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Dana-Farber-AIOS / pathml

Tools for computational pathology
https://pathml.org
GNU General Public License v2.0
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MultiparametricSlide java #23

Closed jacob-rosenthal closed 4 years ago

jacob-rosenthal commented 4 years ago

I am able to import bioformats and javabridge, although javabridge.start_vm(class_path=bioformats.JARS) fails. This error should be caught so that we can give a message to the user telling them how to resolve

On MacOS 10.15.4

>>> from pathml.preprocessing.multiparametricslide import MultiparametricSlide
Could not find Java JRE compatible with x86_64 architecture
>>> wsi = MultiparametricSlide(path = "tests/testdata/smalltif.tif")
Could not find Java JRE compatible with x86_64 architecture
Could not find Java JRE compatible with x86_64 architecture
Traceback (most recent call last):
  File "/Users/jacobrosenthal/.conda/envs/pathml/lib/python3.7/site-packages/javabridge/jutil.py", line 114, in _find_mac_lib
    cmd = ["find", os.path.dirname(jvm_dir), "-name", library+extension]
  File "/Users/jacobrosenthal/.conda/envs/pathml/lib/python3.7/posixpath.py", line 156, in dirname
    p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not NoneType
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "/Users/jacobrosenthal/.conda/envs/pathml/lib/python3.7/site-packages/javabridge/jutil.py", line 278, in start_thread
    library_path = _find_mac_lib("libjvm")
  File "/Users/jacobrosenthal/.conda/envs/pathml/lib/python3.7/site-packages/javabridge/jutil.py", line 125, in _find_mac_lib
    (cmd, library), exc_info=1)
UnboundLocalError: local variable 'cmd' referenced before assignment
Failed to create Java VM
Traceback (most recent call last):
  File "/Users/jacobrosenthal/.conda/envs/pathml/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3331, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-3-81b83c29b5ca>", line 1, in <module>
    wsi = MultiparametricSlide(path = "tests/testdata/smalltif.tif")
  File "/Users/jacobrosenthal/PycharmProjects/pathml/pathml/preprocessing/multiparametricslide.py", line 46, in __init__
    javabridge.start_vm(class_path=bioformats.JARS)
  File "/Users/jacobrosenthal/.conda/envs/pathml/lib/python3.7/site-packages/javabridge/jutil.py", line 319, in start_vm
    raise RuntimeError("Failed to start Java VM")
RuntimeError: Failed to start Java VM
jacob-rosenthal commented 4 years ago

Solved by exporting JAVA_HOME variable:

import os
os.environ["JAVA_HOME"] = '/Library/Java/JavaVirtualMachines/jdk1.8.0_261.jdk/Contents/Home'

Will try to put this info in a useful error message

jacob-rosenthal commented 4 years ago

The Could not find Java JRE compatible with x86_64 architecture message comes from the logger (see here). After looking around for a little while, can't find how to capture log messages. In the meantime, will add a check to the imports that looks for JAVA_HOME in environment variables