Add peak_sign to sd_ratio (#4362)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Chris Halcrow <57948917+chrishalcrow@users.noreply.github.com>

Author: 3 people

src/spikeinterface/metrics/quality/misc_metrics.py

@@ -15,8 +15,7 @@
 import numpy as np
 
 from spikeinterface.core.analyzer_extension_core import BaseMetric
-from spikeinterface.core.job_tools import fix_job_kwargs, split_job_kwargs
-from spikeinterface.core import SortingAnalyzer, get_noise_levels, NumpySorting
+from spikeinterface.core import SortingAnalyzer, NumpySorting
 from spikeinterface.core.template_tools import (
     get_template_extremum_channel,
     get_template_extremum_amplitude,
@@ -1359,7 +1358,8 @@ def compute_sd_ratio(
     censored_period_ms: float = 4.0,
     correct_for_drift: bool = True,
     correct_for_template_itself: bool = True,
-    **kwargs,
+    peak_sign: str = "neg",
+    **job_kwargs,
 ):
     """
     Computes the SD (Standard Deviation) of each unit's spike amplitudes, and compare it to the SD of noise.
@@ -1384,20 +1384,21 @@ def compute_sd_ratio(
     correct_for_template_itself : bool, default:  True
         If true, will take into account that the template itself impacts the standard deviation of the noise,
         and will make a rough estimation of what that impact is (and remove it).
-    **kwargs : dict, default: {}
-        Keyword arguments for computing spike amplitudes and extremum channel.
+    peak_sign : "neg" | "pos" | "both", default: "neg"
+        The peak sign used to select the template extremum channel.
+    **job_kwargs : dict, default: {}
+        Keyword arguments sent to get_noise_levels.
 
     Returns
     -------
-    num_spikes : dict
-        The number of spikes, across all segments, for each unit ID.
+    sd_ratio : dict
+        The ratio of the standard deviation of spike amplitudes to the standard deviation of noise, for each unit ID.
     """
 
     from spikeinterface.curation.curation_tools import find_duplicated_spikes
+    from spikeinterface.core import get_noise_levels
 
     check_has_required_extensions("sd_ratio", sorting_analyzer)
-    kwargs, job_kwargs = split_job_kwargs(kwargs)
-    job_kwargs = fix_job_kwargs(job_kwargs)
 
     sorting = sorting_analyzer.sorting
     sorting = sorting.select_periods(periods=periods)
@@ -1429,11 +1430,11 @@ def compute_sd_ratio(
     noise_levels = get_noise_levels(
         sorting_analyzer.recording, return_in_uV=sorting_analyzer.return_in_uV, method="std", **job_kwargs
     )
-    best_channels = get_template_extremum_channel(sorting_analyzer, outputs="index", **kwargs)
-    n_spikes = sorting_analyzer.sorting.count_num_spikes_per_unit(unit_ids=unit_ids)
+    best_channels = get_template_extremum_channel(sorting_analyzer, outputs="index", peak_sign=peak_sign)
 
     if correct_for_template_itself:
-        tamplates_array = get_dense_templates_array(sorting_analyzer, return_in_uV=sorting_analyzer.return_in_uV)
+        n_spikes = sorting_analyzer.sorting.count_num_spikes_per_unit(unit_ids=unit_ids)
+        templates_array = get_dense_templates_array(sorting_analyzer, return_in_uV=sorting_analyzer.return_in_uV)
 
     sd_ratio = {}
 
@@ -1468,21 +1469,17 @@ def compute_sd_ratio(
             best_channel = best_channels[unit_id]
             std_noise = noise_levels[best_channel]
 
-            n_samples = sorting_analyzer.get_total_samples()
-
             if correct_for_template_itself:
                 # template = sorting_analyzer.get_template(unit_id, force_dense=True)[:, best_channel]
                 unit_index = sorting.id_to_index(unit_id)
-
-                template = tamplates_array[unit_index, :, :][:, best_channel]
-                nsamples = template.shape[0]
+                template = templates_array[unit_index, :, best_channel]
 
                 # Computing the variance of a trace that is all 0 and n_spikes non-overlapping template.
                 # TODO: Take into account that templates for different segments might differ.
-                p = nsamples * n_spikes[unit_id] / n_samples
-                total_variance = p * np.mean(template**2) - p**2 * np.mean(template) ** 2
+                p = len(template) * n_spikes[unit_id] / sorting_analyzer.get_total_samples()
+                template_variance = p * np.mean(template**2) - p**2 * np.mean(template) ** 2
 
-                std_noise = np.sqrt(std_noise**2 - total_variance)
+                std_noise = np.sqrt(std_noise**2 - template_variance)
 
             sd_ratio[unit_id] = unit_std / std_noise
 
@@ -1496,6 +1493,7 @@ class SDRatio(BaseMetric):
         "censored_period_ms": 4.0,
         "correct_for_drift": True,
         "correct_for_template_itself": True,
+        "peak_sign": "neg",
     }
     metric_columns = {"sd_ratio": float}
     metric_descriptions = {