vml]><img width=700 height=600
1901src="Small%20Angle%20Image%20Processing_files/image038.png" v:shapes="Picture_x0020_66"><![endif]></span></p>
1902
1903<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1904
1905<p class=MsoNormal>And the <b style='mso-bidi-font-weight:normal'><span
1906style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1907mso-hansi-theme-font:minor-latin'>Masks</span></b> window will have new
1908information</p>
1909
1910<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1911 id="Picture_x0020_47" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:453.75pt;
1912 height:227.25pt;visibility:visible;mso-wrap-style:square'>
1913 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image039.png"
1914  o:title=""/>
1915</v:shape><![endif]--><![if !vml]><img width=605 height=303
1916src="Small%20Angle%20Image%20Processing_files/image039.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
1917
1918<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1919
1920<p class=MsoNormal>You can change the diameter of the spot, I used <b
1921style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1922mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>7.0</span></b>;
1923the plot now shows a ring that just covers the beam stop. You may have to drag
1924it a bit (Hint: drag the center of the spot) to get it well centered.</p>
1925
1926<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1927 id="Picture_x0020_67" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
1928 height:450pt;visibility:visible;mso-wrap-style:square'>
1929 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image040.png"
1930  o:title=""/>
1931</v:shape><![endif]--><![if !vml]><img width=700 height=600
1932src="Small%20Angle%20Image%20Processing_files/image040.png" v:shapes="Picture_x0020_67"><![endif]></span></p>
1933
1934<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1935
1936<p class=MsoNormal>Next we need to mask the stick holding the beam stop; we’ll
1937use a 4 sided polygon for this. Adjust the zoom &amp; position so you can see
1938the entire beam stop stick. Make sure all zoom buttons are off, press ‘<b
1939style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1940mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>p</span></b>’
1941on the plot, then press the mouse <b style='mso-bidi-font-weight:normal'><span
1942style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1943mso-hansi-theme-font:minor-latin'>LB</span></b> at four points in succession
1944around the beam stop stick. A line segment for the polygon will be drawn
1945following your mouse clicks. Finally press the mouse <b style='mso-bidi-font-weight:
1946normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1947minor-latin;mso-hansi-theme-font:minor-latin'>RB</span></b> to close the
1948polygon. You should see something like</p>
1949
1950<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1951 id="Picture_x0020_68" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
1952 height:450pt;visibility:visible;mso-wrap-style:square'>
1953 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image041.png"
1954  o:title=""/>
1955</v:shape><![endif]--><![if !vml]><img width=700 height=600
1956src="Small%20Angle%20Image%20Processing_files/image041.png" v:shapes="Picture_x0020_68"><![endif]></span></p>
1957
1958<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1959
1960<p class=MsoNormal>You can adjust the position of the polygon vertices by
1961closely dragging it with mouse <b style='mso-bidi-font-weight:normal'><span
1962style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1963mso-hansi-theme-font:minor-latin'>LB</span></b> pressed; a new vertex can be
1964added by dragging an existing vertex with the mouse <b style='mso-bidi-font-weight:
1965normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1966minor-latin;mso-hansi-theme-font:minor-latin'>RB</span></b> pressed. If you
1967drag one vertex onto another, they are merged and cannot be separated.</p>
1968
1969<p class=MsoNormal>We want to use these masks for all the Sa1-4 images. Do <b
1970style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1971mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Copy
1972mask</span></b>; a <b style='mso-bidi-font-weight:normal'><span
1973style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1974mso-hansi-theme-font:minor-latin'>Copy mask information</span></b> dialog box
1975will appear. Select the <b style='mso-bidi-font-weight:normal'><span
1976style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1977mso-hansi-theme-font:minor-latin'>Sa1-4</span></b> items and press <b
1978style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1979mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.
1980Here is a useful place to save your project; do <b style='mso-bidi-font-weight:
1981normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1982minor-latin;mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from
1983the main GSAS-II data tree menu.</p>
1984
1985<h2>Step 3: Integration of images</h2>
1986
1987<p class=MsoNormal>We are now ready to integrate the glassy carbon and the four
1988Sa images. Select any <b style='mso-bidi-font-weight:normal'><span
1989style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1990mso-hansi-theme-font:minor-latin'>Image Controls</span></b> and then do <b
1991style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1992mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Integration/Integrate
1993all</span></b>. A selection dialog will appear; select only the <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</span></b>
1996and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1997mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b>
1998data sets and press <b style='mso-bidi-font-weight:normal'><span
1999style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2000mso-hansi-theme-font:minor-latin'>Ok</span></b>. The image integration will
2001proceed; a progress bar increments as each one is done. Five SASD data items
2002will appear on the GSAS-II data tree; the last one (<b style='mso-bidi-font-weight:
2003normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2004minor-latin;mso-hansi-theme-font:minor-latin'>SASD Sa4_40s_061.tif <span
2005class=SpellE>Azm</span>=0.00</span></b>) will be expanded and plotted (you may
2006have to select the <b style='mso-bidi-font-weight:normal'><span
2007style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2008mso-hansi-theme-font:minor-latin'>Powder Patterns</span></b> tab to see it).</p>
2009
2010<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2011 id="Picture_x0020_26" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
2012 height:450pt;visibility:visible;mso-wrap-style:square'>
2013 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image042.png"
2014  o:title=""/>
2015</v:shape><![endif]--><![if !vml]><img width=700 height=600
2016src="Small%20Angle%20Image%20Processing_files/image042.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
2017
2018<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2019
2020<p class=MsoNormal>Pretty obviously the SASD pattern is down to background at
2021Q~0.25Å<sup>-1</sup>; the other Sa1-Sa4 patterns are similar. The glassy carbon
2022pattern extends nicely to the highest Q (~1.0Å<sup>-1</sup>) measured.</p>
2023
2024<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2025 id="_x0000_i1036" type="#_x0000_t75" style='width:525pt;height:450pt;
2026 visibility:visible;mso-wrap-style:square'>
2027 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image043.png"
2028  o:title=""/>
2029</v:shape><![endif]--><![if !vml]><img width=700 height=600
2030src="Small%20Angle%20Image%20Processing_files/image043.png" v:shapes="_x0000_i1036"><![endif]></span></p>
2031
2032<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2033
2034<h2>Step 4: Scaling of SASD patterns</h2>
2035
2036<p class=MsoNormal>To set this data on an absolute scale, we compare it to an
2037absolute scaled glassy carbon scan. One of these is in the same directory as
2038the image data; do <b style='mso-bidi-font-weight:normal'><span
2039style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2040mso-hansi-theme-font:minor-latin'>Import/Small Angle Data/ from q(A-1) step
2041X-ray QIE data file</span></b> and select <b style='mso-bidi-font-weight:normal'><span
2042style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2043mso-hansi-theme-font:minor-latin'>GC calibrated data.txt</span></b> from the
2044file selection dialog. You will need to select <b style='mso-bidi-font-weight:
2045normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2046minor-latin;mso-hansi-theme-font:minor-latin'>any <span class=GramE>file(</span>*.*)</span></b>
2047to see it. A <b style='mso-bidi-font-weight:normal'><span style='font-family:
2048"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2049minor-latin'>Is this the file you want</span></b> dialog will appear – respond <b
2050style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2051mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b>
2052to read the file; it will be plotted.</p>
2053
2054<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2055 id="_x0000_i1035" type="#_x0000_t75" style='width:525pt;height:450pt;
2056 visibility:visible;mso-wrap-style:square'>
2057 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image044.png"
2058  o:title=""/>
2059</v:shape><![endif]--><![if !vml]><img width=700 height=600
2060src="Small%20Angle%20Image%20Processing_files/image044.png" v:shapes="_x0000_i1035"><![endif]></span></p>
2061
2062<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2063
2064<p class=MsoNormal>If you enter ‘<b style='mso-bidi-font-weight:normal'><span
2065style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2066mso-hansi-theme-font:minor-latin'>m</span></b>’ on the plot window, all of the
2067SASD patterns will be plotted together (I’ve adjusted the zoom to see them
2068all).</p>
2069
2070<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2071 id="_x0000_i1034" type="#_x0000_t75" style='width:525pt;height:450pt;
2072 visibility:visible;mso-wrap-style:square'>
2073 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image045.png"
2074  o:title=""/>
2075</v:shape><![endif]--><![if !vml]><img width=700 height=600
2076src="Small%20Angle%20Image%20Processing_files/image045.png" v:shapes="_x0000_i1034"><![endif]></span></p>
2077
2078<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2079
2080<p class=MsoNormal>Clearly the measured image data need to be scaled down to have
2081them on absolute scale. First is to discover the scaling between the two glassy
2082carbon patterns. Go to the measured one (<b style='mso-bidi-font-weight:normal'><span
2083style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2084mso-hansi-theme-font:minor-latin'>SASD GC_5s_200.tif <span class=SpellE>Azm</span>=0.00</span></b>)
2085and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2086"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2087minor-latin'>Sample Parameters</span></b>.</p>
2088
2089<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2090 id="Picture_x0020_48" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:304.5pt;
2091 height:460.5pt;visibility:visible;mso-wrap-style:square'>
2092 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image046.png"
2093  o:title=""/>
2094</v:shape><![endif]--><![if !vml]><img width=406 height=614
2095src="Small%20Angle%20Image%20Processing_files/image046.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
2096
2097<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2098
2099<p class=MsoNormal>We will change <b style='mso-bidi-font-weight:normal'><span
2100style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2101mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> by
2102comparison with the absolute glassy carbon scan. Do <b style='mso-bidi-font-weight:
2103normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2104minor-latin;mso-hansi-theme-font:minor-latin'>Command/Set scale</span></b> from
2105the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2106mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
2107Parameters</span></b> menu; a <b style='mso-bidi-font-weight:normal'><span
2108style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2109mso-hansi-theme-font:minor-latin'>Reference histogram</span></b> dialog will
2110appear.</p>
2111
2112<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2113 id="Picture_x0020_49" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:192.75pt;
2114 height:168pt;visibility:visible;mso-wrap-style:square'>
2115 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image047.png"
2116  o:title=""/>
2117</v:shape><![endif]--><![if !vml]><img width=257 height=224
2118src="Small%20Angle%20Image%20Processing_files/image047.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
2119
2120<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2121
2122<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2123style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2124mso-hansi-theme-font:minor-latin'>SASD GC calibrated data.txt</span></b> (shown
2125in blue above) and press <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'>Ok</span></b>; the <b style='mso-bidi-font-weight:
2128normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2129minor-latin;mso-hansi-theme-font:minor-latin'>GC_5s_200.tif</span></b> data
2130will be rescaled to the <b style='mso-bidi-font-weight:normal'><span
2131style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2132mso-hansi-theme-font:minor-latin'>GC calibrated data</span></b> and the <b
2133style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2134mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
2135scale factor</span></b> will be changed to the new scaling factor (<b
2136style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2137mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.0008519</span></b>).
2138The plot will be redrawn with the scaled data.</p>
2139
2140<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2141 id="_x0000_i1031" type="#_x0000_t75" style='width:525pt;height:450pt;
2142 visibility:visible;mso-wrap-style:square'>
2143 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image048.png"
2144  o:title=""/>
2145</v:shape><![endif]--><![if !vml]><img width=700 height=600
2146src="Small%20Angle%20Image%20Processing_files/image048.png" v:shapes="_x0000_i1031"><![endif]></span></p>
2147
2148<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2149
2150<p class=MsoNormal>The divergence at high Q is probably from a background
2151contribution to the standard that is not present in our measured one. Next we
2152have to apply this scale factor to the Sa1-Sa4 data sets. Do <b
2153style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2154mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Command/Copy
2155selected…</span></b> from the <b style='mso-bidi-font-weight:normal'><span
2156style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2157mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> menu; a <b
2158style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2159mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select
2160sample parameters</span></b> dialog will appear</p>
2161
2162<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2163 id="Picture_x0020_50" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:240pt;
2164 height:318pt;visibility:visible;mso-wrap-style:square'>
2165 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image049.png"
2166  o:title=""/>
2167</v:shape><![endif]--><![if !vml]><img width=320 height=424
2168src="Small%20Angle%20Image%20Processing_files/image049.png" v:shapes="Picture_x0020_50"><![endif]></span></p>
2169
2170<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2171
2172<p class=MsoNormal>Select only <b style='mso-bidi-font-weight:normal'><span
2173style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2174mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> (#8) and
2175press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2176mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>;
2177a <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2178mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Copy sample
2179parameters</span></b> dialog will appear</p>
2180
2181<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2182 id="Picture_x0020_51" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:226.5pt;
2183 height:254.25pt;visibility:visible;mso-wrap-style:square'>
2184 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image050.png"
2185  o:title=""/>
2186</v:shape><![endif]--><![if !vml]><img width=302 height=339
2187src="Small%20Angle%20Image%20Processing_files/image050.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
2188
2189<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2190
2191<p class=MsoNormal>Select only the <b style='mso-bidi-font-weight:normal'><span
2192style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2193mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b> data sets and press <b
2194style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2195mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.
2196The copy will occur and the plot redrawn</p>
2197
2198<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2199 id="Picture_x0020_53" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
2200 height:450pt;visibility:visible;mso-wrap-style:square'>
2201 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image051.png"
2202  o:title=""/>
2203</v:shape><![endif]--><![if !vml]><img width=700 height=600
2204src="Small%20Angle%20Image%20Processing_files/image051.png" v:shapes="Picture_x0020_53"><![endif]></span></p>
2205
2206<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2207
2208<p class=MsoNormal>I’ve changed the zoom to show all the data. We are not quite
2209done; the scales for the Sa1-Sa4 data sets have to be further reduced by a factor
2210of 8 to account for the longer exposure time. Select <b style='mso-bidi-font-weight:
2211normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2212minor-latin;mso-hansi-theme-font:minor-latin'>SASD Sa1_40s_067.tif</span></b>
2213from the GSAS-II data tree, expand it and choose <b style='mso-bidi-font-weight:
2214normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2215minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b></p>
2216
2217<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2218 id="Picture_x0020_52" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:304.5pt;
2219 height:460.5pt;visibility:visible;mso-wrap-style:square'>
2220 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image052.png"
2221  o:title=""/>
2222</v:shape><![endif]--><![if !vml]><img width=406 height=614
2223src="Small%20Angle%20Image%20Processing_files/image052.png" v:shapes="Picture_x0020_52"><![endif]></span></p>
2224
2225<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2226
2227<p class=MsoNormal>The data items here can take simple mathematical expressions
2228so change <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2229mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
2230scale factor</span></b> to <b style='mso-bidi-font-weight:normal'><span
2231style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2232mso-hansi-theme-font:minor-latin'>0.0008519/8</span></b> and press <b
2233style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2234mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>.
2235The value will change to <b style='mso-bidi-font-weight:normal'><span
2236style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2237mso-hansi-theme-font:minor-latin'>0.0001065</span></b> and the plot redrawn.</p>
2238
2239<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2240 id="Picture_x0020_56" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
2241 height:450pt;visibility:visible;mso-wrap-style:square'>
2242 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image053.png"
2243  o:title=""/>
2244</v:shape><![endif]--><![if !vml]><img width=700 height=600
2245src="Small%20Angle%20Image%20Processing_files/image053.png" v:shapes="Picture_x0020_56"><![endif]></span></p>
2246
2247<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2248
2249<p class=MsoNormal>Next do <b style='mso-bidi-font-weight:normal'><span
2250style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2251mso-hansi-theme-font:minor-latin'>Command/Copy selected</span></b> as before to
2252copy this new scale factor to the other Sa data sets. The plot will again be
2253redrawn</p>
2254
2255<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2256 id="Picture_x0020_57" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
2257 height:450pt;visibility:visible;mso-wrap-style:square'>
2258 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image054.png"
2259  o:title=""/>
2260</v:shape><![endif]--><![if !vml]><img width=700 height=600
2261src="Small%20Angle%20Image%20Processing_files/image054.png" v:shapes="Picture_x0020_57"><![endif]></span></p>
2262
2263<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2264
2265<p class=MsoNormal>Everything is now on absolute scale and these polymer
2266samples are quite weak small angle <span class=SpellE>scatterers</span>. This
2267is a good point to do a <b style='mso-bidi-font-weight:normal'><span
2268style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2269mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from the main
2270GSAS-II data tree menu. You can try to fit unified &amp; <span class=SpellE>Porod</span>
2271models to them following the procedures demonstrated in the <strong><span
2272style='font-weight:normal'>Fitting Small Angle X-Ray Data</span></strong><strong><span
2273style='font-weight:normal;mso-bidi-font-weight:bold'> tutorial. I’d set the
2274high Q limit to about 0.25Å<sup>-1</sup> as above that is only noisy
2275background.</span></strong></p>
2276
2277</div>
2278
2279</body>
2280
2281</html>
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