Open Microscopy Environment

I tried to use `loci.formats.tools.TiffComment`from Bio-Formats MATLAB toolbox and realized that `loci.formats` and `loci.common` are both empty in 5.9.2 by checking the content of the `bioformats_package.jar` file with Java Decompiler. They were there in 5.9.1. I can't really find an announcement about deprecation of them.

The command line tools also include `bioformats_package.jar`, but this apparently still contains both `loci.formats` and `loci.common`. Aren't they meant to be the same?

Hi Kouichi,

There was no change on the class packaging in 5.9.2.

How did you download the artifacts? Retrieving for instance the Bio-Formats MATLAB bundle from the official downloads page, I can confirm all the classes are available within the 30MB JAR:

Code: Select all

sbesson@ls30630:tmp $ wget -q http://downloads.openmicroscopy.org/bio-formats/5.9.2/artifacts/bfmatlab.zip
sbesson@ls30630:tmp $ unzip -q bfmatlab.zip
sbesson@ls30630:tmp $ jar tf bfmatlab/bioformats_package.jar | grep loci/formats
...
sbesson@ls30630:tmp $ jar tf bfmatlab/bioformats_package.jar | grep loci/formats | wc
     563     563   21955
sbesson@ls30630:tmp $ jar tf bfmatlab/bioformats_package.jar | grep loci/common | wc
      63      63    2121


Best,
Sebastien

Maybe I should've tested it earlier, but downloading the same 5.9.2 matlab toolbox again, the jar file contained the TiffComment class.

On a related note, `loci.formats.tools.TiffComment` class is not found in 5.9.2 documentation. I can find it in 5.1.10, but not in 5.2.1 and up. Is this on purpose?
https://downloads.openmicroscopy.org/bi ... frame.html
https://downloads.openmicroscopy.org/bi ... frame.html

Hi Kouichi
Thanks for spotting it,
This is definitely not intentional. We worked on our build system for the doc and it seems that some packages got inadvertently ignored.
We will need to review that.


Cheers
Jmarie

Good to hear that. This was part of the reasons why I thought these classes might be being deprecated.