Working simulation.

src/quackseq/spectrometer/simulator.py

@@ -0,0 +1,17 @@
+from quackseq.spectrometer.spectrometer import Spectrometer
+
+from .simulator_model import SimulatorModel
+from .simulator_controller import SimulatorController
+
+class Simulator(Spectrometer):
+
+    def __init__(self):
+        self.model = SimulatorModel()
+        self.controller = SimulatorController(self.model)
+
+    def run_sequence(self, sequence):
+        result =self.controller.run_sequence(sequence)
+        return result
+
+    def set_averages(self, value: int):
+        self.model.average = value

src/quackseq/spectrometer/simulator_controller.py

@@ -0,0 +1,354 @@
+"""The controller module for the simulator spectrometer."""
+
+import logging
+from datetime import datetime
+import numpy as np
+
+from quackseq.spectrometer.spectrometer_controller import SpectrometerController
+from quackseq.measurement import Measurement
+from quackseq.pulseparameters import TXPulse, RXReadout
+from quackseq.pulsesequence import QuackSequence
+
+from nqr_blochsimulator.classes.pulse import PulseArray
+from nqr_blochsimulator.classes.sample import Sample
+from nqr_blochsimulator.classes.simulation import Simulation
+
+logger = logging.getLogger(__name__)
+
+
+class SimulatorController(SpectrometerController):
+    """The controller class for the nqrduck simulator module."""
+
+    def __init__(self, model):
+        """Initializes the SimulatorController."""
+        super().__init__()
+        self.model = model
+
+    def run_sequence(self, sequence: QuackSequence) -> None:
+        """This method  is called when the start_measurement signal is received from the core.
+
+        It will becalled if the simulator is the  active  spectrometer.
+        This will start the simulation based on the settings and the pulse sequence.
+        """
+        logger.debug("Starting simulation")
+        sample = self.get_sample_from_settings()
+        logger.debug("Sample: %s", sample.name)
+
+        dwell_time = self.calculate_dwelltime(sequence)
+        logger.debug("Dwell time: %s", dwell_time)
+
+        try:
+            pulse_array = self.translate_pulse_sequence(sequence, dwell_time)
+        except AttributeError:
+            logger.warning("Could not translate pulse sequence")
+            return
+
+        simulation = self.get_simulation(sample, pulse_array)
+
+        result = simulation.simulate()
+
+        tdx = (
+            np.linspace(0, float(self.calculate_simulation_length(sequence)), len(result)) * 1e6
+        )
+
+        rx_begin, rx_stop = self.translate_rx_event(sequence)
+        # If we have a RX event, we need to cut the result to the RX event
+        if rx_begin and rx_stop:
+            evidx = np.where((tdx > rx_begin) & (tdx < rx_stop))[0]
+            tdx = tdx[evidx]
+            result = result[evidx]
+
+        # Measurement name date + module + target frequency + averages + sequence name
+        name = f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S')} - Simulator - {self.model.target_frequency / 1e6} MHz - {self.model.averages} averages - {sequence.name}"
+        logger.debug(f"Measurement name: {name}")
+
+        measurement_data = Measurement(
+            name,
+            tdx,
+            result / simulation.averages,
+            sample.resonant_frequency,
+            # frequency_shift=self.module.model.if_frequency,
+        )
+
+        return measurement_data
+
+    def get_sample_from_settings(self) -> Sample:
+        """This method creates a sample object based on the settings in the model.
+
+        Returns:
+            Sample: The sample object created from the settings.
+        """
+        model = self.model
+        atom_density = None
+        sample_volume = None
+        sample_length = None
+        sample_diameter = None
+
+        for samplesetting in model.settings[self.model.SAMPLE]:
+            logger.debug("Sample setting: %s", samplesetting.name)
+
+            if samplesetting.name == model.NAME:
+                name = samplesetting.value
+            elif samplesetting.name == model.DENSITY:
+                density = float(samplesetting.value)
+            elif samplesetting.name == model.MOLAR_MASS:
+                molar_mass = float(samplesetting.value)
+            elif samplesetting.name == model.RESONANT_FREQUENCY:
+                resonant_frequency = float(samplesetting.value)
+            elif samplesetting.name == model.GAMMA:
+                gamma = float(samplesetting.value)
+            elif samplesetting.name == model.NUCLEAR_SPIN:
+                nuclear_spin = float(samplesetting.value)
+            elif samplesetting.name == model.SPIN_FACTOR:
+                spin_factor = float(samplesetting.value)
+            elif samplesetting.name == model.POWDER_FACTOR:
+                powder_factor = float(samplesetting.value)
+            elif samplesetting.name == model.FILLING_FACTOR:
+                filling_factor = float(samplesetting.value)
+            elif samplesetting.name == model.T1:
+                T1 = float(samplesetting.value)
+            elif samplesetting.name == model.T2:
+                T2 = float(samplesetting.value)
+            elif samplesetting.name == model.T2_STAR:
+                T2_star = float(samplesetting.value)
+            elif samplesetting.name == model.ATOM_DENSITY:
+                atom_density = float(samplesetting.value)
+            elif samplesetting.name == model.SAMPLE_VOLUME:
+                sample_volume = float(samplesetting.value)
+            elif samplesetting.name == model.SAMPLE_LENGTH:
+                sample_length = float(samplesetting.value)
+            elif samplesetting.name == model.SAMPLE_DIAMETER:
+                sample_diameter = float(samplesetting.value)
+            else:
+                logger.warning("Unknown sample setting: %s", samplesetting.name)
+                self.module.nqrduck_signal.emit(
+                    "notification",
+                    ["Error", "Unknown sample setting: " + samplesetting.name],
+                )
+                return None
+
+        sample = Sample(
+            name=name,
+            density=density,
+            molar_mass=molar_mass,
+            resonant_frequency=resonant_frequency,
+            gamma=gamma,
+            nuclear_spin=nuclear_spin,
+            spin_factor=spin_factor,
+            powder_factor=powder_factor,
+            filling_factor=filling_factor,
+            T1=T1,
+            T2=T2,
+            T2_star=T2_star,
+            atom_density=atom_density,
+            sample_volume=sample_volume,
+            sample_length=sample_length,
+            sample_diameter=sample_diameter,
+        )
+        return sample
+
+    def translate_pulse_sequence(self,  sequence : QuackSequence, dwell_time: float) -> PulseArray:
+        """This method translates the pulse sequence from the core to a PulseArray object needed for the simulation.
+
+        Args:
+            sequence (QuackSequence): The pulse sequence from the core.
+            dwell_time (float): The dwell time in seconds.
+
+        Returns:
+            PulseArray: The pulse sequence translated to a PulseArray object.
+        """
+        events = sequence.events
+
+        amplitude_array = list()
+        for event in events:
+            logger.debug("Event %s has parameters: %s", event.name, event.parameters)
+            for parameter in event.parameters.values():
+                logger.debug(
+                    "Parameter %s has options: %s", parameter.name, parameter.options
+                )
+
+                if (
+                    parameter.name == sequence.TX_PULSE
+                    and parameter.get_option_by_name(TXPulse.RELATIVE_AMPLITUDE).value
+                    > 0
+                ):
+                    logger.debug(f"Adding pulse: {event.duration} s")
+                    # If we have a pulse, we need to add it to the pulse array
+                    pulse_shape = parameter.get_option_by_name(
+                        TXPulse.TX_PULSE_SHAPE
+                    ).value
+                    pulse_amplitude = abs(
+                        pulse_shape.get_pulse_amplitude(
+                            event.duration, resolution=dwell_time
+                        )
+                    )
+
+                    amplitude_array.append(pulse_amplitude)
+                elif (
+                    parameter.name == sequence.TX_PULSE
+                    and parameter.get_option_by_name(TXPulse.RELATIVE_AMPLITUDE).value
+                    == 0
+                ):
+                    # If we have a wait, we need to add it to the pulse array
+                    amplitude_array.append(np.zeros(int(event.duration / dwell_time)))
+
+        amplitude_array = np.concatenate(amplitude_array)
+
+        # This has not yet been implemented right now the phase is always 0
+        phase_array = np.zeros(len(amplitude_array))
+
+        pulse_array = PulseArray(
+            pulseamplitude=amplitude_array,
+            pulsephase=phase_array,
+            dwell_time=float(dwell_time),
+        )
+
+        return pulse_array
+
+    def get_simulation(self, sample: Sample, pulse_array: PulseArray) -> Simulation:
+        """This method creates a simulation object based on the settings and the pulse sequence.
+
+        Args:
+            sample (Sample): The sample object created from the settings.
+            pulse_array (PulseArray): The pulse sequence translated to a PulseArray object.
+
+        Returns:
+            Simulation: The simulation object created from the settings and the pulse sequence.
+        """
+        model = self.model
+
+        # noise = float(model.get_setting_by_name(model.NOISE).value)
+        simulation = Simulation(
+            sample=sample,
+            pulse=pulse_array,
+            number_isochromats=int(
+                model.get_setting_by_name(model.NUMBER_ISOCHROMATS).value
+            ),
+            initial_magnetization=float(
+                model.get_setting_by_name(model.INITIAL_MAGNETIZATION).value
+            ),
+            gradient=float(model.get_setting_by_name(model.GRADIENT).value),
+            noise=float(model.get_setting_by_name(model.NOISE).value),
+            length_coil=float(model.get_setting_by_name(model.LENGTH_COIL).value),
+            diameter_coil=float(model.get_setting_by_name(model.DIAMETER_COIL).value),
+            number_turns=float(model.get_setting_by_name(model.NUMBER_TURNS).value),
+            q_factor_transmit=float(
+                model.get_setting_by_name(model.Q_FACTOR_TRANSMIT).value
+            ),
+            q_factor_receive=float(
+                model.get_setting_by_name(model.Q_FACTOR_RECEIVE).value
+            ),
+            power_amplifier_power=float(
+                model.get_setting_by_name(model.POWER_AMPLIFIER_POWER).value
+            ),
+            gain=float(model.get_setting_by_name(model.GAIN).value),
+            temperature=float(model.get_setting_by_name(model.TEMPERATURE).value),
+            averages=int(model.averages),
+            loss_TX=float(model.get_setting_by_name(model.LOSS_TX).value),
+            loss_RX=float(model.get_setting_by_name(model.LOSS_RX).value),
+            conversion_factor=float(
+                model.get_setting_by_name(model.CONVERSION_FACTOR).value
+            ),
+        )
+        return simulation
+
+    def calculate_dwelltime(self, sequence : QuackSequence) -> float:
+        """This method calculates the dwell time based on the settings and the pulse sequence.
+
+        Returns:
+            float: The dwell time in seconds.
+        """
+        n_points = int(
+            self.model.get_setting_by_name(self.model.NUMBER_POINTS).value
+        )
+        simulation_length = self.calculate_simulation_length(sequence)
+        dwell_time = simulation_length / n_points
+        return dwell_time
+
+    def calculate_simulation_length(self, sequence : QuackSequence) -> float:
+        """This method calculates the simulation length based on the settings and the pulse sequence.
+
+        Returns:
+            float: The simulation length in seconds.
+        """
+        events = sequence.events
+        simulation_length = 0
+        for event in events:
+            simulation_length += event.duration
+        return simulation_length
+
+    def translate_rx_event(self, sequence : QuackSequence) -> tuple:
+        """This method translates the RX event of the pulse sequence to the limr object.
+
+        Returns:
+        tuple: A tuple containing the start and stop time of the RX event in µs
+        """
+        # This is a correction factor for the RX event. The offset of the first pulse is 2.2µs longer than from the specified samples.
+        events =  sequence.events
+
+        previous_events_duration = 0
+        # offset = 0
+        rx_duration = 0
+        for event in events:
+            logger.debug("Event %s has parameters: %s", event.name, event.parameters)
+            for parameter in event.parameters.values():
+                logger.debug(
+                    "Parameter %s has options: %s", parameter.name, parameter.options
+                )
+
+                if (
+                    parameter.name == sequence.RX_READOUT
+                    and parameter.get_option_by_name(RXReadout.RX).value
+                ):
+                    # Get the length of all previous events
+                    previous_events = events[: events.index(event)]
+                    previous_events_duration = sum(
+                        [event.duration for event in previous_events]
+                    )
+                    rx_duration = event.duration
+
+        rx_begin = float(previous_events_duration)
+        if rx_duration:
+            rx_stop = rx_begin + float(rx_duration)
+            return rx_begin * 1e6, rx_stop * 1e6
+
+        else:
+            return None, None
+
+    def set_frequency(self, value: str) -> None:
+        """This method is called when the set_frequency signal is received from the core.
+
+        For the simulator this just prints a  warning that the simulator is selected.
+
+        Args:
+            value (str) : The new frequency in MHz.
+        """
+        logger.debug("Setting frequency to: %s", value)
+        try:
+            self.module.model.target_frequency = float(value)
+            logger.debug("Successfully set frequency to: %s", value)
+        except ValueError:
+            logger.warning("Could not set frequency to: %s", value)
+            self.module.nqrduck_signal.emit(
+                "notification", ["Error", "Could not set frequency to: " + value]
+            )
+            self.module.nqrduck_signal.emit("failure_set_frequency", value)
+
+    def set_averages(self, value: str) -> None:
+        """This method is called when the set_averages signal is received from the core.
+
+        It sets the averages in the model used for the simulation.
+
+        Args:
+            value (str): The value to set the averages to.
+        """
+        logger.debug("Setting averages to: %s", value)
+        try:
+            self.module.model.averages = int(value)
+            logger.debug("Successfully set averages to: %s", value)
+        except ValueError:
+            logger.warning("Could not set averages to: %s", value)
+            self.module.nqrduck_signal.emit(
+                "notification", ["Error", "Could not set averages to: " + value]
+            )
+            self.module.nqrduck_signal.emit("failure_set_averages", value)

src/quackseq/spectrometer/simulator_model.py

@@ -0,0 +1,327 @@
+"""The model module for the simulator spectrometer."""
+
+import logging
+from quackseq.spectrometer.spectrometer_model import SpectrometerModel
+from quackseq.spectrometer.spectrometer_settings import IntSetting, FloatSetting, StringSetting
+from quackseq.pulseparameters import TXPulse, RXReadout
+
+logger = logging.getLogger(__name__)
+
+
+class SimulatorModel(SpectrometerModel):
+    """Model class for the simulator spectrometer."""
+
+    # Simulation settings
+    NUMBER_POINTS = "N. simulation points"
+    NUMBER_ISOCHROMATS = "N. of isochromats"
+    INITIAL_MAGNETIZATION = "Initial magnetization"
+    GRADIENT = "Gradient (mT/m))"
+    NOISE = "Noise (uV)"
+
+    # Hardware settings
+    LENGTH_COIL = "Length coil (m)"
+    DIAMETER_COIL = "Diameter coil (m)"
+    NUMBER_TURNS = "Number turns"
+    Q_FACTOR_TRANSMIT = "Q factor Transmit"
+    Q_FACTOR_RECEIVE = "Q factor Receive"
+    POWER_AMPLIFIER_POWER = "PA power (W)"
+    GAIN = "Gain"
+    TEMPERATURE = "Temperature (K)"
+    AVERAGES = "Averages"
+    LOSS_TX = "Loss TX (dB)"
+    LOSS_RX = "Loss RX (dB)"
+    CONVERSION_FACTOR = "Conversion factor"
+
+    # Sample settings, this will  be done in a separate module later on
+    NAME = "Name"
+    DENSITY = "Density (g/cm^3)"
+    MOLAR_MASS = "Molar mass (g/mol)"
+    RESONANT_FREQUENCY = "Resonant freq. (Hz)"
+    GAMMA = "Gamma (Hz/T)"
+    NUCLEAR_SPIN = "Nuclear spin"
+    SPIN_FACTOR = "Spin factor"
+    POWDER_FACTOR = "Powder factor"
+    FILLING_FACTOR = "Filling factor"
+    T1 = "T1 (s)"
+    T2 = "T2 (s)"
+    T2_STAR = "T2* (s)"
+    ATOM_DENSITY = "Atom density (1/cm^3)"
+    SAMPLE_VOLUME = "Sample volume (m^3)"
+    SAMPLE_LENGTH = "Sample length (m)"
+    SAMPLE_DIAMETER = "Sample diameter (m)"
+
+    # Categories of the settings
+    SIMULATION = "Simulation"
+    HARDWARE = "Hardware"
+    EXPERIMENTAL_Setup = "Experimental Setup"
+    SAMPLE = "Sample"
+
+    def __init__(self):
+        """Initializes the SimulatorModel."""
+        super().__init__()
+
+        # Simulation settings
+        number_of_points_setting = IntSetting(
+            self.NUMBER_POINTS,
+            8192,
+            "Number of points used for the simulation. This influences the dwell time in combination with the total event simulation given by the pulse sequence.",
+            min_value=0,
+        )
+        self.add_setting(
+            number_of_points_setting,
+            self.SIMULATION,
+        )
+
+        number_of_isochromats_setting = IntSetting(
+            self.NUMBER_ISOCHROMATS,
+            1000,
+            "Number of isochromats used for the simulation. This influences the computation time.",
+            min_value=0,
+            max_value=10000,
+        )
+        self.add_setting(number_of_isochromats_setting, self.SIMULATION)
+
+        initial_magnetization_setting = FloatSetting(
+            self.INITIAL_MAGNETIZATION,
+            1,
+            "Initial magnetization",
+            min_value=0,
+        )
+        self.add_setting(initial_magnetization_setting, self.SIMULATION)
+
+        # This doesn't really do anything yet
+        gradient_setting = FloatSetting(
+            self.GRADIENT,
+            1,
+            "Gradient",
+        )
+        self.add_setting(gradient_setting, self.SIMULATION)
+
+        noise_setting = FloatSetting(
+            self.NOISE,
+            2,
+            "Adds a specified level of random noise to the simulation to mimic real-world signal variations.",
+            min_value=0,
+            max_value=100,
+        )
+        self.add_setting(noise_setting, self.SIMULATION)
+
+        # Hardware settings
+        coil_length_setting = FloatSetting(
+            self.LENGTH_COIL,
+            30e-3,
+            "The length of the sample coil within the hardware setup.",
+            min_value=1e-3,
+        )
+        self.add_setting(coil_length_setting, self.HARDWARE)
+
+        coil_diameter_setting = FloatSetting(
+            self.DIAMETER_COIL,
+            8e-3,
+            "The diameter of the sample coil.",
+            min_value=1e-3,
+        )
+        self.add_setting(coil_diameter_setting, self.HARDWARE)
+
+        number_turns_setting = FloatSetting(
+            self.NUMBER_TURNS,
+            8,
+            "The total number of turns of the sample coil.",
+            min_value=1,
+        )
+        self.add_setting(number_turns_setting, self.HARDWARE)
+
+        q_factor_transmit_setting = FloatSetting(
+            self.Q_FACTOR_TRANSMIT,
+            80,
+            "The quality factor of the transmit path, which has an effect on the field strength for excitation.",
+            min_value=1,
+        )
+        self.add_setting(q_factor_transmit_setting, self.HARDWARE)
+
+        q_factor_receive_setting = FloatSetting(
+            self.Q_FACTOR_RECEIVE,
+            80,
+            "The quality factor of the receive path, which has an effect on the final SNR.",
+            min_value=1,
+        )
+        self.add_setting(q_factor_receive_setting, self.HARDWARE)
+
+        power_amplifier_power_setting = FloatSetting(
+            self.POWER_AMPLIFIER_POWER,
+            110,
+            "The power output capability of the power amplifier, determines the strength of pulses that can be generated.",
+            min_value=0.1,
+        )
+        self.add_setting(power_amplifier_power_setting, self.HARDWARE)
+
+        gain_setting = FloatSetting(
+            self.GAIN,
+            6000,
+            "The amplification factor of the receiver chain, impacting the final measured signal amplitude.",
+            min_value=0.1,
+        )
+        self.add_setting(gain_setting, self.HARDWARE)
+
+        temperature_setting = FloatSetting(
+            self.TEMPERATURE,
+            300,
+            "The absolute temperature during the experiment. This influences the SNR of the measurement.",
+            min_value=0.1,
+            max_value=400,
+        )
+        self.add_setting(temperature_setting, self.EXPERIMENTAL_Setup)
+
+        loss_tx_setting = FloatSetting(
+            self.LOSS_TX,
+            25,
+            "The signal loss occurring in the transmission path, affecting the effective RF pulse power.",
+            min_value=0.1,
+            max_value=60,
+        )
+        self.add_setting(loss_tx_setting, self.EXPERIMENTAL_Setup)
+
+        loss_rx_setting = FloatSetting(
+            self.LOSS_RX,
+            25,
+            "The signal loss in the reception path, which can reduce the signal that is ultimately detected.",
+            min_value=0.1,
+            max_value=60,
+        )
+        self.add_setting(loss_rx_setting, self.EXPERIMENTAL_Setup)
+
+        conversion_factor_setting = FloatSetting(
+            self.CONVERSION_FACTOR,
+            2884,
+            "Conversion factor  (spectrometer units / V)",
+        )
+        self.add_setting(
+            conversion_factor_setting,
+            self.EXPERIMENTAL_Setup,
+        )  # Conversion factor for the LimeSDR based spectrometer
+
+        # Sample settings
+        sample_name_setting = StringSetting(
+            self.NAME,
+            "BiPh3",
+            "The name of the sample.",
+        )
+        self.add_setting(sample_name_setting, self.SAMPLE)
+
+        density_setting = FloatSetting(
+            self.DENSITY,
+            1.585e6,
+            "The density of the sample. This is used to calculate the number of spins in the sample volume.",
+            min_value=0.1,
+        )
+        self.add_setting(density_setting, self.SAMPLE)
+
+        molar_mass_setting = FloatSetting(
+            self.MOLAR_MASS,
+            440.3,
+            "The molar mass of the sample. This is used to calculate the number of spins in the sample volume.",
+            min_value=0.1,
+        )
+        self.add_setting(molar_mass_setting, self.SAMPLE)
+
+        resonant_frequency_setting = FloatSetting(
+            self.RESONANT_FREQUENCY,
+            83.56e6,
+            "The resonant frequency of the observed transition.",
+            min_value=1e5,
+        )
+        self.add_setting(resonant_frequency_setting, self.SAMPLE)
+
+        gamma_setting = FloatSetting(
+            self.GAMMA,
+            4.342e7,
+            "The gyromagnetic ratio of the sample’s nuclei.",
+            min_value=0,
+        )
+        self.add_setting(gamma_setting, self.SAMPLE)
+
+        # This could be updated to a selection setting
+        nuclear_spin_setting = FloatSetting(
+            self.NUCLEAR_SPIN,
+            9 / 2,
+            "The nuclear spin of the sample’s nuclei.",
+            min_value=0,
+        )
+        self.add_setting(nuclear_spin_setting, self.SAMPLE)
+
+        spin_factor_setting = FloatSetting(
+            self.SPIN_FACTOR,
+            2,
+            "The spin factor represents the scaling coefficient for observable nuclear spin transitions along the x-axis, derived from the Pauli I x 0 -matrix elements.",
+            min_value=0,
+        )
+        self.add_setting(spin_factor_setting, self.SAMPLE)
+
+        powder_factor_setting = FloatSetting(
+            self.POWDER_FACTOR,
+            0.75,
+            "A factor representing the crystallinity of the solid sample. A value of 0.75 corresponds to a powder sample.",
+            min_value=0,
+            max_value=1,
+        )
+        self.add_setting(powder_factor_setting, self.SAMPLE)
+
+        filling_factor_setting = FloatSetting(
+            self.FILLING_FACTOR,
+            0.7,
+            "The ratio of the sample volume that occupies the coil’s sensitive volume.",
+            min_value=0,
+            max_value=1,
+        )
+        self.add_setting(filling_factor_setting, self.SAMPLE)
+
+        t1_setting = FloatSetting(
+            self.T1,
+            83.5e-5,
+            "The longitudinal or spin-lattice relaxation time of the sample, influencing signal recovery between pulses.",
+            min_value=1e-6,
+        )
+        self.add_setting(t1_setting, self.SAMPLE)
+
+        t2_setting = FloatSetting(
+            self.T2,
+            396e-6,
+            "The transverse or spin-spin relaxation time, determining the rate at which spins dephase and the signal decays in the xy plane",
+            min_value=1e-6,
+        )
+        self.add_setting(t2_setting, self.SAMPLE)
+
+        t2_star_setting = FloatSetting(
+            self.T2_STAR,
+            50e-6,
+            "The effective transverse relaxation time, incorporating effects of EFG inhomogeneities and other dephasing factors.",
+            min_value=1e-6,
+        )
+        self.add_setting(t2_star_setting, self.SAMPLE)
+
+        self.averages = 1
+        self.target_frequency = 100e6
+
+    @property
+    def averages(self):
+        """The number of averages used for the simulation.
+
+        More averages improve the signal-to-noise ratio of the simulated signal.
+        """
+        return self._averages
+
+    @averages.setter
+    def averages(self, value):
+        self._averages = value
+
+    @property
+    def target_frequency(self):
+        """The target frequency for the simulation.
+
+        Doesn't do anything at the moment.
+        """
+        return self._target_frequency
+
+    @target_frequency.setter
+    def target_frequency(self, value):
+        self._target_frequency = value

src/quackseq/spectrometer/spectrometer.py

@@ -0,0 +1,39 @@
+class Spectrometer():
+    """Base class for spectrometers.
+
+    This class should be inherited by all spectrometers.
+    The spectrometers then need to implement the methods of this class.
+    """
+
+    def run_sequence(self, sequence):
+        """Starts the measurement.
+
+        This method should be called when the measurement is started.
+        """
+        raise NotImplementedError
+
+    def set_frequency(self, value : float):
+        """Sets the frequency of the spectrometer."""
+        raise NotImplementedError
+
+    def set_averages(self, value : int):
+        """Sets the number of averages."""
+        raise NotImplementedError
+    
+    @property
+    def controller(self):
+        """The controller of the spectrometer."""
+        return self._controller
+    
+    @controller.setter
+    def controller(self, controller):
+        self._controller = controller
+
+    @property
+    def model(self):
+        """The model of the spectrometer."""
+        return self._model
+    
+    @model.setter
+    def model(self, model):
+        self._model = model

src/quackseq/spectrometer/spectrometer_controller.py

@@ -0,0 +1,19 @@
+"""Base class for all spectrometer controllers."""
+
+class SpectrometerController():
+    """The base class for all spectrometer controllers."""
+
+    def run_sequence(self, sequence):
+        """Starts the measurement.
+
+        This method should be called when the measurement is started.
+        """
+        raise NotImplementedError
+
+    def set_frequency(self, value : float):
+        """Sets the frequency of the spectrometer."""
+        raise NotImplementedError
+
+    def set_averages(self, value : int):
+        """Sets the number of averages."""
+        raise NotImplementedError

src/quackseq/spectrometer/spectrometer_model.py

@@ -2,7 +2,7 @@
 
 import logging
 from collections import OrderedDict
-from quackseq.spectrometer.spectrometer_setting import Setting
+from quackseq.spectrometer.spectrometer_settings import Setting
 
 logger = logging.getLogger(__name__)
 
@@ -12,22 +12,14 @@ class SpectrometerModel():
 
     It contains the settings and pulse parameters of the spectrometer.
 
-    Args:
-        module (Module) : The module that the spectrometer is connected to
-
     Attributes:
         settings (OrderedDict) : The settings of the spectrometer
     """
 
     settings: OrderedDict
 
-    def __init__(self, module):
+    def __init__(self):
-        """Initializes the spectrometer model.
+        """Initializes the spectrometer model."""
-
-        Args:
-            module (Module) : The module that the spectrometer is connected to
-        """
-        super().__init__(module)
         self.settings = OrderedDict()
 
     def add_setting(self, setting: Setting, category: str) -> None:

src/quackseq/spectrometer/spectrometer_settings.py

@@ -109,7 +109,6 @@ class FloatSetting(NumericalSetting):
     def value(self, value):
         logger.debug(f"Setting {self.name} to {value}")
         self._value = float(value)
-        self.settings_changed.emit()
 
 
 class IntSetting(NumericalSetting):
@@ -130,10 +129,8 @@ class IntSetting(NumericalSetting):
         description: str,
         min_value=None,
         max_value=None,
-        spin_box: tuple = (False, False),
     ) -> None:
         """Create a new int setting."""
-        self.spin_box = spin_box
         super().__init__(name, description, default, min_value, max_value)
 
     @property

tests/simulator.py

@@ -1,8 +1,13 @@
 # Dummy test to communicate the structure
+import logging
+import matplotlib.pyplot as plt
+
 from quackseq.pulsesequence import QuackSequence
 from quackseq.event import Event
 from quackseq.functions import RectFunction
+from quackseq.spectrometer.simulator import Simulator
 
+logging.basicConfig(level=logging.DEBUG)
 
 seq = QuackSequence("test")
 
@@ -17,11 +22,11 @@ rect = RectFunction()
 
 seq.set_tx_shape(tx, rect)
 
-blank = Event("blank", "10u", seq)
+blank = Event("blank", "3u", seq)
 
 seq.add_event(blank)
 
-rx = Event("rx", "10u", seq)
+rx = Event("rx", "50u", seq)
 #rx.set_rx_phase(0)
 
 seq.set_rx(rx, True)
@@ -36,11 +41,12 @@ json = seq.to_json()
 
 print(json)
 
-#sim = Simulator()
+sim = Simulator()
 
-#sim.set_averages(100)
+sim.set_averages(100)
 
 # Returns the data at the  RX event
-#result = sim.run(seq)
+result = sim.run_sequence(seq)
 
-#result.plot()
+plt.plot(result.tdx, abs(result.tdy))
+plt.show()