def create_new_object_proxy(self):
"""def on_accept(mixture_type):
if mixture_type == "mixture":
self.add_object(Mixture(parent=self.model))
#elif mixture_type == "insitu":
# self.add_object(InSituMixture(parent=self.model))
# TODO re-use this and reset the COMBO etc.
self.add_model = Model()
self.add_view = AddMixtureView(types_dict={
'mixture': "Create a regular mixture",
#'insitu': "Create an in-situ mixture"
}, parent=self.view)
self.add_ctrl = AddMixtureController(
model=self.add_model, view=self.add_view, parent=self.parent,
callback=on_accept
)
self.add_view.present()"""
return Mixture(parent=self.model) #None
def setUp(self):
self.project = Project(name="TestProject")
self.mixture = Mixture(name="TestMixture", parent=self.project)
class TestMixture(unittest.TestCase):
atom_type = None
def setUp(self):
self.project = Project(name="TestProject")
self.mixture = Mixture(name="TestMixture", parent=self.project)
def tearDown(self):
del self.mixture
del self.project
def test_not_none(self):
self.assertIsNotNone(self.mixture)
def test_data_object(self):
self.assertIsNotNone(self.mixture.data_object)
test_name = create_object_attribute_test("mixture", "name", "Test Name")
def test_parent(self):
parent_project = Project(name="Parent2")
self.mixture.parent = parent_project
self.assertEqual(self.mixture.parent, parent_project)
def test_add_phase_slot(self):
index = self.mixture.add_phase_slot("TestPhase", 0.5)
self.assertEqual(index, 0, "Adding a phase slot should return the correct index!")
def test_add_specimen_slot(self):
index = self.mixture.add_specimen_slot(None, 1.0, 0)
self.assertEqual(index, 0, "Adding a specimen slot should return the correct index!")
def test_add_order1(self):
"""Test if addition works when 1st specimen slot is added before 1st phase slot"""
self.mixture.add_specimen_slot(None, 1.0, 0)
self.assertEqual(len(self.mixture.specimens), 1)
self.assertEqual(len(self.mixture.phases), 0)
self.assertEqual(len(self.mixture.fractions), 0)
self.assertEqual(self.mixture.phase_matrix.shape, (1, 0))
self.mixture.add_phase_slot("TestPhase", 0.5)
self.assertEqual(len(self.mixture.specimens), 1)
self.assertEqual(len(self.mixture.phases), 1)
self.assertEqual(len(self.mixture.fractions), 1)
self.assertEqual(self.mixture.phase_matrix.shape, (1, 1))
self.assertEqual(self.mixture.phase_matrix[0, 0], None)
def test_add_order2(self):
"""Test if addition works when 1st phase slot is added before 1st specimen slot"""
self.mixture.add_phase_slot("TestPhase", 0.5)
self.assertEqual(len(self.mixture.specimens), 0)
self.assertEqual(len(self.mixture.phases), 1)
self.assertEqual(len(self.mixture.fractions), 1)
self.assertEqual(self.mixture.phase_matrix.shape, (0, 1))
self.mixture.add_specimen_slot(None, 1.0, 0)
self.assertEqual(len(self.mixture.specimens), 1)
self.assertEqual(len(self.mixture.phases), 1)
self.assertEqual(len(self.mixture.fractions), 1)
self.assertEqual(self.mixture.phase_matrix.shape, (1, 1))
self.assertEqual(self.mixture.phase_matrix[0, 0], None)
def test_add_multiple(self):
"""Test if addition for multiple phases and specimens works as expected"""
self.mixture.add_phase_slot("TestPhase", 0.5)
self.mixture.add_specimen_slot(None, 1.0, 0)
self.mixture.add_specimen_slot(None, 1.0, 0)
self.mixture.add_phase_slot("TestPhase2", 0.5)
self.mixture.add_phase_slot("TestPhase3", 0.5)
self.assertEqual(len(self.mixture.specimens), 2)
self.assertEqual(len(self.mixture.phases), 3)
self.assertEqual(len(self.mixture.fractions), 3)
self.assertEqual(self.mixture.phase_matrix.shape, (2, 3))
def test_del_phase_slot(self):
"""Test if deleting a phase works as expected"""
self.mixture.add_phase_slot("TestPhase1", 0.1)
self.mixture.add_phase_slot("TestPhase2", 0.1)
self.mixture.del_phase_slot(1)
self.assertEqual(len(self.mixture.phases), 1)
self.assertEqual(len(self.mixture.fractions), 1)
self.assertEqual(self.mixture.phase_matrix.shape, (0, 1))
self.mixture.del_phase_slot(0)
self.assertEqual(len(self.mixture.phases), 0)
self.assertEqual(len(self.mixture.fractions), 0)
self.assertEqual(self.mixture.phase_matrix.shape, (0, 0))
def test_del_specimen_slot(self):
"""Test if deleting a specimen works as expected"""
self.mixture.add_specimen_slot(None, 0.5, 0)
self.mixture.add_specimen_slot(None, 0.5, 0)
self.mixture.del_specimen_slot(1)
self.assertEqual(len(self.mixture.specimens), 1)
self.assertEqual(self.mixture.phase_matrix.shape, (1, 0))
self.mixture.del_specimen_slot(0)
self.assertEqual(len(self.mixture.specimens), 0)
self.assertEqual(self.mixture.phase_matrix.shape, (0, 0))
def test_del_phase_slot_by_name(self):
self.mixture.add_phase_slot("TestPhase1", 0.1)
self.mixture.del_phase_slot_by_name("TestPhase1")
self.assertEqual(len(self.mixture.phases), 0)
self.assertEqual(len(self.mixture.fractions), 0)
self.assertEqual(self.mixture.phase_matrix.shape, (0, 0))
def test_del_specimen_slot_by_object(self):
dummy = Specimen(name="Test Specimen", parent=self.project)
self.project.specimens.append(dummy)
self.mixture.add_specimen_slot(dummy, 0.5, 0)
self.mixture.del_specimen_slot_by_object(dummy)
self.assertEqual(len(self.mixture.specimens), 0)
self.assertEqual(self.mixture.phase_matrix.shape, (0, 0))
def test_set_specimen(self):
dummy = Specimen(name="Test Specimen", parent=self.project)
self.project.specimens.append(dummy)
self.mixture.add_specimen_slot(None, 0.5, 0)
self.mixture.set_specimen(0, dummy)
self.assertEqual(self.mixture.specimens[0], dummy)
def test_unset_specimen(self):
dummy = Specimen(name="Test Specimen", parent=self.project)
self.project.specimens.append(dummy)
self.mixture.add_specimen_slot(dummy, 0.5, 0)
self.mixture.unset_specimen(dummy)
self.assertEqual(self.mixture.specimens[0], None)
def test_unset_phase(self):
specimen = Specimen(name="Test Specimen", parent=self.project)
self.project.specimens.append(specimen)
self.mixture.add_specimen_slot(specimen, 0.5, 0)
self.mixture.add_phase_slot("Test Phase1", 0.5)
dummy = Phase(name="Test Phase", parent=self.project)
self.project.phases.append(dummy)
self.mixture.set_phase(0, 0, dummy)
self.mixture.unset_phase(dummy)
self.assertEqual(self.mixture.phase_matrix[0, 0], None)
def test_randomize_empty_mixture(self):
self.mixture.refiner.randomize()
def _refinement_setup(self):
# TODO maybe add some more variation in the type of Phases?
specimen = Specimen(name="Test Specimen", parent=self.project)
self.project.specimens.append(specimen)
phase1 = Phase(name="Test Phase1", parent=self.project)
self.project.phases.append(phase1)
phase2 = Phase(name="Test Phase2", parent=self.project)
self.project.phases.append(phase2)
self.mixture.add_specimen_slot(specimen, 0.5, 0)
self.mixture.add_phase_slot("Test Phase1", 0.5)
self.mixture.add_phase_slot("Test Phase2", 0.5)
self.mixture.set_phase(0, 0, phase1)
self.mixture.set_phase(0, 1, phase2)
def test_randomize(self):
self._refinement_setup()
# Mark the attribute(s) for refinement & get their values:
refinables = []
for node in self.mixture.refinables.iter_children():
ref_prop = node.object
if ref_prop.refinable:
ref_prop.refine = True
refinables.append((ref_prop, ref_prop.value))
# Randomize:
self.mixture.refiner.randomize()
# Check all of them have been randomized:
# It is possible (but unlikely) that the randomized value
# is the same as the pre-randomized value. If so run this test again
# to make sure it is really failing.
for ref_prop, pre_val in refinables:
self.assertNotEqual(pre_val, ref_prop.value)
def test_auto_restrict_empy_mixture(self):
self.mixture.refiner.auto_restrict()
def test_auto_restrict(self):
self._refinement_setup()
# Mark the attribute(s) for refinement & get their values:
refinables = []
for node in self.mixture.refinables.iter_children():
ref_prop = node.object
if ref_prop.refinable:
ref_prop.refine = True
refinables.append((ref_prop, ref_prop.value))
# Randomize:
self.mixture.refiner.auto_restrict()
# Check all of them have been restricted:
for ref_prop, pre_val in refinables:
self.assertEqual(pre_val * 0.8, ref_prop.value_min)
self.assertEqual(pre_val * 1.2, ref_prop.value_max)
# TODO:
# - set_data_object
# - optimize
# - apply_current_data_object
# - update
# - get_refinement_method
# - setup_refine_options
pass # end of class
def setUp(self):
mock_settings()
self.project = Project(name="TestProject")
self.mixture = Mixture(name="TestMixture", parent=self.project)
class TestMixture(unittest.TestCase):
atom_type = None
def setUp(self):
mock_settings()
self.project = Project(name="TestProject")
self.mixture = Mixture(name="TestMixture", parent=self.project)
def tearDown(self):
del self.mixture
del self.project
def test_not_none(self):
self.assertIsNotNone(self.mixture)
def test_data_object(self):
self.assertIsNotNone(self.mixture.data_object)
test_name = create_object_attribute_test("mixture", "name", "Test Name")
def test_parent(self):
parent_project = Project(name="Parent2")
self.mixture.parent = parent_project
self.assertEqual(self.mixture.parent, parent_project)
def test_add_phase_slot(self):
index = self.mixture.add_phase_slot("TestPhase", 0.5)
self.assertEqual(index, 0, "Adding a phase slot should return the correct index!")
def test_add_specimen_slot(self):
index = self.mixture.add_specimen_slot(None, 1.0, 0)
self.assertEqual(index, 0, "Adding a specimen slot should return the correct index!")
def test_add_order1(self):
"""Test if addition works when 1st specimen slot is added before 1st phase slot"""
self.mixture.add_specimen_slot(None, 1.0, 0)
self.assertEqual(len(self.mixture.specimens), 1)
self.assertEqual(len(self.mixture.phases), 0)
self.assertEqual(len(self.mixture.fractions), 0)
self.assertEqual(self.mixture.phase_matrix.shape, (1, 0))
self.mixture.add_phase_slot("TestPhase", 0.5)
self.assertEqual(len(self.mixture.specimens), 1)
self.assertEqual(len(self.mixture.phases), 1)
self.assertEqual(len(self.mixture.fractions), 1)
self.assertEqual(self.mixture.phase_matrix.shape, (1, 1))
self.assertEqual(self.mixture.phase_matrix[0, 0], None)
def test_add_order2(self):
"""Test if addition works when 1st phase slot is added before 1st specimen slot"""
self.mixture.add_phase_slot("TestPhase", 0.5)
self.assertEqual(len(self.mixture.specimens), 0)
self.assertEqual(len(self.mixture.phases), 1)
self.assertEqual(len(self.mixture.fractions), 1)
self.assertEqual(self.mixture.phase_matrix.shape, (0, 1))
self.mixture.add_specimen_slot(None, 1.0, 0)
self.assertEqual(len(self.mixture.specimens), 1)
self.assertEqual(len(self.mixture.phases), 1)
self.assertEqual(len(self.mixture.fractions), 1)
self.assertEqual(self.mixture.phase_matrix.shape, (1, 1))
self.assertEqual(self.mixture.phase_matrix[0, 0], None)
def test_add_multiple(self):
"""Test if addition for multiple phases and specimens works as expected"""
self.mixture.add_phase_slot("TestPhase", 0.5)
self.mixture.add_specimen_slot(None, 1.0, 0)
self.mixture.add_specimen_slot(None, 1.0, 0)
self.mixture.add_phase_slot("TestPhase2", 0.5)
self.mixture.add_phase_slot("TestPhase3", 0.5)
self.assertEqual(len(self.mixture.specimens), 2)
self.assertEqual(len(self.mixture.phases), 3)
self.assertEqual(len(self.mixture.fractions), 3)
self.assertEqual(self.mixture.phase_matrix.shape, (2, 3))
def test_del_phase_slot(self):
"""Test if deleting a phase works as expected"""
self.mixture.add_phase_slot("TestPhase1", 0.1)
self.mixture.add_phase_slot("TestPhase2", 0.1)
self.mixture.del_phase_slot(1)
self.assertEqual(len(self.mixture.phases), 1)
self.assertEqual(len(self.mixture.fractions), 1)
self.assertEqual(self.mixture.phase_matrix.shape, (0, 1))
self.mixture.del_phase_slot(0)
self.assertEqual(len(self.mixture.phases), 0)
self.assertEqual(len(self.mixture.fractions), 0)
self.assertEqual(self.mixture.phase_matrix.shape, (0, 0))
def test_del_specimen_slot(self):
"""Test if deleting a specimen works as expected"""
self.mixture.add_specimen_slot(None, 0.5, 0)
self.mixture.add_specimen_slot(None, 0.5, 0)
self.mixture.del_specimen_slot(1)
self.assertEqual(len(self.mixture.specimens), 1)
self.assertEqual(self.mixture.phase_matrix.shape, (1, 0))
self.mixture.del_specimen_slot(0)
self.assertEqual(len(self.mixture.specimens), 0)
self.assertEqual(self.mixture.phase_matrix.shape, (0, 0))
def test_del_phase_slot_by_name(self):
self.mixture.add_phase_slot("TestPhase1", 0.1)
self.mixture.del_phase_slot_by_name("TestPhase1")
self.assertEqual(len(self.mixture.phases), 0)
self.assertEqual(len(self.mixture.fractions), 0)
self.assertEqual(self.mixture.phase_matrix.shape, (0, 0))
def test_del_specimen_slot_by_object(self):
dummy = Specimen(name="Test Specimen", parent=self.project)
self.project.specimens.append(dummy)
self.mixture.add_specimen_slot(dummy, 0.5, 0)
self.mixture.del_specimen_slot_by_object(dummy)
self.assertEqual(len(self.mixture.specimens), 0)
self.assertEqual(self.mixture.phase_matrix.shape, (0, 0))
def test_set_specimen(self):
dummy = Specimen(name="Test Specimen", parent=self.project)
self.project.specimens.append(dummy)
self.mixture.add_specimen_slot(None, 0.5, 0)
self.mixture.set_specimen(0, dummy)
self.assertEqual(self.mixture.specimens[0], dummy)
def test_unset_specimen(self):
dummy = Specimen(name="Test Specimen", parent=self.project)
self.project.specimens.append(dummy)
self.mixture.add_specimen_slot(dummy, 0.5, 0)
self.mixture.unset_specimen(dummy)
self.assertEqual(self.mixture.specimens[0], None)
def test_unset_phase(self):
specimen = Specimen(name="Test Specimen", parent=self.project)
self.project.specimens.append(specimen)
self.mixture.add_specimen_slot(specimen, 0.5, 0)
self.mixture.add_phase_slot("Test Phase1", 0.5)
dummy = Phase(name="Test Phase", parent=self.project)
self.project.phases.append(dummy)
self.mixture.set_phase(0, 0, dummy)
self.mixture.unset_phase(dummy)
self.assertEqual(self.mixture.phase_matrix[0, 0], None)
def test_randomize_empty_mixture(self):
self.mixture.refinement.randomize()
def _refinement_setup(self):
# TODO maybe add some more variation in the type of Phases?
specimen = Specimen(name="Test Specimen", parent=self.project)
self.project.specimens.append(specimen)
phase1 = Phase(name="Test Phase1", parent=self.project)
self.project.phases.append(phase1)
phase2 = Phase(name="Test Phase2", parent=self.project)
self.project.phases.append(phase2)
self.mixture.add_specimen_slot(specimen, 0.5, 0)
self.mixture.add_phase_slot("Test Phase1", 0.5)
self.mixture.add_phase_slot("Test Phase2", 0.5)
self.mixture.set_phase(0, 0, phase1)
self.mixture.set_phase(0, 1, phase2)
def test_randomize(self):
self._refinement_setup()
# Mark the attribute(s) for refinement & get their values:
refinables = []
for node in self.mixture.refinables.iter_children():
ref_prop = node.object
if ref_prop.refinable:
ref_prop.refine = True
refinables.append((ref_prop, ref_prop.value))
# Randomize:
self.mixture.refinement.randomize()
# Check all of them have been randomized:
# It is possible (but unlikely) that the randomized value
# is the same as the pre-randomized value. If so run this test again
# to make sure it is really failing.
for ref_prop, pre_val in refinables:
self.assertNotEqual(pre_val, ref_prop.value)
def test_auto_restrict_empy_mixture(self):
self.mixture.refinement.auto_restrict()
def test_auto_restrict(self):
self._refinement_setup()
# Mark the attribute(s) for refinement & get their values:
refinables = []
for node in self.mixture.refinables.iter_children():
ref_prop = node.object
if ref_prop.refinable:
ref_prop.refine = True
refinables.append((ref_prop, ref_prop.value))
# Randomize:
self.mixture.refinement.auto_restrict()
# Check all of them have been restricted:
for ref_prop, pre_val in refinables:
self.assertEqual(pre_val * 0.8, ref_prop.value_min)
self.assertEqual(pre_val * 1.2, ref_prop.value_max)
# TODO:
# - set_data_object
# - optimize
# - apply_current_data_object
# - update
# - get_refinement_method
# - setup_refine_options
pass # end of class
def create_new_object_proxy(self):
return Mixture(parent=self.model)
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
