def test02_copy(self):
"""Checking (X)Array.copy() method ('numetic' flavor)"""
srcfile = test_filename("oldflavor_numeric.h5")
tmpfile = tempfile.mktemp(".h5")
shutil.copy(srcfile, tmpfile)
try:
# Open the HDF5 with old numeric flavor
with tables.open_file(tmpfile, "r+") as h5file:
# Copy to another location
self.assertWarns(FlavorWarning,
h5file.root.array1.copy, '/', 'array1copy')
h5file.root.array2.copy('/', 'array2copy')
h5file.root.carray1.copy('/', 'carray1copy')
h5file.root.carray2.copy('/', 'carray2copy')
h5file.root.vlarray1.copy('/', 'vlarray1copy')
h5file.root.vlarray2.copy('/', 'vlarray2copy')
if self.close:
h5file.close()
h5file = tables.open_file(tmpfile)
else:
h5file.flush()
# Assert other properties in array
self.assertEqual(h5file.root.array1copy.flavor, 'numeric')
self.assertEqual(h5file.root.array2copy.flavor, 'python')
self.assertEqual(h5file.root.carray1copy.flavor, 'numeric')
self.assertEqual(h5file.root.carray2copy.flavor, 'python')
self.assertEqual(h5file.root.vlarray1copy.flavor, 'numeric')
self.assertEqual(h5file.root.vlarray2copy.flavor, 'python')
finally:
os.remove(tmpfile)
def test01_readTable(self):
"""Checking backward compatibility of old formats of tables."""
if common.verbose:
print('\n', '-=' * 30)
print("Running %s.test01_readTable..." % self.__class__.__name__)
# Create an instance of an HDF5 Table
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=UserWarning)
h5file = tables.open_file(test_filename(self.h5fname), "r")
try:
table = h5file.get_node("/tuple0")
# Read the 100 records
result = [rec['var2'] for rec in table]
if common.verbose:
print("Nrows in", table._v_pathname, ":", table.nrows)
print("Last record in table ==>", rec)
print("Total selected records in table ==> ", len(result))
self.assertEqual(len(result), 100)
finally:
h5file.close()
class ContiguousCompoundAppendTestCase(common.TestFileMixin, TestCase):
"""Test for appending data to native contiguous compound datasets."""
h5fname = test_filename('non-chunked-table.h5')
def test(self):
self.assertIn('/test_var/structure variable', self.h5file)
self.h5file.close()
# Do a copy to a temporary to avoid modifying the original file
h5fname_copy = tempfile.mktemp(".h5")
shutil.copy(self.h5fname, h5fname_copy)
# Reopen in 'a'ppend mode
try:
self.h5file = tables.open_file(h5fname_copy, 'a')
except IOError:
# Problems for opening (probably not permisions to write the file)
return
tbl = self.h5file.get_node('/test_var/structure variable')
# Try to add rows to a non-chunked table (this should raise an error)
self.assertRaises(tables.HDF5ExtError, tbl.append,
[(4.0, 5.0, [2.0, 3.0], 'd')])
# Appending using the Row interface
self.assertRaises(tables.HDF5ExtError, tbl.row.append)
# Remove the file copy
self.h5file.close() # Close the handler first
os.remove(h5fname_copy)
class EnumTestCase(common.TestFileMixin, TestCase):
"""Test for enumerated datatype.
See ftp://ftp.hdfgroup.org/HDF5/current/src/unpacked/test/enum.c.
"""
h5fname = test_filename('smpl_enum.h5')
def test(self):
self.assertIn('/EnumTest', self.h5file)
arr = self.h5file.get_node('/EnumTest')
self.assertIsInstance(arr, tables.Array)
enum = arr.get_enum()
expectedEnum = tables.Enum(['RED', 'GREEN', 'BLUE', 'WHITE', 'BLACK'])
self.assertEqual(enum, expectedEnum)
data = list(arr.read())
expectedData = [
enum[name] for name in [
'RED', 'GREEN', 'BLUE', 'WHITE', 'BLACK', 'RED', 'GREEN',
'BLUE', 'WHITE', 'BLACK'
]
]
self.assertEqual(data, expectedData)
class ExtendibleTestCase(common.TestFileMixin, TestCase):
"""Test for extendible datasets.
See the example programs in the Introduction to HDF5.
"""
h5fname = test_filename('smpl_SDSextendible.h5')
def test(self):
self.assertIn('/ExtendibleArray', self.h5file)
arr = self.h5file.get_node('/ExtendibleArray')
self.assertIsInstance(arr, tables.EArray)
self.assertEqual(arr.byteorder, 'big')
self.assertEqual(arr.atom.type, 'int32')
self.assertEqual(arr.shape, (10, 5))
self.assertEqual(arr.extdim, 0)
self.assertEqual(len(arr), 10)
data = arr.read()
expectedData = numpy.array(
[[1, 1, 1, 3, 3], [1, 1, 1, 3, 3], [1, 1, 1, 0, 0], [
2, 0, 0, 0, 0
], [2, 0, 0, 0, 0], [2, 0, 0, 0, 0], [2, 0, 0, 0, 0],
[2, 0, 0, 0, 0], [2, 0, 0, 0, 0], [2, 0, 0, 0, 0]],
dtype=arr.atom.type)
self.assertTrue(common.areArraysEqual(data, expectedData))
def test01_readTable(self):
"""Checking backward compatibility of old formats of tables."""
if common.verbose:
print('\n', '-=' * 30)
print("Running %s.test01_readTable..." % self.__class__.__name__)
# Create an instance of an HDF5 Table
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=UserWarning)
h5file = tables.open_file(test_filename(self.h5fname), "r")
try:
table = h5file.get_node("/tuple0")
# Read the 100 records
result = [rec['var2'] for rec in table]
if common.verbose:
print("Nrows in", table._v_pathname, ":", table.nrows)
print("Last record in table ==>", rec)
print("Total selected records in table ==> ", len(result))
self.assertEqual(len(result), 100)
finally:
h5file.close()
class PaddedArrayTestCase(common.TestFileMixin, TestCase):
"""Test for H5T_COMPOUND (Table) datatype with padding.
Regression test for issue gh-734
itemsize.h5 was created with h5py with the array `expectedData` (see below)
in the table `/Test`:
'A' and 'B' are 4 + 4 bytes, with 8 bytes padding.
$ h5ls -v itemsize.h5
Test Dataset {3/3}
Location: 1:800
Links: 1
Storage: 48 logical bytes, 48 allocated bytes, 100.00% utilization
Type: struct {
"A" +0 native unsigned int
"B" +4 native unsigned int
} 16 bytes
"""
h5fname = test_filename('itemsize.h5')
def test(self):
arr = self.h5file.get_node('/Test')
data = arr.read()
expectedData = numpy.array(
[(1, 11), (2, 12), (3, 13)],
dtype={
'names': ['A', 'B'],
'formats': ['<u4', '<u4'],
'offsets': [0, 4],
'itemsize': 16
})
self.assertTrue(common.areArraysEqual(data, expectedData))
def test02_copy(self):
"""Checking (X)Array.copy() method ('numetic' flavor)"""
srcfile = test_filename("oldflavor_numeric.h5")
tmpfile = tempfile.mktemp(".h5")
shutil.copy(srcfile, tmpfile)
try:
# Open the HDF5 with old numeric flavor
with tables.open_file(tmpfile, "r+") as h5file:
# Copy to another location
self.assertWarns(FlavorWarning,
h5file.root.array1.copy, '/', 'array1copy')
h5file.root.array2.copy('/', 'array2copy')
h5file.root.carray1.copy('/', 'carray1copy')
h5file.root.carray2.copy('/', 'carray2copy')
h5file.root.vlarray1.copy('/', 'vlarray1copy')
h5file.root.vlarray2.copy('/', 'vlarray2copy')
if self.close:
h5file.close()
h5file = tables.open_file(tmpfile)
else:
h5file.flush()
# Assert other properties in array
self.assertEqual(h5file.root.array1copy.flavor, 'numeric')
self.assertEqual(h5file.root.array2copy.flavor, 'python')
self.assertEqual(h5file.root.carray1copy.flavor, 'numeric')
self.assertEqual(h5file.root.carray2copy.flavor, 'python')
self.assertEqual(h5file.root.vlarray1copy.flavor, 'numeric')
self.assertEqual(h5file.root.vlarray2copy.flavor, 'python')
finally:
os.remove(tmpfile)
class SzipTestCase(common.TestFileMixin, TestCase):
"""Test for native HDF5 files with datasets compressed with szip."""
h5fname = test_filename('test_szip.h5')
def test(self):
self.assertIn('/dset_szip', self.h5file)
arr = self.h5file.get_node('/dset_szip')
filters = ("Filters(complib='szip', shuffle=False, bitshuffle=False, "
"fletcher32=False, least_significant_digit=None)")
self.assertEqual(repr(arr.filters), filters)
class VLArrayTestCase(common.TestFileMixin, TestCase):
h5fname = test_filename("flavored_vlarrays-format1.6.h5")
def test01_backCompat(self):
"""Checking backward compatibility with old flavors of VLArray."""
# Check that we can read the contents without problems (nor warnings!)
vlarray1 = self.h5file.root.vlarray1
self.assertEqual(vlarray1.flavor, "numeric")
vlarray2 = self.h5file.root.vlarray2
self.assertEqual(vlarray2.flavor, "python")
self.assertEqual(vlarray2[1], [b'5', b'6', b'77'])
class ChunkedCompoundTestCase(common.TestFileMixin, TestCase):
"""Test for a more complex and chunked compound structure.
This is generated by a chunked version of the example in
ftp://ftp.ncsa.uiuc.edu/HDF/files/hdf5/samples/compound2.c.
"""
h5fname = test_filename('smpl_compound_chunked.h5')
def test(self):
self.assertIn('/CompoundChunked', self.h5file)
tbl = self.h5file.get_node('/CompoundChunked')
self.assertIsInstance(tbl, tables.Table)
self.assertEqual(
tbl.colnames,
['a_name', 'c_name', 'd_name', 'e_name', 'f_name', 'g_name'])
self.assertEqual(tbl.coltypes['a_name'], 'int32')
self.assertEqual(tbl.coldtypes['a_name'].shape, ())
self.assertEqual(tbl.coltypes['c_name'], 'string')
self.assertEqual(tbl.coldtypes['c_name'].shape, ())
self.assertEqual(tbl.coltypes['d_name'], 'int16')
self.assertEqual(tbl.coldtypes['d_name'].shape, (5, 10))
self.assertEqual(tbl.coltypes['e_name'], 'float32')
self.assertEqual(tbl.coldtypes['e_name'].shape, ())
self.assertEqual(tbl.coltypes['f_name'], 'float64')
self.assertEqual(tbl.coldtypes['f_name'].shape, (10, ))
self.assertEqual(tbl.coltypes['g_name'], 'uint8')
self.assertEqual(tbl.coldtypes['g_name'].shape, ())
for m in range(len(tbl)):
row = tbl[m]
# This version of the loop seems to fail because of ``iterrows()``.
# for (m, row) in enumerate(tbl):
self.assertEqual(row['a_name'], m)
self.assertEqual(row['c_name'], b"Hello!")
dRow = row['d_name']
for n in range(5):
for o in range(10):
self.assertEqual(dRow[n][o], m + n + o)
self.assertAlmostEqual(row['e_name'], m * 0.96, places=6)
fRow = row['f_name']
for n in range(10):
self.assertAlmostEqual(fRow[n], m * 1024.9637)
self.assertEqual(row['g_name'], ord('m'))
class ObjectReferenceTestCase(common.TestFileMixin, TestCase):
h5fname = test_filename('test_ref_array1.mat')
def test_node_var(self):
array = self.h5file.get_node('/ANN/my_arr')
self.assertEqual(array.shape, (1, 3))
def test_ref_utf_str(self):
array = self.h5file.get_node('/ANN/my_arr')
self.assertTrue(
common.areArraysEqual(array[0][0][0],
numpy.array([0, 0], dtype=numpy.uint64)))
def test01_open(self):
"""Checking opening of (X)Array (old 'numeric' flavor)"""
# Open the HDF5 with old numeric flavor
h5fname = test_filename("oldflavor_numeric.h5")
with tables.open_file(h5fname) as h5file:
# Assert other properties in array
self.assertEqual(h5file.root.array1.flavor, 'numeric')
self.assertEqual(h5file.root.array2.flavor, 'python')
self.assertEqual(h5file.root.carray1.flavor, 'numeric')
self.assertEqual(h5file.root.carray2.flavor, 'python')
self.assertEqual(h5file.root.vlarray1.flavor, 'numeric')
self.assertEqual(h5file.root.vlarray2.flavor, 'python')
def test01_open(self):
"""Checking opening of (X)Array (old 'numeric' flavor)"""
# Open the HDF5 with old numeric flavor
h5fname = test_filename("oldflavor_numeric.h5")
with tables.open_file(h5fname) as h5file:
# Assert other properties in array
self.assertEqual(h5file.root.array1.flavor, 'numeric')
self.assertEqual(h5file.root.array2.flavor, 'python')
self.assertEqual(h5file.root.carray1.flavor, 'numeric')
self.assertEqual(h5file.root.carray2.flavor, 'python')
self.assertEqual(h5file.root.vlarray1.flavor, 'numeric')
self.assertEqual(h5file.root.vlarray2.flavor, 'python')
class MatlabFileTestCase(common.TestFileMixin, TestCase):
h5fname = test_filename('matlab_file.mat')
def test_unicode(self):
array = self.h5file.get_node('/', 'a')
self.assertEqual(array.shape, (3, 1))
# in Python 3 this will be the same as the test above
def test_string(self):
array = self.h5file.get_node('/', 'a')
self.assertEqual(array.shape, (3, 1))
def test_numpy_str(self):
array = self.h5file.get_node(numpy.str_('/'), numpy.str_('a'))
self.assertEqual(array.shape, (3, 1))
class TimeTestCase(common.TestFileMixin, TestCase):
# Open a PYTABLES_FORMAT_VERSION=1.x file
h5fname = test_filename("time-table-vlarray-1_x.h5")
def test00_table(self):
"""Checking backward compatibility with old TimeXX types (tables)."""
# Check that we can read the contents without problems (nor warnings!)
table = self.h5file.root.table
self.assertEqual(table.byteorder, "little")
def test01_vlarray(self):
"""Checking backward compatibility with old TimeXX types (vlarrays)."""
# Check that we can read the contents without problems (nor warnings!)
vlarray4 = self.h5file.root.vlarray4
self.assertEqual(vlarray4.byteorder, "little")
vlarray8 = self.h5file.root.vlarray4
self.assertEqual(vlarray8.byteorder, "little")
class ObjectReferenceRecursiveTestCase(common.TestFileMixin, TestCase):
h5fname = test_filename('test_ref_array2.mat')
def test_var(self):
array = self.h5file.get_node('/var')
self.assertEqual(array.shape, (3, 1))
def test_ref_str(self):
array = self.h5file.get_node('/var')
self.assertTrue(common.areArraysEqual(
array[1][0][0],
numpy.array([[116], [101], [115], [116]],
dtype=numpy.uint16)))
def test_double_ref(self):
array = self.h5file.get_node('/var')
self.assertTrue(common.areArraysEqual(
array[2][0][0][1][0],
numpy.array([[105], [110], [115], [105], [100], [101]],
dtype=numpy.uint16)))
class ContiguousCompoundTestCase(common.TestFileMixin, TestCase):
"""Test for support of native contiguous compound datasets.
This example has been provided by Dav Clark.
"""
h5fname = test_filename('non-chunked-table.h5')
def test(self):
self.assertIn('/test_var/structure variable', self.h5file)
tbl = self.h5file.get_node('/test_var/structure variable')
self.assertIsInstance(tbl, tables.Table)
self.assertEqual(
tbl.colnames,
['a', 'b', 'c', 'd'])
self.assertEqual(tbl.coltypes['a'], 'float64')
self.assertEqual(tbl.coldtypes['a'].shape, ())
self.assertEqual(tbl.coltypes['b'], 'float64')
self.assertEqual(tbl.coldtypes['b'].shape, ())
self.assertEqual(tbl.coltypes['c'], 'float64')
self.assertEqual(tbl.coldtypes['c'].shape, (2,))
self.assertEqual(tbl.coltypes['d'], 'string')
self.assertEqual(tbl.coldtypes['d'].shape, ())
for row in tbl.iterrows():
self.assertEqual(row['a'], 3.0)
self.assertEqual(row['b'], 4.0)
self.assertTrue(allequal(row['c'], numpy.array([2.0, 3.0],
dtype="float64")))
self.assertEqual(row['d'], b"d")
self.h5file.close()
class F64LETestCase(NumericTestCase):
h5fname = test_filename('smpl_f64le.h5')
type = 'float64'
byteorder = 'little'
def setUp(self):
self.h5fname = test_filename(self.FILENAME % self.format)
super(BackCompatAttrsTestCase, self).setUp()
def setUp(self):
self.h5fname = test_filename(self.FILENAME % self.format)
super().setUp()
class I64LETestCase(NumericTestCase):
h5fname = test_filename('smpl_i64le.h5')
type = 'int64'
byteorder = 'little'
def setUp(self):
super().setUp()
filename = common.test_filename('times-nested-be.h5')
self.h5file = tb.open_file(filename, 'r')
class I32LETestCase(NumericTestCase):
h5fname = test_filename('smpl_i32le.h5')
type = 'int32'
byteorder = 'little'
class F64BETestCase(NumericTestCase):
h5fname = test_filename('smpl_f64be.h5')
type = 'float64'
byteorder = 'big'
def setUp(self):
self.h5fname = test_filename(self.FILENAME % self.format)
super(BackCompatAttrsTestCase, self).setUp()
class I64BETestCase(NumericTestCase):
h5fname = test_filename('smpl_i64be.h5')
type = 'int64'
byteorder = 'big'
def setUp(self):
super(BigEndianTestCase, self).setUp()
filename = test_filename('times-nested-be.h5')
self.h5file = tables.open_file(filename, 'r')
class Indexes2_1TestCase(IndexesTestCase):
h5fname = test_filename("indexes_2_1.h5")
class I32BETestCase(NumericTestCase):
h5fname = test_filename('smpl_i32be.h5')
type = 'int32'
byteorder = 'big'
class ReadFloatTestCase(common.TestFileMixin, TestCase):
h5fname = test_filename("float.h5")
nrows = 5
ncols = 6
def setUp(self):
super(ReadFloatTestCase, self).setUp()
x = numpy.arange(self.ncols)
y = numpy.arange(self.nrows)
y.shape = (self.nrows, 1)
self.values = x + y
def test01_read_float16(self):
dtype = "float16"
if hasattr(numpy, dtype):
ds = getattr(self.h5file.root, dtype)
self.assertFalse(isinstance(ds, tables.UnImplemented))
self.assertEqual(ds.shape, (self.nrows, self.ncols))
self.assertEqual(ds.dtype, dtype)
self.assertTrue(
common.allequal(ds.read(), self.values.astype(dtype)))
else:
with self.assertWarns(UserWarning):
ds = getattr(self.h5file.root, dtype)
self.assertTrue(isinstance(ds, tables.UnImplemented))
def test02_read_float32(self):
dtype = "float32"
ds = getattr(self.h5file.root, dtype)
self.assertFalse(isinstance(ds, tables.UnImplemented))
self.assertEqual(ds.shape, (self.nrows, self.ncols))
self.assertEqual(ds.dtype, dtype)
self.assertTrue(common.allequal(ds.read(), self.values.astype(dtype)))
def test03_read_float64(self):
dtype = "float64"
ds = getattr(self.h5file.root, dtype)
self.assertFalse(isinstance(ds, tables.UnImplemented))
self.assertEqual(ds.shape, (self.nrows, self.ncols))
self.assertEqual(ds.dtype, dtype)
self.assertTrue(common.allequal(ds.read(), self.values.astype(dtype)))
def test04_read_longdouble(self):
dtype = "longdouble"
if hasattr(tables, "Float96Atom") or hasattr(tables, "Float128Atom"):
ds = getattr(self.h5file.root, dtype)
self.assertFalse(isinstance(ds, tables.UnImplemented))
self.assertEqual(ds.shape, (self.nrows, self.ncols))
self.assertEqual(ds.dtype, dtype)
self.assertTrue(
common.allequal(ds.read(), self.values.astype(dtype)))
if hasattr(tables, "Float96Atom"):
self.assertEqual(ds.dtype, "float96")
elif hasattr(tables, "Float128Atom"):
self.assertEqual(ds.dtype, "float128")
else:
# XXX: check
# the behavior depends on the HDF5 lib configuration
try:
with self.assertWarns(UserWarning):
ds = getattr(self.h5file.root, dtype)
self.assertTrue(isinstance(ds, tables.UnImplemented))
except AssertionError:
from tables.utilsextension import _broken_hdf5_long_double
if not _broken_hdf5_long_double():
ds = getattr(self.h5file.root, dtype)
self.assertEqual(ds.dtype, "float64")
def test05_read_quadprecision_float(self):
# XXX: check
try:
with self.assertWarns(UserWarning):
ds = self.h5file.root.quadprecision
self.assertTrue(isinstance(ds, tables.UnImplemented))
except AssertionError:
# NOTE: it would be nice to have some sort of message that warns
# against the potential precision loss: the quad-precision
# dataset actually uses 128 bits for each element, not just
# 80 bits (longdouble)
ds = self.h5file.root.quadprecision
self.assertEqual(ds.dtype, "longdouble")
class Indexes2_0TestCase(IndexesTestCase):
h5fname = common.test_filename("indexes_2_0.h5")