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Queuing option » History » Version 2

Amber Herold, 04/27/2010 11:44 AM

1 1 Amber Herold
h1. Queuing option
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h2. Introduction
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Queuing option puts in a queue the selected targets on multiple images from the same
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acquisition node. The queue can then processed as a batch. Therefore, targets from multiple
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squares can be selected before any hole image image is acquired in any grid square.
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Alternatively, targets from multiple holes of the same square can be selected before any
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exposure is taken. Because the event bindings are identical in MSI application. Target
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processing scheme can be switched between the queuing (breadth-first) mode and the
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depth-first mode at appropriate point.
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!http://emg.nysbc.org/software/leginon/images/images/MSIQtree.png!
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In queuing mode, the movement of the stage is more complicated as targets in the same
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suptree are not acquired in close time frame and often need readjustment of targets when it
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is finally the time to acquire the child image. This is all taken care of by the drift
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manager by revesing the stage position (including stage z) of the parent image when the
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first child image is to be acquired after the drift declared event. Users of the queuing
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mode should know that this frequent interaction with the drift manager makes the time for
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completing the target list longer but is necessary when targeting accuracy is
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importent.
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The other consideration is that if queuing is activated at Hole Targeting node so that a
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large number of images are acquired in "sq" preset at LM mode in a batch without ever
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cycling to HM presets, the objective lens may cool down sufficianly that the image alignment
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is different from during normal acquisition cycle. We recommand that either setting the
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scope to one of the HM mode, wait for 30 or more minute and recheck the image alignment or
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processing a smaller batch of "sq" preset each time so that the scope does not operate in LM
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for extended amount of time. Our experience is that it is better not to activate queuing at
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Hole Targeting but queue up only at exposure targeting so that the above problem is less
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likely to occur.
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<link linkend="MSI_troubleshooting">Trouble shooting</link>
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h2.  Initial Queuing set-up
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The user should start with <link linkend="MSI_pref">the preference and
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configuration</link> of the nodes in MSI application in the depth-first mode and follow
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the <link linkend="MISQuickStart">quick start procedure</link>. Once the function of all
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nodes are confirmed to be normal, then switch to queuing. There are two possible points for
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queuing, at Hole Targeting or at Exposure Targeting. The two can be used in any combination
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with the depth-first mode.
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h2. Configuration and operation rules for a chosen queuing point
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Configuration of two nodes are affected by each queuing and they should be set in the
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following order if the two are currently processing data:
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*  The option for "Queue up targets" should be selected in the HoleFinder. "Declare
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drift when queue is submitted" is optional. Use it if accurate targeting is required.
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The time required to finish target will be longer.
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*  The acquisition node that acquires the image on which targets will be selected do
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not need to wait for HoleFinder node to process the image before next acquisition. This
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option is deselected in /Tool/Setup/. Leave it on if you are willing to wait for
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HoleFinder before next image acquisition.
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In operation, the behavior of the above two nodes plus the acquisition node after the
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queuing holefinder are affected
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*  All targets submited to the above-mentioned acquisition node will be acquired
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first(Waiting off) rather than one after each target submission (Waiting on). These
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targets would be considered "done" by Leginon at restart or target refresh.
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*  The normal "submit"<inlinegraphic
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fileref="http://emg.nysbc.org/software/leginon/images/icons/play.png" format="PNG"/>
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in the targetfinder only stores the selected targets in the queue rather than proceeding
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to target processing.
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*  Upon "Submit Queue"<inlinegraphic
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fileref="http://emg.nysbc.org/software/leginon/images/icons/send_queue_out.png"
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format="PNG"/> the queued target list is processed by the next acquisition node in
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which individual targets can be aborted by the abort button <inlinegraphic
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fileref="http://emg.nysbc.org/software/leginon/images/icons/stop.png" format="PNG"
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/>, paused as in MSI, and the whole queue list can be aborted using the abort queue
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button <inlinegraphic
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fileref="http://emg.nysbc.org/software/leginon/images/icons/stop_queue.png"
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format="PNG"/>.
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*  The queued target list is in fact a list of lists where targets are grouped by
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their parent images. At the start of target processing of any unfinished sub-list by an
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acquisition node, leginon reverts the z stage position to that of the parent and
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processes rejected targets (i.e., the focus targets) first if the option is on as it is
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for "Hole" and "Exposure" nodes whether they have been processed previously. The rest of
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the unfinished acquisition targets are then processed.
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*  The targets that generate images in the non-waiting acquisition node is considered
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done once acquired. Therefore, if Leginon is interrupted and restarted, you can not
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continue the acquisition and process the queued targets by submiting refreshed targets
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in "Square Targeting" node as in MSI. Instead, you shoulde resubmit the queue in the
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corresponding holefinder node. Leginon will find out which targets have not been
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completed and continue the acquisition.
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[[MSI Operation|< MSI Operation]] | [[Queuing Example 1 - Exposure Targeting|Queuing Example 1 - Exposure Targeting >]]
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