[OpenSPIM] Picard stage error after update
Luke Stuyvenberg
stuyvenberg at wisc.edu
Wed Aug 20 21:19:47 CDT 2014
Hi Veli-Pekka,
On 8/18/2014 4:18 AM, Veli-Pekka Ronkainen wrote:
>
> Hi Luke,
>
>
> Thanks for your reply! I attach here different CoreLogs created by two
> different software versions:
>
Thanks! These have really helped.
> The first CoreLog pid3156 is generated by the latest SW version.
> Here we tried to make a new configuration and adding/editing
> Picard Z-stage is not possible [IFO,dev:Picard Z Stage] Could not
> initialize motor -1 (PiUsb error code 1).
>
From the core log, I see the line "2014-08-18T09:27:19.082080 tid860
[IFO,dev:Picard Twister] Found 0 motors and 1 twisters." -- in essence,
it isn't finding any of your stages. Probably this is because the
version of mmgr_dal_PicardStage.dll is out-of-date, and only checks the
serial numbers up to 250. (A newer version is available in vanilla
Micro-Manager that checks up to 500, and I've been looking into a more
reasonable detector that should discover any regardless of serial
number...) I will try to upload a newer version of the DAL to the update
site, once I'm sure it's compatible.
> The next one pid4032 is generated by the same SW version, and we tried
> to modify an existing older .cfg-file which is also attached here.
>
Another odd issue. I think it's related, but I'm not totally sure how --
something about the first failure to communicate with the stage seems to
trigger a series of Java errors referring to the rest of the devices in
the configuration (I think).
> The last CoreLog (no pid number) is generated by the non-updated SW
> version downloaded from openspim.org. Here everything is fine.
>
>
> There is no possibility to edit the old .cfg-file with notepad like
> you suggested, since there is no mention about the Twister step
> size. Maybe because there is no possibility to edit step sizes in the
> older SW version, only serial numbers?
>
You're probably right. It may work to simply add the line I mentioned,
only with the '1' instead of '1.8'. (Again, this isn't a fix for the
underlying problem, but I'll be looking at that.)
I hope this all helps, and I'll see what I can do about causing a more
permanent change. Thanks!
Luke
On 8/18/2014 4:18 AM, Veli-Pekka Ronkainen wrote:
>
> Hi Luke,
>
>
> Thanks for your reply! I attach here different CoreLogs created by two
> different software versions:
>
>
> The first CoreLog pid3156 is generated by the latest SW version.
> Here we tried to make a new configuration and adding/editing
> Picard Z-stage is not possible [IFO,dev:Picard Z Stage] Could not
> initialize motor -1 (PiUsb error code 1).
>
>
> The next one pid4032 is generated by the same SW version, and we tried
> to modify an existing older .cfg-file which is also attached here.
>
>
> The last CoreLog (no pid number) is generated by the non-updated SW
> version downloaded from openspim.org. Here everything is fine.
>
>
> There is no possibility to edit the old .cfg-file with notepad like
> you suggested, since there is no mention about the Twister step
> size. Maybe because there is no possibility to edit step sizes in the
> older SW version, only serial numbers?
>
>
> Regards,
>
> Veli-Pekka
>
>
> ------------------------------------------------------------------------
> *Lähettäjä:* openspim-bounces at openspim.org
> <openspim-bounces at openspim.org> käyttäjän puolestaLuke Stuyvenberg
> <stuyvenberg at wisc.edu>
> *Lähetetty:* 16. elokuuta 2014 4:10
> *Vastaanottaja:* openspim at openspim.org
> *Aihe:* Re: [OpenSPIM] Picard stage error after update
> Hi Veli-Pekka,
>
> On 8/14/2014 7:01 AM, Veli-Pekka Ronkainen wrote:
>
> However, now after using the Fiji updater Picard USB-stage
> rotation angle coordinates are not right anymore. Changing angle
> from -180 deg to 180 deg rotates the sample holder only ~180
> degrees, and rotation in general spins the sample much less than
> indicated by the slider. In addition, we can not access and modify
> old .cfg-files, so that it would be possible to change step size
> of the twister from 1.8 to 1, as it was discussed earlier:
> http://openspim.org/pipermail/openspim/2014-July/000482.html .
>
> As you suspected, this is because of the change in step size.
>
> Modification of an existing configuration starts with an error
> "Error in device Picard Z Stage: Unable to communicate with the
> device" followed by lots of COM and "No device with label _device
> name_" -errors. Creating a new configuration doesn't help since it
> is not possible to add Picard stage z-axis to the config file
> or modify the serial number.
>
> The error when modifying a configuration or creating new
> configurations is a different problem entirely, and one I wasn't aware
> of. If you could, please, attach a CoreLog or two from after the
> update, when you've received these errors. (If you can't tell which
> one contains these errors, you can open them and search, or just run
> the program again and produce a new one.) This would go a long way
> towards figuring out what's causing this problem.
>
> But in the meantime, an easy, dirty solution to the problem
> interfering with your experiments is to open a working configuration
> file in Notepad. You should see a line in there that reads something like
>
> "Device,Picard Twister,StepSize,1.8"
>
> Changing the 1.8 to 1 should resolve at least the rotational stage
> problem.
>
> We've tried to copy the latest Picard .dll-files from the recent
> Micro-Manager nightly build but the problem persists. Are there
> some other files we should copy and replace as well? Of course we
> can still download and configure the non-updated package from
> openspim.org and be happy using that older version without any
> problems. Still it would be nice to be up-to-date. Anyone
> having the same problems or some solutions? Thanks!
>
> You shouldn't need any other files; hopefully the above is all it
> takes to get things running until I can figure out what's causing the
> trouble with editing configurations.
>
> Hope this helps,
> Luke Stuyvenberg
>
> P.S. If you get a few moments, please feel free to update
> http://openspim.org/Who_has_an_OpenSPIM%3F with your location and
> information! We love hearing about people using the system.
>
> On 8/14/2014 7:01 AM, Veli-Pekka Ronkainen wrote:
>
> Dear all,
>
>
> We've been scanning some mouse tissue test samples with our
> dual-side illumination OpenSPIM for a short while now, and we are
> very happy with the first results!
>
>
> We have used the original software package downloaded
> from openspim.org without any updates, and it has been working
> fine. However, now after using the Fiji updater Picard USB-stage
> rotation angle coordinates are not right anymore. Changing angle
> from -180 deg to 180 deg rotates the sample holder only ~180
> degrees, and rotation in general spins the sample much less than
> indicated by the slider. In addition, we can not access and modify
> old .cfg-files, so that it would be possible to change step size
> of the twister from 1.8 to 1, as it was discussed earlier:
> http://openspim.org/pipermail/openspim/2014-July/000482.html .
> Modification of an existing configuration starts with an error
> "Error in device Picard Z Stage: Unable to communicate with the
> device" followed by lots of COM and "No device with label _device
> name_" -errors. Creating a new configuration doesn't help since it
> is not possible to add Picard stage z-axis to the config file
> or modify the serial number.
>
>
> We've tried to copy the latest Picard .dll-files from the recent
> Micro-Manager nightly build but the problem persists. Are there
> some other files we should copy and replace as well? Of course we
> can still download and configure the non-updated package from
> openspim.org and be happy using that older version without any
> problems. Still it would be nice to be up-to-date. Anyone
> having the same problems or some solutions? Thanks!
>
>
> Regards,
>
> Veli-Pekka Ronkainen
>
> Light Microscopy Core Facility
>
> Biocenter Oulu, University of Oulu
>
> Finland
>
>
>
>
> _______________________________________________
> OpenSPIM mailing list
> OpenSPIM at openspim.org
> http://openspim.org/mailman/listinfo/openspim
>
>
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