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"""
Python h5 module and octave h5 module have different ways to deal with
h5 files.
This module is used to make the link between octave and python using such files.
(python is using a dictionary and octave a struct )
This module provides tool to set HDF5 file for fasttomo input.
Here is an example of a simple read and write :
.. code-block:: python
:emphasize-lines: 3,5
# writing a structure
myStruct = {'MKEEP_MASK': 0.0, 'UNSHARP_SIGMA': 0.80000000000000004 }
writer = Octaveh5().open("my_h5file", 'a')
writer.write('mt_struct_name', myStruct)
# reading a h5 file
reader = Octaveh5().open("my_h5file")
strucDict = reader.get('mt_struct_name')
.. note:: These functions depend on the `h5py <http://www.h5py.org/>`_
library, which is a mandatory dependency for `silx`.
"""
import logging
logger = logging.getLogger(__name__)
import numpy as np
import h5py
__authors__ = ["C. Nemoz", "H. Payno"]
__license__ = "MIT"
__date__ = "05/10/2016"
[docs]
class Octaveh5(object):
"""This class allows communication between octave and python using hdf5 format."""
def __init__(self, octave_targetted_version=3.8):
"""Constructor
:param octave_targetted_version: the version of Octave for which we want to write this hdf5 file.
This is needed because for old Octave version we need to had a hack(adding one extra character)
"""
self.file = None
self.octave_targetted_version = octave_targetted_version
[docs]
def open(self, h5file, mode="r"):
"""Open the h5 file which has been write by octave
:param h5file: The path of the file to read
:param mode: the opening mode of the file :'r', 'w'...
"""
try:
self.file = h5py.File(h5file, mode)
return self
except IOError as e:
if mode == "a":
reason = "\n %s: Can t find or create " % h5file
else:
reason = "\n %s: File not found" % h5file
self.file = None
logger.info(reason)
raise e
[docs]
def get(self, struct_name):
"""Read octave equivalent structures in hdf5 file
:param struct_name: the identification of the top level identity we want to get from an hdf5 structure
:return: the dictionnary of the requested struct. None if can t find it
"""
if self.file is None:
info = "No file currently open"
logger.info(info)
return None
data_dict = {}
grr = (list(self.file[struct_name].items())[1])[1]
try:
gr_level2 = grr.items()
except AttributeError:
reason = "no gr_level2"
logger.info(reason)
return None
for key, val in iter(dict(gr_level2).items()):
data_dict[str(key)] = list(val.items())[1][1][()]
if list(val.items())[0][1][()] != np.bytes_("sq_string"):
data_dict[str(key)] = float(data_dict[str(key)])
else:
if list(val.items())[0][1][()] == np.bytes_("sq_string"):
# in the case the string has been stored as an nd-array of char
if type(data_dict[str(key)]) is np.ndarray:
data_dict[str(key)] = "".join(
chr(item) for item in data_dict[str(key)]
)
else:
data_dict[str(key)] = data_dict[str(key)].decode("UTF-8")
# In the case Octave have added an extra character at the end
if self.octave_targetted_version < 3.8:
data_dict[str(key)] = data_dict[str(key)][:-1]
return data_dict
[docs]
def write(self, struct_name, data_dict):
"""write data_dict under the group struct_name in the open hdf5 file
:param struct_name: the identificatioon of the structure to write in the hdf5
:param data_dict: The python dictionnary containing the informations to write
"""
if self.file is None:
info = "No file currently open"
logger.info(info)
return
group_l1 = self.file.create_group(struct_name)
group_l1.attrs["OCTAVE_GLOBAL"] = np.uint8(1)
group_l1.attrs["OCTAVE_NEW_FORMAT"] = np.uint8(1)
group_l1.create_dataset("type", data=np.bytes_("scalar struct"), dtype="|S14")
group_l2 = group_l1.create_group("value")
for ftparams in data_dict:
group_l3 = group_l2.create_group(ftparams)
group_l3.attrs["OCTAVE_NEW_FORMAT"] = np.uint8(1)
if type(data_dict[ftparams]) == str:
group_l3.create_dataset(
"type", (), data=np.bytes_("sq_string"), dtype="|S10"
)
if self.octave_targetted_version < 3.8:
group_l3.create_dataset(
"value", data=np.bytes_(data_dict[ftparams] + "0")
)
else:
group_l3.create_dataset(
"value", data=np.bytes_(data_dict[ftparams])
)
else:
group_l3.create_dataset(
"type", (), data=np.bytes_("scalar"), dtype="|S7"
)
group_l3.create_dataset("value", data=data_dict[ftparams])
[docs]
def close(self):
"""Close the file after calling read function"""
if self.file:
self.file.close()
def __del__(self):
"""Destructor"""
self.close()
