def test_data(comm):
with temporary_data() as (data, tmpfile):
# read
f = HDFFile(tmpfile, header='Header')
# check columns
cols = ['X/Mass', 'X/Position', 'Y/Mass', 'Y/Position']
assert (all(col in cols for col in f.columns))
assert f.attrs['Value'] == 333
# make sure data is the same
for col in cols:
field = col.rsplit('/', 1)[-1]
numpy.testing.assert_almost_equal(data[field], f[col][:])
# try a slice
data2 = f.read(cols, 0, 512, 1)
for col in cols:
field = col.rsplit('/', 1)[-1]
numpy.testing.assert_almost_equal(data[field][:512], data2[col])
# check size
numpy.testing.assert_equal(f.size, 1024)
def test_data(comm):
with temporary_data() as (data, tmpfile):
# read
f = HDFFile(tmpfile, header='Header')
# check columns
cols = ['X/Mass', 'X/Position', 'Y/Mass', 'Y/Position']
assert(all(col in cols for col in f.columns))
assert f.attrs['Value'] == 333
# make sure data is the same
for col in cols:
field = col.rsplit('/', 1)[-1]
numpy.testing.assert_almost_equal(data[field], f[col][:])
# try a slice
data2 = f.read(cols, 0, 512, 1)
for col in cols:
field = col.rsplit('/', 1)[-1]
numpy.testing.assert_almost_equal(data[field][:512], data2[col])
# check size
numpy.testing.assert_equal(f.size, 1024)
def test_nonzero_root(comm):
with temporary_data() as (data, tmpfile):
# read
f = HDFFile(tmpfile, dataset='Y')
# non-zero root
f = HDFFile(tmpfile, dataset='Y')
assert (all(col in ['Mass', 'Position'] for col in f.columns))
# wrong root
with pytest.raises(ValueError):
f = HDFFile(tmpfile, dataset='Z')
def test_nonzero_exclude(comm):
with temporary_data() as (data, tmpfile):
# read
f = HDFFile(tmpfile, exclude=['Y', 'Header'])
# non-zero exclude
f = HDFFile(tmpfile, exclude=['Y', 'Header'])
assert (all(col in ['Mass', 'Position'] for col in f.columns))
# non-zero exclude and root
f = HDFFile(tmpfile, exclude=['Mass'], dataset='Y')
assert all(col in ['Position'] for col in f.columns)
# bad exclude
with pytest.raises(ValueError):
f = HDFFile(tmpfile, exclude=['Z'])
def test_empty(comm):
# create empty file
tmpfile = tempfile.mkstemp()[1]
with h5py.File(tmpfile, 'w') as ff:
ff.create_group('Y')
# no datasets!
with pytest.raises(ValueError):
f = HDFFile(tmpfile)
os.unlink(tmpfile)
def test_data_mismatch(comm):
# generate data
pos = numpy.random.random(size=(1024, 3))
mass = numpy.random.random(size=512)
# write to file
tmpfile = tempfile.mkstemp()[1]
with h5py.File(tmpfile, 'w') as ff:
ff.create_dataset('Mass', data=mass)
ff.create_dataset('Position', data=pos)
# fails due to mismatched sizes
with pytest.raises(ValueError):
f = HDFFile(tmpfile)
# only one dataset now, so this works
f = HDFFile(tmpfile, exclude=['Mass'])
assert f.size == 1024
os.unlink(tmpfile)