diff --git a/src/spikeanalysis/intrinsic_plotter.py b/src/spikeanalysis/intrinsic_plotter.py index cc4951f..760f2a0 100644 --- a/src/spikeanalysis/intrinsic_plotter.py +++ b/src/spikeanalysis/intrinsic_plotter.py @@ -324,7 +324,7 @@ def _plot_cdf_pdf(self, df: pd.DataFrame): def _generate_amp_depth_bins( self, - sp, + sp: SpikeData, spike_amps: np.ndarray, probe_len: float, pitch: float, @@ -349,7 +349,12 @@ def _generate_amp_depth_bins( return depth_bins, amp_bins, recording_duration def _compute_cdf_pdf( - self, spike_amps, spike_depths, amp_bins, depth_bins, recording_dur + self, + spike_amps: np.ndarray, + spike_depths: np.ndarray, + amp_bins: np.ndarray, + depth_bins: np.ndarray, + recording_dur: float, ) -> tuple[np.ndarray, np.ndarray]: n_depth_bins = len(depth_bins) - 1 n_amp_bins = len(amp_bins) - 1 diff --git a/src/spikeanalysis/spike_analysis.py b/src/spikeanalysis/spike_analysis.py index aa03fec..a73f7b0 100644 --- a/src/spikeanalysis/spike_analysis.py +++ b/src/spikeanalysis/spike_analysis.py @@ -869,7 +869,7 @@ def get_responsive_neurons(self, z_parameters: Optional[dict] = None): self.responsive_neurons[stim][key] = responsive_neurons - def _merge_events(self, event_0, event_1): + def _merge_events(self, event_0: dict, event_1: dict): """Utility function for merging digital and analog events into one dictionary""" events = {**event_0, **event_1} return events diff --git a/src/spikeanalysis/stimulus_data.py b/src/spikeanalysis/stimulus_data.py index c81114e..88853db 100644 --- a/src/spikeanalysis/stimulus_data.py +++ b/src/spikeanalysis/stimulus_data.py @@ -131,6 +131,17 @@ def create_neo_reader(self, file_name: Optional[str] = None): """ Function that creates a Neo IntanRawIO reader and then parses the header + Parameters + ---------- + file_name: Optional[filename] + Default None uses the internal function, whereas providing a file_name will call + the neo function `get_rawio_class` to return a neo reader that can be used + + Returns + ------- + neo_class: neo.rawio + Returns a neo.rawio class if filename is given otherwise stores values internally + """ if file_name is None: reader = neo.rawio.IntanRawIO(filename=self._filename) @@ -146,7 +157,7 @@ def create_neo_reader(self, file_name: Optional[str] = None): self.sample_frequency = sample_freq self.reader = reader - def get_analog_data(self, time_slice=(None, None)): + def get_analog_data(self, time_slice: tuple = (None, None)): """ Function to load analog data from an Intan file. Requires the IntanRawIO to be generated with `create_neo_reader` @@ -259,7 +270,7 @@ def _valueround(self, x: float, precision: int = 2, base: float = 0.25) -> float """ return round(base * round(float(x) / base), precision) - def get_raw_digital_data(self, time_slice=(None, None)): + def get_raw_digital_data(self, time_slice: tuple = (None, None)): """ This is a function that in the future will get the digital data, but currently due to the inability to grab digital from neo automatically. Calls on internal hack to