Merge pull request #1948 from samuelgarcia/generator

Refactor generate.py
SpikeInterface · Sep 1, 2023 · 23aef27 · 23aef27
2 parents 3817ee0 + 20f5108
commit 23aef27
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Showing 14 changed files with 1,466 additions and 1,124 deletions.
diff --git a/src/spikeinterface/comparison/hybrid.py b/src/spikeinterface/comparison/hybrid.py
@@ -6,11 +6,9 @@
     BaseSorting,
     WaveformExtractor,
     NumpySorting,
-    NpzSortingExtractor,
-    InjectTemplatesRecording,
 )
 from spikeinterface.core.core_tools import define_function_from_class
-from spikeinterface.core import generate_sorting
+from spikeinterface.core.generate import generate_sorting, InjectTemplatesRecording, _ensure_seed
 
 
 class HybridUnitsRecording(InjectTemplatesRecording):
@@ -60,6 +58,7 @@ def __init__(
         amplitude_std: float = 0.0,
         refractory_period_ms: float = 2.0,
         injected_sorting_folder: Union[str, Path, None] = None,
+        seed=None,
     ):
         num_samples = [
             parent_recording.get_num_frames(seg_index) for seg_index in range(parent_recording.get_num_segments())
@@ -80,8 +79,8 @@ def __init__(
                 num_units=len(templates),
                 sampling_frequency=fs,
                 durations=durations,
-                firing_rate=firing_rate,
-                refractory_period=refractory_period_ms,
+                firing_rates=firing_rate,
+                refractory_period_ms=refractory_period_ms,
             )
         # save injected sorting if necessary
         self.injected_sorting = injected_sorting
@@ -90,17 +89,10 @@ def __init__(
             self.injected_sorting = self.injected_sorting.save(folder=injected_sorting_folder)
 
         if amplitude_factor is None:
-            amplitude_factor = [
-                [
-                    np.random.normal(
-                        loc=1.0,
-                        scale=amplitude_std,
-                        size=len(self.injected_sorting.get_unit_spike_train(unit_id, segment_index=seg_index)),
-                    )
-                    for unit_id in self.injected_sorting.unit_ids
-                ]
-                for seg_index in range(parent_recording.get_num_segments())
-            ]
+            seed = _ensure_seed(seed)
+            rng = np.random.default_rng(seed=seed)
+            num_spikes = self.injected_sorting.to_spike_vector().size
+            amplitude_factor = rng.normal(loc=1.0, scale=amplitude_std, size=num_spikes)
 
         InjectTemplatesRecording.__init__(
             self, self.injected_sorting, templates, nbefore, amplitude_factor, parent_recording, num_samples
@@ -116,6 +108,7 @@ def __init__(
             amplitude_std=amplitude_std,
             refractory_period_ms=refractory_period_ms,
             injected_sorting_folder=None,
+            seed=seed,
         )
 
 

diff --git a/src/spikeinterface/core/__init__.py b/src/spikeinterface/core/__init__.py
@@ -34,6 +34,13 @@
     inject_some_duplicate_units,
     inject_some_split_units,
     synthetize_spike_train_bad_isi,
+    generate_templates,
+    NoiseGeneratorRecording,
+    noise_generator_recording,
+    generate_recording_by_size,
+    InjectTemplatesRecording,
+    inject_templates,
+    generate_ground_truth_recording,
 )
 
 # utils to append and concatenate segment (equivalent to OLD MultiRecordingTimeExtractor)
@@ -109,7 +116,7 @@
 )
 
 # templates addition
-from .injecttemplates import InjectTemplatesRecording, InjectTemplatesRecordingSegment, inject_templates
+# from .injecttemplates import InjectTemplatesRecording, InjectTemplatesRecordingSegment, inject_templates
 
 # template tools
 from .template_tools import (