39b841aee3
converted from a Word document to docbook, for integration into Gumtree help, and to have under source control.
228 lines
20 KiB
XML
228 lines
20 KiB
XML
<?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>
|