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

pymodaq/extensions/optimizers_base/optimizer.py

@@ -0,0 +1,1016 @@
+import abc
+from typing import List,  Optional
+import tempfile
+from pathlib import Path
+
+
+from qtpy import QtWidgets, QtCore
+import time
+import numpy as np
+
+from collections import OrderedDict
+
+
+from pymodaq.utils.managers.modules_manager import ModulesManager
+from pymodaq_gui.messenger import messagebox
+from pymodaq_utils import utils
+
+from pymodaq_utils.enums import BaseEnum, StrEnum
+from pymodaq_utils.logger import set_logger, get_module_name
+try:
+    from pymodaq_gui.config_saver_loader import ConfigSaverLoader
+except ModuleNotFoundError:
+    from pymodaq_gui.config import ConfigSaverLoader #backcompatibility
+
+from pymodaq_utils.config import Config as ConfigUtils
+
+from pymodaq_data.h5modules.data_saving import DataEnlargeableSaver
+
+from pymodaq_gui.plotting.data_viewers.viewer0D import Viewer0D
+from pymodaq_gui.plotting.data_viewers.viewer import ViewerDispatcher
+from pymodaq_gui.utils import QLED
+from pymodaq_gui.utils.widgets.spinbox import QSpinBox_ro
+from pymodaq_gui import utils as gutils
+from pymodaq_gui.parameter import utils as putils
+from pymodaq_gui.h5modules.saving import H5Saver
+
+from pymodaq.utils.data import DataToExport, DataToActuators, DataCalculated, DataActuator
+from pymodaq.post_treatment.load_and_plot import LoaderPlotter
+from pymodaq.extensions.utils import CustomExt
+
+from pymodaq.utils.h5modules import module_saving
+from pymodaq.utils import config as config_mod
+
+from pymodaq.extensions.optimizers_base.utils import (
+    get_optimizer_models, OptimizerModelGeneric,
+    GenericAlgorithm, StopType, StoppingParameters,
+    OptimizerConfig, individual_as_dta, individual_as_dte)
+from pymodaq.extensions.optimizers_base.thread_commands import OptimizerToRunner, OptimizerThreadStatus
+
+
+logger = set_logger(get_module_name(__file__))
+config = config_mod.Config()
+config_utils = ConfigUtils()
+
+PREDICTION_PARAMS = []  # to be subclassed in real optimizer implementations
+MODELS = get_optimizer_models()
+
+
+class OptimizerAction(StrEnum):
+    QUIT = 'quit'
+    INI_MODEL = 'ini_model'
+    MODELS = 'models'
+    SAVE = 'save'
+    INI_RUNNER = 'ini_runner'
+    RUN = 'run'
+    RESTART = 'restart'
+    STOP = 'stop'
+    GO_TO_BEST = 'gotobest'
+    GO_TO = 'goto'
+
+
+class DataNames(StrEnum):
+    Fitness = 'fitness'
+    Individual = 'individual'
+    ProbedData = 'probed_data'
+    Actuators = 'actuators'
+    Tradeoff = 'tradeoff'
+
+
+def optimizer_params(prediction_params: list[dict]):
+    return [
+        {'title': 'Main Settings:', 'name': 'main_settings', 'expanded': True, 'type': 'group',
+         'children': [
+             {'title': 'Prediction Function:', 'name': 'prediction', 'expanded': False, 'type': 'group',
+              'children': prediction_params
+
+              },
+             {'title': 'Stopping Criteria:', 'name': 'stopping', 'expanded': False, 'type': 'group',
+              'children': [
+                  {'title': 'Niteration', 'name': 'niter', 'type': 'int',
+                   'value': config('optimizer', 'n_iter'), 'min': 5},
+                  {'title': 'Type:', 'name': 'stop_type', 'type': 'list',
+                   'limits': StopType.values(), 'value': str(StopType.ITER),
+                   'tip': StopType.ITER.tip()},
+                  {'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. Random Points', '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': ''}]},
+
+    ]
+
+
+class DataToActuatorsOpti(DataToActuators):
+    """ Specific class including the step in the optimization loop for further use"""
+    ind_iter: int
+    def __init__(self, *args, ind_iter=0, **kwargs):
+        super().__init__(*args, ind_iter=ind_iter, **kwargs)
+
+    def __repr__(self):
+        return f'{super().__repr__()} iter:{self.ind_iter}'
+
+
+
+class OptimizationRunner(QtCore.QObject):
+    algo_live_plot_signal = QtCore.Signal(DataToExport)
+    algo_finished = QtCore.Signal(DataToExport)
+    saver_signal = QtCore.Signal(DataToActuatorsOpti)
+
+    runner_command = QtCore.Signal(utils.ThreadCommand)
+
+    def __init__(self, model_class: OptimizerModelGeneric, modules_manager: ModulesManager,
+                 algorithm: GenericAlgorithm, stopping_params: StoppingParameters):
+        super().__init__()
+
+        self.det_done_datas: DataToExport = None
+        self.input_from_dets: float = None
+        self.outputs: List[np.ndarray] = []
+        self.output_to_actuators: DataToActuators = None
+        self.dte_actuators: DataToExport = None
+        self.stopping_params: StoppingParameters = stopping_params
+
+        self.model_class: OptimizerModelGeneric = model_class
+        self.modules_manager: ModulesManager = modules_manager
+
+        self.running = True
+        self.converged = False
+        self._ind_iter = -1
+
+        self.optimization_algorithm: GenericAlgorithm = algorithm
+
+
+    def queue_command(self, command: utils.ThreadCommand):
+        """
+        """
+        if command.command == OptimizerToRunner.RUN:
+            if command.attribute is None:
+                command.attribute = {}
+            self.run_opti(**command.attribute)
+
+        elif command.command == OptimizerToRunner.PAUSE:
+            self.running = False
+
+        elif command.command == OptimizerToRunner.STOP:
+            self.converged = True
+
+        elif command.command == OptimizerToRunner.STOPPING:
+            self.stopping_params: StoppingParameters = command.attribute
+
+        elif command.command == OptimizerToRunner.BOUNDS:
+            self.optimization_algorithm.bounds = command.attribute
+
+        elif command.command == OptimizerToRunner.RESTART:
+            self.optimization_algorithm = command.attribute
+            self._ind_iter = -1
+
+    def run_opti(self, sync_detectors=True, sync_acts=True):
+        """Start the optimization 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
+        self.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: dict[str, float] = self.optimization_algorithm.ask()
+
+                self.outputs = next_target
+                self.output_to_actuators: DataToActuators = \
+                    self.model_class.convert_output(
+                        self.outputs,
+                        best_individual=self.optimization_algorithm.best_individual
+                    )
+                for dwa in self.output_to_actuators:
+                    dwa.origin = DataNames.Actuators
+
+                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)
+
+                #log data
+                self.runner_command.emit(
+                    utils.ThreadCommand(OptimizerThreadStatus.ADD_DATA,))
+
+                # Run the algo internal mechanic
+                self.optimization_algorithm.tell(self.input_from_dets)
+
+                dte_algo = individual_as_dte(self.optimization_algorithm.best_individual,
+                                             self.modules_manager.actuators,
+                                             DataNames.Individual)
+                dte_algo.append([DataCalculated(DataNames.Fitness,
+                                               data=[np.atleast_1d(self.optimization_algorithm.best_fitness)]),
+                                 ])
+                dte_algo.append(self.output_to_actuators)
+                dte_algo.append(DataCalculated(DataNames.ProbedData,
+                                               data=[np.array([self.input_from_dets])],
+                                               origin='algo'))
+                self.algo_live_plot_signal.emit(dte_algo)
+
+                
+                self.saver_signal.emit(DataToActuatorsOpti(DataNames.Actuators,
+                                                           data = self.output_to_actuators.deepcopy().data,
+                                                           mode=self.output_to_actuators.mode,
+                                                           ind_iter=self._ind_iter))
+
+                self.optimization_algorithm.update_prediction_function()
+                self.runner_command.emit(
+                    utils.ThreadCommand(OptimizerThreadStatus.TRADE_OFF, attribute=self.optimization_algorithm.tradeoff))
+
+
+                self.converged = (self.converged or
+                                  self.optimization_algorithm.stopping(self._ind_iter, self.stopping_params))
+                if self.converged:
+                    break
+
+                self.current_time = time.perf_counter()
+                QtWidgets.QApplication.processEvents()
+                QtWidgets.QApplication.processEvents()
+            logger.info('Optimisation loop exiting')
+            self.modules_manager.connect_actuators(False)
+            self.modules_manager.connect_detectors(False)
+
+            if self.converged:
+                self.algo_finished.emit(dte_algo)
+
+        except Exception as e:
+            logger.exception(str(e))
+
+
+class GenericOptimization(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)
+    explored_viewer_name = f'algo/{DataNames.ProbedData}'
+    optimization_done_signal = QtCore.Signal(DataToExport)
+
+    runner = OptimizationRunner  # replace in real implementation if customization is needed
+    DISPLAY_BEST = True
+
+    params = optimizer_params(PREDICTION_PARAMS)
+
+    config_saver = OptimizerConfig  #to be redefined in real implementation if needed
+
+    def __init__(self, dockarea, dashboard):
+        super().__init__(dockarea, dashboard)
+
+        self._ini_runner = False
+
+        self.algorithm: Optional[GenericAlgorithm] = None
+        self.viewer_observable: Optional[ViewerDispatcher] = None
+        self.model_class: Optional[OptimizerModelGeneric] = None
+        self._save_main_settings = True
+
+        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._h5saver: H5Saver = None
+        self.h5saver.settings.child('do_save').hide()
+        self.h5saver.settings.child('custom_name').hide()
+        self.h5saver.new_file_sig.connect(self.create_new_file)
+
+        self.setup_ui()
+
+        self.optimizer_config = self.config_saver()
+
+        self.mainsettings_saver_loader = ConfigSaverLoader(
+            self.settings.child('main_settings'), self.optimizer_config)
+
+        self._base_name: str = None
+
+        self.h5temp: H5Saver = None
+        self.temp_path: tempfile.TemporaryDirectory = None
+        self.enlargeable_saver: DataEnlargeableSaver = None
+        self.live_plotter = LoaderPlotter(self.dockarea)
+
+        self._module_and_data_saver: module_saving.OptimizerSaver = None
+
+        self._ind_iter: int = 0
+        self.enl_index = 0
+
+        self.settings.child('models', 'ini_model').sigActivated.connect(
+            self.get_action(OptimizerAction.INI_MODEL).trigger)
+
+        self.settings.child('models', 'ini_runner').sigActivated.connect(
+            self.get_action(OptimizerAction.INI_RUNNER).trigger)
+
+        self.ini_custom_attributes()
+
+        if len(MODELS) == 1:
+            self.get_action(OptimizerAction.INI_MODEL).trigger()
+
+
+    @property
+    def title(self):
+        return f'{self.__class__.__name__}'
+
+    def ini_custom_attributes(self):
+        """ Here you can reimplement specific attributes"""
+        self._base_name: str = 'Optimizer'  # base name used for naming the hdf5 file
+
+    @property
+    def h5saver(self):
+        if self._h5saver is None:
+            self._h5saver = H5Saver(save_type='optimizer', backend=config_utils('general', 'hdf5_backend'))
+            self._h5saver.settings.child('base_name').setValue('Optimizer')
+        if self._h5saver.h5_file is None:
+            self._h5saver.init_file(update_h5=True)
+        if not self._h5saver.isopen():
+            self._h5saver.init_file(addhoc_file_path=self._h5saver.settings['current_h5_file'])
+        return self._h5saver
+
+    @h5saver.setter
+    def h5saver(self, h5saver_temp: H5Saver):
+        self._h5saver = h5saver_temp
+
+    @property
+    def module_and_data_saver(self):
+        if not self._module_and_data_saver.h5saver.isopen():
+            self._module_and_data_saver.h5saver = self.h5saver
+        return self._module_and_data_saver
+
+    @module_and_data_saver.setter
+    def module_and_data_saver(self, mod: module_saving.OptimizerSaver):
+        self._module_and_data_saver = mod
+        self._module_and_data_saver.h5saver = self.h5saver
+
+    def create_new_file(self, new_file):
+        if new_file:
+            self.close_file()
+        self.module_and_data_saver.h5saver = self.h5saver  # force all control modules to update their h5saver
+
+    def close_file(self):
+        self.h5saver.close_file()
+
+    def add_data(self, dta: DataToActuatorsOpti):
+        if self.is_action_checked(OptimizerAction.SAVE):
+            self.module_and_data_saver.add_data(axis_values=[dwa[0] for dwa in dta],
+                                                init_step=dta.ind_iter == 0)
+
+    @abc.abstractmethod
+    def validate_config(self) -> bool:
+        pass
+
+    @property
+    def config_path(self) -> Path:
+        return self.optimizer_config.config_path
+
+    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['saving'] = gutils.Dock('Saving')
+        self.docks['saving'].addWidget(self.h5saver.settings_tree)
+        self.dockarea.addDock(self.docks['saving'])
+
+        self.docks['settings'] = gutils.Dock('Settings')
+        self.dockarea.addDock(self.docks['settings'], 'below', self.docks['saving'])
+        splitter = QtWidgets.QSplitter(QtCore.Qt.Orientation.Vertical)
+        self.docks['settings'].addWidget(splitter)
+        splitter.addWidget(self.modules_manager.settings_tree)
+        splitter.addWidget(self.settings_tree)
+        self.modules_manager.show_only_control_modules(True)
+        self.modules_manager.settings_tree.setEnabled(False)
+
+        splitter.setSizes((int(self.dockarea.height() / 2),
+                           int(self.dockarea.height() / 2)))
+        if self.DISPLAY_BEST:
+            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(MODELS) != 0:
+            self.get_set_model_params(MODELS[0]['name'])
+
+
+        self._statusbar = QtWidgets.QStatusBar()
+        self.mainwindow.setStatusBar(self._statusbar)
+        self.populate_status_bar()
+
+
+    def populate_status_bar(self):
+        self._status_message_label = QtWidgets.QLabel('Initializing')
+        self._optimizing_step = QSpinBox_ro()
+        self._optimizing_step.setToolTip('Current Optimizing step')
+
+        self._optimizing_done_LED = QLED()
+        self._optimizing_done_LED.set_as_false()
+        self._optimizing_done_LED.clickable = False
+        self._optimizing_done_LED.setToolTip('Scan done state')
+        self._statusbar.addPermanentWidget(self._status_message_label)
+
+        self._statusbar.addPermanentWidget(self._optimizing_step)
+        self._statusbar.addPermanentWidget(self._optimizing_done_LED)
+
+
+    def get_set_model_params(self, model_name):
+        self.settings.child('models', 'model_params').clearChildren()
+        if len(MODELS) > 0:
+            model_class = utils.find_dict_in_list_from_key_val(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())
+            self.get_action(OptimizerAction.MODELS).setCurrentText(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', 'bounds'), []):
+            self.update_bounds()
+        elif param.name() in putils.iter_children(
+            self.settings.child('main_settings', 'stopping'), []):
+            self.update_stopping_criteria()
+            if param.name() == 'stop_type' and param.value() is not None:
+                self.settings.child('main_settings', 'stopping', 'stop_type').setOpts(
+                    tip=StopType(param.value()).tip())
+        elif param.name() in putils.iter_children(
+                self.settings.child('main_settings', 'prediction'), []):
+            if param.name() != 'tradeoff_actual':
+                self.update_prediction_function()
+
+        if self._save_main_settings and self.model_class is not None and param.name() in putils.iter_children(
+               self.settings.child('main_settings'), []):
+            self.mainsettings_saver_loader.save_config()
+
+    def update_prediction_function(self):
+        """ Get the selected prediction function options and pass them to the Runner
+
+        Should be reimplemented in real Optimizer implementation
+        Something like:
+
+        utility_settings = self.settings.child('main_settings', 'prediction')
+        kind = utility_settings.child('kind').value()
+        uparams = {child.name() : child.value() for child in utility_settings.child('options').children()}
+        uparams['kind'] = kind
+        self.command_runner.emit(
+            utils.ThreadCommand(OptimizerToRunner.PREDICTION, uparams))
+        """
+        pass
+
+    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(OptimizerToRunner.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(OptimizerToRunner.BOUNDS, bounds))
+
+    def setup_actions(self):
+        logger.debug('setting actions')
+        self.add_action(OptimizerAction.QUIT, 'Quit', 'close2', "Quit program")
+        combo_model = QtWidgets.QComboBox()
+        combo_model.addItems([model['name'] for  model in MODELS])
+        self.add_widget(OptimizerAction.MODELS, combo_model, tip='List of available models')
+        self.add_action(OptimizerAction.INI_MODEL, 'Init Model', 'ini')
+        self.add_widget('model_led', QLED, toolbar=self.toolbar)
+        self.add_action(OptimizerAction.SAVE, 'Save?', 'SaveAs', tip='If checked, data will be saved',
+                        checkable=True)
+        self.add_action(OptimizerAction.INI_RUNNER, 'Init the Optimisation Algorithm', 'ini', checkable=True,
+                        enabled=False)
+        self.add_widget('runner_led', QLED, toolbar=self.toolbar)
+        self.add_action(OptimizerAction.RUN, 'Run Optimisation', 'run2', checkable=True, enabled=False)
+        self.add_action(OptimizerAction.RESTART, 'Restart algo', 'Refresh2', checkable=False, enabled=False)
+        self.add_action(OptimizerAction.STOP, 'Stop algo', 'stop', checkable=False, enabled=False,
+                        tip='Stop algo and go to best individual')
+
+        self.add_action(OptimizerAction.GO_TO_BEST, 'Go to best', 'Rendezvous', enabled=False,
+                        tip='Go to the position optimizing the signal')
+        self.add_action(OptimizerAction.GO_TO, 'Go to ', 'move_contour', enabled=False, checkable=True,
+                        tip='Go to the double clicked position in the plot')
+        logger.debug('actions set')
+
+    def connect_things(self):
+        logger.debug('connecting things')
+        self.connect_action(OptimizerAction.QUIT, self.quit)
+        self.connect_action('models', self.update_model_settings_from_action,
+                            signal_name='currentTextChanged')
+
+        self.connect_action(OptimizerAction.SAVE, self.do_save)
+        self.connect_action(OptimizerAction.INI_MODEL, self.ini_model)
+        self.connect_action(OptimizerAction.INI_RUNNER, self.ini_optimization_runner)
+        self.connect_action(OptimizerAction.RUN, self.run_optimization)
+        self.connect_action(OptimizerAction.RESTART, self.restart_algo)
+        self.connect_action(OptimizerAction.STOP, self.stop_algo)
+        self.connect_action(OptimizerAction.GO_TO_BEST, self.go_to_best)
+        self.connect_action(OptimizerAction.GO_TO, self.allow_go_to)
+        self.h5saver.new_file_sig.connect(self.create_new_file)
+
+
+    def update_model_settings_from_action(self, model: str):
+        self.settings.child('models', 'model_class').setValue(model)
+
+    def go_to_best(self):
+        best_individual = self.algorithm.best_individual
+        if best_individual is not None:
+            actuators = self.modules_manager.actuators
+            dte_act = DataToActuators('best',
+                                      data=[
+                                          DataActuator(actuators[ind].title,
+                                                       data=float(best_individual[actuators[ind].title]),
+                                                       units=actuators[ind].units)
+                                          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)
+
+    def allow_go_to(self, enable=True):
+        if len(self.live_plotter.viewers) > 0:
+            if enable:
+                self.live_plotter.viewers[0].sig_double_clicked.connect(self.go_to)
+            else:
+                self.live_plotter.viewers[0].sig_double_clicked.disconnect(self.go_to)
+
+    def go_to(self, *positions):
+        actuators = self.modules_manager.actuators
+        dte_act = DataToActuators('best',
+                                  data=[
+                                      DataActuator(actuators[ind].title,
+                                                   data=float(positions[ind]),
+                                                   units=actuators[ind].units)
+                                      for ind in range(len(positions))
+                                  ],
+                                  mode='abs')
+        self.modules_manager.connect_actuators(True)
+        self.modules_manager.move_actuators(dte_act, polling=True)
+        self.modules_manager.connect_actuators(False)
+
+
+    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(
+            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()
+            if viewer.has_action('autolevels'):
+                if viewer.is_action_checked('autolevels'):
+                    viewer.get_action('autolevels').trigger()
+                    viewer.get_action('autolevels').trigger()
+            if viewer.has_action('aspect_ratio'):
+                if viewer.is_action_checked('aspect_ratio'):
+                    viewer.get_action('aspect_ratio').trigger()
+
+        QtWidgets.QApplication.processEvents()
+        win_width = self.dockarea.width()
+        self.docks['settings'].container().parent().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(OptimizerAction.INI_RUNNER):
+            self.get_action(OptimizerAction.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': config('optimizer', 'bounds', 'actuator_min')},
+                {'title': 'max', 'name': 'max', 'type': 'float',
+                 'value': config('optimizer', 'bounds','actuator_max')},
+            ]})
+        self.settings.child('main_settings', 'bounds').addChildren(params)
+
+        try:
+            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
+        except Exception as e:
+            logger.exception(f'Could not load the configuration')
+
+        self.update_after_actuators_changed(self.modules_manager.selected_actuators_name)
+
+    @abc.abstractmethod
+    def update_after_actuators_changed(self, actuators: list[str]):
+        """ Actions to do after the actuators have been updated
+
+        To be implemented
+        """
+        ...
+
+    def format_bounds(self):
+        bound_dict = OrderedDict([])
+        for bound in self.settings.child('main_settings', 'bounds').children():
+            bound_dict.update({bound.name(): (bound['min'], bound['max'])})
+        return bound_dict
+
+    @abc.abstractmethod
+    def set_algorithm(self):
+        self.algorithm = ...
+
+    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(OptimizerAction.INI_MODEL, False)
+            self.set_action_enabled(OptimizerAction.MODELS, False)
+
+            if self.DISPLAY_BEST:
+                self.viewer_observable.update_viewers(['Viewer0D'] + ['Viewer0D' for _ in self.modules_manager.selected_actuators_name],
+                                                      ['Fitness'] + [act for act in self.modules_manager.selected_actuators_name])
+            self.settings.child('models', 'ini_model').setValue(True)
+            self.settings.child('models', 'ini_runner').setOpts(enabled=True)
+            self.set_action_enabled(OptimizerAction.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()
+
+            self.modules_manager.settings_tree.setEnabled(True)
+            self.settings.child('models', 'ini_model').hide()
+
+            #Warning the activate method here is blocking???
+            # 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 do_save(self):
+        """ Properly prepare the extension for saving """
+        if self.is_action_checked(OptimizerAction.SAVE):
+            if self.is_action_checked(OptimizerAction.INI_RUNNER):
+                if self.is_action_checked(OptimizerAction.RUN):
+                    self.get_action(OptimizerAction.RUN).trigger()
+                    QtWidgets.QApplication.processEvents()
+                self.get_action(OptimizerAction.INI_RUNNER).trigger()  # for the model/algo de-initialization to correctly resave data
+                # afterwards
+                QtWidgets.QApplication.processEvents()
+                self.get_action(OptimizerAction.INI_RUNNER).trigger()
+
+    def ini_saver(self):
+        if self.is_action_checked(OptimizerAction.SAVE):
+            self.module_and_data_saver = module_saving.OptimizerSaver(
+                self, enl_axis_names=self.modules_manager.selected_actuators_name,
+                enl_axis_units=[act.units for act in self.modules_manager.actuators])
+            self.create_new_file(True)
+            self.module_and_data_saver.h5saver = self.h5saver
+            self.check_create_save_node()
+        else:
+            self.module_and_data_saver.forget_h5()
+            self.module_and_data_saver.h5saver.close_file()
+
+    def recursive_enable(self, param: putils.Parameter, enable=True):
+        param.setOpts(enabled=enable)
+        for child in param.children():
+            self.recursive_enable(child, enable)
+
+    def enable_settings_run(self, enable=True):
+        self.modules_manager.settings_tree.setEnabled(enable)
+        self.recursive_enable(self.settings.child('models'), enable)
+        self.recursive_enable(self.settings.child('main_settings', 'bounds'), enable)
+        self.recursive_enable(self.settings.child('main_settings', 'ini_random'), enable)
+
+    def stop_algo(self):
+        self.command_runner.emit(utils.ThreadCommand(OptimizerToRunner.STOP))
+
+    def restart_algo(self):
+
+        if self.is_action_checked(OptimizerAction.RUN):
+            self.get_action(OptimizerAction.RUN).trigger()
+            QtWidgets.QApplication.processEvents()
+
+        self.set_algorithm()
+        self.model_class.runner_initialized()
+        self.command_runner.emit(utils.ThreadCommand(OptimizerToRunner.RESTART, self.algorithm))
+        self.update_prediction_function()
+        if self.viewer_observable is not None:
+            for viewer in self.viewer_observable.viewers:
+                if isinstance(viewer, Viewer0D):
+                    viewer.view.data_displayer.clear_data()
+
+        self.enl_index = 0
+        self._optimizing_done_LED.set_as_false()
+        self.ini_temp_file()
+        self.ini_live_plot()
+
+        if self.is_action_checked(OptimizerAction.SAVE):
+            self.check_create_save_node()
+
+        self.get_action(OptimizerAction.RUN).trigger()
+
+    def check_create_save_node(self):
+        node_is_empty = (
+            len(self.module_and_data_saver.get_set_node().children()) == 0 or
+            len(self.module_and_data_saver.get_set_node().get_child('Detector000').children()) == 0)
+        node = self.module_and_data_saver.get_set_node(new= not node_is_empty)
+        self.h5saver.settings.child('current_scan_name').setValue(node.name)
+
+    def ini_optimization_runner(self):
+        self._status_message_label.setText('Initializing Algorithm and thread')
+        if self.is_action_checked(OptimizerAction.INI_RUNNER):
+            self._optimizing_done_LED.set_as_false()
+            if not self.model_class.has_fitness_observable():
+                messagebox(title='Warning', text='No 0D observable has been chosen as a fitness value for the algorithm')
+                self.set_action_checked(OptimizerAction.INI_RUNNER, False)
+                return
+
+            self.enable_settings_run(False)
+            if not self._ini_runner:
+                self._ini_runner = True
+                self.set_algorithm()
+
+                if self.is_action_checked(OptimizerAction.SAVE):
+                    self.ini_saver()
+                    self.check_create_save_node()
+
+                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 = self.runner(self.model_class, self.modules_manager, self.algorithm,
+                                     self.get_stopping_parameters())
+                self.runner_thread.runner = runner
+                runner.algo_live_plot_signal.connect(self.do_live_plot)
+                runner.algo_finished.connect(self.optimization_done)
+                runner.runner_command.connect(self.thread_status)
+                runner.saver_signal.connect(self.add_data)
+                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(OptimizerAction.RUN, True)
+                self.set_action_enabled(OptimizerAction.RESTART, True)
+                self.set_action_enabled(OptimizerAction.STOP, True)
+                self.model_class.runner_initialized()
+                self.update_prediction_function()
+        else:
+            self.set_action_enabled(OptimizerAction.INI_RUNNER, False)
+            self.enable_settings_run(True)
+            if self.is_action_checked(OptimizerAction.RUN):
+                self.get_action(OptimizerAction.RUN).trigger()
+                QtWidgets.QApplication.processEvents()
+
+            self._status_message_label.setText('Quitting Runner Thread')
+            try:
+                self.command_runner.disconnect()
+            except TypeError:
+                pass
+            if self.runner_thread is not None:
+                self.runner_thread.quit()
+                self.runner_thread.wait(5000)
+                if not self.runner_thread.isFinished():
+                    self.runner_thread.terminate()
+                    self.runner_thread.wait()
+            self.splash.setVisible(False)
+            self.get_action('runner_led').set_as_false()
+            self._ini_runner = False
+            self.set_action_enabled(OptimizerAction.RUN, False)
+            self.set_action_enabled(OptimizerAction.RESTART, False)
+            self.set_action_enabled(OptimizerAction.STOP, False)
+            self.set_action_enabled(OptimizerAction.INI_RUNNER, True)  # reactivate the action only when the thread is finished
+
+    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 optimization_done(self, dte: DataToExport):
+        self.go_to_best()
+        self.get_action(OptimizerAction.RUN).trigger()
+        self.optimization_done_signal.emit(dte)
+        self._optimizing_done_LED.set_as_true()
+        self._status_message_label.setText('Optimization Done')
+
+    def do_live_plot(self, dte_algo: DataToExport):
+        self.enl_index += 1
+        self._optimizing_step.setValue(self.enl_index)
+        self.model_class.update_plots()
+
+        dwa_data = dte_algo.pop(dte_algo.index_from_name_origin(DataNames.ProbedData, 'algo'))
+
+        actuators_values = [
+            dte_algo.get_data_from_name_origin(
+                act,
+                DataNames.Actuators)
+            .value() for act in self.modules_manager.selected_actuators_name]
+
+        best_individual = [
+            dte_algo.get_data_from_name_origin(
+                act,
+                DataNames.Individual)
+            .value() for act in self.modules_manager.selected_actuators_name]
+
+        fitness = dte_algo.get_data_from_name('fitness')
+
+        dte_live = DataToExport('Live', data=[
+            DataCalculated('Fitness',
+                           data=[np.atleast_1d(dwa_data.value()), np.atleast_1d(fitness.value())],
+                           labels=['Fitness', 'Fitness_best']
+                           ),])
+        for ind, act in enumerate(self.modules_manager.actuators):
+            dte_live.append([
+                DataCalculated(act.title,
+                               data=[np.atleast_1d(actuators_values[ind]),
+                                     np.atleast_1d(best_individual[ind])],
+                               labels=[act.title, f'{act.title}_best'],
+                               units=act.units
+                           ),
+                                ])
+
+        if self.DISPLAY_BEST:
+            self.viewer_observable.show_data(dte_live)
+
+
+        self.enlargeable_saver.add_data('/RawData', dwa_data,
+                                        axis_values=actuators_values)
+        if len(best_individual) == 1 or (
+                len(best_individual) == 2 and self.enl_index >= 3):
+            self.update_data_plot(target_at=actuators_values,
+                                  crosshair_at=best_individual)
+
+    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_optimization(self):
+        if self.is_action_checked(OptimizerAction.RUN):
+            self._status_message_label.setText('Running Optimization')
+            self.set_action_enabled(OptimizerAction.SAVE, False)
+            self.get_action(OptimizerAction.RUN).set_icon('pause')
+            self.set_action_enabled(OptimizerAction.GO_TO_BEST, False)
+            self.set_action_checked(OptimizerAction.GO_TO, False)
+            self.set_action_enabled(OptimizerAction.GO_TO, False)
+            self.set_action_enabled(OptimizerAction.INI_RUNNER, False)
+            self.command_runner.emit(utils.ThreadCommand(OptimizerToRunner.START))
+            QtWidgets.QApplication.processEvents()
+            QtWidgets.QApplication.processEvents()
+            self.command_runner.emit(utils.ThreadCommand(OptimizerToRunner.RUN))
+        else:
+            self._status_message_label.setText('Pausing Optimization')
+            self.get_action(OptimizerAction.RUN).set_icon('run2')
+            self.set_action_enabled(OptimizerAction.SAVE, True)
+            self.command_runner.emit(utils.ThreadCommand(OptimizerToRunner.PAUSE))
+            self.set_action_enabled(OptimizerAction.GO_TO_BEST, True)
+            self.set_action_enabled(OptimizerAction.GO_TO, True)
+            self.set_action_enabled(OptimizerAction.INI_RUNNER, True)
+            QtWidgets.QApplication.processEvents()
+
+    def thread_status(self, status: utils.ThreadCommand):
+        """To reimplement if needed"""
+
+
+
+