def test_addPhaseDefinition(cal):
calc = CryspyCalculator('')
interface = QtCalculatorInterface(calc)
interface.addPhaseDefinition(phase_path)
phase_added = interface.getPhase('Fe3O4')
phase_ref = cal.getPhase('Fe3O4')
assert phase_added['phasename'] == phase_ref['phasename']
assert phase_added['spacegroup']['crystal_system'].value == phase_ref[
'spacegroup']['crystal_system'].value
assert phase_added['spacegroup'][
'space_group_name_HM_ref'].value == phase_ref['spacegroup'][
'space_group_name_HM_ref'].value
assert phase_added['spacegroup'][
'space_group_IT_number'].value == phase_ref['spacegroup'][
'space_group_IT_number'].value
assert phase_added['spacegroup']['origin_choice'].value == phase_ref[
'spacegroup']['origin_choice'].value
assert phase_added['cell']['length_a'].value == phase_ref['cell'][
'length_a'].value
assert phase_added['cell']['length_b'].value == phase_ref['cell'][
'length_b'].value
assert phase_added['cell']['length_c'].value == phase_ref['cell'][
'length_c'].value
assert phase_added['cell']['angle_alpha'].value == phase_ref['cell'][
'angle_alpha'].value
assert phase_added['cell']['angle_beta'].value == phase_ref['cell'][
'angle_beta'].value
assert phase_added['cell']['angle_gamma'].value == phase_ref['cell'][
'angle_gamma'].value
assert phase_added['atoms']['Fe3A']['fract_x'].value == phase_ref['atoms'][
'Fe3A']['fract_x'].value
assert phase_added['atoms']['Fe3B']['fract_y'].value == phase_ref['atoms'][
'Fe3B']['fract_y'].value
assert phase_added['atoms']['O']['fract_z'].value == phase_ref['atoms'][
'O']['fract_z'].value
class ProxyPyQml(QObject):
def __init__(self, release_config_file_path, parent=None):
self.__log = logger.getLogger(__name__)
self.__log.info("")
super().__init__(parent)
self.info = Config(release_config_file_path)['release']
self.projectChanged.connect(self.onProjectChanged)
self._project_rcif_path = None
self._samples_rcif_path = None
self._experiment_rcif_path = None
self._calculator_interface = QtCalculatorInterface(CryspyCalculator())
self._project_dict_copy = {}
self._project_control = ProjectControl()
self._measured_data_model = MeasuredDataModel()
self._calculated_data_model = CalculatedDataModel()
self._bragg_peaks_model = BraggPeaksModel()
self._cell_parameters_model = CellParametersModel()
self._cell_box_model = CellBoxModel()
self._atom_sites_model = AtomSitesModel()
self._atom_adps_model = AtomAdpsModel()
self._atom_msps_model = AtomMspsModel()
self._fitables_model = FitablesModel()
self._status_model = StatusModel()
self._refine_thread = None
self._refinement_running = False
self._refinement_done = False
self._refinement_result = {}
self._calculator_interface.clearUndoStack()
self._need_to_save = False
@Slot()
def loadPhasesFromFile(self):
"""
Replace internal structure models based on requested content from CIF
"""
self._samples_rcif_path = self._project_control.phases_rcif_path
self._calculator_interface.addPhaseDefinition(self._samples_rcif_path)
# explicit emit required for the view to reload the model content
self._calculator_interface.clearUndoStack()
self.projectChanged.emit()
self._need_to_save = False
self.projectSaveStateChanged.emit()
#self.onProjectUnsaved()
@Slot()
def loadExperiment(self):
"""
Selects the appropriate loading algorithm
"""
if self._project_control.experiment_file_format == "cif":
self.loadExperimentFromCif()
elif self._project_control.experiment_file_format == "xye":
self.loadExperimentFromXye()
else:
raise IOError(
"Unexpected experiment_file_format in ProjectControl.")
def loadExperimentFromXye(self):
"""
Loads non cif data files, adds fake cif information, and loads
"""
cif_string = self._project_control._cif_string
cif_string = cif_string.replace(
"PHASE_NAME",
self._calculator_interface.phasesIds()[0])
self._calculator_interface.addExperimentDefinitionFromString(
cif_string)
self._measured_data_model.setCalculatorInterface(
self._calculator_interface)
# explicit emit required for the view to reload the model content
self._calculator_interface.clearUndoStack()
self.projectChanged.emit()
self._need_to_save = False
self.projectSaveStateChanged.emit()
#self.onProjectUnsaved()
def loadExperimentFromCif(self):
"""
Replace internal experiment models based on requested content from CIF
"""
self._experiment_rcif_path = self._project_control.experiment_rcif_path
self._calculator_interface.addExperimentDefinition(
self._experiment_rcif_path)
self._measured_data_model.setCalculatorInterface(
self._calculator_interface)
# explicit emit required for the view to reload the model content
self._calculator_interface.updateCalculations()
self._calculator_interface.clearUndoStack()
self.projectChanged.emit()
self._need_to_save = False
self.projectSaveStateChanged.emit()
#self.onProjectUnsaved()
@Slot(str)
def updateMainCifFromGui(self, cif_string):
name_list = [
str_line for str_line in cif_string.split('\n')
if str_line.startswith('_name ')
]
if len(name_list) != 1:
self.__log.warning(
'Project name can not be set. Returning previous value')
return
name = name_list[0].split('_name ')[1]
if name[-1] == ' ':
name = name[:-1]
keywords_list = [
str_line for str_line in cif_string.split('\n')
if str_line.startswith('_keywords ')
]
if len(keywords_list) != 1:
self.__log.warning(
'Project keywords can not be set. Returning previous values')
return
keywords = keywords_list[0].split('_keywords ')[1]
if keywords[-1] == ' ':
keywords = keywords[:-1]
keywords = keywords.strip('\'')
keywords = keywords.split(',')
keywords = [
keyword[1:] if keyword[0] == ' ' else keyword
for keyword in keywords
]
keywords = [
keyword[:-1] if keyword[-1] == ' ' else keyword
for keyword in keywords
]
self._project_control.manager.projectName = name
self._calculator_interface.setProjectName(name)
self._project_control.manager.projectKeywords = keywords
self._calculator_interface.setProjectKeywords(keywords)
self._need_to_save = True
self.projectSaveStateChanged.emit()
@Slot(str)
def updatePhaseFromGui(self, cif_string):
phase_name = self._calculator_interface.phasesIds()[0]
cif_string = cif_string[cif_string.find('data_'):]
new_phase = self._calculator_interface.getPhaseFromCif(cif_string)
old_phase = self._calculator_interface.getPhase(phase_name)
keys, values, modifier = old_phase.dictComparison(new_phase)
modded_keys = [['phases', phase_name, *key]
for key, value in zip(keys, values)
if key[-1] != 'mapping' and key[-1] != 'hide']
modded_values = [
value for key, value in zip(keys, values)
if key[-1] != 'mapping' and key[-1] != 'hide'
]
self._calculator_interface.project_dict.startBulkUpdate(
'Manual update of samples.cif')
self._calculator_interface.project_dict.bulkUpdate(
modded_keys, modded_values)
self._calculator_interface.setCalculatorFromProject()
self._calculator_interface.updateCalculations()
self._calculator_interface.project_dict.endBulkUpdate()
#self.projectChanged.emit()
self._calculator_interface.projectDictChanged.emit()
self._need_to_save = True
self.projectSaveStateChanged.emit()
@Slot(str)
def updateExperimentFromGui(self, cif_string):
exp_name = self._calculator_interface.experimentsIds()[0]
cif_string = cif_string[cif_string.find('data_'):]
new_experiment = self._calculator_interface.getExperimentFromCif(
cif_string)
old_exp = self._calculator_interface.getExperiment(exp_name)
keys, values, modifier = old_exp.dictComparison(new_experiment)
modded_keys = [['experiments', exp_name, *key] for key in keys
if key[-1] != 'mapping' and key[-1] != 'hide']
modded_values = [
value for key, value in zip(keys, values)
if key[-1] != 'mapping' and key[-1] != 'hide'
]
self._calculator_interface.project_dict.startBulkUpdate(
'Manual update of experiments.cif')
self._calculator_interface.project_dict.bulkUpdate(
modded_keys, modded_values)
self._calculator_interface.setCalculatorFromProject()
self._calculator_interface.updateCalculations()
self._calculator_interface.project_dict.endBulkUpdate()
#self.projectChanged.emit()
self._calculator_interface.projectDictChanged.emit()
self._need_to_save = True
self.projectSaveStateChanged.emit()
# Load CIF method, accessible from QML
@Slot()
def initialize(self):
self.__log.info("")
self._project_rcif_path = self._project_control.project_rcif_path
#logging.info(self._calculator.asCifDict())
# TODO This is where you would choose the calculator and import the module
self._calculator_interface = QtCalculatorInterface(
CryspyCalculator(self._project_rcif_path))
self._calculator_interface.project_dict['app']['name'] = self.info[
'name']
self._calculator_interface.project_dict['app']['version'] = self.info[
'version']
self._calculator_interface.project_dict['app']['url'] = self.info[
'url']
self._calculator_interface.projectDictChanged.connect(
self.projectChanged)
self._calculator_interface.canUndoOrRedoChanged.connect(
self.canUndoOrRedoChanged)
self._calculator_interface.clearUndoStack()
# TODO generates dictdiffer
# `ValueError: The truth value of an array with more than one element is ambiguous`
# Temp fix - Andrew
self.onProjectSaved()
models = [
self._measured_data_model, self._calculated_data_model,
self._bragg_peaks_model, self._cell_parameters_model,
self._cell_box_model, self._atom_sites_model,
self._atom_adps_model, self._atom_msps_model, self._fitables_model,
self._status_model
]
for model in models:
model.setCalculatorInterface(self._calculator_interface)
self._refine_thread = Refiner(self._calculator_interface, 'refine')
self._refine_thread.failed.connect(self._thread_failed)
self._refine_thread.finished.connect(self._thread_finished)
self._refine_thread.finished.connect(
self._status_model.onRefinementDone)
# We can't link signals as the manager signals emitted before the dict is updated :-(
self.projectChanged.emit()
@Slot()
def createProjectZip(self):
self.__log.debug("")
self._calculator_interface.writeMainCif(
self._project_control.tempDir.name)
writeEmptyProject(self._project_control,
self._project_control.project_file)
self.onProjectSaved()
@Slot(str)
def createProject(self, file_path):
self.__log.debug("")
self._project_control.createProject(file_path)
# Note that the main rcif of self._project_control.project_rcif_path has not ben cleared
self._project_control.project_rcif_path = ''
self.onProjectSaved()
self.initialize()
self.projectChanged.emit()
@Slot(str)
def saveProjectAs(self, file_path):
self.__log.debug("")
self._project_control.project_file = file_path
self.saveProject()
@Slot()
def saveProject(self):
self.__log.debug("")
self._calculator_interface.saveCifs(self._project_control.tempDir.name)
writeProject(self._project_control, self._project_control.project_file)
self.onProjectSaved()
def onProjectSaved(self):
self.__log.debug("")
self._project_dict_copy = deepcopy(
self._calculator_interface.project_dict)
self._need_to_save = False
self.projectSaveStateChanged.emit()
self.projectChanged.emit(
) # update project.cif in gui (when filenames changed)
def onProjectUnsaved(self):
self.__log.debug("")
self._need_to_save = True
self.projectSaveStateChanged.emit()
def onProjectChanged(self):
keys, _, _ = self._calculator_interface.project_dict.dictComparison(
self._project_dict_copy)
self.__log.debug(f"keys: {keys}")
self._need_to_save = True
if not keys:
self._need_to_save = False
self.__log.debug(f"needToSave: {self._need_to_save}")
self.projectSaveStateChanged.emit()
def calculatorInterface(self):
self.__log.debug("---")
return self._calculator_interface
def needToSave(self):
self.__log.debug("+++")
return self._need_to_save
def projectFilePathSelected(self):
self.__log.debug("***")
return bool(self._project_control.project_file)
# ##############
# QML Properties
# ##############
# Notifications of changes for QML GUI about projectDictChanged,
# which calls another signal projectChanged
projectChanged = Signal()
projectSaveStateChanged = Signal()
canUndoOrRedoChanged = Signal()
_calculatorInterface = Property('QVariant',
calculatorInterface,
notify=projectChanged)
_needToSave = Property(bool, needToSave, notify=projectSaveStateChanged)
_projectFilePathSelected = Property(bool,
projectFilePathSelected,
notify=projectSaveStateChanged)
_undoText = Property('QVariant',
lambda self: self._calculator_interface.undoText(),
notify=canUndoOrRedoChanged)
_redoText = Property('QVariant',
lambda self: self._calculator_interface.redoText(),
notify=canUndoOrRedoChanged)
_canUndo = Property('QVariant',
lambda self: self._calculator_interface.canUndo(),
notify=canUndoOrRedoChanged)
_canRedo = Property('QVariant',
lambda self: self._calculator_interface.canRedo(),
notify=canUndoOrRedoChanged)
# Notifications of changes for QML GUI are done, when needed, in the
# respective classes via dataChanged.emit() or layotChanged.emit() signals
_proxy = Property('QVariant', lambda self: self, constant=True)
_releaseInfo = Property('QVariant',
lambda self: self.releaseInfo,
constant=True)
_projectControl = Property('QVariant',
lambda self: self._project_control,
constant=True)
_projectManager = Property('QVariant',
lambda self: self._project_control.manager,
constant=True)
_measuredData = Property('QVariant',
lambda self: self._measured_data_model,
constant=True)
_calculatedData = Property('QVariant',
lambda self: self._calculated_data_model,
constant=True)
_braggPeaks = Property('QVariant',
lambda self: self._bragg_peaks_model,
constant=True)
_cellParameters = Property(
'QVariant',
lambda self: self._cell_parameters_model.asModel(),
constant=True)
_cellBox = Property('QVariant',
lambda self: self._cell_box_model.asModel(),
constant=True)
_atomSites = Property('QVariant',
lambda self: self._atom_sites_model.asModel(),
constant=True)
_atomAdps = Property('QVariant',
lambda self: self._atom_adps_model.asModel(),
constant=True)
_atomMsps = Property('QVariant',
lambda self: self._atom_msps_model.asModel(),
constant=True)
_fitables = Property('QVariant',
lambda self: self._fitables_model.asModel(),
constant=True)
_statusInfo = Property(
'QVariant',
lambda self: self._status_model.returnStatusBarModel(),
constant=True)
_chartInfo = Property('QVariant',
lambda self: self._status_model.returnChartModel(),
constant=True)
_releaseInfo = Property('QVariant', lambda self: self.info, constant=True)
# ###############
# REFINEMENT TYPE
# ###############
def refineSum(self):
if not self._calculator_interface.experimentsIds():
return False
experiment_name = self._calculator_interface.experimentsIds()[0]
return self._calculator_interface.project_dict['experiments'][
experiment_name]['refinement_type'].sum
def refineDiff(self):
if not self._calculator_interface.experimentsIds():
return False
experiment_name = self._calculator_interface.experimentsIds()[0]
return self._calculator_interface.project_dict['experiments'][
experiment_name]['refinement_type'].diff
def setRefineSum(self, state):
experiment_name = self._calculator_interface.experimentsIds()[0]
if self._calculator_interface.project_dict['experiments'][
experiment_name]['refinement_type'].sum == state:
return
self._calculator_interface.project_dict['experiments'][
experiment_name]['refinement_type'].sum = state
def setRefineDiff(self, state):
experiment_name = self._calculator_interface.experimentsIds()[0]
if self._calculator_interface.project_dict['experiments'][
experiment_name]['refinement_type'].diff == state:
return
self._calculator_interface.project_dict['experiments'][
experiment_name]['refinement_type'].diff = state
_refineSum = Property(bool, refineSum, setRefineSum, notify=projectChanged)
_refineDiff = Property(bool,
refineDiff,
setRefineDiff,
notify=projectChanged)
# ##########
# REFINEMENT
# ##########
def _thread_finished(self, res):
"""
Notfy the listeners about refinement results
"""
self._refinement_running = False
self._refinement_done = True
self._refinement_result = deepcopy(res)
self.refinementStatusChanged.emit()
def _thread_failed(self, reason):
"""
Notify the GUI about failure so a message can be shown
"""
self.__log.info("Refinement failed: " + str(reason))
self._refinement_running = False
self._refinement_done = False
self.refinementStatusChanged.emit()
@Slot()
def refine(self):
"""
Start refinement as a separate thread
"""
self._calculator_interface.setCalculatorFromProject()
self.__log.info("")
if self._refinement_running:
self.__log.info("Fitting stopped")
# This lacks actual stopping functionality, needs to be added
self._refinement_running = False
self._refinement_done = True
self.refinementStatusChanged.emit()
return
self._refinement_running = True
self._refinement_done = False
self.refinementStatusChanged.emit()
self._refine_thread.start()
refinementStatusChanged = Signal()
_refinementStatus = Property('QVariant',
lambda self: [
self._refinement_running, self.
_refinement_done, self._refinement_result
],
notify=refinementStatusChanged)
# ######
# REPORT
# ######
@Slot(str)
def store_report(self, report=""):
"""
Keep the QML generated HTML report for saving
"""
self.report_html = report
@Slot(str, str)
def save_report(self, filename="", extension=".HTML"):
"""
Save the generated report to the specified file
Currently only html
"""
full_filename = filename + extension.lower()
full_filename = os.path.join(
self._project_control.get_project_dir_absolute_path(),
full_filename)
if not self.report_html:
self.__log.info("No report to save")
return
if extension == '.HTML':
# HTML can contain non-ascii, so need to open with right encoding
with open(full_filename, 'w', encoding='utf-8') as report_file:
report_file.write(self.report_html)
self.__log.info("Report written")
elif extension == '.PDF':
document = QTextDocument(parent=None)
document.setHtml(self.report_html)
printer = QPdfWriter(full_filename)
printer.setPageSize(printer.A3) # A3 to fit A4 page
document.print_(printer)
else:
raise NotImplementedError
# Show the generated report in the default browser
url = os.path.realpath(full_filename)
open_url(url=url)