diff --git a/src/nqrduck_spectrometer_simulator/controller.py b/src/nqrduck_spectrometer_simulator/controller.py index 6d63d3d..f987ab8 100644 --- a/src/nqrduck_spectrometer_simulator/controller.py +++ b/src/nqrduck_spectrometer_simulator/controller.py @@ -1,19 +1,13 @@ """The controller module for the simulator spectrometer.""" import logging -from datetime import datetime -import numpy as np from nqrduck_spectrometer.base_spectrometer_controller import BaseSpectrometerController -from nqrduck_spectrometer.measurement import Measurement -from nqrduck_spectrometer.pulseparameters import TXPulse, RXReadout -from nqr_blochsimulator.classes.pulse import PulseArray -from nqr_blochsimulator.classes.sample import Sample -from nqr_blochsimulator.classes.simulation import Simulation +from quackseq_simulator.simulator import Simulator logger = logging.getLogger(__name__) -class SimulatorController(BaseSpectrometerController): +class DuckSimulatorController(BaseSpectrometerController): """The controller class for the nqrduck simulator module.""" def __init__(self, module): @@ -21,301 +15,24 @@ class SimulatorController(BaseSpectrometerController): super().__init__(module) def start_measurement(self): - """This method is called when the start_measurement signal is received from the core. + """This method is called when the start_measurement signal is received.""" + sequence = self.module.model.pulse_programmer.model.pulse_sequence - 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) + simulator = Simulator() - dwell_time = self.calculate_dwelltime() - logger.debug("Dwell time: %s", dwell_time) + simulator.model = self.module.model.quackseq_model - try: - pulse_array = self.translate_pulse_sequence(dwell_time) - except ValueError: - logger.warning("Could not translate pulse sequence") - self.module.nqrduck_signal.emit( - "measurement_error", - "Could not translate pulse sequence. Did you configure one?", - ) - return + simulator.model.target_frequency = self.module.model.target_frequency + simulator.model.averages = self.module.model.averages - simulation = self.get_simulation(sample, pulse_array) - - result = simulation.simulate() - - tdx = ( - np.linspace(0, float(self.calculate_simulation_length()), len(result)) * 1e6 - ) - - rx_begin, rx_stop = self.translate_rx_event() - # 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.module.model.target_frequency / 1e6} MHz - {self.module.model.averages} averages - {self.module.model.pulse_programmer.model.pulse_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, - ) + measurement_data = simulator.run_sequence(sequence) # Emit the data to the nqrduck core logger.debug("Emitting measurement data") self.module.nqrduck_signal.emit("statusbar_message", "Finished Simulation") self.module.nqrduck_signal.emit("measurement_data", 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.module.model - atom_density = None - sample_volume = None - sample_length = None - sample_diameter = None - - for samplesetting in model.settings[self.module.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, dwell_time: float) -> PulseArray: - """This method translates the pulse sequence from the core to a PulseArray object needed for the simulation. - - Args: - dwell_time (float): The dwell time in seconds. - - Returns: - PulseArray: The pulse sequence translated to a PulseArray object. - """ - events = self.module.model.pulse_programmer.model.pulse_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 == self.module.model.TX - and parameter.get_option_by_name(TXPulse.RELATIVE_AMPLITUDE).value - > 0 - ): - # 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 == self.module.model.TX - 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.module.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) -> 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.module.model.get_setting_by_name(self.module.model.NUMBER_POINTS).value - ) - simulation_length = self.calculate_simulation_length() - dwell_time = simulation_length / n_points - return dwell_time - - def calculate_simulation_length(self) -> float: - """This method calculates the simulation length based on the settings and the pulse sequence. - - Returns: - float: The simulation length in seconds. - """ - events = self.module.model.pulse_programmer.model.pulse_sequence.events - simulation_length = 0 - for event in events: - simulation_length += event.duration - return simulation_length - - def translate_rx_event(self) -> 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 = self.module.model.pulse_programmer.model.pulse_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 == self.module.model.RX - 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. diff --git a/src/nqrduck_spectrometer_simulator/model.py b/src/nqrduck_spectrometer_simulator/model.py index d74e2f8..3bfcaf2 100644 --- a/src/nqrduck_spectrometer_simulator/model.py +++ b/src/nqrduck_spectrometer_simulator/model.py @@ -2,328 +2,23 @@ import logging from nqrduck_spectrometer.base_spectrometer_model import BaseSpectrometerModel -from nqrduck_spectrometer.pulseparameters import TXPulse, RXReadout -from nqrduck_spectrometer.settings import ( - FloatSetting, - IntSetting, - StringSetting, -) +from quackseq_simulator.simulator_model import SimulatorModel + logger = logging.getLogger(__name__) -class SimulatorModel(BaseSpectrometerModel): - """Model class for the simulator spectrometer.""" +class DuckSimulatorModel(BaseSpectrometerModel): - # 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" - - # Pulse parameter constants - TX = "TX" - RX = "RX" def __init__(self, module): """Initializes the SimulatorModel.""" super().__init__(module) - # 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, - spin_box=(True, False), - ) - self.add_setting( - number_of_points_setting, - self.SIMULATION, - ) + self.quackseq_model = SimulatorModel() + self.visualize_settings() - 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, - spin_box=(True, False), - ) - self.add_setting(number_of_isochromats_setting, self.SIMULATION) - - initial_magnetization_setting = FloatSetting( - self.INITIAL_MAGNETIZATION, - 1, - "Initial magnetization", - min_value=0, - spin_box=(True, False), - ) - self.add_setting(initial_magnetization_setting, self.SIMULATION) - - # This doesn't really do anything yet - gradient_setting = FloatSetting( - self.GRADIENT, - 1, - "Gradient", - spin_box=(True, False), - ) - 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, - spin_box=(True, False), - ) - 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, - spin_box=(True, True), - ) - 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, - spin_box=(True, True), - ) - 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, - spin_box=(True, True), - ) - 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, - spin_box=(True, False), - ) - 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, - spin_box=(True, False), - ) - 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) - - # Pulse parameter options - self.add_pulse_parameter_option(self.TX, TXPulse) - # self.add_pulse_parameter_option(self.GATE, Gate) - self.add_pulse_parameter_option(self.RX, RXReadout) - - self.averages = 1 - self.target_frequency = 100e6 + self.quackseq_visuals # Try to load the pulse programmer module try: @@ -331,7 +26,7 @@ class SimulatorModel(BaseSpectrometerModel): self.pulse_programmer = pulse_programmer logger.debug("Pulse programmer found.") - self.pulse_programmer.controller.on_loading(self.pulse_parameter_options) + self.pulse_programmer.controller.on_loading() except ImportError: logger.warning("No pulse programmer found.") diff --git a/src/nqrduck_spectrometer_simulator/simulator.py b/src/nqrduck_spectrometer_simulator/simulator.py index 84d7936..c309c49 100644 --- a/src/nqrduck_spectrometer_simulator/simulator.py +++ b/src/nqrduck_spectrometer_simulator/simulator.py @@ -1,8 +1,8 @@ """Creation of the Simulator Spectrometer.""" from nqrduck_spectrometer.base_spectrometer import BaseSpectrometer -from .model import SimulatorModel -from .view import SimulatorView -from .controller import SimulatorController +from .model import DuckSimulatorModel +from .view import DuckSimulatorView +from .controller import DuckSimulatorController -Simulator = BaseSpectrometer(SimulatorModel, SimulatorView, SimulatorController) +Simulator = BaseSpectrometer(DuckSimulatorModel, DuckSimulatorView, DuckSimulatorController) diff --git a/src/nqrduck_spectrometer_simulator/view.py b/src/nqrduck_spectrometer_simulator/view.py index 9ba62d3..8eaaaa9 100644 --- a/src/nqrduck_spectrometer_simulator/view.py +++ b/src/nqrduck_spectrometer_simulator/view.py @@ -3,7 +3,7 @@ from nqrduck_spectrometer.base_spectrometer_view import BaseSpectrometerView -class SimulatorView(BaseSpectrometerView): +class DuckSimulatorView(BaseSpectrometerView): """The View class for the simulator module.""" def __init__(self, module):