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soft-matter / pims

Python Image Sequence: Load video and sequential images in many formats with a simple, consistent interface.
http://soft-matter.github.io/pims/
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loci_tools.jar issue #426

Open perdigao1 opened 2 years ago

perdigao1 commented 2 years ago

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 commented 1 year ago

You could try branch https://github.com/soft-matter/pims/pull/403 (using bioformats_package.jar instead of loci_tools.jar)

jstriebel commented 1 year ago

@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