source: Tutorials/SAimages/Small Angle Image Processing.htm @ 3623

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finish web tutorials for now
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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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1166</head>
1167
1168<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1169
1170<div class=WordSection1>
1171
1172<h1><strong>Small Angle X-Ray Data – Image Processing<o:p></o:p></strong></h1>
1173
1174<P><B>A video version of this tutorial is available at
1175<A href="https://anl.box.com/v/SmallAngleImageProcessing" target="_blank">
1176https://anl.box.com/v/SmallAngleImageProcessing</A></B></P>
1177
1178<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
1179this tutorial you will reduce 2D SAXS data to create 1D absolute scaled data.
1180The data were collected at APS on beam line 15ID on some polymer base materials
1181to be used for liquid crystal displays. The processing has several steps
1182including detector calibration (i.e. determine sample-detector distance &amp;
1183tilt), integration and scaling to an absolute scaled glassy carbon measurement.
1184The data were collected at a wavelength of 1.0332Å with a <span class=SpellE>MarCCD</span>
1185detector placed ~570mm from the sample. Note that menu entries are listed in
1186bold face below as <b style='mso-bidi-font-weight:normal'><span
1187style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1188mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Help/About
1189GSAS-II</span></b>, which lists first the name of the menu (here <b
1190style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1191mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
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1193(here <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1194mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1195minor-latin'>About GSAS-II</span></b>).<span style='mso-spacerun:yes'>  </span><span
1196style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
1197mso-bidi-font-weight:bold;mso-bidi-font-style:italic'><o:p></o:p></span></p>
1198
1199<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1200
1201<h2>Step 1: Detector calibration</h2>
1202
1203<p class=MsoNormal>The detector position is determined by using an image
1204collected from silver <span class=SpellE>behenate</span>; do <b
1205style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1206mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data/Read
1207Image data…</span></b> and a file selection dialog box will appear. Go to <span
1208class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1209"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
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1211style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1212mso-hansi-theme-font:minor-latin'>/data</span></b> and select <b
1213style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1214mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>AgBehenate_003.tif</span></b>
1215with either a mouse button double click or <b style='mso-bidi-font-weight:normal'><span
1216style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1217mso-hansi-theme-font:minor-latin'>Open</span></b>; the image will appear</p>
1218
1219<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1220 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1221 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1222 <v:stroke joinstyle="miter"/>
1223 <v:formulas>
1224  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1225  <v:f eqn="sum @0 1 0"/>
1226  <v:f eqn="sum 0 0 @1"/>
1227  <v:f eqn="prod @2 1 2"/>
1228  <v:f eqn="prod @3 21600 pixelWidth"/>
1229  <v:f eqn="prod @3 21600 pixelHeight"/>
1230  <v:f eqn="sum @0 0 1"/>
1231  <v:f eqn="prod @6 1 2"/>
1232  <v:f eqn="prod @7 21600 pixelWidth"/>
1233  <v:f eqn="sum @8 21600 0"/>
1234  <v:f eqn="prod @7 21600 pixelHeight"/>
1235  <v:f eqn="sum @10 21600 0"/>
1236 </v:formulas>
1237 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1238 <o:lock v:ext="edit" aspectratio="t"/>
1239</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1062" type="#_x0000_t75"
1240 style='width:525pt;height:450pt;visibility:visible;mso-wrap-style:square'>
1241 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image001.png"
1242  o:title=""/>
1243</v:shape><![endif]--><![if !vml]><img width=700 height=600
1244src="Small%20Angle%20Image%20Processing_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
1245
1246<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1247
1248<p class=MsoNormal>And the <b style='mso-bidi-font-weight:normal'><span
1249style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1250mso-hansi-theme-font:minor-latin'>Image controls</span></b> window will show
1251(you may have to select the <b style='mso-bidi-font-weight:normal'><span
1252style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1253mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>IMG</span></b>
1254tree entry &amp; then it’s <b style='mso-bidi-font-weight:normal'><span
1255style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1256mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Image
1257Controls</span></b>).</p>
1258
1259<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1260 id="_x0000_i1061" type="#_x0000_t75" style='width:468pt;height:402pt;
1261 visibility:visible;mso-wrap-style:square'>
1262 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image002.png"
1263  o:title=""/>
1264</v:shape><![endif]--><![if !vml]><img width=624 height=536
1265src="Small%20Angle%20Image%20Processing_files/image003.png" v:shapes="_x0000_i1061"><![endif]></span></p>
1266
1267<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1268
1269<p class=MsoNormal>Note the default <b style='mso-bidi-font-weight:normal'><span
1270style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1271mso-hansi-theme-font:minor-latin'>Type of image data</span></b> is <b
1272style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1273mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR -
1274powder diffraction data</span></b>; you will change that <span
1275style='mso-no-proof:yes'>now.</span> Select <b style='mso-bidi-font-weight:
1276normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1277minor-latin;mso-hansi-theme-font:minor-latin'>SASD – small angle scattering
1278data</span></b> (the window will change). Enter the <b style='mso-bidi-font-weight:
1279normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1280minor-latin;mso-hansi-theme-font:minor-latin'>wavelength</span></b> (<b
1281style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1282mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.0332</span></b>),
1283and select the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1284style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1285mso-hansi-theme-font:minor-latin'>Calibrant</span></b></span> (near bottom of
1286window) as <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'>Ag <span class=SpellE>behenate</span></span></b>. Note that the
1289calibration info for Ag <span class=SpellE>behenate</span> was read from a
1290python file – <b style='mso-bidi-font-weight:normal'><span style='font-family:
1291"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1292minor-latin'>GSASII/ImageCalibrants.py</span></b>. If you have a <span
1293class=SpellE>calibrant</span> that isn’t in this file you should enter it in
1294the file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1295mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UserCalibrants.py</span></b>;
1296just follow the format of the examples within <b style='mso-bidi-font-weight:
1297normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1298minor-latin;mso-hansi-theme-font:minor-latin'>ImageCalibrants.py</span></b>.
1299You should move the <b style='mso-bidi-font-weight:normal'><span
1300style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1301mso-hansi-theme-font:minor-latin'>Max intensity</span></b> slider to near the
1302middle of the range – that will improve the image. When done the <b
1303style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1304mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1305controls</span></b> window should look like</p>
1306
1307<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1308 id="_x0000_i1060" type="#_x0000_t75" style='width:468pt;height:402pt;
1309 visibility:visible;mso-wrap-style:square'>
1310 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image004.png"
1311  o:title=""/>
1312</v:shape><![endif]--><![if !vml]><img width=624 height=536
1313src="Small%20Angle%20Image%20Processing_files/image005.png" v:shapes="_x0000_i1060"><![endif]></span></p>
1314
1315<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1316
1317<p class=MsoNormal>And the image will be</p>
1318
1319<p class=MsoNormal><!--[if gte vml 1]><v:shapetype id="_x0000_t32" coordsize="21600,21600"
1320 o:spt="32" o:oned="t" path="m,l21600,21600e" filled="f">
1321 <v:path arrowok="t" fillok="f" o:connecttype="none"/>
1322 <o:lock v:ext="edit" shapetype="t"/>
1323</v:shapetype><v:shape id="Straight_x0020_Arrow_x0020_Connector_x0020_21"
1324 o:spid="_x0000_s1026" type="#_x0000_t32" style='position:absolute;
1325 margin-left:150pt;margin-top:194.25pt;width:48pt;height:15.75pt;flip:y;
1326 z-index:251659264;visibility:visible;mso-wrap-style:square;
1327 mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:9pt;
1328 mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
1329 mso-wrap-distance-bottom:0;mso-position-horizontal:absolute;
1330 mso-position-horizontal-relative:text;mso-position-vertical:absolute;
1331 mso-position-vertical-relative:text;mso-width-percent:0;mso-height-percent:0;
1332 mso-width-relative:page;mso-height-relative:page' o:gfxdata="UEsDBBQABgAIAAAAIQC2gziS/gAAAOEBAAATAAAAW0NvbnRlbnRfVHlwZXNdLnhtbJSRQU7DMBBF
133390jcwfIWJU67QAgl6YK0S0CoHGBkTxKLZGx5TGhvj5O2G0SRWNoz/78nu9wcxkFMGNg6quQqL6RA
13340s5Y6ir5vt9lD1JwBDIwOMJKHpHlpr69KfdHjyxSmriSfYz+USnWPY7AufNIadK6MEJMx9ApD/oD
1335OlTrorhX2lFEilmcO2RdNtjC5xDF9pCuTyYBB5bi6bQ4syoJ3g9WQ0ymaiLzg5KdCXlKLjvcW893
1336SUOqXwnz5DrgnHtJTxOsQfEKIT7DmDSUCaxw7Rqn8787ZsmRM9e2VmPeBN4uqYvTtW7jvijg9N/y
1337JsXecLq0q+WD6m8AAAD//wMAUEsDBBQABgAIAAAAIQA4/SH/1gAAAJQBAAALAAAAX3JlbHMvLnJl
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1345RVWWm2IAbD2CVCHQ7e2U5LvMr7WS8aPWQUVmG069xRwxx4cUi91W1CcUvjNybkP8Qxe9MI6KLlS3
1346Igr2Dc0fVL2RCAF0XEnoC9DaSJU1kJp1+ZuaYye8ylrInOAXm8L/o5Ufzgdkpm34i4ozJ3qa0TGi
1347MKcusjeIMLA9OEc+ArJqnfwafKgJtncHTIrl6I7+DuTXQLnil2Q6BD89GzX2TFvjv9CaZKtIPBvz
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1351H777DgAA//8DAFBLAwQUAAYACAAAACEAuvjFqd8AAAALAQAADwAAAGRycy9kb3ducmV2LnhtbEyP
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1354T987jLL2lbY9DmLuWn2fJHPtsGFJqLGjp5rK793JGWieh3e7Hj4O+4Ozr1+b7cs0WDTm9mZcL0FF
1355GuNFDH/4gg6FMB39iW1QrYFZkkiXKEOaPoISxWwxl8vRwIMkgy5y/b9D8QsAAP//AwBQSwECLQAU
1356AAYACAAAACEAtoM4kv4AAADhAQAAEwAAAAAAAAAAAAAAAAAAAAAAW0NvbnRlbnRfVHlwZXNdLnht
1357bFBLAQItABQABgAIAAAAIQA4/SH/1gAAAJQBAAALAAAAAAAAAAAAAAAAAC8BAABfcmVscy8ucmVs
1358c1BLAQItABQABgAIAAAAIQB9d1Df6wEAACkEAAAOAAAAAAAAAAAAAAAAAC4CAABkcnMvZTJvRG9j
1359LnhtbFBLAQItABQABgAIAAAAIQC6+MWp3wAAAAsBAAAPAAAAAAAAAAAAAAAAAEUEAABkcnMvZG93
1360bnJldi54bWxQSwUGAAAAAAQABADzAAAAUQUAAAAA
1361" strokecolor="#c0504d [3205]" strokeweight="3pt">
1362 <v:stroke endarrow="open"/>
1363 <v:shadow on="t" color="black" opacity="22937f" origin=",.5" offset="0,.63889mm"/>
1364 <o:lock v:ext="edit" shapetype="f"/>
1365</v:shape><![endif]--><![if !vml]><span style='mso-ignore:vglayout;position:
1366absolute;z-index:251659264;margin-left:198px;margin-top:246px;width:73px;
1367height:39px'><img width=73 height=39
1368src="Small%20Angle%20Image%20Processing_files/image006.png" v:shapes="Straight_x0020_Arrow_x0020_Connector_x0020_21"></span><![endif]><span
1369style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_41"
1370 o:spid="_x0000_i1059" type="#_x0000_t75" style='width:468pt;height:401.25pt;
1371 visibility:visible;mso-wrap-style:square'>
1372 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image007.png"
1373  o:title=""/>
1374</v:shape><![endif]--><![if !vml]><img width=624 height=535
1375src="Small%20Angle%20Image%20Processing_files/image008.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
1376
1377<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1378
1379<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
1380style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1381mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calibration</span></b><b
1382style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1383mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>/Calibrate</span></b>
1384from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1385mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1386Controls</span></b> menu; a bit of instruction will appear on the status line
1387of this window. Select 5 points on the innermost ring (arrowed above); a small
1388red cross will appear at each selection point. Press the right mouse button to
1389finish; calibration will proceed. A sequence of concentric red rings will
1390appear; they will switch to blue when calibration is finished. Select <b
1391style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1392mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show ring
1393picks</span></b> (near bottom right of <b style='mso-bidi-font-weight:normal'><span
1394style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1395mso-hansi-theme-font:minor-latin'>Image Controls</span></b> window). The <b
1396style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1397mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1398Controls</span></b> window will show the results of the calibration</p>
1399
1400<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1401 id="Picture_x0020_5" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:468pt;
1402 height:402pt;visibility:visible;mso-wrap-style:square'>
1403 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image009.png"
1404  o:title=""/>
1405</v:shape><![endif]--><![if !vml]><img width=624 height=536
1406src="Small%20Angle%20Image%20Processing_files/image010.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
1407
1408<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1409
1410<p class=MsoNormal>And the plot will show the points used in the calibration
1411calculations.</p>
1412
1413<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1414 id="Picture_x0020_6" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:468pt;
1415 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1416 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image011.png"
1417  o:title=""/>
1418</v:shape><![endif]--><![if !vml]><img width=624 height=535
1419src="Small%20Angle%20Image%20Processing_files/image012.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
1420
1421<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1422
1423<p class=MsoNormal>You would like to use more points from just the visible
1424rings. I suggest you change <b style='mso-bidi-font-weight:normal'><span
1425style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1426mso-hansi-theme-font:minor-latin'>Min ring I/<span class=SpellE>Ib</span></span></b>
1427to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1428mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.5</span></b>
1429and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1430mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Min <span
1431class=SpellE>calib</span> d-spacing</span></b> to <b style='mso-bidi-font-weight:
1432normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1433minor-latin;mso-hansi-theme-font:minor-latin'>10.0</span></b>. 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'>Calibrate/Recalibrate</span></b>;
1436more points will be used and they will be limited to the 5 visible rings in the
1437pattern.</p>
1438
1439<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1440 id="Picture_x0020_7" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:468pt;
1441 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1442 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image013.png"
1443  o:title=""/>
1444</v:shape><![endif]--><![if !vml]><img width=624 height=535
1445src="Small%20Angle%20Image%20Processing_files/image014.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
1446
1447<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1448
1449<p class=MsoNormal>And give the calibration result as</p>
1450
1451<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1452 id="Picture_x0020_8" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:468pt;
1453 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1454 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image013.png"
1455  o:title=""/>
1456</v:shape><![endif]--><![if !vml]><img width=624 height=535
1457src="Small%20Angle%20Image%20Processing_files/image015.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
1458
1459<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1460
1461<p class=MsoNormal>You will need this calibration information to process the
1462other images in this tutorial. To save it for future use do <span class=SpellE><b
1463style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1464mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Parms</span></b></span><b
1465style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1466mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>/Save
1467controls</span></b>; a file dialog will appear. Makeup a file name (no
1468extension needed) for this; I chose <b style='mso-bidi-font-weight:normal'><span
1469style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1470mso-hansi-theme-font:minor-latin'>SASD</span></b>. Press <b style='mso-bidi-font-weight:
1471normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1472minor-latin;mso-hansi-theme-font:minor-latin'>Save</span></b> and the file <span
1473class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1474"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1475minor-latin'>SASD.imctrl</span></b></span> will be written to the local
1476directory. If you are continuing on to the next step do <b style='mso-bidi-font-weight:
1477normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1478minor-latin;mso-hansi-theme-font:minor-latin'>File/New Project</span></b>
1479(don’t bother saving the project file unless you want it; we will not need it
1480here); otherwise you can exit GSAS-II.</p>
1481
1482<h2>Step 2: Data image integration</h2>
1483
1484<p class=MsoNormal>The objective here is to read in the four polymer sample
1485images, a glassy carbon image, an empty container image and a dark image. The
1486images will be integrated after creating masks to remove the beam stop and
1487other objectionable parts of the images. If you have not done so already, start
1488GSAS-II. </p>
1489
1490<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1491
1492<p class=MsoNormal>First do <b style='mso-bidi-font-weight:normal'><span
1493style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1494mso-hansi-theme-font:minor-latin'>Data/Read image data…</span></b>, go to <b
1495style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1496mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>exercises/<span
1497class=SpellE>SAimages</span></span></b> and select all images except <b
1498style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1499mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>AgBehenate_003.tif</span></b>;
1500then press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1501"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1502minor-latin'>Open</span></b> to read all of them. The GSAS-II data tree window
1503will show entries for 7 images and will expand the last one</p>
1504
1505<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1506 id="Picture_x0020_9" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:300pt;
1507 height:310.5pt;visibility:visible;mso-wrap-style:square'>
1508 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image016.png"
1509  o:title=""/>
1510</v:shape><![endif]--><![if !vml]><img width=400 height=414
1511src="Small%20Angle%20Image%20Processing_files/image016.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
1512
1513<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1514
1515<p class=MsoNormal>Notice that the Dark, Empty and GC (glassy carbon) are all
15165s images and the Sa1-4 ones are 40s images; this time information is needed
1517later to obtain correct scaling. First select the <b style='mso-bidi-font-weight:
1518normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1519minor-latin;mso-hansi-theme-font:minor-latin'>IMG GC_5s_200.tif</span></b>
1520entry from the tree and expand it (press the <b style='mso-bidi-font-weight:
1521normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1522minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b> box); then select <b
1523style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1524mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1525controls</span></b>. The data window (<b style='mso-bidi-font-weight:normal'><span
1526style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1527mso-hansi-theme-font:minor-latin'>Image Controls</span></b>) will show the
1528default settings.</p>
1529
1530<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1531 id="Picture_x0020_10" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:468pt;
1532 height:402pt;visibility:visible;mso-wrap-style:square'>
1533 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image017.png"
1534  o:title=""/>
1535</v:shape><![endif]--><![if !vml]><img width=624 height=536
1536src="Small%20Angle%20Image%20Processing_files/image018.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
1537
1538<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1539
1540<p class=MsoNormal>Do <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1541style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1542mso-hansi-theme-font:minor-latin'>Parms</span></b></span><b style='mso-bidi-font-weight:
1543normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1544minor-latin;mso-hansi-theme-font:minor-latin'>/Load controls</span></b> from
1545the menu; a file selection dialog will appear showing the available *.<span
1546class=SpellE>imctrl</span> files (the one you made in Step 1 should be seen).
1547Select it and press <b style='mso-bidi-font-weight:normal'><span
1548style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1549mso-hansi-theme-font:minor-latin'>Open</span></b>; the <b style='mso-bidi-font-weight:
1550normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1551minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> window
1552will be redrawn with the settings obtained in <b style='mso-bidi-font-weight:
1553normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1554minor-latin;mso-hansi-theme-font:minor-latin'>Step 1: Detector calibration</span></b></p>
1555
1556<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1557 id="Picture_x0020_11" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:468pt;
1558 height:402pt;visibility:visible;mso-wrap-style:square'>
1559 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image019.png"
1560  o:title=""/>
1561</v:shape><![endif]--><![if !vml]><img width=624 height=536
1562src="Small%20Angle%20Image%20Processing_files/image020.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
1563
1564<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1565
1566<p class=MsoNormal>and the image will be that of glassy carbon. Changing the <b
1567style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1568mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Max
1569intensity</span></b> slider on the <b style='mso-bidi-font-weight:normal'><span
1570style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1571mso-hansi-theme-font:minor-latin'>Image Controls</span></b> window will show
1572that the image from the <span class=SpellE>MarCCD</span> is circular and
1573slightly offset from the beam center. You can also select from the drop down to
1574the left of the intensity sliders; <b style='mso-bidi-font-weight:normal'><span
1575style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1576mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>90%</span></b>
1577will suffice. A beam stop shadow is evident as well as an arc-like fault in the
1578image (a bit hard to see - toward the upper left corner of the image). We will
1579sort those out later.</p>
1580
1581<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1582 id="Picture_x0020_12" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:468pt;
1583 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1584 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image021.png"
1585  o:title=""/>
1586</v:shape><![endif]--><![if !vml]><img width=624 height=535
1587src="Small%20Angle%20Image%20Processing_files/image022.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
1588
1589<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1590
1591<p class=MsoNormal>The next step we will be doing is to set up the integration
1592controls. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
1593"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1594minor-latin'>Dark image</span></b> is <b style='mso-bidi-font-weight:normal'><span
1595style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1596mso-hansi-theme-font:minor-latin'>IMG Dark_5s_003.tif</span></b>, the <b
1597style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1598mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background
1599image</span></b> is <b style='mso-bidi-font-weight:normal'><span
1600style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1601mso-hansi-theme-font:minor-latin'>IMG Empty_5s_014.tif</span></b>. We will be
1602needing the background image; the dark is not needed as it would be subtracted
1603from both sample and background thus cancelling out. Select just <b
1604style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1605mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>IMG
1606Empty_5s_<span class=GramE>014.tif<span style='font-family:"Times New Roman",serif;
1607font-weight:normal'><span style='mso-spacerun:yes'>  </span>for</span></span></span></b>
1608the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1609mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1610minor-latin'>Background image</span></b>; leave Dark image blank. The <b
1611style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1612mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multiplier</span></b>
1613is <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1614mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-1.0</span></b>
1615because its exposure was the same as this glassy carbon image (5s). Notice that
1616the background is instantly applied to the image. Next check the boxes for <b
1617style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1618mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show
1619integration limits?</span></b> and <b style='mso-bidi-font-weight:normal'><span
1620style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1621mso-hansi-theme-font:minor-latin'>Do full integration?</span></b> A pair of
1622circles with a connecting diagonal line will appear on the plot. Set the <b
1623style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1624mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Inner/Outer
1625q</span></b> values to <b style='mso-bidi-font-weight:normal'><span
1626style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1627mso-hansi-theme-font:minor-latin'>0.05</span></b> and <b style='mso-bidi-font-weight:
1628normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1629minor-latin;mso-hansi-theme-font:minor-latin'>0.9</span></b>, respectively, and
1630set the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1631mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Start
1632azimuth</span></b> to <b style='mso-bidi-font-weight:normal'><span
1633style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1634mso-hansi-theme-font:minor-latin'>0</span></b>. Set the <b style='mso-bidi-font-weight:
1635normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1636minor-latin;mso-hansi-theme-font:minor-latin'>No. 2-theta bins</span></b> to <b
1637style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1638mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>250</span></b>,
1639which is more appropriate for small angle scattering, and set the <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'>Bin style:
1642Constant step bins in</span></b> to <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'>log(q)</span></b>. You should also check the <b
1645style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1646mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Apply sample
1647absorption?</span></b> and <b style='mso-bidi-font-weight:normal'><span
1648style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1649mso-hansi-theme-font:minor-latin'>Apply polarization?</span></b> <span
1650class=GramE>boxes</span>; set the sample shape to <b style='mso-bidi-font-weight:
1651normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1652minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Fixed
1653flat plate</span></b> and enter the measured <b style='mso-bidi-font-weight:
1654normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1655minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> (<b
1656style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1657mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.818</span></b>)
1658for the glassy carbon sample. When done the <b style='mso-bidi-font-weight:
1659normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1660minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> data
1661window should look like</p>
1662
1663<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1664 id="Picture_x0020_13" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:468pt;
1665 height:402pt;visibility:visible;mso-wrap-style:square'>
1666 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image023.png"
1667  o:title=""/>
1668</v:shape><![endif]--><![if !vml]><img width=624 height=536
1669src="Small%20Angle%20Image%20Processing_files/image024.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1670
1671<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1672
1673<p class=MsoNormal>And the plot should look like</p>
1674
1675<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1676 id="Picture_x0020_14" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:468pt;
1677 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1678 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image025.png"
1679  o:title=""/>
1680</v:shape><![endif]--><![if !vml]><img width=624 height=535
1681src="Small%20Angle%20Image%20Processing_files/image026.png" v:shapes="Picture_x0020_14"><![endif]></span></p>
1682
1683<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1684
1685<p class=MsoNormal>Now copy these controls to the other images. Do <span
1686class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1687"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1688minor-latin'>Parms</span></b></span><b style='mso-bidi-font-weight:normal'><span
1689style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1690mso-hansi-theme-font:minor-latin'>/Copy controls</span></b> and select just the
1691<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1692mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-4</span></b>
1693data names. </p>
1694
1695<p class=MsoNormal>We now need to go to the <b style='mso-bidi-font-weight:
1696normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1697minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> for
1698each of <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1699mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b>
1700to enter the correct transmission for each and change the Background <b
1701style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1702mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multiplier</span></b>
1703to account for the different exposure times. Start with <b style='mso-bidi-font-weight:
1704normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1705minor-latin;mso-hansi-theme-font:minor-latin'>IMG Sa1_40s_067.tif</span></b>
1706and change <b style='mso-bidi-font-weight:normal'><span style='font-family:
1707"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1708minor-latin'>transmission</span></b> to <b style='mso-bidi-font-weight:normal'><span
1709style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1710mso-hansi-theme-font:minor-latin'>0.943</span></b> and the <b style='mso-bidi-font-weight:
1711normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1712minor-latin;mso-hansi-theme-font:minor-latin'>multiplier</span></b> to <b
1713style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1714mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1715Then go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1716"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1717minor-latin'>IMG Sa2_40s_069.tif</span></b> and change <b style='mso-bidi-font-weight:
1718normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1719minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1720style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1721mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.979</span></b>;
1722<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'>multiplier</span></b>
1724to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1725mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1726Next go <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1727mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>to IMG
1728Sa3_40s_059.tif</span></b> and change <b style='mso-bidi-font-weight:normal'><span
1729style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1730mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1731style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1732mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.960</span></b>;
1733<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1734mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multiplier</span></b>
1735to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1736mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1737Finally, go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1738"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1739minor-latin'>IMG Sa4_40s_061.tif</span></b> and change <b style='mso-bidi-font-weight:
1740normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1741minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> to <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'>0.968</span></b>;
1744<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'>multiplier</span></b>
1746to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1747mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1748The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1749mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1750Controls</span></b> data window for this should look like</p>
1751
1752<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1753 id="Picture_x0020_39" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt;
1754 height:402pt;visibility:visible;mso-wrap-style:square'>
1755 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image027.png"
1756  o:title=""/>
1757</v:shape><![endif]--><![if !vml]><img width=624 height=536
1758src="Small%20Angle%20Image%20Processing_files/image028.png" v:shapes="Picture_x0020_39"><![endif]></span></p>
1759
1760<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1761
1762<p class=MsoNormal>You will notice that the image changes as you change the Background
1763image multiplier; it applies this correction immediately. Pretty clearly much
1764of the Sa1-4 images are largely background (intensities ~0; negative ones shown
1765as red); we’ll see the result of this when we integrate them. </p>
1766
1767<p class=MsoNormal>This is a reasonable time to save the project; do <b
1768style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1769mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>File/Save
1770project as…</span></b> from the main GSAS-II data tree menu. Choose a file name
1771(I assumed <b style='mso-bidi-font-weight:normal'><span style='font-family:
1772"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1773minor-latin'>image</span></b>) and it will be written on the local file
1774directory. </p>
1775
1776<p class=MsoNormal>As noted earlier, the images contain some unwanted features;
1777so let’s create masks to remove them. Select <b style='mso-bidi-font-weight:
1778normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1779minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b> from the GSAS-II
1780data tree under <b style='mso-bidi-font-weight:normal'><span style='font-family:
1781"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1782minor-latin'>IMG GC_5s_200.tif</span></b>; the data window will show</p>
1783
1784<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1785 id="Picture_x0020_40" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:453.75pt;
1786 height:140.25pt;visibility:visible;mso-wrap-style:square'>
1787 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image029.png"
1788  o:title=""/>
1789</v:shape><![endif]--><![if !vml]><img width=605 height=187
1790src="Small%20Angle%20Image%20Processing_files/image029.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
1791
1792<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1793
1794<p class=MsoNormal>To mask out the regions beyond the circular <span
1795class=SpellE>MarCCD</span> image change the <span class=GramE><b
1796style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1797mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Lower<span
1798style='mso-spacerun:yes'>  </span><span class=SpellE>threshhold</span></span></b></span>
1799from <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1800mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0</span></b>
1801to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1802mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>;
1803the image will be redrawn with these regions in red</p>
1804
1805<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1806 id="Picture_x0020_43" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:468pt;
1807 height:430.5pt;visibility:visible;mso-wrap-style:square'>
1808 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image030.png"
1809  o:title=""/>
1810</v:shape><![endif]--><![if !vml]><img width=624 height=574
1811src="Small%20Angle%20Image%20Processing_files/image031.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
1812
1813<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1814
1815<p class=MsoNormal>These are now excluded. The status line for the <b
1816style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1817mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b>
1818data window gives the directions for adding additional masks. You can make arcs
1819(we’ll use that here), rings, spots (this too) and polygons (this as well) as
1820masks. These enclose areas to be excluded. The frame works in the opposite
1821sense in that everything outside the frame is excluded (NB: only one frame is
1822allowed). So let’s first mask the bad arc in the upper left – zoom in on that
1823part of the image</p>
1824
1825<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1826 id="Picture_x0020_44" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:468pt;
1827 height:430.5pt;visibility:visible;mso-wrap-style:square'>
1828 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image032.png"
1829  o:title=""/>
1830</v:shape><![endif]--><![if !vml]><img width=624 height=574
1831src="Small%20Angle%20Image%20Processing_files/image033.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
1832
1833<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1834
1835<p class=MsoNormal>To add the mask 1: be sure the focus is on the image and the
1836zoom buttons are off, 2: type <b style='mso-bidi-font-weight:normal'><span
1837style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1838mso-hansi-theme-font:minor-latin'>a</span></b> to activate the arc mask entry
18393: press the left mouse button (<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'>LB</span></b>) with the cursor centered on
1842the bad arc. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
1843"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1844minor-latin'>Masks</span></b> window will show a new entry </p>
1845
1846<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1847 id="Picture_x0020_45" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:453.75pt;
1848 height:183.75pt;visibility:visible;mso-wrap-style:square'>
1849 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image034.png"
1850  o:title=""/>
1851</v:shape><![endif]--><![if !vml]><img width=605 height=245
1852src="Small%20Angle%20Image%20Processing_files/image034.png" v:shapes="Picture_x0020_45"><![endif]></span><span
1853style='mso-spacerun:yes'> </span></p>
1854
1855<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1856
1857<p class=MsoNormal>and an arc mask will be drawn on the plot.</p>
1858
1859<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1860 id="Picture_x0020_46" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:468pt;
1861 height:430.5pt;visibility:visible;mso-wrap-style:square'>
1862 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image035.png"
1863  o:title=""/>
1864</v:shape><![endif]--><![if !vml]><img width=624 height=574
1865src="Small%20Angle%20Image%20Processing_files/image036.png" v:shapes="Picture_x0020_46"><![endif]></span></p>
1866
1867<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1868
1869<p class=MsoNormal>You can change the angular width of the arc by changing <b
1870style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1871mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>thickness</span></b>
1872in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1873mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b>
1874data window, you can change the angular range of the arc by RB dragging either
1875end of the arc (NB: increments only in whole degrees), and you can move the
1876arc<span style='mso-spacerun:yes'>  </span>along a constant 2&#920; angle by LB
1877dragging on any edge of the mask. The curvature is centered on the beam center
1878position and follows a constant 2&#920; curve established by the detector
1879calibration.<span style='mso-no-proof:yes'> </span></p>
1880
1881<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1882 id="Picture_x0020_65" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
1883 height:450pt;visibility:visible;mso-wrap-style:square'>
1884 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image037.png"
1885  o:title=""/>
1886</v:shape><![endif]--><![if !vml]><img width=700 height=600
1887src="Small%20Angle%20Image%20Processing_files/image037.png" v:shapes="Picture_x0020_65"><![endif]></span></p>
1888
1889<p class=MsoNormal>Next let’s deal with the beam stop. I’m going to use both a
1890polygon and a spot to cover it. Move the zoom area to be around the center,
1891make sure the zoom buttons are off, enter ‘<b style='mso-bidi-font-weight:normal'><span
1892style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1893mso-hansi-theme-font:minor-latin'>s</span></b>’ on the plot and press mouse <b
1894style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1895mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>LB</span></b>
1896with the cursor positioned where you want the spot (probably on the ‘X’ – beam center
1897position). A 1mm diameter red circle will appear on the plot</p>
1898
1899<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1900 id="Picture_x0020_66" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;
1901 height:450pt;visibility:visible;mso-wrap-style:square'>
1902 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image038.png"
1903  o:title=""/>
1904</v:shape><![endif]--><![if !vml]><img width=700 height=600
1905src="Small%20Angle%20Image%20Processing_files/image038.png" v:shapes="Picture_x0020_66"><![endif]></span></p>
1906
1907<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1908
1909<p class=MsoNormal>And the <b style='mso-bidi-font-weight:normal'><span
1910style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1911mso-hansi-theme-font:minor-latin'>Masks</span></b> window will have new
1912information</p>
1913
1914<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1915 id="Picture_x0020_47" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:453.75pt;
1916 height:227.25pt;visibility:visible;mso-wrap-style:square'>
1917 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image039.png"
1918  o:title=""/>
1919</v:shape><![endif]--><![if !vml]><img width=605 height=303
1920src="Small%20Angle%20Image%20Processing_files/image039.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
1921
1922<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1923
1924<p class=MsoNormal>You can change the diameter of the spot, I used <b
1925style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1926mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>7.0</span></b>;
1927the plot now shows a ring that just covers the beam stop. You may have to drag
1928it a bit (Hint: drag the center of the spot) to get it well centered.</p>
1929
1930<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1931 id="Picture_x0020_67" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
1932 height:450pt;visibility:visible;mso-wrap-style:square'>
1933 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image040.png"
1934  o:title=""/>
1935</v:shape><![endif]--><![if !vml]><img width=700 height=600
1936src="Small%20Angle%20Image%20Processing_files/image040.png" v:shapes="Picture_x0020_67"><![endif]></span></p>
1937
1938<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1939
1940<p class=MsoNormal>Next we need to mask the stick holding the beam stop; we’ll
1941use a 4 sided polygon for this. Adjust the zoom &amp; position so you can see
1942the entire beam stop stick. Make sure all zoom buttons are off, press ‘<b
1943style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1944mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>p</span></b>’
1945on the plot, then press the mouse <b style='mso-bidi-font-weight:normal'><span
1946style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1947mso-hansi-theme-font:minor-latin'>LB</span></b> at four points in succession
1948around the beam stop stick. A line segment for the polygon will be drawn
1949following your mouse clicks. Finally press the mouse <b style='mso-bidi-font-weight:
1950normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1951minor-latin;mso-hansi-theme-font:minor-latin'>RB</span></b> to close the
1952polygon. You should see something like</p>
1953
1954<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1955 id="Picture_x0020_68" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
1956 height:450pt;visibility:visible;mso-wrap-style:square'>
1957 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image041.png"
1958  o:title=""/>
1959</v:shape><![endif]--><![if !vml]><img width=700 height=600
1960src="Small%20Angle%20Image%20Processing_files/image041.png" v:shapes="Picture_x0020_68"><![endif]></span></p>
1961
1962<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1963
1964<p class=MsoNormal>You can adjust the position of the polygon vertices by
1965closely dragging it with mouse <b style='mso-bidi-font-weight:normal'><span
1966style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1967mso-hansi-theme-font:minor-latin'>LB</span></b> pressed; a new vertex can be
1968added by dragging an existing vertex with the mouse <b style='mso-bidi-font-weight:
1969normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1970minor-latin;mso-hansi-theme-font:minor-latin'>RB</span></b> pressed. If you
1971drag one vertex onto another, they are merged and cannot be separated.</p>
1972
1973<p class=MsoNormal>We want to use these masks for all the Sa1-4 images. Do <b
1974style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1975mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Copy
1976mask</span></b>; a <b style='mso-bidi-font-weight:normal'><span
1977style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1978mso-hansi-theme-font:minor-latin'>Copy mask information</span></b> dialog box
1979will appear. Select the <b style='mso-bidi-font-weight:normal'><span
1980style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1981mso-hansi-theme-font:minor-latin'>Sa1-4</span></b> items and press <b
1982style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1983mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.
1984Here is a useful place to save your project; do <b style='mso-bidi-font-weight:
1985normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1986minor-latin;mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from
1987the main GSAS-II data tree menu.</p>
1988
1989<h2>Step 3: Integration of images</h2>
1990
1991<p class=MsoNormal>We are now ready to integrate the glassy carbon and the four
1992Sa images. Select any <b style='mso-bidi-font-weight:normal'><span
1993style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1994mso-hansi-theme-font:minor-latin'>Image Controls</span></b> and then do <b
1995style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1996mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Integration/Integrate
1997all</span></b>. A selection dialog will appear; select only the <b
1998style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1999mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>GC</span></b>
2000and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2001mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b>
2002data sets and press <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'>Ok</span></b>. The image integration will
2005proceed; a progress bar increments as each one is done. Five SASD data items
2006will appear on the GSAS-II data tree; the last one (<b style='mso-bidi-font-weight:
2007normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2008minor-latin;mso-hansi-theme-font:minor-latin'>SASD Sa4_40s_061.tif <span
2009class=SpellE>Azm</span>=0.00</span></b>) will be expanded and plotted (you may
2010have to select the <b style='mso-bidi-font-weight:normal'><span
2011style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2012mso-hansi-theme-font:minor-latin'>Powder Patterns</span></b> tab to see it).</p>
2013
2014<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2015 id="Picture_x0020_26" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
2016 height:450pt;visibility:visible;mso-wrap-style:square'>
2017 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image042.png"
2018  o:title=""/>
2019</v:shape><![endif]--><![if !vml]><img width=700 height=600
2020src="Small%20Angle%20Image%20Processing_files/image042.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
2021
2022<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2023
2024<p class=MsoNormal>Pretty obviously the SASD pattern is down to background at
2025Q~0.25Å<sup>-1</sup>; the other Sa1-Sa4 patterns are similar. The glassy carbon
2026pattern extends nicely to the highest Q (~1.0Å<sup>-1</sup>) measured.</p>
2027
2028<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2029 id="_x0000_i1036" type="#_x0000_t75" style='width:525pt;height:450pt;
2030 visibility:visible;mso-wrap-style:square'>
2031 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image043.png"
2032  o:title=""/>
2033</v:shape><![endif]--><![if !vml]><img width=700 height=600
2034src="Small%20Angle%20Image%20Processing_files/image043.png" v:shapes="_x0000_i1036"><![endif]></span></p>
2035
2036<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2037
2038<h2>Step 4: Scaling of SASD patterns</h2>
2039
2040<p class=MsoNormal>To set this data on an absolute scale, we compare it to an
2041absolute scaled glassy carbon scan. One of these is in the same directory as
2042the image data; do <b style='mso-bidi-font-weight:normal'><span
2043style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2044mso-hansi-theme-font:minor-latin'>Import/Small Angle Data/ from q(A-1) step
2045X-ray QIE data file</span></b> and select <b style='mso-bidi-font-weight:normal'><span
2046style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2047mso-hansi-theme-font:minor-latin'>GC calibrated data.txt</span></b> from the
2048file selection dialog. You will need to select <b style='mso-bidi-font-weight:
2049normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2050minor-latin;mso-hansi-theme-font:minor-latin'>any <span class=GramE>file(</span>*.*)</span></b>
2051to see it. A <b style='mso-bidi-font-weight:normal'><span style='font-family:
2052"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2053minor-latin'>Is this the file you want</span></b> dialog will appear – respond <b
2054style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2055mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b>
2056to read the file; it will be plotted.</p>
2057
2058<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2059 id="_x0000_i1035" type="#_x0000_t75" style='width:525pt;height:450pt;
2060 visibility:visible;mso-wrap-style:square'>
2061 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image044.png"
2062  o:title=""/>
2063</v:shape><![endif]--><![if !vml]><img width=700 height=600
2064src="Small%20Angle%20Image%20Processing_files/image044.png" v:shapes="_x0000_i1035"><![endif]></span></p>
2065
2066<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2067
2068<p class=MsoNormal>If you enter ‘<b style='mso-bidi-font-weight:normal'><span
2069style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2070mso-hansi-theme-font:minor-latin'>m</span></b>’ on the plot window, all of the
2071SASD patterns will be plotted together (I’ve adjusted the zoom to see them
2072all).</p>
2073
2074<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2075 id="_x0000_i1034" type="#_x0000_t75" style='width:525pt;height:450pt;
2076 visibility:visible;mso-wrap-style:square'>
2077 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image045.png"
2078  o:title=""/>
2079</v:shape><![endif]--><![if !vml]><img width=700 height=600
2080src="Small%20Angle%20Image%20Processing_files/image045.png" v:shapes="_x0000_i1034"><![endif]></span></p>
2081
2082<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2083
2084<p class=MsoNormal>Clearly the measured image data need to be scaled down to have
2085them on absolute scale. First is to discover the scaling between the two glassy
2086carbon patterns. Go to the measured one (<b style='mso-bidi-font-weight:normal'><span
2087style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2088mso-hansi-theme-font:minor-latin'>SASD GC_5s_200.tif <span class=SpellE>Azm</span>=0.00</span></b>)
2089and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2090"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2091minor-latin'>Sample Parameters</span></b>.</p>
2092
2093<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2094 id="Picture_x0020_48" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:304.5pt;
2095 height:460.5pt;visibility:visible;mso-wrap-style:square'>
2096 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image046.png"
2097  o:title=""/>
2098</v:shape><![endif]--><![if !vml]><img width=406 height=614
2099src="Small%20Angle%20Image%20Processing_files/image046.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
2100
2101<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2102
2103<p class=MsoNormal>We will change <b style='mso-bidi-font-weight:normal'><span
2104style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2105mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> by
2106comparison with the absolute glassy carbon scan. Do <b style='mso-bidi-font-weight:
2107normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2108minor-latin;mso-hansi-theme-font:minor-latin'>Command/Set scale</span></b> from
2109the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2110mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
2111Parameters</span></b> menu; a <b style='mso-bidi-font-weight:normal'><span
2112style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2113mso-hansi-theme-font:minor-latin'>Reference histogram</span></b> dialog will
2114appear.</p>
2115
2116<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2117 id="Picture_x0020_49" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:192.75pt;
2118 height:168pt;visibility:visible;mso-wrap-style:square'>
2119 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image047.png"
2120  o:title=""/>
2121</v:shape><![endif]--><![if !vml]><img width=257 height=224
2122src="Small%20Angle%20Image%20Processing_files/image047.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
2123
2124<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2125
2126<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2127style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2128mso-hansi-theme-font:minor-latin'>SASD GC calibrated data.txt</span></b> (shown
2129in blue above) and press <b style='mso-bidi-font-weight:normal'><span
2130style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2131mso-hansi-theme-font:minor-latin'>Ok</span></b>; the <b style='mso-bidi-font-weight:
2132normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2133minor-latin;mso-hansi-theme-font:minor-latin'>GC_5s_200.tif</span></b> data
2134will be rescaled to the <b style='mso-bidi-font-weight:normal'><span
2135style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2136mso-hansi-theme-font:minor-latin'>GC calibrated data</span></b> and the <b
2137style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2138mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
2139scale factor</span></b> will be changed to the new scaling factor (<b
2140style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2141mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.0008519</span></b>).
2142The plot will be redrawn with the scaled data.</p>
2143
2144<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2145 id="_x0000_i1031" type="#_x0000_t75" style='width:525pt;height:450pt;
2146 visibility:visible;mso-wrap-style:square'>
2147 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image048.png"
2148  o:title=""/>
2149</v:shape><![endif]--><![if !vml]><img width=700 height=600
2150src="Small%20Angle%20Image%20Processing_files/image048.png" v:shapes="_x0000_i1031"><![endif]></span></p>
2151
2152<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2153
2154<p class=MsoNormal>The divergence at high Q is probably from a background
2155contribution to the standard that is not present in our measured one. Next we
2156have to apply this scale factor to the Sa1-Sa4 data sets. Do <b
2157style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2158mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Command/Copy
2159selected…</span></b> from the <b style='mso-bidi-font-weight:normal'><span
2160style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2161mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> menu; a <b
2162style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2163mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select
2164sample parameters</span></b> dialog will appear</p>
2165
2166<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2167 id="Picture_x0020_50" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:240pt;
2168 height:318pt;visibility:visible;mso-wrap-style:square'>
2169 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image049.png"
2170  o:title=""/>
2171</v:shape><![endif]--><![if !vml]><img width=320 height=424
2172src="Small%20Angle%20Image%20Processing_files/image049.png" v:shapes="Picture_x0020_50"><![endif]></span></p>
2173
2174<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2175
2176<p class=MsoNormal>Select only <b style='mso-bidi-font-weight:normal'><span
2177style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2178mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> (#8) and
2179press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2180mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>;
2181a <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2182mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Copy sample
2183parameters</span></b> dialog will appear</p>
2184
2185<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2186 id="Picture_x0020_51" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:226.5pt;
2187 height:254.25pt;visibility:visible;mso-wrap-style:square'>
2188 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image050.png"
2189  o:title=""/>
2190</v:shape><![endif]--><![if !vml]><img width=302 height=339
2191src="Small%20Angle%20Image%20Processing_files/image050.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
2192
2193<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2194
2195<p class=MsoNormal>Select only the <b style='mso-bidi-font-weight:normal'><span
2196style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2197mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b> data sets and press <b
2198style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2199mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.
2200The copy will occur and the plot redrawn</p>
2201
2202<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2203 id="Picture_x0020_53" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
2204 height:450pt;visibility:visible;mso-wrap-style:square'>
2205 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image051.png"
2206  o:title=""/>
2207</v:shape><![endif]--><![if !vml]><img width=700 height=600
2208src="Small%20Angle%20Image%20Processing_files/image051.png" v:shapes="Picture_x0020_53"><![endif]></span></p>
2209
2210<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2211
2212<p class=MsoNormal>I’ve changed the zoom to show all the data. We are not quite
2213done; the scales for the Sa1-Sa4 data sets have to be further reduced by a factor
2214of 8 to account for the longer exposure time. Select <b style='mso-bidi-font-weight:
2215normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2216minor-latin;mso-hansi-theme-font:minor-latin'>SASD Sa1_40s_067.tif</span></b>
2217from the GSAS-II data tree, expand it and choose <b style='mso-bidi-font-weight:
2218normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2219minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b></p>
2220
2221<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2222 id="Picture_x0020_52" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:304.5pt;
2223 height:460.5pt;visibility:visible;mso-wrap-style:square'>
2224 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image052.png"
2225  o:title=""/>
2226</v:shape><![endif]--><![if !vml]><img width=406 height=614
2227src="Small%20Angle%20Image%20Processing_files/image052.png" v:shapes="Picture_x0020_52"><![endif]></span></p>
2228
2229<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2230
2231<p class=MsoNormal>The data items here can take simple mathematical expressions
2232so change <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2233mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
2234scale factor</span></b> to <b style='mso-bidi-font-weight:normal'><span
2235style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2236mso-hansi-theme-font:minor-latin'>0.0008519/8</span></b> and press <b
2237style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2238mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>.
2239The value will change to <b style='mso-bidi-font-weight:normal'><span
2240style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2241mso-hansi-theme-font:minor-latin'>0.0001065</span></b> and the plot redrawn.</p>
2242
2243<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2244 id="Picture_x0020_56" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
2245 height:450pt;visibility:visible;mso-wrap-style:square'>
2246 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image053.png"
2247  o:title=""/>
2248</v:shape><![endif]--><![if !vml]><img width=700 height=600
2249src="Small%20Angle%20Image%20Processing_files/image053.png" v:shapes="Picture_x0020_56"><![endif]></span></p>
2250
2251<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2252
2253<p class=MsoNormal>Next do <b style='mso-bidi-font-weight:normal'><span
2254style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2255mso-hansi-theme-font:minor-latin'>Command/Copy selected</span></b> as before to
2256copy this new scale factor to the other Sa data sets. The plot will again be
2257redrawn</p>
2258
2259<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2260 id="Picture_x0020_57" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
2261 height:450pt;visibility:visible;mso-wrap-style:square'>
2262 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image054.png"
2263  o:title=""/>
2264</v:shape><![endif]--><![if !vml]><img width=700 height=600
2265src="Small%20Angle%20Image%20Processing_files/image054.png" v:shapes="Picture_x0020_57"><![endif]></span></p>
2266
2267<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2268
2269<p class=MsoNormal>Everything is now on absolute scale and these polymer
2270samples are quite weak small angle <span class=SpellE>scatterers</span>. This
2271is a good point to do a <b style='mso-bidi-font-weight:normal'><span
2272style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2273mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from the main
2274GSAS-II data tree menu. You can try to fit unified &amp; <span class=SpellE>Porod</span>
2275models to them following the procedures demonstrated in the <strong><span
2276style='font-weight:normal'>Fitting Small Angle X-Ray Data</span></strong><strong><span
2277style='font-weight:normal;mso-bidi-font-weight:bold'> tutorial. I’d set the
2278high Q limit to about 0.25Å<sup>-1</sup> as above that is only noisy
2279background.</span></strong></p>
2280
2281</div>
2282
2283</body>
2284
2285</html>
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