Heap space error

[yoda-vid]

While loading a relatively large, multi-series CZI file, I encountered a Java heap space error in formatreader.get_omexml_metadata. The call worked fine in Python-Bioformats v.1.1.0, and I noticed it on the current release (v.1.3.2) but can reproduce it with v.1.2.0 (all tested with Javabridge 1.0.15).

Normally I initialize with 8GB of Java heap space. I tried increasing to 16 and then 30GB to no avail. Processor usages also rises very high with all cores running for several minutes before the error.

Here's the stacktrace when running on v.1.2.0 (similar on v.1.3.2):

  File "/home/ec2-user/miniconda3/envs/clr2/lib/python3.6/site-packages/bioformats/formatreader.py", line 1025, in get_omexml_metadata
    xml = jutil.run_script(script, dict(path=rdr.path, reader = rdr.rdr))
  File "/home/ec2-user/miniconda3/envs/clr2/lib/python3.6/site-packages/javabridge/jutil.py", line 384, in run_script
    scope, script, "<java-python-bridge>", 0, None)
  File "/home/ec2-user/miniconda3/envs/clr2/lib/python3.6/site-packages/javabridge/jutil.py", line 887, in call
    result = fn(*nice_args)
  File "/home/ec2-user/miniconda3/envs/clr2/lib/python3.6/site-packages/javabridge/jutil.py", line 854, in fn
    raise JavaException(x)
javabridge.jutil.JavaException: Java heap space

I didn't see any changes in formatreader between v.1.1.0 and v.1.2.0, but could it be related to the change in loci_tools?

Thanks.