<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=iso-8859-1"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><title>RE: [GSAS-II] Masking Bad Data Points In Image Data</title><style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
@font-face
{font-family:"Courier New \;color\:black";
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:"Courier New \;color\:\#0563C1";
panose-1:0 0 0 0 0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";
color:black;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:12.0pt;
font-family:"Times New Roman","serif";
color:black;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0in;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";
color:black;}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0in;
margin-right:0in;
margin-bottom:0in;
margin-left:.5in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";
color:black;}
span.EmailStyle19
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:#1F497D;}
span.EmailStyle20
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:windowtext;}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:Consolas;
color:black;}
span.EmailStyle23
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:1530876951;
mso-list-type:hybrid;
mso-list-template-ids:-2010192718 600474764 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l0:level1
{mso-level-text:%1-;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
ol
{margin-bottom:0in;}
ul
{margin-bottom:0in;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body bgcolor=white lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks, <o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span style='mso-list:Ignore'>1-<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I was able to export calibration data ( wavelength, distance etc) to other image files by using “copy” in “Image Controls”. Somehow checking the “Use as defaults for all images?” does not work for me.<o:p></o:p></span></p><p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>(Problem Solved)<o:p></o:p></span></p><p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span style='mso-list:Ignore'>2-<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>To export all the integrated data, I tried “export” , “powder data as”. I was previously trying to export “text” data, in “text” data I don’t see “select all” but for CSV, FXYE, XYE. I am able to select all and export all data in a single go.<o:p></o:p></span></p><p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>(Problem Solved)<o:p></o:p></span></p><p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span style='mso-list:Ignore'>3-<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>May be I am asking too much about this “feature request” . I agree that by converting the wavelength of final data, some information will be lost and one would not be able to perform “Rietveld Refinement etc”, but still I believe it can be helpful to many users for easy comparison of data with ICDD or other published data etc.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Regards,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>/Shoaib<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:windowtext'>From:</span></b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:windowtext'> Andrzej Falenty [mailto:afalent@gwdg.de] <br><b>Sent:</b> Thursday, July 3, 2014 12:53 AM<br><b>To:</b> Shoaib Muhammad<br><b>Subject:</b> Re: [GSAS-II] Masking Bad Data Points In Image Data<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Here is some further help<br><br>Cheers<br><br>Andrzej<br><br>Am 02.07.2014 11:55, schrieb Shoaib Muhammad:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Dear All</span><o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks all for the excellent help, I was able to calibrate, import all data together, mask it and integrate it. Data qulity is not so good, so Rietveld refinement is not meaningful. I have few more questions:</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>1- First, I imported LaB6 image file to do the calibrations and saved the “controls file”. Then I imported in situ image data files together but I had to add “control file” (to add “sample to detector” distance and beam center etc) individually to each image file. I have around 90 image files so it took long to add control file to every image file. I tried different ways but could not figure out any way to add control parameters to each image file. In Fit2d usually after calibration, calibration data is exported to all other image files. Is there any way to do this in GSAS2?</span><o:p></o:p></p></blockquote><p class=MsoNormal><br>After finishing the calibration with LaB6 image you should select a box "Use as default for all images" in the "Image controls" window . If I remember correctly when you load your 2D data the image control settings should be automatically applied to every image.<br><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>2- After integrating all the image file, I could not find a way to export all the integrated data together. I had to export each integrated data file individually. How can I export all the integrated data together?</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p></blockquote><p class=MsoNormal><br>You can export all your 1D patterns in one go via GSASII data tree>Export>Powder Data As>GSAS FXYE file. Then a window "Item Selector" opens. There you can select your data for export individually or all of them (Toggle All or Set All will do the job). The export of 2D images is one-by-one only...<br><br><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Feature Request:</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Usually data recorded at synchrotron beamlines is not at CuKa wavelength but one is supposed to report this data in CuKa for easy comparison. It would be very helpful if GSAS2 users can export integrated diffraction image data, directly to CuKa wavelength</span><o:p></o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks,</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>/Shoaib</span><o:p></o:p></p><p><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'>Hi Shoaib,<br><br>I'm still working myself into the GSASII but I think I have figured of most of the often used options. I'm not sure to what extent you are familiar with the idea of masking but here are the basics. You can "draw" or select a region of different shape (e.g spot, polygon, arc etc) and that area is ignored in the integration. If you are familiar with masks in Fit2D program you will find nearly the same functionality in GSASII.<br><br><br>1) ....is there any way in GSAS2 to mask unwanted spots or sometimes even unwanted peaks...<br><br>-In order to create a mask you should load an image and in "GSAS II data tree" go to the sub tree: "Mask>Operations>Create new> ....." How to use individual mask types is written on the bottom of the "Mask" window. You can save, copy and load created masks. You can do it individually to selected images apply it to all images.<br><br>-If you have an interference showing up always in the same area (e.g. a beam stop) you may also limit the angular range of the integrated area ("Set Start/End azimuth" and "Inner/Outer 2-theta" in the "Image controls" window)<br><br>2) ...integrating this data and then make a sequence file to integrate...<br><br>Yeas you can. Prepare masks for your images and go: Image Controls>Operations>Integrate all> (Select 2D images) and Integrate. You will get a bunch of 1D diffraction patterns in the "GSAS II data tree".<br><br>3)...refine many image files together...<br><br>Hmm, this is a tough one and I had not opportunity to try this one out. An option to sum up diffraction patterns might help here if there is no crystallographic argument against it (like change in: T, detector-sample distance, wavelength and so on.... )<br><br>Good luck!<br><br>Andrzej</span><o:p></o:p></p><p><b><span style='font-family:"Calibri","sans-serif"'>From:</span></b><span style='font-family:"Calibri","sans-serif"'> Brian Toby [<a href="mailto:bhtoby@comcast.net">mailto:bhtoby@comcast.net</a>]<br><b>Sent:</b> Wednesday, July 2, 2014 10:47 AM<br><b>To:</b> Shoaib Muhammad<br><b>Cc:</b> Robert Von Dreele<br><b>Subject:</b> Re: [GSAS-II] Masking Bad Data Points In Image Data</span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'>Yes, you can mask sections of the detector. You can read in a series of images and then once you have settings you are happy with the masking and integration for one image you can copy those settings to the rest of the images and then integrate them while you get a cup of coffee. </span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'>Brian</span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'>Yes. Go to the Mask data tree item for your 1st image & add spots where you need them. Then change the size of the spot to fit. Use other masks as well; frame outlines the image to remove edge features. Masks can be copied to other images; they all can be integrated at once. Use sequential refinement to fit a sequence of images.<br>Bob Von Dreele<br>On 7/1/2014 8:33 PM, Shoaib Muhammad wrote:</span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'>Dear All,</span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'>Recently I noticed many updates in GSAS2 about image plate diffraction data integration and Rietveld refinement. I have some MAR345 type image plate diffraction data which I can successfully read in GSAS2. Data is recorded in situ on lithium ion battery cell so quality is not the best and has couple of unwanted bright spots. I was wondering, is there any way in GSAS2 to mask unwanted spots or sometimes even unwanted peaks while integrating this data and then make a sequence file to integrate and refine many image files together?</span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'>Regards,</span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'>/Shoaib</span> <o:p></o:p></p><p style='margin-bottom:12.0pt'> <o:p></o:p></p><p><span style='font-size:10.0pt;font-family:"Courier New ;color:black","serif"'>_______________________________________________</span><o:p></o:p></p><p><span style='font-size:10.0pt;font-family:"Courier New ;color:black","serif"'>GSAS-II mailing list</span><o:p></o:p></p><p><a href="mailto:GSAS-II@mailman.aps.anl.gov"><span style='font-size:10.0pt;font-family:"Courier New ;color:#0563C1","serif"'>GSAS-II@mailman.aps.anl.gov</span></a><o:p></o:p></p><p><a href="https://mailman.aps.anl.gov/mailman/listinfo/gsas-ii"><span style='font-size:10.0pt;font-family:"Courier New ;color:#0563C1","serif"'>https://mailman.aps.anl.gov/mailman/listinfo/gsas-ii</span></a><o:p></o:p></p></blockquote><p class=MsoNormal><br><br><br><o:p></o:p></p><pre>-- <o:p></o:p></pre><pre>--<o:p></o:p></pre><pre>Dr. Andrzej Falenty <a href="mailto:afalent@gwdg.de"><afalent@gwdg.de></a><o:p></o:p></pre><pre>Abt. Kristallographie<o:p></o:p></pre><pre>GZG, Georg-August-Universit�t<o:p></o:p></pre><pre>Goldschmidtstra�e 1<o:p></o:p></pre><pre>D-37077 G�ttingen<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Tel. 0049 551 3912150 <o:p></o:p></pre><pre><a href="http://kristall.uni-mki.gwdg.de/">http://kristall.uni-mki.gwdg.de/</a><o:p></o:p></pre></div></body></html>