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1164
1165	<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1166
1167	<div class=WordSection1>
1168
1169	<h1><strong>Small Angle X-Ray Data Image Processing<o:p></o:p></strong></h1>
1170
1171	<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
1172	this tutorial you will reduce 2D SAXS data to create 1D absolute scaled data.
1173	The data were collected at APS on beam line 15ID on some polymer base materials
1174	to be used for liquid crystal displays. The processing has several steps
1175	including detector calibration (i.e. determine sample-detector distance &
1176	tilt), integration and scaling to an absolute scaled glassy carbon measurement.
1177	The data were collected at a wavelength of 1.0332Å with a <span class=SpellE>MarCCD</span>
1178	detector placed ~570mm from the sample. Note that menu entries are listed in
1179	bold face below as <b style='mso-bidi-font-weight:normal'><span
1180	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1181	mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1182	minor-latin'>Help/About GSAS-II</span></b>, which lists first the name of the
1183	menu (here <b style='mso-bidi-font-weight:normal'><span style='font-family:
1184	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1185	minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Help</span></b>)
1186	and second the name of the entry in the menu (here <b style='mso-bidi-font-weight:
1187	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1188	minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1189	mso-bidi-theme-font:minor-latin'>About GSAS-II</span></b>).<span
1190	style='mso-spacerun:yes'> </span><span style='mso-fareast-font-family:Calibri;
1191	mso-fareast-theme-font:minor-latin;mso-bidi-font-weight:bold;mso-bidi-font-style:
1192	italic'><o:p></o:p></span></p>
1193
1194	<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1195
1196	<h2>Step 1: Detector calibration</h2>
1197
1198	<p class=MsoNormal>The detector position is determined by using an image
1199	collected from silver <span class=SpellE>behenate</span>; do <b
1200	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1201	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data/Read
1202	Image data</span></b> and a file selection dialog box will appear. Go to <span
1203	class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1204	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1205	minor-latin'>SAimages</span></b></span><b style='mso-bidi-font-weight:normal'><span
1206	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1207	mso-hansi-theme-font:minor-latin'>/data</span></b> and select <b
1208	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1209	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>AgBehenate_003.tif</span></b>
1210	with either a mouse button double click or <b style='mso-bidi-font-weight:normal'><span
1211	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1212	mso-hansi-theme-font:minor-latin'>Open</span></b>; the image will appear</p>
1213
1214	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1215	id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1216	path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1217	<v:stroke joinstyle="miter"/>
1218	<v:formulas>
1219	<v:f eqn="if lineDrawn pixelLineWidth 0"/>
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1221	<v:f eqn="sum 0 0 @1"/>
1222	<v:f eqn="prod @2 1 2"/>
1223	<v:f eqn="prod @3 21600 pixelWidth"/>
1224	<v:f eqn="prod @3 21600 pixelHeight"/>
1225	<v:f eqn="sum @0 0 1"/>
1226	<v:f eqn="prod @6 1 2"/>
1227	<v:f eqn="prod @7 21600 pixelWidth"/>
1228	<v:f eqn="sum @8 21600 0"/>
1229	<v:f eqn="prod @7 21600 pixelHeight"/>
1230	<v:f eqn="sum @10 21600 0"/>
1231	</v:formulas>
1232	<v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1233	<o:lock v:ext="edit" aspectratio="t"/>
1234	</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1062" type="#_x0000_t75"
1235	style='width:525pt;height:450pt;visibility:visible;mso-wrap-style:square'>
1236	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image001.png"
1237	o:title=""/>
1238	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1239	src="Small%20Angle%20Image%20Processing_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
1240
1241	<p class=MsoNormal><o:p> </o:p></p>
1242
1243	<p class=MsoNormal>And the <b style='mso-bidi-font-weight:normal'><span
1244	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1245	mso-hansi-theme-font:minor-latin'>Image controls</span></b> window will show</p>
1246
1247	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1248	id="Picture_x0020_2" o:spid="_x0000_i1061" type="#_x0000_t75" style='width:472.5pt;
1249	height:388.5pt;visibility:visible;mso-wrap-style:square'>
1250	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image002.png"
1251	o:title=""/>
1252	</v:shape><![endif]--><![if !vml]><img width=630 height=518
1253	src="Small%20Angle%20Image%20Processing_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1254
1255	<p class=MsoNormal><o:p> </o:p></p>
1256
1257	<p class=MsoNormal>Note the default <b style='mso-bidi-font-weight:normal'><span
1258	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1259	mso-hansi-theme-font:minor-latin'>Type of image data</span></b> is <b
1260	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1261	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR -
1262	powder diffraction data</span></b>; you will change that <span
1263	style='mso-no-proof:yes'>now.</span> Select <b style='mso-bidi-font-weight:
1264	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1265	minor-latin;mso-hansi-theme-font:minor-latin'>SASD small angle scattering
1266	data</span></b> (the window will change). Enter the <b style='mso-bidi-font-weight:
1267	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1268	minor-latin;mso-hansi-theme-font:minor-latin'>wavelength</span></b> (<b
1269	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1270	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.0332</span></b>),
1271	and select the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1272	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1273	mso-hansi-theme-font:minor-latin'>Calibrant</span></b></span> (near bottom of
1274	window) as <b style='mso-bidi-font-weight:normal'><span style='font-family:
1275	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1276	minor-latin'>Ag <span class=SpellE>behenate</span></span></b>. Note that the
1277	calibration info for Ag <span class=SpellE>behenate</span> was read from a
1278	python file <b style='mso-bidi-font-weight:normal'><span style='font-family:
1279	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1280	minor-latin'>GSASII/ImageCalibrants.py</span></b>. If you have a <span
1281	class=SpellE>calibrant</span> that isnt in this file you should enter it in
1282	the file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1283	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UserCalibrants.py</span></b>;
1284	just follow the format of the examples within <b style='mso-bidi-font-weight:
1285	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1286	minor-latin;mso-hansi-theme-font:minor-latin'>ImageCalibrants.py</span></b>.
1287	You should move the <b style='mso-bidi-font-weight:normal'><span
1288	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1289	mso-hansi-theme-font:minor-latin'>Max intensity</span></b> slider to near the
1290	middle of the range that will improve the image. When done the <b
1291	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1292	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1293	controls</span></b> window should look like</p>
1294
1295	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1296	id="Picture_x0020_3" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:472.5pt;
1297	height:388.5pt;visibility:visible;mso-wrap-style:square'>
1298	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image003.png"
1299	o:title=""/>
1300	</v:shape><![endif]--><![if !vml]><img width=630 height=518
1301	src="Small%20Angle%20Image%20Processing_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
1302
1303	<p class=MsoNormal><o:p> </o:p></p>
1304
1305	<p class=MsoNormal>And the image will be</p>
1306
1307	<p class=MsoNormal><!--[if gte vml 1]><v:shapetype id="_x0000_t32" coordsize="21600,21600"
1308	o:spt="32" o:oned="t" path="m,l21600,21600e" filled="f">
1309	<v:path arrowok="t" fillok="f" o:connecttype="none"/>
1310	<o:lock v:ext="edit" shapetype="t"/>
1311	</v:shapetype><v:shape id="Straight_x0020_Arrow_x0020_Connector_x0020_21"
1312	o:spid="_x0000_s1026" type="#_x0000_t32" style='position:absolute;
1313	margin-left:177pt;margin-top:214.5pt;width:48pt;height:15.75pt;flip:y;
1314	z-index:251659264;visibility:visible;mso-wrap-style:square;
1315	mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:9pt;
1316	mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
1317	mso-wrap-distance-bottom:0;mso-position-horizontal:absolute;
1318	mso-position-horizontal-relative:text;mso-position-vertical:absolute;
1319	mso-position-vertical-relative:text;mso-width-percent:0;mso-height-percent:0;
1320	mso-width-relative:page;mso-height-relative:page' o:gfxdata="UEsDBBQABgAIAAAAIQC2gziS/gAAAOEBAAATAAAAW0NvbnRlbnRfVHlwZXNdLnhtbJSRQU7DMBBF
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1334	Igr2Dc0fVL2RCAF0XEnoC9DaSJU1kJp1+ZuaYye8ylrInOAXm8L/o5Ufzgdkpm34i4ozJ3qa0TGi
1335	MKcusjeIMLA9OEc+ArJqnfwafKgJtncHTIrl6I7+DuTXQLnil2Q6BD89GzX2TFvjv9CaZKtIPBvz
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1339	H777DgAA//8DAFBLAwQUAAYACAAAACEAgdKpXd8AAAALAQAADwAAAGRycy9kb3ducmV2LnhtbEyP
1340	wU7DMBBE70j8g7VI3KjTklQQ4lQVohfEpS1FHLfxkgTidRS7Tfh7lhPc3mhHszPFanKdOtMQWs8G
1341	5rMEFHHlbcu1gdf95uYOVIjIFjvPZOCbAqzKy4sCc+tH3tJ5F2slIRxyNNDE2Odah6ohh2Hme2K5
1342	ffjBYRQ51NoOOEq46/QiSZbaYcvyocGeHhuqvnYnZ6B9Gt/senw/7A/Ovnxuts/zYNGY66tp/QAq
1343	0hT/zPBbX6pDKZ2O/sQ2qM7AbZbKlmggXdwLiCPNEoGjwDLJQJeF/r+h/AEAAP//AwBQSwECLQAU
1344	AAYACAAAACEAtoM4kv4AAADhAQAAEwAAAAAAAAAAAAAAAAAAAAAAW0NvbnRlbnRfVHlwZXNdLnht
1345	bFBLAQItABQABgAIAAAAIQA4/SH/1gAAAJQBAAALAAAAAAAAAAAAAAAAAC8BAABfcmVscy8ucmVs
1346	c1BLAQItABQABgAIAAAAIQB9d1Df6wEAACkEAAAOAAAAAAAAAAAAAAAAAC4CAABkcnMvZTJvRG9j
1347	LnhtbFBLAQItABQABgAIAAAAIQCB0qld3wAAAAsBAAAPAAAAAAAAAAAAAAAAAEUEAABkcnMvZG93
1348	bnJldi54bWxQSwUGAAAAAAQABADzAAAAUQUAAAAA
1349	" strokecolor="#c0504d [3205]" strokeweight="3pt">
1350	<v:stroke endarrow="open"/>
1351	<v:shadow on="t" color="black" opacity="22937f" origin=",.5" offset="0,.63889mm"/>
1352	<o:lock v:ext="edit" shapetype="f"/>
1353	</v:shape><![endif]--><![if !vml]><span style='mso-ignore:vglayout;position:
1354	absolute;z-index:251659264;margin-left:234px;margin-top:273px;width:73px;
1355	height:38px'><img width=73 height=38
1356	src="Small%20Angle%20Image%20Processing_files/image040.png" v:shapes="Straight_x0020_Arrow_x0020_Connector_x0020_21"></span><![endif]><span
1357	style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_4"
1358	o:spid="_x0000_i1059" type="#_x0000_t75" style='width:525pt;height:450pt;
1359	visibility:visible;mso-wrap-style:square'>
1360	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image005.png"
1361	o:title=""/>
1362	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1363	src="Small%20Angle%20Image%20Processing_files/image005.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
1364
1365	<p class=MsoNormal><o:p> </o:p></p>
1366
1367	<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
1368	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1369	mso-hansi-theme-font:minor-latin'>Operations/Calibrate</span></b> from the <b
1370	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1371	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1372	Controls</span></b> menu; a bit of instruction will appear on the status line
1373	of this window. Select 5 points on the innermost ring (arrowed above); a small
1374	red cross will appear at each selection point. Press the right mouse button to
1375	finish; calibration will proceed. A sequence of concentric red rings will
1376	appear; they will switch to blue when calibration is finished. Select <b
1377	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1378	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show ring
1379	picks</span></b> (near bottom right of <b style='mso-bidi-font-weight:normal'><span
1380	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1381	mso-hansi-theme-font:minor-latin'>Image Controls</span></b> window). The <b
1382	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1383	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1384	Controls</span></b> window will show the results of the calibration</p>
1385
1386	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1387	id="Picture_x0020_5" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:472.5pt;
1388	height:388.5pt;visibility:visible;mso-wrap-style:square'>
1389	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image006.png"
1390	o:title=""/>
1391	</v:shape><![endif]--><![if !vml]><img width=630 height=518
1392	src="Small%20Angle%20Image%20Processing_files/image006.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
1393
1394	<p class=MsoNormal><o:p> </o:p></p>
1395
1396	<p class=MsoNormal>And the plot will show the points (very sparse!) used in the
1397	calibration calculations.</p>
1398
1399	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1400	id="Picture_x0020_6" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:525pt;
1401	height:450pt;visibility:visible;mso-wrap-style:square'>
1402	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image007.png"
1403	o:title=""/>
1404	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1405	src="Small%20Angle%20Image%20Processing_files/image007.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
1406
1407	<p class=MsoNormal><o:p> </o:p></p>
1408
1409	<p class=MsoNormal>You would like to use more points from just the visible
1410	rings. I suggest you change <b style='mso-bidi-font-weight:normal'><span
1411	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1412	mso-hansi-theme-font:minor-latin'>Min ring I/<span class=SpellE>Ib</span></span></b>
1413	to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1414	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.5</span></b>
1415	and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1416	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Min <span
1417	class=SpellE>calib</span> d-spacing</span></b> to <b style='mso-bidi-font-weight:
1418	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1419	minor-latin;mso-hansi-theme-font:minor-latin'>10.0</span></b>. Do <b
1420	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1421	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Recalibrate</span></b>;
1422	more points will be used and they will be limited to the 5 visible rings in the
1423	pattern.</p>
1424
1425	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1426	id="Picture_x0020_7" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:525pt;
1427	height:450pt;visibility:visible;mso-wrap-style:square'>
1428	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image008.png"
1429	o:title=""/>
1430	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1431	src="Small%20Angle%20Image%20Processing_files/image008.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
1432
1433	<p class=MsoNormal><o:p> </o:p></p>
1434
1435	<p class=MsoNormal>And give the calibration result as</p>
1436
1437	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1438	id="Picture_x0020_8" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:472.5pt;
1439	height:388.5pt;visibility:visible;mso-wrap-style:square'>
1440	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image009.png"
1441	o:title=""/>
1442	</v:shape><![endif]--><![if !vml]><img width=630 height=518
1443	src="Small%20Angle%20Image%20Processing_files/image009.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
1444
1445	<p class=MsoNormal><o:p> </o:p></p>
1446
1447	<p class=MsoNormal>You will need this calibration information to process the
1448	other images in this tutorial. To save it for future use do <b
1449	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1450	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Save
1451	controls</span></b>; a file dialog will appear. Makeup a file name (no
1452	extension needed) for this; I chose <b style='mso-bidi-font-weight:normal'><span
1453	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1454	mso-hansi-theme-font:minor-latin'>SASD</span></b>. Press <b style='mso-bidi-font-weight:
1455	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1456	minor-latin;mso-hansi-theme-font:minor-latin'>Save</span></b> and the file <span
1457	class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1458	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1459	minor-latin'>SASD.imctrl</span></b></span> will be written to the local
1460	directory. If you are continuing on to the next step do <b style='mso-bidi-font-weight:
1461	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1462	minor-latin;mso-hansi-theme-font:minor-latin'>File/New Project</span></b>
1463	(dont bother saving the project file unless you want it; we will not need it
1464	here); otherwise you can exit GSAS-II.</p>
1465
1466	<h2>Step 2: Data image integration</h2>
1467
1468	<p class=MsoNormal>The objective here is to read in the four polymer sample
1469	images, a glassy carbon image, an empty container image and a dark image. The
1470	images will be integrated after creating masks to remove the beam stop and
1471	other objectionable parts of the images. If you have not done so already, start
1472	GSAS-II. </p>
1473
1474	<p class=MsoNormal><o:p> </o:p></p>
1475
1476	<p class=MsoNormal>First do <b style='mso-bidi-font-weight:normal'><span
1477	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1478	mso-hansi-theme-font:minor-latin'>Data/Read image data</span></b>, go to <b
1479	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1480	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>exercises/<span
1481	class=SpellE>SAimages</span></span></b> and select all images except <b
1482	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1483	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>AgBehenate_003.tif</span></b>;
1484	then press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1485	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1486	minor-latin'>Open</span></b> to read all of them. The GSAS-II data tree window
1487	will show entries for 7 images and will expand the last one</p>
1488
1489	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1490	id="Picture_x0020_9" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:300pt;
1491	height:310.5pt;visibility:visible;mso-wrap-style:square'>
1492	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image010.png"
1493	o:title=""/>
1494	</v:shape><![endif]--><![if !vml]><img width=400 height=414
1495	src="Small%20Angle%20Image%20Processing_files/image010.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
1496
1497	<p class=MsoNormal><o:p> </o:p></p>
1498
1499	<p class=MsoNormal>Notice that the Dark, Empty and GC (glassy carbon) are all
1500	5s images and the Sa1-4 ones are 40s images; this time information is needed
1501	later to obtain correct scaling. First select the <b style='mso-bidi-font-weight:
1502	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1503	minor-latin;mso-hansi-theme-font:minor-latin'>IMG GC_5s_200.tif</span></b>
1504	entry from the tree and expand it (press the <b style='mso-bidi-font-weight:
1505	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1506	minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b> box); then select <b
1507	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1508	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1509	controls</span></b>. The data window (<b style='mso-bidi-font-weight:normal'><span
1510	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1511	mso-hansi-theme-font:minor-latin'>Image Controls</span></b>) will show the
1512	default settings.</p>
1513
1514	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1515	id="Picture_x0020_10" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:472.5pt;
1516	height:388.5pt;visibility:visible;mso-wrap-style:square'>
1517	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image011.png"
1518	o:title=""/>
1519	</v:shape><![endif]--><![if !vml]><img width=630 height=518
1520	src="Small%20Angle%20Image%20Processing_files/image011.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
1521
1522	<p class=MsoNormal><o:p> </o:p></p>
1523
1524	<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
1525	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1526	mso-hansi-theme-font:minor-latin'>Operations/Load controls</span></b> from the
1527	menu; a file selection dialog will appear showing the available *.<span
1528	class=SpellE>imctrl</span> files (the one you made in Step 1 should be seen).
1529	Select it and press <b style='mso-bidi-font-weight:normal'><span
1530	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1531	mso-hansi-theme-font:minor-latin'>Open</span></b>; the <b style='mso-bidi-font-weight:
1532	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1533	minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> window
1534	will be redrawn with the settings obtained in <b style='mso-bidi-font-weight:
1535	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1536	minor-latin;mso-hansi-theme-font:minor-latin'>Step 1: Detector calibration</span></b></p>
1537
1538	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1539	id="Picture_x0020_11" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:472.5pt;
1540	height:388.5pt;visibility:visible;mso-wrap-style:square'>
1541	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image012.png"
1542	o:title=""/>
1543	</v:shape><![endif]--><![if !vml]><img width=630 height=518
1544	src="Small%20Angle%20Image%20Processing_files/image012.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
1545
1546	<p class=MsoNormal><o:p> </o:p></p>
1547
1548	<p class=MsoNormal>and the image will be that of glassy carbon. Changing the <b
1549	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1550	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Max intensity</span></b>
1551	slider on the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1552	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1553	minor-latin'>Image Controls</span></b> window will show that the image from the
1554	<span class=SpellE>MarCCD</span> is circular and slightly offset from the beam
1555	center. A beam stop shadow is evident as well as an arc-like fault in the image
1556	(toward the upper left corner of the image). We will sort those out later.</p>
1557
1558	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1559	id="Picture_x0020_55" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:525pt;
1560	height:450pt;visibility:visible;mso-wrap-style:square'>
1561	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image013.png"
1562	o:title=""/>
1563	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1564	src="Small%20Angle%20Image%20Processing_files/image013.png" v:shapes="Picture_x0020_55"><![endif]></span></p>
1565
1566	<p class=MsoNormal><o:p> </o:p></p>
1567
1568	<p class=MsoNormal>The next step we will be doing is to set up the integration
1569	controls. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
1570	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1571	minor-latin'>Dark image</span></b> is <b style='mso-bidi-font-weight:normal'><span
1572	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1573	mso-hansi-theme-font:minor-latin'>IMG Dark_5s_003.tif</span></b>, the <b
1574	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1575	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background
1576	image</span></b> is <b style='mso-bidi-font-weight:normal'><span
1577	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1578	mso-hansi-theme-font:minor-latin'>IMG Empty_5s_014.tif</span></b>; select these
1579	two. The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1580	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1581	for each are <b style='mso-bidi-font-weight:normal'><span style='font-family:
1582	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1583	minor-latin'>-1.0</span></b> because their exposures were the same as this
1584	glassy carbon image (5s). Next check the boxes for <b style='mso-bidi-font-weight:
1585	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1586	minor-latin;mso-hansi-theme-font:minor-latin'>Show integration limits?</span></b>
1587	and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1588	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Do full
1589	integration?</span></b> A pair of circles with a connecting diagonal line will
1590	appear on the plot. Set the <b style='mso-bidi-font-weight:normal'><span
1591	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1592	mso-hansi-theme-font:minor-latin'>Inner/Outer q</span></b> values to <b
1593	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1594	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.05</span></b>
1595	and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1596	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.9</span></b>,
1597	respectively, and set the <b style='mso-bidi-font-weight:normal'><span
1598	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1599	mso-hansi-theme-font:minor-latin'>Start azimuth</span></b> to <b
1600	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1601	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0</span></b>.
1602	Set the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1603	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. 2-theta
1604	bins</span></b> to <b style='mso-bidi-font-weight:normal'><span
1605	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1606	mso-hansi-theme-font:minor-latin'>250</span></b>, which is more appropriate for
1607	small angle scattering, and set the <b style='mso-bidi-font-weight:normal'><span
1608	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1609	mso-hansi-theme-font:minor-latin'>Bin style: Constant step bins in</span></b>
1610	to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1611	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>log(q)</span></b>.
1612	You should also check the <b style='mso-bidi-font-weight:normal'><span
1613	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1614	mso-hansi-theme-font:minor-latin'>Apply sample absorption?</span></b> and <b
1615	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1616	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Apply
1617	polarization?</span></b> boxes; enter the measured <b style='mso-bidi-font-weight:
1618	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1619	minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> (<b
1620	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1621	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.818</span></b>)
1622	for the glassy carbon sample. When done the <b style='mso-bidi-font-weight:
1623	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1624	minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> data
1625	window should look like</p>
1626
1627	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1628	id="Picture_x0020_40" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:472.5pt;
1629	height:388.5pt;visibility:visible;mso-wrap-style:square'>
1630	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image014.png"
1631	o:title=""/>
1632	</v:shape><![endif]--><![if !vml]><img width=630 height=518
1633	src="Small%20Angle%20Image%20Processing_files/image014.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
1634
1635	<p class=MsoNormal><o:p> </o:p></p>
1636
1637	<p class=MsoNormal>And the plot should look like</p>
1638
1639	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1640	id="Picture_x0020_41" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:525pt;
1641	height:450pt;visibility:visible;mso-wrap-style:square'>
1642	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image015.png"
1643	o:title=""/>
1644	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1645	src="Small%20Angle%20Image%20Processing_files/image015.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
1646
1647	<p class=MsoNormal><o:p> </o:p></p>
1648
1649	<p class=MsoNormal>Now copy these controls to the other images. Do <b
1650	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1651	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Copy
1652	controls</span></b> and select just the <b style='mso-bidi-font-weight:normal'><span
1653	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1654	mso-hansi-theme-font:minor-latin'>Sa1-4</span></b> data names. </p>
1655
1656	<p class=MsoNormal>We now need to go to the <b style='mso-bidi-font-weight:
1657	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1658	minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> for
1659	each of <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1660	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b>
1661	to enter the correct transmission for each and change the Dark & Background
1662	<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1663	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1664	to account for the different exposure times. Start with <b style='mso-bidi-font-weight:
1665	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1666	minor-latin;mso-hansi-theme-font:minor-latin'>IMG Sa1_40s_067.tif</span></b>
1667	and change <b style='mso-bidi-font-weight:normal'><span style='font-family:
1668	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1669	minor-latin'>transmission</span></b> to <b style='mso-bidi-font-weight:normal'><span
1670	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1671	mso-hansi-theme-font:minor-latin'>0.943</span></b> and the two <b
1672	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1673	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1674	to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1675	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1676	Then go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1677	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1678	minor-latin'>IMG Sa2_40s_069.tif</span></b> and change <b style='mso-bidi-font-weight:
1679	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1680	minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1681	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1682	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.979</span></b>;
1683	<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1684	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1685	to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1686	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1687	Next go <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1688	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>to IMG
1689	Sa3_40s_059.tif</span></b> and change <b style='mso-bidi-font-weight:normal'><span
1690	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1691	mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1692	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1693	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.960</span></b>;
1694	<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1695	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1696	to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1697	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1698	Finally, go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1699	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1700	minor-latin'>IMG Sa4_40s_061.tif</span></b> and change <b style='mso-bidi-font-weight:
1701	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1702	minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> to <b
1703	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1704	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.968</span></b>;
1705	<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1706	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>multipliers</span></b>
1707	to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1708	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-8.0</span></b>.
1709	The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1710	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
1711	Controls</span></b> data window for this should look like</p>
1712
1713	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1714	id="Picture_x0020_43" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:472.5pt;
1715	height:388.5pt;visibility:visible;mso-wrap-style:square'>
1716	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image016.png"
1717	o:title=""/>
1718	</v:shape><![endif]--><![if !vml]><img width=630 height=518
1719	src="Small%20Angle%20Image%20Processing_files/image016.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
1720
1721	<p class=MsoNormal><o:p> </o:p></p>
1722
1723	<p class=MsoNormal>This is a reasonable time to save the project; do <b
1724	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1725	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>File/Save
1726	project as</span></b> from the main GSAS-II data tree menu. Choose a file name
1727	(I assumed <b style='mso-bidi-font-weight:normal'><span style='font-family:
1728	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1729	minor-latin'>image</span></b>) and it will be written on the local file
1730	directory. </p>
1731
1732	<p class=MsoNormal>As noted earlier, the images contain some unwanted features;
1733	so lets create masks to remove them. Select <b style='mso-bidi-font-weight:
1734	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1735	minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b> from the GSAS-II
1736	data tree under <b style='mso-bidi-font-weight:normal'><span style='font-family:
1737	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1738	minor-latin'>IMG GC_5s_200.tif</span></b>; the data window will show</p>
1739
1740	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1741	id="Picture_x0020_17" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:337.5pt;
1742	height:99.75pt;visibility:visible;mso-wrap-style:square'>
1743	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image017.png"
1744	o:title=""/>
1745	</v:shape><![endif]--><![if !vml]><img width=450 height=133
1746	src="Small%20Angle%20Image%20Processing_files/image017.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1747
1748	<p class=MsoNormal><o:p> </o:p></p>
1749
1750	<p class=MsoNormal>To mask out the regions beyond the circular <span
1751	class=SpellE>MarCCD</span> image change the <span class=GramE><b
1752	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1753	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Lower<span
1754	style='mso-spacerun:yes'> </span><span class=SpellE>threshhold</span></span></b></span>
1755	from <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1756	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0</span></b>
1757	to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1758	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>;
1759	the image will be redrawn with these regions in red</p>
1760
1761	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1762	id="Picture_x0020_45" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
1763	height:450pt;visibility:visible;mso-wrap-style:square'>
1764	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image018.png"
1765	o:title=""/>
1766	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1767	src="Small%20Angle%20Image%20Processing_files/image018.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
1768
1769	<p class=MsoNormal><o:p> </o:p></p>
1770
1771	<p class=MsoNormal>These are now excluded. The status line for the <b
1772	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1773	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b>
1774	data window gives the directions for adding additional masks. You can make arcs
1775	(well use that here), rings, spots (this too) and polygons (this as well) as
1776	masks. These enclose areas to be excluded. The frame works in the opposite
1777	sense in that everything outside the frame is excluded (NB: only one frame is
1778	allowed). So lets first mask the bad arc in the upper left zoom in on that
1779	part of the image</p>
1780
1781	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1782	id="Picture_x0020_62" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt;
1783	height:450pt;visibility:visible;mso-wrap-style:square'>
1784	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image019.png"
1785	o:title=""/>
1786	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1787	src="Small%20Angle%20Image%20Processing_files/image019.png" v:shapes="Picture_x0020_62"><![endif]></span></p>
1788
1789	<p class=MsoNormal><o:p> </o:p></p>
1790
1791	<p class=MsoNormal>To add the mask 1: be sure the focus is on the image and the
1792	zoom buttons are off, 2: type <b style='mso-bidi-font-weight:normal'><span
1793	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1794	mso-hansi-theme-font:minor-latin'>a</span></b> to activate the arc mask entry
1795	3: press the left mouse button (<b style='mso-bidi-font-weight:normal'><span
1796	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1797	mso-hansi-theme-font:minor-latin'>LB</span></b>) with the cursor centered on
1798	the bad arc. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
1799	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1800	minor-latin'>Masks</span></b> window will show a new entry </p>
1801
1802	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1803	id="Picture_x0020_63" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:342pt;
1804	height:136.5pt;visibility:visible;mso-wrap-style:square'>
1805	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image020.png"
1806	o:title=""/>
1807	</v:shape><![endif]--><![if !vml]><img width=456 height=182
1808	src="Small%20Angle%20Image%20Processing_files/image020.png" v:shapes="Picture_x0020_63"><![endif]></span><span
1809	style='mso-spacerun:yes'> </span></p>
1810
1811	<p class=MsoNormal><o:p> </o:p></p>
1812
1813	<p class=MsoNormal>and an arc mask will be drawn on the plot.</p>
1814
1815	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1816	id="Picture_x0020_64" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
1817	height:450pt;visibility:visible;mso-wrap-style:square'>
1818	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image021.png"
1819	o:title=""/>
1820	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1821	src="Small%20Angle%20Image%20Processing_files/image021.png" v:shapes="Picture_x0020_64"><![endif]></span></p>
1822
1823	<p class=MsoNormal><o:p> </o:p></p>
1824
1825	<p class=MsoNormal>You can change the angular width of the arc by changing <b
1826	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1827	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>thickness</span></b>
1828	in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1829	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Masks</span></b>
1830	data window, you can change the angular range of the arc by dragging either end
1831	of the arc (NB: increments only in whole degrees), and you can move the
1832	arc<span style='mso-spacerun:yes'> </span>along a constant 2Θ angle by
1833	dragging on any point inside the mask. The curvature is centered on the beam
1834	center position and follows a constant 2Θ curve established by the
1835	detector calibration.<span style='mso-no-proof:yes'> </span></p>
1836
1837	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1838	id="Picture_x0020_65" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
1839	height:450pt;visibility:visible;mso-wrap-style:square'>
1840	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image022.png"
1841	o:title=""/>
1842	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1843	src="Small%20Angle%20Image%20Processing_files/image022.png" v:shapes="Picture_x0020_65"><![endif]></span></p>
1844
1845	<p class=MsoNormal>Next lets deal with the beam stop. Im going to use both a
1846	polygon and a spot to cover it. Move the zoom area to be around the center,
1847	make sure the zoom buttons are off, enter <b style='mso-bidi-font-weight:normal'><span
1848	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1849	mso-hansi-theme-font:minor-latin'>s</span></b> on the plot and press mouse <b
1850	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1851	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>LB</span></b>
1852	with the cursor positioned where you want the spot. A 1mm diameter red circle
1853	will appear 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_66" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;
1857	height:450pt;visibility:visible;mso-wrap-style:square'>
1858	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image023.png"
1859	o:title=""/>
1860	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1861	src="Small%20Angle%20Image%20Processing_files/image023.png" v:shapes="Picture_x0020_66"><![endif]></span></p>
1862
1863	<p class=MsoNormal><o:p> </o:p></p>
1864
1865	<p class=MsoNormal>And the <b style='mso-bidi-font-weight:normal'><span
1866	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1867	mso-hansi-theme-font:minor-latin'>Masks</span></b> window will have new
1868	information</p>
1869
1870	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1871	id="Picture_x0020_24" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:337.5pt;
1872	height:170.25pt;visibility:visible;mso-wrap-style:square'>
1873	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image024.png"
1874	o:title=""/>
1875	</v:shape><![endif]--><![if !vml]><img width=450 height=227
1876	src="Small%20Angle%20Image%20Processing_files/image024.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
1877
1878	<p class=MsoNormal><o:p> </o:p></p>
1879
1880	<p class=MsoNormal>You can change the diameter of the spot, I used <b
1881	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1882	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>7.0</span></b>;
1883	the plot now shows a ring that just covers the beam stop. You may have to drag
1884	it a bit (Hint: drag the center of the spot) to get it well centered.</p>
1885
1886	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1887	id="Picture_x0020_67" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
1888	height:450pt;visibility:visible;mso-wrap-style:square'>
1889	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image025.png"
1890	o:title=""/>
1891	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1892	src="Small%20Angle%20Image%20Processing_files/image025.png" v:shapes="Picture_x0020_67"><![endif]></span></p>
1893
1894	<p class=MsoNormal><o:p> </o:p></p>
1895
1896	<p class=MsoNormal>Next we need to mask the stick holding the beam stop; well
1897	use a 4 sided polygon for this. Adjust the zoom & position so you can see
1898	the entire beam stop stick. Make sure all zoom buttons are off, press <b
1899	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1900	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>p</span></b>
1901	on the plot, then press the mouse <b style='mso-bidi-font-weight:normal'><span
1902	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1903	mso-hansi-theme-font:minor-latin'>LB</span></b> at four points in succession
1904	around the beam stop stick. A line segment for the polygon will be drawn
1905	following your mouse clicks. Finally press the mouse <b style='mso-bidi-font-weight:
1906	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1907	minor-latin;mso-hansi-theme-font:minor-latin'>RB</span></b> to close the
1908	polygon. You should see something like</p>
1909
1910	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1911	id="Picture_x0020_68" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
1912	height:450pt;visibility:visible;mso-wrap-style:square'>
1913	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image026.png"
1914	o:title=""/>
1915	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1916	src="Small%20Angle%20Image%20Processing_files/image026.png" v:shapes="Picture_x0020_68"><![endif]></span></p>
1917
1918	<p class=MsoNormal><o:p> </o:p></p>
1919
1920	<p class=MsoNormal>You can adjust the position of the polygon vertices by
1921	closely dragging it with mouse <b style='mso-bidi-font-weight:normal'><span
1922	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1923	mso-hansi-theme-font:minor-latin'>LB</span></b> pressed; a new vertex can be
1924	added by dragging an existing vertex with the mouse <b style='mso-bidi-font-weight:
1925	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1926	minor-latin;mso-hansi-theme-font:minor-latin'>RB</span></b> pressed. If you
1927	drag one vertex onto another, they are merged and cannot be separated.</p>
1928
1929	<p class=MsoNormal>We want to use these masks for all the Sa1-4 images. Do <b
1930	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1931	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Copy
1932	mask</span></b>; a <b style='mso-bidi-font-weight:normal'><span
1933	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1934	mso-hansi-theme-font:minor-latin'>Copy mask information</span></b> dialog box
1935	will appear. Select the <b style='mso-bidi-font-weight:normal'><span
1936	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1937	mso-hansi-theme-font:minor-latin'>Sa1-4</span></b> items and press <b
1938	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1939	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.
1940	Here is a useful place to save your project; do <b style='mso-bidi-font-weight:
1941	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1942	minor-latin;mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from
1943	the main GSAS-II data tree menu.</p>
1944
1945	<h2>Step 3: Integration of images</h2>
1946
1947	<p class=MsoNormal>We are now ready to integrate the glassy carbon and the four
1948	Sa images. Select any <b style='mso-bidi-font-weight:normal'><span
1949	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1950	mso-hansi-theme-font:minor-latin'>Image Controls</span></b> and then do <b
1951	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1952	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Integrate
1953	all</span></b>. A selection dialog will appear; select only the <b
1954	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1955	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>GC</span></b>
1956	and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1957	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b>
1958	data sets and press <b style='mso-bidi-font-weight:normal'><span
1959	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1960	mso-hansi-theme-font:minor-latin'>Ok</span></b>. The image integration will
1961	proceed; a progress bar shows as each one is done. Five SASD data items will
1962	appear on the GSAS-II data tree; the last one (<b style='mso-bidi-font-weight:
1963	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1964	minor-latin;mso-hansi-theme-font:minor-latin'>SASD Sa4_40s_061.tif <span
1965	class=SpellE>Azm</span>=45.00</span></b>) will be expanded and plotted (you may
1966	have to select the <b style='mso-bidi-font-weight:normal'><span
1967	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1968	mso-hansi-theme-font:minor-latin'>Powder Patterns</span></b> tab to see it).</p>
1969
1970	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1971	id="Picture_x0020_26" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
1972	height:450pt;visibility:visible;mso-wrap-style:square'>
1973	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image027.png"
1974	o:title=""/>
1975	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1976	src="Small%20Angle%20Image%20Processing_files/image027.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
1977
1978	<p class=MsoNormal><o:p> </o:p></p>
1979
1980	<p class=MsoNormal>Pretty obviously the SASD pattern is down to background at
1981	Q~0.25Å<sup>-1</sup>; the other Sa1-Sa4 patterns are similar. The glassy carbon
1982	pattern extends nicely to the highest Q (~1.0Å<sup>-1</sup>) measured.</p>
1983
1984	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1985	id="Picture_x0020_48" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:525pt;
1986	height:450pt;visibility:visible;mso-wrap-style:square'>
1987	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image028.png"
1988	o:title=""/>
1989	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1990	src="Small%20Angle%20Image%20Processing_files/image028.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
1991
1992	<p class=MsoNormal><o:p> </o:p></p>
1993
1994	<h2>Step 4: Scaling of SASD patterns</h2>
1995
1996	<p class=MsoNormal>To set this data on an absolute scale, we compare it to an
1997	absolute scaled glassy carbon scan. One of these is in the same directory as
1998	the image data; do <b style='mso-bidi-font-weight:normal'><span
1999	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2000	mso-hansi-theme-font:minor-latin'>Import/Small Angle Data/ from q(A-1) step
2001	X-ray QIE data file</span></b> and select <b style='mso-bidi-font-weight:normal'><span
2002	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2003	mso-hansi-theme-font:minor-latin'>GC calibrated data.txt</span></b> from the
2004	file selection dialog. You will need to select <b style='mso-bidi-font-weight:
2005	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2006	minor-latin;mso-hansi-theme-font:minor-latin'>any <span class=GramE>file(</span>.)</span></b>
2007	to see it. A <b style='mso-bidi-font-weight:normal'><span style='font-family:
2008	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2009	minor-latin'>Is this the file you want</span></b> dialog will appear respond <b
2010	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2011	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b>
2012	to read the file; it will be plotted.</p>
2013
2014	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2015	id="Picture_x0020_49" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
2016	height:450pt;visibility:visible;mso-wrap-style:square'>
2017	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image029.png"
2018	o:title=""/>
2019	</v:shape><![endif]--><![if !vml]><img width=700 height=600
2020	src="Small%20Angle%20Image%20Processing_files/image029.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
2021
2022	<p class=MsoNormal><o:p> </o:p></p>
2023
2024	<p class=MsoNormal>If you enter <b style='mso-bidi-font-weight:normal'><span
2025	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2026	mso-hansi-theme-font:minor-latin'>m</span></b> on the plot window, all of the
2027	SASD patterns will be plotted together (Ive adjusted the zoom to see them
2028	all).</p>
2029
2030	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2031	id="Picture_x0020_50" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
2032	height:450pt;visibility:visible;mso-wrap-style:square'>
2033	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image030.png"
2034	o:title=""/>
2035	</v:shape><![endif]--><![if !vml]><img width=700 height=600
2036	src="Small%20Angle%20Image%20Processing_files/image030.png" v:shapes="Picture_x0020_50"><![endif]></span></p>
2037
2038	<p class=MsoNormal><o:p> </o:p></p>
2039
2040	<p class=MsoNormal>Clearly the measured image data need to be scaled down to
2041	have them on absolute scale. First is to discover the scaling between the two
2042	glassy carbon patterns. Go to the measured one (<b style='mso-bidi-font-weight:
2043	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2044	minor-latin;mso-hansi-theme-font:minor-latin'>SASD GC_5s_200.tif</span></b>)
2045	and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2046	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2047	minor-latin'>Sample Parameters</span></b>.</p>
2048
2049	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2050	id="Picture_x0020_51" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:291.75pt;
2051	height:408pt;visibility:visible;mso-wrap-style:square'>
2052	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image031.png"
2053	o:title=""/>
2054	</v:shape><![endif]--><![if !vml]><img width=389 height=544
2055	src="Small%20Angle%20Image%20Processing_files/image031.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
2056
2057	<p class=MsoNormal><o:p> </o:p></p>
2058
2059	<p class=MsoNormal>We will change <b style='mso-bidi-font-weight:normal'><span
2060	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2061	mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> by
2062	comparison with the absolute glassy carbon scan. Do <b style='mso-bidi-font-weight:
2063	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2064	minor-latin;mso-hansi-theme-font:minor-latin'>Command/Set scale</span></b> from
2065	the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2066	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
2067	Parameters</span></b> menu; a <b style='mso-bidi-font-weight:normal'><span
2068	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2069	mso-hansi-theme-font:minor-latin'>Reference histogram</span></b> dialog will
2070	appear.</p>
2071
2072	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2073	id="Picture_x0020_44" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:259.5pt;
2074	height:252pt;visibility:visible;mso-wrap-style:square'>
2075	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image032.png"
2076	o:title=""/>
2077	</v:shape><![endif]--><![if !vml]><img width=346 height=336
2078	src="Small%20Angle%20Image%20Processing_files/image032.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
2079
2080	<p class=MsoNormal><o:p> </o:p></p>
2081
2082	<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2083	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2084	mso-hansi-theme-font:minor-latin'>SASD GC calibrated data.txt</span></b> (shown
2085	in blue above) and press <b style='mso-bidi-font-weight:normal'><span
2086	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2087	mso-hansi-theme-font:minor-latin'>Ok</span></b>; the <b style='mso-bidi-font-weight:
2088	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2089	minor-latin;mso-hansi-theme-font:minor-latin'>GC_5s_200.tif</span></b> data
2090	will be rescaled to the <b style='mso-bidi-font-weight:normal'><span
2091	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2092	mso-hansi-theme-font:minor-latin'>GC calibrated data</span></b> and the <b
2093	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2094	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale
2095	factor</span></b> will be changed to the new scaling factor (<b
2096	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2097	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.0008536</span></b>).
2098	The plot will be redrawn with the scaled data.</p>
2099
2100	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2101	id="Picture_x0020_52" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:525pt;
2102	height:450pt;visibility:visible;mso-wrap-style:square'>
2103	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image033.png"
2104	o:title=""/>
2105	</v:shape><![endif]--><![if !vml]><img width=700 height=600
2106	src="Small%20Angle%20Image%20Processing_files/image033.png" v:shapes="Picture_x0020_52"><![endif]></span></p>
2107
2108	<p class=MsoNormal><o:p> </o:p></p>
2109
2110	<p class=MsoNormal>The divergence at high Q is probably from a background
2111	contribution to the standard that is not present in our measured one. Next we
2112	have to apply this scale factor to the Sa1-Sa4 data sets. Do <b
2113	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2114	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Command/Copy
2115	selected</span></b> from the <b style='mso-bidi-font-weight:normal'><span
2116	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2117	mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> menu; a <b
2118	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2119	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select
2120	sample parameters</span></b> dialog will appear</p>
2121
2122	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2123	id="Picture_x0020_46" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:240pt;
2124	height:232.5pt;visibility:visible;mso-wrap-style:square'>
2125	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image034.png"
2126	o:title=""/>
2127	</v:shape><![endif]--><![if !vml]><img width=320 height=310
2128	src="Small%20Angle%20Image%20Processing_files/image034.png" v:shapes="Picture_x0020_46"><![endif]></span></p>
2129
2130	<p class=MsoNormal><o:p> </o:p></p>
2131
2132	<p class=MsoNormal>Select only <b style='mso-bidi-font-weight:normal'><span
2133	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2134	mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> and press <b
2135	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2136	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>;
2137	a <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2138	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Copy sample
2139	parameters</span></b> dialog will appear</p>
2140
2141	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2142	id="Picture_x0020_47" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:240pt;
2143	height:232.5pt;visibility:visible;mso-wrap-style:square'>
2144	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image035.png"
2145	o:title=""/>
2146	</v:shape><![endif]--><![if !vml]><img width=320 height=310
2147	src="Small%20Angle%20Image%20Processing_files/image035.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
2148
2149	<p class=MsoNormal><o:p> </o:p></p>
2150
2151	<p class=MsoNormal>Select only the <b style='mso-bidi-font-weight:normal'><span
2152	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2153	mso-hansi-theme-font:minor-latin'>Sa1-Sa4</span></b> data sets and press <b
2154	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2155	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.
2156	The copy will occur and the plot redrawn</p>
2157
2158	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2159	id="Picture_x0020_53" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
2160	height:450pt;visibility:visible;mso-wrap-style:square'>
2161	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image036.png"
2162	o:title=""/>
2163	</v:shape><![endif]--><![if !vml]><img width=700 height=600
2164	src="Small%20Angle%20Image%20Processing_files/image036.png" v:shapes="Picture_x0020_53"><![endif]></span></p>
2165
2166	<p class=MsoNormal><o:p> </o:p></p>
2167
2168	<p class=MsoNormal>Ive changed the zoom to show all the data. We are not quite
2169	done; the scales for the Sa1-Sa4 data sets have to be further reduced by a factor
2170	of 8 to account for the longer exposure time. Select <b style='mso-bidi-font-weight:
2171	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2172	minor-latin;mso-hansi-theme-font:minor-latin'>SASD Sa1_40s_067.tif</span></b>
2173	from the GSAS-II data tree, expand it and choose <b style='mso-bidi-font-weight:
2174	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2175	minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b></p>
2176
2177	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2178	id="Picture_x0020_54" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:291.75pt;
2179	height:408pt;visibility:visible;mso-wrap-style:square'>
2180	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image037.png"
2181	o:title=""/>
2182	</v:shape><![endif]--><![if !vml]><img width=389 height=544
2183	src="Small%20Angle%20Image%20Processing_files/image037.png" v:shapes="Picture_x0020_54"><![endif]></span></p>
2184
2185	<p class=MsoNormal><o:p> </o:p></p>
2186
2187	<p class=MsoNormal>The data items here can take simple mathematical expressions
2188	so change <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2189	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
2190	scale factor</span></b> to <b style='mso-bidi-font-weight:normal'><span
2191	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2192	mso-hansi-theme-font:minor-latin'>0.0008536/8</span></b> and press <b
2193	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2194	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>.
2195	The value will change to <b style='mso-bidi-font-weight:normal'><span
2196	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2197	mso-hansi-theme-font:minor-latin'>0.0001067</span></b> and the plot redrawn.</p>
2198
2199	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2200	id="Picture_x0020_56" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
2201	height:450pt;visibility:visible;mso-wrap-style:square'>
2202	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image038.png"
2203	o:title=""/>
2204	</v:shape><![endif]--><![if !vml]><img width=700 height=600
2205	src="Small%20Angle%20Image%20Processing_files/image038.png" v:shapes="Picture_x0020_56"><![endif]></span></p>
2206
2207	<p class=MsoNormal><o:p> </o:p></p>
2208
2209	<p class=MsoNormal>Next do <b style='mso-bidi-font-weight:normal'><span
2210	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2211	mso-hansi-theme-font:minor-latin'>Command/Copy selected</span></b> as before to
2212	copy this new scale factor to the other Sa data sets. The plot will again be
2213	redrawn</p>
2214
2215	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2216	id="Picture_x0020_57" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
2217	height:450pt;visibility:visible;mso-wrap-style:square'>
2218	<v:imagedata src="Small%20Angle%20Image%20Processing_files/image039.png"
2219	o:title=""/>
2220	</v:shape><![endif]--><![if !vml]><img width=700 height=600
2221	src="Small%20Angle%20Image%20Processing_files/image039.png" v:shapes="Picture_x0020_57"><![endif]></span></p>
2222
2223	<p class=MsoNormal><o:p> </o:p></p>
2224
2225	<p class=MsoNormal>Everything is now on absolute scale and these polymer
2226	samples are quite weak small angle <span class=SpellE>scatterers</span>. This
2227	is a good point to do a <b style='mso-bidi-font-weight:normal'><span
2228	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2229	mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from the main
2230	GSAS-II data tree menu. You can try to fit unified & <span class=SpellE>Porod</span>
2231	models to them following the procedures demonstrated in the <strong><span
2232	style='font-weight:normal'>Fitting Small Angle X-Ray Data</span></strong><strong><span
2233	style='font-weight:normal;mso-bidi-font-weight:bold'> tutorial. Id set the
2234	high Q limit to about 0.25Å<sup>-1</sup> as above that is only noisy
2235	background.</span></strong></p>
2236
2237	</div>
2238
2239	</body>
2240
2241	</html>

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