multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
? File "/usr/lib/python3.5/multiprocessing/pool.py", line 119, in worker
? ? result = (True, func(*args, **kwds))
? File "/usr/local/lib/python3.5/dist-packages/keras/utils/data_utils.py", line 626, in next_sample
? ? return six.next(_SHARED_SEQUENCES[uid])
? File "/media/amax/partion2/xdh/tensorflow/3DUnetCNN-master/unet3d/generator.py", line 155, in data_generator
? ? skip_blank=skip_blank, permute=permute)
? File "/media/amax/partion2/xdh/tensorflow/3DUnetCNN-master/unet3d/generator.py", line 210, in add_data
? ? data, truth = get_data_from_file(data_file, index, patch_shape=patch_shape)
? File "/media/amax/partion2/xdh/tensorflow/3DUnetCNN-master/unet3d/generator.py", line 238, in get_data_from_file
? ? x, y = data_file.root.data[index], data_file.root.truth[index, 0]
? File "/usr/local/lib/python3.5/dist-packages/tables/array.py", line 662, in __getitem__
? ? arr = self._read_slice(startl, stopl, stepl, shape)
? File "/usr/local/lib/python3.5/dist-packages/tables/array.py", line 766, in _read_slice
? ? self._g_read_slice(startl, stopl, stepl, nparr)
? File "tables/hdf5extension.pyx", line 1585, in tables.hdf5extension.Array._g_read_slice
tables.exceptions.HDF5ExtError: HDF5 error back trace
? File "H5Dio.c", line 216, in H5Dread
? ? can't read data
? File "H5Dio.c", line 587, in H5D__read
? ? can't read data
? File "H5Dchunk.c", line 2304, in H5D__chunk_read
? ? unable to read raw data chunk
? File "H5Dchunk.c", line 3659, in H5D__chunk_lock
? ? data pipeline read failed
? File "H5Z.c", line 1279, in H5Z_pipeline
? ? filter returned failure during read
? File "hdf5-blosc/src/blosc_filter.c", line 254, in blosc_filter
? ? Blosc decompression error
End of HDF5 error back trace
Problems reading the array data.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
? File "brats/train_isensee2017.py", line 117, in <module>
? ? main(overwrite=config["overwrite"])
? File "brats/train_isensee2017.py", line 112, in main
? ? n_epochs=config["n_epochs"])
? File "/media/amax/partion2/xdh/tensorflow/3DUnetCNN-master/unet3d/training.py", line 90, in train_model
? ? use_multiprocessing = True)
? File "/usr/local/lib/python3.5/dist-packages/keras/legacy/interfaces.py", line 91, in wrapper
? ? return func(*args, **kwargs)
? File "/usr/local/lib/python3.5/dist-packages/keras/engine/training.py", line 1418, in fit_generator
? ? initial_epoch=initial_epoch)
? File "/usr/local/lib/python3.5/dist-packages/keras/engine/training_generator.py", line 181, in fit_generator
? ? generator_output = next(output_generator)
? File "/usr/local/lib/python3.5/dist-packages/keras/utils/data_utils.py", line 709, in get
? ? six.reraise(*sys.exc_info())
? File "/home/amax/.local/lib/python3.5/site-packages/six.py", line 693, in reraise
? ? raise value
? File "/usr/local/lib/python3.5/dist-packages/keras/utils/data_utils.py", line 685, in get
? ? inputs = self.queue.get(block=True).get()
? File "/usr/lib/python3.5/multiprocessing/pool.py", line 608, in get
? ? raise self._value
tables.exceptions.HDF5ExtError: HDF5 error back trace
? File "H5Dio.c", line 216, in H5Dread
? ? can't read data
? File "H5Dio.c", line 587, in H5D__read
? ? can't read data
? File "H5Dchunk.c", line 2304, in H5D__chunk_read
? ? unable to read raw data chunk
? File "H5Dchunk.c", line 3659, in H5D__chunk_lock
? ? data pipeline read failed
? File "H5Z.c", line 1279, in H5Z_pipeline
? ? filter returned failure during read
? File "hdf5-blosc/src/blosc_filter.c", line 254, in blosc_filter
? ? Blosc decompression error
End of HDF5 error back trace
Problems reading the array data.
Closing remaining open files:/media/amax/partion2/xdh/tensorflow/3DUnetCNN-master/brats_data.h5...done
