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162 lines
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162 lines
11 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<?oxygen RNGSchema="http://www.oasis-open.org/docbook/xml/5.0/rng/docbook.rng" type="xml"?>
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<chapter xmlns="http://docbook.org/ns/docbook" xmlns:xlink="http://www.w3.org/1999/xlink"
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version="5.0">
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<info><title>Quick guide to Quokka data reduction</title><author>
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<personname>Katy Wood</personname>
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</author>
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<date>2008-08-29 16:47</date>
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</info>
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<sect1>
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<title></title>
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<para>Note: Any data publication with quokka data reduced with the NIST macros should cite:
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Kline SR (2006) Reduction and analysis of SANS and USANS data using IGOR Pro. <emphasis
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role="italic">Journal of Applied Crystallography</emphasis><emphasis role="bold"
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>39:</emphasis> 895-900. </para>
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<para>The following is a ‘quick guide’ to treating quokka data. More detailled help about the macros is found in the ‘help’ buttons in Igor. </para>
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</sect1>
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<sect1><title>Chose a workspace and copy across report files </title>
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<para>Data can be treated either on the instrument control PC, or the NBI PC on the left in
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cabin (DAV2-Quokka), or your own PC with Quokka Igor macros installed.</para>
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<para>If working on DAV2-Quokka, please work under D:\Quokka Users. Any old (pre- April
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2012) reduced data is now under D:\NSVIS.backup.</para>
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<para>On DAV2-Quokka, your data can be copied across from J:\proposal\xxx where xxx is your
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proposal number.</para>
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<para>Report files are saved which associates the relevant transmission measurements with
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the scattering files – copy across the report files associated with your data to your
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working directory. These are under</para>
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<para>/data/current/reports on the Instrument control PC.</para>
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<para>J:\current\reports on the DAV2-quokka PC.</para>
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<para>Your local contact should give you the relevant sensitivity and mask files.</para>
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</sect1>
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<sect1><title>Open Igor macros</title>
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<para>Open “Igor with Quokka macros”, then in the ‘Macros’ menu select ‘Load Quokka data reduction’. You should be able to see the following window:</para>
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<figure><title>Data Reduction Controls</title><mediaobject>
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<imageobject>
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<imagedata align="center" width="80mm" fileref="igorReductionControls.jpg"/>
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</imageobject>
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</mediaobject>
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</figure>
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</sect1>
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<sect1><title>Select working directory</title><para>On the SANS Reduction controls, ‘Pick path’ (select path where all your data is), then ‘file catalogue’.
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A table with all data files + characteristics appears, this table takes some time to appear the first time, the small sign on the bottom left of Igor tells you it’s working.... </para>
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<figure><title></title><mediaobject>
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<imageobject>
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<imagedata align="left" width="40mm" fileref="igorAbort.jpg"/>
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</imageobject>
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</mediaobject>
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</figure>
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</sect1>
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<sect1><title>Patch the data </title>
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<para>This step is only necessary on data taken prior to April 2011, later data does not
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need to be patched, unless advised by your local contact. </para>
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<sect2><title>Write correct λ and Δλ/λ to all files</title>
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<para>Select ‘patch’ on the ‘raw data’ tab. With a * in the ‘match string’ box, hit enter.
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The ‘files to patch’ drop down menu should then be populated with all the files in your
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working directory. </para>
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<figure><title></title><mediaobject>
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<imageobject>
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<imagedata align="left" width="80mm" fileref="igorPatchFiles.jpg"/>
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</imageobject>
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</mediaobject>
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</figure>
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<para>The wavelength and wavelength spread values have been measured experimentally and
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should be changed to 5.078 and 0.14, respectively. These values are for data collected
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on Quokka after October 2010. Enter these number into the ‘Wavelength’ and ‘Wavelength
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spread’ boxes, tick the boxes and click ‘Change All Headers in List’.</para></sect2>
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<sect2>
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<title>Determine beam centres for each configuration and
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write to file</title>
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<para>In the green ‘patch’ window, select the ‘SDD’ box under ‘Match String’.</para>
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<figure><title></title><mediaobject>
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<imageobject>
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<imagedata align="left" width="80mm" fileref="igorPatchSDD.jpg"/>
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</imageobject>
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</mediaobject>
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</figure>
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<para>Enter the SDD distance of the configuration you wish to treat in the ‘Match
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String’ box and hit enter. If the SDD=1.31531, writing 1.3* is enough.</para>
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<para>The drop down menu under ‘Files to patch’ should now only contain the files at the
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specified SDD distance.</para>
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<para>Select a transmission file for the first configuration you wish to treat by usinig
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the ‘Display raw data’ in the ‘raw data’ tab. Select the direct beam using the
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marquee, right click and ‘find beam centre’. The X and Y-centers will be displayed
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in the Igor ‘history’ window (cntrl +J will bring this window to the front if it is
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hidden). </para>
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<para>Copy and paste the beam centre values which are displayed in the Igor ‘history’
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window into the ‘patch’ window. Then ‘change all headers in List’. By selecting
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‘File catalog’ again, the table ‘Data File Catalog’ will be refreshed and the
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columns Xcenter and Ycenter should be filled.</para>
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<para>Repeat this step for the other configurations you wish to treat.</para>
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</sect2>
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</sect1>
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<sect1><title>Calculating transmissions</title>
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<sect2><title>Read the report file & create table</title>
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<para>Select ‘transmission’ in the ‘raw data’ tab.
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‘pick path’ then select the xml report generated by gumtree, then ‘List Files’. A table
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is then created with all the correct file associations. </para></sect2>
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<sect2>
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<title>Calculate transmissions </title><para>Select the ‘empty beam’ transmission file for the first configuration you want to treat by
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clicking on the appropriate box in the table (should appear in the column
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‘EMP_Filenames’), and click ‘set BCENT file’ on the ‘calculate transmissions’ window
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(this sets this to beam centre). Click ‘Set XY Box’ and use the square to select the
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beam centre. Right click and select ‘SetXY box coords’. Then highlight the
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scattering files in the ‘scattering files table’ at the configuration for which
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you’ve just set the empty beam transmission, and click ‘calculate selected files’ in
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the Calculate transmissions window. The S_Transmission column in the
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‘ScatteringFiles’ window should now be populated.</para>
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<para>Repeat this step for the other configuations. </para>
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<para>Click ‘done’ when finished with transmissions’. If you click ‘File catalog’ the
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data File catalog window will be updated, and you should be able to see the
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transmission values. These are ‘patched’ into the data files.</para>
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<para>If your report is incomplete (ie you have stopped a MSW early and the different
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files are now in different reports) you can easily modify the report by opening it
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in a text editor.</para>
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</sect2>
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</sect1>
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<sect1>
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<title>Reduce data</title>
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<para>This section is not complete, but gives a quick overview. More info is available in the NIST help document.
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In the ‘reduction tab’ choose ‘build protocol’. The following appears:
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</para>
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<figure><title></title><mediaobject>
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<imageobject>
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<imagedata align="left" width="80mm" fileref="igorBuildProtocolAll.jpg"/>
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</imageobject>
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</mediaobject>
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</figure>
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<para/>
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<para>Leaving ‘ask’ will mean that during the reduction Igor will prompt you to select the
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file you wish to use:</para>
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<para>‘Sample’ will typically remain ‘ask’.</para>
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<para>‘Background’ is a scan of the blocked beam.</para>
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<para>‘Empty Cell’. If you are always subtracting the same empty cell/buffer run this can be
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set to the empty file by clicking on the appropriate ‘filename’ in the ‘Data File
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Catalog’ table, then clicking ‘set EMP file’ (or the filename can be copied and pasted
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in). (If you are using an empty cell from a previous run, you need to copy the file to
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the current directory – these will have different beam centres, unless obviously far off
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warnings about this can be ignored).</para>
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<para>‘Sensitivity’. Take the sensitivity file in S:\Bragg\Quokka\Sensitivity and
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standards\</para>
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<para>or one given by your local contact. Copy and paste the sensitivity file name or select
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it in the ‘data file catalog’, then ‘set DIV file’ on the data reduction window.</para>
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<para>‘Absolute’ – for absolute scaling. Click ‘set ABS params’, then select method of
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absolute calibration ‘Empty Beam Flux’. Select the empty beam transmission file, and
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draw a box around the beam with the cursor, then click ‘continue’.</para>
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<para>‘Mask’. Take the mask file in S:\Bragg\Quokka\Sensitivity and standards\</para>
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<para>or one given by your local contact, or make up your own!</para>
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<para>‘Average’ can be left as is for isotropic data.</para>
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<para>The data reduction protocol that you’ve now created can be saved ‘Save Protocol’. You
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can now reduce a file by selecting ‘Reduce a file’ directly in the blue ‘Data Reduction
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Protocol’ panel, or if you have saved the protocol, directly on the yellow ‘SANS
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Reduction Control’ panel. Via the ‘SANS Reduction Control’ panel you can then select the
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protocol (useful if you want to make multiple protocols).</para>
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<para>During the reduction, you’ll be prompted to select files to use. Each time Igor asks
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‘Do you want to add another xxx file’? This is for if you wish to add multiple runs
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together, if you only have one run, select no.</para>
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<para>Reduced data are then saved in the file: QKK00xxx.ABS</para>
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<para>To merge several configurations together: 1D Ops, ‘sort’ button</para>
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</sect1>
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</chapter>
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