spectre-core 0.0.21__py3-none-any.whl → 0.0.23__py3-none-any.whl

spectre_core/spectrograms/_spectrogram.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: © 2024 Jimmy Fitzpatrick <jcfitzpatrick12@gmail.com>
+# SPDX-FileCopyrightText: © 2024-2025 Jimmy Fitzpatrick <jcfitzpatrick12@gmail.com>
 # This file is part of SPECTRE
 # SPDX-License-Identifier: GPL-3.0-or-later
 
@@ -26,27 +26,29 @@ from ._array_operations import (
 
 class SpectrumUnit(Enum):
     """A defined unit for dynamic spectra values.
-    
+
     :ivar AMPLITUDE: Formal definition TBC.
     :ivar POWER: Formal definition TBC.
     :ivar DIGITS: Formal definition TBC.
     """
+
     AMPLITUDE = "amplitude"
-    POWER     = "power"
-    DIGITS    = "digits"
-    
+    POWER = "power"
+    DIGITS = "digits"
+
 
 @dataclass
 class FrequencyCut:
-    """A cut of a dynamic spectra, at a particular instant of time. Equivalently, some spectrum in 
+    """A cut of a dynamic spectra, at a particular instant of time. Equivalently, some spectrum in
     the spectrogram.
-    
+
     :ivar time: The time of the frequency cut, either in relative time (if time is a float)
     or as a datetime.
     :ivar frequencies: The physical frequencies assigned to each spectral component, in Hz.
     :ivar cut: The spectrum values.
     :ivar spectrum_unit: The unit of each spectrum value.
     """
+
     time: float | datetime
     frequencies: npt.NDArray[np.float32]
     cut: npt.NDArray[np.float32]
@@ -57,13 +59,14 @@ class FrequencyCut:
 class TimeCut:
     """A cut of a dynamic spectra, at some fixed frequency. Equivalently, a time series of
     some spectral component in the spectrogram.
-    
+
     :ivar frequency: The physical frequency assigned to the spectral component, in Hz.
-    :ivar times: The time for each time series value, either as a relative time (if 
+    :ivar times: The time for each time series value, either as a relative time (if
     the elements are floats) or as a datetimes.
     :ivar cut: The time series values of the spectral component.
     :ivar spectrum_unit: The unit of each time series value.
     """
+
     frequency: float
     times: npt.NDArray[np.float32 | np.datetime64]
     cut: npt.NDArray[np.float32]
@@ -72,27 +75,29 @@ class TimeCut:
 
 class TimeType(Enum):
     """The type of time we can assign to each spectrum in the dynamic spectra.
-    
+
     :ivar RELATIVE: The elapsed time from the first spectrum, in seconds.
     :ivar DATETIMES: The datetime associated with each spectrum.
     """
-    RELATIVE   = "relative"
-    DATETIMES  = "datetimes"
+
+    RELATIVE = "relative"
+    DATETIMES = "datetimes"
 
 
 class Spectrogram:
     """Standardised wrapper for spectrogram data, providing a consistent
-    interface for storing, accessing, and manipulating spectrogram data, 
+    interface for storing, accessing, and manipulating spectrogram data,
     along with associated metadata.
     """
+
     def __init__(
-        self, 
+        self,
         dynamic_spectra: npt.NDArray[np.float32],
-        times          : npt.NDArray[np.float32], 
-        frequencies    : npt.NDArray[np.float32], 
-        tag            : str,
-        spectrum_unit  : SpectrumUnit,
-        start_datetime : Optional[datetime | np.datetime64] = None
+        times: npt.NDArray[np.float32],
+        frequencies: npt.NDArray[np.float32],
+        tag: str,
+        spectrum_unit: SpectrumUnit,
+        start_datetime: Optional[datetime | np.datetime64] = None,
     ) -> None:
         """Initialise a Spectrogram instance.
 
@@ -105,145 +110,109 @@ class Spectrogram:
         :param start_datetime: The datetime corresponding to the first spectrum, defaults to None.
         :raises ValueError: If times does not start at 0 or array shapes are inconsistent.
         """
-        
+
         self._dynamic_spectra = dynamic_spectra
 
         if times[0] != 0:
             raise ValueError(f"The first spectrum must correspond to t=0")
         self._times = times
-        
+
         self._frequencies = frequencies
         self._tag = tag
         self._spectrum_unit = spectrum_unit
         self._start_datetime = np.datetime64(start_datetime)
-        
+
         # by default, the background is evaluated over the whole spectrogram
-        self._start_background_index = 0 
-        self._end_background_index   = self.num_times 
+        self._start_background_index = 0
+        self._end_background_index = self.num_times
         # the background interval can be set after instantiation
-        self._start_background: Optional[str]   = None 
-        self._end_background  : Optional[str]   = None
-        
+        self._start_background: Optional[str] = None
+        self._end_background: Optional[str] = None
+
         # finally check that the spectrogram arrays are matching in shape
         self._check_shapes()
 
-
     @property
-    def dynamic_spectra(
-        self
-    ) -> npt.NDArray[np.float32]:
+    def dynamic_spectra(self) -> npt.NDArray[np.float32]:
         """The dynamic spectra array.
-        
-        Returns the 2D array of spectrogram data with shape (num_frequencies, num_times), 
+
+        Returns the 2D array of spectrogram data with shape (num_frequencies, num_times),
         where values are in the units specified by `spectrum_unit`.
         """
         return self._dynamic_spectra
-    
 
     @property
-    def times(
-        self
-    ) -> npt.NDArray[np.float32]:
+    def times(self) -> npt.NDArray[np.float32]:
         """A 1D array representing the elapsed time of each spectrum, in seconds, relative to the first
         in the spectrogram."""
         return self._times
-    
-    
+
     @property
-    def num_times(
-        self
-    ) -> int:
+    def num_times(self) -> int:
         """The size of the times array. Equivalent to the number of spectrums in the spectrogram."""
         return len(self._times)
-    
 
     @property
-    def time_resolution(
-        self
-    ) -> float:
+    def time_resolution(self) -> float:
         """The time resolution of the dynamic spectra.
 
-        Represents the spacing between consecutive time values in the times array, 
+        Represents the spacing between consecutive time values in the times array,
         calculated as the median difference between adjacent elements.
         """
         return compute_resolution(self._times)
-    
 
     @property
-    def time_range(
-        self
-    ) -> float:
+    def time_range(self) -> float:
         """The time range of the dynamic spectra.
 
-        Represents the difference between the first and last time values 
+        Represents the difference between the first and last time values
         in the times array.
         """
         return compute_range(self._times)
-    
 
     @property
-    def frequencies(
-        self
-    ) -> npt.NDArray[np.float32]:
+    def frequencies(self) -> npt.NDArray[np.float32]:
         """A 1D array representing the physical frequencies assigned to each spectral component, in Hz."""
         return self._frequencies
 
-
     @property
-    def num_frequencies(
-        self
-    ) -> int:
+    def num_frequencies(self) -> int:
         """The number of spectral components in the spectrogram.
 
         Equivalent to the size of the frequencies array.
         """
         return len(self._frequencies)
-    
-    
+
     @property
-    def frequency_resolution(
-        self
-    ) -> float:
+    def frequency_resolution(self) -> float:
         """The frequency resolution of the dynamic spectra.
 
-        Represents the spacing between consecutive frequency values in the frequencies array, 
+        Represents the spacing between consecutive frequency values in the frequencies array,
         calculated as the median difference between adjacent elements.
         """
         return compute_resolution(self._frequencies)
-    
 
     @property
-    def frequency_range(
-        self
-    ) -> float:
+    def frequency_range(self) -> float:
         """The frequency range covered by the dynamic spectra.
 
-        Represents the difference between the minimum and maximum frequency 
+        Represents the difference between the minimum and maximum frequency
         values in the frequencies array.
         """
         return compute_range(self._frequencies)
-    
 
     @property
-    def tag(
-        self
-    ) -> str:
+    def tag(self) -> str:
         """The tag identifier for the spectrogram"""
         return self._tag
-    
 
     @property
-    def start_datetime_is_set(
-        self
-    ) -> bool:
+    def start_datetime_is_set(self) -> bool:
         """Indicates whether the start datetime for the spectrogram has been set."""
-        return (self._start_datetime is not None)
-    
-    
+        return self._start_datetime is not None
+
     @property
-    def start_datetime(
-        self
-    ) -> np.datetime64:
+    def start_datetime(self) -> np.datetime64:
         """The datetime assigned to the first spectrum in `dynamic_spectra`.
 
         :raises AttributeError: If the start_datetime has not been set.
@@ -251,166 +220,151 @@ class Spectrogram:
         if self._start_datetime is None:
             raise AttributeError(f"A start time has not been set.")
         return self._start_datetime
-    
-    
+
     @property
-    def datetimes(
-        self
-    ) -> npt.NDArray[np.datetime64]:
+    def datetimes(self) -> npt.NDArray[np.datetime64]:
         """The datetimes associated with each spectrum in `dynamic_spectra`.
 
-        Returns a list of datetime objects, calculated by adding the elapsed 
+        Returns a list of datetime objects, calculated by adding the elapsed
         times in the times array to the start_datetime.
         """
-        return self.start_datetime + (1e6*self._times).astype('timedelta64[us]')
-    
+        return self.start_datetime + (1e6 * self._times).astype("timedelta64[us]")
 
     @property
-    def spectrum_unit(
-        self
-    ) -> SpectrumUnit:
+    def spectrum_unit(self) -> SpectrumUnit:
         """The units associated with the `dynamic_spectra` array."""
         return self._spectrum_unit
-    
 
     @property
-    def start_background(
-        self
-    ) -> Optional[str]:
+    def start_background(self) -> Optional[str]:
         """The start of the background interval.
 
-        Returns a string-formatted datetime up to seconds precision, or None 
+        Returns a string-formatted datetime up to seconds precision, or None
         if the background interval has not been set.
         """
         return self._start_background
-    
 
     @property
-    def end_background(
-        self
-    ) -> Optional[str]:
+    def end_background(self) -> Optional[str]:
         """The end of the background interval.
 
-        Returns a string-formatted datetime up to seconds precision, or None 
+        Returns a string-formatted datetime up to seconds precision, or None
         if the background interval has not been set.
         """
         return self._end_background
-    
 
-    def compute_background_spectrum(
-        self
-    ) -> npt.NDArray[np.float32]:
+    def compute_background_spectrum(self) -> npt.NDArray[np.float32]:
         """Compute the background spectrum by averaging the dynamic spectra in time.
 
-        By default, the entire dynamic spectra is averaged. Use set_background to 
+        By default, the entire dynamic spectra is averaged. Use set_background to
         specify a custom background interval.
 
-        :return: A 1D array representing the time-averaged dynamic spectra over the 
+        :return: A 1D array representing the time-averaged dynamic spectra over the
         specified background interval.
         """
-        return np.nanmean(self._dynamic_spectra[:, self._start_background_index:self._end_background_index+1], 
-                                                   axis=-1)
-    
-
-    def compute_dynamic_spectra_dBb(
-        self
-    ) -> npt.NDArray[np.float32]:
+        return np.nanmean(
+            self._dynamic_spectra[
+                :, self._start_background_index : self._end_background_index + 1
+            ],
+            axis=-1,
+        )
+
+    def compute_dynamic_spectra_dBb(self) -> npt.NDArray[np.float32]:
         """Compute the dynamic spectra in units of decibels above the background spectrum.
 
-        The computation applies logarithmic scaling based on the `spectrum_unit`. 
+        The computation applies logarithmic scaling based on the `spectrum_unit`.
 
         :raises NotImplementedError: If the spectrum_unit is unrecognised.
-        :return: A 2D array with the same shape as `dynamic_spectra`, representing 
+        :return: A 2D array with the same shape as `dynamic_spectra`, representing
         the values in decibels above the background.
         """
         # Create a 'background' spectrogram where each spectrum is identically the background spectrum
         background_spectrum = self.compute_background_spectrum()
         background_spectra = background_spectrum[:, np.newaxis]
         # Suppress divide by zero and invalid value warnings for this block of code
-        with np.errstate(divide='ignore', invalid='ignore'):
-            if self._spectrum_unit == SpectrumUnit.AMPLITUDE or self._spectrum_unit == SpectrumUnit.DIGITS:
-                dynamic_spectra_dBb = 10 * np.log10(self._dynamic_spectra / background_spectra)
+        with np.errstate(divide="ignore", invalid="ignore"):
+            if (
+                self._spectrum_unit == SpectrumUnit.AMPLITUDE
+                or self._spectrum_unit == SpectrumUnit.DIGITS
+            ):
+                dynamic_spectra_dBb = 10 * np.log10(
+                    self._dynamic_spectra / background_spectra
+                )
             elif self._spectrum_unit == SpectrumUnit.POWER:
-                dynamic_spectra_dBb = 20 * np.log10(self._dynamic_spectra / background_spectra)
+                dynamic_spectra_dBb = 20 * np.log10(
+                    self._dynamic_spectra / background_spectra
+                )
             else:
-                raise NotImplementedError(f"{self._spectrum_unit} is unrecognised; decibel conversion is uncertain!")
+                raise NotImplementedError(
+                    f"{self._spectrum_unit} is unrecognised; decibel conversion is uncertain!"
+                )
         return dynamic_spectra_dBb.astype(np.float32)
-    
-    
-    def format_start_time(
-        self
-    ) -> str:
+
+    def format_start_time(self) -> str:
         """Format the datetime assigned to the first spectrum in the dynamic spectra.
 
         :return: A string representation of the `start_datetime`, up to seconds precision.
         """
         dt = self.start_datetime.astype(datetime)
         return datetime.strftime(dt, TimeFormat.DATETIME)
-    
-    
-    def set_background(
-        self, 
-        start_background: str, 
-        end_background: str
-    ) -> None:
+
+    def set_background(self, start_background: str, end_background: str) -> None:
         """Set the background interval for computing the background spectrum, and doing
         background subtractions.
 
-        :param start_background: The start time of the background interval, formatted as 
+        :param start_background: The start time of the background interval, formatted as
         a string in the format `TimeFormat.DATETIME` (up to seconds precision).
-        :param end_background: The end time of the background interval, formatted as 
+        :param end_background: The end time of the background interval, formatted as
         a string in the format `TimeFormat.DATETIME` (up to seconds precision).
         """
         self._start_background = start_background
-        self._end_background   = end_background
-        self._update_background_indices_from_interval(self._start_background, 
-                                                      self._end_background)
-    
-    
-    
+        self._end_background = end_background
+        self._update_background_indices_from_interval(
+            self._start_background, self._end_background
+        )
+
     def _update_background_indices_from_interval(
-        self,
-        start_background: str,
-        end_background: str
-    ) -> None:
-        start_background_datetime = np.datetime64( datetime.strptime(start_background, TimeFormat.DATETIME) )
-        end_background_datetime   = np.datetime64( datetime.strptime(end_background,   TimeFormat.DATETIME) )
-        self._start_background_index = find_closest_index(start_background_datetime, 
-                                                          self.datetimes, 
-                                                          enforce_strict_bounds=True)
-        self._end_background_index   = find_closest_index(end_background_datetime, 
-                                                          self.datetimes, 
-                                                          enforce_strict_bounds=True)
-
-
-    def _check_shapes(
-        self
+        self, start_background: str, end_background: str
     ) -> None:
+        start_background_datetime = np.datetime64(
+            datetime.strptime(start_background, TimeFormat.DATETIME)
+        )
+        end_background_datetime = np.datetime64(
+            datetime.strptime(end_background, TimeFormat.DATETIME)
+        )
+        self._start_background_index = find_closest_index(
+            start_background_datetime, self.datetimes, enforce_strict_bounds=True
+        )
+        self._end_background_index = find_closest_index(
+            end_background_datetime, self.datetimes, enforce_strict_bounds=True
+        )
+
+    def _check_shapes(self) -> None:
         """Check that the data array shapes are consistent with one another."""
         num_spectrogram_dims = np.ndim(self._dynamic_spectra)
         # Check if 'dynamic_spectra' is a 2D array
         if num_spectrogram_dims != 2:
-            raise ValueError(f"Expected dynamic spectrogram to be a 2D array, but got {num_spectrogram_dims}D array")
+            raise ValueError(
+                f"Expected dynamic spectrogram to be a 2D array, but got {num_spectrogram_dims}D array"
+            )
         dynamic_spectra_shape = self.dynamic_spectra.shape
         # Check if the dimensions of 'dynamic_spectra' are consistent with the time and frequency arrays
         if dynamic_spectra_shape[0] != self.num_frequencies:
-            raise ValueError(f"Mismatch in number of frequency bins: Expected {self.num_frequencies}, but got {dynamic_spectra_shape[0]}")
-        
+            raise ValueError(
+                f"Mismatch in number of frequency bins: Expected {self.num_frequencies}, but got {dynamic_spectra_shape[0]}"
+            )
+
         if dynamic_spectra_shape[1] != self.num_times:
-            raise ValueError(f"Mismatch in number of time bins: Expected {self.num_times}, but got {dynamic_spectra_shape[1]}")
-        
+            raise ValueError(
+                f"Mismatch in number of time bins: Expected {self.num_times}, but got {dynamic_spectra_shape[1]}"
+            )
 
-    def save(
-        self
-    ) -> None:
+    def save(self) -> None:
         """Write the spectrogram and its associated metadata to a batch file in the FITS format."""
         _save_spectrogram(self)
-    
 
     def integrate_over_frequency(
-        self, 
-        correct_background: bool = False, 
-        peak_normalise: bool = False
+        self, correct_background: bool = False, peak_normalise: bool = False
     ) -> npt.NDArray[np.float32]:
         """Numerically integrate the spectrogram over the frequency axis.
 
@@ -418,278 +372,291 @@ class Spectrogram:
         computing the integral, defaults to False
         :param peak_normalise: Indicates whether to normalise the integral such that
         the peak value is equal to unity, defaults to False
-        :return: A 1D array containing each spectrum numerically integrated over the 
+        :return: A 1D array containing each spectrum numerically integrated over the
         frequency axis.
         """
         # numerically integrate over frequency
         I = np.trapz(self._dynamic_spectra, self._frequencies, axis=0)
 
         if correct_background:
-            I = subtract_background(I, 
-                                    self._start_background_index, 
-                                    self._end_background_index)
+            I = subtract_background(
+                I, self._start_background_index, self._end_background_index
+            )
         if peak_normalise:
             I = normalise_peak_intensity(I)
         return I
 
-
     def get_frequency_cut(
-        self, 
-        at_time: float | str,
-        dBb: bool = False,
-        peak_normalise: bool = False
+        self, at_time: float | str, dBb: bool = False, peak_normalise: bool = False
     ) -> FrequencyCut:
         """Retrieve a cut of the dynamic spectra at a specific time.
 
-        If `at_time` does not match exactly with a time in `times`, the closest match 
+        If `at_time` does not match exactly with a time in `times`, the closest match
         is selected. The cut represents one of the spectrums in the spectrogram.
 
-        :param at_time: The requested time for the cut. If a string, it is parsed 
+        :param at_time: The requested time for the cut. If a string, it is parsed
         as a datetime. If a float, it is treated as elapsed time since the first spectrum.
-        :param dBb: If True, returns the cut in decibels above the background, 
+        :param dBb: If True, returns the cut in decibels above the background,
         defaults to False.
-        :param peak_normalise: If True, normalises the cut such that its peak value 
+        :param peak_normalise: If True, normalises the cut such that its peak value
         is equal to 1. Ignored if dBb is True, defaults to False.
         :raises ValueError: If at_time is not a recognised type.
         :return: A FrequencyCut object containing the spectral values and associated metadata.
         """
 
         if isinstance(at_time, str):
-            _at_datetime = np.datetime64( datetime.strptime(at_time, TimeFormat.DATETIME) )
-            index_of_cut = find_closest_index(_at_datetime, 
-                                              self.datetimes,  
-                                              enforce_strict_bounds = True)
-            time_of_cut = self.datetimes[index_of_cut]  
+            _at_datetime = np.datetime64(
+                datetime.strptime(at_time, TimeFormat.DATETIME)
+            )
+            index_of_cut = find_closest_index(
+                _at_datetime, self.datetimes, enforce_strict_bounds=True
+            )
+            time_of_cut = self.datetimes[index_of_cut]
 
         elif isinstance(at_time, float):
             _at_time = np.float32(at_time)
-            index_of_cut = find_closest_index(_at_time, 
-                                              self._times, 
-                                              enforce_strict_bounds = True)
+            index_of_cut = find_closest_index(
+                _at_time, self._times, enforce_strict_bounds=True
+            )
             time_of_cut = self.times[index_of_cut]
-        
+
         else:
             raise ValueError(f"'at_time' type '{type(at_time)}' is unsupported.")
-        
+
         if dBb:
             ds = self.compute_dynamic_spectra_dBb()
         else:
             ds = self._dynamic_spectra
-        
-        cut = ds[:, index_of_cut].copy() # make a copy so to preserve the spectrum on transformations of the cut
+
+        cut = ds[
+            :, index_of_cut
+        ].copy()  # make a copy so to preserve the spectrum on transformations of the cut
 
         if dBb:
             if peak_normalise:
-                warn("Ignoring frequency cut normalisation, since dBb units have been specified")
+                warn(
+                    "Ignoring frequency cut normalisation, since dBb units have been specified"
+                )
         else:
             if peak_normalise:
                 cut = normalise_peak_intensity(cut)
-        
-        return FrequencyCut(time_of_cut, 
-                            self._frequencies, 
-                            cut, 
-                            self._spectrum_unit)
 
-        
+        return FrequencyCut(time_of_cut, self._frequencies, cut, self._spectrum_unit)
+
     def get_time_cut(
         self,
         at_frequency: float,
         dBb: bool = False,
-        peak_normalise = False, 
-        correct_background = False, 
-        return_time_type: TimeType = TimeType.RELATIVE
+        peak_normalise=False,
+        correct_background=False,
+        return_time_type: TimeType = TimeType.RELATIVE,
     ) -> TimeCut:
         """Retrieve a cut of the dynamic spectra at a specific frequency.
 
-        If `at_frequency` does not exactly match a frequency in `frequencies`, the 
+        If `at_frequency` does not exactly match a frequency in `frequencies`, the
         closest match is selected. The cut represents the time series of some spectral
         component.
 
         :param at_frequency: The requested frequency for the cut, in Hz.
-        :param dBb: If True, returns the cut in decibels above the background. 
+        :param dBb: If True, returns the cut in decibels above the background.
         Defaults to False.
-        :param peak_normalise: If True, normalises the cut so its peak value is 1. 
+        :param peak_normalise: If True, normalises the cut so its peak value is 1.
         Ignored if dBb is True. Defaults to False.
-        :param correct_background: If True, subtracts the background from the cut. 
+        :param correct_background: If True, subtracts the background from the cut.
         Ignored if dBb is True. Defaults to False.
-        :param return_time_type: Specifies the type of time values in the cut 
+        :param return_time_type: Specifies the type of time values in the cut
         (TimeType.RELATIVE or TimeType.DATETIMES). Defaults to TimeType.RELATIVE.
         :raises ValueError: If return_time_type is not recognised.
         :return: A TimeCut object containing the temporal values and associated metadata.
         """
         _at_frequency = np.float32(at_frequency)
-        index_of_cut = find_closest_index(_at_frequency, 
-                                          self._frequencies, 
-                                          enforce_strict_bounds = True)
-        frequency_of_cut = float( self.frequencies[index_of_cut] )
+        index_of_cut = find_closest_index(
+            _at_frequency, self._frequencies, enforce_strict_bounds=True
+        )
+        frequency_of_cut = float(self.frequencies[index_of_cut])
 
         # dependent on the requested cut type, we return the dynamic spectra in the preferred units
         if dBb:
             ds = self.compute_dynamic_spectra_dBb()
         else:
             ds = self.dynamic_spectra
-        
-        cut = ds[index_of_cut,:].copy() # make a copy so to preserve the spectrum on transformations of the cut
+
+        cut = ds[
+            index_of_cut, :
+        ].copy()  # make a copy so to preserve the spectrum on transformations of the cut
 
         # Warn if dBb is used with background correction or peak normalisation
         if dBb:
             if correct_background or peak_normalise:
-                warn("Ignoring time cut normalisation, since dBb units have been specified")
+                warn(
+                    "Ignoring time cut normalisation, since dBb units have been specified"
+                )
         else:
             # Apply background correction if required
             if correct_background:
-                cut = subtract_background(cut, 
-                                          self._start_background_index,
-                                          self._end_background_index)
-            
+                cut = subtract_background(
+                    cut, self._start_background_index, self._end_background_index
+                )
+
             # Apply peak normalisation if required
             if peak_normalise:
                 cut = normalise_peak_intensity(cut)
 
         if return_time_type == TimeType.DATETIMES:
-            return TimeCut(frequency_of_cut,
-                           self.datetimes,
-                           cut,
-                           self.spectrum_unit)
+            return TimeCut(frequency_of_cut, self.datetimes, cut, self.spectrum_unit)
         elif return_time_type == TimeType.RELATIVE:
-            return TimeCut(frequency_of_cut, 
-                           self.times, 
-                           cut,
-                           self.spectrum_unit)
+            return TimeCut(frequency_of_cut, self.times, cut, self.spectrum_unit)
         else:
-            raise ValueError(f"Invalid return_time_type. Got {return_time_type}, "
-                             f"expected one of 'datetimes' or 'seconds'")
+            raise ValueError(
+                f"Invalid return_time_type. Got {return_time_type}, "
+                f"expected one of 'datetimes' or 'seconds'"
+            )
 
-    
 
-def _seconds_of_day(
-    dt: datetime
-) -> float:
+def _seconds_of_day(dt: datetime) -> float:
     start_of_day = datetime(dt.year, dt.month, dt.day)
     return (dt - start_of_day).total_seconds()
 
 
 # Function to create a FITS file with the specified structure
-def _save_spectrogram(
-    spectrogram: Spectrogram
-) -> None:
+def _save_spectrogram(spectrogram: Spectrogram) -> None:
     """Save the input spectrogram and associated metadata to a fits file. Some metadata
     will be fetched from the corresponding capture config.
-    
+
     :param spectrogram: The spectrogram containing the data to be saved.
     """
     dt = spectrogram.start_datetime.astype(datetime)
     # making the write path
-    batch_parent_path = get_batches_dir_path(year  = dt.year,
-                                             month = dt.month,
-                                             day   = dt.day)
+    batch_parent_path = get_batches_dir_path(year=dt.year, month=dt.month, day=dt.day)
     # file name formatted as a batch file
     file_name = f"{spectrogram.format_start_time()}_{spectrogram.tag}.fits"
-    write_path = os.path.join(batch_parent_path, 
-                                file_name)
-    
+    write_path = os.path.join(batch_parent_path, file_name)
+
     # get optional metadata from the capture config
     capture_config = CaptureConfig(spectrogram.tag)
-    ORIGIN    = cast(str,   capture_config.get_parameter_value(PName.ORIGIN))
-    INSTRUME  = cast(str,   capture_config.get_parameter_value(PName.INSTRUMENT))
-    TELESCOP  = cast(str,   capture_config.get_parameter_value(PName.TELESCOPE))
-    OBJECT    = cast(str,   capture_config.get_parameter_value(PName.OBJECT))
-    OBS_ALT   = cast(float, capture_config.get_parameter_value(PName.OBS_ALT))
-    OBS_LAT   = cast(float, capture_config.get_parameter_value(PName.OBS_LAT))
-    OBS_LON   = cast(float, capture_config.get_parameter_value(PName.OBS_LON))
-    
+    ORIGIN = cast(str, capture_config.get_parameter_value(PName.ORIGIN))
+    INSTRUME = cast(str, capture_config.get_parameter_value(PName.INSTRUMENT))
+    TELESCOP = cast(str, capture_config.get_parameter_value(PName.TELESCOPE))
+    OBJECT = cast(str, capture_config.get_parameter_value(PName.OBJECT))
+    OBS_ALT = cast(float, capture_config.get_parameter_value(PName.OBS_ALT))
+    OBS_LAT = cast(float, capture_config.get_parameter_value(PName.OBS_LAT))
+    OBS_LON = cast(float, capture_config.get_parameter_value(PName.OBS_LON))
+
     # Primary HDU with data
-    primary_data = spectrogram.dynamic_spectra.astype(dtype=np.float32) 
+    primary_data = spectrogram.dynamic_spectra.astype(dtype=np.float32)
     primary_hdu = fits.PrimaryHDU(primary_data)
 
-    primary_hdu.header.set('SIMPLE', True, 'file does conform to FITS standard')
-    primary_hdu.header.set('BITPIX', -32, 'number of bits per data pixel')
-    primary_hdu.header.set('NAXIS', 2, 'number of data axes')
-    primary_hdu.header.set('NAXIS1', spectrogram.dynamic_spectra.shape[1], 'length of data axis 1')
-    primary_hdu.header.set('NAXIS2', spectrogram.dynamic_spectra.shape[0], 'length of data axis 2')
-    primary_hdu.header.set('EXTEND', True, 'FITS dataset may contain extensions')
+    primary_hdu.header.set("SIMPLE", True, "file does conform to FITS standard")
+    primary_hdu.header.set("BITPIX", -32, "number of bits per data pixel")
+    primary_hdu.header.set("NAXIS", 2, "number of data axes")
+    primary_hdu.header.set(
+        "NAXIS1", spectrogram.dynamic_spectra.shape[1], "length of data axis 1"
+    )
+    primary_hdu.header.set(
+        "NAXIS2", spectrogram.dynamic_spectra.shape[0], "length of data axis 2"
+    )
+    primary_hdu.header.set("EXTEND", True, "FITS dataset may contain extensions")
 
     # Add comments
     comments = [
         "FITS (Flexible Image Transport System) format defined in Astronomy and",
         "Astrophysics Supplement Series v44/p363, v44/p371, v73/p359, v73/p365.",
         "Contact the NASA Science Office of Standards and Technology for the",
-        "FITS Definition document #100 and other FITS information."
+        "FITS Definition document #100 and other FITS information.",
     ]
-    
+
     # The comments section remains unchanged since add_comment is the correct approach
     for comment in comments:
         primary_hdu.header.add_comment(comment)
 
     start_datetime = cast(datetime, spectrogram.datetimes[0].astype(datetime))
-    start_date     = start_datetime.strftime("%Y-%m-%d")
-    start_time     = start_datetime.strftime("%H:%M:%S.%f")
-
-    end_datetime   = cast(datetime, spectrogram.datetimes[-1].astype(datetime))
-    end_date       = end_datetime.strftime("%Y-%m-%d")
-    end_time       = end_datetime.strftime("%H:%M:%S.%f")
-
-    primary_hdu.header.set('DATE', start_date, 'time of observation')
-    primary_hdu.header.set('CONTENT', f'{start_date} dynamic spectrogram', 'title of image')
-    primary_hdu.header.set('ORIGIN', f'{ORIGIN}')
-    primary_hdu.header.set('TELESCOP', f'{TELESCOP}', 'type of instrument')
-    primary_hdu.header.set('INSTRUME', f'{INSTRUME}') 
-    primary_hdu.header.set('OBJECT', f'{OBJECT}', 'object description')
-
-    primary_hdu.header.set('DATE-OBS', f'{start_date}', 'date observation starts')
-    primary_hdu.header.set('TIME-OBS', f'{start_time}', 'time observation starts')
-    primary_hdu.header.set('DATE-END', f'{end_date}', 'date observation ends')
-    primary_hdu.header.set('TIME-END', f'{end_time}', 'time observation ends')
-
-    primary_hdu.header.set('BZERO', 0, 'scaling offset')
-    primary_hdu.header.set('BSCALE', 1, 'scaling factor')
-    primary_hdu.header.set('BUNIT', f"{spectrogram.spectrum_unit.value}", 'z-axis title') 
-
-    primary_hdu.header.set('DATAMIN', np.nanmin(spectrogram.dynamic_spectra), 'minimum element in image')
-    primary_hdu.header.set('DATAMAX', np.nanmax(spectrogram.dynamic_spectra), 'maximum element in image')
-
-    primary_hdu.header.set('CRVAL1', f'{_seconds_of_day( start_datetime)}', 'value on axis 1 at reference pixel [sec of day]')
-    primary_hdu.header.set('CRPIX1', 0, 'reference pixel of axis 1')
-    primary_hdu.header.set('CTYPE1', 'TIME [UT]', 'title of axis 1')
-    primary_hdu.header.set('CDELT1', spectrogram.time_resolution, 'step between first and second element in x-axis')
-
-    primary_hdu.header.set('CRVAL2', 0, 'value on axis 2 at reference pixel')
-    primary_hdu.header.set('CRPIX2', 0, 'reference pixel of axis 2')
-    primary_hdu.header.set('CTYPE2', 'Frequency [Hz]', 'title of axis 2')
-    primary_hdu.header.set('CDELT2', spectrogram.frequency_resolution, 'step between first and second element in axis')
-
-    primary_hdu.header.set('OBS_LAT', f'{OBS_LAT}', 'observatory latitude in degree')
-    primary_hdu.header.set('OBS_LAC', 'N', 'observatory latitude code {N,S}')
-    primary_hdu.header.set('OBS_LON', f'{OBS_LON}', 'observatory longitude in degree')
-    primary_hdu.header.set('OBS_LOC', 'W', 'observatory longitude code {E,W}')
-    primary_hdu.header.set('OBS_ALT', f'{OBS_ALT}', 'observatory altitude in meter asl')
-
+    start_date = start_datetime.strftime("%Y-%m-%d")
+    start_time = start_datetime.strftime("%H:%M:%S.%f")
+
+    end_datetime = cast(datetime, spectrogram.datetimes[-1].astype(datetime))
+    end_date = end_datetime.strftime("%Y-%m-%d")
+    end_time = end_datetime.strftime("%H:%M:%S.%f")
+
+    primary_hdu.header.set("DATE", start_date, "time of observation")
+    primary_hdu.header.set(
+        "CONTENT", f"{start_date} dynamic spectrogram", "title of image"
+    )
+    primary_hdu.header.set("ORIGIN", f"{ORIGIN}")
+    primary_hdu.header.set("TELESCOP", f"{TELESCOP}", "type of instrument")
+    primary_hdu.header.set("INSTRUME", f"{INSTRUME}")
+    primary_hdu.header.set("OBJECT", f"{OBJECT}", "object description")
+
+    primary_hdu.header.set("DATE-OBS", f"{start_date}", "date observation starts")
+    primary_hdu.header.set("TIME-OBS", f"{start_time}", "time observation starts")
+    primary_hdu.header.set("DATE-END", f"{end_date}", "date observation ends")
+    primary_hdu.header.set("TIME-END", f"{end_time}", "time observation ends")
+
+    primary_hdu.header.set("BZERO", 0, "scaling offset")
+    primary_hdu.header.set("BSCALE", 1, "scaling factor")
+    primary_hdu.header.set(
+        "BUNIT", f"{spectrogram.spectrum_unit.value}", "z-axis title"
+    )
+
+    primary_hdu.header.set(
+        "DATAMIN", np.nanmin(spectrogram.dynamic_spectra), "minimum element in image"
+    )
+    primary_hdu.header.set(
+        "DATAMAX", np.nanmax(spectrogram.dynamic_spectra), "maximum element in image"
+    )
+
+    primary_hdu.header.set(
+        "CRVAL1",
+        f"{_seconds_of_day( start_datetime)}",
+        "value on axis 1 at reference pixel [sec of day]",
+    )
+    primary_hdu.header.set("CRPIX1", 0, "reference pixel of axis 1")
+    primary_hdu.header.set("CTYPE1", "TIME [UT]", "title of axis 1")
+    primary_hdu.header.set(
+        "CDELT1",
+        spectrogram.time_resolution,
+        "step between first and second element in x-axis",
+    )
+
+    primary_hdu.header.set("CRVAL2", 0, "value on axis 2 at reference pixel")
+    primary_hdu.header.set("CRPIX2", 0, "reference pixel of axis 2")
+    primary_hdu.header.set("CTYPE2", "Frequency [Hz]", "title of axis 2")
+    primary_hdu.header.set(
+        "CDELT2",
+        spectrogram.frequency_resolution,
+        "step between first and second element in axis",
+    )
+
+    primary_hdu.header.set("OBS_LAT", f"{OBS_LAT}", "observatory latitude in degree")
+    primary_hdu.header.set("OBS_LAC", "N", "observatory latitude code {N,S}")
+    primary_hdu.header.set("OBS_LON", f"{OBS_LON}", "observatory longitude in degree")
+    primary_hdu.header.set("OBS_LOC", "W", "observatory longitude code {E,W}")
+    primary_hdu.header.set("OBS_ALT", f"{OBS_ALT}", "observatory altitude in meter asl")
 
     # Wrap arrays in an additional dimension to mimic the e-CALLISTO storage
     times_wrapped = np.array([spectrogram.times.astype(np.float32)])
     # To mimic e-Callisto storage, convert frequencies to MHz
     frequencies_MHz = spectrogram.frequencies * 1e-6
     frequencies_wrapped = np.array([frequencies_MHz.astype(np.float32)])
-    
+
     # Binary Table HDU (extension)
-    col1 = fits.Column(name='TIME', format='PD', array=times_wrapped)
-    col2 = fits.Column(name='FREQUENCY', format='PD', array=frequencies_wrapped)
+    col1 = fits.Column(name="TIME", format="PD", array=times_wrapped)
+    col2 = fits.Column(name="FREQUENCY", format="PD", array=frequencies_wrapped)
     cols = fits.ColDefs([col1, col2])
 
     bin_table_hdu = fits.BinTableHDU.from_columns(cols)
 
-    bin_table_hdu.header.set('PCOUNT', 0, 'size of special data area')
-    bin_table_hdu.header.set('GCOUNT', 1, 'one data group (required keyword)')
-    bin_table_hdu.header.set('TFIELDS', 2, 'number of fields in each row')
-    bin_table_hdu.header.set('TTYPE1', 'TIME', 'label for field 1')
-    bin_table_hdu.header.set('TFORM1', 'D', 'data format of field: 8-byte DOUBLE')
-    bin_table_hdu.header.set('TTYPE2', 'FREQUENCY', 'label for field 2')
-    bin_table_hdu.header.set('TFORM2', 'D', 'data format of field: 8-byte DOUBLE')
-    bin_table_hdu.header.set('TSCAL1', 1, '')
-    bin_table_hdu.header.set('TZERO1', 0, '')
-    bin_table_hdu.header.set('TSCAL2', 1, '')
-    bin_table_hdu.header.set('TZERO2', 0, '')
+    bin_table_hdu.header.set("PCOUNT", 0, "size of special data area")
+    bin_table_hdu.header.set("GCOUNT", 1, "one data group (required keyword)")
+    bin_table_hdu.header.set("TFIELDS", 2, "number of fields in each row")
+    bin_table_hdu.header.set("TTYPE1", "TIME", "label for field 1")
+    bin_table_hdu.header.set("TFORM1", "D", "data format of field: 8-byte DOUBLE")
+    bin_table_hdu.header.set("TTYPE2", "FREQUENCY", "label for field 2")
+    bin_table_hdu.header.set("TFORM2", "D", "data format of field: 8-byte DOUBLE")
+    bin_table_hdu.header.set("TSCAL1", 1, "")
+    bin_table_hdu.header.set("TZERO1", 0, "")
+    bin_table_hdu.header.set("TSCAL2", 1, "")
+    bin_table_hdu.header.set("TZERO2", 0, "")
 
     # Create HDU list and write to file
     hdul = fits.HDUList([primary_hdu, bin_table_hdu])
-    hdul.writeto(write_path, overwrite=True)
+    hdul.writeto(write_path, overwrite=True)