def test_add_hdf_dataset(self):
"""
Test adding a name and an array
"""
testencoder = HDFEncoder()
testencoder.add_hdf_dataset('test_dataset', self.known_array)
testencoder.encoder_close()
def test_add_hdf_dataset_with_bad_array(self):
"""
Test adding a name and a something other than an array
"""
testencoder = HDFEncoder()
with self.assertRaises(HDFEncoderException):
testencoder.add_hdf_dataset(self.dataset_name,'bad array')
testencoder.encoder_close()
def test_add_hdf_dataset_with_bad_name(self):
"""
Test adding a bad name and an array
"""
testencoder = HDFEncoder()
with self.assertRaises(HDFEncoderException):
self.dataset = testencoder.add_hdf_dataset('bad name', self.known_array)
testencoder.encoder_close()
def test_encode_known_and_compare(self):
"""
Create an encoder and add some (one) dataset/array
"""
hdfencoder = HDFEncoder()
hdfencoder.add_hdf_dataset(self.path_to_dataset, self.known_array)
# Serialize to string and compare to a know value
hdf_string = hdfencoder.encoder_close()
self.assertEqual(hdf_string,self.known_hdf_as_string)
def test_encode_decode(self):
"""
Encode some arrays
"""
hdfencoder = HDFEncoder() # put array into the encoder
hdfencoder.add_hdf_dataset(self.path_to_dataset, self.known_array)
# get the string out from encoder
hdf_string = hdfencoder.encoder_close()
# Compare the arrays
hdfdecoder = HDFDecoder(hdf_string) # put string in decoder...
nparray = hdfdecoder.read_hdf_dataset(self.path_to_dataset) # get array out
self.assertEqual(nparray.tostring(), self.known_array.tostring()) # works for arbitrarily shaped arrays
def test_decode_encode(self):
"""
Try a decode-encode sequence and compare if its the same string
"""
# decode an existing hdf file and read out an array
hdfdecoder = HDFDecoder(self.known_hdf_as_string) # put known string in decoder...
nparray = hdfdecoder.read_hdf_dataset(self.path_to_dataset) # get array out
# encode the array and get the binary string containing the encoded hdf file
hdfencoder = HDFEncoder() # put the array in the encoder...
hdfencoder.add_hdf_dataset(self.path_to_dataset, self.known_array)
hdf_string = hdfencoder.encoder_close() # get string out
# compare the two strings
self.assertEqual(hdf_string,self.known_hdf_as_string)
def test_encode_with_filename_and_compare(self):
"""
Create an encoder and add some (one) dataset/array
"""
testfilename = '/tmp/testFile.hdf5'
hdfencoder = HDFEncoder(testfilename)
hdfencoder.add_hdf_dataset(self.path_to_dataset, self.known_array)
# get the string out from encoder
hdf_string = hdfencoder.encoder_close()
self.assertEqual(hdf_string,self.known_hdf_as_string)
hdfdecoder = HDFDecoder(self.known_hdf_as_string)
nparray = hdfdecoder.read_hdf_dataset(self.path_to_dataset)
self.assertEqual(nparray.tostring(), self.known_array.tostring())
def add_two_datasets_read_compare(self, filename, dataset_name1, dataset_name2):
array1 = numpy.ones((4,5))
array2 = numpy.ones((2,3))
# first create the file
hdfencoder = HDFEncoder(filename)
hdfencoder.add_hdf_dataset(dataset_name1, array1)
hdfstring = hdfencoder.encoder_close()
# now open the file and add another branch
hdfencoder = HDFEncoder(filename)
hdfencoder.add_hdf_dataset(dataset_name2, array2)
hdfstring = hdfencoder.encoder_close()
hdfdecoder = HDFDecoder(hdfstring)
# Read the first dataset
array_decoded_1 = hdfdecoder.read_hdf_dataset(dataset_name1)
hdfdecoder = HDFDecoder(hdfstring)
# Read the second dataset
array_decoded_2 = hdfdecoder.read_hdf_dataset(dataset_name2)
self.assertEqual(array1.tostring(), array_decoded_1.tostring())
self.assertEqual(array2.tostring(), array_decoded_2.tostring())
import numpy, h5py
from prototype.hdf.science_object_codec import HDFEncoder, HDFDecoder
array1 = numpy.ones((4,5))
array2 = numpy.ones((2,3))
array3 = numpy.ones((10,2))
dataset_name1 = 'rootgroup/mygroup/data/temperature'
dataset_name2 = 'rootgroup/mygroup/data/pressure'
dname = 'aGroup/adataset'
###########################################################
# Create an encoder object
hdfencoder = HDFEncoder()
# Add data as an array
hdfencoder.add_hdf_dataset(dataset_name1, array1)
hdfencoder.add_hdf_dataset(dataset_name2, array2)
# Convert all the data to a binary string for easy transportation
hdfstring1 = hdfencoder.encoder_close()
# Create another encoder. This time pass on name of hdf5 file to write
hdfencoder = HDFEncoder('/tmp/testHDFEncoder.hdf5')
hdfencoder.add_hdf_dataset(dataset_name1, array1)
hdfencoder.add_hdf_dataset(dataset_name2, array2)
# Convert all the data to a binary string for easy transportation
hdfstring2 = hdfencoder.encoder_close()
# Create another encoder. This time pass on name of hdf5 file to write
hdfencoder = HDFEncoder('/tmp/testHDFEncoder.hdf5')
hdfencoder.add_hdf_dataset(dname, array3)
