From 00b208c04d39980c7d67e45d0afb445456b2824b Mon Sep 17 00:00:00 2001 From: Zach McKenzie <92116279+zm711@users.noreply.github.com> Date: Fri, 13 Oct 2023 15:34:49 -0400 Subject: [PATCH 1/3] fix for waveform parameter change --- .../modules_gallery/core/plot_4_waveform_extractor.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/examples/modules_gallery/core/plot_4_waveform_extractor.py b/examples/modules_gallery/core/plot_4_waveform_extractor.py index 6c886c1eb0..bee8f4061b 100644 --- a/examples/modules_gallery/core/plot_4_waveform_extractor.py +++ b/examples/modules_gallery/core/plot_4_waveform_extractor.py @@ -49,7 +49,8 @@ ############################################################################### # A :py:class:`~spikeinterface.core.WaveformExtractor` object can be created with the -# :py:func:`~spikeinterface.core.extract_waveforms` function: +# :py:func:`~spikeinterface.core.extract_waveforms` function (this defaults to a sparse +# representation of the waveforms): folder = 'waveform_folder' we = extract_waveforms( @@ -87,6 +88,7 @@ recording, sorting, folder, + sparse=False, ms_before=3., ms_after=4., max_spikes_per_unit=500, @@ -149,7 +151,7 @@ # # Option 1) Save a dense waveform extractor to sparse: # -# In this case, from an existing waveform extractor, we can first estimate a +# In this case, from an existing (dense) waveform extractor, we can first estimate a # sparsity (which channels each unit is defined on) and then save to a new # folder in sparse mode: @@ -173,7 +175,7 @@ ############################################################################### -# Option 2) Directly extract sparse waveforms: +# Option 2) Directly extract sparse waveforms (current spikeinterface default): # # We can also directly extract sparse waveforms. To do so, dense waveforms are # extracted first using a small number of spikes (:code:`'num_spikes_for_sparsity'`) From 21e2e974a8c56c091300b77e76c3ac5f9d98b103 Mon Sep 17 00:00:00 2001 From: Zach McKenzie <92116279+zm711@users.noreply.github.com> Date: Fri, 13 Oct 2023 15:41:18 -0400 Subject: [PATCH 2/3] fix sparsity here as well. --- .../modules_gallery/qualitymetrics/plot_3_quality_mertics.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/modules_gallery/qualitymetrics/plot_3_quality_mertics.py b/examples/modules_gallery/qualitymetrics/plot_3_quality_mertics.py index 209f357457..986680e798 100644 --- a/examples/modules_gallery/qualitymetrics/plot_3_quality_mertics.py +++ b/examples/modules_gallery/qualitymetrics/plot_3_quality_mertics.py @@ -30,7 +30,7 @@ # because it contains a reference to the "Recording" and the "Sorting" objects: folder = 'waveforms_mearec' -we = si.extract_waveforms(recording, sorting, folder, +we = si.extract_waveforms(recording, sorting, folder, sparsity=False, ms_before=1, ms_after=2., max_spikes_per_unit=500, n_jobs=1, chunk_durations='1s') print(we) From bf8c5d1ccbe85b22e0397af562df1a21f256331f Mon Sep 17 00:00:00 2001 From: Zach McKenzie <92116279+zm711@users.noreply.github.com> Date: Fri, 13 Oct 2023 18:24:48 -0400 Subject: [PATCH 3/3] sparse=False for dense --- .../modules_gallery/qualitymetrics/plot_3_quality_mertics.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/modules_gallery/qualitymetrics/plot_3_quality_mertics.py b/examples/modules_gallery/qualitymetrics/plot_3_quality_mertics.py index 986680e798..7b6aae3e30 100644 --- a/examples/modules_gallery/qualitymetrics/plot_3_quality_mertics.py +++ b/examples/modules_gallery/qualitymetrics/plot_3_quality_mertics.py @@ -30,7 +30,7 @@ # because it contains a reference to the "Recording" and the "Sorting" objects: folder = 'waveforms_mearec' -we = si.extract_waveforms(recording, sorting, folder, sparsity=False, +we = si.extract_waveforms(recording, sorting, folder, sparse=False, ms_before=1, ms_after=2., max_spikes_per_unit=500, n_jobs=1, chunk_durations='1s') print(we)