saving a multi-image file programmatically

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saving a multi-image file programmatically

Roy Wollman-2
Hi, 

I would like to use the exciting new multi-image file programmatically in my scripts (matlab in my case, but doesn't really matter). I couldn't find any related method in the doxygen documentations. Any pointers on how to do that will be appreciated!

Right now I am creating a new acquisition using: 
>> gui.openAcquisition(acqname,expPath),1,n, 1,showflag,saveflag)

I change scope state (channels, exposure, etc) in a loop adding new images to it using 
>> gui.snapAndAddImage(acqname, 0, i-1, 0);

How should I specify for it to save into the multi-image file format?  

As a note, the doxygen docs are probably out of date, a few methods that I found related to the new TaggedImage classes (core.getTaggedImage) where not there. 

Thanks, 
Roy 


--

Roy Wollman, PhD

University of California - San Diego
Department Chemistry and Biochemistry & 
San Diego Center for Systems Biology

Room 5202 Urey Hall, 9500 Gilman Drive 

La Jolla, CA 92093-0356
Lab Phone: 858-224-2249
E-mail: [hidden email]
http://wollmanlab.ucsd.edu



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Re: saving a multi-image file programmatically

Arthur D. Edelstein
Hi Roy,

> I would like to use the exciting new multi-image file programmatically in my
> scripts (matlab in my case, but doesn't really matter).
> [...]
> How should I specify for it to save into the multi-image file format?

You can use the line:
gui.setImageSavingFormat(org.micromanager.acquisition.TaggedImageStorageMultipageTiff.class);

Best regards,
Arthur

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Re: saving a multi-image file programmatically

Nico Stuurman
Administrator
In reply to this post by Roy Wollman-2
Hi Roy,

> As a note, the doxygen docs are probably out of date, a few methods that I found related to the new TaggedImage classes (core.getTaggedImage) where not there.

Some functions are added in the SWIG layer, which translates C++ to Java.  Regretfully, creating documentation for functions that are generated there is complicated.  They do not show in the doxygen-generated files that describe the C++ files.  We can generate Javadoc from the generated Java classes, but those do not include comments.  We once looked at importing comments through the SWIG layer but failed to find a nice solution.

In any case, I updated the javadoc and doxygen generated files.  Those should have been updated automatically, not sure why that did not happen..

Best,

Nico




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Re: saving a multi-image file programmatically

Roy Wollman-2
In reply to this post by Roy Wollman-2
Thanks Arthur, 

That almost did the trick, matlab doesn't like the call for *.class but I added the call: 

gui.setImageSavingFormat(org.micromanager.acquisition.TaggedImageStorageMultipageTiff.class);


to the MMStartup.bsh and it seems to work, i.e. it does save a mutli-image tiff. However, while doing so I get an error message: "summary metadata not found or corrupt". From the Logfile:

LOG(2012-10-18T14:23:02.920219, 7096, 00000000210867D0:): > Error: Couldn't find SlicesFirst or TimeFirst in summary metadata
LOG(2012-10-18T14:23:02.920219, 7096, 00000000210867D0:): > Error: Summary metadata not found or corrupt.  Is this a Micro-Manager dataset?

Do I need to do anything else to attach the metadata to the tagged image before / after the call to snapAndAddImage

Best, 
Roy 


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Re: saving a multi-image file programmatically

Nico Stuurman
Administrator
Hi Roy,

> However, while doing so I get an error message: "summary metadata not found or corrupt". From the Logfile:
>
> LOG(2012-10-18T14:23:02.920219, 7096, 00000000210867D0:): > Error: Couldn't find SlicesFirst or TimeFirst in summary metadata
> LOG(2012-10-18T14:23:02.920219, 7096, 00000000210867D0:): > Error: Summary metadata not found or corrupt.  Is this a Micro-Manager dataset?

I remember this error from a few days ago.  Are you using the very latest nightly build?

Best,

Nico


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Re: saving a multi-image file programmatically

Roy Wollman-2
In reply to this post by Roy Wollman-2
Hi Nico, 

I remember this error from a few days ago.  Are you using the very latest nightly build?

Yes. The previous error message was generated by the 20121016 and I just reproduced it with the 20121018 (64bit)

This matlab script snippet reproduces the error on the demo config:

%%%%
gui.openAcquisition('testing123',pathtosave,1,3, 1,true,true)
chnl={'DAPI','FITC','Cy5'};
for i=1:3
    mmc.setConfig(mmc.getChannelGroup,chnl{i});
    mmc.waitForConfig(mmc.getChannelGroup, chnl{i});
    gui.snapAndAddImage('testing123', 0, i-1, 0);
end
gui.closeAcquisition('testing123');
%%%%

I pasted below the entire log generated in case there is anything else hiding there. This is done with the demo camera, matlab interface where I added all the loci jars (4 of them) to the classpath. 

Thanks for your help, 

Best, 
Roy  



=================
LOG(2012-10-18T17:56:24.801684, 5708, 000000000FEA2190:): Device Z debug message: Reporting position
DBG(2012-10-18T17:56:24.804684, 5708, t:000000000FEA2190:) Configuration Channel/Cy5 applied.
DBG(2012-10-18T17:56:24.804684, 5708, t:000000000FEA2190:) Waiting for device Dichroic...
DBG(2012-10-18T17:56:24.804684, 5708, t:000000000FEA2190:) Finished waiting.
DBG(2012-10-18T17:56:24.804684, 5708, t:000000000FEA2190:) Waiting for device Emission...
DBG(2012-10-18T17:56:24.804684, 5708, t:000000000FEA2190:) Finished waiting.
DBG(2012-10-18T17:56:24.804684, 5708, t:000000000FEA2190:) Waiting for device Excitation...
DBG(2012-10-18T17:56:24.804684, 5708, t:000000000FEA2190:) Finished waiting.
LOG(2012-10-18T17:56:24.804684, 5708, 000000000FEA2190:): Auto-focus device set to Autofocus
LOG(2012-10-18T17:56:24.805684, 5708, 000000000FEA2190:): Device Z debug message: Reporting position
LOG(2012-10-18T17:56:24.807684, 5708, 000000000FEA2190:): Device Camera debug message: Reading property ScanMode
LOG(2012-10-18T17:56:24.807684, 5708, 000000000FEA2190:): Device Camera debug message: Reading property ScanMode
LOG(2012-10-18T17:56:24.808684, 5708, 000000000FEA2190:): System state cache updated.
LOG(2012-10-18T17:56:24.809684, 5708, 000000000FEA2190:): Channel group set to Channel
LOG(2012-10-18T17:56:24.809684, 5708, 000000000FEA2190:): Auto-focus device set to Autofocus
LOG(2012-10-18T17:56:24.809684, 5708, 000000000FEA2190:): Device Z debug message: Reporting position
DBG(2012-10-18T17:56:24.811684, 5708, t:000000000FEA2190:) Exposure set to 300.000 ms
DBG(2012-10-18T17:56:24.811684, 5708, t:000000000FEA2190:) Waiting for device Shutter...
DBG(2012-10-18T17:56:24.811684, 5708, t:000000000FEA2190:) Finished waiting.
DBG(2012-10-18T17:56:25.111701, 5708, t:000000000FEA2190:) Waiting for device Shutter...
DBG(2012-10-18T17:56:25.111701, 5708, t:000000000FEA2190:) Finished waiting.
DBG(2012-10-18T17:56:25.111701, 5708, t:000000000FEA2190:) Image acquired at 2012-10-18T17:56:25.111701
LOG(2012-10-18T17:56:25.113702, 5708, 000000000FEA2190:): > Error: Couldn't find SlicesFirst or TimeFirst in summary metadata
LOG(2012-10-18T17:56:25.113702, 5708, 000000000FEA2190:): > Error: Summary metadata not found or corrupt.  Is this a Micro-Manager dataset?
LOG(2012-10-18T17:56:25.571728, 5708, 000000000FEA2190:): > 
org.json.JSONException: Positions tag not found in summary metadata in Thread[main,5,main]
  at org.micromanager.utils.MDUtils.getNumPositions(MDUtils.java:114)
  at org.micromanager.acquisition.TaggedImageStorageMultipageTiff.processSummaryMD(TaggedImageStorageMultipageTiff.java:121)
  at org.micromanager.acquisition.TaggedImageStorageMultipageTiff.setSummaryMetadata(TaggedImageStorageMultipageTiff.java:302)
  at org.micromanager.acquisition.TaggedImageStorageMultipageTiff.<init>(TaggedImageStorageMultipageTiff.java:95)
  at org.micromanager.acquisition.TaggedImageStorageMultipageTiff.<init>(TaggedImageStorageMultipageTiff.java:79)
  at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
  at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
  at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
  at java.lang.reflect.Constructor.newInstance(Unknown Source)
  at org.micromanager.utils.ImageUtils.newImageStorageInstance(ImageUtils.java:369)
  at org.micromanager.acquisition.MMAcquisition.initialize(MMAcquisition.java:300)
  at org.micromanager.MMStudioMainFrame.snapAndAddImage(MMStudioMainFrame.java:4117)
  at org.micromanager.MMStudioMainFrame.snapAndAddImage(MMStudioMainFrame.java:4090)


LOG(2012-10-18T17:56:25.571728, 5708, 000000000FEA2190:): > Error: Summary metadata not found or corrupt.  Is this a Micro-Manager dataset?
LOG(2012-10-18T17:56:25.985751, 5708, 000000000FEA2190:): > 
org.json.JSONException: Positions tag not found in summary metadata in Thread[main,5,main]
  at org.micromanager.utils.MDUtils.getNumPositions(MDUtils.java:114)
  at org.micromanager.acquisition.TaggedImageStorageMultipageTiff.processSummaryMD(TaggedImageStorageMultipageTiff.java:121)
  at org.micromanager.acquisition.TaggedImageStorageMultipageTiff.<init>(TaggedImageStorageMultipageTiff.java:99)
  at org.micromanager.acquisition.TaggedImageStorageMultipageTiff.<init>(TaggedImageStorageMultipageTiff.java:79)
  at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
  at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
  at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
  at java.lang.reflect.Constructor.newInstance(Unknown Source)
  at org.micromanager.utils.ImageUtils.newImageStorageInstance(ImageUtils.java:369)
  at org.micromanager.acquisition.MMAcquisition.initialize(MMAcquisition.java:300)
  at org.micromanager.MMStudioMainFrame.snapAndAddImage(MMStudioMainFrame.java:4117)
  at org.micromanager.MMStudioMainFrame.snapAndAddImage(MMStudioMainFrame.java:4090)


LOG(2012-10-18T17:56:26.035754, 5708, 000000000FEA2190:): > 
java.lang.reflect.InvocationTargetException in Thread[main,5,main]
  at java.awt.EventQueue.invokeAndWait(Unknown Source)
  at javax.swing.SwingUtilities.invokeAndWait(Unknown Source)
  at org.micromanager.utils.GUIUtils.invokeAndWait(GUIUtils.java:181)
  at org.micromanager.acquisition.VirtualAcquisitionDisplay.show(VirtualAcquisitionDisplay.java:1966)
  at org.micromanager.acquisition.MMAcquisition.initialize(MMAcquisition.java:357)
  at org.micromanager.MMStudioMainFrame.snapAndAddImage(MMStudioMainFrame.java:4117)
  at org.micromanager.MMStudioMainFrame.snapAndAddImage(MMStudioMainFrame.java:4090)
Caused by: java.lang.NullPointerException
  at org.micromanager.acquisition.TaggedImageStorageMultipageTiff.lastAcquiredFrame(TaggedImageStorageMultipageTiff.java:360)
  at org.micromanager.acquisition.MMImageCache.lastAcquiredFrame(MMImageCache.java:97)
  at org.micromanager.acquisition.VirtualAcquisitionDisplay.startup(VirtualAcquisitionDisplay.java:554)
  at org.micromanager.acquisition.VirtualAcquisitionDisplay.access$2100(VirtualAcquisitionDisplay.java:64)
  at org.micromanager.acquisition.VirtualAcquisitionDisplay$18.run(VirtualAcquisitionDisplay.java:1969)
  at java.awt.event.InvocationEvent.dispatch(Unknown Source)
  at java.awt.EventQueue.dispatchEvent(Unknown Source)
  at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
  at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
  at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
  at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
  at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
  at java.awt.EventDispatchThread.run(Unknown Source)


LOG(2012-10-18T17:56:26.036754, 5708, 000000000FEA2190:): > Error: Can't find Prefix in summary metadata
DBG(2012-10-18T17:56:26.048755, 5708, t:000000000FEA2190:) Configuration Channel/DAPI applied.
DBG(2012-10-18T17:56:26.048755, 5708, t:000000000FEA2190:) Waiting for device Dichroic...
DBG(2012-10-18T17:56:26.048755, 5708, t:000000000FEA2190:) Finished waiting.
DBG(2012-10-18T17:56:26.048755, 5708, t:000000000FEA2190:) Waiting for device Emission...
DBG(2012-10-18T17:56:26.048755, 5708, t:000000000FEA2190:) Finished waiting.
DBG(2012-10-18T17:56:26.048755, 5708, t:000000000FEA2190:) Waiting for device Excitation...
DBG(2012-10-18T17:56:26.048755, 5708, t:000000000FEA2190:) Finished waiting.
LOG(2012-10-18T17:56:26.049755, 5708, 000000000FEA2190:): Auto-focus device set to Autofocus
LOG(2012-10-18T17:56:26.049755, 5708, 000000000FEA2190:): Device Z debug message: Reporting position
LOG(2012-10-18T17:56:26.050755, 5708, 000000000FEA2190:): Device Camera debug message: Reading property ScanMode
LOG(2012-10-18T17:56:26.050755, 5708, 000000000FEA2190:): Device Camera debug message: Reading property ScanMode
LOG(2012-10-18T17:56:26.051755, 5708, 000000000FEA2190:): System state cache updated.
LOG(2012-10-18T17:56:26.052755, 5708, 000000000FEA2190:): Channel group set to Channel
LOG(2012-10-18T17:56:26.052755, 5708, 000000000FEA2190:): Auto-focus device set to Autofocus
LOG(2012-10-18T17:56:26.052755, 5708, 000000000FEA2190:): Device Z debug message: Reporting position
DBG(2012-10-18T17:56:26.056755, 5708, t:000000000FEA2190:) Exposure set to 300.000 ms
DBG(2012-10-18T17:56:26.056755, 5708, t:000000000FEA2190:) Waiting for device Shutter...
DBG(2012-10-18T17:56:26.056755, 5708, t:000000000FEA2190:) Finished waiting.
DBG(2012-10-18T17:56:26.355773, 5708, t:000000000FEA2190:) Waiting for device Shutter...
DBG(2012-10-18T17:56:26.355773, 5708, t:000000000FEA2190:) Finished waiting.
DBG(2012-10-18T17:56:26.355773, 5708, t:000000000FEA2190:) Image acquired at 2012-10-18T17:56:26.355773
DBG(2012-10-18T17:56:26.370773, 5708, t:000000000FEA2190:) Configuration Channel/FITC applied.
DBG(2012-10-18T17:56:26.370773, 5708, t:000000000FEA2190:) Waiting for device Dichroic...
DBG(2012-10-18T17:56:26.370773, 5708, t:000000000FEA2190:) Finished waiting.
DBG(2012-10-18T17:56:26.370773, 5708, t:000000000FEA2190:) Waiting for device Emission...
DBG(2012-10-18T17:56:26.370773, 5708, t:000000000FEA2190:) Finished waiting.
DBG(2012-10-18T17:56:26.370773, 5708, t:000000000FEA2190:) Waiting for device Excitation...
DBG(2012-10-18T17:56:26.370773, 5708, t:000000000FEA2190:) Finished waiting.
LOG(2012-10-18T17:56:26.371774, 5708, 000000000FEA2190:): Auto-focus device set to Autofocus
LOG(2012-10-18T17:56:26.371774, 5708, 000000000FEA2190:): Device Z debug message: Reporting position
LOG(2012-10-18T17:56:26.372774, 5708, 000000000FEA2190:): Device Camera debug message: Reading property ScanMode
LOG(2012-10-18T17:56:26.372774, 5708, 000000000FEA2190:): Device Camera debug message: Reading property ScanMode
LOG(2012-10-18T17:56:26.373774, 5708, 000000000FEA2190:): System state cache updated.
LOG(2012-10-18T17:56:26.378774, 5708, 000000000FEA2190:): Channel group set to Channel
LOG(2012-10-18T17:56:26.378774, 5708, 000000000FEA2190:): Auto-focus device set to Autofocus
LOG(2012-10-18T17:56:26.378774, 5708, 000000000FEA2190:): Device Z debug message: Reporting position
DBG(2012-10-18T17:56:26.386774, 5708, t:000000000FEA2190:) Exposure set to 300.000 ms
DBG(2012-10-18T17:56:26.386774, 5708, t:000000000FEA2190:) Waiting for device Shutter...
DBG(2012-10-18T17:56:26.386774, 5708, t:000000000FEA2190:) Finished waiting.
DBG(2012-10-18T17:56:26.685791, 5708, t:000000000FEA2190:) Waiting for device Shutter...
DBG(2012-10-18T17:56:26.685791, 5708, t:000000000FEA2190:) Finished waiting.
DBG(2012-10-18T17:56:26.685791, 5708, t:000000000FEA2190:) Image acquired at 2012-10-18T17:56:26.685791


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Re: saving a multi-image file programmatically

Nico Stuurman
Administrator
In reply to this post by Nico Stuurman
Hi Roy,

>> As a note, the doxygen docs are probably out of date, a few methods that I found related to the new TaggedImage classes (core.getTaggedImage) where not there.

Arthur updated our code generating documentation and there is now a link on the website to the Java version of the Core API at:

https://valelab.ucsf.edu/~MM/doc/mmcorej/mmcorej/CMMCore.html

Best,

Nico
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Re: saving a multi-image file programmatically

Roy Wollman-2
In reply to this post by Nico Stuurman
Thanks!

Just for future users, I figured out how to get around the error message I was getting.

After  the call:   
>> gui.openAcquisition(...)

I get the image cache with 

>> imgcache = acq.getImageCache;


and use the summary date I get from that to set the acqusition summary: 

>> gui.setAcquisitionSummary(acqname,imgcache.getSummaryMetadata)


That seems to do that trick... I guess since I wasn't using the the acquisition engine before but directly calling the snapAndAddImage something about the metadata didn't get updated.  


Thanks for your help, 


Best, 

Roy 


--

Roy Wollman, PhD

University of California - San Diego
Department Chemistry and Biochemistry & 
San Diego Center for Systems Biology

Room 5202 Urey Hall, 9500 Gilman Drive 

La Jolla, CA 92093-0356
Lab Phone: 858-224-2249
E-mail: [hidden email]
http://wollmanlab.ucsd.edu




On Fri, Oct 19, 2012 at 5:38 PM, Nico Stuurman <[hidden email]> wrote:
Hi Roy,

>> As a note, the doxygen docs are probably out of date, a few methods that I found related to the new TaggedImage classes (core.getTaggedImage) where not there.

Arthur updated our code generating documentation and there is now a link on the website to the Java version of the Core API at:

https://valelab.ucsf.edu/~MM/doc/mmcorej/mmcorej/CMMCore.html

Best,

Nico
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Re: saving a multi-image file programmatically

Nico Stuurman
Administrator
Hi Roy,

I think that I now fixed this problem (thanks for finding the work-around, that helped a lot in finding the bug)!  In the next nightly build you should no longer need the work-around.

Best,

Nico


On Oct 19, 2012, at 6:16 PM, Roy Wollman wrote:

Thanks!

Just for future users, I figured out how to get around the error message I was getting.

After  the call:   
>> gui.openAcquisition(...)

I get the image cache with 

>> imgcache = acq.getImageCache;

and use the summary date I get from that to set the acqusition summary: 
>> gui.setAcquisitionSummary(acqname,imgcache.getSummaryMetadata)

That seems to do that trick... I guess since I wasn't using the the acquisition engine before but directly calling the snapAndAddImage something about the metadata didn't get updated.  

Thanks for your help, 

Best, 
Roy 

--
Roy Wollman, PhD
University of California - San Diego
Department Chemistry and Biochemistry & 
San Diego Center for Systems Biology
Room 5202 Urey Hall, 9500 Gilman Drive 
La Jolla, CA 92093-0356
Lab Phone: 858-224-2249
E-mail: [hidden email]
http://wollmanlab.ucsd.edu




On Fri, Oct 19, 2012 at 5:38 PM, Nico Stuurman <[hidden email]> wrote:
Hi Roy,

>> As a note, the doxygen docs are probably out of date, a few methods that I found related to the new TaggedImage classes (core.getTaggedImage) where not there.

Arthur updated our code generating documentation and there is now a link on the website to the Java version of the Core API at:

https://valelab.ucsf.edu/~MM/doc/mmcorej/mmcorej/CMMCore.html

Best,

Nico
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