109 lines
3.6 KiB
Python
109 lines
3.6 KiB
Python
# -*- coding: UTF-8 no BOM -*-
|
|
|
|
import os
|
|
import sys
|
|
import h5py
|
|
import numpy as np
|
|
import xml.etree.cElementTree as ET
|
|
|
|
# ---------------------------------------------------------------- #
|
|
# python 3 has no unicode object, this ensures that the code works #
|
|
# on Python 2&3 #
|
|
# ---------------------------------------------------------------- #
|
|
try:
|
|
test=isinstance('test', unicode)
|
|
except(NameError):
|
|
unicode=str
|
|
|
|
|
|
# ------------------------------------------------------- #
|
|
# Singleton class for converting feature name to H5F path #
|
|
# ------------------------------------------------------- #
|
|
# NOTE:
|
|
# use simple function to mimic the singleton class in
|
|
# C++/Java
|
|
def lables_to_path(label, dsXMLPath=None):
|
|
""" read the xml definition file and return the path."""
|
|
if dsXMLPath is None:
|
|
dsXMLPath = os.path.abspath(__file__).replace("h5table.py",
|
|
"DS_HDF5.xml")
|
|
tree = ET.parse(dsXMLPath)
|
|
dataType = tree.find('{}/type'.format(label)).text
|
|
h5path = tree.find('{}/h5path'.format(label)).text
|
|
return (dataType, h5path)
|
|
|
|
|
|
# ----------------------- #
|
|
# H5Table interface class #
|
|
# ----------------------- #
|
|
class H5Table(object):
|
|
"""
|
|
DESCRIPTION
|
|
-----------
|
|
Interface class for manipulating data in HDF5 with DAMASK
|
|
specialized data structure.
|
|
PARAMETERS
|
|
----------
|
|
h5f_path: str
|
|
Absolute path the HDF5 file
|
|
METHOD
|
|
------
|
|
del_entry()
|
|
get_attr()
|
|
add_attr()
|
|
get_data()
|
|
add_data()
|
|
NOTE
|
|
----
|
|
1. As an interface class, it uses the lazy evaluation design
|
|
that read the data only when its absolutely necessary.
|
|
2. The command line used to generate new feature is stored with
|
|
each dataset as dataset attribute.
|
|
"""
|
|
|
|
def __init__(self, h5f_path):
|
|
"""
|
|
"""
|
|
self.h5f_path = h5f_path
|
|
|
|
def del_entry(self, feature_name):
|
|
""" delete entry in HDF5 table """
|
|
dataType, h5f_path = lables_to_path(feature_name)
|
|
h5f = h5py.File(self.h5f_path, 'a')
|
|
del h5f[h5f_path]
|
|
|
|
def get_attr(self, attr_name):
|
|
h5f = h5py.File(self.h5f_path, 'r')
|
|
dataType, h5f_path = lables_to_path(attr_name)
|
|
return h5f[h5f_path].attrs[attr_name]
|
|
|
|
def add_attr(self, attr_name, attr_data):
|
|
h5f = h5py.File(self.h5f_path, 'a')
|
|
dataType, h5f_path = lables_to_path(attr_name)
|
|
if dataType == "attr":
|
|
h5f[h5f_path].attrs[attr_name] = attr_data
|
|
else:
|
|
raise ValueError("Unspported attr: {}".format(attr_name))
|
|
|
|
def get_data(self, feature_name=None):
|
|
""" extract dataset from HDF5 table and return it in a numpy array """
|
|
dataType, h5f_path = lables_to_path(feature_name)
|
|
h5f = h5py.File(self.h5f_path, 'r')
|
|
h5f_dst = h5f[h5f_path] # get the handle for target dataset(table)
|
|
return h5f_dst.read_direct(np.zeros(h5f_dst.shape))
|
|
|
|
def add_data(self, feature_name, dataset=None):
|
|
""" adding new feature into existing HDF5 file """
|
|
dataType, h5f_path = lables_to_path(feature_name)
|
|
if dataType is not "attr":
|
|
h5f = h5py.File(self.h5f_path, 'a')
|
|
h5f.create_dataset(h5f_path, data=dataset)
|
|
else:
|
|
raise ValueError("feature {} isn't valid".format(feature_name))
|
|
|
|
def get_log(self, feature_name):
|
|
""" get cmd history used to generate the data"""
|
|
dataType, h5f_path = lables_to_path(feature_name)
|
|
h5f = ht5py.File(self.h5f_path, 'r')
|
|
return h5f[h5f_path].attrs['log']
|