Linting.

src/nqrduck_spectrometer_limenqr/__init__.py

@@ -0,0 +1 @@
+"""Init file for the nqrduck_spectrometer_limenqr package."""

src/nqrduck_spectrometer_limenqr/controller.py

@@ -1,3 +1,5 @@
+"""Controller module for the Lime NQR spectrometer."""
+
 import logging
 import tempfile
 from pathlib import Path
@@ -10,24 +12,33 @@ from nqrduck_spectrometer.base_spectrometer_controller import BaseSpectrometerCo
 from nqrduck_spectrometer.measurement import Measurement
 from nqrduck_spectrometer.pulseparameters import TXPulse, RXReadout
 
+
 logger = logging.getLogger(__name__)
 
 
 class LimeNQRController(BaseSpectrometerController):
+    """Controller class for the Lime NQR spectrometer."""
+
     def __init__(self, module):
+        """Initializes the LimeNQRController."""
         super().__init__(module)
 
     def start_measurement(self):
+        """Starts the measurement procedure."""
         self.log_start_message()
 
         lime = self.initialize_lime()
         if lime is None:
             # Emit error message
-            self.emit_measurement_error("Error with Lime driver. Is the Lime driver installed?")
+            self.emit_measurement_error(
+                "Error with Lime driver. Is the Lime driver installed?"
+            )
             return -1
         elif lime.Npulses == 0:
             # Emit error message
-            self.emit_measurement_error("Error with pulse sequence. Is the pulse sequence empty?")
+            self.emit_measurement_error(
+                "Error with pulse sequence. Is the pulse sequence empty?"
+            )
             return -1
 
         self.setup_lime_parameters(lime)
@@ -37,7 +48,9 @@ class LimeNQRController(BaseSpectrometerController):
 
         if not self.perform_measurement(lime):
             self.emit_status_message("Measurement failed")
-            self.emit_measurement_error("Error with measurement data. Did you set an RX event?")
+            self.emit_measurement_error(
+                "Error with measurement data. Did you set an RX event?"
+            )
             return -1
 
         measurement_data = self.process_measurement_results(lime)
@@ -48,12 +61,14 @@ class LimeNQRController(BaseSpectrometerController):
         else:
             self.emit_measurement_error("Measurement failed. Unable to retrieve data.")
 
-    def log_start_message(self):
+    def log_start_message(self) -> None:
-        """This method logs a message when the measurement is started."""
+        """Logs a message when the measurement is started."""
-        logger.debug("Starting measurement with spectrometer: %s", self.module.model.name)
+        logger.debug(
+            "Starting measurement with spectrometer: %s", self.module.model.name
+        )
 
-    def initialize_lime(self):
+    def initialize_lime(self) -> PyLimeConfig:
-        """This method initializes the limr object that is used to communicate with the pulseN driver.
+        """Initializes the limr object that is used to communicate with the pulseN driver.
 
         Returns:
             PyLimeConfig: The PyLimeConfig object that is used to communicate with the pulseN driver
@@ -67,17 +82,18 @@ class LimeNQRController(BaseSpectrometerController):
         except Exception as e:
             logger.error("Error while initializing Lime driver: %s", e)
             import traceback
+
             traceback.print_exc()
 
         return None
 
-    def setup_lime_parameters(self, lime):
+    def setup_lime_parameters(self, lime: PyLimeConfig) -> None:
-        """This method sets the parameters of the lime config according to the settings set in the spectrometer module.
+        """Sets the parameters of the lime config according to the settings set in the spectrometer module.
 
         Args:
             lime (PyLimeConfig): The PyLimeConfig object that is used to communicate with the pulseN driver
         """
-        #lime.noi = -1
+        # lime.noi = -1
         lime.override_init = -1
         #
         # lime.nrp = 1
@@ -87,19 +103,19 @@ class LimeNQRController(BaseSpectrometerController):
         lime.averages = self.module.model.averages
         self.log_lime_parameters(lime)
 
-    def setup_temporary_storage(self, lime):
+    def setup_temporary_storage(self, lime: PyLimeConfig) -> None:
-        """This method sets up the temporary storage for the measurement data.
+        """Sets up the temporary storage for the measurement data.
 
         Args:
             lime (PyLimeConfig): The PyLimeConfig object that is used to communicate with the pulseN driver
         """
         temp_dir = tempfile.TemporaryDirectory()
         logger.debug("Created temporary directory at: %s", temp_dir.name)
-        lime.save_path = str(Path(temp_dir.name)) + "/"   # Temporary storage path
+        lime.save_path = str(Path(temp_dir.name)) + "/"  # Temporary storage path
-        lime.file_pattern = "temp"                # Temporary filename prefix or related config
+        lime.file_pattern = "temp"  # Temporary filename prefix or related config
 
-    def perform_measurement(self, lime):
+    def perform_measurement(self, lime: PyLimeConfig) -> bool:
-        """This method executes the measurement procedure.
+        """Executes the measurement procedure.
 
         Args:
             lime (PyLimeConfig): The PyLimeConfig object that is used to communicate with the pulseN driver
@@ -115,8 +131,8 @@ class LimeNQRController(BaseSpectrometerController):
             logger.error("Failed to execute the measurement: %s", e)
             return False
 
-    def process_measurement_results(self, lime):
+    def process_measurement_results(self, lime: PyLimeConfig) -> Measurement:
-        """This method processes the measurement results and returns a Measurement object.
+        """Processes the measurement results and returns a Measurement object.
 
         Args:
             lime (PyLimeConfig): The PyLimeConfig object that is used to communicate with the pulseN driver
@@ -133,8 +149,10 @@ class LimeNQRController(BaseSpectrometerController):
         logger.debug("RX event begins at: %sµs and ends at: %sµs", rx_begin, rx_stop)
         return self.calculate_measurement_data(lime, rx_begin, rx_stop)
 
-    def calculate_measurement_data(self, lime, rx_begin, rx_stop):
+    def calculate_measurement_data(
-        """This method calculates the measurement data from the limr object.
+        self, lime: PyLimeConfig, rx_begin: float, rx_stop: float
+    ) -> Measurement:
+        """Calculates the measurement data from the limr object.
 
         Args:
             lime (PyLimeConfig): The PyLimeConfig object that is used to communicate with the pulseN driver
@@ -146,34 +164,44 @@ class LimeNQRController(BaseSpectrometerController):
         """
         try:
             path = lime.get_path()
-            hdf =  HDF(path)
+            hdf = HDF(path)
             evidx = self.find_evaluation_range_indices(hdf, rx_begin, rx_stop)
             tdx, tdy = self.extract_measurement_data(lime, hdf, evidx)
             fft_shift = self.get_fft_shift()
-            return Measurement(tdx, tdy, self.module.model.target_frequency, frequency_shift=fft_shift, IF_frequency=self.module.model.if_frequency)
+            return Measurement(
+                tdx,
+                tdy,
+                self.module.model.target_frequency,
+                frequency_shift=fft_shift,
+                IF_frequency=self.module.model.if_frequency,
+            )
         except Exception as e:
             logger.error("Error processing measurement result: %s", e)
             return None
 
-    def find_evaluation_range_indices(self, hdf, rx_begin, rx_stop):
+    def find_evaluation_range_indices(
-        """This method finds the indices of the evaluation range in the measurement data.
+        self, hdf: HDF, rx_begin: float, rx_stop: float
+    ) -> list:
+        """Finds the indices of the evaluation range in the measurement data.
 
         Args:
-            HDF (HDF): The HDF object that is used to read the measurement data
+            hdf (HDF): The HDF object that is used to read the measurement data
             rx_begin (float): The start time of the RX event in µs
             rx_stop (float): The stop time of the RX event in µs
 
         Returns:
-        list: The indices of the evaluation range in the measurement data
+            list: The indices of the evaluation range in the measurement data
         """
         return np.where((hdf.tdx > rx_begin) & (hdf.tdx < rx_stop))[0]
 
-    def extract_measurement_data(self, lime, hdf, indices):
+    def extract_measurement_data(
-        """This method extracts the measurement data from the limr object.
+        self, lime: PyLimeConfig, hdf: HDF, indices: list
+    ) -> tuple:
+        """Extracts the measurement data from the PyLimeConfig object.
 
         Args:
             lime (PyLimeConfig): The PyLimeConfig object that is used to communicate with the pulseN driver
-            HDF (HDF): The HDF object that is used to read the measurement data
+            hdf (HDF): The HDF object that is used to read the measurement data
             indices (list): The indices of the evaluation range in the measurement data
 
         Returns:
@@ -185,17 +213,19 @@ class LimeNQRController(BaseSpectrometerController):
         tdy = tdy.flatten()
         return tdx, tdy
 
-    def get_fft_shift(self):
+    def get_fft_shift(self) -> int:
-        """This method returns the FFT shift value from the settings.
+        """Rreturns the FFT shift value from the settings.
 
         Returns:
-        int: The FFT shift value
+            int: The FFT shift value
         """
-        fft_shift_enabled = self.module.model.get_setting_by_name(self.module.model.FFT_SHIFT).value
+        fft_shift_enabled = self.module.model.get_setting_by_name(
+            self.module.model.FFT_SHIFT
+        ).value
         return self.module.model.if_frequency if fft_shift_enabled else 0
 
-    def emit_measurement_data(self, measurement_data):
+    def emit_measurement_data(self, measurement_data: Measurement) -> None:
-        """This method emits the measurement data to the GUI.
+        """Emits the measurement data to the GUI.
 
         Args:
             measurement_data (Measurement): The measurement data
@@ -203,16 +233,16 @@ class LimeNQRController(BaseSpectrometerController):
         logger.debug("Emitting measurement data")
         self.module.nqrduck_signal.emit("measurement_data", measurement_data)
 
-    def emit_status_message(self, message):
+    def emit_status_message(self, message: str) -> None:
-        """This method emits a status message to the GUI.
+        """Emits a status message to the GUI.
 
         Args:
             message (str): The status message
         """
         self.module.nqrduck_signal.emit("statusbar_message", message)
 
-    def emit_measurement_error(self, error_message):
+    def emit_measurement_error(self, error_message: str) -> None:
-        """This method emits a measurement error to the GUI.
+        """Emits a measurement error to the GUI.
 
         Args:
             error_message (str): The error message
@@ -220,24 +250,24 @@ class LimeNQRController(BaseSpectrometerController):
         logger.error(error_message)
         self.module.nqrduck_signal.emit("measurement_error", error_message)
 
-    def log_lime_parameters(self, lime):
+    def log_lime_parameters(self, lime: PyLimeConfig) -> None:
-        """This method logs the parameters of the limr object.
+        """Logs the parameters of the limr object.
 
         Args:
             lime (PyLimeConfig): The PyLimeConfig object that is used to communicate with the pulseN driver
         """
         # for key, value in lime.__dict__.items():
-            # logger.debug("Lime parameter %s has value %s", key, value)
+        # logger.debug("Lime parameter %s has value %s", key, value)
         logger.debug("Lime parameter %s has value %s", "srate", lime.srate)
 
-    def update_settings(self, lime):
+    def update_settings(self, lime: PyLimeConfig) -> PyLimeConfig:
-        """This method sets the parameters of the limr object according to the settings set in the spectrometer module.
+        """Sets the parameters of the limr object according to the settings set in the spectrometer module.
 
         Args:
             lime (PyLimeConfig): The PyLimeConfig object that is used to communicate with the pulseN driver
 
         Returns:
-        lime: The updated limr object
+            lime: The updated limr object
         """
         logger.debug(
             "Updating settings for spectrometer: %s for measurement",
@@ -259,7 +289,9 @@ class LimeNQRController(BaseSpectrometerController):
                     lime.RX_matching = setting.get_setting()
                 # Careful this doesn't only set the IF frequency but the local oscillator frequency
                 elif setting.name == self.module.model.IF_FREQUENCY:
-                    lime.frq = self.module.model.target_frequency - setting.get_setting()
+                    lime.frq = (
+                        self.module.model.target_frequency - setting.get_setting()
+                    )
                     self.module.model.if_frequency = setting.get_setting()
                 elif setting.name == self.module.model.ACQUISITION_TIME:
                     lime.rectime_secs = setting.get_setting()
@@ -309,8 +341,8 @@ class LimeNQRController(BaseSpectrometerController):
         lime.c3_tim = c3_tim
         return lime
 
-    def translate_pulse_sequence(self, lime):
+    def translate_pulse_sequence(self, lime: PyLimeConfig) -> PyLimeConfig:
-        """This method translates the pulse sequence to the limr object.
+        """Ttranslates the pulse sequence to the limr object.
 
         Args:
             lime (PyLimeConfig): The PyLimeConfig object that is used to communicate with the pulseN driver
@@ -325,15 +357,25 @@ class LimeNQRController(BaseSpectrometerController):
                 self.log_parameter_details(parameter)
 
                 if self.is_translatable_tx_parameter(parameter):
-                    pulse_shape, pulse_amplitude = self.prepare_pulse_amplitude(event, parameter)
+                    pulse_shape, pulse_amplitude = self.prepare_pulse_amplitude(
-                    pulse_amplitude, modulated_phase = self.modulate_pulse_amplitude(pulse_amplitude, event, lime)
+                        event, parameter
+                    )
+                    pulse_amplitude, modulated_phase = self.modulate_pulse_amplitude(
+                        pulse_amplitude, event, lime
+                    )
 
                     if first_pulse:  # If the pulse frequency list is empty
-                        pfr, pdr, pam, pof, pph = self.initialize_pulse_lists(lime, pulse_amplitude, pulse_shape, modulated_phase)
+                        pfr, pdr, pam, pof, pph = self.initialize_pulse_lists(
+                            lime, pulse_amplitude, pulse_shape, modulated_phase
+                        )
                         first_pulse = False
                     else:
-                        pfr_ext, pdr_ext, pam_ext, pph_ext = self.extend_pulse_lists(lime, pulse_amplitude, pulse_shape, modulated_phase)
+                        pfr_ext, pdr_ext, pam_ext, pph_ext = self.extend_pulse_lists(
-                        pof_ext =  self.calculate_and_set_offsets(lime, pulse_shape, events, event, pulse_amplitude)
+                            pulse_amplitude, pulse_shape, modulated_phase
+                        )
+                        pof_ext = self.calculate_and_set_offsets(
+                            lime, pulse_shape, events, event, pulse_amplitude
+                        )
 
                         pfr.extend(pfr_ext)
                         pdr.extend(pdr_ext)
@@ -351,8 +393,9 @@ class LimeNQRController(BaseSpectrometerController):
         lime.Npulses = len(lime.p_frq)
         return lime
 
-    def get_number_of_pulses(self):
+    def get_number_of_pulses(self) -> int:
-        """This method calculates the number of pulses in the pulse sequence before the LimeDriverBinding is initialized.
+        """Calculates the number of pulses in the pulse sequence before the LimeDriverBinding is initialized.
+
         This makes sure it"s initialized with the correct size of the pulse lists.
 
         Returns:
@@ -371,31 +414,35 @@ class LimeNQRController(BaseSpectrometerController):
 
     # Helper functions below:
 
-    def fetch_pulse_sequence_events(self):
+    def fetch_pulse_sequence_events(self) -> list:
-        """This method fetches the pulse sequence events from the pulse programmer module.
+        """Fetches the pulse sequence events from the pulse programmer module.
 
         Returns:
             list: The pulse sequence events
         """
         return self.module.model.pulse_programmer.model.pulse_sequence.events
 
-    def log_event_details(self, event):
+    def log_event_details(self, event) -> None:
+        """Logs the details of an event."""
         logger.debug("Event %s has parameters: %s", event.name, event.parameters)
 
-    def log_parameter_details(self, parameter):
+    def log_parameter_details(self, parameter) -> None:
+        """Logs the details of a parameter."""
         logger.debug("Parameter %s has options: %s", parameter.name, parameter.options)
 
     def is_translatable_tx_parameter(self, parameter):
-        """This method checks if a parameter a pulse with a transmit pulse shape (amplitude nonzero)
+        """Checks if a parameter a pulse with a transmit pulse shape (amplitude nonzero).
 
         Args:
-        parameter (Parameter): The parameter to check
+            parameter (Parameter): The parameter to check
         """
-        return (parameter.name == self.module.model.TX and
+        return (
-                parameter.get_option_by_name(TXPulse.RELATIVE_AMPLITUDE).value > 0)
+            parameter.name == self.module.model.TX
+            and parameter.get_option_by_name(TXPulse.RELATIVE_AMPLITUDE).value > 0
+        )
 
     def prepare_pulse_amplitude(self, event, parameter):
-        """This method prepares the pulse amplitude for the limr object.
+        """Prepares the pulse amplitude for the limr object.
 
         Args:
             event (Event): The event that contains the parameter
@@ -405,13 +452,16 @@ class LimeNQRController(BaseSpectrometerController):
         tuple: A tuple containing the pulse shape and the pulse amplitude
         """
         pulse_shape = parameter.get_option_by_name(TXPulse.TX_PULSE_SHAPE).value
-        pulse_amplitude = abs(pulse_shape.get_pulse_amplitude(event.duration)) * \
+        pulse_amplitude = abs(pulse_shape.get_pulse_amplitude(event.duration)) * (
-                          (parameter.get_option_by_name(TXPulse.RELATIVE_AMPLITUDE).value / 100)
+            parameter.get_option_by_name(TXPulse.RELATIVE_AMPLITUDE).value / 100
+        )
         pulse_amplitude = np.clip(pulse_amplitude, -0.99, 0.99)
         return pulse_shape, pulse_amplitude
 
-    def modulate_pulse_amplitude(self, pulse_amplitude, event, lime):
+    def modulate_pulse_amplitude(
-        """This method modulates the pulse amplitude for the limr object. We need to do this to have the pulse at IF frequency instead  of LO frequency.
+        self, pulse_amplitude: float, event, lime: PyLimeConfig
+    ) -> tuple:
+        """Modulates the pulse amplitude for the limr object. We need to do this to have the pulse at IF frequency instead  of LO frequency.
 
         Args:
             pulse_amplitude (float): The pulse amplitude
@@ -430,58 +480,72 @@ class LimeNQRController(BaseSpectrometerController):
         modulated_phase = self.unwrap_phase(np.angle(pulse_complex))
         return modulated_amplitude, modulated_phase
 
-    def unwrap_phase(self, phase):
+    def unwrap_phase(self, phase: float) -> float:
         """This method unwraps the phase of the pulse.
 
         Args:
-        phase (float): The phase of the pulse
+            phase (float): The phase of the pulse
         """
         return (np.unwrap(phase) + 2 * np.pi) % (2 * np.pi)
 
-    def initialize_pulse_lists(self, lime, pulse_amplitude, pulse_shape, modulated_phase):
+    def initialize_pulse_lists(
+        self,
+        lime: PyLimeConfig,
+        pulse_amplitude: np.array,
+        pulse_shape,
+        modulated_phase: np.array,
+    ) -> tuple:
         """This method initializes the pulse lists of the limr object.
 
         Args:
             lime (PyLimeConfig): The PyLimeConfig object that is used to communicate with the pulseN driver
-            pulse_amplitude (float): The pulse amplitude
+            pulse_amplitude (np.array): The pulse amplitude
-            pulse_shape (PulseShape): The pulse shape
+            pulse_shape (Function): The pulse shape
-            modulated_phase (float): The modulated phase
+            modulated_phase (np.array): The modulated phase
         """
         pfr = [float(self.module.model.if_frequency)] * len(pulse_amplitude)
         # We set the first  len(pulse_amplitude) of the p_dur
         pdr = [float(pulse_shape.resolution)] * len(pulse_amplitude)
         pam = list(pulse_amplitude)
-        pof = ([self.module.model.OFFSET_FIRST_PULSE] +
+        pof = [self.module.model.OFFSET_FIRST_PULSE] + [
-                    [int(pulse_shape.resolution * lime.srate)] * (len(pulse_amplitude) - 1))
+            int(pulse_shape.resolution * lime.srate)
+        ] * (len(pulse_amplitude) - 1)
         pph = list(modulated_phase)
 
-        return  pfr, pdr, pam, pof, pph
+        return pfr, pdr, pam, pof, pph
 
-    def extend_pulse_lists(self, lime, pulse_amplitude, pulse_shape, modulated_phase):
+    def extend_pulse_lists(self, pulse_amplitude, pulse_shape, modulated_phase):
         """This method extends the pulse lists of the limr object.
 
         Args:
-            lime (PyLimeConfig): The PyLimeConfig object that is used to communicate with the pulseN driver
             pulse_amplitude (float): The pulse amplitude
             pulse_shape (PulseShape): The pulse shape
             modulated_phase (float): The modulated phase
+
+        Returns:
+            tuple: A tuple containing the extended pulse lists (frequency, duration, amplitude, phase)
         """
-        pfr = ([float(self.module.model.if_frequency)] * len(pulse_amplitude))
+        pfr = [float(self.module.model.if_frequency)] * len(pulse_amplitude)
-        pdr = ([float(pulse_shape.resolution)] * len(pulse_amplitude))
+        pdr = [float(pulse_shape.resolution)] * len(pulse_amplitude)
-        pam = (list(pulse_amplitude))
+        pam = list(pulse_amplitude)
-        pph = (list(modulated_phase))
+        pph = list(modulated_phase)
 
         return pfr, pdr, pam, pph
 
-    def calculate_and_set_offsets(self, lime, pulse_shape, events, current_event, pulse_amplitude):
+    def calculate_and_set_offsets(
+        self, lime: PyLimeConfig, pulse_shape, events, current_event, pulse_amplitude
+    ) -> list:
         """This method calculates and sets the offsets for the limr object.
 
         Args:
             lime (PyLimeConfig): The PyLimeConfig object that is used to communicate with the pulseN driver
-            pulse_shape (PulseShape): The pulse shape
+            pulse_shape (Function): The pulse shape
             events (list): The pulse sequence events
             current_event (Event): The current event
             pulse_amplitude (float): The pulse amplitude
+
+        Returns:
+            list: The offsets for the limr object
         """
         blank_durations = self.get_blank_durations_before_event(events, current_event)
 
@@ -500,7 +564,8 @@ class LimeNQRController(BaseSpectrometerController):
         pof.extend([offset_per_sample] * (len(pulse_amplitude) - 1))
         return pof
 
-    def get_blank_durations_before_event(self, events, current_event):
+    # This method could be refactored in a potential pulse sequence module
+    def get_blank_durations_before_event(self, events, current_event) -> list:
         """This method returns the blank durations before the current event.
 
         Args:
@@ -511,12 +576,15 @@ class LimeNQRController(BaseSpectrometerController):
             list: The blank durations before the current event
         """
         blank_durations = []
-        previous_events_without_tx_pulse = self.get_previous_events_without_tx_pulse(events, current_event)
+        previous_events_without_tx_pulse = self.get_previous_events_without_tx_pulse(
+            events, current_event
+        )
         for event in previous_events_without_tx_pulse:
             blank_durations.append(float(event.duration))
         return blank_durations
 
-    def get_previous_events_without_tx_pulse(self, events, current_event):
+    # This method could be refactored in a potential pulse sequence module
+    def get_previous_events_without_tx_pulse(self, events, current_event) -> list:
         """This method returns the previous events without a transmit pulse.
 
         Args:
@@ -530,15 +598,19 @@ class LimeNQRController(BaseSpectrometerController):
         previous_events = events[:index]
         result = []
         for event in reversed(previous_events):
-            translatable = any(self.is_translatable_tx_parameter(param) for param in event.parameters.values())
+            translatable = any(
+                self.is_translatable_tx_parameter(param)
+                for param in event.parameters.values()
+            )
             if not translatable:
                 result.append(event)
             else:
                 break
-        return reversed(result)  # Reversed to maintain the original order if needed elsewhere
+        return reversed(
+            result
+        )  # Reversed to maintain the original order if needed elsewhere
 
-
+    def translate_rx_event(self, lime : PyLimeConfig) -> tuple:
-    def translate_rx_event(self, lime):
         """This method translates the RX event of the pulse sequence to the limr object.
 
         Args:
@@ -547,19 +619,25 @@ class LimeNQRController(BaseSpectrometerController):
         Returns:
             tuple: A tuple containing the start and stop time of the RX event in µs
         """
-        CORRECTION_FACTOR = self.module.model.get_setting_by_name(self.module.model.RX_OFFSET).value
+        CORRECTION_FACTOR = self.module.model.get_setting_by_name(
+            self.module.model.RX_OFFSET
+        ).value
         events = self.module.model.pulse_programmer.model.pulse_sequence.events
 
         rx_event = self.find_rx_event(events)
         if not rx_event:
             return None, None
 
-        previous_events_duration = self.calculate_previous_events_duration(events, rx_event)
+        previous_events_duration = self.calculate_previous_events_duration(
+            events, rx_event
+        )
         rx_duration = float(rx_event.duration)
 
         offset = self.calculate_offset(lime)
 
-        rx_begin = float(previous_events_duration) + float(offset) + float(CORRECTION_FACTOR)
+        rx_begin = (
+            float(previous_events_duration) + float(offset) + float(CORRECTION_FACTOR)
+        )
         rx_stop = rx_begin + rx_duration
         return rx_begin * 1e6, rx_stop * 1e6
 
@@ -593,7 +671,7 @@ class LimeNQRController(BaseSpectrometerController):
         previous_events = events[: events.index(rx_event)]
         return sum(event.duration for event in previous_events)
 
-    def calculate_offset(self, lime):
+    def calculate_offset(self, lime :PyLimeConfig) -> float:
         """This method calculates the offset for the RX event.
 
         Args:
@@ -604,8 +682,7 @@ class LimeNQRController(BaseSpectrometerController):
         """
         return self.module.model.OFFSET_FIRST_PULSE * (1 / lime.srate)
 
-
+    def set_frequency(self, value: float) -> None:
-    def set_frequency(self, value: float):
         """This method sets the target frequency of the spectrometer.
 
         Args:
@@ -622,7 +699,7 @@ class LimeNQRController(BaseSpectrometerController):
             )
             self.module.nqrduck_signal.emit("failure_set_frequency", value)
 
-    def set_averages(self, value: int):
+    def set_averages(self, value: int) -> None:
         """This method sets the number of averages for the spectrometer.
 
         Args:

src/nqrduck_spectrometer_limenqr/limenqr.py

@@ -1,3 +1,5 @@
+"""BaseSpectrometer for Lime NQR spectrometer."""
+
 from nqrduck_spectrometer.base_spectrometer import BaseSpectrometer
 from .model import LimeNQRModel
 from .view import LimeNQRView

src/nqrduck_spectrometer_limenqr/model.py

@@ -1,12 +1,20 @@
+"""Model for the Lime NQR spectrometer."""
+
 import logging
 from nqrduck_spectrometer.base_spectrometer_model import BaseSpectrometerModel
 from nqrduck_spectrometer.pulseparameters import TXPulse, RXReadout
-from nqrduck_spectrometer.settings import FloatSetting, IntSetting, BooleanSetting, SelectionSetting
+from nqrduck_spectrometer.settings import (
+    FloatSetting,
+    IntSetting,
+    BooleanSetting,
+    SelectionSetting,
+)
 
 logger = logging.getLogger(__name__)
 
 
 class LimeNQRModel(BaseSpectrometerModel):
+    """Model for the Lime NQR spectrometer."""
     # Setting constants for the names of the spectrometer settings
     CHANNEL = "TX/RX Channel"
     TX_MATCHING = "TX Matching"
@@ -49,91 +57,228 @@ class LimeNQRModel(BaseSpectrometerModel):
     # Settings that are not changed by the user
     OFFSET_FIRST_PULSE = 300
 
-
     def __init__(self, module) -> None:
+        """Initializes the Lime NQR model."""
         super().__init__(module)
         # Acquisition settings
         channel_options = ["0", "1"]
-        channel_setting = SelectionSetting(self.CHANNEL, channel_options, "0", "TX/RX Channel")
+        channel_setting = SelectionSetting(
+            self.CHANNEL, channel_options, "0", "TX/RX Channel"
+        )
         self.add_setting(channel_setting, self.ACQUISITION)
 
         tx_matching_options = ["0", "1"]
-        tx_matching_setting = SelectionSetting(self.TX_MATCHING, tx_matching_options, "0", "TX Matching")
+        tx_matching_setting = SelectionSetting(
+            self.TX_MATCHING, tx_matching_options, "0", "TX Matching"
+        )
         self.add_setting(tx_matching_setting, self.ACQUISITION)
 
         rx_matching_options = ["0", "1"]
-        rx_matching_setting = SelectionSetting(self.RX_MATCHING, rx_matching_options, "0", "RX Matching")
+        rx_matching_setting = SelectionSetting(
+            self.RX_MATCHING, rx_matching_options, "0", "RX Matching"
+        )
         self.add_setting(rx_matching_setting, self.ACQUISITION)
 
-        sampling_frequency_setting = FloatSetting(self.SAMPLING_FREQUENCY, 30.72e6, "The rate at which the spectrometer samples the input signal.", min_value=0, max_value=30.72e6)
+        sampling_frequency_setting = FloatSetting(
+            self.SAMPLING_FREQUENCY,
+            30.72e6,
+            "The rate at which the spectrometer samples the input signal.",
+            min_value=0,
+            max_value=30.72e6,
+        )
         self.add_setting(sampling_frequency_setting, self.ACQUISITION)
 
-        if_frequency_setting = FloatSetting(self.IF_FREQUENCY, 5e6, "The intermediate frequency to which the input signal is down converted during analog-to-digital conversion.", min_value=0)
+        if_frequency_setting = FloatSetting(
+            self.IF_FREQUENCY,
+            5e6,
+            "The intermediate frequency to which the input signal is down converted during analog-to-digital conversion.",
+            min_value=0,
+        )
         self.add_setting(if_frequency_setting, self.ACQUISITION)
         self.if_frequency = 5e6
 
-        acquisition_time_setting = FloatSetting(self.ACQUISITION_TIME, 82e-6, "Acquisition time - this is from the beginning of the pulse sequence", min_value=0)
+        acquisition_time_setting = FloatSetting(
+            self.ACQUISITION_TIME,
+            82e-6,
+            "Acquisition time - this is from the beginning of the pulse sequence",
+            min_value=0,
+        )
         self.add_setting(acquisition_time_setting, self.ACQUISITION)
 
         # Gate Settings
-        gate_enable_setting = BooleanSetting(self.GATE_ENABLE, True, "Setting that controls whether gate is on during transmitting.")
+        gate_enable_setting = BooleanSetting(
+            self.GATE_ENABLE,
+            True,
+            "Setting that controls whether gate is on during transmitting.",
+        )
         self.add_setting(gate_enable_setting, self.GATE_SETTINGS)
 
-        gate_padding_left_setting = IntSetting(self.GATE_PADDING_LEFT, 10, "The number of samples by which to extend the gate window to the left.", min_value=0)
+        gate_padding_left_setting = IntSetting(
+            self.GATE_PADDING_LEFT,
+            10,
+            "The number of samples by which to extend the gate window to the left.",
+            min_value=0,
+        )
         self.add_setting(gate_padding_left_setting, self.GATE_SETTINGS)
 
-        gate_padding_right_setting = IntSetting(self.GATE_PADDING_RIGHT, 10, "The number of samples by which to extend the gate window to the right.", min_value=0)
+        gate_padding_right_setting = IntSetting(
+            self.GATE_PADDING_RIGHT,
+            10,
+            "The number of samples by which to extend the gate window to the right.",
+            min_value=0,
+        )
         self.add_setting(gate_padding_right_setting, self.GATE_SETTINGS)
 
-        gate_shift_setting = IntSetting(self.GATE_SHIFT, 53, "The delay, in number of samples, by which the gate window is shifted.", min_value=0)
+        gate_shift_setting = IntSetting(
+            self.GATE_SHIFT,
+            53,
+            "The delay, in number of samples, by which the gate window is shifted.",
+            min_value=0,
+        )
         self.add_setting(gate_shift_setting, self.GATE_SETTINGS)
 
         # RX/TX settings
-        rx_gain_setting = IntSetting(self.RX_GAIN, 55, "The gain level of the receiver’s amplifier.", min_value=0, max_value=55, spin_box=(True, True))
+        rx_gain_setting = IntSetting(
+            self.RX_GAIN,
+            55,
+            "The gain level of the receiver’s amplifier.",
+            min_value=0,
+            max_value=55,
+            spin_box=(True, True),
+        )
         self.add_setting(rx_gain_setting, self.RX_TX_SETTINGS)
 
-        tx_gain_setting = IntSetting(self.TX_GAIN, 30, "The gain level of the transmitter’s amplifier.", min_value=0, max_value=55, spin_box=(True, True))
+        tx_gain_setting = IntSetting(
+            self.TX_GAIN,
+            30,
+            "The gain level of the transmitter’s amplifier.",
+            min_value=0,
+            max_value=55,
+            spin_box=(True, True),
+        )
         self.add_setting(tx_gain_setting, self.RX_TX_SETTINGS)
 
-        rx_lpf_bw_setting = FloatSetting(self.RX_LPF_BW, 30.72e6/2, "The bandwidth of the receiver’s low-pass filter which attenuates frequencies below a certain threshold.")
+        rx_lpf_bw_setting = FloatSetting(
+            self.RX_LPF_BW,
+            30.72e6 / 2,
+            "The bandwidth of the receiver’s low-pass filter which attenuates frequencies below a certain threshold.",
+        )
         self.add_setting(rx_lpf_bw_setting, self.RX_TX_SETTINGS)
 
-        tx_lpf_bw_setting = FloatSetting(self.TX_LPF_BW, 130.0e6, "The bandwidth of the transmitter’s low-pass filter which limits the frequency range of the transmitted signa")
+        tx_lpf_bw_setting = FloatSetting(
+            self.TX_LPF_BW,
+            130.0e6,
+            "The bandwidth of the transmitter’s low-pass filter which limits the frequency range of the transmitted signa",
+        )
         self.add_setting(tx_lpf_bw_setting, self.RX_TX_SETTINGS)
 
         # Calibration settings
-        tx_i_dc_correction_setting = IntSetting(self.TX_I_DC_CORRECTION, -45, "Adjusts the direct current offset errors in the in-phase (I) component of the transmit (TX) path.", min_value=-128, max_value=127, spin_box=(True, True))
+        tx_i_dc_correction_setting = IntSetting(
+            self.TX_I_DC_CORRECTION,
+            -45,
+            "Adjusts the direct current offset errors in the in-phase (I) component of the transmit (TX) path.",
+            min_value=-128,
+            max_value=127,
+            spin_box=(True, True),
+        )
         self.add_setting(tx_i_dc_correction_setting, self.CALIBRATION)
 
-        tx_q_dc_correction_setting = IntSetting(self.TX_Q_DC_CORRECTION, 0, "Adjusts the direct current offset errors in the quadrature (Q) component of the transmit (TX) path.", min_value=-128, max_value=127, spin_box=(True, True))
+        tx_q_dc_correction_setting = IntSetting(
+            self.TX_Q_DC_CORRECTION,
+            0,
+            "Adjusts the direct current offset errors in the quadrature (Q) component of the transmit (TX) path.",
+            min_value=-128,
+            max_value=127,
+            spin_box=(True, True),
+        )
         self.add_setting(tx_q_dc_correction_setting, self.CALIBRATION)
 
-        tx_i_gain_correction_setting = IntSetting(self.TX_I_GAIN_CORRECTION, 2047, "Modifies the gain settings for the I channel of the TX path, adjusting for imbalances.", min_value=0, max_value=2047, spin_box=(True, True))
+        tx_i_gain_correction_setting = IntSetting(
+            self.TX_I_GAIN_CORRECTION,
+            2047,
+            "Modifies the gain settings for the I channel of the TX path, adjusting for imbalances.",
+            min_value=0,
+            max_value=2047,
+            spin_box=(True, True),
+        )
         self.add_setting(tx_i_gain_correction_setting, self.CALIBRATION)
 
-        tx_q_gain_correction_setting = IntSetting(self.TX_Q_GAIN_CORRECTION, 2039, "Modifies the gain settings for the Q channel of the TX path, adjusting for imbalances.", min_value=0, max_value=2047, spin_box=(True, True))
+        tx_q_gain_correction_setting = IntSetting(
+            self.TX_Q_GAIN_CORRECTION,
+            2039,
+            "Modifies the gain settings for the Q channel of the TX path, adjusting for imbalances.",
+            min_value=0,
+            max_value=2047,
+            spin_box=(True, True),
+        )
         self.add_setting(tx_q_gain_correction_setting, self.CALIBRATION)
 
-        tx_phase_adjustment_setting = IntSetting(self.TX_PHASE_ADJUSTMENT, 3, "Corrects the Phase of I Q signals in the TX path.", min_value=-2048, max_value=2047, spin_box=(True, True))
+        tx_phase_adjustment_setting = IntSetting(
+            self.TX_PHASE_ADJUSTMENT,
+            3,
+            "Corrects the Phase of I Q signals in the TX path.",
+            min_value=-2048,
+            max_value=2047,
+            spin_box=(True, True),
+        )
         self.add_setting(tx_phase_adjustment_setting, self.CALIBRATION)
 
-        rx_i_dc_correction_setting = IntSetting(self.RX_I_DC_CORRECTION, 0, "Adjusts the direct current offset errors in the in-phase (I) component of the receive (RX) path.", min_value=-63, max_value=63, spin_box=(True, True))
+        rx_i_dc_correction_setting = IntSetting(
+            self.RX_I_DC_CORRECTION,
+            0,
+            "Adjusts the direct current offset errors in the in-phase (I) component of the receive (RX) path.",
+            min_value=-63,
+            max_value=63,
+            spin_box=(True, True),
+        )
         self.add_setting(rx_i_dc_correction_setting, self.CALIBRATION)
 
-        rx_q_dc_correction_setting = IntSetting(self.RX_Q_DC_CORRECTION, 0, "Adjusts the direct current offset errors in the quadrature (Q) component of the receive (RX) path.", min_value=-63, max_value=63, spin_box=(True, True))
+        rx_q_dc_correction_setting = IntSetting(
+            self.RX_Q_DC_CORRECTION,
+            0,
+            "Adjusts the direct current offset errors in the quadrature (Q) component of the receive (RX) path.",
+            min_value=-63,
+            max_value=63,
+            spin_box=(True, True),
+        )
         self.add_setting(rx_q_dc_correction_setting, self.CALIBRATION)
 
-        rx_i_gain_correction_setting = IntSetting(self.RX_I_GAIN_CORRECTION, 2047, "Modifies the gain settings for the I channel of the RX path, adjusting for imbalances.", min_value=0, max_value=2047, spin_box=(True, True))
+        rx_i_gain_correction_setting = IntSetting(
+            self.RX_I_GAIN_CORRECTION,
+            2047,
+            "Modifies the gain settings for the I channel of the RX path, adjusting for imbalances.",
+            min_value=0,
+            max_value=2047,
+            spin_box=(True, True),
+        )
         self.add_setting(rx_i_gain_correction_setting, self.CALIBRATION)
 
-        rx_q_gain_correction_setting = IntSetting(self.RX_Q_GAIN_CORRECTION, 2047, "Modifies the gain settings for the Q channel of the RX path, adjusting for imbalances.", min_value=0, max_value=2047, spin_box=(True, True))
+        rx_q_gain_correction_setting = IntSetting(
+            self.RX_Q_GAIN_CORRECTION,
+            2047,
+            "Modifies the gain settings for the Q channel of the RX path, adjusting for imbalances.",
+            min_value=0,
+            max_value=2047,
+            spin_box=(True, True),
+        )
         self.add_setting(rx_q_gain_correction_setting, self.CALIBRATION)
 
-        rx_phase_adjustment_setting = IntSetting(self.RX_PHASE_ADJUSTMENT, 0, "Corrects the Phase of I Q signals in the RX path.", min_value=-2048, max_value=2047, spin_box=(True, True))
+        rx_phase_adjustment_setting = IntSetting(
+            self.RX_PHASE_ADJUSTMENT,
+            0,
+            "Corrects the Phase of I Q signals in the RX path.",
+            min_value=-2048,
+            max_value=2047,
+            spin_box=(True, True),
+        )
         self.add_setting(rx_phase_adjustment_setting, self.CALIBRATION)
 
         # Signal Processing settings
-        rx_offset_setting = FloatSetting(self.RX_OFFSET, 2.4e-6, "The offset of the RX event, this changes all the time")
+        rx_offset_setting = FloatSetting(
+            self.RX_OFFSET,
+            2.4e-6,
+            "The offset of the RX event, this changes all the time",
+        )
         self.add_setting(rx_offset_setting, self.SIGNAL_PROCESSING)
 
         fft_shift_setting = BooleanSetting(self.FFT_SHIFT, False, "FFT shift")
@@ -147,6 +292,7 @@ class LimeNQRModel(BaseSpectrometerModel):
         # Try to load the pulse programmer module
         try:
             from nqrduck_pulseprogrammer.pulseprogrammer import pulse_programmer
+
             self.pulse_programmer = pulse_programmer
             logger.debug("Pulse programmer found.")
             self.pulse_programmer.controller.on_loading(self.pulse_parameter_options)
@@ -157,6 +303,7 @@ class LimeNQRModel(BaseSpectrometerModel):
 
     @property
     def target_frequency(self):
+        """The target frequency of the spectrometer."""
         return self._target_frequency
 
     @target_frequency.setter
@@ -165,6 +312,7 @@ class LimeNQRModel(BaseSpectrometerModel):
 
     @property
     def averages(self):
+        """The number of averages to be taken."""
         return self._averages
 
     @averages.setter
@@ -173,10 +321,9 @@ class LimeNQRModel(BaseSpectrometerModel):
 
     @property
     def if_frequency(self):
+        """The intermediate frequency to which the input signal is down converted during analog-to-digital conversion."""
         return self._if_frequency
 
     @if_frequency.setter
     def if_frequency(self, value):
         self._if_frequency = value
-
-

src/nqrduck_spectrometer_limenqr/view.py

@@ -1,9 +1,13 @@
+"""View  for LimeNQR spectrometer."""
 from nqrduck_spectrometer.base_spectrometer_view import BaseSpectrometerView
 
 
 class LimeNQRView(BaseSpectrometerView):
+    """View class for LimeNQR spectrometer."""
+
     def __init__(self, module):
+        """Initialize the LimeNQRView object."""
         super().__init__(module)
 
+        # Setting UI is automatically generated based on the settings specified in the model
         self.widget = self.load_settings_ui()
-