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