Re: Use BioFormat in java

Posted by ctrueden on Oct 17, 2017; 3:18pm
URL: http://imagej.273.s1.nabble.com/Use-BioFormat-in-java-tp5019558p5019559.html

Hi Philippe,

> this code is already not compiling as soon as it finds either one of
> the two Bio-formats imports

I have created and pushed a repository with a sample Maven project that
uses Bio-Formats 5.1.0 + ImageJ 1.x + Java 6:
    https://github.com/imagej/example-bio-formats-legacy-plugin

> I tried to write a java code that would retrieve the X and Y
> calibration values and symbols from a stack of pictures.

Is there some reason you need Bio-Formats specifically, rather than
examining the Calibration of the ImagePlus?

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
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On Tue, Oct 17, 2017 at 8:09 AM, Philippe CARL <[hidden email]>
wrote:

> Dear all,
>
> I’m using the last version of ImageJ (1.51r) running under Java 1.6.0_24
> (64-bit) and using the Bio-formats 5.1.10 (which seems to be the last
> version running with java < 1.7).
>
> With this configuration, I tried to write a java code that would retrieve
> the X and Y calibration values and symbols from a stack of pictures.
>
> Thus I started with something quite easy at the beginning, by trying to
> make
> run the code found under the following link (which should actually be
> formatted for the version 5.1.10 of the Bio-formats):
>
> https://github.com/openmicroscopy/bioformats/blob/v5.1.10/
> components/bio-for
> mats-plugins/utils/Simple_Read.java
> <https://github.com/openmicroscopy/bioformats/blob/v5.1.10/components/bio-formats-plugins/utils/Simple_Read.java>
>
> But this code is already not compiling as soon as it finds either one of
> the
> two Bio-formats imports, i.e.:
>
> import loci.formats.FormatException;
>
> or
>
> import loci.plugins.BF;
>
> For trying to solve this issue, I moved the "bioformats_package.jar" file
> from the "plugins" into the "plugins/jars" folder, but this had no effect.
>
> What am I doing wrong?
>
> Also I have the impression that it is quite easy to use the bio-formats
> within a macro code, but once moving to java there are way more issues
> which
> are as well connected with the library version. Am I right with this?
>
> I thank you very much in advance for your answers and help.
>
> My best regards,
>
> Philippe
>
>
>
> Philippe CARL
>
> Laboratoire de Biophotonique et Pharmacologie
>
> UMR 7213 CNRS - Université de Strasbourg
>
> Faculté de Pharmacie
>
> 74 route du Rhin
>
> 67401 ILLKIRCH
>
> Tel : [phone]
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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