Open Microscopy Environment

Hi all,

I ran into a problem when trying to add the OIB -> OME-TIFF converter (https://www.openmicroscopy.org/site/sup ... rsion.html) to my workflow in Matlab (R2013 in Ubuntu 14.04) as a new user to OME.

I managed to get the FileConvert.java finally compiled (by downgrading my default JDK) so that it was accessible by Matlab without the

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"java.lang.UnsupportedClassVersionError: FileConvert: Unsupported major.minor version 51.0"

error due to my default JDK being 1.7.xx in Ubuntu while the Matlab still wanted the 1.6.xx (Major version 51.0).

However now I got the following error which I do not understand really as I am not that familiar with Java (and using Java files in Matlab) when I try to create an instance to the FileConvert

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>> i = FileConvert()
No constructor 'FileConvert' with matching signature found.

Which according to this (http://undocumentedmatlab.com/blog/java ... s-pitfalls) would be due to non-public class but this does not seem to be the case with FileConvert.java, so any idea of how to get the converter working in Matlab?

Thanks

Hi,

the default constructor of the FileConvert class assuming you didn't modify it is:

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  public FileConvert(String inputFile, String outputFile) {


So you are likely missing the input and output arguments to construct the object. Could you try something like:

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converted = FileConvert('/path/to/input_file' ,'/path/to/output_file');
converter.convert()


If that does not work out of the box, you may try to cast the MATLAB strings as Java strings, e.g.

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converted = FileConvert(java.lang.String('/path/to/input_file'), java.lang.String('/path/to/output_file'));


Let us know if the solution above does not work.
Best,
Sebastien

Thank you Sebastian for your quick reply,

That indeed did the trick of getting the system of doing something, as this:

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filenameFull = '~/Desktop/CP-20150323-TR70-mouse2-1-son.oib'
filenameFullTIF = '~/Desktop/CP-20150323-TR70-mouse2-1-son.tif'

converted = FileConvert(java.lang.String(filenameFull), java.lang.String(filenameFullTIF))


Returns me this:

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converted = FileConvert@6c4bc43a

with no conversion taking place, as no TIF file was saved?

Hi,

thanks for the update. Indeed

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converted = FileConvert(java.lang.String(filenameFull), java.lang.String(filenameFullTIF))


solely initializes a FileConvert object. To perform the conversion operation, you will need to invoke the convert method:

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converted.convert()


Best,
Sebastien