[OpenSPIM] Problems with OpenSPIM system

[Ke Li]

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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