pymodaq 5.0.17__py3-none-any.whl → 5.1.0__py3-none-any.whl

pymodaq/extensions/bayesian/bayesian_optimisation.py

@@ -1,685 +0,0 @@
-from typing import List, Union, Optional
-import tempfile
-from pathlib import Path
-
-from qtpy import QtWidgets, QtCore
-import time
-import numpy as np
-
-from pymodaq.utils.data import DataToExport, DataToActuators, DataCalculated, DataActuator
-from pymodaq.utils.managers.modules_manager import ModulesManager
-from pymodaq_utils import utils
-from pymodaq_utils import config as config_mod
-from pymodaq_utils.enums import BaseEnum
-
-from pymodaq_gui.config import ConfigSaverLoader
-from pymodaq_utils.logger import set_logger, get_module_name
-
-from pymodaq_gui.plotting.data_viewers.viewer0D import Viewer0D
-from pymodaq_gui.plotting.data_viewers.viewer import ViewerDispatcher, ViewersEnum
-from pymodaq_gui.utils import QLED
-from pymodaq_gui.utils.utils import mkQApp
-from pymodaq_gui import utils as gutils
-from pymodaq_gui.parameter import utils as putils
-from pymodaq_gui.h5modules.saving import H5Saver
-
-from pymodaq_data.h5modules.data_saving import DataEnlargeableSaver
-
-
-from pymodaq.extensions.bayesian.utils import (get_bayesian_models, BayesianModelGeneric,
-                                               BayesianAlgorithm, UtilityKind,
-                                               UtilityParameters, StopType, StoppingParameters)
-from pymodaq.post_treatment.load_and_plot import LoaderPlotter
-from pymodaq.extensions.bayesian.utils import BayesianConfig
-from pymodaq.extensions.utils import CustomExt
-
-EXTENSION_NAME = 'BayesianOptimisation'
-CLASS_NAME = 'BayesianOptimisation'
-
-logger = set_logger(get_module_name(__file__))
-config = config_mod.Config()
-
-
-class DataNames(BaseEnum):
-    Fitness = 0
-    Individual = 1
-    ProbedData = 2
-    Actuators = 3
-    Kappa = 4
-
-
-class BayesianOptimisation(CustomExt):
-    """ PyMoDAQ extension of the DashBoard to perform the optimization of a target signal
-    taken form the detectors as a function of one or more parameters controlled by the actuators.
-    """
-
-    command_runner = QtCore.Signal(utils.ThreadCommand)
-    models = get_bayesian_models()
-    explored_viewer_name = 'algo/ProbedData'
-    optimisation_done_signal = QtCore.Signal(DataToExport)
-
-    params = [
-        {'title': 'Main Settings:', 'name': 'main_settings', 'expanded': True, 'type': 'group',
-         'children': [
-             {'title': 'Utility Function:', 'name': 'utility', 'expanded': False, 'type': 'group',
-              'children': [
-                  {'title': 'Kind', 'name': 'kind', 'type': 'list',
-                   'limits': UtilityKind.to_dict_value()},
-                  {'title': 'Kappa:', 'name': 'kappa', 'type': 'slide', 'value': 2.576,
-                   'min': 0.001, 'max': 100, 'subtype': 'log',
-                   'tip': 'Parameter to indicate how closed are the next parameters sampled.'
-                          'Higher value = favors spaces that are least explored.'
-                          'Lower value = favors spaces where the regression function is the '
-                          'highest.'},
-                  {'title': 'Kappa actual:', 'name': 'kappa_actual', 'type': 'float', 'value': 2.576,
-                   'tip': 'Current value of the kappa parameter', 'readonly': True},
-                  {'title': 'xi:', 'name': 'xi', 'type': 'slide', 'value': 0,
-                   'tip': 'Governs the exploration/exploitation tradeoff.'
-                          'Lower prefers exploitation, higher prefers exploration.'},
-                  {'title': 'Kappa decay:', 'name': 'kappa_decay', 'type': 'float', 'value': 0.9,
-                   'tip': 'kappa is multiplied by this factor every iteration.'},
-                  {'title': 'Kappa decay delay:', 'name': 'kappa_decay_delay', 'type': 'int',
-                   'value': 20, 'tip': 'Number of iterations that must have passed before applying '
-                                      'the decay to kappa.'},
-              ]},
-             {'title': 'Stopping Criteria:', 'name': 'stopping', 'expanded': False, 'type': 'group',
-              'children': [
-                  {'title': 'Niteration', 'name': 'niter', 'type': 'int', 'value': 100, 'min': -1},
-                  {'title': 'Type:', 'name': 'stop_type', 'type': 'list',
-                   'limits': StopType.names()},
-                  {'title': 'Tolerance', 'name': 'tolerance', 'type': 'slide', 'value': 1e-2,
-                   'min': 1e-8, 'max': 1, 'subtype': 'log',},
-                  {'title': 'Npoints', 'name': 'npoints', 'type': 'int', 'value': 5, 'min': 1},
-              ]},
-             {'title': 'Ini. State', 'name': 'ini_random', 'type': 'int', 'value': 5},
-             {'title': 'bounds', 'name': 'bounds', 'type': 'group', 'children': []},
-         ]},
-
-        {'title': 'Models', 'name': 'models', 'type': 'group', 'expanded': True, 'visible': True,
-         'children': [
-            {'title': 'Models class:', 'name': 'model_class', 'type': 'list',
-             'limits': [d['name'] for d in models]},
-            {'title': 'Ini Model', 'name': 'ini_model', 'type': 'action', },
-            {'title': 'Ini Algo', 'name': 'ini_runner', 'type': 'action', 'enabled': False},
-            {'title': 'Model params:', 'name': 'model_params', 'type': 'group', 'children': []},
-        ]},
-        {'title': 'Move settings:', 'name': 'move_settings', 'expanded': True, 'type': 'group',
-         'visible': False, 'children': [
-             {'title': 'Units:', 'name': 'units', 'type': 'str', 'value': ''}]},
-
-    ]
-
-    def __init__(self, dockarea, dashboard):
-        super().__init__(dockarea, dashboard)
-
-        self.algorithm: Optional[BayesianAlgorithm] = None
-        self.viewer_fitness: Optional[Viewer0D] = None
-        self.viewer_observable: Optional[ViewerDispatcher] = None
-        self.model_class: Optional[BayesianModelGeneric] = None
-        self._save_main_settings = True
-        self._modules_manager = ModulesManager(self.dashboard.detector_modules,
-                                               self.dashboard.actuators_modules)
-        self.modules_manager.actuators_changed[list].connect(self.update_actuators)
-        self.modules_manager.settings.child('data_dimensions').setOpts(expanded=False)
-        self.modules_manager.settings.child('actuators_positions').setOpts(expanded=False)
-        self.setup_ui()
-
-        self.bayesian_config = BayesianConfig()
-        self.mainsettings_saver_loader = ConfigSaverLoader(
-            self.settings.child('main_settings'), self.bayesian_config)
-
-        self.h5temp: H5Saver = None
-        self.temp_path: tempfile.TemporaryDirectory = None
-
-        self.enlargeable_saver: DataEnlargeableSaver = None
-        self.live_plotter = LoaderPlotter(self.dockarea)
-
-        self.enl_index = 0
-
-        self.settings.child('models', 'ini_model').sigActivated.connect(
-            self.get_action('ini_model').trigger)
-
-        self.settings.child('models', 'ini_runner').sigActivated.connect(
-            self.get_action('ini_runner').trigger)
-
-    @property
-    def modules_manager(self) -> ModulesManager:
-        return self._modules_manager
-
-    def setup_docks(self):
-        """
-        to be subclassed to setup the docks layout
-        for instance:
-
-        self.docks['ADock'] = gutils.Dock('ADock name)
-        self.dockarea.addDock(self.docks['ADock"])
-        self.docks['AnotherDock'] = gutils.Dock('AnotherDock name)
-        self.dockarea.addDock(self.docks['AnotherDock"], 'bottom', self.docks['ADock"])
-
-        See Also
-        ########
-        pyqtgraph.dockarea.Dock
-        """
-        self.docks['settings'] = gutils.Dock('Settings')
-        self.dockarea.addDock(self.docks['settings'])
-        splitter = QtWidgets.QSplitter(QtCore.Qt.Vertical)
-        self.docks['settings'].addWidget(splitter)
-        splitter.addWidget(self.settings_tree)
-        splitter.addWidget(self.modules_manager.settings_tree)
-        self.modules_manager.show_only_control_modules(False)
-        splitter.setSizes((int(self.dockarea.height() / 2),
-                           int(self.dockarea.height() / 2)))
-
-        widget_observable = QtWidgets.QWidget()
-        widget_observable.setLayout(QtWidgets.QHBoxLayout())
-        observable_dockarea = gutils.DockArea()
-        widget_observable.layout().addWidget(observable_dockarea)
-        self.viewer_observable = ViewerDispatcher(observable_dockarea, direction='bottom')
-        self.docks['observable'] = gutils.Dock('Observable')
-        self.dockarea.addDock(self.docks['observable'], 'right', self.docks['settings'])
-        self.docks['observable'].addWidget(widget_observable)
-
-        if len(self.models) != 0:
-            self.get_set_model_params(self.models[0]['name'])
-
-    def get_set_model_params(self, model_name):
-        self.settings.child('models', 'model_params').clearChildren()
-        if len(self.models) > 0:
-            model_class = utils.find_dict_in_list_from_key_val(self.models, 'name', model_name)['class']
-            params = getattr(model_class, 'params')
-            self.settings.child('models', 'model_params').addChildren(params)
-
-    def setup_menu(self, menubar: QtWidgets.QMenuBar = None):
-        '''
-        to be subclassed
-        create menu for actions contained into the self.actions_manager, for instance:
-
-        For instance:
-
-        file_menu = self.menubar.addMenu('File')
-        self.actions_manager.affect_to('load', file_menu)
-        self.actions_manager.affect_to('save', file_menu)
-
-        file_menu.addSeparator()
-        self.actions_manager.affect_to('quit', file_menu)
-        '''
-        pass
-
-    def value_changed(self, param):
-        ''' to be subclassed for actions to perform when one of the param's value in self.settings is changed
-
-        For instance:
-        if param.name() == 'do_something':
-            if param.value():
-                print('Do something')
-                self.settings.child('main_settings', 'something_done').setValue(False)
-
-        Parameters
-        ----------
-        param: (Parameter) the parameter whose value just changed
-        '''
-        if param.name() == 'model_class':
-            self.get_set_model_params(param.value())
-        elif param.name() in putils.iter_children(self.settings.child('models', 'model_params'), []):
-            if self.model_class is not None:
-                self.model_class.update_settings(param)
-        elif param.name() in putils.iter_children(
-                self.settings.child('main_settings', 'utility'), []):
-            if param.name() != 'kappa_actual':
-                self.update_utility_function()
-        elif param.name() in putils.iter_children(
-                self.settings.child('main_settings', 'bounds'), []):
-            self.update_bounds()
-        elif param.name() in putils.iter_children(
-            self.settings.child('main_settings', 'stopping'), []):
-            self.update_stopping_criteria()
-        if self._save_main_settings and param.name() in putils.iter_children(
-                self.settings.child('main_settings'), []):
-            self.mainsettings_saver_loader.save_config()
-
-    def update_utility_function(self):
-        utility_settings = self.settings.child('main_settings', 'utility')
-        uparams = UtilityParameters(utility_settings['kind'], utility_settings['kappa'],
-                                    utility_settings['xi'], utility_settings['kappa_decay'],
-                                    utility_settings['kappa_decay_delay'])
-        self.command_runner.emit(utils.ThreadCommand('utility', uparams))
-
-    def get_stopping_parameters(self) -> StoppingParameters:
-        stopping_settings = self.settings.child('main_settings', 'stopping')
-        stopping_params = StoppingParameters(stopping_settings['niter'],
-                                             stopping_settings['stop_type'],
-                                             stopping_settings['tolerance'],
-                                             stopping_settings['npoints'])
-        return stopping_params
-
-    def update_stopping_criteria(self):
-        self.command_runner.emit(utils.ThreadCommand('stopping', self.get_stopping_parameters()))
-
-    def update_bounds(self):
-        bounds = {}
-        for child in self.settings.child('main_settings', 'bounds').children():
-            bounds[child.name()] = (child['min'], child['max'])
-
-        self.command_runner.emit(utils.ThreadCommand('bounds', bounds))
-
-    def setup_actions(self):
-        logger.debug('setting actions')
-        self.add_action('quit', 'Quit', 'close2', "Quit program")
-        self.add_action('ini_model', 'Init Model', 'ini')
-        self.add_widget('model_led', QLED, toolbar=self.toolbar)
-        self.add_action('ini_runner', 'Init the Optimisation Algorithm', 'ini', checkable=True,
-                        enabled=False)
-        self.add_widget('runner_led', QLED, toolbar=self.toolbar)
-        self.add_action('run', 'Run Optimisation', 'run2', checkable=True, enabled=False)
-        self.add_action('gotobest', 'Got to best individual', 'move_contour', enabled=False,
-                        tip='Go to the best individual guessed by the algorithm')
-        logger.debug('actions set')
-
-    def connect_things(self):
-        logger.debug('connecting things')
-        self.connect_action('quit', self.quit, )
-        self.connect_action('ini_model', self.ini_model)
-        self.connect_action('ini_runner', self.ini_optimisation_runner)
-        self.connect_action('run', self.run_optimisation)
-        self.connect_action('gotobest', self.go_to_best)
-
-    def go_to_best(self):
-        best_individual = self.algorithm.best_individual
-        actuators = self.modules_manager.selected_actuators_name
-        dte_act = DataToActuators('best', data=[
-            DataActuator(actuators[ind], data=float(best_individual[ind])) for ind in range(len(best_individual))
-        ],
-                                  mode='abs')
-        self.modules_manager.connect_actuators(True)
-        self.modules_manager.move_actuators(dte_act, polling=True)
-        self.modules_manager.connect_actuators(False)
-
-        self.modules_manager.grab_datas()
-
-    def quit(self):
-        self.dockarea.parent().close()
-        self.clean_h5_temp()
-
-    def set_model(self):
-        model_name = self.settings.child('models', 'model_class').value()
-        self.model_class = utils.find_dict_in_list_from_key_val(
-            self.models, 'name', model_name)['class'](self)
-        self.model_class.ini_model_base()
-
-    def ini_temp_file(self):
-        self.clean_h5_temp()
-
-        self.h5temp = H5Saver()
-        self.temp_path = tempfile.TemporaryDirectory(prefix='pymo')
-        addhoc_file_path = Path(self.temp_path.name).joinpath('bayesian_temp_data.h5')
-        self.h5temp.init_file(custom_naming=True, addhoc_file_path=addhoc_file_path)
-        act_names = [child.name() for child in self.settings.child( 'main_settings',
-                                                                    'bounds').children()]
-        act_units = [self.modules_manager.get_mod_from_name(act_name, 'act').units for act_name
-                     in act_names]
-        self.enlargeable_saver = DataEnlargeableSaver(
-            self.h5temp,
-            enl_axis_names=act_names,
-            enl_axis_units=act_units)
-
-    def ini_live_plot(self):
-        self.live_plotter.h5saver = self.h5temp
-        act_names = [child.name() for child in self.settings.child('main_settings',
-                                                                   'bounds').children()]
-        act_units = [self.modules_manager.get_mod_from_name(act_name, 'act').units for act_name
-                     in act_names]
-        if len(act_names) == 1:
-            viewer_enum = 'Viewer1D'
-        elif len(act_names) == 2:
-            viewer_enum = 'Viewer2D'
-        else:
-            viewer_enum = 'ViewerND'
-        viewers = self.live_plotter.prepare_viewers([viewer_enum],
-                                                    viewers_name=[self.explored_viewer_name])
-        for viewer in viewers:
-            if viewer.has_action('crosshair'):
-                viewer.get_action('crosshair').trigger()
-                if hasattr(viewer.view, 'collapse_lineout_widgets'):
-                    viewer.view.collapse_lineout_widgets()
-            if viewer.has_action('sort'):
-                if not viewer.is_action_checked('sort'):
-                   viewer.get_action('sort').trigger()
-            if viewer.has_action('scatter'):
-                if not viewer.is_action_checked('scatter'):
-                    viewer.get_action('scatter').trigger()
-
-        QtWidgets.QApplication.processEvents()
-        win_width = self.dockarea.width()
-        self.docks['settings'].container().setSizes((int(win_width / 5),
-                                                     int(2 * win_width / 5),
-                                                     int(2 * win_width / 5), 10, 10))
-
-    def update_actuators(self, actuators: List[str]):
-        if self.is_action_checked('ini_runner'):
-            self.get_action('ini_runner').trigger()
-            QtWidgets.QApplication.processEvents()
-
-        self._save_main_settings = False
-
-        for child in self.settings.child('main_settings', 'bounds').children():
-            self.settings.child('main_settings', 'bounds').removeChild(child)
-        params = []
-        for actuator in actuators:
-            params.append({'title': actuator, 'name': actuator, 'type': 'group', 'children': [
-                {'title': 'min', 'name': 'min', 'type': 'float', 'value': -5},
-                {'title': 'max', 'name': 'max', 'type': 'float', 'value': 5},
-            ]})
-        self.settings.child('main_settings', 'bounds').addChildren(params)
-        self.mainsettings_saver_loader.base_path = [self.model_class.__class__.__name__] + \
-            self.modules_manager.selected_actuators_name
-        self.mainsettings_saver_loader.load_config()
-        self._save_main_settings = True
-
-    def format_bounds(self):
-        bound_dict = {}
-        for bound in self.settings.child('main_settings', 'bounds').children():
-            bound_dict.update({bound.name(): (bound['min'], bound['max'])})
-        return bound_dict
-
-    def set_algorithm(self):
-        self.algorithm = BayesianAlgorithm(
-            ini_random=self.settings['main_settings', 'ini_random'],
-            bounds=self.format_bounds(),)
-
-    def ini_model(self):
-        try:
-            if self.model_class is None:
-                self.set_model()
-
-            self.modules_manager.selected_actuators_name = self.model_class.actuators_name
-            self.modules_manager.selected_detectors_name = self.model_class.detectors_name
-
-            self.enable_controls_opti(True)
-            self.get_action('model_led').set_as_true()
-            self.set_action_enabled('ini_model', False)
-
-            self.viewer_observable.update_viewers(['Viewer0D', 'Viewer0D'],
-                                                  ['Fitness', 'Individual'])
-            self.settings.child('models', 'ini_model').setValue(True)
-            self.settings.child('models', 'ini_runner').setOpts(enabled=True)
-            self.set_action_enabled('ini_runner', True)
-
-            self.mainsettings_saver_loader.base_path = [self.model_class.__class__.__name__] + \
-                self.modules_manager.selected_actuators_name
-            self.mainsettings_saver_loader.load_config()
-
-            try:  # this is correct for Default Model and probably for all models...
-                self.model_class.settings.child('optimizing_signal', 'data_probe').activate()
-            except Exception:
-                pass
-
-        except Exception as e:
-            logger.exception(str(e))
-
-    def ini_optimisation_runner(self):
-        if self.is_action_checked('ini_runner'):
-            self.set_algorithm()
-
-            self.settings.child('models', 'ini_runner').setValue(True)
-            self.enl_index = 0
-
-            self.ini_temp_file()
-            self.ini_live_plot()
-
-            self.runner_thread = QtCore.QThread()
-            runner = OptimisationRunner(self.model_class, self.modules_manager, self.algorithm,
-                                        self.get_stopping_parameters())
-            self.runner_thread.runner = runner
-            runner.algo_output_signal.connect(self.process_output)
-            runner.algo_finished.connect(self.optimisation_done)
-            self.command_runner.connect(runner.queue_command)
-
-            runner.moveToThread(self.runner_thread)
-
-            self.runner_thread.start()
-            self.get_action('runner_led').set_as_true()
-            self.set_action_enabled('run', True)
-            self.model_class.runner_initialized()
-            self.update_utility_function()
-        else:
-            if self.is_action_checked('run'):
-                self.get_action('run').trigger()
-                QtWidgets.QApplication.processEvents()
-            self.runner_thread.terminate()
-            self.get_action('runner_led').set_as_false()
-
-    def clean_h5_temp(self):
-        if self.temp_path is not None:
-            try:
-                self.h5temp.close()
-                self.temp_path.cleanup()
-            except Exception as e:
-                logger.exception(str(e))
-
-    def optimisation_done(self, dte: DataToExport):
-        self.go_to_best()
-        self.optimisation_done_signal.emit(dte)
-
-    def process_output(self, dte: DataToExport):
-
-        self.enl_index += 1
-        dwa_kappa = dte.remove(dte.get_data_from_name(DataNames.Kappa.name))
-        self.settings.child('main_settings', 'utility', 'kappa_actual').setValue(
-            float(dwa_kappa[0][0])
-        )
-
-        dwa_data = dte.remove(dte.get_data_from_name(DataNames.ProbedData.name))
-        dwa_actuators: DataActuator = dte.remove(dte.get_data_from_name(DataNames.Actuators.name))
-        self.viewer_observable.show_data(dte)
-
-        # dwa_observations = self.algorithm.get_dwa_obervations(
-        #     self.modules_manager.selected_actuators_name)
-        self.model_class.update_plots()
-
-        best_individual = dte.get_data_from_name(DataNames.Individual.name)
-        best_indiv_as_list = [float(best_individual[ind][0]) for ind in range(len(best_individual))]
-
-
-        self.enlargeable_saver.add_data('/RawData', dwa_data,
-                                        axis_values=dwa_actuators.values())
-        if len(best_indiv_as_list) == 1 or (
-                len(best_indiv_as_list) == 2 and self.enl_index >= 3):
-            self.update_data_plot(target_at=dwa_actuators.values(),
-                                  crosshair_at=best_indiv_as_list)
-
-    def update_data_plot(self, target_at=None, crosshair_at=None):
-        self.live_plotter.load_plot_data(remove_navigation=False,
-                                         crosshair_at=crosshair_at,
-                                         target_at=target_at)
-
-    def enable_controls_opti(self, enable: bool):
-        pass
-
-    def run_optimisation(self):
-        if self.is_action_checked('run'):
-            self.get_action('run').set_icon('pause')
-            self.command_runner.emit(utils.ThreadCommand('start', {}))
-            QtWidgets.QApplication.processEvents()
-            QtWidgets.QApplication.processEvents()
-            self.command_runner.emit(utils.ThreadCommand('run', {}))
-        else:
-            self.get_action('run').set_icon('run2')
-            self.command_runner.emit(utils.ThreadCommand('stop', {}))
-            self.set_action_enabled('gotobest', True)
-
-            QtWidgets.QApplication.processEvents()
-
-
-class OptimisationRunner(QtCore.QObject):
-    algo_output_signal = QtCore.Signal(DataToExport)
-    algo_finished = QtCore.Signal(DataToExport)
-
-    def __init__(self, model_class: BayesianModelGeneric, modules_manager: ModulesManager,
-                 algorithm: BayesianAlgorithm, stopping_params: StoppingParameters):
-        super().__init__()
-
-        self.det_done_datas: DataToExport = None
-        self.input_from_dets: float = None
-        self.outputs: List[np.ndarray] = []
-        self.dte_actuators: DataToExport = None
-        self.stopping_params: StoppingParameters = stopping_params
-
-        self.model_class: BayesianModelGeneric = model_class
-        self.modules_manager: ModulesManager = modules_manager
-
-        self.running = True
-
-        self.optimisation_algorithm: BayesianAlgorithm = algorithm
-
-        self._ind_iter: int = 0
-
-    @QtCore.Slot(utils.ThreadCommand)
-    def queue_command(self, command: utils.ThreadCommand):
-        """
-        """
-        if command.command == "run":
-            self.run_opti(**command.attribute)
-
-        elif command.command == "stop":
-            self.running = False
-
-        elif command.command == 'utility':
-            utility_params: UtilityParameters = command.attribute
-            self.optimisation_algorithm.set_utility_function(
-                utility_params.kind,
-                kappa=utility_params.kappa,
-                xi=utility_params.xi,
-                kappa_decay=utility_params.kappa_decay,
-                kappa_decay_delay=utility_params.kappa_decay_delay)
-
-        elif command.command == 'stopping':
-            self.stopping_params: StoppingParameters = command.attribute
-
-        elif command.command == 'bounds':
-            self.optimisation_algorithm.set_bounds(command.attribute)
-
-    def run_opti(self, sync_detectors=True, sync_acts=True):
-        """Start the optimisation loop
-
-        Parameters
-        ----------
-        sync_detectors: (bool) if True will make sure all selected detectors (if any) all got their data before calling
-            the model
-        sync_acts: (bool) if True will make sure all selected actuators (if any) all reached their target position
-         before calling the model
-        """
-        self.running = True
-        converged = False
-        try:
-            if sync_detectors:
-                self.modules_manager.connect_detectors()
-            if sync_acts:
-                self.modules_manager.connect_actuators()
-
-            self.current_time = time.perf_counter()
-            logger.info('Optimisation loop starting')
-            while self.running:
-                self._ind_iter += 1
-
-                next_target = self.optimisation_algorithm.ask()
-
-                self.outputs = next_target
-                self.output_to_actuators: DataToActuators =\
-                    self.model_class.convert_output(
-                        self.outputs,
-                        best_individual=self.optimisation_algorithm.best_individual
-                    )
-
-                self.modules_manager.move_actuators(self.output_to_actuators,
-                                                    self.output_to_actuators.mode,
-                                                    polling=sync_acts)
-
-                # Do the evaluation (measurements)
-                self.det_done_datas = self.modules_manager.grab_data()
-                self.input_from_dets = self.model_class.convert_input(self.det_done_datas)
-
-                # Run the algo internal mechanic
-                self.optimisation_algorithm.tell(float(self.input_from_dets))
-
-                dte = DataToExport('algo',
-                                   data=[self.individual_as_data(
-                                       np.array([self.optimisation_algorithm.best_fitness]),
-                                       DataNames.Fitness.name),
-                                       self.individual_as_data(
-                                           self.optimisation_algorithm.best_individual,
-                                           DataNames.Individual.name),
-                                       DataCalculated(DataNames.ProbedData.name,
-                                                      data=[np.array([self.input_from_dets])],
-                                                      ),
-                                       self.output_to_actuators.merge_as_dwa(
-                                           'Data0D', DataNames.Actuators.name),
-                                       DataCalculated(
-                                           DataNames.Kappa.name,
-                                           data=[
-                                               np.array([self.optimisation_algorithm.kappa])])
-                                         ])
-                self.algo_output_signal.emit(dte)
-
-                self.optimisation_algorithm.update_utility_function()
-
-                if self.optimisation_algorithm.stopping(self._ind_iter, self.stopping_params):
-                    converged = True
-                    break
-
-            self.current_time = time.perf_counter()
-            QtWidgets.QApplication.processEvents()
-
-            logger.info('Optimisation loop exiting')
-            self.modules_manager.connect_actuators(False)
-            self.modules_manager.connect_detectors(False)
-
-            if converged:
-                self.algo_finished.emit(dte)
-
-        except Exception as e:
-            logger.exception(str(e))
-
-    @staticmethod
-    def individual_as_data(individual: np.ndarray, name: str = 'Individual') -> DataCalculated:
-        return DataCalculated(name, data=[np.atleast_1d(np.squeeze(coordinate)) for coordinate in
-                                          np.atleast_1d(np.squeeze(individual))])
-
-
-def main(init_qt=True):
-    import sys
-    from pathlib import Path
-    from pymodaq.utils.daq_utils import get_set_preset_path
-
-    if init_qt:  # used for the test suite
-        app = mkQApp("PyMoDAQ Dashboard")
-
-    from pymodaq.dashboard import DashBoard
-
-    win = QtWidgets.QMainWindow()
-    area = gutils.dock.DockArea()
-    win.setCentralWidget(area)
-    win.resize(1000, 500)
-
-    dashboard = DashBoard(area)
-    daq_scan = None
-    file = Path(get_set_preset_path()).joinpath(f"{'beam_steering_mock'}.xml")
-
-    if file.exists():
-        dashboard.set_preset_mode(file)
-        daq_scan = dashboard.load_bayesian()
-    else:
-        msgBox = QtWidgets.QMessageBox()
-        msgBox.setText(f"The default file specified in the configuration file does not exists!\n"
-                       f"{file}\n"
-                       f"Impossible to load the DAQScan Module")
-        msgBox.setStandardButtons(msgBox.Ok)
-        ret = msgBox.exec()
-
-    if init_qt:
-        sys.exit(app.exec_())
-    return dashboard, daq_scan, win
-
-
-if __name__ == '__main__':
-    main()
-

pymodaq/utils/leco/desktop.ini

@@ -1,2 +0,0 @@
-[LocalizedFileNames]
-Command Prompt.lnk=@%SystemRoot%\system32\shell32.dll,-22022