def test_GIVEN_stream_in_group_children_WHEN_handling_group_THEN_stream_is_appended_to_children(
file, ):
group_name = "test_group"
group = file.create_group(group_name)
group.attrs["NX_class"] = "NCstream"
group_contents = {
"writer_module": "f142",
"topic": "topic1",
"source": "SIMPLE:DOUBLE",
"type": "double",
"value_units": "cubits",
"array_size": 32,
}
for name, value in group_contents.items():
group.create_dataset(name, data=value)
converter = NexusToDictConverter()
root_dict = converter.convert(file)
assert len(root_dict["children"]) == 1, "The stream group has been omitted"
assert group_name == root_dict["children"][0]["name"]
assert group_contents == root_dict["children"][0]["children"][0]["stream"]
assert "attributes" not in root_dict["children"][0]
def test_GIVEN_nx_class_and_attributes_are_bytes_WHEN_output_to_json_THEN_they_are_written_as_utf8(
file, ):
dataset_name = "test_ds"
dataset_value = 1
dataset_dtype = np.int32
dataset = file.create_dataset(dataset_name,
data=dataset_value,
dtype=dataset_dtype)
test_nx_class = b"NXpinhole"
test_string_attr = b"some_string"
dataset.attrs["NX_class"] = test_nx_class
dataset.attrs["string_attr"] = test_string_attr
converter = NexusToDictConverter()
root_dict = converter.convert(file)
ds = root_dict["children"][0]
for attribute in ds["attributes"]:
assert attribute["name"] in ["NX_class", "string_attr"]
if attribute["name"] == "NX_class":
assert attribute["values"] == test_nx_class.decode("utf8")
elif attribute["name"] == "string_attr":
assert attribute["values"] == test_string_attr.decode("utf8")
def test_GIVEN_group_with_multiple_attributes_WHEN_converting_nexus_to_dict_THEN_attributes_end_up_in_file(
file, ):
group_name = "test_group"
group = file.create_group(group_name)
group.attrs["NX_class"] = "NXgroup"
field1name = "field1"
field1value = "field1val"
field2name = "field2"
field2value = 3
arbitrary_field_name = "arbitrary_field"
arbitrary_field_value = "something"
field1 = group.create_dataset(field1name, data=field1value)
field1.attrs["NX_class"] = "NXfield"
field1.attrs[arbitrary_field_name] = arbitrary_field_value
field2 = group.create_dataset(field2name, data=field2value)
field2.attrs["NX_class"] = "NXfield"
converter = NexusToDictConverter()
root_dict = converter.convert(file)
assert group.name.split("/")[-1] == root_dict["children"][0]["name"]
assert field1.name.split(
"/")[-1] == root_dict["children"][0]["children"][0]["name"]
assert field1value == root_dict["children"][0]["children"][0]["values"]
assert ("NX_class" == root_dict["children"][0]["children"][0]["attributes"]
[0]["name"])
assert (field1.attrs["NX_class"] == root_dict["children"][0]["children"][0]
["attributes"][0]["values"])
assert (arbitrary_field_name == root_dict["children"][0]["children"][0]
["attributes"][1]["name"])
assert (field1.attrs[arbitrary_field_name] == root_dict["children"][0]
["children"][0]["attributes"][1]["values"])
assert field2.name.split(
"/")[-1] == root_dict["children"][0]["children"][1]["name"]
assert field2value == root_dict["children"][0]["children"][1]["values"]
def test_GIVEN_multiple_values_WHEN_handling_dataset_THEN_size_field_does_exist_in_root_dict(
file, ):
dataset_name = "test_ds"
dataset_value = [1.1, 1.2, 1.3]
dataset_dtype = np.float
dataset = file.create_dataset(dataset_name,
data=dataset_value,
dtype=dataset_dtype)
dataset.attrs["NX_class"] = "NXpinhole"
converter = NexusToDictConverter()
root_dict = converter.convert(file)
ds = root_dict["children"][0]
assert ds["name"].lstrip("/") == dataset_name
assert ds["type"] == "dataset"
assert ds["values"] == dataset_value
assert ds["dataset"]["size"] == (len(dataset_value), )
def test_GIVEN_dataset_with_an_array_attribute_WHEN_output_to_json_THEN_attribute_is_present_in_json(
file, test_input):
dataset_name = "test_ds"
dataset_value = 1
dataset_dtype = np.int32
dataset = file.create_dataset(dataset_name,
data=dataset_value,
dtype=dataset_dtype)
test_attr_name = "test_attr"
dataset.attrs[test_attr_name] = test_input
converter = NexusToDictConverter()
root_dict = converter.convert(file)
ds = root_dict["children"][0]
assert ds["attributes"][0]["name"] == test_attr_name
assert ds["attributes"][0]["values"].tolist() == test_input
def test_GIVEN_link_in_group_children_that_is_a_dataset_WHEN_handling_group_THEN_link_is_appended_to_children(
file, ):
root_group = file.create_group("root")
ds_to_be_linked_name = "test_linked_dataset"
dataset_to_be_linked = root_group.create_dataset(ds_to_be_linked_name,
data=1)
dataset_to_be_linked.attrs["NX_class"] = "NXgroup"
group_name = "test_group_with_link"
root_group[group_name] = h5py.SoftLink(dataset_to_be_linked.name)
root_group[group_name].attrs["NX_class"] = "NXgroup"
converter = NexusToDictConverter()
root_dict = converter.convert(file)
assert root_dict["children"][0]["children"][0]["type"] == "link"
assert (root_group[group_name].name.split("/")[-1] == root_dict["children"]
[0]["children"][0]["name"])
assert (dataset_to_be_linked.name == root_dict["children"][0]["children"]
[0]["target"])
def test_GIVEN_link_in_group_children_WHEN_handling_group_THEN_link_is_appended_to_children(
file, ):
root_group = file.create_group("root")
group_to_be_linked_name = "test_linked_group"
group_to_be_linked = root_group.create_group(group_to_be_linked_name)
group_to_be_linked.attrs["NX_class"] = "NXgroup"
group_name = "test_group_with_link"
root_group[group_name] = h5py.SoftLink(group_to_be_linked.name)
root_group[group_name].attrs["NX_class"] = "NXgroup"
converter = NexusToDictConverter()
root_dict = converter.convert(file)
assert len(root_dict["children"]) == 1, "The link group has been omitted"
assert root_dict["children"][0]["children"][0]["type"] == "link"
assert (root_group[group_name].name.split("/")[-1] == root_dict["children"]
[0]["children"][0]["name"])
assert group_to_be_linked.name == root_dict["children"][0]["children"][0][
"target"]
def send_command(self):
if self.command_producer is not None:
(
nexus_file_name,
broker,
start_time,
stop_time,
service_id,
abort_on_uninitialised_stream,
) = self.command_widget.get_arguments()
self.command_producer.send_command(
bytes(
run_start_pl72.serialise_pl72(
job_id=str(uuid.uuid4()),
filename=nexus_file_name,
start_time=start_time,
stop_time=stop_time,
broker=broker,
nexus_structure=generate_nexus_string(
NexusToDictConverter(), self.instrument),
service_id=service_id,
)))
self.command_widget.ok_button.setEnabled(False)