Merge branch 'main' into ibl-extractor-pid

Author: alejoe91

src/spikeinterface/postprocessing/principal_component.py

@@ -1,12 +1,14 @@
 from __future__ import annotations
 
-import shutil
-import pickle
 import warnings
-import tempfile
+import platform
 from pathlib import Path
 from tqdm.auto import tqdm
 
+from concurrent.futures import ProcessPoolExecutor
+import multiprocessing as mp
+from threadpoolctl import threadpool_limits
+
 import numpy as np
 
 from spikeinterface.core.sortinganalyzer import register_result_extension, AnalyzerExtension
@@ -314,11 +316,13 @@ def _run(self, verbose=False, **job_kwargs):
         job_kwargs = fix_job_kwargs(job_kwargs)
         n_jobs = job_kwargs["n_jobs"]
         progress_bar = job_kwargs["progress_bar"]
+        max_threads_per_process = job_kwargs["max_threads_per_process"]
+        mp_context = job_kwargs["mp_context"]
 
         # fit model/models
         # TODO : make parralel  for by_channel_global and concatenated
         if mode == "by_channel_local":
-            pca_models = self._fit_by_channel_local(n_jobs, progress_bar)
+            pca_models = self._fit_by_channel_local(n_jobs, progress_bar, max_threads_per_process, mp_context)
             for chan_ind, chan_id in enumerate(self.sorting_analyzer.channel_ids):
                 self.data[f"pca_model_{mode}_{chan_id}"] = pca_models[chan_ind]
             pca_model = pca_models
@@ -411,12 +415,16 @@ def run_for_all_spikes(self, file_path=None, verbose=False, **job_kwargs):
         )
         processor.run()
 
-    def _fit_by_channel_local(self, n_jobs, progress_bar):
+    def _fit_by_channel_local(self, n_jobs, progress_bar, max_threads_per_process, mp_context):
         from sklearn.decomposition import IncrementalPCA
-        from concurrent.futures import ProcessPoolExecutor
 
         p = self.params
 
+        if mp_context is not None and platform.system() == "Windows":
+            assert mp_context != "fork", "'fork' mp_context not supported on Windows!"
+        elif mp_context == "fork" and platform.system() == "Darwin":
+            warnings.warn('As of Python 3.8 "fork" is no longer considered safe on macOS')
+
         unit_ids = self.sorting_analyzer.unit_ids
         channel_ids = self.sorting_analyzer.channel_ids
         # there is one PCA per channel for independent fit per channel
@@ -436,13 +444,18 @@ def _fit_by_channel_local(self, n_jobs, progress_bar):
                     pca = pca_models[chan_ind]
                     pca.partial_fit(wfs[:, :, wf_ind])
             else:
-                # parallel
+                # create list of args to parallelize. For convenience, the max_threads_per_process is passed
+                # as last argument
                 items = [
-                    (chan_ind, pca_models[chan_ind], wfs[:, :, wf_ind]) for wf_ind, chan_ind in enumerate(channel_inds)
+                    (chan_ind, pca_models[chan_ind], wfs[:, :, wf_ind], max_threads_per_process)
+                    for wf_ind, chan_ind in enumerate(channel_inds)
                 ]
                 n_jobs = min(n_jobs, len(items))
 
-                with ProcessPoolExecutor(max_workers=n_jobs) as executor:
+                with ProcessPoolExecutor(
+                    max_workers=n_jobs,
+                    mp_context=mp.get_context(mp_context),
+                ) as executor:
                     results = executor.map(_partial_fit_one_channel, items)
                     for chan_ind, pca_model_updated in results:
                         pca_models[chan_ind] = pca_model_updated
@@ -674,6 +687,12 @@ def _init_work_all_pc_extractor(recording, sorting, all_pcs_args, nbefore, nafte
 
 
 def _partial_fit_one_channel(args):
-    chan_ind, pca_model, wf_chan = args
-    pca_model.partial_fit(wf_chan)
-    return chan_ind, pca_model
+    chan_ind, pca_model, wf_chan, max_threads_per_process = args
+
+    if max_threads_per_process is None:
+        pca_model.partial_fit(wf_chan)
+        return chan_ind, pca_model
+    else:
+        with threadpool_limits(limits=int(max_threads_per_process)):
+            pca_model.partial_fit(wf_chan)
+            return chan_ind, pca_model

src/spikeinterface/postprocessing/tests/test_principal_component.py

@@ -18,6 +18,18 @@ class TestPrincipalComponentsExtension(AnalyzerExtensionCommonTestSuite):
     def test_extension(self, params):
         self.run_extension_tests(ComputePrincipalComponents, params=params)
 
+    def test_multi_processing(self):
+        """
+        Test the extension works with multiple processes.
+        """
+        sorting_analyzer = self._prepare_sorting_analyzer(
+            format="memory", sparse=False, extension_class=ComputePrincipalComponents
+        )
+        sorting_analyzer.compute("principal_components", mode="by_channel_local", n_jobs=2)
+        sorting_analyzer.compute(
+            "principal_components", mode="by_channel_local", n_jobs=2, max_threads_per_process=4, mp_context="spawn"
+        )
+
     def test_mode_concatenated(self):
         """
         Replicate the "extension_function_params_list" test outside of

src/spikeinterface/preprocessing/tests/test_filter.py

@@ -46,7 +46,7 @@ def test_causal_filter_main_kwargs(self, recording_and_data):
 
         filt_data = causal_filter(recording, direction="forward", **options, margin_ms=0).get_traces()
 
-        assert np.allclose(test_data, filt_data, rtol=0, atol=1e-6)
+        assert np.allclose(test_data, filt_data, rtol=0, atol=1e-4)
 
         # Then, change all kwargs to ensure they are propagated
         # and check the backwards version.
@@ -66,7 +66,7 @@ def test_causal_filter_main_kwargs(self, recording_and_data):
 
         filt_data = causal_filter(recording, direction="backward", **options, margin_ms=0).get_traces()
 
-        assert np.allclose(test_data, filt_data, rtol=0, atol=1e-6)
+        assert np.allclose(test_data, filt_data, rtol=0, atol=1e-4)
 
     def test_causal_filter_custom_coeff(self, recording_and_data):
         """
@@ -89,7 +89,7 @@ def test_causal_filter_custom_coeff(self, recording_and_data):
 
         filt_data = causal_filter(recording, direction="forward", **options, margin_ms=0).get_traces()
 
-        assert np.allclose(test_data, filt_data, rtol=0, atol=1e-6, equal_nan=True)
+        assert np.allclose(test_data, filt_data, rtol=0, atol=1e-4, equal_nan=True)
 
         # Next, in "sos" mode
         options["filter_mode"] = "sos"
@@ -100,7 +100,7 @@ def test_causal_filter_custom_coeff(self, recording_and_data):
 
         filt_data = causal_filter(recording, direction="forward", **options, margin_ms=0).get_traces()
 
-        assert np.allclose(test_data, filt_data, rtol=0, atol=1e-6, equal_nan=True)
+        assert np.allclose(test_data, filt_data, rtol=0, atol=1e-4, equal_nan=True)
 
     def test_causal_kwarg_error_raised(self, recording_and_data):
         """

src/spikeinterface/qualitymetrics/pca_metrics.py

@@ -2,15 +2,16 @@
 
 from __future__ import annotations
 
-
+import warnings
 from copy import deepcopy
-
-import numpy as np
+import platform
 from tqdm.auto import tqdm
-from concurrent.futures import ProcessPoolExecutor
 
+import numpy as np
 
-import warnings
+import multiprocessing as mp
+from concurrent.futures import ProcessPoolExecutor
+from threadpoolctl import threadpool_limits
 
 from .misc_metrics import compute_num_spikes, compute_firing_rates
 
@@ -56,6 +57,8 @@ def compute_pc_metrics(
     seed=None,
     n_jobs=1,
     progress_bar=False,
+    mp_context=None,
+    max_threads_per_process=None,
 ) -> dict:
     """
     Calculate principal component derived metrics.
@@ -144,17 +147,7 @@ def compute_pc_metrics(
         pcs = dense_projections[np.isin(all_labels, neighbor_unit_ids)][:, :, neighbor_channel_indices]
         pcs_flat = pcs.reshape(pcs.shape[0], -1)
 
-        func_args = (
-            pcs_flat,
-            labels,
-            non_nn_metrics,
-            unit_id,
-            unit_ids,
-            qm_params,
-            seed,
-            n_spikes_all_units,
-            fr_all_units,
-        )
+        func_args = (pcs_flat, labels, non_nn_metrics, unit_id, unit_ids, qm_params, max_threads_per_process)
         items.append(func_args)
 
     if not run_in_parallel and non_nn_metrics:
@@ -167,7 +160,15 @@ def compute_pc_metrics(
             for metric_name, metric in pca_metrics_unit.items():
                 pc_metrics[metric_name][unit_id] = metric
     elif run_in_parallel and non_nn_metrics:
-        with ProcessPoolExecutor(n_jobs) as executor:
+        if mp_context is not None and platform.system() == "Windows":
+            assert mp_context != "fork", "'fork' mp_context not supported on Windows!"
+        elif mp_context == "fork" and platform.system() == "Darwin":
+            warnings.warn('As of Python 3.8 "fork" is no longer considered safe on macOS')
+
+        with ProcessPoolExecutor(
+            max_workers=n_jobs,
+            mp_context=mp.get_context(mp_context),
+        ) as executor:
             results = executor.map(pca_metrics_one_unit, items)
             if progress_bar:
                 results = tqdm(results, total=len(unit_ids), desc="calculate_pc_metrics")
@@ -976,26 +977,19 @@ def _compute_isolation(pcs_target_unit, pcs_other_unit, n_neighbors: int):
 
 
 def pca_metrics_one_unit(args):
-    (
-        pcs_flat,
-        labels,
-        metric_names,
-        unit_id,
-        unit_ids,
-        qm_params,
-        seed,
-        # we_folder,
-        n_spikes_all_units,
-        fr_all_units,
-    ) = args
-
-    # if "nn_isolation" in metric_names or "nn_noise_overlap" in metric_names:
-    #     we = load_waveforms(we_folder)
+    (pcs_flat, labels, metric_names, unit_id, unit_ids, qm_params, max_threads_per_process) = args
+
+    if max_threads_per_process is None:
+        return _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, qm_params)
+    else:
+        with threadpool_limits(limits=int(max_threads_per_process)):
+            return _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, qm_params)
+
 
+def _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, qm_params):
     pc_metrics = {}
     # metrics
     if "isolation_distance" in metric_names or "l_ratio" in metric_names:
-
         try:
             isolation_distance, l_ratio = mahalanobis_metrics(pcs_flat, labels, unit_id)
         except:

src/spikeinterface/qualitymetrics/tests/test_pca_metrics.py

@@ -1,9 +1,7 @@
 import pytest
 import numpy as np
 
-from spikeinterface.qualitymetrics import (
-    compute_pc_metrics,
-)
+from spikeinterface.qualitymetrics import compute_pc_metrics, get_quality_pca_metric_list
 
 
 def test_calculate_pc_metrics(small_sorting_analyzer):
@@ -22,3 +20,24 @@ def test_calculate_pc_metrics(small_sorting_analyzer):
             assert not np.all(np.isnan(res2[metric_name].values))
 
         assert np.array_equal(res1[metric_name].values, res2[metric_name].values)
+
+
+def test_pca_metrics_multi_processing(small_sorting_analyzer):
+    sorting_analyzer = small_sorting_analyzer
+
+    metric_names = get_quality_pca_metric_list()
+    metric_names.remove("nn_isolation")
+    metric_names.remove("nn_noise_overlap")
+
+    print(f"Computing PCA metrics with 1 thread per process")
+    res1 = compute_pc_metrics(
+        sorting_analyzer, n_jobs=-1, metric_names=metric_names, max_threads_per_process=1, progress_bar=True
+    )
+    print(f"Computing PCA metrics with 2 thread per process")
+    res2 = compute_pc_metrics(
+        sorting_analyzer, n_jobs=-1, metric_names=metric_names, max_threads_per_process=2, progress_bar=True
+    )
+    print("Computing PCA metrics with spawn context")
+    res2 = compute_pc_metrics(
+        sorting_analyzer, n_jobs=-1, metric_names=metric_names, max_threads_per_process=2, progress_bar=True
+    )