CODEWITHSUNDEEP
pythonhdf5caffeh5pypycaffe
Atikin
Atikin

Reputation: 11

Python layer can't read hdf5 file in caffe framework

I write python layer for caffe that can read hdf5 with some manipulation needs for me. But I have some issue when open and read hdf5 file in python setup method. Here it is. When I used tables with the code in setup:

def setup(self, bottom, top):
    h5file = tables.open_file("/home/titan/models/hdf5/train_small.h5", driver="H5FD_CORE")

I have this error when run net:

Traceback (most recent call last):
  File "/home/titan/scripts/python_layers/pydata_hdf5.py", line 37, in setup
    h5file = tables.open_file("/home/titan/models/hdf5/train_small.h5", driver="H5FD_CORE")
  File "/home/titan/anaconda/lib/python2.7/site-packages/tables/file.py", line 318, in open_file
    return File(filename, mode, title, root_uep, filters, **kwargs)
  File "/home/titan/anaconda/lib/python2.7/site-packages/tables/file.py", line 784, in __init__
    self._g_new(filename, mode, **params)
  File "tables/hdf5extension.pyx", line 465, in tables.hdf5extension.File._g_new (tables/hdf5extension.c:4872)
tables.exceptions.HDF5ExtError: HDF5 error back trace

  File "../../../src/H5FDcore.c", line 273, in H5Pset_fapl_core
    not a file access property list
  File "../../../src/H5Pint.c", line 3371, in H5P_object_verify
    property list is not a member of the class
  File "../../../src/H5Pint.c", line 3321, in H5P_isa_class
    not a property list

End of HDF5 error back trace

When I used h5py

def setup(self, bottom, top):
    self.data = h5py.File('/home/titan/models/hdf5_nose_mouth/train_small.h5', 'r')

I have the same error:

Traceback (most recent call last):
  File "/home/titan/scripts/python_layers/pydata_hdf5.py", line 11, in <module>
    import h5py
  File "/home/titan/anaconda/lib/python2.7/site-packages/h5py/__init__.py", line 31, in <module>
    from .highlevel import *
  File "/home/titan/anaconda/lib/python2.7/site-packages/h5py/highlevel.py", line 13, in <module>
    from ._hl.base import is_hdf5, HLObject
  File "/home/titan/anaconda/lib/python2.7/site-packages/h5py/_hl/base.py", line 78, in <module>
    dlapl = default_lapl()
  File "/home/titan/anaconda/lib/python2.7/site-packages/h5py/_hl/base.py", line 65, in default_lapl
    lapl = h5p.create(h5p.LINK_ACCESS)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (-------src-dir-------/h5py/_objects.c:2458)
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (-------src-dir-------/h5py/_objects.c:2415)
  File "h5py/h5p.pyx", line 130, in h5py.h5p.create (-------src-dir-------/h5py/h5p.c:2491)
ValueError: Not a property list class (Not a property list class)

When I used deepdish:

def setup(self, bottom, top):
    self.data = dd.io.load('/home/titan/models/hdf5/train_smallest.h5')

I have error too:

Traceback (most recent call last):
  File "/home/titan/scripts/python_layers/pydata_hdf5.py", line 36, in setup
    self.data = dd.io.load('/home/titan/models/hdf5/train_smallest.h5')
  File "/home/titan/anaconda/lib/python2.7/site-packages/deepdish/io/hdf5io.py", line 476, in load
    with tables.open_file(path, mode='r') as h5file:
  File "/home/titan/anaconda/lib/python2.7/site-packages/tables/file.py", line 318, in open_file
    return File(filename, mode, title, root_uep, filters, **kwargs)
  File "/home/titan/anaconda/lib/python2.7/site-packages/tables/file.py", line 784, in __init__
    self._g_new(filename, mode, **params)
  File "tables/hdf5extension.pyx", line 488, in tables.hdf5extension.File._g_new (tables/hdf5extension.c:5081)
tables.exceptions.HDF5ExtError: HDF5 error back trace

  File "../../../src/H5F.c", line 1582, in H5Fopen
    not file access property list
  File "../../../src/H5Pint.c", line 3321, in H5P_isa_class
    not a property list

End of HDF5 error back trace

But when I read simply *.txt file, all is ok. Also I can read this file from console and use it in hdf5 layer in caffe. Please help me, how I can read hdf5 file from python layer?

Upvotes: 1

Views: 820

Answers (1)

prlz77
prlz77

Reputation: 31

Try to install another version of h5py. I just solved it with:

pip install h5py==prev_version

I guess it has something to do with the linking but it would be interesting to know which is the exact cause for this problem.

Upvotes: 3

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