loci_tools.jar missing
bpavie opened this issue · 1 comments
bpavie commented
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