[OpenSPIM] very slow acquisition speed

[Monika Pawłowska]

"What is going on" should be relatively easy if you look at the timestamps  
in the log that you send. "Why" and "How to fix it" is a different matter  
unfortunately.

Did you try to take a time series only with Micromanager, without the  
OpenSPIM plugin? This should be possible somehow.

Regards,
Monika

W dniu .05.2015 o 19:00 <openspim-request at openspim.org> pisze:

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>    1. Re: very slow acquisition speed (Robert Hauschild)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Tue, 12 May 2015 14:41:25 +0200
> From: Robert Hauschild <robert.hauschild at ist.ac.at>
> To: openspim at openspim.org
> Subject: Re: [OpenSPIM] very slow acquisition speed
> Message-ID: <5551F4F5.3050403 at ist.ac.at>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear Monika, All,
>
> thanks for testing! At least my system is not the only one that is so  
> slow.
>
> Would be great if someone could tell me how to figure out what is going
> on during the 75% of time that is unaccounted for in the profiler!
>
> thanks!
>
> Best regards,
>
> Robert
>
> On 07.05.2015 18:20, m.pawlowska at nencki.gov.pl wrote:
>> Dear Robert,
>>
>> since I also have Orca+Picard, I decided to repeat your experiment and
>> did 10 frames, 100 ms. I'm using the new 64-bit version, updated. I
>> got very similar results to yours (see below). Unfortunately I don't
>> know whether it used to be better, I never tried taking very fast
>> measurements.
>>
>> Maybe somebody who is able to get 10 frames/sec could send their
>> CoreLog for comparison...?
>>
>> Opened log file
>> D:\Dane\2015\2015_05\2015_05_07\02time_series_test\log.txt
>> Profiler("performAcquisition")[4 children]: 6,0611s
>> 6,3337%:    Profiler("Output")[0 children]: 0,3839s
>> 0,0000%:    Profiler("Acquisition")[0 children]: 0,0000s
>> 29,7792%:    Profiler("Movement")[0 children]: 1,8049s
>> 0,0005%:    Profiler("Setup")[0 children]: 0,0000s
>>
>> Regards,
>> Monika
>
>> Hi All and especially Pete,
>>
>> My setup is Orca R2, Coherent Cube, Picard stage.
>> I tested a couple of things and it it still unclear to me where the
>> time is wasted.
>>
>> I attached the core log of a 10 frame long time series (100ms
>> exposure) recorded to memory with X/Y/Z Stage/Theta all unchecked and
>> without "Update Live preview".
>>
>> I tried two configurations:
>> 1. Orca  + Cube + Picard
>> 2. Orca  + Picard
>>
>> "1" took 7.6 s of which ("1"- "2") = 1.4 s are communication with
>> laser, which, while way too much, is not the source of the problem.
>>
>> Profiler("performAcquisition")[4 children]: 7.6113s
>> 0.0017%:    Profiler("Output")[0 children]: 0.0001s
>> 0.0000%:    Profiler("Acquisition")[0 children]: 0.0000s
>> 24.0133%:    Profiler("Movement")[0 children]: 1.8277s
>> 0.0013%:    Profiler("Setup")[0 children]: 0.0001s
>>
>> So most of the time the system is doing something that the Profiler is
>> not recording.
>>
>> Looking at the core log I am a bit puzzled why the laser power is
>> queried once  per slice and why the stage is told to move to the very
>> position it currently is even though none of the motors should move at
>> all since X/Y/Z/Theta are all unchecked in the acquisition dialog.
>>
>> I would really appreciate any hint/suggestion on how to get back to
>> reasonable acquisition speeds.
>>
>> Thanks again!
>>
>> Robert
>


-- 
Dr Monika Pawłowska
Nencki Institute
Laboratory of Neurobiology
3, Pasteur Street
02-093 Warsaw, Poland
phone: (+48) 22 5892 427