loci_tools.jar issue

[perdigao1]

Example code

import pims
image = pims.bioformats.BioformatsReader(somefilename)

And error messages that spit out

UserWarning: loci_tools.jar not found, downloading
  warn('loci_tools.jar not found, downloading')

...

HTTPError: HTTP Error 404: Not Found

Note here:

File [...]\site-packages\pims\bioformats.py:78, in download_jar(version)
74 url = ('http://downloads.openmicroscopy.org/bio-formats/' + version +
75 '/artifacts/loci_tools.jar')

which points to https://downloads.openmicroscopy.org/bio-formats/6.10.1/artifacts/loci_tools.jar , but this file/url does not exist

Please fix

[GenevieveBuckley]

You could try branch #403 (using bioformats_package.jar instead of loci_tools.jar)

[jstriebel]

@perdigao1 You can also download an older version of bioformats which still contains the loci_tools.jar. The newest working version seems to be 6.7.0. We use such a workaround here:
https://github.com/scalableminds/webknossos-libs/blob/1d4831dd00862de7ee634137f5bbeaf0ba4c10e8/webknossos/webknossos/dataset/_utils/pims_images.py#L251-L258