Leginon

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

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 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

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 sufficianly that the image alignment

is different from during normal acquisition cycle. We 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.

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

h2.  Initial Queuing set-up

The user should start with <link linkend="MSI_pref">the preference and

configuration</link> of the nodes in MSI application in the depth-first mode and follow

the <link linkend="MISQuickStart">quick start 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:

*  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.

*  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

*  All targets 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.

*  The normal "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.

*  Upon "Submit 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 <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 <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.

*  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 shoulde resubmit the queue in the

corresponding holefinder node. Leginon will find out which targets have not been

completed and continue the acquisition.