def viewResults(r, scenIdall, detector):
"""
Opens Results table
"""
# need a correspondence table in order to display results!
session = Session()
settings = RaseSettings()
default_corr_table = session.query(CorrespondenceTable).filter_by(
is_default=True).one_or_none()
if not default_corr_table:
msgbox = QMessageBox(
QMessageBox.Question, 'No Correspondence Table set!',
'No correspondence table set! Would you like to set a correspondence table now?'
)
msgbox.addButton(QMessageBox.Yes)
msgbox.addButton(QMessageBox.No)
answer = msgbox.exec()
if answer == QMessageBox.Yes:
CorrespondenceTableDialog().exec_()
settings.setIsAfterCorrespondenceTableCall(True)
else:
return
selected_scenarios = scenIdall
r.calculateScenarioStats(1, selected_scenarios, detector)
ViewResultsDialog(r, selected_scenarios, detector).exec_()
def set_otherCols_fromMat(self, units, matName, doseItem):
if matName:
if not doseItem.text():
doseItem.setText('0.1')
if not units.text():
textSet = False
if self.comboDetectorSelect.currentIndex() == 0:
detector_list = [
detector for detector in Session().query(Detector)
]
else:
detector_list = [
Session().query(Detector).filter_by(
name=self.comboDetectorSelect.currentText()).first(
)
]
for detector in detector_list:
for baseSpectrum in detector.base_spectra:
if baseSpectrum.material.name == matName and not textSet:
units.tableWidget().blockSignals(True)
if isinstance(baseSpectrum.rase_sensitivity,
float):
units.setText(units_labels['DOSE'])
units.setData(Qt.UserRole, 'DOSE')
textSet = True
else:
units.setText(units_labels['FLUX'])
units.setData(Qt.UserRole, 'FLUX')
units.tableWidget().blockSignals(False)
def __init__(self, parent=None, groups=[], scens=None, del_groups=False):
QDialog.__init__(self, parent)
self.groups = groups
self.scens = scens
self.del_groups = del_groups
self.session = Session()
self.makeLayout()
def showDetailView(self, index):
scen_det_key = self.results_model.headerData(index.row(), Qt.Vertical, Qt.UserRole)
resultMap = self.parent.result_super_map[scen_det_key]
scen_id = scen_det_key.split('*')[0]
det_name = "".join(scen_det_key.split('*')[1:])
scenario = Session().query(Scenario).filter_by(id=scen_id).first()
detector = Session().query(Detector).filter_by(name=det_name).first()
DetailedResultsDialog(resultMap, scenario, detector).exec_()
def export_scenarios(scenarios_ids, file_path):
"""
Export scenarios from database to xml file
"""
session = Session()
scenarios = [session.query(Scenario).filter_by(id=scenid).first() for scenid in scenarios_ids]
scen_io = ScenariosIO()
xml_str = scen_io.scenario_export(scenarios)
Path(file_path).write_text(xml_str)
def initializeDatabase(databaseFilepath):
"""
binds Session to database and creates new database if none exists
:param databaseFilepath: path to src.sqlite file
"""
Session.remove()
engine = create_engine('sqlite:///' + databaseFilepath)
Session.configure(bind=engine)
if not os.path.exists(databaseFilepath):
Base.metadata.create_all(engine)
def createEditor(self, parent, option, index):
if index.column() == self.matCol:
# generate material list
fd_units = self.tblMat.item(index.row(),
self.unitsCol).data(Qt.UserRole)
material_list = []
if not self.selected_detname:
for detector in Session().query(Detector):
for baseSpectrum in detector.base_spectra:
if baseSpectrum.material.name not in material_list:
if ((isinstance(baseSpectrum.rase_sensitivity,
float) and (fd_units == 'DOSE')) or
(isinstance(baseSpectrum.flux_sensitivity,
float) and (fd_units == 'FLUX'))
or not fd_units):
material_list.append(
baseSpectrum.material.name)
material_list = sorted(material_list)
else:
detector = Session().query(Detector).filter_by(
name=self.selected_detname).first()
material_list = sorted([
baseSpectrum.material.name
for baseSpectrum in detector.base_spectra
if ((isinstance(baseSpectrum.rase_sensitivity, float) and
(fd_units == 'DOSE')) or
(isinstance(baseSpectrum.flux_sensitivity, float) and
(fd_units == 'FLUX')) or not fd_units)
])
# remove any materials already used
for row in range(self.tblMat.rowCount()):
item = self.tblMat.item(row, self.matCol)
if item and item.text() in material_list:
material_list.remove(item.text())
#create and populate comboEdit
comboEdit = QComboBox(parent)
comboEdit.setEditable(self.editable)
comboEdit.setSizeAdjustPolicy(0)
comboEdit.setMaxVisibleItems(25)
comboEdit.addItem('')
comboEdit.addItems(material_list)
return comboEdit
elif index.column() == self.intensityCol:
editor = QLineEdit(parent)
editor.setValidator(RegExpSetValidator(editor, self.auto_s))
return editor
elif index.column() == self.unitsCol:
return self.unitsEditor(parent, index)
else:
return super(MaterialDoseDelegate,
self).createEditor(parent, option, index)
def __init__(self, resultMap, scenario, detector):
QDialog.__init__(self)
self.setupUi(self)
self.settings = RaseSettings()
self.headerLabels = ['File', 'Tp', 'Fn', 'Fp', 'Precision', 'Recall', 'Fscore', 'IDs']
self.NUM_COLS = len(self.headerLabels)
self.session = Session()
self.scenario = scenario
self.detector = detector
self.tblDetailedResults.setContextMenuPolicy(Qt.CustomContextMenu)
self.tblDetailedResults.setColumnCount(self.NUM_COLS)
self.tblDetailedResults.setHorizontalHeaderLabels(self.headerLabels)
self.tblDetailedResults.horizontalHeader().setSectionResizeMode(0, QHeaderView.Stretch)
self.tblDetailedResults.setRowCount(0)
row=0
for file in sorted(resultMap, key=natural_keys):
results = resultMap[file]
results.insert(0, file)
self.tblDetailedResults.insertRow(row)
for col in range(self.NUM_COLS):
self.tblDetailedResults.setItem(row, col, QTableWidgetItem(results[col]))
row = row + 1
results.pop(0)
self.tblDetailedResults.resizeColumnsToContents()
self.tblDetailedResults.horizontalHeader().setSectionResizeMode(0, QHeaderView.Stretch)
self.buttonOK.clicked.connect(self.closeSelected)
self.buttonExport.clicked.connect(self.handleExport)
def cleanup_scenarios(rangefind_rep, scenIds):
"""Remove scenarios from the database that were rangefinders, i.e.: low replication scenarios"""
settings = RaseSettings()
session = Session()
scenarios = []
for scen in scenIds:
scenarios.append(session.query(Scenario).filter_by(id=scen).first())
scens_to_delete = []
for scen in scenarios:
if scen.replication == rangefind_rep:
scens_to_delete.append(scen.id)
delete_scenario(scens_to_delete, settings.getSampleDirectory())
session.commit()
def set_otherCols_fromUnit(self, units, matName, doseItem):
textKeep = False
if self.comboDetectorSelect.currentIndex() == 0:
detector_list = [
detector for detector in Session().query(Detector)
]
else:
detector_list = [
Session().query(Detector).filter_by(
name=self.comboDetectorSelect.currentText()).first()
]
for detector in detector_list:
for baseSpectrum in detector.base_spectra:
if baseSpectrum.material.name == matName.text(
) and not textKeep:
if (units.data(Qt.UserRole) == 'DOSE' and isinstance(baseSpectrum.rase_sensitivity, float)) or \
(units.data(Qt.UserRole) == 'FLUX' and isinstance(baseSpectrum.flux_sensitivity, float)):
textKeep = True
if not textKeep:
matName.setText('')
def delete_scenario(scenario_ids, sample_root_dir):
"""
Delete scenarios from database and cleanup sample folders
"""
session = Session()
for id in scenario_ids:
scenDelete = session.query(Scenario).filter(Scenario.id == id)
matDelete = session.query(ScenarioMaterial).filter(ScenarioMaterial.scenario_id == id)
backgMatDelete = session.query(ScenarioBackgroundMaterial).filter(ScenarioBackgroundMaterial.scenario_id == id)
# folders
folders = [name for name in glob.glob(os.path.join(sample_root_dir, "*" + id + "*"))]
for folder in folders:
shutil.rmtree(folder)
# database
scenObj = scenDelete.first()
scenObj.scenario_groups.clear()
matDelete.delete()
backgMatDelete.delete()
scenDelete.delete()
session.commit()
session.close()
class GroupSettings(QDialog):
"""Simple Dialog to allow the user to select which groups a scenario is in.
This information is stored in the scenario_groups table value for each scenario.
:param parent: the parent dialog
"""
def __init__(self, parent=None, groups=[], scens=None, del_groups=False):
QDialog.__init__(self, parent)
self.groups = groups
self.scens = scens
self.del_groups = del_groups
self.session = Session()
self.makeLayout()
def makeLayout(self):
cols_list = [grp.name for grp in self.session.query(ScenarioGroup)]
cols_list.insert(0, cols_list.pop(cols_list.index('default_group')))
cb_list = [QCheckBox(v.replace('&', '&&')) for v in cols_list]
self.layout = QVBoxLayout()
self.checklayout = QVBoxLayout()
self.buttonlayout = QVBoxLayout()
for cb in cb_list:
self.checklayout.addWidget(cb)
if cb.text() in self.groups:
cb.setChecked(True)
if cb.text() == 'default_group' and self.del_groups:
cb.setEnabled(False)
self.btn_newgroup = QPushButton('Add New Group')
self.buttonlayout.addWidget(self.btn_newgroup)
self.btn_newgroup.clicked.connect(self.addCheckbox)
self.buttonBox = QDialogButtonBox(self)
if self.del_groups:
self.btn_deletegroup = QPushButton('Remove Group(s)')
self.buttonlayout.addWidget(self.btn_deletegroup)
self.btn_deletegroup.clicked.connect(self.delGroup)
self.buttonBox.setStandardButtons(QDialogButtonBox.Close)
self.buttonBox.rejected.connect(self.reject)
else:
self.buttonBox.setStandardButtons(QDialogButtonBox.Cancel
| QDialogButtonBox.Ok)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
self.buttonlayout.addWidget(self.buttonBox)
self.layout.addLayout(self.checklayout)
self.layout.addLayout(self.buttonlayout)
if not self.del_groups and self.scens and len(self.scens) > 1:
self.info = QLabel(
'NOTE: A group box is checked if\nany one of the selected scenarios\nis in that '
'group. Pressing OK will\nadd all selected scenarios to the\nselected groups.'
)
self.layout.addWidget(self.info)
self.setLayout(self.layout)
def _cb_list(self):
return [
self.checklayout.itemAt(i).widget()
for i in range(self.checklayout.count())
]
def addCheckbox(self):
newgroup, okPressed = QInputDialog.getText(self,
"Add New Scenario Group",
"Scenario Group name:",
QLineEdit.Normal, "")
collist = [grp.name for grp in self.session.query(ScenarioGroup)]
if okPressed and (newgroup != '' and newgroup not in collist):
self.checklayout.addWidget(QCheckBox(newgroup))
self.setLayout(self.layout)
self.add_groups(self.session, newgroup)
def delGroup(self):
del_groups = [cb.text() for cb in self._cb_list() if cb.isChecked()]
if len(del_groups) > 1:
answer = QMessageBox(
QMessageBox.Question, 'Delete Scenario Groups',
'Are you sure you want to delete these scenario groups? '
'Scenarios in these groups will not be deleted')
else:
answer = QMessageBox(
QMessageBox.Question, 'Delete Scenario Group',
'Are you sure you want to delete this scenario group? '
'Scenarios in this group will not be deleted')
answer.addButton(QMessageBox.Yes)
answer.addButton(QMessageBox.No)
ans_hold = answer.exec()
if ans_hold == QMessageBox.Yes:
for group in del_groups:
self.delete_groups(self.session, group)
for cb in self._cb_list():
if cb.text() in del_groups:
self.checklayout.removeWidget(cb)
cb.deleteLater()
@staticmethod
def delete_groups(session, group):
group_delete = session.query(ScenarioGroup).filter(
ScenarioGroup.name == group)
group_delete.delete()
session.commit()
@staticmethod
def add_groups(session, group):
session.add(ScenarioGroup(name=group))
session.commit()
@pyqtSlot()
def accept(self):
"""
Adds the scenario to the checked groups
"""
self.n_groups = [cb.text() for cb in self._cb_list() if cb.isChecked()]
if self.scens:
for scen in self.scens:
scen.scenario_groups.clear()
for groupname in self.n_groups:
scen.scenario_groups.append(
self.session.query(ScenarioGroup).filter_by(
name=groupname).first())
self.session.commit()
return QDialog.accept(self)
def __init__(self, rase_gui, id=None, duplicate=[], auto_s=False):
QDialog.__init__(self)
self.setupUi(self)
self.rase_gui = rase_gui
self.tblMaterial.setContextMenuPolicy(Qt.CustomContextMenu)
self.tblBackground.setContextMenuPolicy(Qt.CustomContextMenu)
self.id = id
self.auto_s = auto_s
self.settings = RaseSettings()
self.scenarioHasChanged = False
self.groupHasChanged = False
self.duplicate = duplicate
self.session = Session()
self.txtAcqTime.setText('30')
self.txtAcqTime.setToolTip(
"Enter comma-separated values OR range as min-max:step OR range followed by comma-separated values"
)
self.txtReplication_2.setText('100')
int_validator = QIntValidator()
self.txtAcqTime.setValidator(RegExpSetValidator())
self.txtReplication_2.setValidator(int_validator)
self.tblMaterial.setHorizontalHeaderItem(INTENSITY,
QTableWidgetItem('Intensity'))
self.tblBackground.setHorizontalHeaderItem(
INTENSITY, QTableWidgetItem('Intensity'))
self.tblMaterial.customContextMenuRequested.connect(
lambda x, table=self.tblMaterial: self.context_auto_range(
x, self.tblMaterial))
self.tblBackground.customContextMenuRequested.connect(
lambda x, table=self.tblBackground: self.context_auto_range(
x, self.tblBackground))
# set material table
self.tblMaterial.setItemDelegate(
MaterialDoseDelegate(self.tblMaterial,
unitsCol=UNITS,
materialCol=MATERIAL,
intensityCol=INTENSITY))
self.tblMaterial.setRowCount(10)
for row in range(self.tblMaterial.rowCount()):
self.tblMaterial.setItem(row, UNITS, QTableWidgetItem())
self.tblMaterial.setItem(row, INTENSITY, QTableWidgetItem())
self.tblMaterial.setItem(row, MATERIAL, QTableWidgetItem())
self.tblMaterial.item(row, INTENSITY).setToolTip(
"Enter comma-separated values OR range as min-max:step OR range followed by comma-separated values"
)
self.tblMaterial.setRowHeight(row, 22)
# set background table
self.tblBackground.setItemDelegate(
MaterialDoseDelegate(self.tblBackground,
unitsCol=UNITS,
materialCol=MATERIAL,
intensityCol=INTENSITY,
auto_s=self.auto_s))
self.tblBackground.setRowCount(10)
for row in range(self.tblBackground.rowCount()):
self.tblBackground.setItem(row, UNITS, QTableWidgetItem())
self.tblBackground.setItem(row, INTENSITY, QTableWidgetItem())
self.tblBackground.setItem(row, MATERIAL, QTableWidgetItem())
self.tblBackground.item(row, INTENSITY).setToolTip(
"Enter comma-separated values OR range as min-max:step OR range followed by comma-separated values"
)
self.tblBackground.setRowHeight(row, 22)
# fill influence list
for influence in self.session.query(Influence):
self.lstInfluences.addItem(QListWidgetItem(influence.name))
self.comboDetectorSelect.addItems(
["all detectors"] +
[s.name for s in self.session.query(Detector).all()])
self.comboDetectorSelect.currentIndexChanged.connect(
self.updateTableDelegate)
# display a previous scenario if defined
if self.id:
if not self.duplicate:
self.setWindowTitle("Scenario Edit")
scenario = self.session.query(Scenario).get(id)
materials = scenario.scen_materials
bckg_materials = scenario.scen_bckg_materials
influences = scenario.influences
for table, mat_list in zip(
(self.tblMaterial, self.tblBackground),
(materials, bckg_materials)):
for rowCount, mat in enumerate(mat_list):
item = QTableWidgetItem(units_labels[mat.fd_mode])
item.setData(Qt.UserRole, mat.fd_mode)
table.setItem(rowCount, 0, item)
table.setItem(rowCount, 1,
QTableWidgetItem(mat.material_name))
table.setItem(rowCount, 2,
QTableWidgetItem(str(mat.dose)))
self.txtAcqTime.setText(str(scenario.acq_time))
self.txtReplication_2.setText(str(scenario.replication))
for influence in influences:
lst = self.lstInfluences.findItems(influence.name,
Qt.MatchExactly)[0]
lst.setSelected(True)
self.groups = self.getGroups()
else:
self.setWindowTitle("Build Scenario from Other Scenario")
scens = [
self.session.query(Scenario).filter_by(id=scen).first()
for scen in self.duplicate
]
scenario = scens[0]
materials = scenario.scen_materials
back_materials = scenario.scen_bckg_materials
influences = scenario.influences
mat_dict = {}
back_dict = {}
mat_fd = []
back_fd = []
for mat in materials:
mat_fd.append((mat.material_name, mat.fd_mode))
mat_dict[mat.material_name] = set([mat.dose])
for back in back_materials:
back_fd.append((back.material_name, back.fd_mode))
back_dict[back.material_name] = set([back.dose])
if len(scens) > 1:
for scen in scens[1:]:
mat_dict = self.make_matDict(scen.scen_materials,
mat_dict)
back_dict = self.make_matDict(scen.scen_bckg_materials,
back_dict)
if influences:
influences.append[scen.influences]
else:
influences = scen.influences
for table, material_dictionary, fd_list in \
zip((self.tblMaterial, self.tblBackground), (mat_dict, back_dict), (mat_fd, back_fd)):
mat_list_tup = [(k, v)
for k, v in material_dictionary.items()]
for rowCount, (mat, fd_mode) in enumerate(
zip(mat_list_tup, fd_list)):
doses = [str(d) for d in sorted(mat[1])]
item = QTableWidgetItem(units_labels[fd_mode[1]])
item.setData(Qt.UserRole, fd_mode[1])
table.setItem(rowCount, 0, item)
table.setItem(rowCount, 1,
QTableWidgetItem(str(mat[0])))
table.setItem(rowCount, 2,
QTableWidgetItem(str(','.join(doses))))
self.txtAcqTime.setText(str(scenario.acq_time))
for influence in influences:
lst = self.lstInfluences.findItems(influence.name,
Qt.MatchExactly)[0]
lst.setSelected(True)
self.groups = self.getGroups()
else:
self.groups = []
if self.auto_s and self.rase_gui.static_background:
for rowCount, mat in enumerate(self.rase_gui.static_background):
mat = mat[0]
item = QTableWidgetItem(units_labels[mat[0]])
item.setData(Qt.UserRole, mat[0])
self.tblBackground.setItem(rowCount, 0, item)
self.tblBackground.setItem(rowCount, 1,
QTableWidgetItem(mat[1].name))
self.tblBackground.setItem(rowCount, 2,
QTableWidgetItem(str(mat[2])))
# signal/slot connections (this has to be done after_ the previous scenario is loaded)
self.tblMaterial.cellChanged.connect(self.scenarioChanged)
self.tblBackground.cellChanged.connect(self.scenarioChanged)
self.tblMaterial.cellChanged.connect(self.updateScenariosList)
self.tblBackground.cellChanged.connect(self.updateScenariosList)
self.lstInfluences.itemSelectionChanged.connect(self.scenarioChanged)
self.txtAcqTime.textChanged.connect(self.scenarioChanged)
self.txtReplication_2.textChanged.connect(self.scenarioChanged)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
class ScenarioDialog(ui_create_scenario_dialog.Ui_ScenarioDialog, QDialog):
def __init__(self, rase_gui, id=None, duplicate=[], auto_s=False):
QDialog.__init__(self)
self.setupUi(self)
self.rase_gui = rase_gui
self.tblMaterial.setContextMenuPolicy(Qt.CustomContextMenu)
self.tblBackground.setContextMenuPolicy(Qt.CustomContextMenu)
self.id = id
self.auto_s = auto_s
self.settings = RaseSettings()
self.scenarioHasChanged = False
self.groupHasChanged = False
self.duplicate = duplicate
self.session = Session()
self.txtAcqTime.setText('30')
self.txtAcqTime.setToolTip(
"Enter comma-separated values OR range as min-max:step OR range followed by comma-separated values"
)
self.txtReplication_2.setText('100')
int_validator = QIntValidator()
self.txtAcqTime.setValidator(RegExpSetValidator())
self.txtReplication_2.setValidator(int_validator)
self.tblMaterial.setHorizontalHeaderItem(INTENSITY,
QTableWidgetItem('Intensity'))
self.tblBackground.setHorizontalHeaderItem(
INTENSITY, QTableWidgetItem('Intensity'))
self.tblMaterial.customContextMenuRequested.connect(
lambda x, table=self.tblMaterial: self.context_auto_range(
x, self.tblMaterial))
self.tblBackground.customContextMenuRequested.connect(
lambda x, table=self.tblBackground: self.context_auto_range(
x, self.tblBackground))
# set material table
self.tblMaterial.setItemDelegate(
MaterialDoseDelegate(self.tblMaterial,
unitsCol=UNITS,
materialCol=MATERIAL,
intensityCol=INTENSITY))
self.tblMaterial.setRowCount(10)
for row in range(self.tblMaterial.rowCount()):
self.tblMaterial.setItem(row, UNITS, QTableWidgetItem())
self.tblMaterial.setItem(row, INTENSITY, QTableWidgetItem())
self.tblMaterial.setItem(row, MATERIAL, QTableWidgetItem())
self.tblMaterial.item(row, INTENSITY).setToolTip(
"Enter comma-separated values OR range as min-max:step OR range followed by comma-separated values"
)
self.tblMaterial.setRowHeight(row, 22)
# set background table
self.tblBackground.setItemDelegate(
MaterialDoseDelegate(self.tblBackground,
unitsCol=UNITS,
materialCol=MATERIAL,
intensityCol=INTENSITY,
auto_s=self.auto_s))
self.tblBackground.setRowCount(10)
for row in range(self.tblBackground.rowCount()):
self.tblBackground.setItem(row, UNITS, QTableWidgetItem())
self.tblBackground.setItem(row, INTENSITY, QTableWidgetItem())
self.tblBackground.setItem(row, MATERIAL, QTableWidgetItem())
self.tblBackground.item(row, INTENSITY).setToolTip(
"Enter comma-separated values OR range as min-max:step OR range followed by comma-separated values"
)
self.tblBackground.setRowHeight(row, 22)
# fill influence list
for influence in self.session.query(Influence):
self.lstInfluences.addItem(QListWidgetItem(influence.name))
self.comboDetectorSelect.addItems(
["all detectors"] +
[s.name for s in self.session.query(Detector).all()])
self.comboDetectorSelect.currentIndexChanged.connect(
self.updateTableDelegate)
# display a previous scenario if defined
if self.id:
if not self.duplicate:
self.setWindowTitle("Scenario Edit")
scenario = self.session.query(Scenario).get(id)
materials = scenario.scen_materials
bckg_materials = scenario.scen_bckg_materials
influences = scenario.influences
for table, mat_list in zip(
(self.tblMaterial, self.tblBackground),
(materials, bckg_materials)):
for rowCount, mat in enumerate(mat_list):
item = QTableWidgetItem(units_labels[mat.fd_mode])
item.setData(Qt.UserRole, mat.fd_mode)
table.setItem(rowCount, 0, item)
table.setItem(rowCount, 1,
QTableWidgetItem(mat.material_name))
table.setItem(rowCount, 2,
QTableWidgetItem(str(mat.dose)))
self.txtAcqTime.setText(str(scenario.acq_time))
self.txtReplication_2.setText(str(scenario.replication))
for influence in influences:
lst = self.lstInfluences.findItems(influence.name,
Qt.MatchExactly)[0]
lst.setSelected(True)
self.groups = self.getGroups()
else:
self.setWindowTitle("Build Scenario from Other Scenario")
scens = [
self.session.query(Scenario).filter_by(id=scen).first()
for scen in self.duplicate
]
scenario = scens[0]
materials = scenario.scen_materials
back_materials = scenario.scen_bckg_materials
influences = scenario.influences
mat_dict = {}
back_dict = {}
mat_fd = []
back_fd = []
for mat in materials:
mat_fd.append((mat.material_name, mat.fd_mode))
mat_dict[mat.material_name] = set([mat.dose])
for back in back_materials:
back_fd.append((back.material_name, back.fd_mode))
back_dict[back.material_name] = set([back.dose])
if len(scens) > 1:
for scen in scens[1:]:
mat_dict = self.make_matDict(scen.scen_materials,
mat_dict)
back_dict = self.make_matDict(scen.scen_bckg_materials,
back_dict)
if influences:
influences.append[scen.influences]
else:
influences = scen.influences
for table, material_dictionary, fd_list in \
zip((self.tblMaterial, self.tblBackground), (mat_dict, back_dict), (mat_fd, back_fd)):
mat_list_tup = [(k, v)
for k, v in material_dictionary.items()]
for rowCount, (mat, fd_mode) in enumerate(
zip(mat_list_tup, fd_list)):
doses = [str(d) for d in sorted(mat[1])]
item = QTableWidgetItem(units_labels[fd_mode[1]])
item.setData(Qt.UserRole, fd_mode[1])
table.setItem(rowCount, 0, item)
table.setItem(rowCount, 1,
QTableWidgetItem(str(mat[0])))
table.setItem(rowCount, 2,
QTableWidgetItem(str(','.join(doses))))
self.txtAcqTime.setText(str(scenario.acq_time))
for influence in influences:
lst = self.lstInfluences.findItems(influence.name,
Qt.MatchExactly)[0]
lst.setSelected(True)
self.groups = self.getGroups()
else:
self.groups = []
if self.auto_s and self.rase_gui.static_background:
for rowCount, mat in enumerate(self.rase_gui.static_background):
mat = mat[0]
item = QTableWidgetItem(units_labels[mat[0]])
item.setData(Qt.UserRole, mat[0])
self.tblBackground.setItem(rowCount, 0, item)
self.tblBackground.setItem(rowCount, 1,
QTableWidgetItem(mat[1].name))
self.tblBackground.setItem(rowCount, 2,
QTableWidgetItem(str(mat[2])))
# signal/slot connections (this has to be done after_ the previous scenario is loaded)
self.tblMaterial.cellChanged.connect(self.scenarioChanged)
self.tblBackground.cellChanged.connect(self.scenarioChanged)
self.tblMaterial.cellChanged.connect(self.updateScenariosList)
self.tblBackground.cellChanged.connect(self.updateScenariosList)
self.lstInfluences.itemSelectionChanged.connect(self.scenarioChanged)
self.txtAcqTime.textChanged.connect(self.scenarioChanged)
self.txtReplication_2.textChanged.connect(self.scenarioChanged)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
def make_matDict(self, mats, m_dict):
for mat in mats:
m_dict[mat.material_name].update([mat.dose])
return m_dict
def getGroups(self):
if self.id:
if not self.duplicate:
scen_edit = self.session.query(Scenario).filter_by(
id=self.id).first()
return [grp.name for grp in scen_edit.scenario_groups]
else:
scens = [
self.session.query(Scenario).filter_by(id=scen).first()
for scen in self.duplicate
]
grps = set()
for scen in scens:
grps.update([grp.name for grp in scen.scenario_groups])
return grps
else:
return []
@pyqtSlot()
def scenarioChanged(self):
"""
Listens for Scenario changed
"""
self.scenarioHasChanged = True
@pyqtSlot()
def groupChanged(self):
"""
Listens for group changed
"""
self.groupHasChanged = True
@pyqtSlot(int)
def updateTableDelegate(self, index):
if index == 0:
selected_detname = None
else:
selected_detname = self.comboDetectorSelect.currentText()
self.tblMaterial.setItemDelegate(
MaterialDoseDelegate(self.tblMaterial,
unitsCol=UNITS,
materialCol=MATERIAL,
intensityCol=INTENSITY,
selected_detname=selected_detname))
self.tblBackground.setItemDelegate(
MaterialDoseDelegate(self.tblBackground,
unitsCol=UNITS,
materialCol=MATERIAL,
intensityCol=INTENSITY,
selected_detname=selected_detname,
auto_s=self.auto_s))
@pyqtSlot(QPoint)
def context_auto_range(self, point, table):
current_cell = table.itemAt(point)
# show the context menu only if on an a valid part of the table
if current_cell:
column = current_cell.column()
if column == 2:
autorangeAction = QAction('Auto-Define Range', self)
menu = QMenu(table)
menu.addAction(autorangeAction)
action = menu.exec_(table.mapToGlobal(point))
if action == autorangeAction:
auto_list = self.auto_range()
if auto_list:
current_cell.setText(','.join(auto_list))
@pyqtSlot(bool)
def auto_range(self):
dialog = ScenarioRange(self)
dialog.setWindowModality(Qt.WindowModal)
if dialog.exec_():
if dialog.points:
return dialog.points
@pyqtSlot()
def updateScenariosList(self):
materialStr = ""
for row in range(self.tblMaterial.rowCount()):
untStr = self.tblMaterial.item(row, UNITS).text()
matStr = self.tblMaterial.item(row, MATERIAL).text()
intStr = self.tblMaterial.item(row, INTENSITY).text()
if matStr and untStr and intStr:
if (len(materialStr) > 0):
materialStr = materialStr + "\n "
materialStr = materialStr + '{}({})'.format(matStr, ', '.join("{:.5f}".format(float(dose)) for
dose in self.getSet(self.tblMaterial.item(row, INTENSITY)))) + \
', Units: ' + self.tblMaterial.item(row, UNITS).data(Qt.UserRole).title()
backgroundStr = ""
for row in range(self.tblBackground.rowCount()):
untStr = self.tblBackground.item(row, UNITS).text()
matStr = self.tblBackground.item(row, MATERIAL).text()
intStr = self.tblBackground.item(row, INTENSITY).text()
if matStr and untStr and intStr:
if (len(backgroundStr) > 0):
backgroundStr = backgroundStr + "\n "
backgroundStr = backgroundStr + '{}({})'.format(matStr, ', '.join("{:.5f}".format(float(dose)) for
dose in self.getSet(self.tblBackground.item(row, INTENSITY)))) + \
', Units: ' + self.tblBackground.item(row, UNITS).data(Qt.UserRole).title()
self.txtScenariosList_2.setText(
f"Source materials:\n {materialStr} \n\nBackground materials:\n {backgroundStr}"
)
@pyqtSlot(bool)
def on_btnGroups_clicked(self, checked):
dialog = GroupSettings(self, groups=self.groups)
dialog.setWindowModality(Qt.WindowModal)
if dialog.exec_():
self.groups = dialog.n_groups
@pyqtSlot()
def accept(self):
if self.auto_s:
materials_doses = []
for matsT in [self.tblBackground]:
for row in range(matsT.rowCount()):
matName = matsT.item(row, MATERIAL).text()
if matName:
matArr = []
for dose in self.getSet(matsT.item(row, 2)):
mat = self.session.query(Material).filter_by(
name=matName).first()
fd_mat = matsT.item(row, UNITS).data(Qt.UserRole)
matArr.append((fd_mat, mat, dose))
materials_doses.append(matArr)
self.rase_gui.static_background = materials_doses
return QDialog.accept(self)
self.tblMaterial.setCurrentIndex(QModelIndex(
)) # so that if table item is being edited it will commit the data
# if this is edit rather than create, need to treat differently:
if self.id and not self.duplicate:
# check if the scenario has been changed by the user
# Note that this approach considers a change even if
# the user rewrites the previous entry identically
if not self.scenarioHasChanged:
# update just the group for the same scenario
# so as not to change the scenario ID
scen = self.session.query(Scenario).get(self.id)
self.provide_message_new_groups = False
self.add_groups_to_scen(scen, self.groups, add_groups=True)
self.session.commit()
return QDialog.accept(self)
else:
# clear the existing scenario first
self.scenario_delete()
# replication and influences
replication = int(self.txtReplication_2.text())
influences = [] # element type: Influence
for index in self.lstInfluences.selectedIndexes():
influences.append(
self.session.query(Influence).filter_by(
name=self.lstInfluences.itemFromIndex(
index).text()).first())
materials_doses = [[], []]
for i, matsT in enumerate([self.tblMaterial, self.tblBackground]):
for row in range(matsT.rowCount()):
matName = matsT.item(row, MATERIAL).text()
if matName:
matArr = []
for dose in self.getSet(matsT.item(row, 2)):
mat = self.session.query(Material).filter_by(
name=matName).first()
fd_mat = matsT.item(row, UNITS).data(Qt.UserRole)
matArr.append((fd_mat, mat, dose))
materials_doses[i].append(matArr)
# cartesian product to break out scenarios from scenario group
integrity_fail = False
duplicate = False
self.provide_message_new_groups = True
for acqTime in self.getSet(self.txtAcqTime):
mm = product(*materials_doses[0])
bb = product(*materials_doses[1])
for mat_dose_arr, bckg_mat_dose_arr in product(mm, bb):
scenMaterials = [
ScenarioMaterial(material=m, dose=float(d), fd_mode=u)
for u, m, d in mat_dose_arr
]
bcgkScenMaterials = [
ScenarioBackgroundMaterial(material=m,
dose=float(d),
fd_mode=u)
for u, m, d in bckg_mat_dose_arr
]
scen_groups = []
try:
for groupname in self.groups:
scen_groups.append(
self.session.query(ScenarioGroup).filter_by(
name=groupname).first())
if not scen_groups:
scen_groups.append(
self.session.query(ScenarioGroup).filter_by(
name='default_group').first())
# if just changing groups, add to new group without creating a new scenario
scen_hash = Scenario.scenario_hash(float(acqTime),
scenMaterials,
bcgkScenMaterials,
influences)
scen_exists = self.session.query(Scenario).filter_by(
id=scen_hash).first()
add_groups = False
if scen_exists:
# and (sorted([g.name for g in scen_exists.scenario_groups]) !=
# sorted([g.name for g in scen_groups])):
for group in scen_groups:
if group not in scen_exists.scenario_groups:
add_groups = True
break
all_groups = set(g.name
for g in scen_exists.scenario_groups +
scen_groups)
all_groups.update(self.groups)
# don't allow duplicate scenarios, unless there are other scenarios in the group that are
# simply having their group changed. In which case, pass by those groups without impact.
duplicate = self.add_groups_to_scen(
scen_exists, all_groups, add_groups=add_groups)
else:
Scenario(float(acqTime), replication, scenMaterials,
bcgkScenMaterials, influences, scen_groups)
# if inputting multiple scenarios with at least one preexisting scenario (i.e.: this only happens when
# the loop traverses more than once and the database is accessed again)
except (IntegrityError, FlushError):
self.integrity_message(materials_doses)
integrity_fail = True
break
# if inputting a single scenario that already exists
if not integrity_fail:
if duplicate:
self.integrity_message(materials_doses)
else:
try:
self.session.commit()
return QDialog.accept(self)
except (IntegrityError, FlushError):
self.integrity_message(materials_doses)
def add_groups_to_scen(self, scen, all_groups, add_groups=False):
"""
Clear groups associated with a scenario and append new ones
"""
if add_groups:
scen.scenario_groups.clear()
for groupname in all_groups:
scen.scenario_groups.append(
self.session.query(ScenarioGroup).filter_by(
name=groupname).first())
if self.provide_message_new_groups:
QMessageBox.information(
self, 'Record Exists',
'At least one defined scenario is already in the database; '
'adding scenario to additional groups.')
self.provide_message_new_groups = False
elif self.provide_message_new_groups:
return True
return False
def scenario_delete(self):
"""
Clear existing scenario before adding the modified version
"""
scenDelete = self.session.query(Scenario).filter(
Scenario.id == self.id)
matDelete = self.session.query(ScenarioMaterial).filter(
ScenarioMaterial.scenario_id == self.id)
bckgMatDelete = self.session.query(ScenarioBackgroundMaterial).filter(
ScenarioBackgroundMaterial.scenario_id == self.id)
scenTableAssocDelete = scenDelete.first()
scenTableAssocDelete.scenario_groups.clear()
scenTableAssocDelete.influences.clear()
matDelete.delete()
bckgMatDelete.delete()
scenDelete.delete()
def integrity_message(self, materials_doses):
if (materials_doses[0] and len(list(product(*materials_doses[0]))) > 1) or \
(materials_doses[1] and len(list(product(*materials_doses[1]))) > 1):
QMessageBox.critical(
self, 'Record Exists',
'At least one defined scenario is already in the database! '
'Please change scenarios.')
else:
QMessageBox.critical(
self, 'Record Exists',
'This scenario is already in the database! Please change scenario.'
)
self.session.rollback()
# TODO: combine these two methods using a cellChanged.connect()
@pyqtSlot(int, int)
def on_tblMaterial_cellChanged(self, row, col):
"""
Listens for Material table cell changed
"""
if col == UNITS:
if self.tblMaterial.item(row, MATERIAL) and self.tblMaterial.item(
row, INTENSITY):
if not self.tblMaterial.item(row, UNITS).data(Qt.UserRole):
self.tblMaterial.item(row, MATERIAL).setText('')
self.tblMaterial.item(row, INTENSITY).setText('')
elif self.tblMaterial.item(row, MATERIAL):
units = self.tblMaterial.item(row, UNITS)
matName = self.tblMaterial.item(row, MATERIAL)
doseItem = self.tblMaterial.item(row, INTENSITY)
self.set_otherCols_fromUnit(units, matName, doseItem)
if col == MATERIAL:
units = self.tblMaterial.item(row, UNITS)
matName = self.tblMaterial.item(row, MATERIAL).text()
doseItem = self.tblMaterial.item(row, INTENSITY)
self.set_otherCols_fromMat(units, matName, doseItem)
@pyqtSlot(int, int)
def on_tblBackground_cellChanged(self, row, col):
"""
Listens for Material table cell changed
"""
if col == UNITS:
if self.tblBackground.item(
row, MATERIAL) and self.tblBackground.item(row, INTENSITY):
if not self.tblBackground.item(row, UNITS).data(Qt.UserRole):
self.tblBackground.item(row, MATERIAL).setText('')
self.tblBackground.item(row, INTENSITY).setText('')
elif self.tblBackground.item(row, MATERIAL):
units = self.tblBackground.item(row, UNITS)
matName = self.tblBackground.item(row, MATERIAL)
doseItem = self.tblBackground.item(row, INTENSITY)
self.set_otherCols_fromUnit(units, matName, doseItem)
if col == MATERIAL:
units = self.tblBackground.item(row, UNITS)
matName = self.tblBackground.item(row, MATERIAL).text()
doseItem = self.tblBackground.item(row, INTENSITY)
self.set_otherCols_fromMat(units, matName, doseItem)
def set_otherCols_fromUnit(self, units, matName, doseItem):
textKeep = False
if self.comboDetectorSelect.currentIndex() == 0:
detector_list = [
detector for detector in Session().query(Detector)
]
else:
detector_list = [
Session().query(Detector).filter_by(
name=self.comboDetectorSelect.currentText()).first()
]
for detector in detector_list:
for baseSpectrum in detector.base_spectra:
if baseSpectrum.material.name == matName.text(
) and not textKeep:
if (units.data(Qt.UserRole) == 'DOSE' and isinstance(baseSpectrum.rase_sensitivity, float)) or \
(units.data(Qt.UserRole) == 'FLUX' and isinstance(baseSpectrum.flux_sensitivity, float)):
textKeep = True
if not textKeep:
matName.setText('')
def set_otherCols_fromMat(self, units, matName, doseItem):
if matName:
if not doseItem.text():
doseItem.setText('0.1')
if not units.text():
textSet = False
if self.comboDetectorSelect.currentIndex() == 0:
detector_list = [
detector for detector in Session().query(Detector)
]
else:
detector_list = [
Session().query(Detector).filter_by(
name=self.comboDetectorSelect.currentText()).first(
)
]
for detector in detector_list:
for baseSpectrum in detector.base_spectra:
if baseSpectrum.material.name == matName and not textSet:
units.tableWidget().blockSignals(True)
if isinstance(baseSpectrum.rase_sensitivity,
float):
units.setText(units_labels['DOSE'])
units.setData(Qt.UserRole, 'DOSE')
textSet = True
else:
units.setText(units_labels['FLUX'])
units.setData(Qt.UserRole, 'FLUX')
units.tableWidget().blockSignals(False)
def getSet(self, dialogField):
values = []
groups = dialogField.text().split(',')
for group in groups:
group = group.strip()
if '-' in group and ':' in group:
start, stop, step = [
float(x)
for x in re.match(r'([^-]+)-([^:]+):(.*)', group).groups()
]
if step == 0:
values.append(start)
values.append(stop)
else:
while start <= stop:
values.append(start)
start += step
else:
values.append(group)
return values
class AutomatedSCurve(ui_auto_scurve.Ui_AutoSCurveDialog, QDialog):
def __init__(self, parent):
QDialog.__init__(self, parent)
self.setWindowTitle('Automated S-Curve Generation')
self.Rase = parent
self.settings = RaseSettings()
self.setupUi(self)
self.session = Session()
# setting default states
self.detName = None
self.detReplay = None
self.static_background = []
self.setInstrumentItems()
self.buttonBox.button(QDialogButtonBox.Ok).setEnabled(False)
# Validators
self.line_rep.setValidator(
QRegularExpressionValidator(QRegularExpression("[0-9]{0,9}")))
self.line_initrep.setValidator(
QRegularExpressionValidator(QRegularExpression("[0-9]{0,9}")))
self.line_edge.setValidator(
QRegularExpressionValidator(QRegularExpression("[0-9]{0,9}")))
self.line_dwell.setValidator(
QRegularExpressionValidator(
QRegularExpression("((\d*\.\d*)|(\d*))")))
self.line_minx.setValidator(
QRegularExpressionValidator(
QRegularExpression("((\d*\.\d*)|(\d*))")))
self.line_maxx.setValidator(
QRegularExpressionValidator(
QRegularExpression("((\d*\.\d*)|(\d*))")))
self.line_addpoints.setValidator(
QRegularExpressionValidator(
QRegularExpression(
r"((((\d+\.\d*)|(\d*\.\d+))|(\d+))((((,\d*\.\d+)|(,\d+\.\d*))|(,\d+))*)(,|,\.)?)"
)))
self.line_lowerbound.setValidator(
QRegularExpressionValidator(
QRegularExpression("((\d*\.\d*)|(\d*))")))
self.line_upperbound.setValidator(
QRegularExpressionValidator(
QRegularExpression("((\d*\.\d*)|(\d*))")))
# connections
self.combo_inst.currentTextChanged.connect(self.updateMaterials)
self.combo_mat.currentTextChanged[str].connect(
lambda mat: self.updateUnits(mat, self.combo_matdose))
self.btn_bgnd.clicked.connect(self.defineBackground)
# Confirm enables
self.combo_matdose.currentTextChanged.connect(self.enableOk)
# Set values of various things based on user inputs
self.line_rep.editingFinished.connect(
lambda: self.setminval(self.line_rep, '2'))
self.line_initrep.editingFinished.connect(
lambda: self.setminval(self.line_initrep, '1'))
self.line_edge.editingFinished.connect(
lambda: self.setminval(self.line_edge, '1'))
self.line_dwell.editingFinished.connect(
lambda: self.setminval(self.line_dwell, '1', '0.00000000001'))
self.line_minx.editingFinished.connect(lambda: self.setminval(
self.line_minx, '0.00000001', '0.00000000001'))
self.line_maxx.editingFinished.connect(
lambda: self.setminval(self.line_maxx, '0.001', '0.00000000001'))
self.line_lowerbound.editingFinished.connect(
lambda: self.setminval(self.line_lowerbound, '0'))
self.line_lowerbound.editingFinished.connect(
lambda: self.setmaxval(self.line_lowerbound, '.99'))
self.line_upperbound.editingFinished.connect(
lambda: self.setmaxval(self.line_upperbound, '1'))
self.line_minx.editingFinished.connect(self.checkMaxX)
self.line_maxx.editingFinished.connect(self.checkMaxX)
self.line_lowerbound.editingFinished.connect(self.checkMaxY)
self.line_upperbound.editingFinished.connect(self.checkMaxY)
self.line_addpoints.editingFinished.connect(self.removeZeroPoint)
self.check_minx.stateChanged.connect(self.setDefaultMin)
self.check_maxx.stateChanged.connect(self.setDefaultMax)
self.check_addpoints.stateChanged.connect(self.setAddPoints)
self.check_name.stateChanged.connect(self.setDefaultName)
def setInstrumentItems(self):
for det in self.session.query(Detector):
if det.replay and det.replay.is_cmd_line:
self.combo_inst.addItem(det.name)
@pyqtSlot(str)
def updateMaterials(self, detName):
"""
Updates the possible material selection based on the selected instrument.
Also identify the name of the replay associated with the chosen detector
and set it for S-curve processing
"""
self.combo_mat.clear()
self.combo_mat.addItem('')
if not detName.strip():
self.combo_mat.setCurrentIndex(0)
self.combo_mat.setEnabled(False)
self.btn_bgnd.setEnabled(False)
self.detName = None
self.detReplay = None
else:
self.detName = detName
self.combo_mat.setEnabled(True)
self.btn_bgnd.setEnabled(True)
det = self.session.query(Detector).filter_by(name=detName).first()
self.detReplay = det.replay.name
for baseSpectrum in det.base_spectra:
self.combo_mat.addItem(baseSpectrum.material.name)
def updateUnits(self, matName, combobox):
"""
General function call for updating the flux/dose setting in the
combobox after material has been selected
"""
combobox.clear()
combobox.addItem('')
if not matName.strip():
combobox.setCurrentIndex(0)
combobox.setEnabled(False)
else:
combobox.setEnabled(True)
det = self.session.query(Detector).filter_by(
name=self.detName).first()
for baseSpectrum in det.base_spectra:
if baseSpectrum.material_name == matName:
if baseSpectrum.rase_sensitivity:
combobox.addItem('DOSE (\u00B5Sv/h)')
combobox.setCurrentIndex(1)
if baseSpectrum.flux_sensitivity:
combobox.addItem('FLUX (\u03B3/(cm\u00B2s))')
@pyqtSlot(str)
def enableOk(self, intensity):
"""Only enable the okay button if all the relevant points are selected"""
if self.combo_matdose.currentText() and self.line_dwell.text() and \
self.line_maxx.text() and self.line_minx.text():
self.buttonBox.button(QDialogButtonBox.Ok).setEnabled(True)
else:
self.buttonBox.button(QDialogButtonBox.Ok).setEnabled(False)
def changeMinMax(self):
"""Change the min and max guess based on the background intensity"""
if not self.check_minx.isChecked():
minv = str(1E-7)
minv = self.checkSciNote(minv)
self.line_minx.setText(minv)
self.checkMaxX()
self.setAddPoints()
if not self.check_maxx.isChecked():
maxv = str(1E-2)
maxv = self.checkSciNote(maxv)
self.line_maxx.setText(maxv)
self.checkMaxX()
def checkSciNote(self, val):
"""If there is scientific notation, remove it so as to not break regex"""
if 'E' in val.upper():
sci = val.upper().split('E')
if int(sci[1]) < 0:
val = '0.' + ''.zfill(abs(int(sci[1])) - 1) + sci[0].replace(
'.', '')
else:
val = str(float(sci[0]) * 10**int(sci[1]))
return val
def setminval(self, line, setval='0.00000001', minval=None):
if not minval:
minval = setval
try:
if float(line.text()) <= float(minval):
line.setText(setval)
except: # if the user enters a decimal point or something nonsensical
line.setText(setval)
def setmaxval(self, line, setval='1', maxval=None):
if not maxval:
maxval = setval
try:
if float(line.text()) >= float(maxval):
line.setText(setval)
except: # if the user enters a decimal point or something nonsensical
line.setText(setval)
def checkMaxX(self):
"""Make sure the maximum x value is larger than the minimum x value"""
if self.line_maxx.text() and self.line_minx.text():
if float(self.line_maxx.text()) <= float(self.line_minx.text()):
self.line_maxx.setText(str(float(self.line_minx.text()) * 1E5))
def checkMaxY(self):
"""Make sure that the bounds don't overlap each other"""
if self.line_upperbound.text() and self.line_lowerbound.text():
if float(self.line_upperbound.text()) <= float(
self.line_lowerbound.text()):
self.line_upperbound.setText(
str(max([0.9,
float(self.line_lowerbound.text()) * 1.01])))
def setDefaultMin(self):
"""Set the default minimum x value if it has been unchecked"""
if not self.check_minx.isChecked():
self.line_minx.setText('0.00000001')
self.setAddPoints()
self.checkMaxX()
def setDefaultMax(self):
"""Set the default max x value if it has been unchecked"""
if not self.check_maxx.isChecked():
self.line_maxx.setText('0.001')
self.checkMaxX()
def setAddPoints(self):
"""Set default user-added points and clears them if the box is unchecked"""
if self.check_addpoints.isChecked():
if not self.line_addpoints.text():
self.line_addpoints.setText(self.line_minx.text())
else:
self.line_addpoints.setText('')
def setDefaultName(self):
"""Set name back to [Default] if the checkbox is unchecked"""
if not self.check_name.isChecked():
self.line_name.setText('[Default]')
def removeZeroPoint(self):
"""Disallow the user to add a point with 0 dose/flux"""
if self.line_addpoints.text():
self.line_addpoints.setText(
self.endRecurse(self.line_addpoints.text()))
addpoints = [
float(i) for i in self.line_addpoints.text().split(',')
]
if 0 in addpoints:
addpoints = [i for i in addpoints if i != 0]
addpoints = list(dict.fromkeys(addpoints))
addpoints.sort()
addpoints = [self.checkSciNote(str(i)) for i in addpoints]
addpoints = str(addpoints)[1:-1].replace('\'', '').replace(' ', '')
self.line_addpoints.setText(addpoints)
def endRecurse(self, line):
"""Remove commas/periods at the end of the uesr-adde points list, recursively"""
if (line[-1] == ',') or (line[-1] == '.'):
return self.endRecurse(line[:-1])
else:
return line
def defineBackground(self):
dialog = ScenarioDialog(self, auto_s=True)
dialog.comboDetectorSelect.setCurrentText(
self.combo_inst.currentText())
remove_layouts = [dialog.horizontalLayout, dialog.horizontalLayout_4]
for layout in remove_layouts:
for i in reversed(range(layout.count())):
item = layout.itemAt(i)
if isinstance(item, QWidgetItem):
item.widget().hide()
dialog.pushButton.hide()
dialog.tblMaterial.hide()
dialog.label_scenlist.hide()
dialog.txtScenariosList_2.hide()
dialog.label_influences.hide()
dialog.lstInfluences.hide()
dialog.resize(440, 340)
dialog.setWindowTitle('Set static background for the ' +
self.combo_inst.currentText() + '.')
dialog.exec_()
@pyqtSlot()
def accept(self):
if self.line_addpoints.text():
addpoints = [
float(i) for i in self.line_addpoints.text().split(',')
]
else:
addpoints = []
self.input_d = {
"instrument": self.detName,
"replay": self.detReplay,
"source": self.combo_mat.currentText(),
"source_fd": self.combo_matdose.currentText().split()[0],
"background": self.static_background,
"dwell_time": float(self.line_dwell.text()),
"results_type": self.combo_resulttype.currentText(),
"input_reps": int(self.line_rep.text()),
"invert_curve": self.check_invert.isChecked()
}
self.input_advanced = {
"rise_points": int(self.line_edge.text()),
"min_guess": float(self.line_minx.text()),
"max_guess": float(self.line_maxx.text()),
"repetitions": int(self.line_initrep.text()),
"add_points": addpoints,
"cleanup": self.check_cleanup.isChecked(),
"custom_name": self.line_name.text(),
"num_points": 6, # hardcode for now
"lower_bound": float(self.line_lowerbound.text()),
"upper_bound": float(self.line_upperbound.text())
}
return QDialog.accept(self)
def __init__(self, parent):
QDialog.__init__(self, parent)
self.setWindowTitle('Automated S-Curve Generation')
self.Rase = parent
self.settings = RaseSettings()
self.setupUi(self)
self.session = Session()
# setting default states
self.detName = None
self.detReplay = None
self.static_background = []
self.setInstrumentItems()
self.buttonBox.button(QDialogButtonBox.Ok).setEnabled(False)
# Validators
self.line_rep.setValidator(
QRegularExpressionValidator(QRegularExpression("[0-9]{0,9}")))
self.line_initrep.setValidator(
QRegularExpressionValidator(QRegularExpression("[0-9]{0,9}")))
self.line_edge.setValidator(
QRegularExpressionValidator(QRegularExpression("[0-9]{0,9}")))
self.line_dwell.setValidator(
QRegularExpressionValidator(
QRegularExpression("((\d*\.\d*)|(\d*))")))
self.line_minx.setValidator(
QRegularExpressionValidator(
QRegularExpression("((\d*\.\d*)|(\d*))")))
self.line_maxx.setValidator(
QRegularExpressionValidator(
QRegularExpression("((\d*\.\d*)|(\d*))")))
self.line_addpoints.setValidator(
QRegularExpressionValidator(
QRegularExpression(
r"((((\d+\.\d*)|(\d*\.\d+))|(\d+))((((,\d*\.\d+)|(,\d+\.\d*))|(,\d+))*)(,|,\.)?)"
)))
self.line_lowerbound.setValidator(
QRegularExpressionValidator(
QRegularExpression("((\d*\.\d*)|(\d*))")))
self.line_upperbound.setValidator(
QRegularExpressionValidator(
QRegularExpression("((\d*\.\d*)|(\d*))")))
# connections
self.combo_inst.currentTextChanged.connect(self.updateMaterials)
self.combo_mat.currentTextChanged[str].connect(
lambda mat: self.updateUnits(mat, self.combo_matdose))
self.btn_bgnd.clicked.connect(self.defineBackground)
# Confirm enables
self.combo_matdose.currentTextChanged.connect(self.enableOk)
# Set values of various things based on user inputs
self.line_rep.editingFinished.connect(
lambda: self.setminval(self.line_rep, '2'))
self.line_initrep.editingFinished.connect(
lambda: self.setminval(self.line_initrep, '1'))
self.line_edge.editingFinished.connect(
lambda: self.setminval(self.line_edge, '1'))
self.line_dwell.editingFinished.connect(
lambda: self.setminval(self.line_dwell, '1', '0.00000000001'))
self.line_minx.editingFinished.connect(lambda: self.setminval(
self.line_minx, '0.00000001', '0.00000000001'))
self.line_maxx.editingFinished.connect(
lambda: self.setminval(self.line_maxx, '0.001', '0.00000000001'))
self.line_lowerbound.editingFinished.connect(
lambda: self.setminval(self.line_lowerbound, '0'))
self.line_lowerbound.editingFinished.connect(
lambda: self.setmaxval(self.line_lowerbound, '.99'))
self.line_upperbound.editingFinished.connect(
lambda: self.setmaxval(self.line_upperbound, '1'))
self.line_minx.editingFinished.connect(self.checkMaxX)
self.line_maxx.editingFinished.connect(self.checkMaxX)
self.line_lowerbound.editingFinished.connect(self.checkMaxY)
self.line_upperbound.editingFinished.connect(self.checkMaxY)
self.line_addpoints.editingFinished.connect(self.removeZeroPoint)
self.check_minx.stateChanged.connect(self.setDefaultMin)
self.check_maxx.stateChanged.connect(self.setDefaultMax)
self.check_addpoints.stateChanged.connect(self.setAddPoints)
self.check_name.stateChanged.connect(self.setDefaultName)
def _getCountsDoseAndSensitivity(scenario, detector, degradations=None):
"""
:param scenario:
:param detector:
:return:
"""
session = Session()
# distortion: distort ecal with influence factors
ecal = [detector.ecal3, detector.ecal2, detector.ecal1, detector.ecal0]
energies = np.polyval(ecal, np.arange(detector.chan_count))
new_influences = []
bin_widths = np.zeros([len(scenario.influences), len(energies)])
for index, influence in enumerate(scenario.influences):
detInfl = session.query(DetectorInfluence).filter_by(influence_name=influence.name).first()
new_infl = [detInfl.infl_0, detInfl.infl_1, detInfl.infl_2, detInfl.fixed_smear, detInfl.linear_smear]
if degradations:
new_infl = [infl + deg for infl, deg in zip(new_infl, degradations[index])]
# deal with potential negative values
for position, n_inf in enumerate(new_infl):
if n_inf < 0:
if not position == 1:
new_infl[position] = 0
else:
new_infl[position] = 0.0001
new_influences.append(new_infl)
if new_infl[0] != 0 or new_infl[2] != 0 or new_infl[1] != 1:
energies = np.polyval([new_infl[2], (new_infl[1]), new_infl[0]], energies)
# convert fixed energy smear distortion from energy to bins
if new_infl[3] != 0:
e_width = new_infl[3] / 2
for sub_index, energy in enumerate(energies):
b0 = np.roots([new_infl[2], new_infl[1], new_infl[0] - (energy - e_width)])
b1 = np.roots([new_infl[2], new_infl[1], new_infl[0] - (energy + e_width)])
bin_widths[index][sub_index] = max(b1) - max(b0)
# get dose, counts and sensitivity for each material
countsDoseAndSensitivity = []
for scenMaterial in scenario.scen_materials + scenario.scen_bckg_materials:
baseSpectrum = (session.query(BaseSpectrum)
.filter_by(detector_name=detector.name,
material_name=scenMaterial.material_name)
).first()
counts = baseSpectrum.get_counts_as_np()
if scenario.influences:
for index, infl in enumerate(new_influences):
counts = apply_distortions(infl, counts, bin_widths[index], energies, ecal)
if scenMaterial.fd_mode == 'FLUX':
countsDoseAndSensitivity.append((counts, scenMaterial.dose, baseSpectrum.flux_sensitivity))
else:
countsDoseAndSensitivity.append((counts, scenMaterial.dose, baseSpectrum.rase_sensitivity))
# if the detector has an internal calibration source, it needs to be added with special treatment
if detector.includeSecondarySpectrum and detector.secondary_type == secondary_type['internal']:
secondary_spectrum = (session.query(BackgroundSpectrum).filter_by(detector_name=detector.name)).first()
counts = secondary_spectrum.get_counts_as_np()
# apply distortion on counts
if scenario.influences:
for index, infl in enumerate(new_influences):
counts = apply_distortions(infl, counts, bin_widths[index], energies, ecal)
# extract counts per second
cps = sum(counts)/secondary_spectrum.livetime
# the internal calibration spectrum is scaled only by time
# so the sensitivity parameter is set to the cps and the dose to 1
countsDoseAndSensitivity.append((counts, 1.0, cps))
return countsDoseAndSensitivity
def generate_curve(r, input_data, advanced):
"""Primary function where the points that make up the S-curve are determined"""
session = Session()
if advanced['custom_name'] == '[Default]':
group_name = ("AutoScurve_" + input_data['instrument'] + '_' +
input_data['source'])
else:
suffix = 0
while True:
if session.query(ScenarioGroup).filter_by(
name=advanced['custom_name']).first():
if not session.query(ScenarioGroup).filter_by(
name=advanced['custom_name']).first().scenarios:
group_name = (advanced['custom_name'])
break
else:
suffix += 1
advanced['custom_name'] = advanced[
'custom_name'] + '_' + str(suffix)
else:
group_name = (advanced['custom_name'])
break
detName = [input_data['instrument']]
detector = session.query(Detector).filter_by(name=detName[0]).first()
condition = False
already_done = False
expand = 0
first_run = True
# All scenarios within the group that have the same source/backgrounds
make_scen_group(session, group_name, input_data)
scenIdall = make_scenIdall(session, input_data)
# scenarios that will be rerun in this run
scenIds_no_persist = []
maxback = 0
if input_data['background']:
for bmat in input_data['background']:
bmat = bmat[0]
if bmat[0] == input_data['source_fd']:
if maxback == 0:
maxback = float(bmat[2])
else:
maxback = max(maxback, float(bmat[2]))
if not maxback:
maxback = 0.1
while not condition:
# newly generated scenIds, and all scenIds with source/backgrounds as defined in the auto s-curve gui
scenIds, scenIds_no_persist, scenIdall = gen_scens(
input_data, advanced, session, scenIdall, scenIds_no_persist,
group_name, advanced['repetitions'])
abort = run_scenarios(r, scenIds, detector, input_data['replay'],
condition, expand, first_run)
first_run = False
if abort:
cleanup_scenarios(advanced['repetitions'], scenIds_no_persist)
return
r.calculateScenarioStats(1, scenIdall, detName)
if input_data['results_type'] == 'C&C':
results = r.scenario_stats_df['C&C']
elif input_data['results_type'] == 'TP':
results = r.scenario_stats_df['TP']
elif input_data['results_type'] == 'Precision':
results = r.scenario_stats_df['Precision']
elif input_data['results_type'] == 'Recall':
results = r.scenario_stats_df['Recall']
elif input_data['results_type'] == 'Fscore':
results = r.scenario_stats_df['F_Score']
else: # to add more later
results = r.scenario_stats_df['PID']
if not input_data['invert_curve']:
results = results.sort_values()
else:
results = results.sort_values(ascending=False)
if max(results) >= advanced['upper_bound'] and min(
results) <= advanced['lower_bound']:
"""If there are values surrounding the rising edge"""
# find scenarios in for cases
ids_on_edge = []
start_list = []
end_list = []
prev_point = False
for index, result in enumerate(results):
if (not input_data['invert_curve'] and result <= advanced['lower_bound']) or \
(input_data['invert_curve'] and result >= advanced['upper_bound']):
start_list.append(results.index[index].split('*')[0])
if prev_point:
ids_on_edge = [
] # rose and then dropped back down (i.e.: fluctuations)
prev_point = False
elif advanced['lower_bound'] <= result <= advanced[
'upper_bound']:
ids_on_edge.append(results.index[index].split('*')[0])
prev_point = True
elif (not input_data['invert_curve'] and result >= advanced['upper_bound']) or \
(input_data['invert_curve'] and result <= advanced['lower_bound']):
end_list.append(results.index[index].split('*')[0])
# Grab doses for scenarios on the edges of the S-curve. The first value in each list is
# the value that is the second closest to the rising edge, and the second is the closest
start_val = [-1, -1]
end_val = [-1, -1]
for scenid in scenIdall:
scen = session.query(Scenario).filter_by(id=scenid).first()
if scenid in start_list:
if start_val[1] == -1 or scen.scen_materials[
0].dose >= start_val[1]:
start_val = set_bounds(start_val,
scen.scen_materials[0].dose)
if scen.id in end_list:
if end_val[1] == -1 or scen.scen_materials[
0].dose < end_val[1]:
end_val = set_bounds(end_val,
scen.scen_materials[0].dose)
# check if there are enough points on the rising edge
if len(ids_on_edge) >= advanced['rise_points']:
condition = True
# to avoid persistence errors by reusing a value with the same ID but different replications
edge_count, bound_scens_start, bound_scens_end = check_edge_ids(
session, input_data['input_reps'], start_list, end_list,
ids_on_edge, detector)
if edge_count < advanced[
'rise_points'] or bound_scens_start < 2 or bound_scens_end < 2:
advanced['min_guess'] = start_val[0] * 0.9
advanced['max_guess'] = end_val[0] * 1.1
advanced['num_points'] = advanced['rise_points'] + 4
else:
already_done = True
else:
# avoid infinite loop due to being stuck on edge cases. Moves slightly inward to better populate edge
if start_val[1] == advanced['min_guess']:
advanced['min_guess'] = start_val[1] + (
end_val[1] - start_val[1]) * 0.01
else:
advanced['min_guess'] = start_val[1]
if end_val[1] == advanced['max_guess']:
advanced['max_guess'] = end_val[1] - (end_val[1] -
start_val[1]) * 0.01
else:
advanced['max_guess'] = end_val[1]
advanced['num_points'] = advanced['rise_points'] # + 4
elif min(results) >= advanced['lower_bound']:
"""If the quoted results aren't small enough yet"""
expand += 1
dose_list = []
for scenId in scenIdall:
scen = session.query(Scenario).filter_by(id=scenId).first()
dose_list.append(scen.scen_materials[0].dose)
dose_list.sort()
if not input_data['invert_curve']:
dose_bound = dose_list[0]
if (0 < dose_bound <= 1E-9 * maxback
and len(scenIdall) >= 9) or 0 < dose_bound <= 1E-12:
fail_never(r, scenIdall, [input_data['instrument']])
return
if len(dose_list) > 1:
step_ratio = dose_list[0] / dose_list[1]
else:
step_ratio = dose_list[0] * 0.9
advanced['min_guess'] = advanced['min_guess'] * step_ratio
advanced['max_guess'] = advanced['min_guess']
advanced['num_points'] = 1
else:
dose_bound = dose_list[-1]
if dose_bound >= 40 * maxback and len(scenIdall) >= 9:
fail_never(r, scenIdall, [input_data['instrument']])
return
if len(dose_list) > 1:
step_ratio = dose_list[-1] / dose_list[-2]
else:
step_ratio = dose_list[0] * 1.1
advanced['min_guess'] = advanced['max_guess'] * step_ratio
advanced['max_guess'] = advanced['min_guess']
advanced['num_points'] = 1
elif max(results) <= advanced['upper_bound']:
"""If the quoted results aren't large enough yet"""
expand += 1
dose_list = []
for scenId in scenIdall:
scen = session.query(Scenario).filter_by(id=scenId).first()
# for scen in session.query(ScenarioGroup).filter_by(name=group_name).first().scenarios:
dose_list.append(scen.scen_materials[0].dose)
dose_list.sort()
if not input_data['invert_curve']:
dose_bound = dose_list[-1]
if dose_bound >= 40 * maxback and len(scenIdall) >= 9:
fail_always(r, scenIdall, [input_data['instrument']])
return
if len(dose_list) > 1:
step_ratio = dose_list[-1] / dose_list[-2]
else:
step_ratio = dose_list[0] * 1.1
advanced['min_guess'] = advanced['max_guess'] * step_ratio
advanced['max_guess'] = advanced['min_guess']
advanced['num_points'] = 1
else:
dose_bound = dose_list[0]
if (0 < dose_bound <= 1E-9 * maxback
and len(scenIdall) >= 9) or 0 < dose_bound <= 1E-12:
fail_always(r, scenIdall, [input_data['instrument']])
return
if len(dose_list) > 1:
step_ratio = dose_list[0] / dose_list[1]
else:
step_ratio = dose_list[0] * 0.9
advanced['min_guess'] = advanced['min_guess'] * step_ratio
advanced['max_guess'] = advanced['min_guess']
advanced['num_points'] = 1
if condition:
if not already_done:
scenIds, _, _ = gen_scens(input_data, advanced, session, scenIdall,
scenIds_no_persist, group_name,
input_data['input_reps'], condition)
detector = session.query(Detector).filter_by(
name=detName[0]).first()
abort = run_scenarios(r, scenIds, detector, input_data['replay'],
condition)
if abort:
cleanup_scenarios(advanced['repetitions'], scenIds_no_persist)
cleanup_scenarios(input_data['input_reps'], scenIds)
return
if advanced['cleanup']:
cleanup_scenarios(advanced['repetitions'], scenIds_no_persist)
r.populateScenarios()
msgbox = QMessageBox(QMessageBox.Question,
'S-Curve generation complete!',
'Would you like to view the results?')
msgbox.addButton(QMessageBox.Yes)
msgbox.addButton(QMessageBox.No)
answer = msgbox.exec()
if answer == QMessageBox.Yes:
viewResults(r, scenIds, [input_data['instrument']])