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import sys
import zlib
import itertools
import numpy as np
import tables as tb
from tables.tests import common
class ArrayDirectChunkingTestCase(
common.TempFileMixin, common.PyTablesTestCase
):
obj = np.arange(25, dtype="uint8")
def setUp(self):
super().setUp()
self.array = self.h5file.create_array("/", "array", self.obj)
def test_chunk_info(self):
self.assertRaises(
tb.NotChunkedError, self.array.chunk_info, (0,) * self.array.ndim
)
def test_read_chunk(self):
self.assertRaises(
tb.NotChunkedError, self.array.read_chunk, (0,) * self.array.ndim
)
def test_read_chunk_out(self):
arr = np.zeros(self.obj.shape, dtype=self.obj.dtype)
self.assertRaises(
tb.NotChunkedError,
self.array.read_chunk,
(0,) * self.array.ndim,
out=memoryview(arr),
)
def test_write_chunk(self):
arr = self.obj // 2
self.assertRaises(
tb.NotChunkedError,
self.array.write_chunk,
(0,) * self.array.ndim,
arr,
)
# For enlargeable and non-enlargeable datasets.
class DirectChunkingTestCase(common.TempFileMixin, common.PyTablesTestCase):
# Class attributes:
shape: tuple[int, ...]
chunkshape: tuple[int, ...]
shuffle: bool
obj: np.ndarray
# Instance attributes:
array: tb.Leaf # set by ``setUp()`` and ``_reopen()``
filters: tb.Filters
def setUp(self):
super().setUp()
self.filters = tb.Filters(
complib="zlib", complevel=1, shuffle=self.shuffle
)
def modified(self, obj):
# Return altered copy with same dtype and shape.
raise NotImplementedError
def iter_chunks(self):
chunk_ranges = list(
range(0, s, cs) for (s, cs) in zip(self.shape, self.chunkshape)
)
yield from itertools.product(*chunk_ranges)
def test_chunk_info_aligned(self):
for chunk_start in self.iter_chunks():
chunk_info = self.array.chunk_info(chunk_start)
self.assertEqual(chunk_info.start, chunk_start)
self.assertIsNotNone(chunk_info.filter_mask)
self.assertIsNotNone(chunk_info.offset)
self.assertIsNotNone(chunk_info.size)
def test_chunk_info_unaligned(self):
chunk_info_a = self.array.chunk_info((0,) * self.array.ndim)
chunk_info_u = self.array.chunk_info((1,) * self.array.ndim)
self.assertIsNotNone(chunk_info_a.start)
self.assertEqual(chunk_info_a, chunk_info_u)
def test_chunk_info_aligned_beyond(self):
beyond = tuple(
(1 + s // cs) * cs for (s, cs) in zip(self.shape, self.chunkshape)
)
self.assertRaises(IndexError, self.array.chunk_info, beyond)
def test_chunk_info_unaligned_beyond(self):
beyond = tuple(
1 + (1 + s // cs) * cs
for (s, cs) in zip(self.shape, self.chunkshape)
)
self.assertRaises(IndexError, self.array.chunk_info, beyond)
def shuffled(self, bytes_):
itemsize = self.obj.dtype.itemsize
return b"".join(bytes_[d::itemsize] for d in range(itemsize))
def filter_chunk(self, bytes_, shuffle=None):
assert self.filters.complib == "zlib"
if shuffle is None:
shuffle = self.shuffle
maybe_shuffled = self.shuffled(bytes_) if shuffle else bytes_
return zlib.compress(maybe_shuffled, self.filters.complevel)
def test_read_chunk(self):
# Extended to fit chunk boundaries.
ext_obj = np.pad(
self.obj,
[(0, s % cs) for (s, cs) in zip(self.shape, self.chunkshape)],
)
for chunk_start in self.iter_chunks():
chunk = self.array.read_chunk(chunk_start)
self.assertIsInstance(chunk, bytes)
obj_slice = tuple(
slice(s, s + cs)
for (s, cs) in zip(chunk_start, self.chunkshape)
)
obj_bytes = self.filter_chunk(ext_obj[obj_slice].tobytes())
self.assertEqual(chunk, obj_bytes)
def test_read_chunk_out(self):
# Extended to fit chunk boundaries.
ext_obj = np.pad(
self.obj,
[(0, s % cs) for (s, cs) in zip(self.shape, self.chunkshape)],
)
chunk_start = (0,) * self.obj.ndim
obj_slice = tuple(
slice(s, s + cs) for (s, cs) in zip(chunk_start, self.chunkshape)
)
obj_bytes = self.filter_chunk(ext_obj[obj_slice].tobytes())
chunk_size = len(obj_bytes)
chunk_out = bytearray(chunk_size - 1) # too short
self.assertRaises(
ValueError, self.array.read_chunk, chunk_start, out=chunk_out
)
chunk_out = bytearray(chunk_size)
chunk = self.array.read_chunk(chunk_start, out=chunk_out)
self.assertIsInstance(chunk, memoryview)
self.assertEqual(chunk, obj_bytes)
self.assertEqual(chunk_out, obj_bytes)
def test_read_chunk_unaligned(self):
self.assertRaises(
tb.NotChunkAlignedError,
self.array.read_chunk,
(1,) * self.array.ndim,
)
def test_read_chunk_beyond(self):
beyond = tuple(
(1 + s // cs) * cs for (s, cs) in zip(self.shape, self.chunkshape)
)
self.assertRaises(IndexError, self.array.read_chunk, beyond)
def test_write_chunk(self):
new_obj = self.modified(self.obj)
# Extended to fit chunk boundaries.
ext_obj = np.pad(
new_obj,
[(0, s % cs) for (s, cs) in zip(self.shape, self.chunkshape)],
)
for chunk_start in self.iter_chunks():
obj_slice = tuple(
slice(s, s + cs)
for (s, cs) in zip(chunk_start, self.chunkshape)
)
obj_bytes = self.filter_chunk(ext_obj[obj_slice].tobytes())
self.array.write_chunk(chunk_start, obj_bytes)
self._reopen()
self.assertTrue(common.areArraysEqual(self.array[:], new_obj))
def test_write_chunk_filtermask(self):
no_shuffle_mask = 0x00000004 # to turn shuffle off
chunk_start = (0,) * self.obj.ndim
obj_slice = tuple(
slice(s, s + cs) for (s, cs) in zip(chunk_start, self.chunkshape)
)
new_obj = self.obj.copy()
new_obj[obj_slice] = self.modified(new_obj[obj_slice])
obj_bytes = self.filter_chunk(
new_obj[obj_slice].tobytes(), shuffle=False
)
self.array.write_chunk(
chunk_start, obj_bytes, filter_mask=no_shuffle_mask
)
self._reopen()
arr_obj = self.array[:] # first chunk is shuffled, fix it
fixed_bytes = self.shuffled(arr_obj[obj_slice].tobytes())
fixed_chunk = np.ndarray(
self.chunkshape, dtype=self.obj.dtype, buffer=fixed_bytes
)
arr_obj[obj_slice] = fixed_chunk
self.assertTrue(common.areArraysEqual(arr_obj, new_obj))
chunk_info = self.array.chunk_info(chunk_start)
self.assertEqual(chunk_info.filter_mask, no_shuffle_mask)
def test_write_chunk_unaligned(self):
self.assertRaises(
tb.NotChunkAlignedError,
self.array.write_chunk,
(1,) * self.array.ndim,
b"foobar",
)
def test_write_chunk_beyond(self):
beyond = tuple(
(1 + s // cs) * cs for (s, cs) in zip(self.shape, self.chunkshape)
)
self.assertRaises(
IndexError, self.array.write_chunk, beyond, b"foobar"
)
# For enlargeable datasets only.
class XDirectChunkingTestCase(DirectChunkingTestCase):
def test_chunk_info_miss_extdim(self):
# Next chunk in the enlargeable dimension.
assert self.array.extdim == 0
chunk_start = (
((1 + self.shape[0] // self.chunkshape[0]) * self.chunkshape[0]),
*((0,) * (self.array.ndim - 1)),
)
self.assertRaises(IndexError, self.array.chunk_info, chunk_start)
# Enlarge the array to put the (missing) chunk within the shape.
self.array.truncate(chunk_start[0] + self.chunkshape[0])
chunk_info = self.array.chunk_info(chunk_start)
self.assertIsNone(chunk_info.filter_mask)
self.assertIsNone(chunk_info.offset)
self.assertIsNone(chunk_info.size)
def test_chunk_info_miss_noextdim(self):
if self.array.ndim < 2:
raise common.unittest.SkipTest(
"missing chunk always within enlargeable dimension"
)
# Next chunk in the first non-enlargeable dimension.
assert self.array.extdim != 1
chunk_start = (
0,
((1 + self.shape[1] // self.chunkshape[1]) * self.chunkshape[1]),
*((0,) * (self.array.ndim - 2)),
)
self.assertRaises(IndexError, self.array.chunk_info, chunk_start)
def test_read_chunk_miss_extdim(self):
# Next chunk in the enlargeable dimension.
assert self.array.extdim == 0
chunk_start = (
((1 + self.shape[0] // self.chunkshape[0]) * self.chunkshape[0]),
*((0,) * (self.array.ndim - 1)),
)
self.assertRaises(IndexError, self.array.read_chunk, chunk_start)
# Enlarge the array to put the (missing) chunk within the shape.
self.array.truncate(chunk_start[0] + self.chunkshape[0])
self.assertRaises(
tb.NoSuchChunkError, self.array.read_chunk, chunk_start
)
def _test_write_chunk_missing(self, shrink_after):
# Enlarge array by two chunk rows,
# copy first old chunk in first chunk of new last chunk row.
assert self.array.extdim == 0
chunk_start = (
(
(1 + self.shape[0] // self.chunkshape[0]) * self.chunkshape[0]
+ self.chunkshape[0]
),
*((0,) * (self.array.ndim - 1)),
)
chunk = self.array.read_chunk((0,) * self.array.ndim)
self.array.truncate(chunk_start[0] + self.chunkshape[0])
self.array.write_chunk(chunk_start, chunk)
if shrink_after:
self.array.truncate(self.shape[0] + 1)
self.array.truncate(self.shape[0] - 1)
new_obj = self.obj.copy()
new_obj.resize(self.array.shape, refcheck=False)
obj_slice = tuple(
slice(s, s + cs) for (s, cs) in zip(chunk_start, self.chunkshape)
)
if not shrink_after:
new_obj[obj_slice] = new_obj[
tuple(slice(0, cs) for cs in self.chunkshape)
]
self._reopen()
self.assertTrue(common.areArraysEqual(self.array[:], new_obj))
def test_write_chunk_missing1(self):
return self._test_write_chunk_missing(shrink_after=False)
def test_write_chunk_missing2(self):
return self._test_write_chunk_missing(shrink_after=True)
class CArrayDirectChunkingTestCase(DirectChunkingTestCase):
shape = (5, 5)
chunkshape = (2, 2) # 3 x 3 chunks, incomplete at right/bottom boundaries
shuffle = True
obj = np.arange(np.prod(shape), dtype="u2").reshape(shape)
def setUp(self):
super().setUp()
self.array = self.h5file.create_carray(
"/",
"carray",
chunkshape=self.chunkshape,
obj=self.obj,
filters=self.filters,
)
def _reopen(self):
super()._reopen()
self.array = self.h5file.root.carray
def modified(self, obj):
return obj * 2
class EArrayDirectChunkingTestCase(XDirectChunkingTestCase):
shape = (5, 5) # enlargeable along first dimension
chunkshape = (2, 2) # 3 x 3 chunks, incomplete at right/bottom boundaries
shuffle = True
obj = np.arange(np.prod(shape), dtype="u2").reshape(shape)
def setUp(self):
super().setUp()
atom = tb.Atom.from_dtype(self.obj.dtype)
shape = (0, *self.shape[1:])
self.array = self.h5file.create_earray(
"/",
"earray",
atom,
shape,
chunkshape=self.chunkshape,
filters=self.filters,
)
self.array.append(self.obj)
def _reopen(self):
super()._reopen()
self.array = self.h5file.root.earray
def modified(self, obj):
return obj * 2
class TableDirectChunkingTestCase(XDirectChunkingTestCase):
shape = (5,) # enlargeable along first dimension
chunkshape = (2,) # 3 chunks, incomplete at bottom boundary
shuffle = True
obj = np.array(
[(i, float(i)) for i in range(np.prod(shape))], dtype="u4,f4"
)
def setUp(self):
super().setUp()
desc, _ = tb.descr_from_dtype(self.obj.dtype)
self.array = self.h5file.create_table(
"/",
"table",
desc,
chunkshape=self.chunkshape,
filters=self.filters,
)
self.array.append(self.obj)
def _reopen(self):
super()._reopen()
self.array = self.h5file.root.table
def modified(self, obj):
flat = obj.copy().reshape((np.prod(obj.shape),))
fnames = flat.dtype.names
for i in range(len(flat)):
for f in fnames:
flat[i][f] *= 2
return flat.reshape(obj.shape)
def suite():
theSuite = common.unittest.TestSuite()
niter = 1
for i in range(niter):
theSuite.addTest(common.make_suite(ArrayDirectChunkingTestCase))
theSuite.addTest(common.make_suite(CArrayDirectChunkingTestCase))
theSuite.addTest(common.make_suite(EArrayDirectChunkingTestCase))
theSuite.addTest(common.make_suite(TableDirectChunkingTestCase))
return theSuite
if __name__ == "__main__":
common.parse_argv(sys.argv)
common.print_versions()
common.unittest.main(defaultTest="suite")
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