Merge branch 'main' into fix-randomness-in-tests

Author: alejoe91

doc/modules/comparison.rst

@@ -523,19 +523,19 @@ in the similarity of templates rather than spiking events.
 This enables us to use exactly the same tools for both types of comparisons, just by changing the way that agreement
 scores are computed.
 
-The functions to compare templates take a list of :py:class:`~spikeinterface.core.WaveformExtractor` objects as input,
+The functions to compare templates take a list of :py:class:`~spikeinterface.core.SortingAnalyzer` objects as input,
 which are assumed to be from different sessions of the same animal over time. In this case, let's assume we have 5
-waveform extractors from day 1 (:code:`we_day1`) to day 5 (:code:`we_day5`):
+sorting analyzers from day 1 (:code:`analyzer_day1`) to day 5 (:code:`analyzer_day5`):
 
 .. code-block:: python
 
-    we_list = [we_day1, we_day2, we_day3, we_day4, we_day5]
+    analyzer_list = [analyzer_day1, analyzer_day2, analyzer_day3, analyzer_day4, analyzer_day5]
 
     # match only day 1 and 2
-    p_tcmp = sc.compare_templates(we1=we_day1, we2=we_day2, we1_name="Day1", we2_name="Day2")
+    p_tcmp = sc.compare_templates(sorting_analyzer_1=analyzer_day1, sorting_analyzer2=analyzer_day2, name1="Day1", name2="Day2")
 
     # match all
-    m_tcmp = sc.compare_multiple_templates(waveform_list=we_list,
+    m_tcmp = sc.compare_multiple_templates(waveform_list=analyzer_list,
                                            name_list=["D1", "D2", "D3", "D4", "D5"])
 
 

doc/modules/core.rst

@@ -496,19 +496,21 @@ Sparsity
 In several cases, it is not necessary to have waveforms on all channels. This is especially true for high-density
 probes, such as Neuropixels, because the waveforms of a unit will only appear on a small set of channels.
 Sparsity is defined as the subset of channels on which waveforms (and related information) are defined. Of course,
-sparsity is not global, but it is unit-specific.
+sparsity is not global, but it is unit-specific. Importantly, saving sparse waveforms, especially for high-density probes,
+dramatically reduces the size of the waveforms extension if computed.
 
-**NOTE** As of version :code:`0.99.0` the default for a :code:`extract_waveforms()` has :code:`sparse=True`, i.e. every :code:`waveform_extractor`
-will be sparse by default. Thus for users that wish to have dense waveforms they must set :code:`sparse=False`. Keyword arguments
-can still be input into the :code:`extract_wavforms()` to generate the desired sparsity as explained below.
+**NOTE** As of :code:`0.101.0` all :code:`SortingAnalyzer`'s have a default of :code:`sparse=True`. This was first
+introduced in :code:`0.99.0` for :code:`WaveformExtractor`'s and will be the default going forward. To obtain dense
+waveforms you will need to set :code:`sparse=False` at the creation of the :code:`SortingAnalyzer`.
 
-Sparsity can be computed from a :py:class:`~spikeinterface.core.WaveformExtractor` object with the
-:py:func:`~spikeinterface.core.compute_sparsity` function:
+
+Sparsity can be computed from a :py:class:`~spikeinterface.core.SortingAnalyzer` object with the
+:py:func:`~spikeinterface.core.estimate_sparsity` function:
 
 .. code-block:: python
 
-    # in this case 'we' should be a dense waveform_extractor
-    sparsity = compute_sparsity(we, method="radius", radius_um=40)
+    # in this case 'analyzer' should be a dense SortingAnalyzer
+    sparsity = compute_sparsity(analyzer, method="radius", radius_um=40)
 
 The returned :code:`sparsity` is a :py:class:`~spikeinterface.core.ChannelSparsity` object, which has convenient
 methods to access the sparsity information in several ways:
@@ -529,17 +531,19 @@ There are several methods to compute sparsity, including:
 * | :code:`method="by_property"`: selects channels based on a property, such as :code:`group`. This method is recommended
   | when working with tetrodes.
 
-The computed sparsity can be used in several postprocessing and visualization functions. In addition, a "dense"
-:py:class:`~spikeinterface.core.WaveformExtractor` can be saved as "sparse" as follows:
+The computed sparsity can be used in several postprocessing and visualization functions. In addition, this sparsity can be
+used when creating a :py:class:`~spikeinterface.core.SortingAnalyzer` which cause the :code:`sparse` boolean to be ignored.
 
 .. code-block:: python
 
-    we_sparse = we.save(sparsity=sparsity, folder="waveforms_sparse")
+    analyzer_sparse = si.create_sorting_analyzer(
+        sorting=sorting,
+        recording=recording,
+        sparsity=sparsity,
+        format='binary_folder',
+        folder="sparse_analyzer"
+    )
 
-The :code:`we_sparse` object will now have an associated sparsity (:code:`we.sparsity`), which is automatically taken
-into consideration for downstream analysis (with the :py:meth:`~spikeinterface.core.WaveformExtractor.is_sparse`
-method). Importantly, saving sparse waveforms, especially for high-density probes, dramatically reduces the size of the
-waveforms folder.
 
 .. _save_load:
 

doc/modules/postprocessing.rst

@@ -205,7 +205,7 @@ This extension computes the principal components of the waveforms. There are sev
 * "by_channel_global": fits the same PCA model to all channels (also termed temporal PCA)
 * "concatenated": concatenates all channels and fits a PCA model on the concatenated data
 
-If the input :code:`WaveformExtractor` is sparse, the sparsity is used when computing the PCA.
+If the input :code:`SortingAnalyzer` is sparse, the sparsity is used when computing the PCA.
 For dense waveforms, sparsity can also be passed as an argument.
 
 .. code-block:: python