def test_nxobject_getting_item_that_does_not_exists_raises_KeyError(
nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(builder_with_events_monitor_and_log())() as f:
root = nexus.NXroot(f, loader)
with pytest.raises(KeyError):
root['abcde']
def test_nxobject_grandchild_can_be_accessed_using_path(
nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(builder_with_events_monitor_and_log())() as f:
root = nexus.NXroot(f, loader)
assert root['entry/log'].name == '/entry/log'
assert root['/entry/log'].name == '/entry/log'
def test_field_properties(nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(builder_with_events_monitor_and_log())() as f:
field = nexus.NXroot(f, loader)['entry/events_0/event_time_offset']
assert field.dtype == np.array(1).dtype
assert field.name == '/entry/events_0/event_time_offset'
assert field.shape == (6, )
assert field.unit == sc.Unit('ns')
def test_raises_if_no_data_found(nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
builder = NexusBuilder()
builder.add_detector(Detector(detector_numbers=np.array([1, 2, 3, 4])))
with resource(builder)() as f:
detector = nexus.NXroot(f, loader)['entry/detector_0']
with pytest.raises(KeyError):
detector[...]
def test_nxobject_event_data(nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(builder_with_events_monitor_and_log())() as f:
event_data = nexus.NXroot(f, loader)['entry']['events_0']
assert set(event_data.keys()) == set([
'event_id', 'event_index', 'event_time_offset', 'event_time_zero'
])
assert event_data.nx_class == nexus.NX_class.NXevent_data
def test_event_mode_monitor_without_event_id_can_be_loaded(
nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(
builder_with_events_and_events_monitor_without_event_id())() as f:
monitor = nexus.NXroot(f, loader)['monitor']
da = monitor[...]
assert len(da.bins.coords) == 1
assert 'event_time_offset' in da.bins.coords
def test_nxobject_name_property_is_full_path(
nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(builder_with_events_monitor_and_log())() as f:
root = nexus.NXroot(f, loader)
assert root.name == '/'
assert root['monitor'].name == '/monitor'
assert root['entry'].name == '/entry'
assert root['entry']['log'].name == '/entry/log'
assert root['entry']['events_0'].name == '/entry/events_0'
def test_nxobject_by_nx_class_contains_only_children(
nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(builder_with_events_monitor_and_log())() as f:
root = nexus.NXroot(f, loader)
classes = root['entry'].by_nx_class()
assert list(classes[nexus.NX_class.NXentry]) == []
assert list(classes[nexus.NX_class.NXmonitor]) == []
assert list(classes[nexus.NX_class.NXlog]) == ['log']
assert set(classes[nexus.NX_class.NXevent_data]) == set(
['events_0', 'events_1'])
def test_field_getitem_returns_numpy_array_with_correct_size_and_values(
nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(builder_with_events_monitor_and_log())() as f:
field = nexus.NXroot(f, loader)['entry/events_0/event_time_offset']
assert np.array_equal(
field[...], np.array([456, 743, 347, 345, 632, 23], dtype='int64'))
assert np.array_equal(
field[1:], np.array([743, 347, 345, 632, 23], dtype='int64'))
assert np.array_equal(
field[:-1], np.array([456, 743, 347, 345, 632], dtype='int64'))
def test_loads_data_with_coords(nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
builder = NexusBuilder()
da = sc.DataArray(
sc.array(dims=['xx', 'yy'], unit='K', values=[[1.1, 2.2], [3.3, 4.4]]))
da.coords['xx'] = sc.array(dims=['xx'], unit='m', values=[0.1, 0.2])
builder.add_detector(
Detector(detector_numbers=np.array([1, 2, 3, 4]), data=da))
with resource(builder)() as f:
detector = nexus.NXroot(f, loader)['entry/detector_0']
loaded = detector[...]
assert sc.identical(loaded, da.rename_dims({'yy': 'dim_1'}))
def test_nxobject_monitor(nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(builder_with_events_monitor_and_log())() as f:
monitor = nexus.NXroot(f, loader)['monitor']
assert monitor.nx_class == nexus.NX_class.NXmonitor
assert sc.identical(
monitor[...],
sc.DataArray(sc.array(dims=['time_of_flight'], values=[1.0]),
coords={
'time_of_flight':
sc.array(dims=['time_of_flight'], values=[1.0])
}))
def test_nxobject_log(nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(builder_with_events_monitor_and_log())() as f:
log = nexus.NXroot(f, loader)['entry']['log']
assert log.nx_class == nexus.NX_class.NXlog
assert sc.identical(
log[...],
sc.DataArray(
sc.array(dims=['time'], values=[1.1, 2.2, 3.3]),
coords={
'time':
sc.epoch(unit='ns') + sc.array(
dims=['time'], unit='s', values=[4.4, 5.5, 6.6]).to(
unit='ns', dtype='int64')
}))
def test_raises_if_data_and_event_data_found(
nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
da = sc.DataArray(
sc.array(dims=['xx', 'yy'], values=[[1.1, 2.2], [3.3, 4.4]]))
event_data = EventData(
event_id=np.array([1, 2, 4, 1, 2, 2]),
event_time_offset=np.array([456, 743, 347, 345, 632, 23]),
event_time_zero=np.array([1, 2, 3, 4]),
event_index=np.array([0, 3, 3, 5]),
)
builder = NexusBuilder()
builder.add_detector(
Detector(detector_numbers=np.array([1, 2, 3, 4]),
data=da,
event_data=event_data))
with resource(builder)() as f:
detector = nexus.NXroot(f, loader)['entry/detector_0']
with pytest.raises(nexus.NexusStructureError):
detector[...]
def test_negative_event_index_converted_to_num_event(
nexus_group: Tuple[Callable, LoadFromNexus]):
event_time_offsets = np.array([456, 743, 347, 345, 632, 23])
event_data = EventData(
event_id=np.array([1, 2, 3, 1, 3, 2]),
event_time_offset=event_time_offsets,
event_time_zero=np.array([
1600766730000000000, 1600766731000000000, 1600766732000000000,
1600766733000000000
]),
event_index=np.array([0, 3, 3, -1000]),
)
builder = NexusBuilder()
builder.add_event_data(event_data)
resource, loader = nexus_group
with resource(builder)() as f:
root = nexus.NXroot(f, loader)
events = root['entry/events_0'][...]
assert events.bins.size().values[2] == 3
assert events.bins.size().values[3] == 0
def test_loading_event_data_creates_automatic_detector_numbers_if_not_present_in_file(
nexus_group: Tuple[Callable, LoadFromNexus]):
event_time_offsets = np.array([456, 743, 347, 345, 632, 23])
event_data = EventData(
event_id=np.array([1, 2, 4, 1, 2, 2]),
event_time_offset=event_time_offsets,
event_time_zero=np.array([1, 2, 3]),
event_index=np.array([0, 3, 5]),
)
builder = NexusBuilder()
builder.add_detector(Detector(event_data=event_data))
resource, loader = nexus_group
with resource(builder)() as f:
detector = nexus.NXroot(f, loader)['entry/detector_0']
assert detector.dims == ['detector_number']
with pytest.raises(nexus.NexusStructureError):
assert detector.shape == (4, )
loaded = detector[...]
assert sc.identical(
loaded.bins.size().data,
sc.array(dims=['detector_number'],
dtype='int64',
values=[2, 3, 0, 1]))
def test_loads_event_data_mapped_to_detector_numbers_based_on_their_event_id(
nexus_group: Tuple[Callable, LoadFromNexus]):
event_time_offsets = np.array([456, 743, 347, 345, 632, 23])
event_data = EventData(
event_id=np.array([1, 2, 3, 1, 2, 2]),
event_time_offset=event_time_offsets,
event_time_zero=np.array([1, 2, 3, 4]),
event_index=np.array([0, 3, 3, 5]),
)
builder = NexusBuilder()
builder.add_detector(
Detector(detector_numbers=np.array([1, 2, 3, 4]),
event_data=event_data))
resource, loader = nexus_group
with resource(builder)() as f:
detector = nexus.NXroot(f, loader)['entry/detector_0']
assert detector.dims == ['detector_number']
assert detector.shape == (4, )
loaded = detector[...]
assert sc.identical(
loaded.bins.size().data,
sc.array(dims=['detector_number'],
dtype='int64',
values=[2, 3, 1, 0]))
def test_nxobject_entry(nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(builder_with_events_monitor_and_log())() as f:
entry = nexus.NXroot(f, loader)['entry']
assert entry.nx_class == nexus.NX_class.NXentry
assert set(entry.keys()) == {'events_0', 'events_1', 'log'}
def test_nxobject_root(nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(builder_with_events_monitor_and_log())() as f:
root = nexus.NXroot(f, loader)
assert root.nx_class == nexus.NX_class.NXroot
assert set(root.keys()) == {'entry', 'monitor'}
def test_field_unit_is_none_if_no_units_attribute(
nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(builder_with_events_monitor_and_log())() as f:
field = nexus.NXroot(f, loader)['entry/log']
assert field.unit is None
def test_nxobject_dataset_items_are_returned_as_Field(
nexus_group: Tuple[Callable, LoadFromNexus]):
resource, loader = nexus_group
with resource(builder_with_events_monitor_and_log())() as f:
field = nexus.NXroot(f, loader)['entry/events_0/event_time_offset']
assert isinstance(field, nexus.Field)