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Queuing option » History » Revision 3

Revision 2 (Amber Herold, 04/27/2010 11:44 AM) → Revision 3/10 (Amber Herold, 06/22/2010 01:19 PM)

h1. Queuing option 




 h2. Introduction 



 Queuing option puts in a queue the selected targets on multiple images from the same 
 acquisition node. The queue can then processed as a batch. Therefore, targets from multiple 
 squares can be selected before any hole image image is acquired in any grid square. 
 Alternatively, targets from multiple holes of the same square can be selected before any 
 exposure is taken. Because the event bindings are identical in MSI application. Target 
 processing scheme can be switched between the queuing (breadth-first) mode and the 
 depth-first mode at appropriate point. 


 



 !http://emg.nysbc.org/software/leginon/images/images/MSIQtree.png! 



 In queuing mode, the movement of the stage is more complicated as targets in the same subtree 
 suptree are not acquired in close time frame and often need readjustment of targets when it 
 is finally the time to acquire the child image. This is all taken care of by the drift 
 manager by reversing revesing the stage position (including stage z) of the parent image when the 
 first child image is to be acquired after the drift declared event. Users of the queuing 
 mode should know that this frequent interaction with the drift manager makes the time for 
 completing the target list longer but is necessary when targeting accuracy is important. 
 importent. 


 The other consideration is that if queuing is activated at Hole Targeting node so that a 
 large number of images are acquired in "sq" preset at LM mode in a batch without ever 
 cycling to HM presets, the objective lens may cool down sufficiently sufficianly that the image alignment 
 is different from during normal acquisition cycle. We recommend recommand that either setting the 
 scope to one of the HM mode, wait for 30 or more minute and recheck the image alignment or 
 processing a smaller batch of "sq" preset each time so that the scope does not operate in LM 
 for extended amount of time. Our experience is that it is better not to activate queuing at 
 Hole Targeting but queue up only at exposure targeting so that the above problem is less 
 likely to occur. 


 [[Trouble shooting|Trouble shooting]] 



 <link linkend="MSI_troubleshooting">Trouble shooting</link> 





 h2.    Initial Queuing set-up 



 The user should start with [[Initial MSI application <link linkend="MSI_pref">the preference setup|the preference and configuration]] 
 configuration</link> of the nodes in MSI application in the depth-first mode and follow 
 the [[MSI Quick-start|quick <link linkend="MISQuickStart">quick start procedure]]. procedure</link>. Once the function of all 
 nodes are confirmed to be normal, then switch to queuing. There are two possible points for 
 queuing, at Hole Targeting or at Exposure Targeting. The two can be used in any combination 
 with the depth-first mode. 



 





 h2. Configuration and operation rules for a chosen queuing point 



 Configuration of two nodes are affected by each queuing and they should be set in the 
 following order if the two are currently processing data: 

 1. 


 *    The option for "Queue up targets" should be selected in the HoleFinder. "Declare 
 drift when queue is submitted" is optional. Use it if accurate targeting is required. 
 The time required to finish target will be longer. 

 2. 


 *    The acquisition node that acquires the image on which targets will be selected do 
 not need to wait for HoleFinder node to process the image before next acquisition. This 
 option is deselected in /Tool/Setup/. Leave it on if you are willing to wait for 
 HoleFinder before next image acquisition. 


 




 In operation, the behavior of the above two nodes plus the acquisition node after the 
 queuing holefinder are affected. 

 1. affected 


 *    All targets submitted submited to the above-mentioned acquisition node will be acquired 
 first(Waiting off) rather than one after each target submission (Waiting on). These 
 targets would be considered "done" by Leginon at restart or target refresh. 

 2. 


 *    The normal "submit" !http://emg.nysbc.org/software/leginon/images/icons/play.png! "submit"<inlinegraphic 
 fileref="http://emg.nysbc.org/software/leginon/images/icons/play.png" format="PNG"/> 
 in the targetfinder only stores the selected targets in the queue rather than proceeding 
 to target processing. 

 3. 


 *    Upon "Submit Queue" !http://emg.nysbc.org/software/leginon/images/icons/send_queue_out.png! Queue"<inlinegraphic 
 fileref="http://emg.nysbc.org/software/leginon/images/icons/send_queue_out.png" 
 format="PNG"/> the queued target list is processed by the next acquisition node in 
 which individual targets can be aborted by the abort button !http://emg.nysbc.org/software/leginon/images/icons/stop.png!, <inlinegraphic 
 fileref="http://emg.nysbc.org/software/leginon/images/icons/stop.png" format="PNG" 
 />, paused as in MSI, and the whole queue list can be aborted using the abort queue 
 button !http://emg.nysbc.org/software/leginon/images/icons/stop_queue.png!. 

 4. <inlinegraphic 
 fileref="http://emg.nysbc.org/software/leginon/images/icons/stop_queue.png" 
 format="PNG"/>. 


 *    The queued target list is in fact a list of lists where targets are grouped by 
 their parent images. At the start of target processing of any unfinished sub-list by an 
 acquisition node, leginon reverts the z stage position to that of the parent and 
 processes rejected targets (i.e., the focus targets) first if the option is on as it is 
 for "Hole" and "Exposure" nodes whether they have been processed previously. The rest of 
 the unfinished acquisition targets are then processed. 

 5. 


 *    The targets that generate images in the non-waiting acquisition node is considered 
 done once acquired. Therefore, if Leginon is interrupted and restarted, you can not 
 continue the acquisition and process the queued targets by submiting refreshed targets 
 in "Square Targeting" node as in MSI. Instead, you should shoulde resubmit the queue in the 
 corresponding holefinder node. Leginon will find out which targets have not been 
 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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