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

[Vanessa K. <van...@gm...>]

Hi Kyle,

Your suggestion here worked, I can now save images just fine using the line
you provided. Thank you for the help!

Vanessa

On Tue, Jun 19, 2018 at 1:52 PM, Kyle Douglass <kyl...@gm...>
wrote:

> 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
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> micro-manager-general mailing list
>>> mic...@li...
>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>
>>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>> _________________________________________
>> micro-manager-general mailing list
>> mic...@li...
>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> micro-manager-general mailing list
> mic...@li...
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>