Re: [micro-manager-general] Access live image from Matlab

[Kyle D. <kyl...@gm...>]

Hi Vanessa,

I did a bit more digging. It seems that accessing Java nested classes and
enums (SaveMode is a nested enum) from within MATLAB requires a bit of
trickery.

According to this MATLAB Answers thread (
https://www.mathworks.com/matlabcentral/answers/15711-how-do-i-access-a-java-inner-class-from-matlab),
you should be able to get the value encoded by MULTIPAGE_TIFF using
MATLAB's javaMethod(...). Try the following:

MULTIPAGE_TIFF = javaMethod('valueOf',
'org.micromanager.data.Datastore$SaveMode', 'MULTIPAGE_TIFF')

(If that doesn't work, try changing the dollar sign to a period.)

I think most of your difficulties are coming from how MATLAB accesses Java
objects, but hopefully we can find a workaround.

Best,
Kyle

On Tue, Jun 19, 2018, 18:48 Vanessa King <van...@gm...> wrote:

> I've tried your suggestion of using the full package name, but this
> continued to give the same error. I also tried importing
> org.micromanager.data.Datastore.SaveMode prior to the save function, but
> this failed as well. Matlab did not recognize it as a valid import
> statement, saying that it was not a fully qualified class name. Just in
> case, I also tried using the javaObject(...) method, but this gave an error
> saying that org.micromanager.data.Datastore.SaveMode.MULTIPAGE_TIFF is not
> on the Java class path.
>
> So it appears that this is an import issue. I double checked my static
> Java class path, and it definitely contains all .jar files in the plugins
> folder and the ij.jar from outside the plugins folder. My script currently
> has no issue importing and using all of:
>
> import mmcorej.*
>
> import org.micromanager.data.Datastore;
>
> import org.micromanager.data.Image;
>
> import java.util.List;
>
> import org.micromanager.SnapLiveManager;
>
> I don't see why the class path to SaveMode cannot be found by Matlab but
> the Datastore class path can be. Any more ideas as to what could be causing
> this error or other options I could try would be greatly appreciated!
>
> Thanks,
> Vanessa
>
> On Tue, Jun 19, 2018 at 6:37 AM, Kyle Douglass <kyl...@gm...>
> wrote:
>
>> Hi Vanessa,
>>
>> On Mon, Jun 18, 2018 at 8:52 PM, Vanessa King <van...@gm...>
>> wrote:
>>
>>> Thanks for the help Kyle,
>>>
>>
>> You're welcome!
>>
>>
>>>
>>> However, I am now running into issues while trying to use the save the
>>> datastore. Following the example from the version 2.0 How Do I... page, I
>>> am using store.save(Datastore.SaveMode.MULTIPAGE_TIFF, savePath);
>>> But this throws the error:
>>>
>>> Undefined function or variable 'SaveMode'.
>>>
>>> Error in Focus>pushbutton4_Callback (line 302)
>>> store.save(Datastore.SaveMode.MULTIPAGE_TIFF, savePath);
>>>
>>>
>> According to the Javadocs (
>> https://valelab4.ucsf.edu/~MM/doc-2.0.0-beta2/mmstudio/org/micromanager/data/Datastore.html),
>> SaveMode is a static Java enum nested inside the Datastore class, so you
>> shouldn't need to initialize it using MATLAB's javaObject(...) method. This
>> means that the way you're using it in MATLAB appears correct.
>>
>> However according to this StackOverflow question (
>> https://stackoverflow.com/questions/1223795/using-java-enums-or-public-static-fields-in-matlab)
>> it looks like you may need to access the enum constant named MULTIPAGE_TIFF
>> using the full package name. Try changing Datastore.SaveMode.MULTIPAGE_TIFF
>> to org.micromanager.data.Datastore.SaveMode.MULTIPAGE_TIFF. Or, try
>> adding the import org.micromanager.data.Datastore; statement back to your
>> script if you removed it from the last iteration.
>>
>> Write back if you make any progress.
>> Cheers,
>> Kyle
>>
>>
>>
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>
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