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pnlbwh / pnlpipe

A Python-based framework for processing anatomical (T1, T2) and diffusion weighted images
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Error message from pnlpipe3/lib/python3.6/warnings.py #13

Closed tashrifbillah closed 5 years ago

tashrifbillah commented 6 years ago

See https://github.com/python/cpython/pull/10343

Build against Tashrif's PR until the PR is merged.

tashrifbillah commented 6 years ago

Looks like there is no build step for warnings.py. We shall probably open up an issue here and direct users to that.

The issue on https://github.com/python/cpython/pull/10343, has been told to show a way to reproduce error, which might not be easy.

tashrifbillah commented 6 years ago 
2018-11-06 09:51:27,314 /home/tb571/Downloads/pnlpipe/pnlscripts/wmql.py DEBUG  Running ['/home/tb571/Downloads/pnlpipe/soft_dir/tract_querier-c57d670/scripts/tract_math', '/home/tb571/Downloads/pnlpipe/_data/003_GNX_007/Ukf-003_GNX_007-761f2a551e.vtk', 'tract_remove_short_tracts', '2', '/tmp/tmpq2z9fmfc/ukfpruned.vtk']
Traceback (most recent call last):
  File "/home/tb571/Downloads/pnlpipe/soft_dir/tract_querier-c57d670/scripts/tract_math", line 115, in main
    tractography, *args.operation_parameters)
  File "/home/tb571/Downloads/pnlpipe/soft_dir/tract_querier-c57d670/tract_querier/tract_math/decorator.py", line 141, in wrapper
    process_output(out, file_output=file_output)
  File "/home/tb571/Downloads/pnlpipe/soft_dir/tract_querier-c57d670/tract_querier/tract_math/decorator.py", line 176, in process_output
    tractography_to_file(file_output, output)
  File "/home/tb571/Downloads/pnlpipe/soft_dir/tract_querier-c57d670/tract_querier/tractography/__init__.py", line 85, in tractography_to_file
    return tractography_to_vtk_file(filename, tractography, **kwargs)
  File "/home/tb571/Downloads/pnlpipe/soft_dir/tract_querier-c57d670/tract_querier/tractography/vtkInterface.py", line 29, in tractography_to_vtk_file
    tractography.tracts_data()
  File "/home/tb571/Downloads/pnlpipe/soft_dir/tract_querier-c57d670/tract_querier/tractography/vtkInterface.py", line 324, in write_vtkPolyData
    poly_data = tracts_to_vtkPolyData(tracts, tracts_data=tracts_data)
  File "/home/tb571/Downloads/pnlpipe/soft_dir/tract_querier-c57d670/tract_querier/tractography/vtkInterface.py", line 267, in tracts_to_vtkPolyData
    vtk_ids = ns.numpy_to_vtkIdTypeArray(ids, deep=True)
  File "/home/tb571/miniconda3/envs/pnlpipe3/lib/python3.6/site-packages/vtk/util/numpy_support.py", line 198, in numpy_to_vtkIdTypeArray
    return numpy_to_vtk(num_array, deep, vtk.VTK_ID_TYPE)
  File "/home/tb571/miniconda3/envs/pnlpipe3/lib/python3.6/site-packages/vtk/util/numpy_support.py", line 137, in numpy_to_vtk
    assert not numpy.issubdtype(z.dtype, complex), \
  File "/home/tb571/miniconda3/envs/pnlpipe3/lib/python3.6/site-packages/numpy/core/numerictypes.py", line 743, in issubdtype
    FutureWarning, stacklevel=2
  File "/home/tb571/miniconda3/envs/pnlpipe3/lib/python3.6/warnings.py", line 101, in _showwarnmsg
    _showwarnmsg_impl(msg)
  File "/home/tb571/miniconda3/envs/pnlpipe3/lib/python3.6/warnings.py", line 28, in _showwarnmsg_impl
    text = _formatwarnmsg(msg)
  File "/home/tb571/miniconda3/envs/pnlpipe3/lib/python3.6/warnings.py", line 116, in _formatwarnmsg
    msg.filename, msg.lineno, line= msg.line)
TypeError: custom_formatwarning() got an unexpected keyword argument 'line'
tashrifbillah commented 5 years ago

https://github.com/python/cpython/pull/12130