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

converted from a Word document to docbook, for integration into Gumtree
help, and to have under source control.

site_ansto/manual/db5SICSUserGuideQuokka.xml

@@ -2,11 +2,10 @@
 <?oxygen RNGSchema="http://www.oasis-open.org/docbook/xml/5.0/rng/docbookxi.rng" type="xml"?>
 <book xmlns="http://docbook.org/ns/docbook" xmlns:xi="http://www.w3.org/2001/XInclude"
     xmlns:xlink="http://www.w3.org/1999/xlink" version="5.0">
-    <info><title>UNDER CONSTRUCTION User Guide for Small Angle Scattering. Quokka
-            Edition</title><subtitle>ANSTO version 0.2. May 2013</subtitle>
+    <info><title>User Guide for Small Angle Scattering. Quokka
+            Edition</title><subtitle>SICS 2.6 and Gumtree 1.8. Generated 31st October 2013</subtitle>
         <date/>
-        <author><personname>Katy Wood</personname></author><author><personname>Nick
-            Hauser</personname></author>
+        <author><personname>Katy Wood</personname></author>
         <bibliosource>Manually maintained from this source ie. can't Xinclude a book into a book.
         </bibliosource>
         <cover>
@@ -16,51 +15,32 @@
             contact…</para>
         </cover>
     </info>
-    <part>
-        <title>QUICK START</title>
-        <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="db5quickstart_quokka.xml">
+    <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="dbGTQuokka_ch0_contacts.xml">
         <xi:fallback>
             <para>
                 <emphasis>FIXME: MISSING XINCLUDE CONTENT</emphasis>
             </para>
         </xi:fallback>
     </xi:include>
-        <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="db5sics_login.xml">
+        <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="dbGTQuokka_ch1_experiment.xml">
             <xi:fallback>
                 <para>
                     <emphasis>FIXME: MISSING XINCLUDE CONTENT</emphasis>
                 </para>
             </xi:fallback>
         </xi:include>
-    </part>
-    <part>
-        <title>DETAIL</title>
-        <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="dbSICSch26_magnet_11T.xml">
+        <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="dbGTQuokka_ch2_reduction.xml">
             <xi:fallback>
                 <para>
                     <emphasis>FIXME: MISSING XINCLUDE CONTENT</emphasis>
                 </para>
             </xi:fallback>
         </xi:include>
-    </part>
-    <part>
-        <title>SAMPLE ENVIRONMENT</title>
-        <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="dbSICSch18_programmer_overview.xml">
+         <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="dbGTQuokka_ch3_reduction.xml">
             <xi:fallback>
                 <para>
                     <emphasis>FIXME: MISSING XINCLUDE CONTENT</emphasis>
                 </para>
             </xi:fallback>
         </xi:include>
-    </part>
-    <part>
-        <title>CONFIGURATION AND TROUBLESHOOTING</title>
-        <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="dbSICSch23_extraconfig.xml">
-            <xi:fallback>
-                <para>
-                    <emphasis>FIXME: MISSING XINCLUDE CONTENT</emphasis>
-                </para>
-            </xi:fallback>
-        </xi:include>
-     </part>
  </book>

site_ansto/manual/db5SICSUserGuideTaipan.xml

@@ -2,8 +2,8 @@
 <?oxygen RNGSchema="http://www.oasis-open.org/docbook/xml/5.0/rng/docbookxi.rng" type="xml"?>
 <book xmlns="http://docbook.org/ns/docbook" xmlns:xi="http://www.w3.org/2001/XInclude"
     xmlns:xlink="http://www.w3.org/1999/xlink" version="5.0">
-    <info><title>User Guide for Triple Axis Spectrometer. Taipan Edition</title><subtitle>ANSTO
-            version 0.2. May 2013</subtitle>
+    <info><title>User Guide for Triple Axis Spectrometer. Taipan Edition</title>
+        <subtitle>Gumtree 1.8  SICS 2.6 28th October 2013</subtitle>
         <date/>
         <author><personname>Kirrily Rule</personname></author>
         <cover>

site_ansto/manual/db5SICSUserManual3Axis.xml

@@ -3,9 +3,9 @@
 <book xmlns="http://docbook.org/ns/docbook" xmlns:xi="http://www.w3.org/2001/XInclude"
     xmlns:xlink="http://www.w3.org/1999/xlink" version="5.0">
     <info>
-        <title>SICS User Manual for Triple Axis Spectrometers</title>
-        <subtitle>DRAFT ANSTO version 0.2    27 June 2012</subtitle>
-        <date>27 June 2012</date>
+        <title>SICS User Manual for Triple Axis Spectrometers. Taipan Edition</title>
+        <subtitle>For SICS version 2.6   Generated 28th October 2013</subtitle>
+        <date>28th October 2013</date>
         <author><personname>Mark Koennecke</personname></author>
         <author><personname>Heinz Heer</personname></author>
         <author><personname>Ferdi Franceschini</personname></author>

site_ansto/manual/db5SICSUserManualPelican.xml

@@ -3,9 +3,9 @@
 <book xmlns="http://docbook.org/ns/docbook" xmlns:xi="http://www.w3.org/2001/XInclude"
     xmlns:xlink="http://www.w3.org/1999/xlink" version="5.0">
     <info>
-        <title>SICS User Manual for Pelican TOF Polarisation spectrometer</title>
-        <subtitle>DRAFT ANSTO version 0.1    13 May 2013</subtitle>
-        <date>27 June 2012</date>
+        <title>SICS User Manual for Pelican TOF Polarisation Spectrometer</title>
+        <subtitle>For SICS version 2.6 Generated 28th October 2013</subtitle>
+        <date>28th October 2013</date>
         <author><personname>Mark Koennecke</personname></author>
         <author><personname>Heinz Heer</personname></author>
         <author><personname>Ferdi Franceschini</personname></author>
@@ -44,7 +44,7 @@
             </xi:fallback>
         </xi:include>
     </part>
-    <part><title>COMMANDS IN DETAIL</title>
+    <part><title>PELICAN SPECIFIC COMMANDS</title>
         <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="dbSICSch34_fermi_chopper_shortnames.xml">
             <xi:fallback>
                 <para>
@@ -59,6 +59,8 @@
                 </para>
             </xi:fallback>
         </xi:include>
+    </part>       
+    <part><title>COMMANDS IN DETAIL</title>
         <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="dbSICSch2_motor_control.xml">
             <xi:fallback>
                 <para>

site_ansto/manual/db5SICSUserManualPlatypus.xml

@@ -4,8 +4,8 @@
     xmlns:xlink="http://www.w3.org/1999/xlink" version="5.0">
     <info>
         <title>SICS User Manual for Reflectometry. Platypus Edition</title>
-        <subtitle>ANSTO version 0.2. 1 August 2012</subtitle>
-        <date>1st August 2012</date>
+        <subtitle>For SICS version 2.6 Generated 28th October 2013</subtitle>
+        <date>28th October 2013</date>
         <author><personname>Mark Koennecke</personname></author>
         <author><personname>Heinz Heer</personname></author>
         <author><personname>Ferdi Franceschini</personname></author>

site_ansto/manual/db5SICSUserManualPowder.xml

@@ -4,14 +4,22 @@
     xmlns:xlink="http://www.w3.org/1999/xlink" version="5.0">
     <info>
         <title>SICS User Manual for Diffractometers</title>
-        <subtitle>DRAFT ANSTO version 0.1</subtitle>
-        <date>6th April 2009</date>
-        <author><personname>Mark Koennecke</personname></author>
-        <author><personname>Heinz Heer</personname></author>
-        <author><personname>Ferdi Franceschini</personname></author>
-        <author><personname>Nick Hauser</personname></author>
-        <bibliosource>db5SICSUserManual.xml plus instrument specific chapters. 
-            Manually maintained from this source ie. can't Xinclude a book into a book. </bibliosource>
+        <subtitle>For SICS version 2.6         Generated 28th October 2013</subtitle>
+        <date>28th October 2013</date>
+        <author>
+            <personname>Mark Koennecke</personname>
+        </author>
+        <author>
+            <personname>Heinz Heer</personname>
+        </author>
+        <author>
+            <personname>Ferdi Franceschini</personname>
+        </author>
+        <author>
+            <personname>Nick Hauser</personname>
+        </author>
+               <bibliosource>db5SICSUserManual.xml plus instrument specific chapters. Manually maintained
+            from this source ie. can't Xinclude a book into a book. </bibliosource>
     </info>
     <part><title>INTRODUCTION</title>
         <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="dbSICSch1_intro.xml">

site_ansto/manual/db5SICSUserManualQuokka.xml

@@ -4,8 +4,8 @@
     xmlns:xlink="http://www.w3.org/1999/xlink" version="5.0">
     <info>
         <title>SICS User Manual for Small Angle Scattering. Quokka Edition</title>
-        <subtitle>ANSTO version 0.2. 1 August 2012</subtitle>
-        <date>1st August 2012</date>
+        <subtitle>For SICS version 2.6         Generated 28th October 2013</subtitle>
+        <date>28th October 2013</date>
         <author><personname>Mark Koennecke</personname></author>
         <author><personname>Heinz Heer</personname></author>
         <author><personname>Ferdi Franceschini</personname></author>

site_ansto/manual/db5SICSUserManualSampleEnvironment.xml

@@ -4,8 +4,8 @@
     xmlns:xlink="http://www.w3.org/1999/xlink" version="5.0">
     <info>
         <title>SICS User Manual for Sample Environment</title>
-        <subtitle>DRAFT ANSTO version 0.1    30 October 2012</subtitle>
-        <date>30 October 2012</date>
+        <subtitle>For SICS version 2.6    Generated 28 October 2013</subtitle>
+        <date>28 October 2013</date>
         <author><personname>Mark Koennecke</personname></author>
         <author><personname>Heinz Heer</personname></author>
         <author><personname>Ferdi Francheschini</personname></author>
@@ -43,6 +43,13 @@
                 </para>
             </xi:fallback>
         </xi:include>
+        <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="dbSICSch30_He3.xml">
+            <xi:fallback>
+                <para>
+                    <emphasis>FIXME: MISSING XINCLUDE CONTENT</emphasis>
+                </para>
+            </xi:fallback>
+        </xi:include>
     </part>
     
     

site_ansto/manual/dbGTQuokka_ch0_contacts.xml

@@ -0,0 +1,38 @@
+<?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>Contact information</title><author>
+        <personname>Katy Wood</personname>
+    </author>
+        <date>2008-08-29 16:47</date>
+    </info>
+    <sect1>
+        <title></title>
+        <para><emphasis role="italic">This guide is not intended to replace your local contact, but
+            to jog your memory if you are operating independently. Anything strange, call your
+            local contact…</emphasis></para>
+        <sect2><title>Numbers for Quokka instrument scientists</title>
+            <para>Elliot Gilbert, office – 9470, mobile – 04 09 03 43 05</para>
+            <para>Katy Wood, office – 7100, mobile – 04 17 47 35 37</para>
+            <para>Chris Garvey, office – 9328, mobile – 04 09 22 58 81</para>
+        </sect2>
+        <sect2><title>Instrument and reactor status</title><para>
+            An image of the quokka detector is visible from outside ansto at the following
+            webpage:</para>
+            <para><link xlink:href="http://www.nbi.ansto.gov.au/quokka/status/"
+                >http://www.nbi.ansto.gov.au/quokka/status/</link></para>
+            <para>Reactor status and cold source temperature visible at </para>
+            <para><link xlink:href="https://neutron.ansto.gov.au/reactor/ReactorInfo.php">https://neutron.ansto.gov.au/reactor/ReactorInfo.php</link></para>
+        </sect2>
+        <sect2><title>Other useful numbers</title>
+            <para>Emergencies – SOSS: 888</para>
+            <para>SOSS (not emergency, working alone form etc…): 3434</para>
+            <para>Health Physics: 9779</para>
+            <para>IT helpdesk: 9200</para>
+        </sect2>
+        
+    </sect1>
+</chapter>
+
+

site_ansto/manual/dbGTQuokka_ch1_experiment.xml

@@ -0,0 +1,227 @@
+<?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>Performing an experiment</title><author>
+        <personname>Katy Wood</personname>
+    </author>
+        <date>2008-08-29 16:47</date>
+    </info>
+    
+    <sect1>
+        <title>Performing an experiment</title>
+        <para>Your local contact will train you in how to enter the enclosure and load samples.
+            Before you do this independently you must sign the training form to acknowledge you have
+            received the training. The following describes how to run the acquisition software. </para>
+    </sect1>
+    <sect1><title>Login to data acquisition computer</title>
+        <para>Login and password will be given to you by
+            your local contact 1.2. Start gumtree Currently version 1.5.7, link on desktop Login and
+            password will be given to you by your local contact. Normally gumtree would already be
+            running. </para>
+        <para>Caution – opening gumtree takes approximately 15 seconds</para>
+    </sect1>
+    <sect1><title>Starting a standard experiment</title>
+        <para>Below describes starting an experiment with the 20 position sample changer at ambient
+            temperature.</para>
+        <figure><title>Workflow start page </title><mediaobject>
+            <imageobject>
+                <imagedata align="center" width="160mm" fileref="quokkaGumtree1.jpg"/>
+            </imageobject>
+        </mediaobject>
+        </figure>
+        <para>
+            Click <inlinemediaobject><imageobject><imagedata fileref="buttonBegin.jpg"></imagedata></imageobject></inlinemediaobject> to start workflow
+        </para>
+        <figure><title>Experiment  title and your details</title><mediaobject>
+            <imageobject>
+                <imagedata align="center" width="160mm" fileref="quokkaGumtree2.jpg"/>
+            </imageobject>
+        </mediaobject>
+        </figure>
+        <para>Fill in first four boxes with appropriate details.
+            Ignore next three for now, then click <inlinemediaobject><imageobject><imagedata fileref="buttonNext.jpg"></imagedata></imageobject></inlinemediaobject></para>
+        <figure><title>Loading samples</title><mediaobject>
+            <imageobject>
+                <imagedata align="center" width="160mm" fileref="quokkaGumtree3.jpg"/>
+            </imageobject>
+        </mediaobject>
+        </figure>
+        <para><inlinemediaobject><imageobject><imagedata fileref="buttonDrive.jpg"></imagedata></imageobject></inlinemediaobject> allows you to move the sample changer
+            in the enclosure to a position where you can easily load your samples.
+            Once in this position insert your sample blocks into the changer.</para>
+        <figure><title>Insert sample details</title><mediaobject><imageobject><imagedata align="center" width="160mm" fileref="quokkaGumtree4.jpg"></imagedata></imageobject></mediaobject></figure>
+        <para>
+            Tick the boxes corresponding to where you have put samples, and enter
+            sample name, thickness and description.</para>
+        <para>
+            In the column <guilabel>Type</guilabel> the pull-down menu allows you to select either <userinput>SAMPLE</userinput> or 
+            <userinput>EMPTY_BEAM</userinput>. It’s best to treat your empty cell measurement as a
+            <userinput>SAMPLE</userinput>. Making sure you have made the right selection simplifies data
+            processing.
+        </para>
+        <para>
+            Positions 19 and 20 on the sample changer are generally left with the
+            <userinput>SAMPLE</userinput> (empty cell) and <userinput>EMPTY_BEAM</userinput> respectively.</para>
+        <para><inlinemediaobject><imageobject><imagedata fileref="buttonExport.jpg"></imagedata></imageobject></inlinemediaobject> allows you to save a file with all sample names, thickness
+            etc.. in the different positions. </para>
+        <para>This can then be re-loaded at a later stage
+            if you will be using similar sample names with <inlinemediaobject><imageobject><imagedata fileref="buttonLoad.jpg"></imagedata></imageobject></inlinemediaobject></para>
+        <para>
+            The ‘Clear All’ and ‘Fill from Sample 1’ buttons are self-explanatory…
+        </para> 
+        <para>Clicking <inlinemediaobject><imageobject><imagedata fileref="buttonNext.jpg"></imagedata></imageobject></inlinemediaobject> brings up the following screen, where you can select your configurations:</para>
+        <figure><title>Configuration selection</title><mediaobject><imageobject><imagedata align="center" width="160mm" fileref="quokkaGumtree5.jpg"></imagedata></imageobject></mediaobject></figure>
+        <para>Clicking <inlinemediaobject><imageobject><imagedata fileref="buttonPlus.jpg"></imagedata></imageobject></inlinemediaobject>  under <guilabel>Configurations</guilabel> brings up the following:</para>
+        <figure><title>Configuration selection</title><mediaobject><imageobject><imagedata align="center" width="80mm" fileref="quokkaGumtree6.jpg"></imagedata></imageobject></mediaobject></figure>
+        <para>Select the configuration then <inlinemediaobject>
+                <imageobject>
+                    <imagedata fileref="buttonOK.jpg"/>
+                </imageobject>
+            </inlinemediaobject> Your local contact will discuss suitable instrument configurations
+            with you prior to commencing the experiment. </para>
+        <figure><title>Configuration selection</title><mediaobject><imageobject><imagedata align="center" width="160mm" fileref="quokkaGumtree7.jpg"></imagedata></imageobject></mediaobject></figure>
+        <para>Several configurations can be selected in this way. <inlinemediaobject><imageobject><imagedata fileref="buttonCross.jpg"></imagedata></imageobject></inlinemediaobject> deletes any you have
+            added by mistake. Do not modify any configurations, only your local contact should do this.</para>
+        <para>In the <guilabel>Transmission</guilabel> and <guilabel>Scattering</guilabel> boxes you
+            enter the time the samples will be measured for. (If you would like to measure different
+            samples for different amounts of time, you can change these values for individual
+            samples later – only for the ‘scattering’ runs, not the transmissions). If you chose the
+            <guimenuitem>Timer</guimenuitem> mode, enter the time you choose in seconds. In
+            <guimenuitem>Counter</guimenuitem> mode, it will count to monitor and you should
+            enter a monitor count rate. A table is given on the right of the computer with monitor
+            counts, seconds etc…</para>
+        <para>Enter counting times in all the different configurations.</para>
+        <para>Once you are happy with configurations and counting times, <inlinemediaobject><imageobject><imagedata fileref="buttonNext.jpg"></imagedata></imageobject></inlinemediaobject> brings up the following:</para>
+        <figure><title>Sample environment</title><mediaobject><imageobject><imagedata align="center" width="160mm" fileref="quokkaGumtree8.jpg"></imagedata></imageobject></mediaobject></figure>
+        <para>‘Normal’ environment is left selected if running with the 20 position sample changer
+            at ambient temperatures. Click <inlinemediaobject>
+                <imageobject>
+                    <imagedata fileref="buttonNext.jpg"/>
+                </imageobject>
+            </inlinemediaobject></para>
+        <figure><title>Ready to run</title><mediaobject><imageobject><imagedata align="center" width="160mm" fileref="quokkaGumtree10.jpg"></imagedata></imageobject></mediaobject></figure>
+         <para>A table now appears with your samples and configurations.  (Scroll across to see all).  If you do not with to measure all samples at all configurations, 
+            you can uncheck the appropriate boxes.  If you wish to do absolute normalisation, always leave a transmission measurement of the empty beam as we use this.  
+            At this point the ‘preset’ column can be modified if you wish to count for different times. You do not need to measure the scattering from the empty camera (position 20) 
+            unless you are using this as a background (i.e. not using cuvette, solvent etc.). </para>
+        <para>Underneath the table an estimated experimental time is given. If you change individual
+            run times ‘Update’ will update this. If the runtime looks very long, you’ve probably
+            made an error and selected to count to monitor counts but accidentally left the option
+            selected as ‘time’.</para>
+        <para>Click <inlinemediaobject>
+                <imageobject>
+                    <imagedata fileref="buttonRun.jpg"/>
+                </imageobject>
+            </inlinemediaobject> then starts the run you have setup. If you have not opened the
+            shutter, you will see a prompt ‘shutter not open’. Check it’s open and then click <inlinemediaobject>
+                <imageobject>
+                    <imagedata fileref="buttonOK.jpg"/>
+                </imageobject>
+            </inlinemediaobject> to start your run! </para>
+    </sect1>
+    <sect1><title>Starting an experiment using a controlled environment / running the same experiment multiple times</title>
+        <para>As per Section 1.3 except Instead of selecting 'Normal Environment, select ‘Controlled
+            Environment’. </para>
+<para>Using the “Controlled Environment” option, you may then select a list of sample environment
+            controllers for your experiment. </para>
+        <para>Select <computeroutput>dummy_motor</computeroutput> if you would like to run the same series of samples multiple times.
+        </para>
+        <figure><title>Adding a sample environment controller</title><mediaobject><imageobject><imagedata align="center" width="160mm" fileref="quokkaGumtree12.jpg"></imagedata></imageobject></mediaobject></figure>
+        <para>In the example above, 3 steps will be generated on clicking on the ‘generate’ button, and the table will be updated as follows:</para>
+        <figure><title>Adding a sample environment controller</title><mediaobject><imageobject><imagedata align="center" width="160mm" fileref="quokkaGumtree9.jpg"></imagedata></imageobject></mediaobject></figure>
+        <para>It is then possible to run the samples and configurations selected previously three times with a 2 second wait between each.</para>
+        <para>Select <computeroutput>/sample/tc1/setpoint</computeroutput> to use temperature control (needs to be correctly set up first by your local contact).</para>
+        <figure><title>Setting up a specific temperature controller</title><mediaobject><imageobject><imagedata align="center" width="160mm" fileref="quokkaGumtree11.jpg"></imagedata></imageobject></mediaobject></figure>
+        <para>To enter the preset values for the controller, type the numbers into the text boxes and press “Generate”.  In the example above, the samples will be measured at 5 
+            different temperatures, between 1 to 10 degrees.  Insert a small wait in seconds at the beginning of each step.</para>
+            <para>You may modify the preset values from the table if you do not wish to use the fixed step presets generated by GumTree. 
+                The multi sample workflow can support multiple sample environment controllers in an experiment.  
+                Press <inlinemediaobject><imageobject><imagedata fileref="buttonPlus.jpg"></imagedata></imageobject></inlinemediaobject> button under the controller to add more.  Each additional controller simply adds a one more nested loop to your experiment sequence.
+        </para>
+    </sect1>
+    <sect1><title>Saving run numbers table for log book</title>
+        <para>As data is saved the run numbers appear in the table.  It’s then particularly useful to save this table with 
+            <inlinemediaobject><imageobject><imagedata fileref="buttonTableImage.jpg"></imagedata></imageobject></inlinemediaobject>.  
+            This button exports the table as a jpeg file, which can then be printed.  
+            Note that you only export what is visible on the screen.  (If you wish to save all configurations you will have to scroll to the right).</para>
+    </sect1>
+    <sect1><title>Saving report file during experiment</title>
+        <para>At the end of a multi sample workflow, a ‘report’ file is created.  This file contains all the associations for the different configurations 
+            (which run numbers are scattering files, which are transmissions, empty beam etc…), and simplifies data reduction.  
+            If you’d like to treat your data before the end, you can create a report file by hitting <inlinemediaobject><imageobject><imagedata fileref="buttonResultXML.jpg"></imagedata></imageobject></inlinemediaobject>. 
+            If you want to stop a multi-sample workflow early for some reason, make sure you <inlinemediaobject><imageobject><imagedata fileref="buttonResultXML.jpg"></imagedata></imageobject></inlinemediaobject> 
+            first, as this is not done automatically. </para></sect1>
+    <sect1><title>Where is the data?</title>
+        <para>
+            Data files are written and updated every minute in the directory in /experiments/quokka/data/current.  This directory is read only.</para><para>
+                Report files are in <computeroutput>/experiments/quokka/data/current/reports</computeroutput></para><para>
+                    A read/write copy of the data is also copied to the directory named after the proposal number: <computeroutput>/experiments/quokka/data/proposal/xxx</computeroutput>.  This data can be patched etc… and used to do data reduction (see section 3).  It is updated approximately every 4 minutes.</para>
+        <para>At the end of the cycle the read only copy of the data and report files will be moved into a directory named after the cycle number, eg. <computeroutput>/experiments/quokka/data/cycle/030</computeroutput></para>
+        <para>Links to these directories can be found on the desktop.</para>
+    </sect1>
+    <sect1><title>Is my experiment running OK?</title>
+        <para>As the workflow moves through your run, messages will be displayed at the bottom in the ‘console’ indicating progress.  Any errors will appear in red.</para>
+        <para>Approximate counts/rates on ‘standard’ samples.  A table is given in the log book with approximate count rates for some standard configurations measured on H2O, D2O samples.  You should have similar values.</para>
+        <para>Instrument dashboard: The dashboard displays a 2D image of the detector, most instrument settings and parameters such as L1 and L2.  Do not modify anything from this dashboard.</para></sect1>
+   <sect1><title>Common issues</title>
+   <qandaset><qandaentry>
+       <question><para>I have started a workflow, but would like to stop it.</para></question>
+       <answer><para>Click on the any of the ‘Interrupt buttons’.    A report file will be saved.   </para>
+           <para><inlinemediaobject><imageobject><imagedata fileref="buttonInterrupt.jpg"></imagedata></imageobject></inlinemediaobject></para>
+           <para>Multisample work flow will then go into ‘cleanup mode’, ie will drive the attenuation to a high value, protecting the detector from any possible over-exposure.  
+               By using <inlinemediaobject><imageobject><imagedata fileref="buttonBack.jpg"></imagedata></imageobject></inlinemediaobject>, you can then modify the run and restart.</para>
+       </answer>
+   </qandaentry>
+       <qandaentry>
+           <question><para>I have started a workflow, but would like to pause it.</para> </question>
+           <answer><para>The workflow can be paused if the acquisition is running in the monitor mode. </para>
+               <para><inlinemediaobject><imageobject><imagedata fileref="buttonPause.jpg"></imagedata></imageobject></inlinemediaobject></para>
+               <para>
+                  You can press on the same button to resume from a paused acquisition.</para></answer>
+       </qandaentry>
+    </qandaset>
+   </sect1>
+    <sect1><title>On the fly’ data inspection with Igor</title><para>It is possible to look at data during collection, before the file is complete.  
+        Following the procedure below allows you to open the file and inspect the radial average, which will automatically be updated approximately every minute.</para>
+        <orderedlist>
+            <listitem ><para>Open “Igor with Quokka macros”, and in the macros menu select ‘Load Quokka Sans Reduction Macros’.  Following yellow panel appears.</para>
+                <para><inlinemediaobject><imageobject><imagedata fileref="igorRawData.jpg"></imagedata></imageobject></inlinemediaobject></para>
+            </listitem>
+            <listitem><para>Click on ‘Pick Path’ and navigate to <computeroutput>/experiments/quokka/data/proposal/xxx</computeroutput></para>
+                <para><inlinemediaobject><imageobject><imagedata fileref="igorPickPath.jpg"></imagedata></imageobject></inlinemediaobject></para></listitem>
+            <listitem><para>In the ‘Reduction’ tab ‘Build protocol’. </para>
+                <para><inlinemediaobject><imageobject><imagedata fileref="igorBuildProtocol.jpg"></imagedata></imageobject></inlinemediaobject></para>
+                <para>The following appears:</para>
+                <para><inlinemediaobject><imageobject><imagedata fileref="igorSaveProtocol.jpg"></imagedata></imageobject></inlinemediaobject></para>
+                <para>Uncheck all except Sample and Average and ‘Save protocol’.  Choose a name eg ‘on_line’.</para>
+                   <note><para>Note that it is not possible to put data on an absolute scale on the fly, as the transmission has not yet been calculated, 
+                    you can however add in the other steps of the data reduction protocol if required.</para></note>
+             </listitem>
+            <listitem><para>Select ‘Online Reduction’ on the ‘Raw Data’ tab</para>
+                <para><inlinemediaobject><imageobject><imagedata fileref="igorOnlineReduction.jpg"></imagedata></imageobject></inlinemediaobject></para>
+                <para>The following appears:</para>
+                <para><inlinemediaobject><imageobject><imagedata fileref="igorOnlineFileSelect.jpg"></imagedata></imageobject></inlinemediaobject></para>
+                <para>Select the file file you would like in top drop down menu.</para>
+                 <para>In the second window click ‘…’,
+                </para>
+                <para><inlinemediaobject><imageobject><imagedata fileref="igorOnlineProtocolSelect.jpg"></imagedata></imageobject></inlinemediaobject></para>              
+                <para>The following appears:</para>
+                <para><inlinemediaobject><imageobject><imagedata fileref="igorPickProtocol.jpg"></imagedata></imageobject></inlinemediaobject></para>
+                <para>Select the protocol you have just built in the drop down menu, eg ‘on_line’ and ‘continue’.  </para>
+                <para><inlinemediaobject><imageobject><imagedata fileref="igorPickOnlineProtocol.jpg"></imagedata></imageobject></inlinemediaobject></para>
+                <para>Then click ‘start’ on the pink ‘Online Reduction panel’.</para>
+                <para><inlinemediaobject><imageobject><imagedata fileref="igorStartOnlineProtocol.jpg"></imagedata></imageobject></inlinemediaobject></para>
+                <para>The radial average data will then be displayed and automatically updated.</para>
+            </listitem>
+        </orderedlist>
+     </sect1>
+    <sect1><title>Before you leave</title><para>
+        Before you leave the instrument, please:</para>
+        <orderedlist>
+        <listitem><para>Clean and return your sample holders.  Instructions in the ‘instructions’ section of the manual in the cabin.  We will not lend sample holders to users who have a history of not returning them clean.</para></listitem>
+            <listitem><para>Photocopy/scan the relevant pages of the logbook</para></listitem>
+       <listitem><para>Take all raw and treated data either using a thumb drive, by burning the data to a CD/DVD (ask your local contact nicely) or using ANSTO sharefile (web-based system) at sharefile.ansto.gov.au.</para></listitem>
+        </orderedlist>
+    </sect1>
+</chapter>

site_ansto/manual/dbGTQuokka_ch2_reduction.xml

@@ -0,0 +1,85 @@
+<?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>Data Reduction</title><author>
+        <personname>Katy Wood</personname>
+    </author>
+        <date>2008-08-29 16:47</date>
+    </info>
+    <sect1>
+        <title>Installing data reduction macros on your own
+                computer</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>
+    </sect1>
+    <sect1><title>Install Igor</title>
+        <para>If you don’t already have it… A free 30 day demo version can be downloaded from the wavemetrics website.  You need Igor version 6.2 or later.</para>
+     </sect1>
+    <sect1><title>Remove any older versions of the macros</title>
+        <para>Skip this step if you’ve never had any of the NIST or Quokka macros installed. If you’ve had any older versions of the NIST or 
+            Quokka analysis macros installed, it’s important to remove completely/rename folder so there will be no conflicts.  
+            You will only have to do this once, as the future updates will be done automatically as long as you are connected to the internet.</para>
+        <caution><para>once you have installed the newer versions of the macros, you will not be able to load any
+                Igor project files made with the older ones. This means you should save all the
+                treated ascii files you are likely to need before installing a newer version of the
+                software. </para></caution>
+        <orderedlist>
+            
+        <listitem><para>Delete any old NIST and Quokka macros from the following directories (or move all macros elsewhere if you’d like to keep older versions of the macros):</para>
+            <orderedlist>
+                <listitem><para>C:\Program Files\WaveMetrics\Igor Pro Folder\User Procedures</para></listitem>
+                <listitem><para>C:\Documents and Settings\user_name\My Documents\WaveMetrics\Igor Pro 6 User Files\User Procedures</para></listitem>
+                <listitem><para>C:\Documents and Settings\user_name\My Documents\WaveMetrics\Igor Pro 6 User Files\Igor Procedures</para></listitem>
+               </orderedlist></listitem>
+            <listitem><para>Delete the two shortcuts to HDF5.xop and HDF5 Browser.ipf in: </para>
+            <orderedlist>
+                <listitem><para>C:\Program Files\WaveMetrics\Igor Pro Folder\Igor Extensions</para></listitem>
+            </orderedlist>
+            </listitem>
+        </orderedlist>
+    </sect1>
+    <sect1><title>Install Quokka specific macros</title>
+        <para>Navigate to:
+            <link xlink:href="http://www.nbi.ansto.gov.au/quokka/macros/IgorUserFilesSwitch.exe">http://www.nbi.ansto.gov.au/quokka/macros/IgorUserFilesSwitch.exe</link>
+            and download the executable  ‘IgorUserFilesSwitch.exe’.  Double click on the executable.  
+        </para>
+        <figure><title>Select Quokka Macros</title><mediaobject>
+            <imageobject>
+                <imagedata align="center" width="80mm" fileref="igorSelectMacros.jpg"/>
+            </imageobject>
+        </mediaobject>
+        </figure>
+        <para>Select Quokka macros to install and click OK. You will be asked if it is OK to
+            download the macros, select yes. </para>
+        <para>After installation ‘continue’ will launch Igor. Ticking the ‘continue when done box’
+            will automatically start Igor after you have used the switch. </para>
+        <para>Once this is done you should have a “Igor with Quokka macros” shortcut either under
+            the Start&gt;Igor menu OR on your desktop (depending on which version of windows you are
+            running).</para>
+        <para>Once Igor Pro is open, the Macros menu should now contain ‘Load QUOKKA SANS Reduction
+            Macros’. Selecting this brings up the yellow ‘SANS Reduction Controls’.</para>
+        <figure><title>Data Reduction Controls</title><mediaobject>
+            <imageobject>
+                <imagedata align="center" width="160mm" fileref="igorStartScreen.jpg"/>
+            </imageobject>
+        </mediaobject>
+        </figure>
+        <para>Every time you open the “Igor with Quokka macros” shortcut, if you are connected to
+            the internet, you will be prompted to install any updates as they become
+            available.</para>
+    </sect1>
+    <sect1><title>Switch to NIST macros</title>
+        <para>Double click again on the executable ‘IgorUserFilesSwitch.exe’. (Or select the “Igor
+            Pro Macro Settings” shortcut under either under start&gt;Igor or on the desktop). Select
+            the NIST macros and click OK. As above, you will be asked if it is OK to download
+            macros, select yes. </para>
+        <para>Once this is done you should have a “Igor with NIST macros” shortcut either under the
+            Start&gt;Igor menu OR on your desktop (depending on which version of windows you are
+            running).</para>
+        <para>Both NIST and Quokka macros will now be on your computer and you can switch between by
+            selecting the different shortcuts “Igor with NIST macros” and “Igor with Quokka
+            macros”.</para></sect1>
+</chapter>

site_ansto/manual/dbGTQuokka_ch3_reduction.xml

@@ -0,0 +1,161 @@
+<?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>

site_ansto/manual/dbSICSch30_He3.xml

@@ -2,14 +2,14 @@
 <?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>3He</title><author>
+    <info><title><superscript>3</superscript>He</title><author>
             <personname>Ferdi Franceschini</personname>
         </author>
         <date>2008-08-29 16:47</date>
     </info>
     <sect1>
         <title>Introduction</title>
-        <para>The system of He3 project consists of a polarizer and analyser which are controlled by
+        <para>The system of <superscript>3</superscript>He project consists of a polarizer and analyser which are controlled by
             Labview servers. The two Labview servers run on one machine and communicate with a
             corresponding SICS driver over TCP/IP. The polarizer and analyser share a single NI I/O
             board and a HMP2030 power supply. </para>