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
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