mirror of
https://github.com/nqrduck/nqrduck-spectrometer-simulator.git
synced 2024-12-21 15:10:25 +00:00
Basic implementation of simulator. This is all very buggy and has to be tested thoroughly.
This commit is contained in:
jupfi
parent
f5cdfdda4b
commit
0988406650
4 changed files with 366 additions and 3 deletions
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@ -7,7 +7,7 @@ allow-direct-references = true
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[project]
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name = "nqrduck-spectrometer-simulator"
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version = "0.0.1"
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version = "0.0.2"
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authors = [
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{ name="Julia Pfitzer", email="git@jupfi.me" },
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]
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@ -26,6 +26,8 @@ classifiers = [
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dependencies = [
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"nqrduck-spectrometer",
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"pyqt6",
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"numpy",
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"nqr_blochsimulator@git+https://github.com/jupfi/nqr-blochsimulator.git",
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]
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[project.entry-points."nqrduck"]
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@ -1,5 +1,250 @@
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import logging
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import numpy as np
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from nqrduck_spectrometer.base_spectrometer_controller import BaseSpectrometerController
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from nqrduck_spectrometer.measurement import Measurement
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from nqrduck_spectrometer.pulseparameters import TXPulse, RXReadout
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from nqr_blochsimulator.classes.pulse import PulseArray
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from nqr_blochsimulator.classes.sample import Sample
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from nqr_blochsimulator.classes.simulation import Simulation
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logger = logging.getLogger(__name__)
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class SimulatorController(BaseSpectrometerController):
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def __init__(self, module):
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super().__init__(module)
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def start_measurement(self):
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"""This method is called when the start_measurement signal is received from the core.
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It will becalled if the simulator is the active spectrometer.
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This will start the simulation based on the settings and the pulse sequence.
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"""
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logger.debug("Starting simulation")
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sample = self.get_sample_from_settings()
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logger.debug("Sample: %s", sample.name)
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dwell_time = self.calculate_dwelltime()
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logger.debug("Dwell time: %s", dwell_time)
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pulse_array = self.translate_pulse_sequence(dwell_time)
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simulation = self.get_simulation(sample, pulse_array)
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result = abs(simulation.simulate())
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tdx = np.linspace(0, float(self.calculate_simulation_length()), len(result)) * 1e6
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measurement_data = Measurement(
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tdx,
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result,
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sample.resonant_frequency,
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# frequency_shift=self.module.model.if_frequency,
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)
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# Emit the data to the nqrduck core
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logger.debug("Emitting measurement data")
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self.module.nqrduck_signal.emit("statusbar_message", "Finished Simulation")
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self.module.nqrduck_signal.emit("measurement_data", measurement_data)
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def get_sample_from_settings(self) -> Sample:
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"""This method creates a sample object based on the settings in the model.
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Returns:
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Sample: The sample object created from the settings.
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"""
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model = self.module.model
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atom_density = None
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sample_volume = None
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sample_length = None
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sample_diameter = None
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for samplesetting in model.settings[self.module.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 = samplesetting.value
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elif samplesetting.name == model.MOLAR_MASS:
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molar_mass = samplesetting.value
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elif samplesetting.name == model.RESONANT_FREQUENCY:
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resonant_frequency = samplesetting.value
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elif samplesetting.name == model.GAMMA:
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gamma = samplesetting.value
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elif samplesetting.name == model.NUCLEAR_SPIN:
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nuclear_spin = samplesetting.value
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elif samplesetting.name == model.SPIN_FACTOR:
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spin_factor = samplesetting.value
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elif samplesetting.name == model.POWDER_FACTOR:
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powder_factor = samplesetting.value
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elif samplesetting.name == model.FILLING_FACTOR:
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filling_factor = samplesetting.value
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elif samplesetting.name == model.T1:
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T1 = samplesetting.value
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elif samplesetting.name == model.T2:
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T2 = samplesetting.value
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elif samplesetting.name == model.T2_STAR:
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T2_star = samplesetting.value
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elif samplesetting.name == model.ATOM_DENSITY:
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atom_density = samplesetting.value
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elif samplesetting.name == model.SAMPLE_VOLUME:
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sample_volume = samplesetting.value
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elif samplesetting.name == model.SAMPLE_LENGTH:
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sample_length = samplesetting.value
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elif samplesetting.name == model.SAMPLE_DIAMETER:
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sample_diameter = 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", ["Error", "Unknown sample setting: " + samplesetting.name]
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)
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return None
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sample = Sample(
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name = name,
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density = density,
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molar_mass = molar_mass,
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resonant_frequency = resonant_frequency,
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gamma = gamma,
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nuclear_spin = nuclear_spin,
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spin_factor = spin_factor,
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powder_factor = powder_factor,
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filling_factor = filling_factor,
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T1 = T1,
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T2 = T2,
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T2_star = T2_star,
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atom_density = atom_density,
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sample_volume = sample_volume,
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sample_length = sample_length,
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sample_diameter = sample_diameter
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)
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return sample
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def translate_pulse_sequence(self, dwell_time : float) -> 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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dwell_time (float): The dwell time in seconds.
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Returns:
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PulseArray: The pulse sequence translated to a PulseArray object.
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"""
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events = self.module.model.pulse_programmer.model.pulse_sequence.events
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amplitude_array = list()
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for event in events:
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logger.debug("Event %s has parameters: %s", event.name, event.parameters)
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for parameter in event.parameters.values():
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logger.debug(
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"Parameter %s has options: %s", parameter.name, parameter.options
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)
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if (
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parameter.name == self.module.model.TX
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and parameter.get_option_by_name(TXPulse.RELATIVE_AMPLITUDE).value
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> 0
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):
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# If we have a pulse, we need to add it to the pulse array
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pulse_shape = parameter.get_option_by_name(
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TXPulse.TX_PULSE_SHAPE
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).value
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pulse_amplitude = abs(pulse_shape.get_pulse_amplitude(event.duration, resolution = dwell_time))
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amplitude_array.append(pulse_amplitude)
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elif (parameter.name == self.module.model.TX and parameter.get_option_by_name(TXPulse.RELATIVE_AMPLITUDE).value
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== 0):
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# If we have a wait, we need to add it to the pulse array
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amplitude_array.append(np.zeros(int(event.duration / dwell_time)))
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amplitude_array = np.concatenate(amplitude_array)
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# This has not yet been implemented right now the phase is always 0
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phase_array = np.zeros(len(amplitude_array))
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pulse_array = PulseArray(
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pulseamplitude = amplitude_array,
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pulsephase = phase_array,
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dwell_time = float(dwell_time)
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)
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return pulse_array
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def get_simulation(self, sample : Sample, pulse_array : PulseArray) -> Simulation:
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"""This method creates a simulation object based on the settings and the pulse sequence.
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Args:
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sample (Sample): The sample object created from the settings.
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pulse_array (PulseArray): The pulse sequence translated to a PulseArray object.
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Returns:
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Simulation: The simulation object created from the settings and the pulse sequence.
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"""
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model = self.module.model
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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 = model.get_setting_by_name(model.NUMBER_ISOCHROMATS).value,
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initial_magnetization = model.get_setting_by_name(model.INITIAL_MAGNETIZATION).value,
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gradient = model.get_setting_by_name(model.GRADIENT).value,
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noise = model.get_setting_by_name(model.NOISE).value,
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length_coil = model.get_setting_by_name(model.LENGTH_COIL).value,
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diameter_coil = model.get_setting_by_name(model.DIAMETER_COIL).value,
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number_turns = model.get_setting_by_name(model.NUMBER_TURNS).value,
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power_amplifier_power = model.get_setting_by_name(model.POWER_AMPLIFIER_POWER).value,
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gain = model.get_setting_by_name(model.GAIN).value,
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temperature = model.get_setting_by_name(model.TEMPERATURE).value,
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averages = model.averages,
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loss_TX = model.get_setting_by_name(model.LOSS_TX).value,
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loss_RX = model.get_setting_by_name(model.LOSS_RX).value
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)
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return simulation
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def calculate_dwelltime(self) -> 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 = self.module.model.get_setting_by_name(self.module.model.NUMBER_POINTS).value
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simulation_length = self.calculate_simulation_length()
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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) -> 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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float: The simulation length in seconds.
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"""
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events = self.module.model.pulse_programmer.model.pulse_sequence.events
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simulation_length = 0
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for event in events:
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simulation_length += event.duration
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return simulation_length
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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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"""
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self.module.nqrduck_signal.emit(
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"notification", ["Warning", "Could not set averages to because the simulator is selected as active spectrometer "]
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)
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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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@ -1,5 +1,121 @@
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import logging
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from nqrduck_spectrometer.base_spectrometer_model import BaseSpectrometerModel
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from nqrduck_spectrometer.pulseparameters import TXPulse, RXReadout
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logger = logging.getLogger(__name__)
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class SimulatorModel(BaseSpectrometerModel):
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# Simulation settings
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NUMBER_POINTS = "N. simulation points"
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NUMBER_ISOCHROMATS = "N. of isochromats"
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INITIAL_MAGNETIZATION = "Initial magnetization"
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GRADIENT = "Gradient (mT/m))"
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NOISE = "Noise (uV)"
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LENGTH_COIL = "Length coil (m)"
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DIAMETER_COIL = "Diameter coil (m)"
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NUMBER_TURNS = "Number turns"
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POWER_AMPLIFIER_POWER = "PA power (W)"
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GAIN = "Gain"
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TEMPERATURE = "Temperature (K)"
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AVERAGES = "Averages"
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LOSS_TX = "Loss TX (dB)"
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LOSS_RX = "Loss RX (dB)"
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# Sample settinggs, this will be done in a seperate module later on
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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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GAMMA = "Gamma (Hz/T)"
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NUCLEAR_SPIN = "Nuclear spin"
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SPIN_FACTOR = "Spin factor"
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POWDER_FACTOR = "Powder factor"
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FILLING_FACTOR = "Filling factor"
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T1 = "T1 (s)"
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T2 = "T2 (s)"
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T2_STAR = "T2* (s)"
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ATOM_DENSITY = "Atom density (1/cm^3)"
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SAMPLE_VOLUME = "Sample volume (m^3)"
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SAMPLE_LENGTH = "Sample length (m)"
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SAMPLE_DIAMETER = "Sample diameter (m)"
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# Categories of the settings
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SIMULATION = "Simulation"
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HARDWARE = "Hardware"
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EXPERIMENTAL_Setup = "Experimental Setup"
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SAMPLE = "Sample"
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# Pulse parameter constants
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TX = "TX"
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RX = "RX"
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def __init__(self, module):
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super().__init__(module)
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# Simulation settings
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self.add_setting(
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self.NUMBER_POINTS,
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300,
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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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self.SIMULATION,
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)
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self.add_setting(
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self.NUMBER_ISOCHROMATS, 1000, "Number of isochromats", self.SIMULATION
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)
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self.add_setting(
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self.INITIAL_MAGNETIZATION, 1, "Initial magnetization", self.SIMULATION
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)
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self.add_setting(self.GRADIENT, 1, "Gradient", self.SIMULATION)
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self.add_setting(self.NOISE, 0, "Noise", self.SIMULATION)
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self.add_setting(self.LENGTH_COIL, 6, "Length coil", self.HARDWARE)
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self.add_setting(self.DIAMETER_COIL, 3, "Diameter coil", self.HARDWARE)
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self.add_setting(self.NUMBER_TURNS, 9, "Number turns", self.HARDWARE)
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self.add_setting(
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self.POWER_AMPLIFIER_POWER, 500, "Power amplifier power", self.HARDWARE
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)
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self.add_setting(
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self.GAIN, 6000, "Gain of the complete measurement chain", self.HARDWARE
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)
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self.add_setting(self.TEMPERATURE, 300, "Temperature", self.EXPERIMENTAL_Setup)
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self.add_setting(self.LOSS_TX, 12, "Loss TX", self.EXPERIMENTAL_Setup)
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self.add_setting(self.LOSS_RX, 12, "Loss RX", self.EXPERIMENTAL_Setup)
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# Sample settings
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self.add_setting(self.NAME, "BiPh3", "Name", self.SAMPLE)
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self.add_setting(self.DENSITY, 1.585e6, "Density", self.SAMPLE)
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self.add_setting(self.MOLAR_MASS, 440.3, "Molar mass", self.SAMPLE)
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self.add_setting(
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self.RESONANT_FREQUENCY, 83.56e6, "Resonant frequency", self.SAMPLE
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)
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self.add_setting(self.GAMMA, 4.342e7, "Gamma", self.SAMPLE)
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self.add_setting(self.NUCLEAR_SPIN, 9 / 2, "Nuclear spin", self.SAMPLE)
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self.add_setting(self.SPIN_FACTOR, 2, "Spin factor", self.SAMPLE)
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self.add_setting(self.POWDER_FACTOR, 0.75, "Powder factor", self.SAMPLE)
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self.add_setting(self.FILLING_FACTOR, 0.7, "Filling factor", self.SAMPLE)
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self.add_setting(self.T1, 83.5e-5, "T1", self.SAMPLE)
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self.add_setting(self.T2, 396e-6, "T2", self.SAMPLE)
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self.add_setting(self.T2_STAR, 50e-6, "T2*", self.SAMPLE)
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# Pulse parameter options
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self.add_pulse_parameter_option(self.TX, TXPulse)
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# self.add_pulse_parameter_option(self.GATE, Gate)
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self.add_pulse_parameter_option(self.RX, RXReadout)
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# Try to load the pulse programmer module
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try:
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from nqrduck_pulseprogrammer.pulseprogrammer import pulse_programmer
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self.pulse_programmer = pulse_programmer
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logger.debug("Pulse programmer found.")
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self.pulse_programmer.controller.on_loading(self.pulse_parameter_options)
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except ImportError:
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logger.warning("No pulse programmer found.")
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@property
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def averages(self):
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return self._averages
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@averages.setter
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def averages(self, value):
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self._averages = value
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@ -3,5 +3,5 @@ from nqrduck_spectrometer.base_spectrometer_view import BaseSpectrometerView
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class SimulatorView(BaseSpectrometerView):
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def __init__(self, module):
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super().__init__(module)
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# This automatically generates the settings widget based on the settings in the model
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self.widget = self.load_settings_ui()
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