[OpenSPIM] New Micro-Manager API: Home()
m.pawlowska at nencki.gov.pl
m.pawlowska at nencki.gov.pl
Thu May 7 12:11:23 CDT 2015
I tried to do it, just to see whether I can, but I can't and I feel that
again the problem is not having sufficient information :/ How can I find
out how this "SVN r15408" relates to the version available via
Micro-Manager-Dev update site? Because in this version (the mysterious
MM Studio version: 1.4.22 20150430) calling core.home(label) for the Z
stage, just like it's done for the X/Y stage, throws exception.
Regards,
Monika
---
2015-05-07T18:49:23.194887 tid5692 [dbg,Core] Will home xy stage Picard
XY Stage
2015-05-07T18:49:23.208887 tid5692 [dbg,Core] Did home xy stage Picard
XY Stage
2015-05-07T18:49:23.208887 tid5692 [dbg,Core] Will home xy stage Picard
XY Stage
2015-05-07T18:49:23.224888 tid5692 [dbg,Core] Did home xy stage Picard
XY Stage
2015-05-07T18:49:23.224888 tid5692 [IFO,App] Could not home Z stage.
[ ] java.lang.Exception: Device
"Picard Z Stage" is of the wrong type for the requested operation in
Thread[AWT-EventQueue-0,6,main]
[ ] at
mmcorej.MMCoreJJNI.CMMCore_home(Native Method)
[ ] at
mmcorej.CMMCore.home(CMMCore.java:1202)
[ ] at
spim.setup.Stage.home(Stage.java:152)
[ ] at
spim.SPIMAcquisition$6.actionPerformed(SPIMAcquisition.java:429)
[ ] at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
[ ] at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
[ ] at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
[ ] at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
[ ] at
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
[ ] at
java.awt.Component.processMouseEvent(Component.java:6289)
[ ] at
javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
[ ] at
java.awt.Component.processEvent(Component.java:6054)
[ ] at
java.awt.Container.processEvent(Container.java:2041)
[ ] at
java.awt.Component.dispatchEventImpl(Component.java:4652)
[ ] at
java.awt.Container.dispatchEventImpl(Container.java:2099)
[ ] at
java.awt.Component.dispatchEvent(Component.java:4482)
[ ] at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577)
[ ] at
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
[ ] at
java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
[ ] at
java.awt.Container.dispatchEventImpl(Container.java:2085)
[ ] at
java.awt.Window.dispatchEventImpl(Window.java:2478)
[ ] at
java.awt.Component.dispatchEvent(Component.java:4482)
[ ] at
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644)
[ ] at
java.awt.EventQueue.access$000(EventQueue.java:85)
[ ] at
java.awt.EventQueue$1.run(EventQueue.java:603)
[ ] at
java.awt.EventQueue$1.run(EventQueue.java:601)
[ ] at
java.security.AccessController.doPrivileged(Native Method)
[ ] at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
[ ] at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
[ ] at
java.awt.EventQueue$2.run(EventQueue.java:617)
[ ] at
java.awt.EventQueue$2.run(EventQueue.java:615)
[ ] at
java.security.AccessController.doPrivileged(Native Method)
[ ] at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
[ ] at
java.awt.EventQueue.dispatchEvent(EventQueue.java:614)
[ ] at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
[ ] at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
[ ] at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
[ ] at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
[ ] at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
[ ] at
java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> Message: 2
> Date: Wed, 06 May 2015 08:15:40 +0200
> From: Johannes Schindelin <schindelin at wisc.edu>
> To: openspim at openspim.org
> Subject: [OpenSPIM] New Micro-Manager API: Home(), was Fwd: Re:
> [micro-manager-general] Joystick
> Message-ID: <b96cc9f412568dc18b038dc5ccd8d11b at www.dscho.org>
> Content-Type: text/plain; CHARSET=US-ASCII; format=flowed
>
> Hello fellow OpenSPIMoids, especially of the software developing
> variety,
>
> I just stumbled over this mail that implies that we need to adjust the
> code of the SPIMAcquisition plugin. Takers?
>
> Ciao,
> Johannes
>
> -------- Original Message --------
> Subject: Re: [micro-manager-general] Joystick
> Date: 2015-05-05 22:55
> From: Mark Tsuchida <marktsuchida at gmail.com>
> To: Micro-Manager General <micro-manager-general at lists.sourceforge.net>
> Reply-To: Micro-Manager General
> <micro-manager-general at lists.sourceforge.net>
>
> On Mon, Apr 27, 2015 at 3:37 PM, Mark Tsuchida <marktsuchida at gmail.com>
> wrote:
>>> One more thing, MM::Stage (in MMDevice.h) does not have a home call.
>>> Is this by design?
>>> My Zstage needs to be homed. I believe I need to implement it as a
>>> property??
>>
>> We should add this, but for now you will need to use a property.
>
> Z stages can now implement Home(), as of SVN r15408.
>
> Best,
> Mark
>
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>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 06 May 2015 08:27:51 +0200
> From: Johannes Schindelin <johannes.schindelin at gmx.de>
> To: Monika Paw?owska <m.pawlowska at nencki.gov.pl>
> Cc: openspim at openspim.org
> Subject: [OpenSPIM] About metadata and SPIM reconstruction, was Re:
> OpenSPIM update site
> Message-ID: <a6dc74c3bbefb641dfe50884651fdf78 at www.dscho.org>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Hi Monika,
>
> [I hope you do not mind that I Cc:ed the mailing list; I believe that
> other OpenSPIM people will be interested/helpful]
>
> On 2015-05-05 16:16, Johannes Schindelin wrote:
>
>> On 2015-05-05 16:13, Monika Paw?owska wrote:
>>
>>> Now that I figured out how to use maven I wouldn't mind helping a bit
>>> more with the plugin. For instance I would like to figure out what
>>> would it take to remove this step:
>>> http://openspim.org/Pre-processing
>>> . Do you have any idea what these "metadata conflicts" are?
>>
>> I do not remember, I just found out recently that we (= the lab I am
>> working in) are not writing OME Tiffs at all :-( As far as I can tell,
>> this is the class that *should* do it:
>>
>> https://github.com/openspim/SPIMAcquisition/blob/master/src/main/java/spim/progacq/OMETIFFHandler.java
>>
>> But I have no idea what the metadata conflicts are, and as far as I
>> can tell, nobody recorded the conflicts, either. I guess we will just
>> have to reproduce them, and I half expect the conflicts to have gone
>> away in the meantime, anyway.
>
> There was a bug report yesterday:
> https://github.com/bigdataviewer/SPIM_Registration/issues/41
>
> While it concerned CZI files, I imagine that OME Tiff files might
> expose
> similar problems. If you stumble over such problems, I would suggest
> doing exactly the same as Mario: report the problem on GitHub. Steffi
> is
> always busy, of course, as we all are, yet he is always helpful.
>
> Ciao,
> Dscho
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 6 May 2015 16:42:12 +0200 (CEST)
> From: "Peter Gabriel Pitrone" <pitrone at mpi-cbg.de>
> To: "Johannes Schindelin" <johannes.schindelin at gmx.de>
> Cc: openspim at openspim.org
> Subject: Re: [OpenSPIM] OpenSPIM update site
> Message-ID:
> <13038.128.128.250.98.1430923332.squirrel at webmail.mpi-cbg.de>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Howdy Johannes,
>
> Here's what I got from the Debug console, along with another core log.
> I
> hope it helps... BTW, the console kept on making more and more errors
> after I homed the stage, but I assume that they are the same message.
>
> The motors completely disconnect (go red) from the device manager after
> the procedure, so I have to unplug the hub and reconnect to get them
> back.
>
> Best Regards,
> Pete
>
> Peter Gabriel Pitrone - DipRMS TechRMS FRMS
> Light Sheet Fluorescence Microscopist and Imaging Specialist
> for Dr. Pavel Tomancak's research group at the
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstra?e 108
> 01307 Dresden, Saxony
> Germany
>
>
> http://www.mpi-cbg.de/research/research-groups/pavel-tomancak.html &
> http://www.openspim.org
>
> "I KEEP six honest serving-men (they taught me all I knew); their names
> are What and Why and When and How and Where and Who." Rudyard Kipling -
> The Elephant's Child
>
> On Tue, May 5, 2015 14:13, Johannes Schindelin wrote:
> <|> Hi Pete,
> <|>
> <|> On 2015-05-05 14:10, Peter Gabriel Pitrone wrote:
> <|>
> <|>> I updated the fiji with OpenSPIM, and after the restart it works
> just
> <|>> like you say. However, afterwards when homes the the 4D-stage
> (with
> <|>> the USB-Slide-II motors), the motors lose connection and I need to
> <|>> pull the connection out of the USB hub and restart.
> <|>
> <|> Console output & CoreLog.txt, please?
> <|>
> <|> Ciao,
> <|> Johannes
> <|>
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> ------------------------------
>
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