Merge branch 'main' into fix-unit-id-matching

src/spikeinterface/core/generate.py

@@ -123,6 +123,9 @@ def generate_sorting(
     firing_rates=3.0,
     empty_units=None,
     refractory_period_ms=3.0,  # in ms
+    add_spikes_on_borders=False,
+    num_spikes_per_border=3,
+    border_size_samples=20,
     seed=None,
 ):
     """
@@ -142,6 +145,12 @@ def generate_sorting(
         List of units that will have no spikes. (used for testing mainly).
     refractory_period_ms : float, default: 3.0
         The refractory period in ms
+    add_spikes_on_borders : bool, default: False
+        If True, spikes will be added close to the borders of the segments.
+    num_spikes_per_border : int, default: 3
+        The number of spikes to add close to the borders of the segments.
+    border_size_samples : int, default: 20
+        The size of the border in samples to add border spikes.
     seed : int, default: None
         The random seed
 
@@ -151,11 +160,13 @@ def generate_sorting(
         The sorting object
     """
     seed = _ensure_seed(seed)
+    rng = np.random.default_rng(seed)
     num_segments = len(durations)
     unit_ids = np.arange(num_units)
 
     spikes = []
     for segment_index in range(num_segments):
+        num_samples = int(sampling_frequency * durations[segment_index])
         times, labels = synthesize_random_firings(
             num_units=num_units,
             sampling_frequency=sampling_frequency,
@@ -175,7 +186,23 @@ def generate_sorting(
         spikes_in_seg["unit_index"] = labels
         spikes_in_seg["segment_index"] = segment_index
         spikes.append(spikes_in_seg)
+
+        if add_spikes_on_borders:
+            spikes_on_borders = np.zeros(2 * num_spikes_per_border, dtype=minimum_spike_dtype)
+            spikes_on_borders["segment_index"] = segment_index
+            spikes_on_borders["unit_index"] = rng.choice(num_units, size=2 * num_spikes_per_border, replace=True)
+            # at start
+            spikes_on_borders["sample_index"][:num_spikes_per_border] = rng.integers(
+                0, border_size_samples, num_spikes_per_border
+            )
+            # at end
+            spikes_on_borders["sample_index"][num_spikes_per_border:] = rng.integers(
+                num_samples - border_size_samples, num_samples, num_spikes_per_border
+            )
+            spikes.append(spikes_on_borders)
+
     spikes = np.concatenate(spikes)
+    spikes = spikes[np.lexsort((spikes["sample_index"], spikes["segment_index"]))]
 
     sorting = NumpySorting(spikes, sampling_frequency, unit_ids)
 
@@ -596,6 +623,7 @@ def __init__(
         dtype = np.dtype(dtype).name  # Cast to string for serialization
         if dtype not in ("float32", "float64"):
             raise ValueError(f"'dtype' must be 'float32' or 'float64' but is {dtype}")
+        assert strategy in ("tile_pregenerated", "on_the_fly"), "'strategy' must be 'tile_pregenerated' or 'on_the_fly'"
 
         BaseRecording.__init__(self, sampling_frequency=sampling_frequency, channel_ids=channel_ids, dtype=dtype)
 

src/spikeinterface/core/tests/test_generate.py

@@ -26,15 +26,44 @@
 
 
 def test_generate_recording():
-    # TODO even this is extenssivly tested in all other function
+    # TODO even this is extensively tested in all other functions
     pass
 
 
 def test_generate_sorting():
-    # TODO even this is extenssivly tested in all other function
+    # TODO even this is extensively tested in all other functions
     pass
 
 
+def test_generate_sorting_with_spikes_on_borders():
+    num_spikes_on_borders = 10
+    border_size_samples = 10
+    segment_duration = 10
+    for nseg in [1, 2, 3]:
+        sorting = generate_sorting(
+            durations=[segment_duration] * nseg,
+            sampling_frequency=30000,
+            num_units=10,
+            add_spikes_on_borders=True,
+            num_spikes_per_border=num_spikes_on_borders,
+            border_size_samples=border_size_samples,
+        )
+        # check that segments are correctly sorted
+        all_spikes = sorting.to_spike_vector()
+        np.testing.assert_array_equal(all_spikes["segment_index"], np.sort(all_spikes["segment_index"]))
+
+        spikes = sorting.to_spike_vector(concatenated=False)
+        # at least num_border spikes at borders for all segments
+        for spikes_in_segment in spikes:
+            # check that sample indices are correctly sorted within segments
+            np.testing.assert_array_equal(spikes_in_segment["sample_index"], np.sort(spikes_in_segment["sample_index"]))
+            num_samples = int(segment_duration * 30000)
+            assert np.sum(spikes_in_segment["sample_index"] < border_size_samples) >= num_spikes_on_borders
+            assert (
+                np.sum(spikes_in_segment["sample_index"] >= num_samples - border_size_samples) >= num_spikes_on_borders
+            )
+
+
 def measure_memory_allocation(measure_in_process: bool = True) -> float:
     """
     A local utility to measure memory allocation at a specific point in time.
@@ -399,7 +428,7 @@ def test_generate_ground_truth_recording():
 if __name__ == "__main__":
     strategy = "tile_pregenerated"
     # strategy = "on_the_fly"
-    test_noise_generator_memory()
+    # test_noise_generator_memory()
     # test_noise_generator_under_giga()
     # test_noise_generator_correct_shape(strategy)
     # test_noise_generator_consistency_across_calls(strategy, 0, 5)
@@ -410,3 +439,4 @@ def test_generate_ground_truth_recording():
     # test_generate_templates()
     # test_inject_templates()
     # test_generate_ground_truth_recording()
+    test_generate_sorting_with_spikes_on_borders()

src/spikeinterface/extractors/cbin_ibl.py

@@ -6,13 +6,6 @@
 from spikeinterface.extractors.neuropixels_utils import get_neuropixels_sample_shifts
 from spikeinterface.core.core_tools import define_function_from_class
 
-try:
-    import mtscomp
-
-    HAVE_MTSCOMP = True
-except:
-    HAVE_MTSCOMP = False
-
 
 class CompressedBinaryIblExtractor(BaseRecording):
     """Load IBL data as an extractor object.
@@ -42,7 +35,6 @@ class CompressedBinaryIblExtractor(BaseRecording):
     """
 
     extractor_name = "CompressedBinaryIbl"
-    installed = HAVE_MTSCOMP
     mode = "folder"
     installation_mesg = "To use the CompressedBinaryIblExtractor, install mtscomp: \n\n pip install mtscomp\n\n"
     name = "cbin_ibl"
@@ -51,7 +43,10 @@ def __init__(self, folder_path, load_sync_channel=False, stream_name="ap"):
         # this work only for future neo
         from neo.rawio.spikeglxrawio import read_meta_file, extract_stream_info
 
-        assert HAVE_MTSCOMP
+        try:
+            import mtscomp
+        except:
+            raise ImportError(self.installation_mesg)
         folder_path = Path(folder_path)
 
         # check bands

src/spikeinterface/postprocessing/amplitude_scalings.py

@@ -16,6 +16,7 @@ class AmplitudeScalingsCalculator(BaseWaveformExtractorExtension):
     """
 
     extension_name = "amplitude_scalings"
+    handle_sparsity = True
 
     def __init__(self, waveform_extractor):
         BaseWaveformExtractorExtension.__init__(self, waveform_extractor)
@@ -68,7 +69,6 @@ def _run(self, **job_kwargs):
         delta_collision_samples = int(delta_collision_ms / 1000 * we.sampling_frequency)
 
         return_scaled = we._params["return_scaled"]
-        unit_ids = we.unit_ids
 
         if ms_before is not None:
             assert (
@@ -82,18 +82,22 @@ def _run(self, **job_kwargs):
         cut_out_before = int(ms_before / 1000 * we.sampling_frequency) if ms_before is not None else nbefore
         cut_out_after = int(ms_after / 1000 * we.sampling_frequency) if ms_after is not None else nafter
 
-        if we.is_sparse():
+        if we.is_sparse() and self._params["sparsity"] is None:
             sparsity = we.sparsity
-        elif self._params["sparsity"] is not None:
+        elif we.is_sparse() and self._params["sparsity"] is not None:
+            sparsity = self._params["sparsity"]
+            # assert provided sparsity is sparser than the one in the waveform extractor
+            waveform_sparsity = we.sparsity
+            assert np.all(
+                np.sum(waveform_sparsity.mask, 1) - np.sum(sparsity.mask, 1) > 0
+            ), "The provided sparsity needs to be sparser than the one in the waveform extractor!"
+        elif not we.is_sparse() and self._params["sparsity"] is not None:
             sparsity = self._params["sparsity"]
         else:
             if self._params["max_dense_channels"] is not None:
                 assert recording.get_num_channels() <= self._params["max_dense_channels"], ""
             sparsity = ChannelSparsity.create_dense(we)
-        sparsity_inds = sparsity.unit_id_to_channel_indices
-
-        # easier to use in chunk function as spikes use unit_index instead o id
-        unit_inds_to_channel_indices = {unit_ind: sparsity_inds[unit_id] for unit_ind, unit_id in enumerate(unit_ids)}
+        sparsity_mask = sparsity.mask
         all_templates = we.get_all_templates()
 
         # precompute segment slice
@@ -112,7 +116,7 @@ def _run(self, **job_kwargs):
             self.spikes,
             all_templates,
             segment_slices,
-            unit_inds_to_channel_indices,
+            sparsity_mask,
             nbefore,
             nafter,
             cut_out_before,
@@ -261,7 +265,7 @@ def _init_worker_amplitude_scalings(
     spikes,
     all_templates,
     segment_slices,
-    unit_inds_to_channel_indices,
+    sparsity_mask,
     nbefore,
     nafter,
     cut_out_before,
@@ -281,7 +285,7 @@ def _init_worker_amplitude_scalings(
     worker_ctx["cut_out_before"] = cut_out_before
     worker_ctx["cut_out_after"] = cut_out_after
     worker_ctx["return_scaled"] = return_scaled
-    worker_ctx["unit_inds_to_channel_indices"] = unit_inds_to_channel_indices
+    worker_ctx["sparsity_mask"] = sparsity_mask
     worker_ctx["handle_collisions"] = handle_collisions
     worker_ctx["delta_collision_samples"] = delta_collision_samples
 
@@ -305,7 +309,7 @@ def _amplitude_scalings_chunk(segment_index, start_frame, end_frame, worker_ctx)
     recording = worker_ctx["recording"]
     all_templates = worker_ctx["all_templates"]
     segment_slices = worker_ctx["segment_slices"]
-    unit_inds_to_channel_indices = worker_ctx["unit_inds_to_channel_indices"]
+    sparsity_mask = worker_ctx["sparsity_mask"]
     nbefore = worker_ctx["nbefore"]
     cut_out_before = worker_ctx["cut_out_before"]
     cut_out_after = worker_ctx["cut_out_after"]
@@ -338,7 +342,7 @@ def _amplitude_scalings_chunk(segment_index, start_frame, end_frame, worker_ctx)
             )
             local_spikes_w_margin = spikes_in_segment[i0_margin:i1_margin]
             collisions_local = find_collisions(
-                local_spikes, local_spikes_w_margin, delta_collision_samples, unit_inds_to_channel_indices
+                local_spikes, local_spikes_w_margin, delta_collision_samples, sparsity_mask
             )
         else:
             collisions_local = {}
@@ -353,7 +357,7 @@ def _amplitude_scalings_chunk(segment_index, start_frame, end_frame, worker_ctx)
                 continue
             unit_index = spike["unit_index"]
             sample_index = spike["sample_index"]
-            sparse_indices = unit_inds_to_channel_indices[unit_index]
+            (sparse_indices,) = np.nonzero(sparsity_mask[unit_index])
             template = all_templates[unit_index][:, sparse_indices]
             template = template[nbefore - cut_out_before : nbefore + cut_out_after]
             sample_centered = sample_index - start_frame
@@ -364,7 +368,7 @@ def _amplitude_scalings_chunk(segment_index, start_frame, end_frame, worker_ctx)
                 template = template[cut_out_before - sample_index :]
             elif sample_index + cut_out_after > end_frame + right:
                 local_waveform = traces_with_margin[cut_out_start:, sparse_indices]
-                template = template[: -(sample_index + cut_out_after - end_frame)]
+                template = template[: -(sample_index + cut_out_after - (end_frame + right))]
             else:
                 local_waveform = traces_with_margin[cut_out_start:cut_out_end, sparse_indices]
             assert template.shape == local_waveform.shape
@@ -392,7 +396,7 @@ def _amplitude_scalings_chunk(segment_index, start_frame, end_frame, worker_ctx)
                     right,
                     nbefore,
                     all_templates,
-                    unit_inds_to_channel_indices,
+                    sparsity_mask,
                     cut_out_before,
                     cut_out_after,
                 )
@@ -409,14 +413,14 @@ def _amplitude_scalings_chunk(segment_index, start_frame, end_frame, worker_ctx)
 
 
 ### Collision handling ###
-def _are_unit_indices_overlapping(unit_inds_to_channel_indices, i, j):
+def _are_unit_indices_overlapping(sparsity_mask, i, j):
     """
     Returns True if the unit indices i and j are overlapping, False otherwise
 
     Parameters
     ----------
-    unit_inds_to_channel_indices: dict
-        A dictionary mapping unit indices to channel indices
+    sparsity_mask: boolean mask
+        The sparsity mask
     i: int
         The first unit index
     j: int
@@ -427,13 +431,13 @@ def _are_unit_indices_overlapping(unit_inds_to_channel_indices, i, j):
     bool
         True if the unit indices i and j are overlapping, False otherwise
     """
-    if len(np.intersect1d(unit_inds_to_channel_indices[i], unit_inds_to_channel_indices[j])) > 0:
+    if np.any(sparsity_mask[i] & sparsity_mask[j]):
         return True
     else:
         return False
 
 
-def find_collisions(spikes, spikes_w_margin, delta_collision_samples, unit_inds_to_channel_indices):
+def find_collisions(spikes, spikes_w_margin, delta_collision_samples, sparsity_mask):
     """
     Finds the collisions between spikes.
 
@@ -445,8 +449,8 @@ def find_collisions(spikes, spikes_w_margin, delta_collision_samples, unit_inds_
         An array of spikes within the added margin
     delta_collision_samples: int
         The maximum number of samples between two spikes to consider them as overlapping
-    unit_inds_to_channel_indices: dict
-        A dictionary mapping unit indices to channel indices
+    sparsity_mask: boolean mask
+        The sparsity mask
 
     Returns
     -------
@@ -476,7 +480,7 @@ def find_collisions(spikes, spikes_w_margin, delta_collision_samples, unit_inds_
         # find the overlapping spikes in space as well
         for possible_overlapping_spike_index in possible_overlapping_spike_indices:
             if _are_unit_indices_overlapping(
-                unit_inds_to_channel_indices,
+                sparsity_mask,
                 spike["unit_index"],
                 spikes_w_margin[possible_overlapping_spike_index]["unit_index"],
             ):
@@ -497,7 +501,7 @@ def fit_collision(
     right,
     nbefore,
     all_templates,
-    unit_inds_to_channel_indices,
+    sparsity_mask,
     cut_out_before,
     cut_out_after,
 ):
@@ -524,8 +528,8 @@ def fit_collision(
         The number of samples before the spike to consider for the fit.
     all_templates: np.ndarray
         A numpy array of shape (n_units, n_samples, n_channels) containing the templates.
-    unit_inds_to_channel_indices: dict
-        A dictionary mapping unit indices to channel indices.
+    sparsity_mask: boolean mask
+        The sparsity mask
     cut_out_before: int
         The number of samples to cut out before the spike.
     cut_out_after: int
@@ -543,14 +547,16 @@ def fit_collision(
     sample_last_centered = np.max(collision["sample_index"]) - (start_frame - left)
 
     # construct sparsity as union between units' sparsity
-    sparse_indices = np.array([], dtype="int")
+    common_sparse_mask = np.zeros(sparsity_mask.shape[1], dtype="int")
     for spike in collision:
-        sparse_indices_i = unit_inds_to_channel_indices[spike["unit_index"]]
-        sparse_indices = np.union1d(sparse_indices, sparse_indices_i)
+        mask_i = sparsity_mask[spike["unit_index"]]
+        common_sparse_mask = np.logical_or(common_sparse_mask, mask_i)
+    (sparse_indices,) = np.nonzero(common_sparse_mask)
 
     local_waveform_start = max(0, sample_first_centered - cut_out_before)
     local_waveform_end = min(traces_with_margin.shape[0], sample_last_centered + cut_out_after)
     local_waveform = traces_with_margin[local_waveform_start:local_waveform_end, sparse_indices]
+    num_samples_local_waveform = local_waveform.shape[0]
 
     y = local_waveform.T.flatten()
     X = np.zeros((len(y), len(collision)))
@@ -563,8 +569,10 @@ def fit_collision(
         # deal with borders
         if sample_centered - cut_out_before < 0:
             full_template[: sample_centered + cut_out_after] = template_cut[cut_out_before - sample_centered :]
-        elif sample_centered + cut_out_after > end_frame + right:
-            full_template[sample_centered - cut_out_before :] = template_cut[: -cut_out_after - (end_frame + right)]
+        elif sample_centered + cut_out_after > num_samples_local_waveform:
+            full_template[sample_centered - cut_out_before :] = template_cut[
+                : -(cut_out_after + sample_centered - num_samples_local_waveform)
+            ]
         else:
             full_template[sample_centered - cut_out_before : sample_centered + cut_out_after] = template_cut
         X[:, i] = full_template.T.flatten()