Open bpavie opened 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/ )
loci_tools.jar
[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
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.
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/ )