def read(self, h5_object=None):
"""
Reads all available NSID main datasets or the specified h5_object
Parameters
----------
h5_object : h5py.Dataset or h5py.Group
HDF5 Dataset to read or the HDF5 group under which to read all
datasets
Returns
-------
sidpy.Dataset or list of sidpy.Dataset objects
Datasets present in the provided file
"""
if h5_object is None:
return self.read_all(recursive=True)
if not isinstance(h5_object, (h5py.Group, h5py.Dataset)):
raise TypeError('Provided h5_object was not a h5py.Dataset or '
'h5py.Group object but was of type: {}'
''.format(type(h5_object)))
self.__validate_obj_in_same_file(h5_object)
if isinstance(h5_object, h5py.Dataset):
return read_h5py_dataset(h5_object)
else:
return self.read_all(parent=h5_object)
def test_attrs_datatype(self):
data_types = [
'UNKNOWN', 'SPECTRUM', 'LINE_PLOT', 'LINE_PLOT_FAMILY', 'IMAGE',
'IMAGE_MAP', 'IMAGE_STACK', 'SPECTRAL_IMAGE', 'IMAGE_4D'
]
for dt in data_types:
_meta = {"data_type": dt}
h5file = make_simple_nsid_dataset(_meta)
dset = read_h5py_dataset(h5file['MyGroup']['data'])
self.assertIsInstance(dset, sidpy.Dataset)
self.assertTrue(dset.data_type.name == dt)
def test_valid_nsid_h5_dset(self):
base = {
'quantity': 'Current',
'units': 'nA',
# 'pyNSID_version': 'version',
'title': 'Current-Voltage spectroscopy measurement',
'data_type': 'SPECTRAL_IMAGE',
'modality': 'cAFM',
'source': 'Asylum Research Cypher'
}
h5file = make_simple_nsid_dataset(base)
dset = read_h5py_dataset(h5file['MyGroup']['data'])
self.assertIsInstance(dset, sidpy.Dataset)
# Validate the base attributes first
for key, expected in base.items():
actual = getattr(dset, key)
def read_all(self, recursive=True, parent=None):
"""
Reads all HDF5 datasets formatted according to NSID specifications.
Parameters
----------
recursive : bool, default = True
We might just remove this kwarg
parent : h5py.Group, Default = None
HDF5 group under which to read all available datasets.
By default, all datasets within the HDF5 file are read.
Returns
-------
sidpy.Dataset or list of sidpy.Dataset objects
Datasets present in the provided file
"""
if parent is None:
h5_group = self._h5_file
else:
if not isinstance(parent, h5py.Group):
raise TypeError('parent should be a h5py.Group object')
self.__validate_obj_in_same_file(parent)
h5_group = parent
if recursive:
list_of_main = self._main_dsets
else:
list_of_main = []
for key in h5_group:
if isinstance(h5_group[key], h5py.Dataset):
if check_if_main(h5_group[key]):
list_of_main.append(h5_group[key])
# Go through each of the identified
list_of_datasets = []
for dset in list_of_main:
list_of_datasets.append(read_h5py_dataset(dset))
return list_of_datasets
def test_dims(self) -> None:
h5file = make_simple_nsid_dataset()
dset = read_h5py_dataset(h5file['MyGroup']['data'])
self.assertIsInstance(dset, sidpy.Dataset)
self.assertTrue(dset._axes[0].name == 'a0')
self.assertTrue(dset._axes[1].name == 'b0')
def test_attrs_source(self) -> None:
_meta = {"source": "src"}
h5file = make_simple_nsid_dataset(_meta)
dset = read_h5py_dataset(h5file['MyGroup']['data'])
self.assertIsInstance(dset, sidpy.Dataset)
self.assertTrue(dset.source == 'src')
def test_attrs_modality(self) -> None:
_meta = {"modality": "mod"}
h5file = make_simple_nsid_dataset(_meta)
dset = read_h5py_dataset(h5file['MyGroup']['data'])
self.assertIsInstance(dset, sidpy.Dataset)
self.assertTrue(dset.modality == 'mod')
def test_attrs_quantity(self):
_meta = {"quantity": "Current"}
h5file = make_simple_nsid_dataset(_meta)
dset = read_h5py_dataset(h5file['MyGroup']['data'])
self.assertIsInstance(dset, sidpy.Dataset)
self.assertTrue(dset.quantity == 'Current')
def test_attrs_units(self) -> None:
_meta = {"units": "nA"}
h5file = make_simple_nsid_dataset(_meta)
dset = read_h5py_dataset(h5file['MyGroup']['data'])
self.assertIsInstance(dset, sidpy.Dataset)
self.assertTrue(dset.units == 'nA')
def test_wrong_input_type(self) -> None:
dataset = make_simple_h5_dataset()
err_msg = 'can only read single Dataset'
with self.assertRaises(TypeError) as context:
_ = read_h5py_dataset(dataset)
self.assertTrue(err_msg in str(context.exception))