mirror of
https://github.com/nqrduck/quackseq-simulator.git
synced 2025-01-02 18:08:07 +00:00
Updated to new setting access.
This commit is contained in:
jupfi
parent
fe458ed59e
commit
014bf53efd
4 changed files with 108 additions and 150 deletions
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@ -15,3 +15,7 @@ class Simulator(Spectrometer):
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def set_averages(self, value: int):
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self.model.average = value
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@property
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def settings(self):
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return self.model.settings
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@ -48,7 +48,10 @@ class SimulatorController(SpectrometerController):
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result = simulation.simulate()
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tdx = (
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np.linspace(0, float(self.calculate_simulation_length(sequence)), len(result)) * 1e6
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np.linspace(
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0, float(self.calculate_simulation_length(sequence)), len(result)
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)
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* 1e6
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)
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rx_begin, rx_stop = self.translate_rx_event(sequence)
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@ -84,48 +87,18 @@ class SimulatorController(SpectrometerController):
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sample_length = None
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sample_diameter = None
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for samplesetting in model.settings[self.model.SAMPLE]:
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logger.debug("Sample setting: %s", samplesetting.name)
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if samplesetting.name == model.NAME:
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name = samplesetting.value
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elif samplesetting.name == model.DENSITY:
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density = float(samplesetting.value)
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elif samplesetting.name == model.MOLAR_MASS:
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molar_mass = float(samplesetting.value)
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elif samplesetting.name == model.RESONANT_FREQUENCY:
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resonant_frequency = float(samplesetting.value)
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elif samplesetting.name == model.GAMMA:
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gamma = float(samplesetting.value)
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elif samplesetting.name == model.NUCLEAR_SPIN:
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nuclear_spin = float(samplesetting.value)
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elif samplesetting.name == model.SPIN_FACTOR:
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spin_factor = float(samplesetting.value)
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elif samplesetting.name == model.POWDER_FACTOR:
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powder_factor = float(samplesetting.value)
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elif samplesetting.name == model.FILLING_FACTOR:
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filling_factor = float(samplesetting.value)
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elif samplesetting.name == model.T1:
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T1 = float(samplesetting.value)
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elif samplesetting.name == model.T2:
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T2 = float(samplesetting.value)
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elif samplesetting.name == model.T2_STAR:
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T2_star = float(samplesetting.value)
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elif samplesetting.name == model.ATOM_DENSITY:
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atom_density = float(samplesetting.value)
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elif samplesetting.name == model.SAMPLE_VOLUME:
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sample_volume = float(samplesetting.value)
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elif samplesetting.name == model.SAMPLE_LENGTH:
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sample_length = float(samplesetting.value)
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elif samplesetting.name == model.SAMPLE_DIAMETER:
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sample_diameter = float(samplesetting.value)
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else:
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logger.warning("Unknown sample setting: %s", samplesetting.name)
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self.module.nqrduck_signal.emit(
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"notification",
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["Error", "Unknown sample setting: " + samplesetting.name],
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)
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return None
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name = model.settings.sample_name
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density = model.settings.density
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molar_mass = model.settings.molar_mass
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resonant_frequency = model.settings.resonant_frequency
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gamma = model.settings.gamma
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nuclear_spin = model.settings.nuclear_spin
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spin_factor = model.settings.spin_factor
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powder_factor = model.settings.powder_factor
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filling_factor = model.settings.filling_factor
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T1 = model.settings.T1
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T2 = model.settings.T2
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T2_star = model.settings.T2_star
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sample = Sample(
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name=name,
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@ -147,7 +120,9 @@ class SimulatorController(SpectrometerController):
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)
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return sample
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def translate_pulse_sequence(self, sequence : QuackSequence, dwell_time: float) -> PulseArray:
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def translate_pulse_sequence(
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self, sequence: QuackSequence, dwell_time: float
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) -> PulseArray:
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"""This method translates the pulse sequence from the core to a PulseArray object needed for the simulation.
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Args:
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@ -221,51 +196,39 @@ class SimulatorController(SpectrometerController):
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simulation = Simulation(
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sample=sample,
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pulse=pulse_array,
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number_isochromats=int(
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model.get_setting_by_name(model.NUMBER_ISOCHROMATS).value
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),
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initial_magnetization=float(
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model.get_setting_by_name(model.INITIAL_MAGNETIZATION).value
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),
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gradient=float(model.get_setting_by_name(model.GRADIENT).value),
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noise=float(model.get_setting_by_name(model.NOISE).value),
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length_coil=float(model.get_setting_by_name(model.LENGTH_COIL).value),
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diameter_coil=float(model.get_setting_by_name(model.DIAMETER_COIL).value),
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number_turns=float(model.get_setting_by_name(model.NUMBER_TURNS).value),
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q_factor_transmit=float(
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model.get_setting_by_name(model.Q_FACTOR_TRANSMIT).value
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),
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q_factor_receive=float(
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model.get_setting_by_name(model.Q_FACTOR_RECEIVE).value
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),
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power_amplifier_power=float(
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model.get_setting_by_name(model.POWER_AMPLIFIER_POWER).value
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),
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gain=float(model.get_setting_by_name(model.GAIN).value),
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temperature=float(model.get_setting_by_name(model.TEMPERATURE).value),
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number_isochromats=int(model.settings.number_isochromats),
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initial_magnetization=float(model.settings.initial_magnetization),
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gradient=float(model.settings.gradient),
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noise=float(model.settings.noise),
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length_coil=float(model.settings.length_coil),
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diameter_coil=float(model.settings.diameter_coil),
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number_turns=float(model.settings.number_turns),
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q_factor_transmit=float(model.settings.q_factor_transmit),
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q_factor_receive=float(model.settings.q_factor_receive),
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power_amplifier_power=float(model.settings.power_amplifier_power),
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gain=float(model.settings.gain),
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temperature=float(model.settings.temperature),
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averages=int(model.averages),
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loss_TX=float(model.get_setting_by_name(model.LOSS_TX).value),
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loss_RX=float(model.get_setting_by_name(model.LOSS_RX).value),
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conversion_factor=float(
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model.get_setting_by_name(model.CONVERSION_FACTOR).value
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),
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loss_TX=float(model.settings.loss_tx),
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loss_RX=float(model.settings.loss_rx),
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conversion_factor=float(model.settings.conversion_factor),
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)
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return simulation
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def calculate_dwelltime(self, sequence : QuackSequence) -> float:
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def calculate_dwelltime(self, sequence: QuackSequence) -> float:
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"""This method calculates the dwell time based on the settings and the pulse sequence.
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Returns:
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float: The dwell time in seconds.
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"""
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n_points = int(
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self.model.get_setting_by_name(self.model.NUMBER_POINTS).value
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self.model.get_setting_by_display_name(self.model.NUMBER_POINTS).value
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)
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simulation_length = self.calculate_simulation_length(sequence)
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dwell_time = simulation_length / n_points
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return dwell_time
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def calculate_simulation_length(self, sequence : QuackSequence) -> float:
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def calculate_simulation_length(self, sequence: QuackSequence) -> float:
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"""This method calculates the simulation length based on the settings and the pulse sequence.
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Returns:
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@ -277,7 +240,7 @@ class SimulatorController(SpectrometerController):
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simulation_length += event.duration
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return simulation_length
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def translate_rx_event(self, sequence : QuackSequence) -> tuple:
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def translate_rx_event(self, sequence: QuackSequence) -> tuple:
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"""This method translates the RX event of the pulse sequence to the limr object.
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Returns:
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@ -314,41 +277,3 @@ class SimulatorController(SpectrometerController):
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else:
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return None, None
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def set_frequency(self, value: str) -> None:
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"""This method is called when the set_frequency signal is received from the core.
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For the simulator this just prints a warning that the simulator is selected.
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Args:
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value (str) : The new frequency in MHz.
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"""
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logger.debug("Setting frequency to: %s", value)
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try:
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self.module.model.target_frequency = float(value)
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logger.debug("Successfully set frequency to: %s", value)
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except ValueError:
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logger.warning("Could not set frequency to: %s", value)
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self.module.nqrduck_signal.emit(
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"notification", ["Error", "Could not set frequency to: " + value]
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)
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self.module.nqrduck_signal.emit("failure_set_frequency", value)
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def set_averages(self, value: str) -> None:
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"""This method is called when the set_averages signal is received from the core.
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It sets the averages in the model used for the simulation.
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Args:
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value (str): The value to set the averages to.
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"""
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logger.debug("Setting averages to: %s", value)
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try:
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self.module.model.averages = int(value)
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logger.debug("Successfully set averages to: %s", value)
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except ValueError:
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logger.warning("Could not set averages to: %s", value)
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self.module.nqrduck_signal.emit(
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"notification", ["Error", "Could not set averages to: " + value]
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)
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self.module.nqrduck_signal.emit("failure_set_averages", value)
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@ -2,7 +2,11 @@
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import logging
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from quackseq.spectrometer.spectrometer_model import SpectrometerModel
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from quackseq.spectrometer.spectrometer_settings import IntSetting, FloatSetting, StringSetting
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from quackseq.spectrometer.spectrometer_settings import (
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IntSetting,
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FloatSetting,
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StringSetting,
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)
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from quackseq.pulseparameters import TXPulse, RXReadout
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logger = logging.getLogger(__name__)
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@ -33,7 +37,7 @@ class SimulatorModel(SpectrometerModel):
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CONVERSION_FACTOR = "Conversion factor"
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# Sample settings, this will be done in a separate module later on
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NAME = "Name"
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SAMPLE_NAME = "Name"
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DENSITY = "Density (g/cm^3)"
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MOLAR_MASS = "Molar mass (g/mol)"
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RESONANT_FREQUENCY = "Resonant freq. (Hz)"
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@ -63,241 +67,264 @@ class SimulatorModel(SpectrometerModel):
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# Simulation settings
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number_of_points_setting = IntSetting(
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self.NUMBER_POINTS,
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self.SIMULATION,
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8192,
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"Number of points used for the simulation. This influences the dwell time in combination with the total event simulation given by the pulse sequence.",
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min_value=0,
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)
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self.add_setting(
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"number_points",
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number_of_points_setting,
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self.SIMULATION,
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)
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number_of_isochromats_setting = IntSetting(
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self.NUMBER_ISOCHROMATS,
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self.SIMULATION,
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1000,
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"Number of isochromats used for the simulation. This influences the computation time.",
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min_value=0,
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max_value=10000,
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)
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self.add_setting(number_of_isochromats_setting, self.SIMULATION)
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self.add_setting("number_isochromats", number_of_isochromats_setting)
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initial_magnetization_setting = FloatSetting(
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self.INITIAL_MAGNETIZATION,
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self.SIMULATION,
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1,
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"Initial magnetization",
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min_value=0,
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)
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self.add_setting(initial_magnetization_setting, self.SIMULATION)
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self.add_setting("initial_magnetization", initial_magnetization_setting)
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# This doesn't really do anything yet
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gradient_setting = FloatSetting(
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self.GRADIENT,
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self.SIMULATION,
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1,
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"Gradient",
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)
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self.add_setting(gradient_setting, self.SIMULATION)
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self.add_setting("gradient", gradient_setting)
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noise_setting = FloatSetting(
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self.NOISE,
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self.SIMULATION,
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2,
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"Adds a specified level of random noise to the simulation to mimic real-world signal variations.",
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min_value=0,
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max_value=100,
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)
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self.add_setting(noise_setting, self.SIMULATION)
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self.add_setting("noise", noise_setting)
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# Hardware settings
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coil_length_setting = FloatSetting(
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self.LENGTH_COIL,
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self.HARDWARE,
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30e-3,
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"The length of the sample coil within the hardware setup.",
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min_value=1e-3,
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)
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self.add_setting(coil_length_setting, self.HARDWARE)
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self.add_setting("length_coil", coil_length_setting)
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coil_diameter_setting = FloatSetting(
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self.DIAMETER_COIL,
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self.HARDWARE,
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8e-3,
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"The diameter of the sample coil.",
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min_value=1e-3,
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)
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self.add_setting(coil_diameter_setting, self.HARDWARE)
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self.add_setting("diameter_coil", coil_diameter_setting)
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number_turns_setting = FloatSetting(
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self.NUMBER_TURNS,
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self.HARDWARE,
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8,
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"The total number of turns of the sample coil.",
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min_value=1,
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)
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self.add_setting(number_turns_setting, self.HARDWARE)
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self.add_setting("number_turns", number_turns_setting)
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q_factor_transmit_setting = FloatSetting(
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self.Q_FACTOR_TRANSMIT,
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self.HARDWARE,
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80,
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"The quality factor of the transmit path, which has an effect on the field strength for excitation.",
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min_value=1,
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)
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self.add_setting(q_factor_transmit_setting, self.HARDWARE)
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self.add_setting("q_factor_transmit", q_factor_transmit_setting)
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q_factor_receive_setting = FloatSetting(
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self.Q_FACTOR_RECEIVE,
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self.HARDWARE,
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80,
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"The quality factor of the receive path, which has an effect on the final SNR.",
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min_value=1,
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)
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self.add_setting(q_factor_receive_setting, self.HARDWARE)
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self.add_setting("q_factor_receive", q_factor_receive_setting)
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power_amplifier_power_setting = FloatSetting(
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self.POWER_AMPLIFIER_POWER,
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self.HARDWARE,
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110,
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"The power output capability of the power amplifier, determines the strength of pulses that can be generated.",
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min_value=0.1,
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)
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self.add_setting(power_amplifier_power_setting, self.HARDWARE)
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self.add_setting("power_amplifier_power", power_amplifier_power_setting)
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gain_setting = FloatSetting(
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self.GAIN,
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self.HARDWARE,
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6000,
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"The amplification factor of the receiver chain, impacting the final measured signal amplitude.",
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min_value=0.1,
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)
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self.add_setting(gain_setting, self.HARDWARE)
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self.add_setting("gain", gain_setting)
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temperature_setting = FloatSetting(
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self.TEMPERATURE,
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self.EXPERIMENTAL_Setup,
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300,
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"The absolute temperature during the experiment. This influences the SNR of the measurement.",
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min_value=0.1,
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max_value=400,
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)
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self.add_setting(temperature_setting, self.EXPERIMENTAL_Setup)
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self.add_setting("temperature", temperature_setting)
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loss_tx_setting = FloatSetting(
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self.LOSS_TX,
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self.EXPERIMENTAL_Setup,
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25,
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"The signal loss occurring in the transmission path, affecting the effective RF pulse power.",
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min_value=0.1,
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max_value=60,
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)
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self.add_setting(loss_tx_setting, self.EXPERIMENTAL_Setup)
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self.add_setting("loss_tx", loss_tx_setting)
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loss_rx_setting = FloatSetting(
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self.LOSS_RX,
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self.EXPERIMENTAL_Setup,
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25,
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"The signal loss in the reception path, which can reduce the signal that is ultimately detected.",
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min_value=0.1,
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max_value=60,
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)
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self.add_setting(loss_rx_setting, self.EXPERIMENTAL_Setup)
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self.add_setting("loss_rx", loss_rx_setting)
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conversion_factor_setting = FloatSetting(
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self.CONVERSION_FACTOR,
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self.EXPERIMENTAL_Setup,
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2884,
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"Conversion factor (spectrometer units / V)",
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)
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self.add_setting(
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conversion_factor_setting,
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self.EXPERIMENTAL_Setup,
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) # Conversion factor for the LimeSDR based spectrometer
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self.add_setting("conversion_factor", conversion_factor_setting) # Conversion factor for the LimeSDR based spectrometer
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# Sample settings
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sample_name_setting = StringSetting(
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self.NAME,
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self.SAMPLE_NAME,
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self.SAMPLE,
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"BiPh3",
|
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"The name of the sample.",
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)
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self.add_setting(sample_name_setting, self.SAMPLE)
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self.add_setting("sample_name", sample_name_setting)
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density_setting = FloatSetting(
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self.DENSITY,
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self.SAMPLE,
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1.585e6,
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"The density of the sample. This is used to calculate the number of spins in the sample volume.",
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min_value=0.1,
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)
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self.add_setting(density_setting, self.SAMPLE)
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self.add_setting("density", density_setting)
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molar_mass_setting = FloatSetting(
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self.MOLAR_MASS,
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self.SAMPLE,
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440.3,
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"The molar mass of the sample. This is used to calculate the number of spins in the sample volume.",
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min_value=0.1,
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)
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self.add_setting(molar_mass_setting, self.SAMPLE)
|
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self.add_setting("molar_mass", molar_mass_setting)
|
||||
|
||||
resonant_frequency_setting = FloatSetting(
|
||||
self.RESONANT_FREQUENCY,
|
||||
self.SAMPLE,
|
||||
83.56e6,
|
||||
"The resonant frequency of the observed transition.",
|
||||
min_value=1e5,
|
||||
)
|
||||
self.add_setting(resonant_frequency_setting, self.SAMPLE)
|
||||
self.add_setting("resonant_frequency", resonant_frequency_setting)
|
||||
|
||||
gamma_setting = FloatSetting(
|
||||
self.GAMMA,
|
||||
self.SAMPLE,
|
||||
4.342e7,
|
||||
"The gyromagnetic ratio of the sample’s nuclei.",
|
||||
min_value=0,
|
||||
)
|
||||
self.add_setting(gamma_setting, self.SAMPLE)
|
||||
self.add_setting("gamma", gamma_setting)
|
||||
|
||||
# This could be updated to a selection setting
|
||||
nuclear_spin_setting = FloatSetting(
|
||||
self.NUCLEAR_SPIN,
|
||||
self.SAMPLE,
|
||||
9 / 2,
|
||||
"The nuclear spin of the sample’s nuclei.",
|
||||
min_value=0,
|
||||
)
|
||||
self.add_setting(nuclear_spin_setting, self.SAMPLE)
|
||||
self.add_setting("nuclear_spin", nuclear_spin_setting)
|
||||
|
||||
spin_factor_setting = FloatSetting(
|
||||
self.SPIN_FACTOR,
|
||||
self.SAMPLE,
|
||||
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)
|
||||
self.add_setting("spin_factor", spin_factor_setting)
|
||||
|
||||
powder_factor_setting = FloatSetting(
|
||||
self.POWDER_FACTOR,
|
||||
self.SAMPLE,
|
||||
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)
|
||||
self.add_setting("powder_factor", powder_factor_setting)
|
||||
|
||||
filling_factor_setting = FloatSetting(
|
||||
self.FILLING_FACTOR,
|
||||
self.SAMPLE,
|
||||
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)
|
||||
self.add_setting("filling_factor", filling_factor_setting)
|
||||
|
||||
t1_setting = FloatSetting(
|
||||
self.T1,
|
||||
self.SAMPLE,
|
||||
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)
|
||||
self.add_setting("T1", t1_setting)
|
||||
|
||||
t2_setting = FloatSetting(
|
||||
self.T2,
|
||||
self.SAMPLE,
|
||||
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)
|
||||
self.add_setting("T2", t2_setting)
|
||||
|
||||
t2_star_setting = FloatSetting(
|
||||
self.T2_STAR,
|
||||
self.SAMPLE,
|
||||
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.add_setting("T2_star", t2_star_setting)
|
||||
|
||||
self.averages = 1
|
||||
self.target_frequency = 100e6
|
||||
|
|
|
|||
|
|
@ -24,6 +24,8 @@ class TestQuackSequence(unittest.TestCase):
|
|||
sim = Simulator()
|
||||
sim.set_averages(100)
|
||||
|
||||
sim.settings.noise = 0
|
||||
|
||||
result = sim.run_sequence(seq)
|
||||
self.assertIsNotNone(result)
|
||||
self.assertTrue(hasattr(result, "tdx"))
|
||||
|
|
|
|||
Loading…
Reference in a new issue