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Mouse-Imaging-Centre / pyminc

A python interface to the MINC 2 library, allowing use of numpy arrays to access MINC data, and other such similar goodies, developed by Jason Lerch
http://en.wikibooks.org/wiki/MINC/Tutorials
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exception with malformed minc file doesn't bubble up to show which file is bad #38

Open gdevenyi opened 3 years ago

gdevenyi commented 3 years ago

An interrupted mincresample etc on Niagara sometimes generates broken minc files, which later on break voxel_vote:

/project/m/mchakrav/quarantine/2019b/minc-toolkit/1.9.18/src/minc-toolkit-v2/libminc/libsrc2/volume.c:1420 (from MINC): Error: Trying to open minc file without image variable
Traceback (most recent call last):
  File "/project/m/mchakrav/quarantine/2019b/minc-stuffs/0.1.24/install/bin/voxel_vote", line 4, in <module>
    __import__('pkg_resources').run_script('python-stuffs==0.1.24', 'voxel_vote')
  File "/scinet/intel/2019u4/intelpython3/lib/python3.6/site-packages/pkg_resources/__init__.py", line 658, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/scinet/intel/2019u4/intelpython3/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1445, in run_script
    exec(script_code, namespace, namespace)
  File "/project/m/mchakrav/quarantine/2019b/minc-stuffs/0.1.24/install/lib/python3.6/site-packages/python_stuffs-0.1.24-py3.6.egg/EGG-INFO/scripts/voxel_vote", line 32, in <module>
  File "/gpfs/fs0/project/m/mchakrav/gdevenyi/quarantine/2019b/pyminc/0.51/install/lib/python3.6/site-packages/pyminc-0.51-py3.6.egg/pyminc/volumes/factory.py", line 8, in volumeFromFile
  File "/gpfs/fs0/project/m/mchakrav/gdevenyi/quarantine/2019b/pyminc/0.51/install/lib/python3.6/site-packages/pyminc-0.51-py3.6.egg/pyminc/volumes/volumes.py", line 552, in openFile
  File "/gpfs/fs0/project/m/mchakrav/gdevenyi/quarantine/2019b/pyminc/0.51/install/lib/python3.6/site-packages/pyminc-0.51-py3.6.egg/pyminc/volumes/volumes.py", line 21, in testMincReturn
pyminc.volumes.volumes.mincException
/project/m/mchakrav/quarantine/2019b/minc-toolkit/1.9.18/src/minc-toolkit-v2/libminc/libsrc2/volume.c:1613 (from MINC): Error: Trying to close null volume
Exception ignored in: <bound method mincVolume.__del__ of <pyminc.volumes.volumes.mincVolume object at 0x2af42ee6b2b0>>
Traceback (most recent call last):
  File "/gpfs/fs0/project/m/mchakrav/gdevenyi/quarantine/2019b/pyminc/0.51/install/lib/python3.6/site-packages/pyminc-0.51-py3.6.egg/pyminc/volumes/volumes.py", line 781, in __del__
  File "/gpfs/fs0/project/m/mchakrav/gdevenyi/quarantine/2019b/pyminc/0.51/install/lib/python3.6/site-packages/pyminc-0.51-py3.6.egg/pyminc/volumes/volumes.py", line 768, in closeVolume
  File "/gpfs/fs0/project/m/mchakrav/gdevenyi/quarantine/2019b/pyminc/0.51/install/lib/python3.6/site-packages/pyminc-0.51-py3.6.egg/pyminc/volumes/volumes.py", line 21, in testMincReturn
pyminc.volumes.volumes.mincException: 
Traceback (most recent call last):
  File "/scratch/m/mlepage/marikhal/LAM/MAGeTbrain/bin/mb", line 792, in <module>
    main()
  File "/scratch/m/mlepage/marikhal/LAM/MAGeTbrain/bin/mb", line 220, in main
    options.func(options)
  File "/scratch/m/mlepage/marikhal/LAM/MAGeTbrain/bin/mb", line 329, in command_run
    p.run()
  File "/scratch/m/mlepage/marikhal/LAM/MAGeTbrain/bin/mb", line 608, in run
    self.queue.run(stages=self._get_stage_order())
  File "/scratch/m/mlepage/marikhal/LAM/MAGeTbrain/bin/mb", line 508, in run
    self.parallel(self.commands[stage])
  File "/scratch/m/mlepage/marikhal/LAM/MAGeTbrain/bin/mb", line 514, in parallel
    self.execute(command, input='\n'.join(commands))
  File "/scratch/m/mlepage/marikhal/LAM/MAGeTbrain/bin/mb", line 492, in execute
    raise Exception("Returns %i :: %s" % (proc.returncode, command))
Exception: Returns 1 :: parallel -j8