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Merge pull request #23 from nqrduck/development

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6
CHANGELOG.md
View file

@ -1,5 +1,11 @@
# Changelog
## Version 0.0.12 (27-05-2024)
- Implemented loading and saving of settings and default settings (`6496ec6824da33fa41a38e26fdcac9a03ceb51fb`)
- Added fitting of measurement data (`d43639c2f9796d5055dd01bd2f36bae43877bfe8`)
## Version 0.0.11 (20-05-2024)
- Measurements are now run in a separate worker thread to prevent the GUI from freezing (`27865aa6d44158e74c0e537be8407c12b4e3725b`)

2
pyproject.toml
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@ -7,7 +7,7 @@ allow-direct-references = true
[project]
name = "nqrduck-spectrometer"
version = "0.0.11"
version = "0.0.12"
authors = [
{ name="jupfi", email="support@nqruck.cool" },
]

49
src/nqrduck_spectrometer/base_spectrometer_controller.py
View file

@ -1,7 +1,10 @@
"""Base class for all spectrometer controllers."""
import logging
import ast
from nqrduck.module.module_controller import ModuleController
logger = logging.getLogger(__name__)
class BaseSpectrometerController(ModuleController):
"""The base class for all spectrometer controllers."""
@ -10,6 +13,52 @@ class BaseSpectrometerController(ModuleController):
"""Initializes the spectrometer controller."""
super().__init__(module)
def on_loading(self):
"""Called when the module is loading."""
logger.debug("Loading spectrometer controller")
self.module.model.load_default_settings()
def save_settings(self, path: str) -> None:
"""Saves the settings of the spectrometer."""
# We get the different settings objects from the model
settings = self.module.model.settings
json = {}
json["name"] = self.module.model.name
for category in settings.keys():
for setting in settings[category]:
json[setting.name] = setting.value
with open(path, "w") as f:
f.write(str(json))
def load_settings(self, path: str) -> None:
"""Loads the settings of the spectrometer."""
with open(path) as f:
json = f.read()
# string to dict
json = ast.literal_eval(json)
module_name = self.module.model.name
json_name = json["name"]
# For some reason the notification is shown twice
if module_name != json_name:
message = f"Module: {module_name} not compatible with module specified in settings file: {json_name}. Did you select the correct settings file?"
self.module.nqrduck_signal.emit("notification", ["Error", message])
return
settings = self.module.model.settings
for category in settings.keys():
for setting in settings[category]:
if setting.name in json:
setting.value = json[setting.name]
else:
message = f"Setting {setting.name} not found in settings file. A change in settings might have broken compatibility."
self.module.nqrduck_signal.emit("notification", ["Error", message])
def start_measurement(self):
"""Starts the measurement.

26
src/nqrduck_spectrometer/base_spectrometer_model.py
View file

@ -2,6 +2,7 @@
import logging
from collections import OrderedDict
from PyQt6.QtCore import QSettings
from PyQt6.QtGui import QPixmap
from nqrduck.module.module_model import ModuleModel
from .settings import Setting
@ -22,6 +23,8 @@ class BaseSpectrometerModel(ModuleModel):
pulse_parameter_options (OrderedDict) : The pulse parameter options of the spectrometer
"""
SETTING_FILE_EXTENSION = "setduck"
settings: OrderedDict
pulse_parameter_options: OrderedDict
@ -99,6 +102,29 @@ class BaseSpectrometerModel(ModuleModel):
super().__init__(module)
self.settings = OrderedDict()
self.pulse_parameter_options = OrderedDict()
self.default_settings = QSettings("nqrduck-spectrometer", "nqrduck")
def set_default_settings(self) -> None:
"""Sets the default settings of the spectrometer."""
self.default_settings.clear()
for category in self.settings.keys():
for setting in self.settings[category]:
setting_string = f"{self.module.model.name},{setting.name}"
self.default_settings.setValue(setting_string, setting.value)
logger.debug(f"Setting default value for {setting_string} to {setting.value}")
def load_default_settings(self) -> None:
"""Load the default settings of the spectrometer."""
for category in self.settings.keys():
for setting in self.settings[category]:
setting_string = f"{self.module.model.name},{setting.name}"
if self.default_settings.contains(setting_string):
logger.debug(f"Loading default value for {setting_string}")
setting.value = self.default_settings.value(setting_string)
def clear_default_settings(self) -> None:
"""Clear the default settings of the spectrometer."""
self.default_settings.clear()
def add_setting(self, setting: Setting, category: str) -> None:
"""Adds a setting to the spectrometer.

107
src/nqrduck_spectrometer/base_spectrometer_view.py
View file

@ -8,6 +8,8 @@ from PyQt6.QtWidgets import (
QSizePolicy,
QSpacerItem,
QVBoxLayout,
QPushButton,
QDialog,
)
from nqrduck.module.module_view import ModuleView
from nqrduck.assets.icons import Logos
@ -91,3 +93,108 @@ class BaseSpectrometerView(ModuleView):
# Push all the settings to the top of the widget
self._ui_form.verticalLayout.addStretch(1)
# Now we add a save and load button to the widget
self.button_layout = QHBoxLayout()
# Default Settings Button
self.default_button = QPushButton("Default Settings")
self.default_button.clicked.connect(self.on_default_button_clicked)
self.button_layout.addWidget(self.default_button)
# Save Button
self.save_button = QPushButton("Save Settings")
self.save_button.setIcon(Logos.Save16x16())
self.save_button.setIconSize(Logos.Save16x16().availableSizes()[0])
self.save_button.clicked.connect(self.on_save_button_clicked)
self.button_layout.addWidget(self.save_button)
# Load Button
self.load_button = QPushButton("Load Settings")
self.load_button.setIcon(Logos.Load16x16())
self.load_button.clicked.connect(self.on_load_button_clicked)
self.button_layout.addWidget(self.load_button)
self.load_button.setIconSize(Logos.Load16x16().availableSizes()[0])
self.button_layout.addStretch(1)
self._ui_form.verticalLayout.addLayout(self.button_layout)
def on_save_button_clicked(self):
"""This method is called when the save button is clicked."""
logger.debug("Save button clicked")
# Open a dialog to save the settings to a file
file_manager = self.FileManager(
extension=self.module.model.SETTING_FILE_EXTENSION, parent=self
)
path = file_manager.saveFileDialog()
if path:
self.module.controller.save_settings(path)
def on_load_button_clicked(self):
"""This method is called when the load button is clicked."""
logger.debug("Load button clicked")
# Open a dialog to load the settings from a file
file_manager = self.FileManager(
extension=self.module.model.SETTING_FILE_EXTENSION, parent=self
)
path = file_manager.loadFileDialog()
self.module.controller.load_settings(path)
if path:
self.module.controller.load_settings(path)
def on_default_button_clicked(self):
"""This method is called when the default button is clicked."""
logger.debug("Default button clicked")
dialog = self.DefaultSettingsDialog(self)
dialog.exec()
class DefaultSettingsDialog(QDialog):
"""Dialog to set or clear the default settings of the spectrometer."""
def __init__(self, parent=None):
"""Initializes the default settings dialog."""
super().__init__(parent)
self.parent = parent
self.setWindowTitle("Default Settings")
self.layout = QVBoxLayout()
# Either we set the current settings as default
self.set_current_button = QPushButton("Set Current Settings as Default")
self.set_current_button.clicked.connect(
self.on_set_current_button_clicked
)
# Or we clear the default settings
self.clear_button = QPushButton("Clear Default Settings")
self.clear_button.clicked.connect(
self.on_clear_button_clicked
)
self.layout.addWidget(self.set_current_button)
self.layout.addWidget(self.clear_button)
self.setLayout(self.layout)
# Ok Button
self.ok_button = QPushButton("Ok")
self.ok_button.clicked.connect(self.accept)
self.layout.addWidget(self.ok_button)
def on_set_current_button_clicked(self):
"""This method is called when the set current button is clicked."""
logger.debug("Set current button clicked")
self.parent.module.model.set_default_settings()
# Show notification that the settings have been set as default
self.parent.module.nqrduck_signal.emit(
"notification", ["Info", "Settings have been set as default."]
)
def on_clear_button_clicked(self):
"""This method is called when the clear button is clicked."""
logger.debug("Clear button clicked")
self.parent.module.model.clear_default_settings()
# Show notification that the default settings have been cleared
self.parent.module.nqrduck_signal.emit(
"notification", ["Info", "Default settings have been cleared."]
)

2
src/nqrduck_spectrometer/controller.py
View file

@ -43,6 +43,8 @@ class SpectrometerController(ModuleController):
logger.debug("Adding spectrometer to spectrometer model: %s", module_name)
self._module.model.add_spectrometers(module_name, module)
module.controller.on_loading()
self._module.view.create_menu_entry()
def process_signals(self, key: str, value: object) -> None:

278
src/nqrduck_spectrometer/measurement.py
View file

@ -1,7 +1,8 @@
"""Class for handling measurement data."""
"""This module defines the measurement data structure and the fit class for measurement data."""
import logging
import numpy as np
from scipy.optimize import curve_fit
from nqrduck.helpers.signalprocessing import SignalProcessing as sp
from nqrduck.helpers.functions import Function
@ -28,8 +29,8 @@ class Measurement:
target_frequency (float): Target frequency of the measurement.
frequency_shift (float): Frequency shift of the measurement.
IF_frequency (float): Intermediate frequency of the measurement.
xf (np.array): Frequency axis for the x axis of the measurement data.
yf (np.array): Frequency axis for the y axis of the measurement data.
fdx (np.array): Frequency axis for the x axis of the measurement data.
fdy (np.array): Frequency axis for the y axis of the measurement data.
"""
def __init__(
@ -46,69 +47,89 @@ class Measurement:
self.tdx = tdx
self.tdy = tdy
self.target_frequency = target_frequency
self.fdx, self.fdy = sp.fft(tdx, tdy, frequency_shift)
self.frequency_shift = frequency_shift
self.IF_frequency = IF_frequency
self.fdx, self.fdy = sp.fft(tdx, tdy, frequency_shift)
self.fits = []
def apodization(self, function: Function):
def apodization(self, function: Function) -> "Measurement":
"""Applies apodization to the measurement data.
Args:
function (Function): Apodization function.
returns:
Measurement : The apodized measurement.
Returns:
Measurement: The apodized measurement.
"""
# Get the y data weights from the function
duration = (self.tdx[-1] - self.tdx[0]) * 1e-6
resolution = duration / len(self.tdx)
logger.debug("Resolution: %s", resolution)
y_weight = function.get_pulse_amplitude(duration, resolution)
tdy_measurement = self.tdy * y_weight
tdy_apodized = self.tdy * y_weight
apodized_measurement = Measurement(
self.name,
self.tdx,
tdy_measurement,
tdy_apodized,
target_frequency=self.target_frequency,
IF_frequency=self.IF_frequency,
)
return apodized_measurement
# Data saving and loading
def add_fit(self, fit: "Fit") -> None:
"""Adds a fit to the measurement.
def to_json(self):
"""Converts the measurement to a json-compatible format.
Args:
fit (Fit): The fit to add.
"""
self.fits.append(fit)
def delete_fit(self, fit: "Fit") -> None:
"""Deletes a fit from the measurement.
Args:
fit (Fit): The fit to delete.
"""
self.fits.remove(fit)
def edit_fit_name(self, fit: "Fit", name: str) -> None:
"""Edits the name of a fit.
Args:
fit (Fit): The fit to edit.
name (str): The new name.
"""
logger.debug(f"Editing fit name to {name}.")
fit.name = name
def to_json(self) -> dict:
"""Converts the measurement to a JSON-compatible format.
Returns:
dict : The measurement in json-compatible format.
dict: The measurement in JSON-compatible format.
"""
return {
"name": self.name,
"tdx": self.tdx.tolist(),
"tdy": [
[x.real, x.imag] for x in self.tdy
], # Convert complex numbers to list
"tdy": [[x.real, x.imag] for x in self.tdy],
"target_frequency": self.target_frequency,
"IF_frequency": self.IF_frequency,
"fits": [fit.to_json() for fit in self.fits],
}
@classmethod
def from_json(cls, json: dict):
"""Converts the json format to a measurement.
def from_json(cls, json: dict) -> "Measurement":
"""Converts the JSON format to a measurement.
Args:
json (dict) : The measurement in json-compatible format.
json (dict): The measurement in JSON-compatible format.
Returns:
Measurement : The measurement.
Measurement: The measurement.
"""
tdy = np.array([complex(y[0], y[1]) for y in json["tdy"]])
return cls(
measurement = cls(
json["name"],
np.array(json["tdx"]),
tdy,
@ -116,58 +137,227 @@ class Measurement:
IF_frequency=json["IF_frequency"],
)
# Measurement data
for fit_json in json["fits"]:
measurement.add_fit(Fit.from_json(fit_json, measurement))
return measurement
# Properties for encapsulation
@property
def name(self):
def name(self) -> str:
"""Name of the measurement."""
return self._name
@name.setter
def name(self, value):
def name(self, value: str) -> None:
self._name = value
@property
def tdx(self):
"""Time axis for the x axis of the measurement data."""
def tdx(self) -> np.array:
"""Time domain data for the measurement (x)."""
return self._tdx
@tdx.setter
def tdx(self, value):
def tdx(self, value: np.array) -> None:
self._tdx = value
@property
def tdy(self):
"""Time axis for the y axis of the measurement data."""
def tdy(self) -> np.array:
"""Time domain data for the measurement (y)."""
return self._tdy
@tdy.setter
def tdy(self, value):
def tdy(self, value: np.array) -> None:
self._tdy = value
@property
def fdx(self):
"""Frequency axis for the x axis of the measurement data."""
def fdx(self) -> np.array:
"""Frequency domain data for the measurement (x)."""
return self._fdx
@fdx.setter
def fdx(self, value):
def fdx(self, value: np.array) -> None:
self._fdx = value
@property
def fdy(self):
"""Frequency axis for the y axis of the measurement data."""
def fdy(self) -> np.array:
"""Frequency domain data for the measurement (y)."""
return self._fdy
@fdy.setter
def fdy(self, value):
def fdy(self, value: np.array) -> None:
self._fdy = value
# Pulse parameters
@property
def target_frequency(self):
def target_frequency(self) -> float:
"""Target frequency of the measurement."""
return self._target_frequency
@target_frequency.setter
def target_frequency(self, value):
def target_frequency(self, value: float) -> None:
self._target_frequency = value
@property
def fits(self) -> list:
"""Fits of the measurement."""
return self._fits
@fits.setter
def fits(self, value: list) -> None:
self._fits = value
class Fit:
"""The fit class for measurement data. A fit can be performed on either the frequency or time domain data.
A measurement can have multiple fits.
"""
subclasses = []
def __init_subclass__(cls, **kwargs) -> None:
"""Adds the subclass to the list of subclasses."""
super().__init_subclass__(**kwargs)
cls.subclasses.append(cls)
def __init__(self, name: str, domain: str, measurement: Measurement) -> None:
"""Initializes the fit."""
self.name = name
self.domain = domain
self.measurement = measurement
self.fit()
def fit(self) -> None:
"""Fits the measurement data and sets the fit parameters and covariance."""
if self.domain == "time":
x = self.measurement.tdx
y = self.measurement.tdy
elif self.domain == "frequency":
x = self.measurement.fdx
y = self.measurement.fdy
else:
raise ValueError("Domain not recognized.")
initial_guess = self.initial_guess()
self.parameters, self.covariance = curve_fit(
self.fit_function, x, abs(y), p0=initial_guess
)
self.x = x
self.y = self.fit_function(x, *self.parameters)
def fit_function(self, x: np.array, *parameters) -> np.array:
"""The fit function.
Args:
x (np.array): The x data.
*parameters: The fit parameters.
Returns:
np.array: The y data.
"""
raise NotImplementedError
def initial_guess(self) -> list:
"""Initial guess for the fit.
Returns:
list: The initial guess.
"""
raise NotImplementedError
def to_json(self) -> dict:
"""Converts the fit to a JSON-compatible format.
Returns:
dict: The fit in JSON-compatible format.
"""
return {
"name": self.name,
"class": self.__class__.__name__,
}
@classmethod
def from_json(cls, data: dict, measurement: Measurement) -> "Fit":
"""Converts the JSON format to a fit.
Args:
data (dict): The fit in JSON-compatible format.
measurement (Measurement): The measurement.
Returns:
Fit: The fit.
"""
for subclass in cls.subclasses:
if subclass.__name__ == data["class"]:
return subclass(name=data["name"], measurement=measurement)
raise ValueError(f"Subclass {data['class']} not found.")
@property
def x(self) -> np.array:
"""The x data of the fit."""
return self._x
@x.setter
def x(self, value: np.array) -> None:
self._x = value
@property
def y(self) -> np.array:
"""The y data of the fit."""
return self._y
@y.setter
def y(self, value: np.array) -> None:
self._y = value
class T2StarFit(Fit):
"""T2* fit for measurement data."""
def __init__(self, measurement: Measurement, name: str = "T2*") -> None:
"""Initializes the T2* fit."""
super().__init__(name, "time", measurement)
def fit(self) -> None:
"""Fits the measurement data and sets the fit parameters and covariance."""
super().fit()
self.parameters = {
"S0": self.parameters[0],
"T2Star": self.parameters[1],
"covariance": self.covariance,
}
def fit_function(self, t: np.array, S0: float, T2Star: float) -> np.array:
"""The T2* fit function used for curve fitting."""
return S0 * np.exp(-t / T2Star)
def initial_guess(self) -> list:
"""Initial guess for the T2* fit."""
return [1, 1]
class LorentzianFit(Fit):
"""Lorentzian fit for measurement data."""
def __init__(self, measurement: Measurement, name: str = "Lorentzian") -> None:
"""Initializes the Lorentzian fit."""
super().__init__(name, "frequency", measurement)
def fit(self) -> None:
"""Fits the measurement data and sets the fit parameters and covariance."""
super().fit()
self.parameters = {
"S0": self.parameters[0],
"T2Star": self.parameters[1],
"covariance": self.covariance,
}
logger.debug("Lorentzian fit parameters: %s", self.parameters)
def fit_function(self, f: np.array, S0: float, T2Star: float) -> np.array:
"""The Lorentzian fit function used for curve fitting."""
return S0 / (1 + (2 * np.pi * f * T2Star) ** 2)
def initial_guess(self) -> list:
"""Initial guess for the Lorentzian fit."""
return [1, 1]

54
src/nqrduck_spectrometer/settings.py
View file

@ -36,6 +36,7 @@ class Setting(QObject):
description (str): A description of the setting.
default: The default value of the setting.
"""
self.widget = None
super().__init__()
self.name = name
self.description = description
@ -87,9 +88,16 @@ class NumericalSetting(Setting):
It can additionally have a minimum and maximum value.
"""
def __init__(self, name: str, description: str, default, min_value = None, max_value = None ) -> None:
def __init__(
self, name: str, description: str, default, min_value=None, max_value=None
) -> None:
"""Create a new numerical setting."""
super().__init__(name, self.description_limit_info(description, min_value, max_value), default)
super().__init__(
name,
self.description_limit_info(description, min_value, max_value),
default,
)
def description_limit_info(self, description: str, min_value, max_value) -> str:
"""Updates the description with the limits of the setting if there are any.
@ -103,11 +111,11 @@ class NumericalSetting(Setting):
str: The description of the setting with the limits.
"""
if min_value is not None and max_value is not None:
description += (f"\n (min: {min_value}, max: {max_value})")
description += f"\n (min: {min_value}, max: {max_value})"
elif min_value is not None:
description += (f"\n (min: {min_value})")
description += f"\n (min: {min_value})"
elif max_value is not None:
description += (f"\n (max: {max_value})")
description += f"\n (max: {max_value})"
return description
@ -133,13 +141,19 @@ class FloatSetting(NumericalSetting):
description: str,
min_value: float = None,
max_value: float = None,
spin_box: tuple = (False, False)
spin_box: tuple = (False, False),
) -> None:
"""Create a new float setting."""
self.spin_box = spin_box
super().__init__(name, description, default, min_value, max_value)
if spin_box[0]:
self.widget = DuckSpinBox(min_value=min_value, max_value=max_value, slider=spin_box[1], double_box=True)
self.widget = DuckSpinBox(
min_value=min_value,
max_value=max_value,
slider=spin_box[1],
double_box=True,
)
self.widget.spin_box.setValue(default)
else:
self.widget = DuckFloatEdit(min_value=min_value, max_value=max_value)
@ -169,6 +183,12 @@ class FloatSetting(NumericalSetting):
self._value = float(value)
self.settings_changed.emit()
if self.widget:
if self.spin_box[0]:
self.widget.spin_box.setValue(self._value)
else:
self.widget.setText(str(self._value))
class IntSetting(NumericalSetting):
"""A setting that is an Integer.
@ -189,13 +209,15 @@ class IntSetting(NumericalSetting):
description: str,
min_value=None,
max_value=None,
spin_box: tuple = (False, False)
spin_box: tuple = (False, False),
) -> None:
"""Create a new int setting."""
self.spin_box = spin_box
super().__init__(name, description, default, min_value, max_value)
if spin_box[0]:
self.widget = DuckSpinBox(min_value=min_value, max_value=max_value, slider=spin_box[1])
if self.spin_box[0]:
self.widget = DuckSpinBox(
min_value=min_value, max_value=max_value, slider=spin_box[1]
)
self.widget.spin_box.setValue(default)
else:
self.widget = DuckIntEdit(min_value=min_value, max_value=max_value)
@ -225,7 +247,11 @@ class IntSetting(NumericalSetting):
value = int(float(value))
self._value = value
self.settings_changed.emit()
if self.widget:
if self.spin_box[0]:
self.widget.spin_box.setValue(value)
else:
self.widget.setText(str(value))
class BooleanSetting(Setting):
@ -253,6 +279,8 @@ class BooleanSetting(Setting):
def value(self, value):
try:
self._value = bool(value)
if self.widget:
self.widget.setChecked(self._value)
self.settings_changed.emit()
except ValueError:
raise ValueError("Value must be a bool")
@ -307,6 +335,8 @@ class SelectionSetting(Setting):
try:
if value in self.options:
self._value = value
if self.widget:
self.widget.setCurrentText(value)
self.settings_changed.emit()
else:
raise ValueError("Value must be one of the options")