[OpenSPIM] OpenSPIM Digest, Vol 14, Issue 20

Mon Jun 30 13:00:38 CDT 2014

Sorry, I meant to also say that I can't load individual components, I get
the same error messages about COM3.  The only configuration I can actually
complete is the shutter on its own, but it doesn't function.

On Mon, Jun 30, 2014 at 6:55 PM, Aurelia Honerkamp-Smith <
aureliaomega at gmail.com> wrote:

> Hi!,
> With the SerialManager dll from June 24, I get the same error messages but
> entire system doesn't crash, it seems to be an improvement!  New core log
> is attached again.
>  Thanks again!
> Aurelia
>
>
>
> On Mon, Jun 30, 2014 at 6:01 PM, Luke Stuyvenberg <stuyvenberg at wisc.edu>
> wrote:
>
>> Hi Aurelia,
>>
>> On 06/30/14, Aurelia Honerkamp-Smith wrote:
>> > Thank you! I am still having a problem, probably because I'm using
>> a nonstandard setup. There seems to be a conflict in loading my camera (a
>> PVCam one) and the shutter I use to block the laser (Thorlabs SC10); when I
>> try to configure, I get a message "the specified label COM3 is already in
>> use" before anything has been configured, and then several times after I
>> load both, one that says "Line8: device, COM3, serialmanager, COM3." The
>> shutter should be on COM3 but not the camera, and I don't run into this
>> conflict when I load both shutter and camera in the vanilla MM from 24
>> June. I attach a core log showing an attempt to load shutter and camera.
>>
>>
>>
>> Do the devices work individually in OpenSPIM? i.e. if only one is loaded,
>> do you ever get that message? It sounds like a problem with the
>> SerialManager, a device adapter which I hadn't updated -- you might try
>> pulling mmgr_dal_SerialManager.dll from the 24 June nightly build. I'll
>> also be looking into this.
>>
>>
>> On 06/30/14, Aurelia Honerkamp-Smith wrote:
>> > The Picard stage now appears in the list of available hardware, but
>> when I try to load all three the computer bluescreens.
>>
>>
>> Load all three devices (camera, shutter, stage), or load all three
>> stages? Does it bluescreen reliably? (I've not seen/heard of this happening
>> before...)
>>
>>
>> I'll let you know what I work out. Thanks again!
>> Luke
>>
>>
>> On 06/30/14, Aurelia Honerkamp-Smith  wrote:
>> > Hi Luke,
>> >
>> >
>> > Thank you! I am still having a problem, probably because I'm using
>> a nonstandard setup. There seems to be a conflict in loading my camera (a
>> PVCam one) and the shutter I use to block the laser (Thorlabs SC10); when I
>> try to configure, I get a message "the specified label COM3 is already in
>> use" before anything has been configured, and then several times after I
>> load both, one that says "Line8: device, COM3, serialmanager, COM3." The
>> shutter should be on COM3 but not the camera, and I don't run into this
>> conflict when I load both shutter and camera in the vanilla MM from 24
>> June. I attach a core log showing an attempt to load shutter and camera.
>> The Picard stage now appears in the list of available hardware, but when I
>> try to load all three the computer bluescreens.
>> >
>> >
>> > Thanks again,
>> > Aurelia
>> >
>> >
>> >
>> > On Mon, Jun 30, 2014 at 3:03 PM, Luke Stuyvenberg <
>> openspim at openspim.org <stuyvenberg at wisc.edu')" target="1">
>> stuyvenberg at wisc.edu> wrote:
>> >
>> > > Hi Aurelia,
>> > >
>> > > Sorry about that; it seems a lot more had changed than I had
>> expected. I've updated the update site again, with a number of changes
>> (new MMCore, new versions of the device adapters). It tested okay on my
>> virtual machine, but if there's still a problem, please let me know. If
>> you run into other device adapter problems (i.e. not with PicardStage), try
>> getting updated device adapter versions from the nightly build as of 24
>> June or so.
>> > >
>> > >
>> > > Thanks!
>> > > Luke
>> > >
>> > > On 06/29/14, Aurelia Honerkamp-Smith wrote:
>> > > > 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, <
>> http://openspim.org/mailman/listinfo/openspim(java_script:main.compose('new(javascript:main.compose('new
>> <http://openspim.org/mailman/listinfo/openspim(java_script:main.compose('new(javascript:main.compose('new>',
>> 't=openspim at openspim.org> <openspim-request at openspim.org <
>> openspim-request at openspim.org>')" target="1">
>> openspim-request at openspim.org <openspim-request at openspim.org>> wrote:
>> > > >
>> > > > > Send OpenSPIM mailing list submissions to
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>> > >
>> > > > > <a href=)
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>> openspim-request at openspim.org <openspim-request at openspim.org>>
>> > > > >
>> > > > > You can reach the person managing the list at
>> > >
>> > > > > openspim-owner at openspim.org <openspim-owner at openspim.org> <
>> openspim-owner at openspim.org <openspim-owner at openspim.org>>
>> > > > >
>> > > > > When replying, please edit your Subject line so it is more
>> specific
>> > > > > than "Re: Contents of OpenSPIM digest..."
>> > > > >
>> > > > >
>> > >
>> > > > > Today's Topics:
>> > > > >
>> > > > > 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 <tianlankeke at gmail.com> <
>> tianlankeke at gmail.com <tianlankeke at gmail.com>>>
>> > > > > To: Kieran Short <kieran.short at gmail.com <kieran.short at gmail.com>
>> <kieran.short at gmail.com <kieran.short at gmail.com>>>
>> > > > > Cc: openspim at openspim.org <openspim at openspim.org> <
>> openspim at openspim.org <openspim at openspim.org>>
>> > > > > Subject: Re: [OpenSPIM] Problems with OpenSPIM system
>> > > > > Message-ID:
>> > >
>> > > > > <
>> CANQL1FuGbrN-Sm4v+W4utYF1hQTVW_C__xYaguRgf3dEJ3wGKA at mail.gmail.com <
>> CANQL1FuGbrN-Sm4v+W4utYF1hQTVW_C__xYaguRgf3dEJ3wGKA at mail.gmail.com> <
>> CANQL1FuGbrN-Sm4v+W4utYF1hQTVW_C__xYaguRgf3dEJ3wGKA at mail.gmail.com <
>> 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(tel:410-934-9802)(tel:410-934-9802(tel:
>> 410-934-9802))
>> > > > > Email: kli26 at jhu.edu <kli26 at jhu.edu> <kli26 at jhu.edu <
>> kli26 at jhu.edu>>
>> > > > >
>> > > > >
>> > > > > On Fri, Jun 27, 2014 at 6:49 PM, Kieran Short <
>> kieran.short at gmail.com <kieran.short at gmail.com> <kieran.short at gmail.com <
>> 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 <
>> tianlankeke at gmail.com> <tianlankeke at gmail.com <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(tel:410-934-9802)(tel:410-934-9802(tel:
>> 410-934-9802))
>> > > > > >> Email: kli26 at jhu.edu <kli26 at jhu.edu> <kli26 at jhu.edu <
>> kli26 at jhu.edu>>
>> > > > > >>
>> > > > > >>
>> > > > > >> On Fri, Jun 27, 2014 at 2:55 PM, Luke Stuyvenberg <
>> stuyvenberg at wisc.edu <stuyvenberg at wisc.edu> <stuyvenberg at wisc.edu <
>> 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 <marktsuchida at gmail.com> <
>> marktsuchida at gmail.com <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 <OpenSPIM at openspim.org> <
>> OpenSPIM at openspim.org <OpenSPIM at openspim.org>>
>> > > > > >>> > > http://openspim.org/mailman/listinfo/openspim
>> > > > > >>> >
>> > > > > >>> > _______________________________________________
>> > > > > >>> > OpenSPIM mailing list
>> > >
>> > > > > >>> > OpenSPIM at openspim.org <OpenSPIM at openspim.org> <
>> OpenSPIM at openspim.org <OpenSPIM at openspim.org>>
>> > > > > >>> > http://openspim.org/mailman/listinfo/openspim
>> > > > > >>>
>> > > > > >>
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>> > > > > End of OpenSPIM Digest, Vol 14, Issue 20
>> > > > > ****************************************
>> > > > >
>> > >
>> > >
>> > >
>>
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