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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 missing #456

Open bpavie opened 8 months ago

bpavie commented 8 months ago

Pims cannot download loci_tools.jar when using bioformat, it seems it does not exist since version version 6.9 of bioformat: (see https://downloads.openmicroscopy.org/bio-formats/6.9.0/artifacts/ )

[c:\GBW_MyPrograms\mambaforge\envs\trackpy\lib\site-packages\pims\bioformats.py:50](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:50): UserWarning: loci_tools.jar not found, downloading
  warn('loci_tools.jar not found, downloading')
---------------------------------------------------------------------------
HTTPError                                 Traceback (most recent call last)
Cell In[2], [line 1](vscode-notebook-cell:?execution_count=2&line=1)
----> [1](vscode-notebook-cell:?execution_count=2&line=1) frames = pims.Bioformats('C:\\Users\\u0094799\\Documents\\Projects\\Leuven\\Marlies_leysen\\2024_01\\Image 17_PBS_Airyscan Processing.czi')
      [2](vscode-notebook-cell:?execution_count=2&line=2) frames

File [c:\GBW_MyPrograms\mambaforge\envs\trackpy\lib\site-packages\pims\bioformats.py:335](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:335), in BioformatsReader.__init__(self, filename, meta, java_memory, read_mode, series)
    [332](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:332) if not jpype.isJVMStarted():
    [333](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:333)     from distutils.version import LooseVersion
--> [335](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:335)     loci_path = _find_jar()
    [336](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:336)     # If we can turn off string auto-conversion, do so,
    [337](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:337)     # since this is the recommended practice.
    [338](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:338)     if LooseVersion(jpype.__version__) >= LooseVersion('0.7.0'):

File [c:\GBW_MyPrograms\mambaforge\envs\trackpy\lib\site-packages\pims\bioformats.py:51](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:51), in _find_jar()
     [48](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:48)         return os.path.join(loc, 'loci_tools.jar')
     [50](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:50) warn('loci_tools.jar not found, downloading')
---> [51](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:51) return download_jar()

File [c:\GBW_MyPrograms\mambaforge\envs\trackpy\lib\site-packages\pims\bioformats.py:78](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:78), in download_jar(version)
     [74](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:74) url = ('http://downloads.openmicroscopy.org/bio-formats/' + version +
     [75](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:75)        '/artifacts/loci_tools.jar')
     [77](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:77) path = os.path.join(loc, 'loci_tools.jar')
---> [78](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:78) loci_tools = urlopen(url).read()
     [79](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/site-packages/pims/bioformats.py:79) sha1_checksum = urlopen(url + '.sha1').read().split(b' ')[0].decode()
...
File [c:\GBW_MyPrograms\mambaforge\envs\trackpy\lib\urllib\request.py:641](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/urllib/request.py:641), in HTTPDefaultErrorHandler.http_error_default(self, req, fp, code, msg, hdrs)
    [640](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/urllib/request.py:640) def http_error_default(self, req, fp, code, msg, hdrs):
--> [641](file:///C:/GBW_MyPrograms/mambaforge/envs/trackpy/lib/urllib/request.py:641)     raise HTTPError(req.full_url, code, msg, hdrs, fp)

HTTPError: HTTP Error 404: Not Found
joshmoore commented 8 months ago

Please see #403. loci_tools.jar has been deprecated for some time and was eventually removed due to security vulnerabilities in the third-party logging library.