[OpenSPIM] OpenSPIM Digest, Vol 14, Issue 20

Aurelia Honerkamp-Smith aureliaomega at gmail.com
Wed Jul 2 10:04:24 CDT 2014 

Hi again,

Yes, setting the pixel size lets the camera work again!   I also had to
switch the Picard serial numbers in the configuration file to their actual
values, as I had switched them around initially to get the focus stage to
be the correct one.  The plugin is now functional.  I can create a
configuration file, start the SPIM plugin, then save it to get a pixel
size.  I still need to remove the extra COM3 line from the configuration
file manually, and when I start live view there is a MicroManager error:
Error:
org.micromanager.MMStudioMainFrame.updateCenterAndDragListener(MMStudioMainFrame.java.2240)

but when I dismiss it, everything seems to function normally.  I am still
getting sporadic Acquiring: null errors when I start acquisition, but that
predated this change.  Let me know if I should send any more info.
Thanks very much Luke!

Aurelia


On Tue, Jul 1, 2014 at 7:12 PM, Luke Stuyvenberg <stuyvenberg at wisc.edu>
wrote:

> There certainly seems to be something odd about the camera adapter right
> now. Specifically,
>
> 2014-07-01T18:07:18.997408 tid6872 [IFO,dev:Camera-1] PVCAM API error:
> "C0_CAM_NAME_NOT_FOUND This is not a valid name for opening the camera",
> code: 14
>
> Do you get this error opening only the live view, without starting the
> SPIM Acquisition plugin? The core log seems to suggest that the camera
> works fine until the plugin is launched. Most likely, when the plugin
> defines an automatic pixel size, some sort of reset occurs in the core, but
> the camera adapter doesn't tolerate it well (I feel like I've encountered
> this issue before with a different camera adapter... I'll have to look into
> this; it might be a report for the MM team to look at.). As a short-term
> workaround, you can define a pixel size before launching the software,
> using Tools -> Pixel Size Calibration. (If a pixel size is predefined, the
> SPIM plugin won't try to add one.) After defining a pixel size, save the
> configuration (Tools -> Save Configuration Settings As...) so you won't
> need to re-make the pixel size definition each time.
>
>
> Please try that workaround and let me know if you still have issues; I'll
> add the immediate fixes on the update sites and see what I can do about
> tracking down this bug.
>
>
> Thanks!
> Luke
>
> On 07/01/14, Aurelia Honerkamp-Smith  wrote:
> > Hi again,
> >
> >
> > Yep, the COM3 messages stop when I get rid of the extra line in the
> configuration file. Oh! This is exciting! After I start up and load the
> configuration file without the extra COM3 line, I can start the plugin, and
> move the stage! However, when I try to start live view, I then get a
> Micro-Manager error: "Error in device Camera-1: The device cannot set this
> property at the moment." Trying to use Snap gives "Error Acquiring: null."
> >
> > Well, it was exciting for me anyhow. Another corelog is attached.
> >
> >
> > Aurelia
> >
> >
> >
> >
> > On Tue, Jul 1, 2014 at 5:32 PM, Luke Stuyvenberg <aureliaomega at gmail.com
> <stuyvenberg at wisc.edu')" target="1">stuyvenberg at wisc.edu> wrote:
> >
> > > Hi Aurelia,
> > >
> > > > Thanks! I've replaced rsyntaxtextarea.jar. I can now configure
> all 3 components, although I still get the COM3 error messages. The shutter
> and camera then seem to function, but I can't start the SPIM plugin to
> see if the stage is working. I don't get an error message that says my
> setup is invalid, the plugin just fails to start. I attach the
> configuration file that I have just made, and a corelog showing an attempt
> to start the plugin.
> > >
> > > The COM3 error message is happening because of the duplicate line in
> the configuration file -- though, if the configurator is generating this
> file each time, there is probably an underlying issue that requires
> investigation. (Unfortunately, it isn't obvious to me why this might
> happen; finding this out could take time.) A quick fix would be to edit the
> config file in a text editor and remove line 7 or 8
> ("Device,COM3,SerialManager,COM3").
> > >
> > >
> > > The SPIM plugin won't start because the stage configuration is
> confusing it. Two possibilities: Either the COM3 error is leaving the
> stages only partially initialized, so the stage position is invalid (out of
> the stage's range, according to its properties), or a stage (usually
> the twister) was left in a position outside its accepted range. Given the
> PVCAM exception earlier in the CoreLog, I would assume the former -- but to
> be sure, before starting the system, please try using the Picard software
> to home the three linear stages and zero the rotational stage, leaving them
> all inside the usual position range.
> > >
> > >
> > > On 07/01/14, Aurelia Honerkamp-Smith wrote:
> > > > My system info is:
> > > >
> > > > --------------- S Y S T E M ---------------
> > > >
> > > > OS: Windows 7 Build 7601 Service Pack 1
> > > >
> > > > CPU:total 12 (6 cores per cpu, 2 threads per core) family 6 model 45
> stepping 7, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2,
> popcnt, ht
> > > >
> > > > Memory: 4k page, physical 66506940k(61696496k free), swap
> 133012024k(127977948k free)
> > > >
> > > > vm_info: Java HotSpot(TM) Client VM (19.1-b02) for windows-x86 JRE
> (1.6.0_24-b07), built on Feb 2 2011 17:44:41 by "java_re" with MS VC++ 7.1
> (VS2003)
> > > >
> > > >
> > > > Is that the system information you need?
> > >
> > >
> > >
> > >
> > > Yes, thank you! It doesn't reveal much about the problem, but at
> the very least it confirms that the system should be working...
> > >
> > >
> > > Just to keep track of what we've done so far (so I know what to
> change in the next update):
> > > - Updated mmgr_dal_SerialManager.dll and all system DALs to the latest
> versions.
> > > - Replaced rsyntaxtextarea.jar with Micro-Manager's preferred
> version.
> > >
> > >
> > > Nearly there, I think!
> > > Luke
> > >
> > >
> > > On 07/01/14, Aurelia Honerkamp-Smith wrote:
> > > > Hi again,
> > > >
> > > >
> > > > Thanks! I've replaced rsyntaxtextarea.jar. I can now configure
> all 3 components, although I still get the COM3 error messages. The shutter
> and camera then seem to function, but I can't start the SPIM plugin to
> see if the stage is working. I don't get an error message that says my
> setup is invalid, the plugin just fails to start. I attach the
> configuration file that I have just made, and a corelog showing an attempt
> to start the plugin. My system info is:
> > > >
> > > > --------------- S Y S T E M ---------------
> > > >
> > > > OS: Windows 7 Build 7601 Service Pack 1
> > > >
> > > > CPU:total 12 (6 cores per cpu, 2 threads per core) family 6 model 45
> stepping 7, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2,
> popcnt, ht
> > > >
> > > > Memory: 4k page, physical 66506940k(61696496k free), swap
> 133012024k(127977948k free)
> > > >
> > > > vm_info: Java HotSpot(TM) Client VM (19.1-b02) for windows-x86 JRE
> (1.6.0_24-b07), built on Feb 2 2011 17:44:41 by "java_re" with MS VC++ 7.1
> (VS2003)
> > > >
> > > >
> > > > Is that the system information you need?
> > > >
> > > >
> > > >
> > > >
> > >
> > > > On Mon, Jun 30, 2014 at 7:37 PM, Luke Stuyvenberg <
> http://openspim.org/mailman/listinfo/openspim(java_script:main.compose('new(java_script:main.compose('new(http://openspim.org/mailman/listinfo/openspim(java_script:main.compose('new(java_script:main.compose('new)&#39(java_script:main.compose('new(javascript:main.compose('new',
> 't=aureliaomega at gmail.com> <stuyvenberg at wisc.edu <stuyvenberg at wisc.edu>')"
> target="1">stuyvenberg at wisc.edu <stuyvenberg at wisc.edu>> wrote:
> > > >
> > > > > Hi,
> > > > >
> > >
> > > > > One further thought -- the Java error at the top of the log file
> comes from a conflict in rsyntaxtextarea.jar (some e-mails on the MM
> mailing list discuss this issue, and we're working on porting Fiji/IJ2
> to a newer version of the jar) -- I expected that having these in conflict
> would only disable the Micro-Manager script editor, but some testing
> suggests it might be more disruptive than that. Another fix you can try
> without waiting on me: From vanilla MM, copy:
> "plugins/Micro-Manager/rsyntaxtextarea.jar" -> (in OpenSPIM.app)
> "jars/rsyntaxtextarea.jar"; then, move, rename, or delete
> "jars/rsyntaxtextarea-2.0.4.1.jar".
> > > > >
> > > > >
> > > > > Thanks again,
> > > > > Luke
> > > > >
> > > > > On 06/30/14, Luke Stuyvenberg wrote:
> > > > > > Hi Aurelia,
> > > > > >
> > >
> > > > > > Could you attach your configuration file, and report your system
> specs (OS version/architecture) as well? The core log certainly seems to
> suggest it is attempting to load COM3 multiple times (it also seems to
> reset the serial port properties with each stage loaded from PicardStage),
> but short of that, I'm still not entirely certain what's going on.
> If the 24 June device adapters weren't correct, they probably
> wouldn't load at all, so presumably you've already copied all the
> right DLLs. (SerialManager and ThorlabsSC10 are self-contained, so just
> those files should be enough to run those devices; PVCAM has an external
> DLL, but your core log suggests the camera initializes without a problem.)
> > > > > >
> > > > > >
> > > > > > Thanks,
> > > > > > Luke
> > > > > >
> > > > > > On 06/30/14, Aurelia Honerkamp-Smith wrote:
> > > > > > > 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 <> >
> > > > On Mon, Jun 30, 2014 at 6:01 PM, Luke Stuyvenberg <
> stuyvenberg at wisc.edu <stuyvenberg at wisc.edu> <stuyvenberg at wisc.edu <
> stuyvenberg at wisc.edu>>(java_script:main.compose()> 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 <openspim at openspim.org> <openspim at openspim.org <
> openspim at openspim.org>>(java_script:main.compose() <stuyvenberg at wisc.edu <
> stuyvenberg at wisc.edu> <stuyvenberg at wisc.edu <stuyvenberg at wisc.edu>>(java_script:main.compose()')"
> target="1">stuyvenberg at wisc.edu <stuyvenberg at wisc.edu> <
> stuyvenberg at wisc.edu <stuyvenberg at wisc.edu>>(java_script:main.compose()>
> 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, <>
> _______________________________________________
> > > > > > 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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