Merge pull request #1950 from samuelgarcia/spike_location_with_true_c…

…hannel

Spike location with true channel

src/spikeinterface/core/node_pipeline.py

@@ -213,7 +213,9 @@ def compute(self, traces, start_frame, end_frame, segment_index, max_margin):
                 elif self.peak_sign == "both":
                     local_peaks[i]["channel_index"] = chans[np.argmax(np.abs(sparse_wfs))]
 
-        # TODO: "amplitude" ???
+        # handle amplitude
+        for i, peak in enumerate(local_peaks):
+            local_peaks["amplitude"][i] = traces[peak["sample_index"], peak["channel_index"]]
 
         return (local_peaks,)
 

src/spikeinterface/core/tests/test_node_pipeline.py

@@ -72,7 +72,8 @@ def compute(self, traces, peaks, waveforms):
 def test_run_node_pipeline():
     recording, sorting = generate_ground_truth_recording(num_channels=10, num_units=10, durations=[10.0])
 
-    job_kwargs = dict(chunk_duration="0.5s", n_jobs=2, progress_bar=False)
+    # job_kwargs = dict(chunk_duration="0.5s", n_jobs=2, progress_bar=False)
+    job_kwargs = dict(chunk_duration="0.5s", n_jobs=1, progress_bar=False)
 
     spikes = sorting.to_spike_vector()
 
@@ -104,7 +105,8 @@ def test_run_node_pipeline():
             AmplitudeExtractionNode(recording, parents=[peak_source], param0=6.6),
         ]
         step_one = run_node_pipeline(recording, nodes, job_kwargs, squeeze_output=True)
-        assert np.allclose(np.abs(peaks["amplitude"]), step_one["abs_amplitude"])
+        if loop == 0:
+            assert np.allclose(np.abs(peaks["amplitude"]), step_one["abs_amplitude"])
 
         # 3 nodes two have outputs
         ms_before = 0.5
@@ -132,7 +134,6 @@ def test_run_node_pipeline():
         # gather memory mode
         output = run_node_pipeline(recording, nodes, job_kwargs, gather_mode="memory")
         amplitudes, waveforms_rms, denoised_waveforms_rms = output
-        assert np.allclose(np.abs(peaks["amplitude"]), amplitudes["abs_amplitude"])
 
         num_peaks = peaks.shape[0]
         num_channels = recording.get_num_channels()

src/spikeinterface/postprocessing/spike_locations.py

@@ -5,6 +5,7 @@
 from spikeinterface.core.template_tools import get_template_extremum_channel, get_template_extremum_channel_peak_shift
 
 from spikeinterface.core.waveform_extractor import WaveformExtractor, BaseWaveformExtractorExtension
+from spikeinterface.core.node_pipeline import SpikeRetriever
 
 
 class SpikeLocationsCalculator(BaseWaveformExtractorExtension):
@@ -25,8 +26,21 @@ def __init__(self, waveform_extractor):
         extremum_channel_inds = get_template_extremum_channel(self.waveform_extractor, outputs="index")
         self.spikes = self.waveform_extractor.sorting.to_spike_vector(extremum_channel_inds=extremum_channel_inds)
 
-    def _set_params(self, ms_before=0.5, ms_after=0.5, method="center_of_mass", method_kwargs={}):
-        params = dict(ms_before=ms_before, ms_after=ms_after, method=method)
+    def _set_params(
+        self,
+        ms_before=0.5,
+        ms_after=0.5,
+        spike_retriver_kwargs=dict(
+            channel_from_template=True,
+            radius_um=50,
+            peak_sign="neg",
+        ),
+        method="center_of_mass",
+        method_kwargs={},
+    ):
+        params = dict(
+            ms_before=ms_before, ms_after=ms_after, spike_retriver_kwargs=spike_retriver_kwargs, method=method
+        )
         params.update(**method_kwargs)
         return params
 
@@ -44,13 +58,22 @@ def _run(self, **job_kwargs):
         uses the`sortingcomponents.peak_localization.localize_peaks()` function to triangulate
         spike locations.
         """
-        from spikeinterface.sortingcomponents.peak_localization import localize_peaks
+        from spikeinterface.sortingcomponents.peak_localization import _run_localization_from_peak_source
 
         job_kwargs = fix_job_kwargs(job_kwargs)
 
         we = self.waveform_extractor
 
-        spike_locations = localize_peaks(we.recording, self.spikes, **self._params, **job_kwargs)
+        extremum_channel_inds = get_template_extremum_channel(we, peak_sign="neg", outputs="index")
+
+        params = self._params.copy()
+        spike_retriver_kwargs = params.pop("spike_retriver_kwargs")
+
+        spike_retriever = SpikeRetriever(
+            we.recording, we.sorting, extremum_channel_inds=extremum_channel_inds, **spike_retriver_kwargs
+        )
+        spike_locations = _run_localization_from_peak_source(we.recording, spike_retriever, **params, **job_kwargs)
+
         self._extension_data["spike_locations"] = spike_locations
 
     def get_data(self, outputs="concatenated"):
@@ -101,6 +124,11 @@ def compute_spike_locations(
     load_if_exists=False,
     ms_before=0.5,
     ms_after=0.5,
+    spike_retriver_kwargs=dict(
+        channel_from_template=True,
+        radius_um=50,
+        peak_sign="neg",
+    ),
     method="center_of_mass",
     method_kwargs={},
     outputs="concatenated",
@@ -119,6 +147,17 @@ def compute_spike_locations(
         The left window, before a peak, in milliseconds.
     ms_after : float
         The right window, after a peak, in milliseconds.
+    spike_retriver_kwargs: dict
+        A dictionary to control the behavior for getting the maximum channel for each spike.
+        This dictionary contains:
+            * channel_from_template: bool, default True
+                For each spike is the maximum channel computed from template or re estimated at every spikes.
+                channel_from_template = True is old behavior but less acurate
+                channel_from_template = False is slower but more accurate
+            * radius_um: float, default 50
+                In case channel_from_template=False, this is the radius to get the true peak.
+            * peak_sign="neg"
+                In case channel_from_template=False, this is the peak sign.
     method : str
         'center_of_mass' / 'monopolar_triangulation' / 'grid_convolution'
     method_kwargs : dict
@@ -138,7 +177,13 @@ def compute_spike_locations(
         slc = waveform_extractor.load_extension(SpikeLocationsCalculator.extension_name)
     else:
         slc = SpikeLocationsCalculator(waveform_extractor)
-        slc.set_params(ms_before=ms_before, ms_after=ms_after, method=method, method_kwargs=method_kwargs)
+        slc.set_params(
+            ms_before=ms_before,
+            ms_after=ms_after,
+            spike_retriver_kwargs=spike_retriver_kwargs,
+            method=method,
+            method_kwargs=method_kwargs,
+        )
         slc.run(**job_kwargs)
 
     locs = slc.get_data(outputs=outputs)

src/spikeinterface/postprocessing/tests/test_spike_locations.py

@@ -10,7 +10,12 @@ class SpikeLocationsExtensionTest(WaveformExtensionCommonTestSuite, unittest.Tes
     extension_class = SpikeLocationsCalculator
     extension_data_names = ["spike_locations"]
     extension_function_kwargs_list = [
-        dict(method="center_of_mass", chunk_size=10000, n_jobs=1),
+        dict(
+            method="center_of_mass", chunk_size=10000, n_jobs=1, spike_retriver_kwargs=dict(channel_from_template=True)
+        ),
+        dict(
+            method="center_of_mass", chunk_size=10000, n_jobs=1, spike_retriver_kwargs=dict(channel_from_template=False)
+        ),
         dict(method="center_of_mass", chunk_size=10000, n_jobs=1, outputs="by_unit"),
         dict(method="monopolar_triangulation", chunk_size=10000, n_jobs=1, outputs="by_unit"),
         dict(method="monopolar_triangulation", chunk_size=10000, n_jobs=1, outputs="by_unit"),

src/spikeinterface/sortingcomponents/peak_localization.py

@@ -7,6 +7,7 @@
     run_node_pipeline,
     find_parent_of_type,
     PeakRetriever,
+    SpikeRetriever,
     PipelineNode,
     WaveformsNode,
     ExtractDenseWaveforms,
@@ -27,72 +28,49 @@
 from .tools import get_prototype_spike
 
 
-def localize_peaks(recording, peaks, method="center_of_mass", ms_before=0.5, ms_after=0.5, **kwargs):
-    """Localize peak (spike) in 2D or 3D depending the method.
-
-    When a probe is 2D then:
-       * X is axis 0 of the probe
-       * Y is axis 1 of the probe
-       * Z is orthogonal to the plane of the probe
-
-    Parameters
-    ----------
-    recording: RecordingExtractor
-        The recording extractor object.
-    peaks: array
-        Peaks array, as returned by detect_peaks() in "compact_numpy" way.
-
-    {method_doc}
-
-    {job_doc}
-
-    Returns
-    -------
-    peak_locations: ndarray
-        Array with estimated location for each spike.
-        The dtype depends on the method. ('x', 'y') or ('x', 'y', 'z', 'alpha').
-    """
+def _run_localization_from_peak_source(
+    recording, peak_source, method="center_of_mass", ms_before=0.5, ms_after=0.5, **kwargs
+):
+    # use by localize_peaks() and compute_spike_locations()
     assert (
         method in possible_localization_methods
     ), f"Method {method} is not supported. Choose from {possible_localization_methods}"
 
     method_kwargs, job_kwargs = split_job_kwargs(kwargs)
 
-    peak_retriever = PeakRetriever(recording, peaks)
     if method == "center_of_mass":
         extract_dense_waveforms = ExtractDenseWaveforms(
-            recording, parents=[peak_retriever], ms_before=ms_before, ms_after=ms_after, return_output=False
+            recording, parents=[peak_source], ms_before=ms_before, ms_after=ms_after, return_output=False
         )
         pipeline_nodes = [
-            peak_retriever,
+            peak_source,
             extract_dense_waveforms,
-            LocalizeCenterOfMass(recording, parents=[peak_retriever, extract_dense_waveforms], **method_kwargs),
+            LocalizeCenterOfMass(recording, parents=[peak_source, extract_dense_waveforms], **method_kwargs),
         ]
     elif method == "monopolar_triangulation":
         extract_dense_waveforms = ExtractDenseWaveforms(
-            recording, parents=[peak_retriever], ms_before=ms_before, ms_after=ms_after, return_output=False
+            recording, parents=[peak_source], ms_before=ms_before, ms_after=ms_after, return_output=False
         )
         pipeline_nodes = [
-            peak_retriever,
+            peak_source,
             extract_dense_waveforms,
-            LocalizeMonopolarTriangulation(
-                recording, parents=[peak_retriever, extract_dense_waveforms], **method_kwargs
-            ),
+            LocalizeMonopolarTriangulation(recording, parents=[peak_source, extract_dense_waveforms], **method_kwargs),
         ]
     elif method == "peak_channel":
-        pipeline_nodes = [peak_retriever, LocalizePeakChannel(recording, parents=[peak_retriever], **method_kwargs)]
+        pipeline_nodes = [peak_source, LocalizePeakChannel(recording, parents=[peak_source], **method_kwargs)]
     elif method == "grid_convolution":
         if "prototype" not in method_kwargs:
+            assert isinstance(peak_source, (PeakRetriever, SpikeRetriever))
             method_kwargs["prototype"] = get_prototype_spike(
-                recording, peaks, ms_before=ms_before, ms_after=ms_after, job_kwargs=job_kwargs
+                recording, peak_source.peaks, ms_before=ms_before, ms_after=ms_after, job_kwargs=job_kwargs
             )
         extract_dense_waveforms = ExtractDenseWaveforms(
-            recording, parents=[peak_retriever], ms_before=ms_before, ms_after=ms_after, return_output=False
+            recording, parents=[peak_source], ms_before=ms_before, ms_after=ms_after, return_output=False
         )
         pipeline_nodes = [
-            peak_retriever,
+            peak_source,
             extract_dense_waveforms,
-            LocalizeGridConvolution(recording, parents=[peak_retriever, extract_dense_waveforms], **method_kwargs),
+            LocalizeGridConvolution(recording, parents=[peak_source, extract_dense_waveforms], **method_kwargs),
         ]
 
     job_name = f"localize peaks using {method}"
@@ -101,6 +79,38 @@ def localize_peaks(recording, peaks, method="center_of_mass", ms_before=0.5, ms_
     return peak_locations
 
 
+def localize_peaks(recording, peaks, method="center_of_mass", ms_before=0.5, ms_after=0.5, **kwargs):
+    """Localize peak (spike) in 2D or 3D depending the method.
+
+    When a probe is 2D then:
+       * X is axis 0 of the probe
+       * Y is axis 1 of the probe
+       * Z is orthogonal to the plane of the probe
+
+    Parameters
+    ----------
+    recording: RecordingExtractor
+        The recording extractor object.
+    peaks: array
+        Peaks array, as returned by detect_peaks() in "compact_numpy" way.
+
+    {method_doc}
+
+    {job_doc}
+
+    Returns
+    -------
+    peak_locations: ndarray
+        Array with estimated location for each spike.
+        The dtype depends on the method. ('x', 'y') or ('x', 'y', 'z', 'alpha').
+    """
+    peak_retriever = PeakRetriever(recording, peaks)
+    peak_locations = _run_localization_from_peak_source(
+        recording, peak_retriever, method=method, ms_before=ms_before, ms_after=ms_after, **kwargs
+    )
+    return peak_locations
+
+
 class LocalizeBase(PipelineNode):
     def __init__(self, recording, return_output=True, parents=None, radius_um=75.0):
         PipelineNode.__init__(self, recording, return_output=return_output, parents=parents)

src/spikeinterface/sortingcomponents/tools.py

@@ -19,6 +19,8 @@ def make_multi_method_doc(methods, ident="    "):
 
 
 def get_prototype_spike(recording, peaks, job_kwargs, nb_peaks=1000, ms_before=0.5, ms_after=0.5):
+    # TODO for Pierre: this function is really inefficient because it runs a full pipeline only for a few
+    # spikes, which means that all traces need to be accesses! Please find a better way
     nb_peaks = min(len(peaks), nb_peaks)
     idx = np.sort(np.random.choice(len(peaks), nb_peaks, replace=False))
     peak_retriever = PeakRetriever(recording, peaks[idx])