[OpenSPIM] OpenSPIM Digest, Vol 14, Issue 20

Aurelia Honerkamp-Smith aureliaomega at gmail.com
Sun Jun 29 07:37:42 CDT 2014 

Hello,
I am afraid that after updating to the newest PicardStage dll, my previous
configuration is unable to load the stage.  I get an error message:

Line 8: Device,Picard Twister,PicardStage,Picard Twister
Failed to load device adapter "PicardStage" from
"C:\Users\ah659\Desktop\OPENSP~1\OpenSPIM.app\mm\win32\mmgr_dal_PicardStage.dll"

Line 9: Device,Picard Z Stage,PicardStage,Picard Z Stage
Failed to load device adapter "PicardStage" from
"C:\Users\ah659\Desktop\OPENSP~1\OpenSPIM.app\mm\win32\mmgr_dal_PicardStage.dll"

Line 10: Device,Picard XY Stage,PicardStage,Picard XY Stage
Failed to load device adapter "PicardStage" from
"C:\Users\ah659\Desktop\OPENSP~1\OpenSPIM.app\mm\win32\mmgr_dal_PicardStage.dll"

Line 22: Property,Picard Twister,Serial Number,60
No device with label "Picard Twister"

Line 23: Property,Picard Z Stage,Serial Number,181
No device with label "Picard Z Stage"

Line 24: Property,Picard XY Stage,Serial Number (X),182
No device with label "Picard XY Stage"

Line 25: Property,Picard XY Stage,Serial Number (Y),180
No device with label "Picard XY Stage"

Line 26: Property,Picard XY Stage,X-Max,8000
No device with label "Picard XY Stage"

Line 27: Property,Picard XY Stage,X-Min,1
No device with label "Picard XY Stage"

Line 28: Property,Picard XY Stage,Y-Max,8000
No device with label "Picard XY Stage"

Line 29: Property,Picard XY Stage,Y-Min,1
No device with label "Picard XY Stage"

Line 44: Property,Core,Focus,Picard Z Stage
Cannot set Core property Focus to invalid value "Picard Z Stage"

I can still load the camera and my shutter.  The Picard Stage now appears
unavailable in the hardware configuration wizard.  I am also using 32-bit
Fiji on a 64-bit machine, but haven't had trouble loading the stage before
(it appeared to work normally, with the exception of the occasional
communication delay that I mentioned earlier).  I attach a core log.




On Sat, Jun 28, 2014 at 6:00 PM, <openspim-request at openspim.org> wrote:

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> Today's Topics:
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>    1. Re: Problems with OpenSPIM system (Ke Li)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 27 Jun 2014 22:35:42 -0400
> From: Ke Li <tianlankeke at gmail.com>
> To: Kieran Short <kieran.short at gmail.com>
> Cc: openspim at openspim.org
> Subject: Re: [OpenSPIM] Problems with OpenSPIM system
> Message-ID:
>         <
> CANQL1FuGbrN-Sm4v+W4utYF1hQTVW_C__xYaguRgf3dEJ3wGKA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Kieran,
>
> Thanks for your detailed info. The 4D stage can be controlled normally by
> the software from Picard in my system. While I just can't add the Z stage
> when I try to create the hardware configuration wizard by micro-manager. So
> there is no place I can put the serial number of the Z stage in. (I can add
> XY stage and the twister normally and change -1 into the correct serial
> number of the XY stage).
>
> I can also reproduce the problem exactly as what Mark did and encountered
> (From Mark: I can reproduce the problem: with no Picard hardware connected
> to the computer, no configuration dialog for the pre-initialization
> settings (including the serial number) is displayed in the hardware
> configuration
> wizard. This is the case for the Twister and Z stage, but not the XY stage
> (at least on my computer).)
>
> Thanks,
> Ke
>
> Ke Li
> Research Assistant
> Biomedical Engineering
> Johns Hopkins University
> Phone: 410-934-9802
> Email: kli26 at jhu.edu
>
>
> On Fri, Jun 27, 2014 at 6:49 PM, Kieran Short <kieran.short at gmail.com>
> wrote:
>
> > Hi Ke,
> >
> > You still can add the seral number to the Z in the Picard
> > application/program. This is totally independent of micromanager.
> >
> > The other thing is, the 4D stage axes are labeled with stickers which
> have
> > 2 bits of info . 1st is stage name and the other is the serial number.
> The
> > stage name doesn't necessarily represent what you think it does. Our "Z"
> > actually translates the stage toward and away from the detection
> objective!
> > That doesn't really matter though, I see Z as just a name that doesn't
> > truly reflect its function. It still works fine.
> >
> > Once you enter in the correct serial number in the Picard application the
> > indicators for the stage communication in the software should turn from
> red
> > to green.
> >
> > The picard software is*very* strict about this serial number setting. I
> > could use just about any numbers and micromanager worked -- but this
> really
> > wont.
> > My feeling is that if you at least have picards app working you will know
> > if its a "driver" problem or not.
> >
> > It'll make Luke's job a lot easier if this is done. Have you already done
> > this and is there communication between the 4d stage and its own software
> > once you have entered tge correct serial numbers?
> >
> > Cheers Kieran
> > On 28/06/2014 8:17 AM, "Ke Li" <tianlankeke at gmail.com> wrote:
> >
> >> Hi Luke,
> >>
> >> Thanks so much. Could you please send the link of the changed version to
> >> me? And since my system is 64-bit, how can I solve the Z stage problem
> (no
> >> field to change the serial number since I can't add the Z stage first)?
> >>
> >> Thanks,
> >> Ke
> >>
> >> Ke Li
> >> Research Assistant
> >> Biomedical Engineering
> >> Johns Hopkins University
> >> Phone: 410-934-9802
> >> Email: kli26 at jhu.edu
> >>
> >>
> >> On Fri, Jun 27, 2014 at 2:55 PM, Luke Stuyvenberg <stuyvenberg at wisc.edu
> >
> >> wrote:
> >>
> >>> Hi everyone,
> >>>
> >>> On 06/27/14, Luke Stuyvenberg wrote:
> >>> > I'll report back after fixing/testing and committing/uploading the
> >>> device adapter.
> >>>
> >>>
> >>> And so here I am. I've committed the changes to SVN and uploaded the
> >>> 32-bit version of the DLL to the OpenSPIM update site.
> >>>
> >>>
> >>> Mark -- Following your suggestion, those lines were removed -- in
> >>> hindsight, it's not really the correct behavior, and the possible issue
> >>> with obtaining an invalid serial number shouldn't be common at all.
> Thanks!
> >>>
> >>>
> >>> Kieran -- I recently became aware of the homing problem; the stage
> >>> sometimes resets its internal location (when it loses power,
> perhaps?), so
> >>> over time it will be pushed away. The X/Y stage can be homed using the
> MM
> >>> Script Panel, running mmc.home("Picard XY Stage") -- the Z stage has no
> >>> appropriate API call, so for the time being, there is a property
> "GoHome"
> >>> that will home that stage when set to 1. It's a workaround until I can
> >>> submit a more useful patch to the MM team (though, as an API change,
> that
> >>> may take a little while).
> >>>
> >>>
> >>> Ke -- Please let me know if there are any more problems; hope this
> helps!
> >>>
> >>>
> >>> Luke
> >>>
> >>>
> >>> On 06/27/14, Luke Stuyvenberg  wrote:
> >>> > Hi Ke, Mark, Johannes,
> >>> >
> >>> >
> >>> > On 06/26/14, Mark Tsuchida wrote:
> >>> > > Johannes, I also found the cause: OnSerialGeneric() is calling the
> >>> > > Initialize() function, which fails. This happens before the
> Hardware
> >>> > > Wizard calls Initialize (actually, when the wizard is trying to get
> >>> > > the initial values of the pre-init properties), so the wizard has
> no
> >>> > > chance to display the configuration dialog.
> >>> > >
> >>> > > Simply taking out the calls to Initialize (PicardStage.cpp lines
> >>> > > 243-245, 258) seems to fix this, but I'm not sure if that is all
> that
> >>> > > needs to be done (since I don't have a Picard stage and cannot
> figure
> >>> > > out what the intent of calling Initialize() at this point was).
> >>> > > Johannes, can you take a look at this?
> >>> >
> >>> >
> >>> >
> >>> > The intent of the Initialize call was to test the serial number
> >>> received from the Pi-detector, but I didn't account for the
> possibility of
> >>> CPiDetector returning DEFAULT_SERIAL_UNKNOWN, which it does if the
> >>> requested device hadn't been found. I'm preparing a fix for this that I
> >>> will submit via SVN as soon as possible.
> >>> >
> >>> >
> >>> > The ultimate issue is this: The Pi-detector only tested serial
> numbers
> >>> up to 250. I've doubled this for now, but this is a stop-gap measure
> that
> >>> causes an ugly pause in the device adding process while it probes the
> >>> serial numbers; I will need to seek a different approach to detecting
> the
> >>> motors.
> >>> >
> >>> >
> >>> > I'll report back after fixing/testing and committing/uploading the
> >>> device adapter.
> >>> >
> >>> >
> >>> > Luke
> >>> >
> >>> >
> >>> > On 06/26/14, Mark Tsuchida wrote:
> >>> > > Hi Ke and Johannes,
> >>> > >
> >>> > > On Thu, Jun 26, 2014 at 11:57 AM, Mark Tsuchida <
> >>> marktsuchida at gmail.com> wrote:
> >>> > > > On Wed, Jun 25, 2014 at 10:27:54PM -0400, Ke Li wrote:
> >>> > > >> 1. I still can't add the Z stage when I create the hardware
> >>> configuration.
> >>> > > >> I tried both 64-bit and 32-bit Windows system, neither can work.
> >>> Since the
> >>> > > >> problem report doesn't give much info, I'm not sure whether
> there
> >>> are other
> >>> > > >> ways to solve this problem? And what possible reasons can cause
> >>> the
> >>> > > >> problem?
> >>> > > >
> >>> > > > Are you sure you have the correct serial number for the Z stage
> (as
> >>> > > > Johannes suggested)? In the problem report you sent us, it looked
> >>> like
> >>> > > > you had not set the serial number when adding the Z stage in the
> >>> > > > Hardware Configuration Wizard. This causes the device adapter to
> >>> use the
> >>> > > > serial number "-1", which always results in an error.
> >>> > > >
> >>> > > > Do you see a field to enter the serial number for the Z stage? If
> >>> you cannot
> >>> > > > get it to work even when entering the correct serial number,
> could
> >>> you try
> >>> > > > sending another Problem Report?
> >>> > >
> >>> > > Sorry, I hadn't seen your reply to Johannes that answered that
> >>> question of mine.
> >>> > >
> >>> > > I can reproduce the problem: with no Picard hardware connected to
> the
> >>> > > computer, no configuration dialog for the pre-initialization
> settings
> >>> > > (including the serial number) is displayed in the hardware
> >>> > > configuration wizard. This is the case for the Twister and Z stage,
> >>> > > but not the XY stage (at least on my computer).
> >>> > >
> >>> > > Johannes, I also found the cause: OnSerialGeneric() is calling the
> >>> > > Initialize() function, which fails. This happens before the
> Hardware
> >>> > > Wizard calls Initialize (actually, when the wizard is trying to get
> >>> > > the initial values of the pre-init properties), so the wizard has
> no
> >>> > > chance to display the configuration dialog.
> >>> > >
> >>> > > Simply taking out the calls to Initialize (PicardStage.cpp lines
> >>> > > 243-245, 258) seems to fix this, but I'm not sure if that is all
> that
> >>> > > needs to be done (since I don't have a Picard stage and cannot
> figure
> >>> > > out what the intent of calling Initialize() at this point was).
> >>> > > Johannes, can you take a look at this?
> >>> > >
> >>> > > Best,
> >>> > > Mark
> >>> > >
> >>> > > --
> >>> > > Mark Tsuchida
> >>> > > Micro-Manager Team (UCSF Vale Lab)
> >>> > >
> >>> > > _______________________________________________
> >>> > > OpenSPIM mailing list
> >>> > > OpenSPIM at openspim.org
> >>> > > http://openspim.org/mailman/listinfo/openspim
> >>> >
> >>> > _______________________________________________
> >>> > OpenSPIM mailing list
> >>> > OpenSPIM at openspim.org
> >>> > http://openspim.org/mailman/listinfo/openspim
> >>>
> >>
> >>
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