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

pymodaq/extensions/optimizers_base/thread_commands.py

@@ -0,0 +1,22 @@
+from pymodaq_utils.enums import StrEnum
+
+
+class OptimizerToRunner(StrEnum):
+    """ Allowed Generic commands sent from an Optimizer to its thread running class
+
+    """
+    START = 'start'
+    RUN = 'run'
+    PAUSE = 'pause'
+    STOP = 'stop'
+    STOPPING = 'stopping'
+    BOUNDS = 'bounds'
+    RESTART = 'restart'
+    PREDICTION = 'prediction'
+
+
+class OptimizerThreadStatus(StrEnum):
+
+    ADD_DATA = "add_data"
+    TRADE_OFF = "tradeoff"
+

pymodaq/extensions/optimizers_base/utils.py

@@ -0,0 +1,427 @@
+# -*- coding: utf-8 -*-
+"""
+Created the 31/08/2023
+
+@author: Sebastien Weber
+"""
+import abc
+from abc import ABC
+from collections import OrderedDict
+from typing import List, TYPE_CHECKING, Union, Dict, Tuple, Iterable, Optional
+from pathlib import Path
+import importlib
+import pkgutil
+import inspect
+import numpy as np
+from collections import namedtuple
+
+from pymodaq_utils.abstract import abstract_attribute
+from pymodaq_utils.utils import find_dict_in_list_from_key_val, get_entrypoints
+from pymodaq_utils.logger import set_logger, get_module_name
+from pymodaq_utils.enums import StrEnum
+from pymodaq_utils.config import BaseConfig
+
+from pymodaq_gui.plotting.data_viewers.viewer import ViewersEnum
+from pymodaq_gui.managers.parameter_manager import Parameter
+
+
+from pymodaq_data.data import (DataToExport, DataCalculated,
+                                DataRaw, Axis)
+
+from pymodaq.utils.data import DataActuator, DataToActuators
+from pymodaq.utils.managers.modules_manager import ModulesManager
+
+if TYPE_CHECKING:
+    from pymodaq.control_modules.daq_move import DAQ_Move
+
+logger = set_logger(get_module_name(__file__))
+
+
+class StopType(StrEnum):
+    NONE = 'None'
+    ITER = 'Iter'
+    PREDICT = 'Predict'
+    BEST = 'Best'
+
+    def tip(self):
+        if self == StopType.NONE:
+            return 'Stopping only after the number of iteration has been reached'
+        elif self == StopType.ITER:
+            return 'Stopping only after the number of iteration has been reached'
+        elif self == StopType.PREDICT:
+            return ('Stopping either after the number of iteration has been reached or the last N'
+                    'tested coordinates have a standard deviation less than tolerance')
+        elif self == StopType.BEST:
+            return ('Stopping either after the number of iteration has been reached or the N best '
+                    'coordinates have a standard deviation less than tolerance')
+
+
+StoppingParameters = namedtuple('StoppingParameters',
+                                ['niter', 'stop_type', 'tolerance', 'npoints'])
+
+class PredictionError(Exception):
+    pass
+
+
+def individual_as_dte(individual: dict[str, float], actuators: list['DAQ_Move'],
+                      name: str = 'Individual') -> DataToExport:
+    """ Create a DataToExport from the individual coordinates and the list of selected actuators"""
+    return DataToExport(
+        name,
+        data=[DataCalculated(actuators[ind].title,
+                             data=[np.atleast_1d(individual[actuators[ind].title])],
+                             units=actuators[ind].units,
+                             labels=[actuators[ind].title],
+                             origin=name)
+              for ind in range(len(individual))],)
+
+
+def individual_as_dta(individual: dict[str, float], actuators: list['DAQ_Move'],
+                      name: str = 'Individual', mode='abs') -> DataToActuators:
+    """ Create a DataToActuators from the individual coordinates and the list of selected actuators"""
+    return DataToActuators(
+        name, mode=mode,
+        data=[DataActuator(actuators[ind].title,
+                           data=[np.atleast_1d(individual[actuators[ind].title])],
+                           units=actuators[ind].units,
+                           labels=[actuators[ind].title],
+                           origin=name)
+              for ind in range(len(individual))],)
+
+
+class GenericAlgorithm(abc.ABC):
+
+    def __init__(self, ini_random: int, bounds: OrderedDict[str, tuple[float, float]], actuators: list[str]):
+
+        self._algo = abstract_attribute()  #could be a Bayesian on Adaptive algorithm
+        self._prediction = abstract_attribute()  # could be an acquisition function...
+
+        self.actuators = actuators
+        self.ini_bounds = bounds
+
+        self._next_point: Optional[dict[str, float]] = None
+        self._suggested_coordinates: list[dict[str, float]]  = []
+        self.ini_random_points = ini_random
+
+    @abc.abstractmethod
+    def set_prediction_function(self, kind: str='', **kwargs):
+        """ Set/Load a given function/class to predict next probed points"""
+
+    @abc.abstractmethod
+    def update_prediction_function(self):
+        """ Update the parameters of the prediction function (kappa decay for instance)"""
+
+    def set_acquisition_function(self, kind: str, **kwargs):
+        """ Deprecated"""
+        self.set_prediction_function(kind, **kwargs)
+
+    def update_acquisition_function(self):
+        """ deprecated"""
+        self.update_prediction_function()
+
+    @property
+    def _acquisition(self):
+        """ deprecated """
+        return self._prediction
+
+    @property
+    def tradeoff(self):
+        return self._prediction.tradeoff
+
+    @property
+    @abc.abstractmethod
+    def bounds(self) -> dict[str, tuple[float, float]]:
+        ...
+
+    @bounds.setter
+    def bounds(self, bounds: dict[str, tuple[float, float]]):
+        ...
+
+    @abc.abstractmethod
+    def get_random_point(self) -> dict[str, float]:
+        """ Get a random point coordinates in the defined bounds"""
+        ...
+
+    def ask(self) -> dict[str, float]:
+        """ Predict next actuator values to probe
+
+        Return a DataToActuator, one DataWithAxes per actuator. In general these dwa are 0D
+        """
+        try:
+            self._next_point = self.prediction_ask()
+        except PredictionError:
+            self.ini_random_points -= 1
+            self._next_point = self.get_random_point()
+        self._suggested_coordinates.append(self._next_point)
+        return self._next_point
+
+    @abc.abstractmethod
+    def prediction_ask(self) -> dict[str, float]:
+        """ Ask the prediction function or algo to provide the next point to probe"""
+
+    @abc.abstractmethod
+    def tell(self, function_value: float):
+        """ Add next points and function value into the algo"""
+        
+    @property
+    @abc.abstractmethod
+    def best_fitness(self) -> float:
+        pass
+
+    @property
+    @abc.abstractmethod
+    def best_individual(self) -> Union[dict[str, float], None]:
+        pass
+
+    @abc.abstractmethod
+    def stopping(self, ind_iter: int, stopping_parameters: StoppingParameters) -> bool:
+        pass
+
+
+class OptimizerModelGeneric(ABC):
+
+    optimization_algorithm: GenericAlgorithm = None
+
+    actuators_name: List[str] = []
+    detectors_name: List[str] = []
+
+    observables_dim: List[ViewersEnum] = []
+
+    params = []  # to be subclassed
+
+    def __init__(self, optimization_controller):
+        self.optimization_controller = optimization_controller  # instance of the pid_controller using this model
+        self.modules_manager: ModulesManager = optimization_controller.modules_manager
+
+        self.settings = self.optimization_controller.settings.child('models', 'model_params')  # set of parameters
+        self.check_modules(self.modules_manager)
+
+    @abc.abstractmethod
+    def has_fitness_observable(self) -> bool:
+        """ Should return True if the model defined a 0D data to be used as fitness value"""
+        return False
+
+    def check_modules(self, modules_manager):
+        for act in self.actuators_name:
+            if act not in modules_manager.actuators_name:
+                logger.warning(f'The actuator {act} defined in the model is'
+                               f' not present in the Dashboard')
+                return False
+        for det in self.detectors_name:
+            if det not in modules_manager.detectors_name:
+                logger.warning(f'The detector {det} defined in the model is'
+                               f' not present in the Dashboard')
+
+    def update_detector_names(self):
+        names = self.optimization_controller.settings.child(
+            'main_settings', 'detector_modules').value()['selected']
+        self.data_names = []
+        for name in names:
+            name = name.split('//')
+            self.data_names.append(name)
+
+    def update_settings(self, param: Parameter):
+        """
+        Get a parameter instance whose value has been modified by a user on the UI
+        To be overwritten in child class
+        """
+        ...
+
+    def update_plots(self):
+        """ Called when updating the live plots """
+        pass
+
+    def ini_model_base(self):
+        self.modules_manager.selected_actuators_name = self.actuators_name
+        self.modules_manager.selected_detectors_name = self.detectors_name
+
+        self.ini_model()
+
+    def ini_model(self):
+        """ To be subclassed
+
+        Initialize whatever is needed by your custom model
+        """
+        raise NotImplementedError
+
+    def runner_initialized(self):
+        """ To be subclassed
+
+        Initialize whatever is needed by your custom model after the optimization runner is
+        initialized
+        """
+        pass
+
+    def convert_input(self, measurements: DataToExport) -> float:
+        """
+        Convert the measurements in the units to be fed to the Optimisation Controller
+        Parameters
+        ----------
+        measurements: DataToExport
+            data object exported from the detectors from which the model extract a float value
+            (fitness) to be fed to the algorithm
+
+        Returns
+        -------
+        float
+
+        """
+        raise NotImplementedError
+
+    def convert_output(self, outputs: dict[str, Union[float, np.ndarray]],
+                       best_individual: Optional[dict[str, float]] = None) -> DataToActuators:
+        """ Convert the output of the Optimisation Controller in units to be fed into the actuators
+        Parameters
+        ----------
+        outputs: dict with name of the actuator as key and the value to move to as a float (or ndarray)
+            output value from the controller from which the model extract a value of the same units as the actuators
+        best_individual: dict[str, float]
+            the coordinates of the best individual so far
+        Returns
+        -------
+        DataToActuatorOpti: derived from DataToExport. Contains value to be fed to the actuators with a 'mode'
+            attribute, either 'rel' for relative or 'abs' for absolute.
+
+        """
+        raise NotImplementedError
+
+
+class OptimizerModelDefault(OptimizerModelGeneric):
+
+    actuators_name: List[str] = []  # to be populated dynamically at instantiation
+    detectors_name: List[str] = []  # to be populated dynamically at instantiation
+
+    params = [{'title': 'Optimizing signal', 'name': 'optimizing_signal', 'type': 'group',
+               'children': [
+                   {'title': 'Get data', 'name': 'data_probe', 'type': 'action'},
+                   {'title': 'Optimize 0Ds:', 'name': 'optimize_0d', 'type': 'itemselect',
+                    'checkbox': True},
+               ]},]
+
+    def __init__(self, optimization_controller):
+        self.actuators_name = optimization_controller.modules_manager.selected_actuators_name
+        self.detectors_name = optimization_controller.modules_manager.selected_detectors_name
+        super().__init__(optimization_controller)
+
+        self.settings.child('optimizing_signal', 'data_probe').sigActivated.connect(
+            self.optimize_from)
+
+    def has_fitness_observable(self) -> bool:
+        """ Should return True if the model defined a 0D data to be used as fitness value"""
+        return len(self.settings.child('optimizing_signal', 'optimize_0d').value()['selected']) == 1
+
+    def ini_model(self):
+        pass
+
+    def update_settings(self, param: Parameter):
+        pass
+
+    def convert_input(self, measurements: DataToExport) -> float:
+        """ Convert the measurements in the units to be fed to the Optimisation Controller
+
+        Parameters
+        ----------
+        measurements: DataToExport
+            data object exported from the detectors from which the model extract a float value
+            (fitness) to be fed to the algorithm
+
+        Returns
+        -------
+        float
+
+        """
+        data_name: str = self.settings['optimizing_signal', 'optimize_0d']['selected'][0]
+        origin, name = data_name.split('/')
+        return float(measurements.get_data_from_name_origin(name, origin).data[0][0])
+
+    def convert_output(self, outputs: dict[str, Union[float, np.ndarray]],
+                       best_individual: Optional[dict[str, float]] = None) -> DataToActuators:
+        """ Convert the output of the Optimisation Controller in units to be fed into the actuators
+        Parameters
+        ----------
+        outputs: dict with name of the actuator as key and the value to move to as a float (or ndarray)
+            output value from the controller from which the model extract a value of the same units as the actuators
+        best_individual: dict[str, float]
+            the coordinates of the best individual so far
+        Returns
+        -------
+        DataToActuatorOpti: derived from DataToExport. Contains value to be fed to the actuators with a 'mode'
+            attribute, either 'rel' for relative or 'abs' for absolute.
+
+        """
+        return individual_as_dta(outputs, self.modules_manager.actuators, 'outputs', mode='abs')
+
+    def optimize_from(self):
+        self.modules_manager.get_det_data_list()
+        data0D = self.modules_manager.settings['data_dimensions', 'det_data_list0D']
+        data0D['selected'] = data0D['all_items']
+        self.settings.child('optimizing_signal', 'optimize_0d').setValue(data0D)
+
+
+def get_optimizer_models(model_name=None):
+    """
+    Get Optimizer Models as a list to instantiate Control Actuators per degree of liberty in the model
+
+    Returns
+    -------
+    list: list of disct containting the name and python module of the found models
+    """
+    models_import = []
+    discovered_models = get_entrypoints(group='pymodaq.models')
+    if len(discovered_models) > 0:
+        for pkg in discovered_models:
+            try:
+                module = importlib.import_module(pkg.value)
+                module_name = pkg.value
+
+                for mod in pkgutil.iter_modules([
+                    str(Path(module.__file__).parent.joinpath('models'))]):
+                    try:
+                        model_module = importlib.import_module(f'{module_name}.models.{mod.name}',
+                                                               module)
+                        classes = inspect.getmembers(model_module, inspect.isclass)
+                        for name, klass in classes:
+                            if issubclass(klass, OptimizerModelGeneric):
+                                if find_dict_in_list_from_key_val(models_import, 'name', mod.name)\
+                                        is None:
+                                    models_import.append({'name': klass.__name__,
+                                                          'module': model_module,
+                                                          'class': klass})
+
+                    except Exception as e:
+                        logger.warning(str(e))
+
+            except Exception as e:
+                logger.warning(f'Impossible to import the {pkg.value} optimizer model: {str(e)}')
+
+    if find_dict_in_list_from_key_val(models_import, 'name', 'OptimizerModelDefault') \
+            is None:
+        models_import.append({'name': 'OptimizerModelDefault',
+                              'module': inspect.getmodule(OptimizerModelDefault),
+                              'class': OptimizerModelDefault})
+    if model_name is None:
+        return models_import
+    else:
+        return find_dict_in_list_from_key_val(models_import, 'name', model_name)
+
+
+class OptimizerConfig(BaseConfig):
+    """Main class to deal with configuration values for this plugin
+
+    To b subclassed for real implementation if needed, see Optimizer class attribute config_saver
+    """
+    config_template_path = None
+    config_name = f"optimizer_settings"
+
+
+def find_key_in_nested_dict(dic, key):
+    stack = [dic]
+    while stack:
+        d = stack.pop()
+        if key in d:
+            return d[key]
+        for v in d.values():
+            if isinstance(v, dict):
+                stack.append(v)
+            if isinstance(v, list):
+                stack += v

pymodaq/extensions/pid/actuator_controller.py

@@ -7,7 +7,8 @@ if TYPE_CHECKING:
 class PIDController:
     """ Fake controller object for the DAQ_Move_PID"""
 
-    def __init__(self, daq_pid: 'DAQ_PID'):
+    def __init__(self, daq_pid: 'DAQ_PID', set_point_name: str = 'setpoint'):
         self.curr_point = daq_pid.curr_points_signal
         self.setpoint = daq_pid.setpoints_signal
-        self.emit_curr_points = daq_pid.emit_curr_points_sig
+        self.emit_curr_points = daq_pid.emit_curr_points_sig
+        self.queue_points = daq_pid.queue_points[set_point_name]

pymodaq/extensions/pid/daq_move_PID.py

@@ -1,23 +1,78 @@
-from pymodaq_utils.utils import ThreadCommand
+from collections import deque
 
-from pymodaq.control_modules.move_utility_classes import (DAQ_Move_base, comon_parameters_fun,
-                                                          DataActuatorType, DataActuator)
+import numpy as np
+from pymodaq_utils.utils import ThreadCommand
 
+from pymodaq.control_modules.move_utility_classes import (
+    DAQ_Move_base,
+    DataActuator,
+    DataActuatorType,
+    comon_parameters_fun,
+)
 from pymodaq.extensions.pid.actuator_controller import PIDController
 
 
 class DAQ_Move_PID(DAQ_Move_base):
-    """
-    """
-    _controller_units = ''
+    """ """
+
+    _controller_units = ""
     data_actuator_type = DataActuatorType.DataActuator
     is_multiaxes = False
-    stage_names = ['',]
-
-    params = comon_parameters_fun(is_multiaxes, stage_names, master=False)
+    stage_names = [
+        "",
+    ]
+    params = [  # elements to be added in order to control your custom stage
+        {
+            "title": "Check stability:",
+            "name": "check_stab",
+            "type": "bool",
+            "value": False,
+            "default": "False",
+            "tooltip": "Activate to only trigger move_done once standard deviation over queue length is below threshold",
+            "children": [
+                {
+                    "title": "Stable:",
+                    "name": "is_stab",
+                    "type": "led",
+                    "value": False,
+                    "default": False,
+                    "tooltip": "Red if the standard deviation of the last positions is above threshold, green if below",
+                },
+                {
+                    "title": "Current stability:",
+                    "name": "current_stab",
+                    "type": "float",
+                    "value": 0,
+                    "default": 0,
+                    "readonly": True,
+                    "tooltip": "",
+                },
+                {
+                    "title": "Threshold:",
+                    "name": "threshold",
+                    "type": "float",
+                    "value": 0.1,
+                    "default": 0.1,
+                    "min": 0,
+                    "tooltip": "Standard deviation threshold to consider the stage stable",
+                },
+                {
+                    "title": "Queue length:",
+                    "name": "queue_length",
+                    "type": "int",
+                    "default": 10,
+                    "value": 50,
+                    "min": 0,
+                    "tooltip": "Length of the queue used to compute the standard deviation for stability check",
+                },
+            ],
+        },
+    ] + comon_parameters_fun(is_multiaxes, stage_names, master=False)
+    # params = comon_parameters_fun(is_multiaxes, stage_names, master=False)
 
     def ini_attributes(self):
         self.controller: PIDController = None
+        self.last_positions = deque(maxlen=self.settings["check_stab", "queue_length"])
 
     def update_position(self, dict_val: dict):
         self.current_value = dict_val[self.parent.title]
@@ -30,48 +85,70 @@ class DAQ_Move_PID(DAQ_Move_base):
     def close(self):
         pass
 
-    def commit_settings(self, param):
-        pass
+    def user_condition_to_reach_target(self):
+        cond = super().user_condition_to_reach_target()
+        parameter_stab = self.settings.child("check_stab")
 
-    def ini_stage(self, controller=None):
-        """
-        """
-        self.controller = controller
+        if parameter_stab.value():
+            if len(self.controller.queue_points) >= self.settings["check_stab", "queue_length"]:
+                self.last_positions = deque(
+                    self.controller.queue_points, maxlen=self.settings["check_stab", "queue_length"]
+                )
+                current_stab = np.std(self.last_positions)
+                parameter_stab.child("current_stab").setValue(current_stab)
+                cond = current_stab <= parameter_stab["threshold"]
+            else:
+                cond = False
+
+            parameter_stab.child("is_stab").setValue(cond)
 
+        return cond
+
+    def commit_settings(self, param):
+        if param.name() == "check_stab":
+            pass
+        elif param.name() == "queue_length":
+            self.last_positions = deque(
+                self.controller.queue_points, maxlen=self.settings["check_stab", "queue_length"]
+            )
+            param.setOpts(max=self.controller.queue_points.maxlen)
+
+    def ini_stage(self, controller: PIDController = None):
+        """ """
+        self.controller = controller
         self.controller.curr_point.connect(self.update_position)
 
+        self.settings.child("check_stab", "queue_length").setValue(self.controller.queue_points.maxlen)
+
         info = "PID stage"
         initialized = True
         return info, initialized
 
     def move_abs(self, position: DataActuator):
-        """
-        """
+        """ """
         position = self.check_bound(position)
-        self.target_position = position
+        self.target_value = position
 
-        self.controller.setpoint.emit({self.parent.title: self.target_position})
+        self.controller.setpoint.emit({self.parent.title: self.target_value})
 
     def move_rel(self, position: DataActuator):
-        """
-        """
+        """ """
         position = self.check_bound(self.current_value + position) - self.current_value
-        self.target_position = position + self.current_value
+        self.target_value = position + self.current_value
 
-        self.controller.setpoint.emit({self.parent.title: self.target_position})
+        self.controller.setpoint.emit({self.parent.title: self.target_value})
         self.poll_moving()
 
     def move_home(self):
-        """
-        """
-        self.emit_status(ThreadCommand('Update_Status', ['Move Home not implemented']))
+        """ """
+        self.emit_status(ThreadCommand("Update_Status", ["Move Home not implemented"]))
 
     def stop_motion(self):
         """
-          Call the specific move_done function (depending on the hardware).
+        Call the specific move_done function (depending on the hardware).
 
-          See Also
-          --------
-          move_done
+        See Also
+        --------
+        move_done
         """
         self.move_done()