def test_constructor_with_impossible_val(self):
good_input = 1
good_center_input = [1, 2, 3]
zero_value = 0
negative_value = -0.0000001
negative_int = -1
negative_string = "-1"
# Check it handles zero
with assertRaisesRegex(self, ValueError,
"The value set for height was: 0"):
sample_details.SampleDetails(height=zero_value,
radius=good_input,
center=good_center_input)
# Very small negative
with assertRaisesRegex(self, ValueError,
"which is impossible for a physical object"):
sample_details.SampleDetails(height=good_input,
radius=negative_value,
center=good_center_input)
# Integer negative
with assertRaisesRegex(self, ValueError,
"The value set for height was: -1"):
sample_details.SampleDetails(height=negative_int,
radius=good_input,
center=good_center_input)
# String negative
with assertRaisesRegex(self, ValueError,
"The value set for radius was: -1"):
sample_details.SampleDetails(height=good_input,
radius=negative_string,
center=good_center_input)
def test_generate_geometry_cylinder_with_container(self):
workspace = CreateSampleWorkspace()
# float
radius_float = 1.0
height_float = 2.0
center_float = [1.0, 2.0, 3.0]
sample_details_float = sample_details.SampleDetails(
radius=radius_float,
shape="cylinder",
height=height_float,
center=center_float)
sample_details_float.set_material(chemical_formula='Si')
sample_details_float.set_container(radius=2.0, chemical_formula='V')
# int
radius_int = 1
height_int = 3
center_int = [1, 2, 3]
sample_details_int = sample_details.SampleDetails(radius=radius_int,
shape="cylinder",
height=height_int,
center=center_int)
sample_details_int.set_material(chemical_formula='Si')
sample_details_int.set_container(radius=2, chemical_formula='V')
# string
radius_string = "1"
height_string = "2"
center_string = ["1", "2", "3"]
sample_details_string = sample_details.SampleDetails(
radius=radius_string,
shape="cylinder",
height=height_string,
center=center_string)
sample_details_string.set_material(chemical_formula='Si')
sample_details_string.set_container(radius="2", chemical_formula='V')
# mix
radius_mix = 1.23
height_mix = 2
center_mix = ["1", 2, 3.45]
sample_details_mix = sample_details.SampleDetails(radius=radius_mix,
shape="cylinder",
height=height_mix,
center=center_mix)
sample_details_mix.set_material(chemical_formula='Si')
sample_details_mix.set_container(radius="2", chemical_formula='V')
sample_details_objects = [
sample_details_float, sample_details_int, sample_details_string,
sample_details_mix
]
for sample_details_object in sample_details_objects:
SetSample(
workspace,
Geometry=sample_details_object.generate_sample_geometry(),
Material=sample_details_object.generate_sample_material(),
ContainerGeometry=sample_details_object.
generate_container_geometry(),
ContainerMaterial=sample_details_object.
generate_container_material())
def test_constructor(self):
expected_height = 1.1
expected_radius = 2.2
expected_center = [3.3, 4.4, 5.5]
# Check easiest case
sample_details_obj = sample_details.SampleDetails(
height=expected_height,
radius=expected_radius,
center=expected_center)
self.assertEqual(sample_details_obj.height(), expected_height)
self.assertEqual(sample_details_obj.radius(), expected_radius)
self.assertEqual(sample_details_obj.center(), expected_center)
# Check shape stype defaults to cylinder
self.assertEqual(sample_details_obj.shape_type(), "cylinder")
# Does it handle ints correctly
height_radius_int = 1
center_int = [2, 3, 4]
sample_details_obj_int = sample_details.SampleDetails(
height=height_radius_int,
radius=height_radius_int,
center=center_int,
shape="cylinder")
self.assertTrue(isinstance(sample_details_obj.height(), float))
self.assertTrue(isinstance(sample_details_obj.radius(), float))
self.assertEqual(sample_details_obj_int.height(),
float(height_radius_int))
self.assertEqual(sample_details_obj_int.radius(),
float(height_radius_int))
self.assertEqual(sample_details_obj_int.center(), [2.0, 3.0, 4.0])
# Does it handle strings correctly
height_radius_string = "5"
center_string = ["2.0", "3.0", "5.0"]
sample_details_obj_str = sample_details.SampleDetails(
height=height_radius_string,
radius=height_radius_string,
center=center_string,
shape="cylinder")
self.assertTrue(isinstance(sample_details_obj.height(), float))
self.assertTrue(isinstance(sample_details_obj.radius(), float))
self.assertEqual(sample_details_obj_str.height(),
float(height_radius_string))
self.assertEqual(sample_details_obj_str.radius(),
float(height_radius_string))
self.assertEqual(sample_details_obj_str.center(), [2.0, 3.0, 5.0])
def test_constructor_non_number_input(self):
good_input = 1.0
good_center_input = [1.0, 2.0, 3.0]
empty_input_value = ''
char_input_value = 'a'
# Check it handles empty input
with assertRaisesRegex(self, ValueError,
"Could not convert the height to a number"):
sample_details.SampleDetails(height=empty_input_value,
radius=good_input,
center=good_center_input)
# Does it handle bad input and tell us what we put in
with assertRaisesRegex(
self, ValueError,
".*to a number. The input was: '" + char_input_value + "'"):
sample_details.SampleDetails(height=char_input_value,
radius=good_input,
center=good_center_input)
# Does it indicate which field was incorrect
with assertRaisesRegex(self, ValueError, "radius"):
sample_details.SampleDetails(height=good_input,
radius=char_input_value,
center=good_center_input)
# Can it handle bad center values
with assertRaisesRegex(self, ValueError, "center"):
sample_details.SampleDetails(height=good_input,
radius=good_input,
center=["", 2, 3])
# Does it throw if were not using a list for the input
with assertRaisesRegex(self, ValueError,
"must be specified as a list of X, Y, Z"):
sample_details.SampleDetails(height=good_input,
radius=good_input,
center=1)
# Does it throw if we are using a list of incorrect length (e.g. not 3D)
with assertRaisesRegex(self, ValueError,
"must have three values corresponding to"):
sample_details.SampleDetails(height=good_input,
radius=good_input,
center=[])
with assertRaisesRegex(self, ValueError,
"must have three values corresponding to"):
sample_details.SampleDetails(height=good_input,
radius=good_input,
center=[1, 2])
with assertRaisesRegex(self, ValueError,
"must have three values corresponding to"):
sample_details.SampleDetails(height=good_input,
radius=good_input,
center=[1, 2, 3, 4])
def test_generate_sample_geometry(self):
# Create mock SampleDetails
sample_details_obj = sample_details.SampleDetails(
height=4.0, radius=3.0, center=[0.5, 1.0, -3.2], shape='cylinder')
# Run test
result = sample_details_obj.generate_sample_geometry()
# Validate result
expected = {
'Shape': 'Cylinder',
'Height': 4.0,
'Radius': 3.0,
'Center': [0.5, 1.0, -3.2]
}
self.assertEqual(result, expected)
def test_set_material_properties(self):
sample_details_obj = sample_details.SampleDetails(height=1.0,
radius=1.0,
center=[2, 3, 5])
self.assertIsNone(sample_details_obj.material_object)
# Check we cannot set a material property without setting the underlying material
with assertRaisesRegex(self, RuntimeError,
"The material has not been set"):
sample_details_obj.set_material_properties(
absorption_cross_section=1.0, scattering_cross_section=2.0)
# Check that with a material object we are allowed to set material properties
sample_details_obj.set_material(chemical_formula='V')
# We will test the immutability of the underlying object elsewhere
sample_details_obj.set_material_properties(
scattering_cross_section=2.0, absorption_cross_section=3.0)
def test_generate_sample_material(self):
# Create mock SampleDetails
sample_details_obj = sample_details.SampleDetails(
height=1.0, radius=1.0, center=[0.0, 0.0, 0.0])
sample_details_obj.set_material(chemical_formula='Si',
number_density=1.5)
sample_details_obj.set_material_properties(
absorption_cross_section=123, scattering_cross_section=456)
# Run test
result = sample_details_obj.generate_sample_material()
# Validate
expected = {
'ChemicalFormula': 'Si',
'NumberDensity': 1.5,
'AttenuationXSection': 123.0,
'ScatteringXSection': 456.0
}
self.assertEqual(result, expected)
def test_set_material(self):
sample_details_obj = sample_details.SampleDetails(height=1.0,
radius=1.0,
center=[2, 3, 4])
# Check that we can only set a material once. We will test the underlying class elsewhere
sample_details_obj.set_material(chemical_formula='V')
self.assertIsNotNone(sample_details_obj.material_object)
# Check that the material is now immutable
with assertRaisesRegex(
self, RuntimeError,
"The material has already been set to the above details"):
sample_details_obj.set_material(chemical_formula='V')
# Check resetting it works
sample_details_obj.reset_sample_material()
self.assertIsNone(sample_details_obj.material_object)
# And ensure setting it for a second time works
sample_details_obj.set_material(chemical_formula='V')
self.assertIsNotNone(sample_details_obj.material_object)
def create_vanadium_sample_details_obj(config_dict):
"""
Creates a SampleDetails object based on a vanadium sample which is found
in the advanced config of an instrument.
:param config_dict: The advanced config dictionary of the instrument for the vanadium sample
:return: A sample details object which holds properties used in sample corrections
"""
height_key = "cylinder_sample_height"
radius_key = "cylinder_sample_radius"
pos_key = "cylinder_position"
formula_key = "chemical_formula"
number_density_key = "number_density"
e_msg = "The following key was not found in the advanced configuration for sample correction:\n"
height = common.dictionary_key_helper(dictionary=config_dict,
key=height_key,
exception_msg=e_msg + height_key)
radius = common.dictionary_key_helper(dictionary=config_dict,
key=radius_key,
exception_msg=e_msg + radius_key)
pos = common.dictionary_key_helper(dictionary=config_dict,
key=pos_key,
exception_msg=e_msg + pos_key)
formula = common.dictionary_key_helper(dictionary=config_dict,
key=formula_key,
exception_msg=e_msg + formula_key)
number_density = common.dictionary_key_helper(dictionary=config_dict,
key=number_density_key,
throws=False)
vanadium_sample_details = sample_details.SampleDetails(height=height,
radius=radius,
center=pos,
shape="cylinder")
vanadium_sample_details.set_material(chemical_formula=formula,
number_density=number_density)
return vanadium_sample_details
def test_construct_slab(self):
expected_thickness = 2.2
expected_width = 1.0
expected_height = 2.0
expected_center = [1.0, 2.0, 3.0]
expected_angle = 3.0
# Check easiest case
sample_details_obj = sample_details.SampleDetails(
thickness=expected_thickness,
shape="slab",
height=expected_height,
width=expected_width,
center=expected_center,
angle=expected_angle)
self.assertEqual(sample_details_obj.thickness(), expected_thickness)
self.assertEqual(sample_details_obj.width(), expected_width)
self.assertEqual(sample_details_obj.height(), expected_height)
self.assertEqual(sample_details_obj.center(), expected_center)
self.assertEqual(sample_details_obj.angle(), expected_angle)
# Does it handle ints correctly
thickness_int = 1
width_int = 2
height_int = 3
center_int = [1, 2, 3]
angle_int = 4
sample_details_obj_int = sample_details.SampleDetails(
thickness=thickness_int,
shape="slab",
height=height_int,
width=width_int,
center=center_int,
angle=angle_int)
self.assertTrue(isinstance(sample_details_obj_int.thickness(), float))
self.assertTrue(isinstance(sample_details_obj_int.width(), float))
self.assertTrue(isinstance(sample_details_obj_int.height(), float))
self.assertTrue(isinstance(sample_details_obj_int.center(), list))
self.assertTrue(
all(isinstance(p, float) for p in sample_details_obj_int.center()))
self.assertTrue(isinstance(sample_details_obj_int.angle(), float))
self.assertEqual(sample_details_obj_int.thickness(),
float(thickness_int))
self.assertEqual(sample_details_obj_int.width(), float(width_int))
self.assertEqual(sample_details_obj_int.height(), float(height_int))
self.assertEqual(sample_details_obj_int.center(),
[float(p) for p in center_int])
self.assertEqual(sample_details_obj_int.angle(), float(angle_int))
# Does it handle strings correctly
thickness_string = "5"
width_string = "1"
height_string = "2"
center_string = ["1", "2", "3"]
angle_string = "3"
sample_details_obj_str = sample_details.SampleDetails(
thickness=thickness_string,
shape="slab",
height=height_string,
width=width_string,
center=center_string,
angle=angle_string)
self.assertTrue(isinstance(sample_details_obj_str.thickness(), float))
self.assertTrue(isinstance(sample_details_obj_str.width(), float))
self.assertTrue(isinstance(sample_details_obj_str.height(), float))
self.assertTrue(isinstance(sample_details_obj_str.center(), list))
self.assertTrue(
all(isinstance(p, float) for p in sample_details_obj_str.center()))
self.assertTrue(isinstance(sample_details_obj_str.angle(), float))
self.assertEqual(sample_details_obj_str.thickness(),
float(thickness_string))
self.assertEqual(sample_details_obj_str.width(), float(width_string))
self.assertEqual(sample_details_obj_str.height(), float(height_string))
self.assertEqual(sample_details_obj_str.center(),
[float(p) for p in center_string])
self.assertEqual(sample_details_obj_str.angle(), float(angle_string))
def test_print_sample_details(self):
expected_height = 1
expected_radius = 2
expected_center = [3, 4, 5]
chemical_formula = 'Si'
chemical_formula_two = 'V'
expected_number_density = 1.2345
old_std_out = sys.stdout
# Wrap in try finally so we always restore std out if any exception is thrown
try:
# Redirect std out to a capture object
std_out_buffer = get_std_out_buffer_obj()
sys.stdout = std_out_buffer
sample_details_obj = sample_details.SampleDetails(
height=expected_height,
radius=expected_radius,
center=expected_center,
shape="cylinder")
# Test with most defaults set
sample_details_obj.print_sample_details()
captured_std_out_default = std_out_buffer.getvalue()
assertRegex(self, captured_std_out_default,
"Height: " + str(float(expected_height)))
assertRegex(self, captured_std_out_default,
"Radius: " + str(float(expected_radius)))
assertRegex(self, captured_std_out_default,
"Center X:" + str(float(expected_center[0])))
assertRegex(self, captured_std_out_default,
"Material has not been set")
# Test with material set but not number density
sys.stdout = std_out_buffer = get_std_out_buffer_obj()
sample_details_obj.set_material(chemical_formula=chemical_formula)
sample_details_obj.print_sample_details()
captured_std_out_material_default = std_out_buffer.getvalue()
assertRegex(self, captured_std_out_material_default,
"Material properties:")
assertRegex(self, captured_std_out_material_default,
"Chemical formula: " + chemical_formula)
assertRegex(self, captured_std_out_material_default,
"Number Density: Set from elemental properties")
# Test with material and number density
sys.stdout = std_out_buffer = get_std_out_buffer_obj()
sample_details_obj.reset_sample_material()
sample_details_obj.set_material(
chemical_formula=chemical_formula_two,
number_density=expected_number_density)
sample_details_obj.print_sample_details()
captured_std_out_material_set = std_out_buffer.getvalue()
assertRegex(self, captured_std_out_material_set,
"Chemical formula: " + chemical_formula_two)
assertRegex(self, captured_std_out_material_set,
"Number Density: " + str(expected_number_density))
# Test with no material properties set - we can reuse buffer from previous test
assertRegex(self, captured_std_out_material_default,
"Absorption cross section: Calculated by Mantid")
assertRegex(self, captured_std_out_material_default,
"Scattering cross section: Calculated by Mantid")
assertRegex(self, captured_std_out_material_default,
"Note to manually override these call")
expected_abs_x_section = 2.13
expected_scattering_x_section = 5.32
# Test with material set
sys.stdout = std_out_buffer = get_std_out_buffer_obj()
sample_details_obj.set_material_properties(
absorption_cross_section=expected_abs_x_section,
scattering_cross_section=expected_scattering_x_section)
sample_details_obj.print_sample_details()
captured_std_out_material_props = std_out_buffer.getvalue()
assertRegex(
self, captured_std_out_material_props,
"Absorption cross section: " + str(expected_abs_x_section))
assertRegex(
self, captured_std_out_material_props,
"Scattering cross section: " +
str(expected_scattering_x_section))
finally:
# Ensure std IO is restored. Do NOT remove this line as all std out will pipe into our buffer otherwise
sys.stdout = old_std_out
def test_generate_geometry_slab_with_container(self):
workspace = CreateSampleWorkspace()
thickness_float = 2.2
width_float = 1.0
height_float = 2.0
center_float = [1.0, 2.0, 3.0]
angle_float = 3.0
sample_details_float = sample_details.SampleDetails(
thickness=thickness_float,
shape="slab",
height=height_float,
width=width_float,
center=center_float,
angle=angle_float)
sample_details_float.set_material(chemical_formula='Si')
sample_details_float.set_container(front_thick=2.0,
back_thick=2.2,
chemical_formula='V')
thickness_int = 1
width_int = 2
height_int = 3
center_int = [1, 2, 3]
angle_int = 4
sample_details_int = sample_details.SampleDetails(
thickness=thickness_int,
shape="slab",
height=height_int,
width=width_int,
center=center_int,
angle=angle_int)
sample_details_int.set_material(chemical_formula='Si')
sample_details_int.set_container(front_thick=2,
back_thick=1,
chemical_formula='V')
thickness_string = "5"
width_string = "1"
height_string = "2"
center_string = ["1", "2", "3"]
angle_string = "3"
sample_details_string = sample_details.SampleDetails(
thickness=thickness_string,
shape="slab",
height=height_string,
width=width_string,
center=center_string,
angle=angle_string)
sample_details_string.set_material(chemical_formula='Si')
sample_details_string.set_container(front_thick="2",
back_thick="2.2",
chemical_formula='V')
thickness_mix = "5"
width_mix = 3.5
height_mix = "2"
center_mix = ["1", 2, 3.45]
angle_mix = 3
sample_details_mix = sample_details.SampleDetails(
thickness=thickness_mix,
shape="slab",
height=height_mix,
width=width_mix,
center=center_mix,
angle=angle_mix)
sample_details_mix.set_material(chemical_formula='Si')
sample_details_mix.set_container(front_thick="2.0",
back_thick=2,
chemical_formula='V')
sample_details_objects = [
sample_details_float, sample_details_int, sample_details_string,
sample_details_mix
]
for sample_details_object in sample_details_objects:
SetSample(
workspace,
Geometry=sample_details_object.generate_sample_geometry(),
Material=sample_details_object.generate_sample_material(),
ContainerGeometry=sample_details_object.
generate_container_geometry(),
ContainerMaterial=sample_details_object.
generate_container_material())
