def get_default_characterisation_parameters(self):
"""
:returns: A CharacterisationsParameters object with default parameters.
"""
input_fname = self.data_analysis_hwobj.edna_default_file
hwr_dir = HardwareRepository().getHardwareRepositoryPath()
with open(os.path.join(hwr_dir, input_fname), 'r') as f:
edna_default_input = ''.join(f.readlines())
edna_input = XSDataInputMXCuBE.parseString(edna_default_input)
diff_plan = edna_input.getDiffractionPlan()
#edna_beam = edna_input.getExperimentalCondition().getBeam()
edna_sample = edna_input.getSample()
char_params = queue_model_objects.CharacterisationParameters()
char_params.experiment_type = queue_model_enumerables.EXPERIMENT_TYPE.OSC
# Optimisation parameters
char_params.use_aimed_resolution = False
char_params.aimed_resolution = diff_plan.getAimedResolution().getValue(
)
char_params.use_aimed_multiplicity = False
#char_params.aimed_multiplicity = diff_plan.getAimedMultiplicity().getValue()
char_params.aimed_i_sigma = diff_plan.getAimedIOverSigmaAtHighestResolution(
).getValue()
char_params.aimed_completness = diff_plan.getAimedCompleteness(
).getValue()
char_params.strategy_complexity = 0
char_params.induce_burn = False
char_params.use_permitted_rotation = False
char_params.permitted_phi_start = 0.0
char_params.permitted_phi_end = 360
char_params.low_res_pass_strat = False
# Crystal
char_params.max_crystal_vdim = edna_sample.getSize().getY().getValue()
char_params.min_crystal_vdim = edna_sample.getSize().getZ().getValue()
char_params.max_crystal_vphi = 90
char_params.min_crystal_vphi = 0.0
char_params.space_group = ""
# Characterisation type
char_params.use_min_dose = True
char_params.use_min_time = False
char_params.min_dose = 30.0
char_params.min_time = 0.0
char_params.account_rad_damage = True
char_params.auto_res = True
char_params.opt_sad = False
char_params.sad_res = 0.5
char_params.determine_rad_params = False
char_params.burn_osc_start = 0.0
char_params.burn_osc_interval = 3
# Radiation damage model
char_params.rad_suscept = edna_sample.getSusceptibility().getValue()
char_params.beta = 1
char_params.gamma = 0.06
return char_params
def add_characterisation(node_id, task):
"""
Adds a data characterisation task to the sample with id: <id>
:param int id: id of the sample to which the task belongs
:param dict task: Task data (parameters)
:returns: The queue id of the Data collection
:rtype: int
"""
sample_model, sample_entry = get_entry(node_id)
params = task['parameters']
refdc_model, refdc_entry = _create_dc(task)
refdc_model.set_name('refdc')
char_params = qmo.CharacterisationParameters().set_from_dict(params)
char_model = qmo.Characterisation(refdc_model, char_params)
char_entry = qe.CharacterisationGroupQueueEntry(Mock(), char_model)
char_entry.queue_model_hwobj = mxcube.queue
# Set the characterisation and reference collection parameters
set_char_params(char_model, char_entry, task)
# A characterisation has two TaskGroups one for the characterisation itself
# and its reference collection and one for the resulting diffraction plans.
# But we only create a reference group if there is a result !
refgroup_model = qmo.TaskGroup()
mxcube.queue.add_child(sample_model, refgroup_model)
mxcube.queue.add_child(refgroup_model, char_model)
refgroup_entry = qe.TaskGroupQueueEntry(Mock(), refgroup_model)
refgroup_entry.set_enabled(True)
sample_entry.enqueue(refgroup_entry)
refgroup_entry.enqueue(char_entry)
char_model.set_enabled(task['checked'])
char_entry.set_enabled(task['checked'])
return char_model._node_id
def __init__(self, parent=None, name="parameter_widget"):
"""
Descript. :
"""
QtGui.QWidget.__init__(self, parent)
if name is not None:
self.setObjectName(name)
# Hardware objects ----------------------------------------------------
# Internal variables --------------------------------------------------
self._char = None
self._char_params = queue_model_objects.CharacterisationParameters()
self._char_params_mib = DataModelInputBinder(self._char_params)
self._tree_view_item = None
self.previous_energy = None
self.add_dc_cb = None
# Graphic elements ----------------------------------------------------
rone_widget = QtGui.QWidget(self)
self.reference_img_widget = ReferenceImageWidget(rone_widget)
self.acq_widget = self.reference_img_widget.acq_widget
self.path_widget = self.reference_img_widget.path_widget
self.position_widget = uic.loadUi(
os.path.join(os.path.dirname(__file__),
'ui_files/Qt4_snapshot_widget_layout.ui'))
self.position_widget.setMinimumSize(450, 340)
rtwo_widget = QtGui.QWidget(self)
self.char_type_widget = CharTypeWidget(rtwo_widget)
self.routine_dc_widget = self.char_type_widget.routine_dc_page
self.sad_widget = self.char_type_widget.sad_page
self.rad_dmg_char_widget = self.char_type_widget.rad_damage_page
self.opt_parameters_widget = OptimisationParametersWidgetLayout(self)
rtree_widget = QtGui.QWidget(self)
self.rad_dmg_widget = uic.loadUi(
os.path.join(
os.path.dirname(__file__),
'ui_files/Qt4_radiation_damage_model_widget_layout.ui'))
self.vertical_dimension_widget = uic.loadUi(
os.path.join(
os.path.dirname(__file__),
'ui_files/Qt4_vertical_crystal_dimension_widget_layout.ui'))
# Layout --------------------------------------------------------------
rone_widget_layout = QtGui.QHBoxLayout(self)
rone_widget_layout.addWidget(self.reference_img_widget)
rone_widget_layout.addWidget(self.position_widget)
#rone_widget_layout.addStretch(0)
rone_widget_layout.setSpacing(2)
rone_widget_layout.setContentsMargins(0, 0, 0, 0)
rone_widget.setLayout(rone_widget_layout)
rtwo_widget_layout = QtGui.QHBoxLayout(self)
rtwo_widget_layout.addWidget(self.char_type_widget)
rtwo_widget_layout.addWidget(self.opt_parameters_widget)
rtwo_widget_layout.addStretch(0)
rtwo_widget_layout.setSpacing(2)
rtwo_widget_layout.setContentsMargins(0, 0, 0, 0)
rtwo_widget.setLayout(rtwo_widget_layout)
rtree_widget_layout = QtGui.QHBoxLayout(self)
rtree_widget_layout.addWidget(self.rad_dmg_widget)
rtree_widget_layout.addWidget(self.vertical_dimension_widget)
rtree_widget_layout.addStretch(0)
rtree_widget_layout.setSpacing(2)
rtree_widget_layout.setContentsMargins(0, 0, 0, 0)
rtree_widget.setLayout(rtree_widget_layout)
_main_vlayout = QtGui.QVBoxLayout(self)
_main_vlayout.addWidget(rone_widget)
_main_vlayout.addWidget(rtwo_widget)
_main_vlayout.addWidget(rtree_widget)
_main_vlayout.setSpacing(2)
_main_vlayout.setContentsMargins(0, 0, 0, 0)
self.setLayout(_main_vlayout)
# SizePolicies -------------------------------------------------------
# Qt signal/slot connections ------------------------------------------
self.toggle_permitted_range(self.opt_parameters_widget.\
opt_param_widget.permitted_range_cbx.isChecked())
self.opt_parameters_widget.opt_param_widget.permitted_range_cbx.\
toggled.connect(self.toggle_permitted_range)
# Other ---------------------------------------------------------------
self._char_params_mib.bind_value_update(
'min_dose', self.routine_dc_widget.dose_ledit, float,
QtGui.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'min_time', self.routine_dc_widget.time_ledit, float,
QtGui.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'use_min_dose', self.routine_dc_widget.min_dose_radio, bool, None)
self._char_params_mib.bind_value_update(
'use_min_time', self.routine_dc_widget.min_time_radio, bool, None)
self._char_params_mib.bind_value_update(
'account_rad_damage', self.routine_dc_widget.radiation_damage_cbx,
bool, None)
self._char_params_mib.bind_value_update(
'auto_res', self.sad_widget.automatic_resolution_radio, bool, None)
self._char_params_mib.bind_value_update(
'sad_res', self.sad_widget.sad_resolution_ledit, float,
QtGui.QDoubleValidator(0.5, 20, 3, self))
self._char_params_mib.bind_value_update(
'opt_sad', self.sad_widget.optimised_sad_cbx, bool, None)
self._char_params_mib.bind_value_update(
'determine_rad_params', self.rad_dmg_char_widget.rad_damage_cbx,
bool, None)
self._char_params_mib.bind_value_update(
'burn_osc_start', self.rad_dmg_char_widget.burn_osc_start_ledit,
float, QtGui.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'burn_osc_interval',
self.rad_dmg_char_widget.burn_osc_interval_ledit, float,
QtGui.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'use_aimed_resolution',
self.opt_parameters_widget.opt_param_widget.maximum_res_cbx, bool,
None)
self._char_params_mib.bind_value_update(
'use_aimed_multiplicity',
self.opt_parameters_widget.opt_param_widget.aimed_mult_cbx, bool,
None)
self._char_params_mib.bind_value_update(
'aimed_resolution',
self.opt_parameters_widget.opt_param_widget.maximum_res_ledit,
float, QtGui.QDoubleValidator(0.01, 1000, 2, self))
self._char_params_mib.bind_value_update(\
'aimed_multiplicity',
self.opt_parameters_widget.opt_param_widget.aimed_mult_ledit,
float,
QtGui.QDoubleValidator(0.01, 1000, 2, self))
self._char_params_mib.bind_value_update(
'aimed_i_sigma',
self.opt_parameters_widget.opt_param_widget.i_over_sigma_ledit,
float, QtGui.QDoubleValidator(0.01, 1000, 2, self))
self._char_params_mib.bind_value_update(
'aimed_completness',
self.opt_parameters_widget.opt_param_widget.aimed_comp_ledit,
float, QtGui.QDoubleValidator(0.01, 1000, 2, self))
self._char_params_mib.bind_value_update(
'strategy_complexity',
self.opt_parameters_widget.opt_param_widget.start_comp_cbox, int,
None)
self._char_params_mib.bind_value_update(
'use_permitted_rotation',
self.opt_parameters_widget.opt_param_widget.permitted_range_cbx,
bool, None)
self._char_params_mib.bind_value_update(
'permitted_phi_start',
self.opt_parameters_widget.opt_param_widget.phi_start_ledit, float,
QtGui.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'permitted_phi_end',
self.opt_parameters_widget.opt_param_widget.phi_end_ledit, float,
QtGui.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'low_res_pass_strat',
self.opt_parameters_widget.opt_param_widget.low_res_pass_cbx, bool,
None)
self._char_params_mib.bind_value_update(
'rad_suscept', self.rad_dmg_widget.sensetivity_ledit, float,
QtGui.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'beta', self.rad_dmg_widget.beta_over_gray_ledit, float,
QtGui.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'gamma', self.rad_dmg_widget.gamma_over_gray_ledit, float,
QtGui.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'max_crystal_vdim', self.vertical_dimension_widget.max_vdim_ledit,
float, QtGui.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'min_crystal_vdim', self.vertical_dimension_widget.min_vdim_ledit,
float, QtGui.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'min_crystal_vphi', self.vertical_dimension_widget.min_vphi_ledit,
float, QtGui.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'max_crystal_vphi', self.vertical_dimension_widget.max_vphi_ledit,
float, QtGui.QDoubleValidator(0.0, 1000, 2, self))
#self._char_params_mib.bind_value_update('space_group',
# self.vertical_dimension_widget.space_group_ledit,
# str,
# None)
self.vertical_dimension_widget.space_group_ledit.\
addItems(queue_model_enumerables.XTAL_SPACEGROUPS)
self.char_type_widget.charact_type_tbox.currentChanged.connect(\
self.update_char_type)
self.rad_dmg_char_widget.rad_damage_cbx.toggled.connect(\
self.enable_opt_parameters_widget)
self.opt_parameters_widget.opt_param_widget.maximum_res_cbx.\
toggled.connect(self.enable_maximum_res_ledit)
self.opt_parameters_widget.opt_param_widget.aimed_mult_cbx.\
toggled.connect(self.enable_aimed_mult_ledit)
self.path_widget.data_path_layout.prefix_ledit.textChanged.\
connect(self._prefix_ledit_change)
self.path_widget.data_path_layout.run_number_ledit.textChanged.\
connect(self._run_number_ledit_change)
self.vertical_dimension_widget.space_group_ledit.activated.\
connect(self._space_group_change)
def __init__(self, parent=None, name="parameter_widget"):
qt.QWidget.__init__(self, parent, name)
#
# Private members
#
self._char = None
self._char_params = queue_model_objects.CharacterisationParameters()
self._char_params_mib = DataModelInputBinder(self._char_params)
self._tree_view_item = None
self.previous_energy = None
self.add_dc_cb = None
self.char_type_widget = CharTypeWidget(self)
self.routine_dc_widget = self.char_type_widget.routine_dc_page
self.sad_widget = self.char_type_widget.sad_page
self.rad_dmg_char_widget = self.char_type_widget.rad_damage_page
self.reference_img_widget = ReferenceImageWidget(self)
self.acq_widget = self.reference_img_widget.acq_widget
self.path_widget = self.reference_img_widget.path_widget
self.opt_parameters_widget = OptimisationParametersWidgetLayout(self)
self.rad_dmg_widget = RadiationDamageModelWidgetLayout(self)
self.position_widget = SnapshotWidgetLayout(self)
self.vertical_dimension_widget = VerticalCrystalDimensionWidgetLayout(
self)
# Fix the widths of the widgets to make the layout look nicer,
# and beacuse the qt layout engine is so tremendosly good.
self.opt_parameters_widget.setFixedWidth(600)
self.reference_img_widget.setFixedWidth(772)
#
# Layout
#
v_layout = qt.QVBoxLayout(self, 11, 15, "main_layout")
rone_hlayout = qt.QHBoxLayout(v_layout, 15, "rone")
rone_cone_vlayout = qt.QVBoxLayout(rone_hlayout, 15, "rone_cone")
rtwo_hlayout = qt.QHBoxLayout(v_layout, 15, "rtwo")
rthree_hlayout = qt.QHBoxLayout(v_layout, 15, "rtwo")
rone_hlayout.addWidget(self.position_widget)
rone_cone_vlayout.addWidget(self.reference_img_widget)
rone_hlayout.addStretch()
rtwo_hlayout.addWidget(self.char_type_widget)
rtwo_hlayout.addWidget(self.opt_parameters_widget)
rtwo_hlayout.addStretch(10)
v_layout.addStretch(10)
rthree_hlayout.addWidget(self.rad_dmg_widget)
rthree_hlayout.addWidget(self.vertical_dimension_widget)
rthree_hlayout.addStretch(10)
v_layout.addStretch(10)
#
# Widget logic
#
self.toggle_permitted_range(self.\
opt_parameters_widget.permitted_range_cbx.isOn())
qt.QObject.connect(self.opt_parameters_widget.permitted_range_cbx,
qt.SIGNAL("toggled(bool)"),
self.toggle_permitted_range)
self._char_params_mib.bind_value_update(
'min_dose', self.routine_dc_widget.dose_ledit, float,
qt.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'min_time', self.routine_dc_widget.time_ledit, float,
qt.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'use_min_dose', self.routine_dc_widget.min_dose_radio, bool, None)
self._char_params_mib.bind_value_update(
'use_min_time', self.routine_dc_widget.min_time_radio, bool, None)
self._char_params_mib.bind_value_update(
'account_rad_damage', self.routine_dc_widget.radiation_damage_cbx,
bool, None)
self._char_params_mib.bind_value_update(
'auto_res', self.sad_widget.automatic_resolution_radio, bool, None)
self._char_params_mib.bind_value_update(
'opt_sad', self.sad_widget.optimal_sad_radio, bool, None)
self._char_params_mib.bind_value_update(
'determine_rad_params', self.rad_dmg_char_widget.rad_damage_cbx,
bool, None)
self._char_params_mib.bind_value_update(
'burn_osc_start', self.rad_dmg_char_widget.burn_osc_start_ledit,
float, qt.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'burn_osc_interval',
self.rad_dmg_char_widget.burn_osc_interval_ledit, float,
qt.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'use_aimed_resolution', self.opt_parameters_widget.maximum_res_cbx,
bool, None)
self._char_params_mib.bind_value_update(
'use_aimed_multiplicity',
self.opt_parameters_widget.aimed_mult_cbx, bool, None)
self._char_params_mib.bind_value_update(
'aimed_resolution', self.opt_parameters_widget.maximum_res_ledit,
float, qt.QDoubleValidator(0.01, 1000, 2, self))
self._char_params_mib.bind_value_update(
'aimed_multiplicity', self.opt_parameters_widget.aimed_mult_ledit,
float, qt.QDoubleValidator(0.01, 1000, 2, self))
self._char_params_mib.bind_value_update(
'aimed_i_sigma', self.opt_parameters_widget.i_over_sigma_ledit,
float, qt.QDoubleValidator(0.01, 1000, 2, self))
self._char_params_mib.bind_value_update(
'aimed_completness', self.opt_parameters_widget.aimed_comp_ledit,
float, qt.QDoubleValidator(0.01, 1000, 2, self))
self._char_params_mib.bind_value_update(
'strategy_complexity', self.opt_parameters_widget.start_comp_cbox,
int, None)
self._char_params_mib.bind_value_update(
'use_permitted_rotation',
self.opt_parameters_widget.permitted_range_cbx, bool, None)
self._char_params_mib.bind_value_update(
'permitted_phi_start', self.opt_parameters_widget.phi_start_ledit,
float, qt.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'permitted_phi_end', self.opt_parameters_widget.phi_end_ledit,
float, qt.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'low_res_pass_strat', self.opt_parameters_widget.low_res_pass_cbx,
bool, None)
self._char_params_mib.bind_value_update(
'rad_suscept', self.rad_dmg_widget.sensetivity_ledit, float,
qt.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'beta', self.rad_dmg_widget.beta_over_gray_ledit, float,
qt.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'gamma', self.rad_dmg_widget.gamma_over_gray_ledit, float,
qt.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'max_crystal_vdim', self.vertical_dimension_widget.max_vdim_ledit,
float, qt.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'min_crystal_vdim', self.vertical_dimension_widget.min_vdim_ledit,
float, qt.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'min_crystal_vphi', self.vertical_dimension_widget.min_vphi_ledit,
float, qt.QDoubleValidator(0.0, 1000, 2, self))
self._char_params_mib.bind_value_update(
'max_crystal_vphi', self.vertical_dimension_widget.max_vphi_ledit,
float, qt.QDoubleValidator(0.0, 1000, 2, self))
#self._char_params_mib.bind_value_update('space_group',
# self.vertical_dimension_widget.space_group_ledit,
# str,
# None)
self.vertical_dimension_widget.space_group_ledit.\
insertStrList(queue_model_enumerables.XTAL_SPACEGROUPS)
qt.QObject.connect(self.char_type_widget.charact_type_tbox,
qt.SIGNAL("currentChanged(int)"),
self.update_char_type)
qt.QObject.connect(self.rad_dmg_char_widget.rad_damage_cbx,
qt.SIGNAL("toggled(bool)"),
self.enable_opt_parameters_widget)
qt.QObject.connect(self.opt_parameters_widget.maximum_res_cbx,
qt.SIGNAL("toggled(bool)"),
self.enable_maximum_res_ledit)
qt.QObject.connect(self.opt_parameters_widget.aimed_mult_cbx,
qt.SIGNAL("toggled(bool)"),
self.enable_aimed_mult_ledit)
qt.QObject.connect(
self.path_widget.data_path_widget_layout.child('prefix_ledit'),
qt.SIGNAL("textChanged(const QString &)"),
self._prefix_ledit_change)
qt.QObject.connect(
self.path_widget.data_path_widget_layout.child('run_number_ledit'),
qt.SIGNAL("textChanged(const QString &)"),
self._run_number_ledit_change)
qt.QObject.connect(self.vertical_dimension_widget.space_group_ledit,
qt.SIGNAL("activated(int)"),
self._space_group_change)
qt.QObject.connect(qt.qApp, qt.PYSIGNAL('tab_changed'),
self.tab_changed)