[OpenSPIM] OpenSPIM Digest, Vol 15, Issue 5

Thu Jul 3 12:00:23 CDT 2014

Hi Aurelia,

Glancing at your old configuration file, the twister step size seems to be set to 1.8 -- however, a change to the Picard USB library has altered the correct value for the step size; now, rather than motor steps, the usual set-position command operates in degrees; that is, the correct step size is 1.0. Try changing your configuration to use this value instead and see if that helps.

Luke

On 07/03/14, Aurelia Honerkamp-Smith  wrote:
> Hi everyone, 
> 
> Today, while looking at my calibration grid, I find that the x, y,and z stages behave normally, but that the rotation stage is acting odd. I can't rotate only one step; the stage doesn't move unless I click two steps. Also, the numbers that show up in the angle readout box are surprising; the angle changes in steps of 3.24 instead of 1.8, so it goes from 0 to 3.24, then 6.48, etc. The information in the configuration file seems to be correct, and the stage reacts normally to the Picard controller. 
> Any ideas? No error appears in my core log. 
> Thanks, 
> Aurelia
> 
> 
> 
> 
> 
> On Wed, Jul 2, 2014 at 10:55 PM, <openspim at openspim.org <openspim-request at openspim.org')" target="1">openspim-request at openspim.org> wrote:
> 
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> > Today's Topics:
> > 
> > 1. Re: OpenSPIM Digest, Vol 14, Issue 20 (Aurelia Honerkamp-Smith)
> > 
> > 
> > ----------------------------------------------------------------------
> > 
> > Message: 1
> > Date: Wed, 2 Jul 2014 16:04:24 +0100
> > From: Aurelia Honerkamp-Smith <aureliaomega at gmail.com <aureliaomega at gmail.com>>
> > To: Luke Stuyvenberg <stuyvenberg at wisc.edu <stuyvenberg at wisc.edu>>
> > Subject: Re: [OpenSPIM] OpenSPIM Digest, Vol 14, Issue 20
> > Message-ID:
> > <CAHAw+8aj-ehCPEv-azUKx9nPGm2k6f=LBqiukZg-cdhquJdQvg at mail.gmail.com <LBqiukZg-cdhquJdQvg at mail.gmail.com>>
> > Content-Type: text/plain; charset="utf-8"
> > 
> > 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 <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 <aureliaomega at gmail.com>
> > > <stuyvenberg at wisc.edu <stuyvenberg at wisc.edu>')" target="1">stuyvenberg at wisc.edu <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(java_script:main.compose('new',
> > > 't=aureliaomega at gmail.com <aureliaomega at gmail.com>> <stuyvenberg at wisc.edu <stuyvenberg at wisc.edu> <stuyvenberg at wisc.edu <stuyvenberg at wisc.edu>>')"
> > > target="1">stuyvenberg at wisc.edu <stuyvenberg at wisc.edu> <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>> <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>> <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>> <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>> <
> > > 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
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> > End of OpenSPIM Digest, Vol 15, Issue 5
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