def test_not_h5_dataset(self):
for arg in [
np.arange(3),
da.from_array(np.arange(3)),
self.h5_simple_file['MyGroup'],
self.h5_simple_file,
]:
self.assertFalse(check_if_main(arg))
def test_invalid_types_for_str_attrs(self):
for key in [
'quantity', 'units', 'main_data_name', 'data_type', 'modality',
'source'
]:
attribute = self.h5_nsid_simple['MyGroup']['data'].attrs[key]
self.h5_nsid_simple['MyGroup']['data'].attrs[key] = 1
self.assertFalse(
check_if_main(self.h5_nsid_simple['MyGroup']['data']))
self.h5_nsid_simple['MyGroup']['data'].attrs[key] = attribute
def test_mandatory_attrs_not_present(self):
for key in [
'quantity', 'units', 'main_data_name', 'data_type', 'modality',
'source'
]:
attribute = self.h5_nsid_simple['MyGroup']['data'].attrs[key]
del self.h5_nsid_simple['MyGroup']['data'].attrs[key]
self.assertFalse(
check_if_main(self.h5_nsid_simple['MyGroup']['data']))
self.h5_nsid_simple['MyGroup']['data'].attrs[key] = attribute
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_dset_is_main(self):
self.assertTrue(check_if_main(self.h5_nsid_simple['MyGroup']['data']))
def test_dim_sizes_not_matching_main(self):
h5_nsid_wrong_dim_length = make_nsid_length_dim_wrong()
self.assertFalse(
check_if_main(h5_nsid_wrong_dim_length['MyGroup']['data']))
def test_dim_exist_but_scales_not_attached_to_main(self):
h5_nsid_no_dim_attached = make_nsid_dataset_no_dim_attached()
self.assertFalse(
check_if_main(h5_nsid_no_dim_attached['MyGroup']['data']))
def test_dims_missing(self):
self.assertFalse(check_if_main(self.h5_simple_file['MyGroup']['data']))