def test_set_atom_type(self):
oxygen, hydrogen, component, _, _ = self.get_mocked_hierarchy()
atom = Atom(
parent = component,
name = "O",
atom_type = oxygen,
)
atom.atom_type = hydrogen
self.assertEqual(atom.atom_type, hydrogen)
def test_set_atom_type(self):
oxygen, hydrogen, component, _, _ = self.get_mocked_hierarchy()
atom = Atom(
parent=component,
name="O",
atom_type=oxygen,
)
atom.atom_type = hydrogen
self.assertEqual(atom.atom_type, hydrogen)
def test_z_calculations(self):
# Checks wether the atom can calculate stretched values:
# 1. When everything is set up the way it should be:
default_z = 9.0
lattice_d = 5.4
factor = 0.5
class DummyComponent(object):
def get_interlayer_stretch_factors(self):
return lattice_d, factor
parent = DummyComponent()
atom = Atom(parent=parent)
atom.stretch_values = True
atom.default_z = default_z
z = atom.z
self.assertEqual(z, lattice_d + (default_z - lattice_d) * factor)
# 2. When no component is set, but stretched is True: should not raise an error, but simple ignore the stretching
atom.parent = None
z = atom.z
class TestAtom(unittest.TestCase):
atom_type = None
def setUp(self):
self.atom = Atom()
def tearDown(self):
del self.atom
def test_not_none(self):
self.assertIsNotNone(self.atom)
def test_data_object(self):
self.assertIsNotNone(self.atom.data_object)
test_name = create_object_attribute_test("atom", "name", "Test Name")
test_pn = create_object_attribute_test("atom", "pn", 3)
test_default_z = create_object_attribute_test("atom", "default_z", 5.3)
test_stretch_values = create_object_attribute_test("atom",
"stretch_values", True)
def test_parent(self):
parent_atom = Atom(name="Parent")
self.atom.parent = parent_atom
self.assertEqual(self.atom.parent, parent_atom)
def test_z_calculations(self):
# Checks wether the atom can calculate stretched values:
# 1. When everything is set up the way it should be:
default_z = 9.0
lattice_d = 5.4
factor = 0.5
class DummyComponent(object):
def get_interlayer_stretch_factors(self):
return lattice_d, factor
parent = DummyComponent()
atom = Atom(parent=parent)
atom.stretch_values = True
atom.default_z = default_z
z = atom.z
self.assertEqual(z, lattice_d + (default_z - lattice_d) * factor)
# 2. When no component is set, but stretched is True: should not raise an error, but simple ignore the stretching
atom.parent = None
z = atom.z
def test_structure_factors(self):
import numpy as np
rng = 2.0 * np.sin(np.arange(30)) / 0.154056
res = self.atom.get_structure_factors(rng)
self.assertIsNotNone(res)
pass # end of class
def test_z_calculations(self):
# Checks wether the atom can calculate stretched values:
# 1. When everything is set up the way it should be:
default_z = 9.0
lattice_d = 5.4
factor = 0.5
parent = Mock()
parent.configure_mock(**{
'get_interlayer_stretch_factors.return_value': (lattice_d, factor)
})
atom = Atom(parent=parent)
atom.stretch_values = True
atom.default_z = default_z
z = atom.z
self.assertEqual(z, lattice_d + (default_z - lattice_d) * factor)
# 2. When no component is set, but stretched is True: should not raise an error, but simple ignore the stretching
atom.parent = None
z = atom.z
def test_z_calculations(self):
# Checks wether the atom can calculate stretched values:
# 1. When everything is set up the way it should be:
default_z = 9.0
lattice_d = 5.4
factor = 0.5
class DummyComponent(object):
def get_interlayer_stretch_factors(self):
return lattice_d, factor
parent = DummyComponent()
atom = Atom(parent=parent)
atom.stretch_values = True
atom.default_z = default_z
z = atom.z
self.assertEqual(z, lattice_d + (default_z - lattice_d) * factor)
# 2. When no component is set, but stretched is True: should not raise an error, but simple ignore the stretching
atom.parent = None
z = atom.z
def test_z_calculations(self):
# Checks wether the atom can calculate stretched values:
# 1. When everything is set up the way it should be:
default_z = 9.0
lattice_d = 5.4
factor = 0.5
parent = Mock()
parent.configure_mock(**{
'get_interlayer_stretch_factors.return_value': (lattice_d, factor)
})
atom = Atom(parent=parent)
atom.stretch_values = True
atom.default_z = default_z
z = atom.z
self.assertEqual(z, lattice_d + (default_z - lattice_d) * factor)
# 2. When no component is set, but stretched is True: should not raise an error, but simple ignore the stretching
atom.parent = None
z = atom.z
class TestAtom(unittest.TestCase):
atom_type = None
def setUp(self):
self.atom = Atom()
def tearDown(self):
del self.atom
def test_not_none(self):
self.assertIsNotNone(self.atom)
def test_data_object(self):
self.assertIsNotNone(self.atom.data_object)
test_name = create_object_attribute_test("atom", "name", "Test Name")
test_pn = create_object_attribute_test("atom", "pn", 3)
test_default_z = create_object_attribute_test("atom", "default_z", 5.3)
test_stretch_values = create_object_attribute_test("atom", "stretch_values", True)
def test_parent(self):
parent_atom = Atom(name="Parent")
self.atom.parent = parent_atom
self.assertEqual(self.atom.parent, parent_atom)
def test_z_calculations(self):
# Checks wether the atom can calculate stretched values:
# 1. When everything is set up the way it should be:
default_z = 9.0
lattice_d = 5.4
factor = 0.5
class DummyComponent(object):
def get_interlayer_stretch_factors(self):
return lattice_d, factor
parent = DummyComponent()
atom = Atom(parent=parent)
atom.stretch_values = True
atom.default_z = default_z
z = atom.z
self.assertEqual(z, lattice_d + (default_z - lattice_d) * factor)
# 2. When no component is set, but stretched is True: should not raise an error, but simple ignore the stretching
atom.parent = None
z = atom.z
def test_structure_factors(self):
import numpy as np
rng = 2.0 * np.sin(np.arange(30)) / 0.154056
res = self.atom.get_structure_factors(rng)
self.assertIsNotNone(res)
pass # end of class
def test_loads_atom_type_by_name(self):
atom_json_dict = {
"uuid": "878341b04e9e11e2b238150ae229a525",
"name": "O",
"default_z": 0.66,
"pn": 6.0,
"atom_type_name": "O1-"
}
oxygen, _, component, _, _ = self.get_mocked_hierarchy()
atom = Atom.from_json(parent=component, **atom_json_dict)
atom.resolve_json_references()
self.assertEqual(atom.atom_type, oxygen)
def test_loads_atom_type_by_name(self):
atom_json_dict = {
"uuid": "878341b04e9e11e2b238150ae229a525",
"name": "O",
"default_z": 0.66,
"pn": 6.0,
"atom_type_name": "O1-"
}
oxygen, _, component, _, _ = self.get_mocked_hierarchy()
atom = Atom.from_json(parent = component, **atom_json_dict)
atom.resolve_json_references()
self.assertEqual(atom.atom_type, oxygen)
def on_accept(dialog):
del self.treemodel_data[:] # clears the list
Atom.get_from_csv(dialog.filename, self.treemodel_data.append, self.model)
def on_accept(open_dialog):
filename = self.extract_filename(open_dialog, self.file_filters)
self.treemodel_data.clear()
Atom.get_from_csv(filename, self.treemodel_data.append, self.model)
def on_accept(save_dialog):
Atom.save_as_csv(save_dialog.filename, self.get_all_objects())
class TestAtom(unittest.TestCase):
atom_type = None
def setUp(self):
self.atom = Atom()
def tearDown(self):
del self.atom
def get_mocked_hierarchy(self):
oxygen = Mock()
oxygen.name = "O1-"
hydrogen = Mock()
hydrogen.name = "H+"
project = Mock()
project.atom_types = [oxygen, hydrogen]
phase = Mock()
phase.attach_mock(project, 'project')
component = Mock()
component.attach_mock(phase, 'phase')
return oxygen, hydrogen, component, phase, project
def test_not_none(self):
self.assertIsNotNone(self.atom)
def test_data_object(self):
self.assertIsNotNone(self.atom.data_object)
test_name = create_object_attribute_test("atom", "name", "Test Name")
test_pn = create_object_attribute_test("atom", "pn", 3)
test_default_z = create_object_attribute_test("atom", "default_z", 5.3)
test_stretch_values = create_object_attribute_test("atom", "stretch_values", True)
def test_parent(self):
parent_atom = Atom(name="Parent")
self.atom.parent = parent_atom
self.assertEqual(self.atom.parent, parent_atom)
def test_set_atom_type(self):
oxygen, hydrogen, component, _, _ = self.get_mocked_hierarchy()
atom = Atom(
parent = component,
name = "O",
atom_type = oxygen,
)
atom.atom_type = hydrogen
self.assertEqual(atom.atom_type, hydrogen)
def test_z_calculations(self):
# Checks wether the atom can calculate stretched values:
# 1. When everything is set up the way it should be:
default_z = 9.0
lattice_d = 5.4
factor = 0.5
parent = Mock()
parent.configure_mock(**{
'get_interlayer_stretch_factors.return_value': (lattice_d, factor)
})
atom = Atom(parent=parent)
atom.stretch_values = True
atom.default_z = default_z
z = atom.z
self.assertEqual(z, lattice_d + (default_z - lattice_d) * factor)
# 2. When no component is set, but stretched is True: should not raise an error, but simple ignore the stretching
atom.parent = None
z = atom.z
def test_structure_factors(self):
import numpy as np
rng = 2.0 * np.sin(np.arange(30)) / 0.154056
res = self.atom.get_structure_factors(rng)
self.assertIsNotNone(res)
def test_loads_atom_type_by_name(self):
atom_json_dict = {
"uuid": "878341b04e9e11e2b238150ae229a525",
"name": "O",
"default_z": 0.66,
"pn": 6.0,
"atom_type_name": "O1-"
}
oxygen, _, component, _, _ = self.get_mocked_hierarchy()
atom = Atom.from_json(parent = component, **atom_json_dict)
atom.resolve_json_references()
self.assertEqual(atom.atom_type, oxygen)
pass # end of class
def on_accept(save_dialog):
Atom.save_as_csv(save_dialog.filename, self.get_all_objects())
def create_new_object_proxy(self):
return Atom(name="New Atom", parent=self.model)
def on_accept(dialog):
del self.treemodel_data[:] # clears the list
Atom.get_from_csv(dialog.filename, self.treemodel_data.append,
self.model)
def on_accept(save_dialog):
filename = self.extract_filename(save_dialog, self.file_filters)
Atom.save_as_csv(filename, self.get_all_objects())
def setUp(self):
self.atom = Atom()
def test_parent(self):
parent_atom = Atom(name="Parent")
self.atom.parent = parent_atom
self.assertEqual(self.atom.parent, parent_atom)
def setUp(self):
self.atom = Atom()
class TestAtom(unittest.TestCase):
atom_type = None
def setUp(self):
self.atom = Atom()
def tearDown(self):
del self.atom
def get_mocked_hierarchy(self):
oxygen = Mock()
oxygen.name = "O1-"
hydrogen = Mock()
hydrogen.name = "H+"
project = Mock()
project.atom_types = [oxygen, hydrogen]
phase = Mock()
phase.attach_mock(project, 'project')
component = Mock()
component.attach_mock(phase, 'phase')
return oxygen, hydrogen, component, phase, project
def test_not_none(self):
self.assertIsNotNone(self.atom)
def test_data_object(self):
self.assertIsNotNone(self.atom.data_object)
test_name = create_object_attribute_test("atom", "name", "Test Name")
test_pn = create_object_attribute_test("atom", "pn", 3)
test_default_z = create_object_attribute_test("atom", "default_z", 5.3)
test_stretch_values = create_object_attribute_test("atom",
"stretch_values", True)
def test_parent(self):
parent_atom = Atom(name="Parent")
self.atom.parent = parent_atom
self.assertEqual(self.atom.parent, parent_atom)
def test_set_atom_type(self):
oxygen, hydrogen, component, _, _ = self.get_mocked_hierarchy()
atom = Atom(
parent=component,
name="O",
atom_type=oxygen,
)
atom.atom_type = hydrogen
self.assertEqual(atom.atom_type, hydrogen)
def test_z_calculations(self):
# Checks wether the atom can calculate stretched values:
# 1. When everything is set up the way it should be:
default_z = 9.0
lattice_d = 5.4
factor = 0.5
parent = Mock()
parent.configure_mock(**{
'get_interlayer_stretch_factors.return_value': (lattice_d, factor)
})
atom = Atom(parent=parent)
atom.stretch_values = True
atom.default_z = default_z
z = atom.z
self.assertEqual(z, lattice_d + (default_z - lattice_d) * factor)
# 2. When no component is set, but stretched is True: should not raise an error, but simple ignore the stretching
atom.parent = None
z = atom.z
def test_structure_factors(self):
import numpy as np
rng = 2.0 * np.sin(np.arange(30)) / 0.154056
res = self.atom.get_structure_factors(rng)
self.assertIsNotNone(res)
def test_loads_atom_type_by_name(self):
atom_json_dict = {
"uuid": "878341b04e9e11e2b238150ae229a525",
"name": "O",
"default_z": 0.66,
"pn": 6.0,
"atom_type_name": "O1-"
}
oxygen, _, component, _, _ = self.get_mocked_hierarchy()
atom = Atom.from_json(parent=component, **atom_json_dict)
atom.resolve_json_references()
self.assertEqual(atom.atom_type, oxygen)
pass # end of class
def create_project_from_sybilla_xml(filename, **kwargs):
"""
Creates a new project structure from a Sybilla XML file.
Some information (e.g. the actual XRD pattern) is not present and will
still need to be imported manually.
"""
tree = ET.parse(filename)
root = tree.getroot()
basename = os.path.basename(filename)
# Create the project:
if "name" in kwargs: kwargs.pop("name")
if "layout_mode" in kwargs: kwargs.pop("layout_mode")
project = Project(name=basename, layout_mode="FULL", **kwargs)
# Add a specimen:
specimen = Specimen(name=basename, parent=project)
project.specimens.append(specimen)
# Add a mixture:
mixture = Mixture(name=basename, auto_run=False, parent=project)
mixture.add_specimen_slot(specimen, 1.0, 0.0)
project.mixtures.append(mixture)
with project.data_changed.ignore():
with mixture.data_changed.ignore():
for child in root:
if child.tag == "basic_params":
# Goniometer parameters:
step_size = safe_float(child.attrib['step_size'])
wavelength = safe_float(child.attrib['lambda']) / 10.0
steps = int(1 +
(specimen.goniometer.max_2theta -
specimen.goniometer.min_2theta) / step_size)
specimen.goniometer.min_2theta = safe_float(
child.attrib['min2theta'])
specimen.goniometer.max_2theta = safe_float(
child.attrib['max2theta'])
specimen.goniometer.steps = steps
specimen.goniometer.wavelength = wavelength
elif child.tag == "diffractometer":
# Some more goniometer parameters, and specimen parameters:
specimen.goniometer.radius = safe_float(
child.attrib['gonio_radius'])
specimen.goniometer.divergence = safe_float(
child.attrib['diverg_slit'])
specimen.goniometer.soller1 = safe_float(
child.attrib['Soller1'])
specimen.goniometer.soller2 = safe_float(
child.attrib['Soller2'])
specimen.sample_length = safe_float(
child.attrib['sample_length'])
elif child.tag == "content":
# Content tag contains 'Mixture' data
for xmlPhaseContent in child:
name = xmlPhaseContent.attrib['name']
fraction = safe_float(
xmlPhaseContent.attrib['content']) / 100.
mixture.add_phase_slot(name, fraction)
elif child.tag == "mixture":
# Mixture tag corresponds with the phases in the project level,
# not an actual Mixture object:
for xmlPhase in child:
name = xmlPhase.attrib['name']
sigma = xmlPhase.attrib['sigma_star']
csds = safe_float(
xmlPhase.find('distribution').attrib['Tmean'])
G = 1
R = 0
W = [
1.0,
]
if xmlPhase.attrib['type'] != 'mono':
prob = xmlPhase.find('probability')
G = int(prob.attrib['no_of_comp'])
R = int(prob.attrib['R'])
# create phase and add to project:
phase = Phase(name=name,
sigma_star=sigma,
G=G,
R=R,
parent=project)
phase.CSDS_distribution.average = csds
project.phases.append(phase)
# set probability:
if R == 0 and G != 1:
xmlW = prob.find('W')
W = np.array([
float(
int(
safe_float(xmlW.attrib[
string.ascii_lowercase[i]]) *
1000.)) / 1000. for i in range(G)
])
for i in range(G - 1):
setattr(phase.probabilities, "F%d" % (i + 1),
W[i] / np.sum(W[i:]))
if R == 1 and G == 2:
pass # TODO
# ... TODO other probs
# parse components:
for i, layer in enumerate(
xmlPhase.findall("./layer_and_edge/layer")):
component = phase.components[i]
component.name = layer.attrib['name']
component.d001 = safe_float(
layer.attrib['d_spacing']) / 10.0
component.default_c = safe_float(
layer.attrib['d_spacing']) / 10.0
component.delta_c = safe_float(
layer.attrib['d_spacing_delta']) / 10.0
component.ucp_b.value = 0.9
component.ucp_a.factor = 0.57735
component.ucp_a.prop = (component, 'cell_b')
component.ucp_a.enabled = True
atom_type_map = {
# "NH4": "FIXME"
"K": "K1+",
"O": "O1-",
"Si": "Si2+",
"OH": "OH1-",
"Fe": "Fe1.5+",
"Al": "Al1.5+",
"Mg": "Mg1+",
"H2O": "H2O",
"Gly": "Glycol",
"Ca": "Ca2+",
"Na": "Na1+",
}
# add atoms:
fe_atom = None
encountered_oxygen = False
for atom in layer.findall("atom"):
atom_type_name = atom_type_map.get(
atom.attrib['type'], None)
if atom_type_name:
if atom_type_name == "O1-":
# From this point we're dealing with layer atoms
encountered_oxygen = True
atom = Atom(
name=atom.attrib['type'],
default_z=safe_float(
atom.attrib['position']) / 10.0,
pn=safe_float(atom.attrib['content']),
atom_type_name=atom_type_name,
parent=component)
if encountered_oxygen:
component.layer_atoms.append(atom)
else:
component.interlayer_atoms.append(atom)
atom.resolve_json_references()
# Assume this is the octahedral iron...
if encountered_oxygen and atom_type_name == "Fe1.5+":
fe_atom = atom
# Set the atom relation
if fe_atom is not None:
component.ucp_b.constant = 0.9
component.ucp_b.factor = 0.0043
component.ucp_b.prop = (fe_atom, 'pn')
component.ucp_b.enabled = True
pass # end of if
pass # end of for
# Map phases onto mixture names:
for phase in project.phases:
for slot, phase_name in enumerate(mixture.phases):
if phase.name == phase_name:
mixture.set_phase(0, slot, phase)
return project
def create_project_from_sybilla_xml(filename, **kwargs):
"""
Creates a new project structure from a Sybilla XML file.
Some information (e.g. the actual XRD pattern) is not present and will
still need to be imported manually.
"""
tree = ET.parse(filename)
root = tree.getroot()
basename = os.path.basename(filename)
# Create the project:
if "name" in kwargs: kwargs.pop("name")
if "layout_mode" in kwargs: kwargs.pop("layout_mode")
project = Project(name=basename, layout_mode="FULL", **kwargs)
# Add a specimen:
specimen = Specimen(name=basename, parent=project)
project.specimens.append(specimen)
# Add a mixture:
mixture = Mixture(name=basename, auto_run=False, parent=project)
mixture.add_specimen_slot(specimen, 1.0, 0.0)
project.mixtures.append(mixture)
with project.data_changed.ignore():
with mixture.data_changed.ignore():
for child in root:
if child.tag == "basic_params":
# Goniometer parameters:
step_size = safe_float(child.attrib['step_size'])
wavelength = safe_float(child.attrib['lambda']) / 10.0
steps = int(1 + (specimen.goniometer.max_2theta - specimen.goniometer.min_2theta) / step_size)
specimen.goniometer.min_2theta = safe_float(child.attrib['min2theta'])
specimen.goniometer.max_2theta = safe_float(child.attrib['max2theta'])
specimen.goniometer.steps = steps
specimen.goniometer.wavelength = wavelength
elif child.tag == "diffractometer":
# Some more goniometer parameters, and specimen parameters:
specimen.goniometer.radius = safe_float(child.attrib['gonio_radius'])
specimen.goniometer.divergence = safe_float(child.attrib['diverg_slit'])
specimen.goniometer.soller1 = safe_float(child.attrib['Soller1'])
specimen.goniometer.soller2 = safe_float(child.attrib['Soller2'])
specimen.sample_length = safe_float(child.attrib['sample_length'])
elif child.tag == "content":
# Content tag contains 'Mixture' data
for xmlPhaseContent in child:
name = xmlPhaseContent.attrib['name']
fraction = safe_float(xmlPhaseContent.attrib['content']) / 100.
mixture.add_phase_slot(name, fraction)
elif child.tag == "mixture":
# Mixture tag corresponds with the phases in the project level,
# not an actual Mixture object:
for xmlPhase in child:
name = xmlPhase.attrib['name']
sigma = xmlPhase.attrib['sigma_star']
csds = safe_float(xmlPhase.find('distribution').attrib['Tmean'])
G = 1
R = 0
W = [1.0, ]
if xmlPhase.attrib['type'] != 'mono':
prob = xmlPhase.find('probability')
G = int(prob.attrib['no_of_comp'])
R = int(prob.attrib['R'])
# create phase and add to project:
phase = Phase(name=name, sigma_star=sigma, G=G, R=R, parent=project)
phase.CSDS_distribution.average = csds
project.phases.append(phase)
# set probability:
if R == 0 and G != 1:
xmlW = prob.find('W')
W = np.array([ float(int(safe_float(xmlW.attrib[string.ascii_lowercase[i]]) * 1000.)) / 1000. for i in range(G) ])
for i in range(G - 1):
setattr(phase.probabilities, "F%d" % (i + 1), W[i] / np.sum(W[i:]))
if R == 1 and G == 2:
pass # TODO
# ... TODO other probs
# parse components:
for i, layer in enumerate(xmlPhase.findall("./layer_and_edge/layer")):
component = phase.components[i]
component.name = layer.attrib['name']
component.d001 = safe_float(layer.attrib['d_spacing']) / 10.0
component.default_c = safe_float(layer.attrib['d_spacing']) / 10.0
component.delta_c = safe_float(layer.attrib['d_spacing_delta']) / 10.0
component.ucp_b.value = 0.9
component.ucp_a.factor = 0.57735
component.ucp_a.prop = (component, 'cell_b')
component.ucp_a.enabled = True
atom_type_map = {
# "NH4": "FIXME"
"K": "K1+",
"O": "O1-",
"Si": "Si2+",
"OH": "OH1-",
"Fe": "Fe1.5+",
"Al": "Al1.5+",
"Mg": "Mg1+",
"H2O": "H2O",
"Gly": "Glycol",
"Ca": "Ca2+",
"Na": "Na1+",
}
# add atoms:
fe_atom = None
encountered_oxygen = False
for atom in layer.findall("atom"):
atom_type_name = atom_type_map.get(atom.attrib['type'], None)
if atom_type_name:
if atom_type_name == "O1-":
# From this point we're dealing with layer atoms
encountered_oxygen = True
atom = Atom(
name=atom.attrib['type'],
default_z=safe_float(atom.attrib['position']) / 10.0,
pn=safe_float(atom.attrib['content']),
atom_type_name=atom_type_name,
parent=component
)
if encountered_oxygen:
component.layer_atoms.append(atom)
else:
component.interlayer_atoms.append(atom)
atom.resolve_json_references()
# Assume this is the octahedral iron...
if encountered_oxygen and atom_type_name == "Fe1.5+":
fe_atom = atom
# Set the atom relation
if fe_atom is not None:
component.ucp_b.constant = 0.9
component.ucp_b.factor = 0.0043
component.ucp_b.prop = (fe_atom, 'pn')
component.ucp_b.enabled = True
pass # end of if
pass # end of for
# Map phases onto mixture names:
for phase in project.phases:
for slot, phase_name in enumerate(mixture.phases):
if phase.name == phase_name:
mixture.set_phase(0, slot, phase)
return project
