def test_save_3D_signal(self, tmp_path):
s = BaseSignal(np.zeros((2, 3, 4)))
fname = tmp_path / 'test.nxs'
s.save(fname)
lin = load(fname, nxdata_only=True)
assert lin.axes_manager.signal_dimension == 3
np.testing.assert_array_equal(lin.data, np.zeros((2, 3, 4)))
def test_writing_unsupported_data_type():
data = np.arange(5 * 10).reshape((5, 10))
s = BaseSignal(data.astype('int64'))
with tempfile.TemporaryDirectory() as tmpdir:
with pytest.raises(IOError) as cm:
fname = os.path.join(tmpdir,
'test_writing_unsupported_data_type.unf')
s.save(fname)
cm.match("The SEMPER file format does not support int64 data type",)
def test_writing_unsupported_data_type():
data = np.arange(5 * 10).reshape((5, 10))
s = BaseSignal(data.astype('int64'))
with tempfile.TemporaryDirectory() as tmpdir:
with pytest.raises(IOError) as cm:
fname = os.path.join(tmpdir,
'test_writing_unsupported_data_type.unf')
s.save(fname)
cm.match(
"The SEMPER file format does not support int64 data type", )
def test_writing_loading_metadata():
data = np.arange(5 * 10).reshape((5, 10)).astype(np.int8)
s = BaseSignal(data)
s.metadata.set_item('General.date', "2016-08-06")
s.metadata.set_item('General.time', "11:55:00")
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test_write_with_metadata.unf')
s.save(fname)
s2 = load(fname)
np.testing.assert_allclose(s.data, s2.data)
assert s.metadata.General.date == s2.metadata.General.date
assert s.metadata.General.time == s2.metadata.General.time
def test_writing_loading_metadata():
data = np.arange(5 * 10).reshape((5, 10)).astype(np.int8)
s = BaseSignal(data)
s.metadata.set_item('General.date', "2016-08-06")
s.metadata.set_item('General.time', "11:55:00")
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test_write_with_metadata.unf')
s.save(fname)
s2 = load(fname)
np.testing.assert_allclose(s.data, s2.data)
nt.assert_equal(s.metadata.General.date, s2.metadata.General.date)
nt.assert_equal(s.metadata.General.time, s2.metadata.General.time)
def test_save_and_read(self):
signal_ref = BaseSignal(data_save)
signal_ref.metadata.General.title = test_title
signal_ref.axes_manager[0].name = 'x'
signal_ref.axes_manager[1].name = 'y'
signal_ref.axes_manager[2].name = 'z'
signal_ref.axes_manager[0].scale = 2
signal_ref.axes_manager[1].scale = 3
signal_ref.axes_manager[2].scale = 4
signal_ref.axes_manager[0].offset = 10
signal_ref.axes_manager[1].offset = 20
signal_ref.axes_manager[2].offset = 30
signal_ref.axes_manager[0].units = 'nm'
signal_ref.axes_manager[1].units = 'µm'
signal_ref.axes_manager[2].units = 'mm'
signal_ref.save(os.path.join(my_path, 'emd_files', 'example_temp.emd'),
overwrite=True,
signal_metadata=sig_metadata,
user=user,
microscope=microscope,
sample=sample,
comments=comments)
signal = load(os.path.join(my_path, 'emd_files', 'example_temp.emd'))
np.testing.assert_equal(signal.data, signal_ref.data)
np.testing.assert_equal(signal.axes_manager[0].name, 'x')
np.testing.assert_equal(signal.axes_manager[1].name, 'y')
np.testing.assert_equal(signal.axes_manager[2].name, 'z')
np.testing.assert_equal(signal.axes_manager[0].scale, 2)
np.testing.assert_almost_equal(signal.axes_manager[1].scale, 3.0)
np.testing.assert_almost_equal(signal.axes_manager[2].scale, 4.0)
np.testing.assert_equal(signal.axes_manager[0].offset, 10)
np.testing.assert_almost_equal(signal.axes_manager[1].offset, 20.0)
np.testing.assert_almost_equal(signal.axes_manager[2].offset, 30.0)
np.testing.assert_equal(signal.axes_manager[0].units, 'nm')
np.testing.assert_equal(signal.axes_manager[1].units, 'µm')
np.testing.assert_equal(signal.axes_manager[2].units, 'mm')
np.testing.assert_equal(signal.metadata.General.title, test_title)
np.testing.assert_equal(signal.metadata.General.user.as_dictionary(),
user)
np.testing.assert_equal(
signal.metadata.General.microscope.as_dictionary(), microscope)
np.testing.assert_equal(signal.metadata.General.sample.as_dictionary(),
sample)
np.testing.assert_equal(
signal.metadata.General.comments.as_dictionary(), comments)
for key, ref_value in sig_metadata.items():
np.testing.assert_equal(
signal.metadata.Signal.as_dictionary().get(key), ref_value)
assert isinstance(signal, BaseSignal)
def test_save_and_read(self):
signal_ref = BaseSignal(data_save)
signal_ref.metadata.General.title = test_title
signal_ref.axes_manager[0].name = 'x'
signal_ref.axes_manager[1].name = 'y'
signal_ref.axes_manager[2].name = 'z'
signal_ref.axes_manager[0].scale = 2
signal_ref.axes_manager[1].scale = 3
signal_ref.axes_manager[2].scale = 4
signal_ref.axes_manager[0].offset = 10
signal_ref.axes_manager[1].offset = 20
signal_ref.axes_manager[2].offset = 30
signal_ref.axes_manager[0].units = 'nm'
signal_ref.axes_manager[1].units = 'µm'
signal_ref.axes_manager[2].units = 'mm'
signal_ref.save(os.path.join(my_path, 'emd_files', 'example_temp.emd'),
overwrite=True, signal_metadata=sig_metadata,
user=user, microscope=microscope, sample=sample,
comments=comments)
signal = load(os.path.join(my_path, 'emd_files', 'example_temp.emd'))
np.testing.assert_equal(signal.data, signal_ref.data)
np.testing.assert_equal(signal.axes_manager[0].name, 'x')
np.testing.assert_equal(signal.axes_manager[1].name, 'y')
np.testing.assert_equal(signal.axes_manager[2].name, 'z')
np.testing.assert_equal(signal.axes_manager[0].scale, 2)
np.testing.assert_almost_equal(signal.axes_manager[1].scale, 3.0)
np.testing.assert_almost_equal(signal.axes_manager[2].scale, 4.0)
np.testing.assert_equal(signal.axes_manager[0].offset, 10)
np.testing.assert_almost_equal(signal.axes_manager[1].offset, 20.0)
np.testing.assert_almost_equal(signal.axes_manager[2].offset, 30.0)
np.testing.assert_equal(signal.axes_manager[0].units, 'nm')
np.testing.assert_equal(signal.axes_manager[1].units, 'µm')
np.testing.assert_equal(signal.axes_manager[2].units, 'mm')
np.testing.assert_equal(signal.metadata.General.title, test_title)
np.testing.assert_equal(
signal.metadata.General.user.as_dictionary(), user)
np.testing.assert_equal(
signal.metadata.General.microscope.as_dictionary(),
microscope)
np.testing.assert_equal(
signal.metadata.General.sample.as_dictionary(), sample)
np.testing.assert_equal(
signal.metadata.General.comments.as_dictionary(), comments)
for key, ref_value in sig_metadata.items():
np.testing.assert_equal(
signal.metadata.Signal.as_dictionary().get(key), ref_value)
assert isinstance(signal, BaseSignal)
def test_save_and_read(self, lazy):
signal_ref = BaseSignal(data_save)
signal_ref.metadata.General.title = test_title
signal_ref.axes_manager[0].name = 'x'
signal_ref.axes_manager[1].name = 'y'
signal_ref.axes_manager[2].name = 'z'
signal_ref.axes_manager[0].scale = 2
signal_ref.axes_manager[1].scale = 3
signal_ref.axes_manager[2].scale = 4
signal_ref.axes_manager[0].offset = 10
signal_ref.axes_manager[1].offset = 20
signal_ref.axes_manager[2].offset = 30
signal_ref.axes_manager[0].units = 'nm'
signal_ref.axes_manager[1].units = 'µm'
signal_ref.axes_manager[2].units = 'mm'
signal_ref.original_metadata.add_dictionary({'user': user})
signal_ref.original_metadata.add_dictionary({'microscope': microscope})
signal_ref.original_metadata.add_dictionary({'sample': sample})
signal_ref.original_metadata.add_dictionary({'comments': comments})
signal_ref.save(os.path.join(my_path, 'emd_files', 'example_temp.emd'),
overwrite=True)
signal = load(os.path.join(my_path, 'emd_files', 'example_temp.emd'),
lazy=lazy)
if lazy:
signal.compute(close_file=True)
om = signal.original_metadata
np.testing.assert_equal(signal.data, signal_ref.data)
np.testing.assert_equal(signal.axes_manager[0].name, 'x')
np.testing.assert_equal(signal.axes_manager[1].name, 'y')
np.testing.assert_equal(signal.axes_manager[2].name, 'z')
np.testing.assert_equal(signal.axes_manager[0].scale, 2)
np.testing.assert_almost_equal(signal.axes_manager[1].scale, 3.0)
np.testing.assert_almost_equal(signal.axes_manager[2].scale, 4.0)
np.testing.assert_equal(signal.axes_manager[0].offset, 10)
np.testing.assert_almost_equal(signal.axes_manager[1].offset, 20.0)
np.testing.assert_almost_equal(signal.axes_manager[2].offset, 30.0)
np.testing.assert_equal(signal.axes_manager[0].units, 'nm')
np.testing.assert_equal(signal.axes_manager[1].units, 'µm')
np.testing.assert_equal(signal.axes_manager[2].units, 'mm')
np.testing.assert_equal(signal.metadata.General.title, test_title)
np.testing.assert_equal(om.user.as_dictionary(), user)
np.testing.assert_equal(om.microscope.as_dictionary(), microscope)
np.testing.assert_equal(om.sample.as_dictionary(), sample)
np.testing.assert_equal(om.comments.as_dictionary(), comments)
assert isinstance(signal, BaseSignal)
