def add_specimen(self):
specimen = Specimen(parent=self.model, name="New Specimen")
self.model.specimens.append(specimen)
self.view.specimens_treeview.set_cursor(
self.treemodel.on_get_path(specimen))
self.edit_specimen()
return True
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 load_specimens(stop=None):
for filename in filenames:
if stop is not None and stop.is_set():
return
try:
specimens = Specimen.from_experimental_data(
filename=filename,
parent=self.model,
parser=parser)
except Exception as msg:
message = "An unexpected error has occurred when trying to parse %s:\n\n<i>" % os.path.basename(
filename)
message += str(msg) + "</i>\n\n"
message += "This is most likely caused by an invalid or unsupported file format."
logger.exception(message)
@run_when_idle
def run_dialog():
DialogFactory.get_information_dialog(
message=message,
parent=self.view.get_top_widget()).run()
return False
run_dialog()
else:
status_dict["specimens"] += specimens
status_dict["current_file"] += 1
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 _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 load_specimens(stop=None):
for filename in filenames:
if stop is not None and stop.is_set():
return
# Error message is case parsing fails:
message = "An unexpected error has occurred when trying to parse %s:\n\n<i>" % os.path.basename(filename)
message += "%s</i>\n\n"
message += "This is most likely caused by an invalid or unsupported file format."
# Run & report any errors:
with DialogFactory.error_dialog_handler(
message, self.view.get_top_widget(),
title="Failed to load file", reraise=False):
specimens = Specimen.from_experimental_data(filename=filename, parent=self.model, parser=parser)
status_dict["specimens"] += specimens
status_dict["current_file"] += 1
def load_specimens(stop=None):
for filename in filenames:
if stop is not None and stop.is_set():
return
try:
specimens = Specimen.from_experimental_data(filename=filename, parent=self.model, parser=parser)
except Exception as msg:
message = "An unexpected error has occurred when trying to parse %s:\n\n<i>" % os.path.basename(filename)
message += str(msg) + "</i>\n\n"
message += "This is most likely caused by an invalid or unsupported file format."
logger.exception(message)
@run_when_idle
def run_dialog():
self.run_information_dialog(
message=message,
parent=self.view.get_top_widget()
)
return False
run_dialog()
else:
status_dict["specimens"] += specimens
status_dict["current_file"] += 1
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 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
