def off_component_with_no_pixel_data(
nexus_wrapper, nx_off_geometry_group, off_geometry_file
):
component = Component(nexus_wrapper, nx_off_geometry_group)
component.set_off_shape(off_geometry_file)
return component
def cylindrical_component_with_pixel_mapping(
nexus_wrapper, nx_cylindrical_geometry_group, pixel_mapping_with_single_pixel
):
component = Component(nexus_wrapper, nx_cylindrical_geometry_group)
component.record_pixel_mapping(pixel_mapping_with_single_pixel)
return component
def create_component(nexus_wrapper: NexusWrapper,
component_group: h5py.Group) -> Component:
nx_class = get_nx_class(component_group)
if nx_class == CHOPPER_CLASS_NAME:
return Component(nexus_wrapper, component_group,
ChopperShape(nexus_wrapper, component_group))
if nx_class in PIXEL_COMPONENT_TYPES and "pixel_shape" in component_group:
return Component(nexus_wrapper, component_group,
PixelShape(nexus_wrapper, component_group))
return Component(nexus_wrapper, component_group)
def create_component(nexus_wrapper: NexusWrapper,
component_group: h5py.Group) -> Component:
if (nexus_wrapper.get_attribute_value(
component_group, CommonAttrs.NX_CLASS) == CHOPPER_CLASS_NAME):
return Component(nexus_wrapper, component_group,
ChopperShape(nexus_wrapper, component_group))
if (nexus_wrapper.get_attribute_value(
component_group, CommonAttrs.NX_CLASS) in PIXEL_COMPONENT_TYPES
and "pixel_shape" in component_group):
return Component(nexus_wrapper, component_group,
PixelShape(nexus_wrapper, component_group))
return Component(nexus_wrapper, component_group)
def replace_pixel_grid_in_off_component(
component: Component, pixel_grid: PixelGrid, off_geometry: OFFGeometryNexus
):
"""
Change the pixel grid that is currently stored in a Component. Used to see if everything behaves correctly even
for pixel data with 'special' properties.
:param component: The component to have its pixel data replaced.
:param pixel_grid: The PixelGrid object.
:param off_geometry: The OffGeometry.
"""
component.record_pixel_grid(pixel_grid)
component.set_off_shape(off_geometry, pixel_data=pixel_grid)
def test_transform_dependents_depends_on_are_updated_when_transformation_name_is_changed(
nexus_wrapper, ):
test_name = "slartibartfast"
test_value = 42
test_vector = QVector3D(1.0, 0.0, 0.0)
test_type = "Translation"
transform_dataset = _add_transform_to_file(nexus_wrapper, test_name,
test_value, test_vector,
test_type)
component = nexus_wrapper.create_nx_group("test", "NXaperture",
nexus_wrapper.nexus_file)
component.create_dataset("depends_on", data=transform_dataset.name)
transform = Transformation(nexus_wrapper, transform_dataset)
transform.register_dependent(Component(nexus_wrapper, component))
new_name = test_name + "1"
transform.name = new_name
assert transform.name == new_name
assert str(component["depends_on"][()],
encoding="UTF-8") == transform.dataset.name
def test_no_link_2(nexus_wrapper):
component1 = add_component_to_file(nexus_wrapper, "field", 42,
"component1")
rot = component1.add_rotation(QVector3D(1.0, 0.0, 0.0), 90.0)
component1.depends_on = rot
new_component = Component(component1.file, component1.group)
assert not new_component.transforms.has_link
def test_GIVEN_single_scalar_field_and_string_WHEN_adding_fields_to_component_THEN_field_appears_in_component_fields_with_correct_name_and_value():
file = NexusWrapper("test_fields_2")
component_group = file.nexus_file.create_group("test_component")
component = Component(file, component_group)
field_name = "test_field"
field_value = np.string_(b"some_value")
field = DummyField(field_name, field_value, field_value.dtype)
list_widget = DummyListWidget()
list_widget.addItem(field)
add_fields_to_component(component, list_widget)
assert component.get_field(field_name)
assert bytes(component.get_field(field_name), encoding="ASCII") == field_value
def test_has_one_transformation_2(nexus_wrapper):
component1 = add_component_to_file(nexus_wrapper, "field", 42,
"component1")
rot1 = component1.add_rotation(QVector3D(1.0, 0.0, 0.0), 90.0)
component1.add_rotation(QVector3D(1.0, 0.0, 0.0), 90.0)
component1.depends_on = rot1
new_component = Component(component1.file, component1.group)
assert len(new_component.transforms) == 1
def test_linked_component_via_component_1(nexus_wrapper):
component1 = add_component_to_file(nexus_wrapper, "field", 42, "component1")
component2 = add_component_to_file(nexus_wrapper, "field", 42, "component2")
rot = component2.add_rotation(QVector3D(1.0, 0.0, 0.0), 90.0)
component2.depends_on = rot
component1.transforms.link.linked_component = component2
new_component = Component(component1.file, component1.group)
assert new_component.transforms.link.linked_component == component2
def fill_existing_entries(self, component_to_edit: Component):
"""
Populate the pixel fields based on what is already stored in the NeXus file.
"""
self.reset_pixel_mapping_list()
if component_to_edit.get_field("x_pixel_offset") is not None:
self.single_pixel_radio_button.setChecked(True)
self.update_pixel_layout_visibility(True, False)
self._fill_single_pixel_fields(component_to_edit)
elif component_to_edit.get_field("detector_number") is not None:
self.entire_shape_radio_button.setChecked(True)
self.update_pixel_layout_visibility(False, True)
self._fill_entire_shape_fields(component_to_edit)
else:
self.no_pixels_button.setChecked(True)
self.pixel_options_stack.setVisible(False)
def add_component_to_file(
nexus_wrapper: NexusWrapper,
field_name: str = "test_field",
field_value: Any = 42,
component_name: str = "test_component",
) -> Component:
component_group = nexus_wrapper.nexus_file.create_group(component_name)
component_group.create_dataset(field_name, data=field_value)
component = Component(nexus_wrapper, component_group)
return component
def _find_linked_component(self) -> Optional[Component]:
for transformation in self.parent:
if self.parent._transform_has_external_link(transformation):
component_path = transformation.depends_on.absolute_path[
: transformation.depends_on.absolute_path.find(TRANSFORM_STR)
]
return Component(
self.parent.parent_component.file,
self.parent.parent_component.file.nexus_file[component_path],
)
return None
def test_GIVEN_single_scalar_field_and_float_WHEN_adding_fields_to_component_THEN_field_appears_in_component_fields_with_correct_name_and_value(
nexus_wrapper, ):
component_group = nexus_wrapper.nexus_file.create_group("test_component")
component = Component(nexus_wrapper, component_group)
field_name = "test_field"
field_dtype = np.float32
field_value = field_dtype(32.123)
field = DummyField(field_name, field_value, field_dtype)
list_widget = DummyListWidget()
list_widget.addItem(field)
add_fields_to_component(component, list_widget)
assert component.get_field(field_name)
assert component.get_field(field_name).dtype == field_dtype
assert component.get_field(field_name)[...] == field_value
def off_component_with_pixel_grid(
pixel_grid, nexus_wrapper, nx_off_geometry_group, off_geometry_file
):
component = Component(nexus_wrapper, nx_off_geometry_group)
component.record_pixel_grid(pixel_grid)
component.set_off_shape(off_geometry_file, pixel_data=pixel_grid)
return component
def generate_geometry_model(
self, component: Component, pixel_data: PixelData = None
):
"""
Generates a geometry model depending on the type of geometry selected and the current values
of the line edits that apply to the particular geometry type.
:return: The generated model.
"""
if self.CylinderRadioButton.isChecked():
component.set_cylinder_shape(
QVector3D(
self.cylinderXLineEdit.value(),
self.cylinderYLineEdit.value(),
self.cylinderZLineEdit.value(),
),
self.cylinderHeightLineEdit.value(),
self.cylinderRadiusLineEdit.value(),
self.unitsLineEdit.text(),
pixel_data=pixel_data,
)
elif self.meshRadioButton.isChecked():
mesh_geometry = OFFGeometryNoNexus()
geometry_model = load_geometry(
self.cad_file_name, self.unitsLineEdit.text(), mesh_geometry
)
# Units have already been used during loading the file, but we store them and file name
# so we can repopulate their fields in the edit component window
geometry_model.units = self.unitsLineEdit.text()
geometry_model.file_path = self.cad_file_name
component.set_off_shape(
geometry_model,
units=self.unitsLineEdit.text(),
filename=self.fileLineEdit.text(),
pixel_data=pixel_data,
)
def linked_component(self) -> Optional[Component]:
if not self.parent.has_link:
return None
if self._has_direct_component_link():
component_path = self.parent.parent_component.depends_on.absolute_path[
: self.parent.parent_component.depends_on.absolute_path.find(
TRANSFORM_STR
)
]
return Component(
self.parent.parent_component.file,
self.parent.parent_component.file.nexus_file[component_path],
)
return self._find_linked_component()
def _fill_single_pixel_fields(self, component_to_edit: Component):
"""
Fill the "single pixel" fields of a component that's being edited and contains pixel information.
:param component_to_edit: The component that's being edited.
"""
# Retrieve the pixel offsets and detector number from the component
x_pixel_offset = component_to_edit.get_field("x_pixel_offset")
y_pixel_offset = component_to_edit.get_field("y_pixel_offset")
detector_numbers = component_to_edit.get_field("detector_number")
# Check that x offset is more than one value
if data_is_an_array_with_more_than_one_element(x_pixel_offset):
# Set the number of rows and the row height
n_rows, row_height = self._get_row_information(y_pixel_offset)
self.row_count_spin_box.setValue(n_rows)
self.row_height_spin_box.setValue(row_height)
# Set the number of columns and the column width
n_cols, col_width = self._get_column_information(x_pixel_offset)
self.column_count_spin_box.setValue(n_cols)
self.column_width_spin_box.setValue(col_width)
# Set the first ID, start counting option, and the count direction option
(
first_id,
start_counting_text,
count_along_text,
) = self._get_detector_number_information(detector_numbers)
self.first_id_spin_box.setValue(first_id)
self.start_counting_combo_box.setCurrentText(start_counting_text)
self.count_first_combo_box.setCurrentText(count_along_text)
else:
# If the pixel offset information represents a single pixel
pass
def test_transforms_has_no_link(nexus_wrapper):
component1 = add_component_to_file(
nexus_wrapper, "some_field", 42, "component_name"
)
component2 = add_component_to_file(
nexus_wrapper, "some_field", 42, "other_component_name"
)
transform1 = component1.add_rotation(QVector3D(1.0, 0.0, 0.0), 90.0)
transform2 = component2.add_rotation(QVector3D(1.0, 0.0, 0.0), 90.0)
component1.depends_on = transform1
component2.depends_on = transform2
new_component = Component(component1.file, component1.group)
assert not new_component.transforms.has_link
def off_component_with_pixel_mapping(
nexus_wrapper,
nx_off_geometry_group,
pixel_mapping_with_six_pixels,
off_geometry_file,
):
component = Component(nexus_wrapper, nx_off_geometry_group)
component.record_pixel_mapping(pixel_mapping_with_six_pixels)
component.set_off_shape(off_geometry_file, pixel_data=pixel_mapping_with_six_pixels)
return component
def write_pixel_data_to_component(
component: Component, nx_class: str, pixel_data: PixelData
):
"""
Writes the detector number/pixel grid data to a component.
:param component: The component to modify.
:param nx_class: The NXclass of the component.
:param pixel_data: The pixel data.
"""
component.clear_pixel_data()
if pixel_data is None or nx_class not in PIXEL_COMPONENT_TYPES:
return
if isinstance(pixel_data, PixelMapping):
component.record_pixel_mapping(pixel_data)
if isinstance(pixel_data, PixelGrid):
component.record_pixel_grid(pixel_data)
def add_component(self, name: str, nx_class: str, description: str):
nexus_wrapper = NexusWrapper(str(uuid1()))
component_group = _add_component_to_file(nexus_wrapper, name, 42,
"component_name")
return Component(nexus_wrapper, component_group)
def test_does_not_have_transformations_2(nexus_wrapper):
component1 = add_component_to_file(nexus_wrapper, "field", 42,
"component1")
component1.add_rotation(QVector3D(1.0, 0.0, 0.0), 90.0)
new_component = Component(component1.file, component1.group)
assert len(new_component.transforms) == 0
def component(nexus_wrapper, component_group):
return Component(nexus_wrapper, component_group)
def test_does_not_have_transformations_1(nexus_wrapper):
component1 = add_component_to_file(nexus_wrapper, "field", 42,
"component1")
new_component = Component(component1.file, component1.group)
assert len(new_component.transforms) == 0
def test_no_link_1(nexus_wrapper):
component1 = add_component_to_file(nexus_wrapper, "field", 42,
"component1")
new_component = Component(component1.file, component1.group)
assert not new_component.transforms.has_link
def get_component():
nexus_wrapper = NexusWrapper(str(uuid1()))
component_group = _add_component_to_file(nexus_wrapper, "some_field", 42,
"component_name")
return Component(nexus_wrapper, component_group)
def test_linked_component_is_none_3(nexus_wrapper):
component1 = add_component_to_file(nexus_wrapper, "field", 42, "component1")
new_component = Component(component1.file, component1.group)
assert new_component.transforms.link.linked_component is None