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import io
import lzma
import os
import numpy as np
import pytest
import asdf
from asdf import compression, config_context, generic_io
from asdf.extension import Compressor, Extension
from ..tests import helpers
def _get_large_tree():
np.random.seed(0)
x = np.random.rand(128, 128)
tree = {
"science_data": x,
}
return tree
def _get_sparse_tree():
np.random.seed(0)
arr = np.zeros((128, 128))
for x, y, z in np.random.rand(64, 3):
arr[int(x * 127), int(y * 127)] = z
arr[0, 0] = 5.0
tree = {"science_data": arr}
return tree
def _roundtrip(tmp_path, tree, compression=None, write_options={}, read_options={}):
write_options = write_options.copy()
write_options.update(all_array_compression=compression)
tmpfile = os.path.join(str(tmp_path), "test.asdf")
ff = asdf.AsdfFile(tree)
ff.write_to(tmpfile, **write_options)
with asdf.open(tmpfile, mode="rw") as ff:
ff.update(**write_options)
with asdf.open(tmpfile, **read_options) as ff:
helpers.assert_tree_match(tree, ff.tree)
# Also test saving to a buffer
buff = io.BytesIO()
ff = asdf.AsdfFile(tree)
ff.write_to(buff, **write_options)
buff.seek(0)
with asdf.open(buff, **read_options) as ff:
helpers.assert_tree_match(tree, ff.tree)
# Test saving to a non-seekable buffer
buff = io.BytesIO()
ff = asdf.AsdfFile(tree)
ff.write_to(generic_io.OutputStream(buff), **write_options)
buff.seek(0)
with asdf.open(generic_io.InputStream(buff), **read_options) as ff:
helpers.assert_tree_match(tree, ff.tree)
return tmpfile
def test_invalid_compression():
tree = _get_large_tree()
ff = asdf.AsdfFile(tree)
with pytest.raises(ValueError):
ff.set_array_compression(tree["science_data"], "foo")
with pytest.raises(ValueError):
compression._get_compressor("foo")
def test_get_compressed_size():
assert compression.get_compressed_size(b"0" * 1024, "zlib") < 1024
def test_decompress_too_long_short():
fio = io.BytesIO()
compression.compress(fio, b"0" * 1024, "zlib")
size = fio.tell()
fio.seek(0)
blocks = lambda us: [fio.read(us)] # noqa: E731
fio.read_blocks = blocks
compression.decompress(fio, size, 1024, "zlib")
fio.seek(0)
with pytest.raises(ValueError):
compression.decompress(fio, size, 1025, "zlib")
fio.seek(0)
with pytest.raises(ValueError):
compression.decompress(fio, size, 1023, "zlib")
def test_zlib(tmp_path):
tree = _get_large_tree()
_roundtrip(tmp_path, tree, "zlib")
def test_bzp2(tmp_path):
tree = _get_large_tree()
_roundtrip(tmp_path, tree, "bzp2")
def test_lz4(tmp_path):
pytest.importorskip("lz4")
tree = _get_large_tree()
_roundtrip(tmp_path, tree, "lz4")
def test_recompression(tmp_path):
tree = _get_large_tree()
tmpfile = os.path.join(str(tmp_path), "test1.asdf")
afile = asdf.AsdfFile(tree)
afile.write_to(tmpfile, all_array_compression="zlib")
afile.close()
afile = asdf.open(tmpfile)
tmpfile = os.path.join(str(tmp_path), "test2.asdf")
afile.write_to(tmpfile, all_array_compression="bzp2")
afile.close()
afile = asdf.open(tmpfile)
helpers.assert_tree_match(tree, afile.tree)
afile.close()
def test_input(tmp_path):
tree = _get_large_tree()
tmpfile = os.path.join(str(tmp_path), "test1.asdf")
afile = asdf.AsdfFile(tree)
afile.write_to(tmpfile, all_array_compression="zlib")
afile.close()
afile = asdf.open(tmpfile)
tmpfile = os.path.join(str(tmp_path), "test2.asdf")
afile.write_to(tmpfile)
afile.close()
afile = asdf.open(tmpfile)
helpers.assert_tree_match(tree, afile.tree)
assert afile.get_array_compression(afile.tree["science_data"]) == "zlib"
afile.close()
def test_none(tmp_path):
tree = _get_large_tree()
tmpfile1 = os.path.join(str(tmp_path), "test1.asdf")
with asdf.AsdfFile(tree) as afile:
afile.write_to(tmpfile1)
tmpfile2 = os.path.join(str(tmp_path), "test2.asdf")
with asdf.open(tmpfile1) as afile:
assert afile.get_array_compression(afile.tree["science_data"]) is None
afile.write_to(tmpfile2, all_array_compression="zlib")
assert afile.get_array_compression(afile.tree["science_data"]) == "zlib"
with asdf.open(tmpfile2) as afile:
afile.write_to(tmpfile1, all_array_compression=None)
with asdf.open(tmpfile1) as afile:
helpers.assert_tree_match(tree, afile.tree)
assert afile.get_array_compression(afile.tree["science_data"]) is None
def test_set_array_compression(tmp_path):
tmpfile = os.path.join(str(tmp_path), "compressed.asdf")
zlib_data = np.array([x for x in range(1000)])
bzp2_data = np.array([x for x in range(1000)])
tree = dict(zlib_data=zlib_data, bzp2_data=bzp2_data)
with asdf.AsdfFile(tree) as af_out:
af_out.set_array_compression(zlib_data, "zlib", level=1)
af_out.set_array_compression(bzp2_data, "bzp2", compresslevel=9000)
with pytest.raises(ValueError):
af_out.write_to(tmpfile)
af_out.set_array_compression(bzp2_data, "bzp2", compresslevel=9)
af_out.write_to(tmpfile)
with asdf.open(tmpfile) as af_in:
assert af_in.get_array_compression(af_in.tree["zlib_data"]) == "zlib"
assert af_in.get_array_compression(af_in.tree["bzp2_data"]) == "bzp2"
def test_nonnative_endian_compression(tmp_path):
ledata = np.arange(1000, dtype="<i8")
bedata = np.arange(1000, dtype=">i8")
_roundtrip(tmp_path, dict(ledata=ledata, bedata=bedata), "lz4")
class LzmaCompressor(Compressor):
def compress(self, data, **kwargs):
comp = lzma.compress(data, **kwargs)
yield comp
def decompress(self, blocks, out, **kwargs):
decompressor = lzma.LZMADecompressor(**kwargs)
i = 0
for block in blocks:
decomp = decompressor.decompress(block)
out[i : i + len(decomp)] = decomp
i += len(decomp)
return i
@property
def label(self):
return b"lzma"
class LzmaExtension(Extension):
@property
def extension_uri(self):
return "asdf://somewhere.org/extensions/lzma-1.0"
@property
def compressors(self):
return [LzmaCompressor()]
def test_compression_with_extension(tmp_path):
tree = _get_large_tree()
with config_context() as config:
config.add_extension(LzmaExtension())
with pytest.raises(lzma.LZMAError):
_roundtrip(tmp_path, tree, "lzma", write_options=dict(compression_kwargs={"preset": 9000}))
fn = _roundtrip(tmp_path, tree, "lzma", write_options=dict(compression_kwargs={"preset": 6}))
hist = {
"extension_class": "asdf.tests.test_compression.LzmaExtension",
"extension_uri": "asdf://somewhere.org/extensions/lzma-1.0",
"supported_compression": ["lzma"],
}
with asdf.open(fn) as af:
assert hist in af["history"]["extensions"]
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