[OpenSPIM] Problems with OpenSPIM system

[Kieran Short]

Hi all (mainly to Ke),

Just a word from my experience using Win7/64bit. Ke - in order for Picard's
own application to work, you need to have the serial numbers for the XY, Z
and R components exactly right. I didn't receive any documentation on what
to do. I just copied the serial numbers that i saw in some simple
documentation that came with it... but using these never got the Picard
application to work. However, the OpenSPIM system worked fine. Anyway,
after having this for some months (and just putting down the Picard program
not working to some weird bug), I only realised today when the serial
number stickers on the 4d stage itself jumped out at me (which aren't
hidden, they're pretty obvious actually now that I look at them!). Anyway,
entering in *those* number, *ding* the Picard application worked, and I
could control the application from that piece of software. FWIW, our
serials were 198, 199, 200. R was much lower, 60-something. :)
What I've also found, is that the "home" position was never set correctly
until I managed to get the 4D stage to properly talk to its own software. X
and Y were extending far too much into the sample chamber. Now that we
could properly 'Home' the stage in its own software once, it's much better
now and we have much better range. :)

Other comments about Win7/6: In our hands the Fiji/ImageJ and the
Micromanager>OpenSpim plugin work fine. I launch it as a WindowsXP/32 bit
compatibility application and it seems to be happy so far. It didn't like
being opened natively. I also tried compiling a Win7/64 build from GIT, but
I never spent the time to properly work out how to roll the plugins for the
hardware into it, so on that basis it never worked properly. As for the
system itself, we still haven't actually captured anything yet as we've had
all sorts of fun getting the sample chamber right -- and we're just
aligning/calibrating it now. But the stage, camera, and laser are all
happily being controlled by the OpenSPIM micromanager plugin.

cheers,
Kieran


On Fri, Jun 27, 2014 at 11:05 PM, Luke Stuyvenberg <stuyvenberg at wisc.edu>
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
>
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