예제 #1
0
파일: test_io.py 프로젝트: Eric89GXL/h5io
def test_hdf5():
    """Test HDF5 IO
    """
    tempdir = _TempDir()
    test_file = op.join(tempdir, "test.hdf5")
    sp = np.eye(3) if sparse is None else sparse.eye(3, 3, format="csc")
    sp[2, 2] = 2
    x = dict(
        a=dict(b=np.zeros(3)),
        c=np.zeros(2, np.complex128),
        d=[dict(e=(1, -2.0, "hello", u"goodbyeu\u2764")), None],
        f=sp,
    )
    write_hdf5(test_file, 1)
    assert_equal(read_hdf5(test_file), 1)
    assert_raises(IOError, write_hdf5, test_file, x)  # file exists
    write_hdf5(test_file, x, overwrite=True)
    assert_raises(IOError, read_hdf5, test_file + "FOO")  # not found
    xx = read_hdf5(test_file)
    assert_true(object_diff(x, xx) == "")  # no assert_equal, ugly output

    # bad title
    assert_raises(ValueError, read_hdf5, test_file, title="nonexist")
    assert_raises(ValueError, write_hdf5, test_file, x, overwrite=True, title=1)
    assert_raises(ValueError, read_hdf5, test_file, title=1)
    # unsupported objects
    assert_raises(TypeError, write_hdf5, test_file, {1: "foo"}, overwrite=True)
    assert_raises(TypeError, write_hdf5, test_file, object, overwrite=True)
예제 #2
0
파일: test_io.py 프로젝트: kingjr/h5io
def test_path_support():
    tempdir = _TempDir()
    test_file = op.join(tempdir, 'test.hdf5')
    write_hdf5(test_file, 1, title='first')
    write_hdf5(test_file, 2, title='second/third', overwrite='update')
    assert_raises(ValueError, read_hdf5, test_file, title='second')
    assert_equal(read_hdf5(test_file, 'first'), 1)
    assert_equal(read_hdf5(test_file, 'second/third'), 2)
예제 #3
0
파일: test_io.py 프로젝트: kingjr/h5io
def test_path_support():
    tempdir = _TempDir()
    test_file = op.join(tempdir, 'test.hdf5')
    write_hdf5(test_file, 1, title='first')
    write_hdf5(test_file, 2, title='second/third', overwrite='update')
    assert_raises(ValueError, read_hdf5, test_file, title='second')
    assert_equal(read_hdf5(test_file, 'first'), 1)
    assert_equal(read_hdf5(test_file, 'second/third'), 2)
예제 #4
0
def test_numpy_values():
    tempdir = _TempDir()
    test_file = op.join(tempdir, 'test.hdf5')
    for cast in [np.int8, np.int16, np.int32, np.int64, np.bool_,
                 np.float16, np.float32, np.float64]:
        value = cast(1)
        write_hdf5(test_file, value, title='first', overwrite='update')
        assert_equal(read_hdf5(test_file, 'first'), value)
예제 #5
0
파일: test_io.py 프로젝트: whigg/h5io
def test_multi_dim_array():
    rng = np.random.RandomState(0)
    traj = np.array([rng.randn(2, 1), rng.randn(3, 1)])
    tempdir = _TempDir()
    test_file = op.join(tempdir, 'test.hdf5')
    write_hdf5(test_file, traj, title='first', overwrite='update')
    for traj_read, traj_sub in zip(read_hdf5(test_file, 'first'), traj):
        assert (np.equal(traj_read, traj_sub).all())
    traj_no_structure = np.array([rng.randn(2, 1, 1), rng.randn(3, 1, 2)])
    pytest.raises(ValueError,
                  write_hdf5,
                  test_file,
                  traj_no_structure,
                  title='second',
                  overwrite='update')
예제 #6
0
파일: test_io.py 프로젝트: kingjr/h5io
def test_hdf5():
    """Test HDF5 IO
    """
    tempdir = _TempDir()
    test_file = op.join(tempdir, 'test.hdf5')
    sp = np.eye(3) if sparse is None else sparse.eye(3, 3, format='csc')
    df = np.eye(3) if isinstance(DataFrame, type(None)) else DataFrame(
        np.eye(3))
    sr = np.eye(3) if isinstance(Series, type(None)) else Series(
        np.random.randn(3))
    sp[2, 2] = 2
    x = dict(a=dict(b=np.zeros(3)),
             c=np.zeros(2, np.complex128),
             d=[dict(e=(1, -2., 'hello', u'goodbyeu\u2764')), None],
             f=sp,
             g=dict(dfa=df, srb=sr))
    write_hdf5(test_file, 1)
    assert_equal(read_hdf5(test_file), 1)
    assert_raises(IOError, write_hdf5, test_file, x)  # file exists
    write_hdf5(test_file, x, overwrite=True)
    assert_raises(IOError, read_hdf5, test_file + 'FOO')  # not found
    xx = read_hdf5(test_file)
    assert_true(object_diff(x, xx) == '')  # no assert_equal, ugly output

    # bad title
    assert_raises(ValueError, read_hdf5, test_file, title='nonexist')
    assert_raises(ValueError,
                  write_hdf5,
                  test_file,
                  x,
                  overwrite=True,
                  title=1)
    assert_raises(ValueError, read_hdf5, test_file, title=1)
    # unsupported objects
    assert_raises(TypeError, write_hdf5, test_file, {1: 'foo'}, overwrite=True)
    assert_raises(TypeError, write_hdf5, test_file, object, overwrite=True)

    write_hdf5(test_file, 1, title='first', overwrite=True)
    write_hdf5(test_file, 2, title='second', overwrite='update')
    assert_equal(read_hdf5(test_file, title='first'), 1)
    assert_equal(read_hdf5(test_file, title='second'), 2)
    assert_raises(IOError, write_hdf5, test_file, 3, title='second')
    write_hdf5(test_file, 3, title='second', overwrite='update')
    assert_equal(read_hdf5(test_file, title='second'), 3)

    write_hdf5(test_file, 5, title='second', overwrite='update', compression=5)
    assert_equal(read_hdf5(test_file, title='second'), 5)
예제 #7
0
파일: test_io.py 프로젝트: whigg/h5io
def test_hdf5_use_json():
    """Test HDF5 IO
    """
    tempdir = _TempDir()
    test_file = op.join(tempdir, 'test.hdf5')
    splash_dict = {'first/second': {'one/more': 'value'}}
    pytest.raises(ValueError,
                  write_hdf5,
                  test_file,
                  splash_dict,
                  overwrite=True,
                  slash='error',
                  use_json=True)
    spec_dict = {'first/second': 'third'}
    write_hdf5(test_file,
               spec_dict,
               overwrite=True,
               slash='replace',
               use_json=True)
    assert_equal(
        read_hdf5(test_file, slash='replace').keys(), spec_dict.keys())
    in_keys = list(read_hdf5(test_file, slash='ignore').keys())
    assert ('{FWDSLASH}' in in_keys[0])
    comp_dict = {'first': [1, 2], 'second': 'str', 'third': {'a': 1}}
    write_hdf5(test_file, comp_dict, overwrite=True, use_json=True)
    assert_equal(sorted(read_hdf5(test_file, slash='replace').keys()),
                 sorted(comp_dict.keys()))
    numpy_dict = {'first': np.array([1])}
    write_hdf5(test_file, numpy_dict, overwrite=True, use_json=True)
    assert_equal(
        list(read_hdf5(test_file, slash='replace').values())[0],
        list(numpy_dict.values())[0])
    pytest.raises(ValueError, read_hdf5, test_file, slash='brains')
    # Testing that title slashes aren't replaced
    write_hdf5(test_file,
               spec_dict,
               title='one/two',
               overwrite=True,
               slash='replace',
               use_json=True)
    assert_equal(
        read_hdf5(test_file, title='one/two', slash='replace').keys(),
        spec_dict.keys())
예제 #8
0
파일: test_io.py 프로젝트: kingjr/h5io
def test_hdf5():
    """Test HDF5 IO
    """
    tempdir = _TempDir()
    test_file = op.join(tempdir, 'test.hdf5')
    sp = np.eye(3) if sparse is None else sparse.eye(3, 3, format='csc')
    df = np.eye(3) if isinstance(DataFrame, type(None)) else DataFrame(
        np.eye(3))
    sr = np.eye(3) if isinstance(Series, type(None)) else Series(
        np.random.randn(3))
    sp[2, 2] = 2
    x = dict(a=dict(b=np.zeros(3)), c=np.zeros(2, np.complex128),
             d=[dict(e=(1, -2., 'hello', u'goodbyeu\u2764')), None], f=sp,
             g=dict(dfa=df, srb=sr))
    write_hdf5(test_file, 1)
    assert_equal(read_hdf5(test_file), 1)
    assert_raises(IOError, write_hdf5, test_file, x)  # file exists
    write_hdf5(test_file, x, overwrite=True)
    assert_raises(IOError, read_hdf5, test_file + 'FOO')  # not found
    xx = read_hdf5(test_file)
    assert_true(object_diff(x, xx) == '')  # no assert_equal, ugly output

    # bad title
    assert_raises(ValueError, read_hdf5, test_file, title='nonexist')
    assert_raises(ValueError, write_hdf5, test_file, x, overwrite=True,
                  title=1)
    assert_raises(ValueError, read_hdf5, test_file, title=1)
    # unsupported objects
    assert_raises(TypeError, write_hdf5, test_file, {1: 'foo'},
                  overwrite=True)
    assert_raises(TypeError, write_hdf5, test_file, object, overwrite=True)

    write_hdf5(test_file, 1, title='first', overwrite=True)
    write_hdf5(test_file, 2, title='second', overwrite='update')
    assert_equal(read_hdf5(test_file, title='first'), 1)
    assert_equal(read_hdf5(test_file, title='second'), 2)
    assert_raises(IOError, write_hdf5, test_file, 3, title='second')
    write_hdf5(test_file, 3, title='second', overwrite='update')
    assert_equal(read_hdf5(test_file, title='second'), 3)

    write_hdf5(test_file, 5, title='second', overwrite='update', compression=5)
    assert_equal(read_hdf5(test_file, title='second'), 5)
예제 #9
0
def test_hdf5():
    """Test HDF5 IO
    """
    tempdir = _TempDir()
    test_file = op.join(tempdir, 'test.hdf5')
    sp = np.eye(3) if sparse is None else sparse.eye(3, 3, format='csc')
    sp_csr = np.eye(3) if sparse is None else sparse.eye(3, 3, format='csr')
    df = np.eye(3) if isinstance(DataFrame, type(None)) else DataFrame(
        np.eye(3))
    sr = np.eye(3) if isinstance(Series, type(None)) else Series(
        np.random.randn(3))
    sp[2, 2] = 2
    sp_csr[2, 2] = 2
    x = dict(a=dict(b=np.zeros(3)), c=np.zeros(2, np.complex128),
             d=[dict(e=(1, -2., 'hello', u'goodbyeu\u2764')), None], f=sp,
             g=dict(dfa=df, srb=sr), h=sp_csr, i=sr, j='hi')
    write_hdf5(test_file, 1)
    assert_equal(read_hdf5(test_file), 1)
    assert_raises(IOError, write_hdf5, test_file, x)  # file exists
    write_hdf5(test_file, x, overwrite=True)
    assert_raises(IOError, read_hdf5, test_file + 'FOO')  # not found
    xx = read_hdf5(test_file)
    assert_true(object_diff(x, xx) == '')  # no assert_equal, ugly output
    list_file_contents(test_file)  # Testing the h5 listing
    assert_raises(TypeError, list_file_contents, sp)  # Only string works
    write_hdf5(test_file, np.bool_(True), overwrite=True)
    assert_equal(read_hdf5(test_file), np.bool_(True))

    # bad title
    assert_raises(ValueError, read_hdf5, test_file, title='nonexist')
    assert_raises(ValueError, write_hdf5, test_file, x, overwrite=True,
                  title=1)
    assert_raises(ValueError, read_hdf5, test_file, title=1)
    # unsupported objects
    assert_raises(TypeError, write_hdf5, test_file, {1: 'foo'},
                  overwrite=True)
    assert_raises(TypeError, write_hdf5, test_file, object, overwrite=True)
    # special_chars
    spec_dict = {'first/second': 'third'}
    assert_raises(ValueError, write_hdf5, test_file, spec_dict, overwrite=True)
    assert_raises(ValueError, write_hdf5, test_file, spec_dict, overwrite=True,
                  slash='brains')
    write_hdf5(test_file, spec_dict, overwrite=True, slash='replace')
    assert_equal(
        read_hdf5(test_file, slash='replace').keys(), spec_dict.keys())
    in_keys = list(read_hdf5(test_file, slash='ignore').keys())
    assert_true('{FWDSLASH}' in in_keys[0])
    assert_raises(ValueError, read_hdf5, test_file, slash='brains')
    # Testing that title slashes aren't replaced
    write_hdf5(
        test_file, spec_dict, title='one/two', overwrite=True, slash='replace')
    assert_equal(read_hdf5(test_file, title='one/two', slash='replace').keys(),
                 spec_dict.keys())

    write_hdf5(test_file, 1, title='first', overwrite=True)
    write_hdf5(test_file, 2, title='second', overwrite='update')
    assert_equal(read_hdf5(test_file, title='first'), 1)
    assert_equal(read_hdf5(test_file, title='second'), 2)
    assert_raises(IOError, write_hdf5, test_file, 3, title='second')
    write_hdf5(test_file, 3, title='second', overwrite='update')
    assert_equal(read_hdf5(test_file, title='second'), 3)

    write_hdf5(test_file, 5, title='second', overwrite='update', compression=5)
    assert_equal(read_hdf5(test_file, title='second'), 5)