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db5SICSUserGuideQuokka.xml is Katy Wood's document that has been manually

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