import os
import tempfile, tarfile
import logging
logger = logging.getLogger("bob.bio.base")
import bob.io.base
[docs]def check_file(filename, force, expected_file_size = 1):
"""Checks if the file with the given ``filename`` exists and has size greater or equal to ``expected_file_size``.
If the file is to small, **or** if the ``force`` option is set to ``True``, the file is removed.
This function returns ``True`` is the file exists (and has not been removed), otherwise ``False``"""
if os.path.exists(filename):
if force or os.path.getsize(filename) < expected_file_size:
logger.debug(" .. Removing old file '%s'.", filename)
os.remove(filename)
return False
else:
return True
return False
[docs]def load(file):
"""Loads data from file. The given file might be an HDF5 file open for reading or a string."""
if isinstance(file, bob.io.base.HDF5File):
return file.read("array")
else:
return bob.io.base.load(file)
[docs]def save(data, file, compression=0):
"""Saves the data to file using HDF5. The given file might be an HDF5 file open for writing, or a string.
If the given data contains a ``save`` method, this method is called with the given HDF5 file.
Otherwise the data is written to the HDF5 file using the given compression."""
f = file if isinstance(file, bob.io.base.HDF5File) else bob.io.base.HDF5File(file, 'w')
if hasattr(data, 'save'):
data.save(f)
else:
f.set("array", data, compression=compression)
[docs]def open_compressed(filename, open_flag = 'r', compression_type='bz2'):
"""Opens a compressed HDF5File with the given opening flags.
For the 'r' flag, the given compressed file will be extracted to a local space.
For 'w', an empty HDF5File is created.
In any case, the opened HDF5File is returned, which needs to be closed using the close_compressed() function.
"""
# create temporary HDF5 file name
hdf5_file_name = tempfile.mkstemp('.hdf5', 'bob_')[1]
if open_flag == 'r':
# extract the HDF5 file from the given file name into a temporary file name
tar = tarfile.open(filename, mode="r:"+compression_type)
memory_file = tar.extractfile(tar.next())
real_file = open(hdf5_file_name, 'wb')
real_file.write(memory_file.read())
del memory_file
real_file.close()
tar.close()
return bob.io.base.HDF5File(hdf5_file_name, open_flag)
[docs]def close_compressed(filename, hdf5_file, compression_type='bz2', create_link=False):
"""Closes the compressed hdf5_file that was opened with open_compressed.
When the file was opened for writing (using the 'w' flag in open_compressed), the created HDF5 file is compressed into the given file name.
To be able to read the data using the real tools, a link with the correct extension might is created, when create_link is set to True.
"""
hdf5_file_name = hdf5_file.filename
is_writable = hdf5_file.writable
hdf5_file.close()
if is_writable:
# create compressed tar file
tar = tarfile.open(filename, mode="w:"+compression_type)
tar.add(hdf5_file_name, os.path.basename(filename))
tar.close()
if create_link:
extension = {'':'.tar', 'bz2':'.tar.bz2', 'gz':'tar.gz'}[compression_type]
link_file = filename+extension
if not os.path.exists(link_file):
os.symlink(os.path.basename(filename), link_file)
# clean up locally generated files
os.remove(hdf5_file_name)
[docs]def load_compressed(filename, compression_type='bz2'):
"""Extracts the data to a temporary HDF5 file using HDF5 and reads its contents.
Note that, though the file name is .hdf5, it contains compressed data!
Accepted compression types are 'gz', 'bz2', ''"""
# read from compressed HDF5
hdf5 = open_compressed(filename, 'r')
data = hdf5.read("array")
close_compressed(filename, hdf5)
return data
[docs]def save_compressed(data, filename, compression_type='bz2', create_link=False):
"""Saves the data to a temporary file using HDF5.
Afterwards, the file is compressed using the given compression method and saved using the given file name.
Note that, though the file name will be .hdf5, it will contain compressed data!
Accepted compression types are 'gz', 'bz2', ''"""
# write to compressed HDF5 file
hdf5 = open_compressed(filename, 'w')
save(data, hdf5)
close_compressed(filename, hdf5, compression_type, create_link)
