We're Hiring!

What happened to loci.formats in 5.9.2?

Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats
Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

What happened to loci.formats in 5.9.2?

Postby Kouichi_C_Nakamura » Wed Nov 14, 2018 11:56 am

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?
Kouichi_C_Nakamura
 
Posts: 165
Joined: Thu Oct 19, 2017 1:35 pm

Re: What happened to loci.formats in 5.9.2?

Postby sbesson » Wed Nov 14, 2018 12:08 pm

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
User avatar
sbesson
Team Member
 
Posts: 421
Joined: Tue Feb 28, 2012 7:20 pm

Re: What happened to loci.formats in 5.9.2?

Postby Kouichi_C_Nakamura » Wed Nov 14, 2018 1:29 pm

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
Kouichi_C_Nakamura
 
Posts: 165
Joined: Thu Oct 19, 2017 1:35 pm

Re: What happened to loci.formats in 5.9.2?

Postby jburel » Thu Nov 15, 2018 2:47 pm

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
User avatar
jburel
Team Member
 
Posts: 348
Joined: Thu May 21, 2009 6:38 pm
Location: dundee

Re: What happened to loci.formats in 5.9.2?

Postby Kouichi_C_Nakamura » Thu Nov 15, 2018 3:51 pm

Good to hear that. This was part of the reasons why I thought these classes might be being deprecated.
Kouichi_C_Nakamura
 
Posts: 165
Joined: Thu Oct 19, 2017 1:35 pm


Return to User Discussion [Legacy]

Who is online

Users browsing this forum: No registered users and 1 guest