Merge branch 'main' into add_name_to_repr

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 24.4.0
+    rev: 24.4.2
     hooks:
     -   id: black
         files: ^src/

doc/conf.py

@@ -63,6 +63,7 @@
 extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
+    'sphinx.ext.autosectionlabel',
     'sphinx_gallery.gen_gallery',
     'numpydoc',
     'sphinx_design',

doc/how_to/get_started.rst

@@ -230,7 +230,7 @@ object to disk.
                              float32 dtype - 39.06 MiB
     CommonReferenceRecording: 32 channels - 32.0kHz - 1 segments - 320,000 samples - 10.00s
                               float32 dtype - 39.06 MiB
-    Use cache_folder=/tmp/spikeinterface_cache/tmpsgoh2z3y/DLGW1J8V
+    Use cache_folder=/tmp/spikeinterface_cache/tmpxozot7du/PS8C5MPU
     write_binary_recording with n_jobs = 4 and chunk_size = 32000
 
 
@@ -245,7 +245,9 @@ object to disk.
     BinaryFolderRecording: 32 channels - 32.0kHz - 1 segments - 320,000 samples - 10.00s
                            float32 dtype - 39.06 MiB
 
-To reload a preprocessed recording that was saved to disk, you can use ``load_extractor()`` function from the ``core`` module.
+
+To reload a preprocessed recording that was saved to disk, you can use
+``load_extractor()`` function from the ``core`` module.
 
 Now you are ready to spike sort using the ``spikeinterface.sorters``
 module! Let’s first check which sorters are implemented and which are
@@ -294,7 +296,7 @@ available parameters are dictionaries and can be accessed with:
     {'apply_preprocessing': True,
      'cache_preprocessing': {'delete_cache': True,
                              'memory_limit': 0.5,
-                             'mode': None},
+                             'mode': 'memory'},
      'clustering': {'legacy': False},
      'debug': False,
      'detection': {'detect_threshold': 4, 'peak_sign': 'neg'},
@@ -306,6 +308,7 @@ available parameters are dictionaries and can be accessed with:
      'selection': {'method': 'smart_sampling_amplitudes',
                    'min_n_peaks': 100000,
                    'n_peaks_per_channel': 5000,
+                   'seed': 42,
                    'select_per_channel': False},
      'sparsity': {'method': 'ptp', 'threshold': 0.25}}
 
@@ -351,9 +354,15 @@ Let’s run ``spykingcircus2`` as well, with default parameters:
     print(sorting_SC2)
 
 
+
 .. parsed-literal::
 
-    NumpyFolderSorting: 10 units - 1 segments - 32.0kHz
+    write_memory_recording:   0%|          | 0/1 [00:00<?, ?it/s]
+
+
+.. parsed-literal::
+
+    NumpyFolderSorting: 8 units - 1 segments - 32.0kHz
 
 
 The ``sorting_TDC`` and ``sorting_SC2`` are ``BaseSorting`` objects. We
@@ -368,7 +377,7 @@ can print the units found using:
 .. parsed-literal::
 
     Units found by tridesclous: [0 1 2 3 4 5 6 7 8 9]
-    Units found by spyking-circus2: [0 1 2 3 4 5 6 7 8 9]
+    Units found by spyking-circus2: [0 1 2 3 4 5 6 7]
 
 
 If a sorter is not installed locally, we can also avoid installing it
@@ -436,7 +445,7 @@ and then to compute, for example, quality metrics. Computations with the
 
 .. parsed-literal::
 
-    <spikeinterface.core.analyzer_extension_core.ComputeWaveforms at 0x7f49d5ddabb0>
+    <spikeinterface.core.analyzer_extension_core.ComputeWaveforms at 0x7fa6f222c5b0>
 
 
 
@@ -476,7 +485,7 @@ There are many more properties we can calculate
 
 .. parsed-literal::
 
-    <spikeinterface.postprocessing.spike_amplitudes.ComputeSpikeAmplitudes at 0x7f49d5e36340>
+    <spikeinterface.postprocessing.spike_amplitudes.ComputeSpikeAmplitudes at 0x7fa6f241cb20>
 
 
 
@@ -500,12 +509,56 @@ Many of the extensions have parameters you can tune
 
 .. parsed-literal::
 
-    <spikeinterface.postprocessing.template_similarity.ComputeTemplateSimilarity at 0x7f49d5e0ed90>
+    <spikeinterface.postprocessing.template_similarity.ComputeTemplateSimilarity at 0x7fa6f2379ac0>
+
+
+
+As you can see, it becomes a bit overwhelming if you’re computing lots
+of extensions. Luckily, there’s some nice syntax for this very
+situation. We can redo the last nine compute statements in one command
+as follows:
+
+.. code:: ipython3
+
+    extensions_to_compute = [
+        "random_spikes",
+        "waveforms",
+        "noise_levels",
+        "templates",
+        "spike_amplitudes",
+        "unit_locations",
+        "spike_locations",
+        "correlograms",
+        "template_similarity"
+    ]
+
+    extension_params = {
+        "unit_locations": {"method": "center_of_mass"},
+        "spike_locations": {"ms_before": 0.1},
+        "correlograms": {"bin_ms": 0.1},
+        "template_similarity": {"method": "cosine_similarity"}
+    }
+
+    analyzer_TDC.compute(extensions_to_compute, extension_params=extension_params)
 
 
 
+.. parsed-literal::
+
+    compute_waveforms:   0%|          | 0/10 [00:00<?, ?it/s]
+
+
+
+.. parsed-literal::
+
+    Compute : spike_amplitudes + spike_locations:   0%|          | 0/10 [00:00<?, ?it/s]
+
+
+Which you might find easier. Note that if we pass no extension
+parameters, the computation simply uses the default parameters.
+
 Find out more about the available parameters and extensions
-`here <https://spikeinterface.readthedocs.io/en/latest/modules/postprocessing.html#available-postprocessing-extensions>`__.
+`here <https://spikeinterface.readthedocs.io/en/latest/modules/postprocessing.html>`__.
 
 The calculations are saved in the ``extensions`` subfolder of the
 ``SortingAnalyzer`` folder. Similar to the waveforms we can access them
@@ -520,7 +573,7 @@ a historgram of spike amplitudes
 
 
 
-.. image:: get_started_files/get_started_52_0.png
+.. image:: get_started_files/get_started_55_0.png
 
 
 You can check which extensions have been saved (in your local folder)
@@ -534,8 +587,8 @@ and which have been loaded (in your enviroment)…
 
 .. parsed-literal::
 
-    ['random_spikes', 'waveforms', 'templates', 'noise_levels', 'template_similarity', 'spike_amplitudes', 'correlograms', 'spike_locations', 'unit_locations']
-    ['random_spikes', 'waveforms', 'noise_levels', 'templates', 'spike_amplitudes', 'unit_locations', 'spike_locations', 'correlograms', 'template_similarity']
+    ['noise_levels', 'spike_locations', 'template_similarity', 'waveforms', 'spike_amplitudes', 'templates', 'correlograms', 'unit_locations', 'random_spikes']
+    ['random_spikes', 'noise_levels', 'correlograms', 'waveforms', 'templates', 'unit_locations', 'template_similarity', 'spike_amplitudes', 'spike_locations']
 
 
 …or delete an extension…
@@ -559,7 +612,7 @@ since we just deleted it)
 
 .. parsed-literal::
 
-    ['random_spikes', 'waveforms', 'templates', 'noise_levels', 'template_similarity', 'correlograms', 'spike_locations', 'unit_locations']
+    ['noise_levels', 'templates', 'spike_locations', 'template_similarity', 'waveforms', 'correlograms', 'unit_locations', 'random_spikes']
 
 
 And any deleted extensions are easily recomputed
@@ -579,7 +632,7 @@ And any deleted extensions are easily recomputed
 
 .. parsed-literal::
 
-    <spikeinterface.postprocessing.spike_amplitudes.ComputeSpikeAmplitudes at 0x7f49b80eadc0>
+    <spikeinterface.postprocessing.spike_amplitudes.ComputeSpikeAmplitudes at 0x7fa6f2095310>
 
 
 
@@ -656,6 +709,19 @@ in the same way as earlier
     analyzer_TDC.compute("quality_metrics", qm_params)
     analyzer_TDC.get_extension("quality_metrics").get_data()
 
+
+.. parsed-literal::
+
+    /home/nolanlab/Chris/Developing/spikeinterface/src/spikeinterface/qualitymetrics/misc_metrics.py:846: UserWarning: Some units have too few spikes : amplitude_cutoff is set to NaN
+      warnings.warn(f"Some units have too few spikes : amplitude_cutoff is set to NaN")
+    /home/nolanlab/Chris/Developing/spikeinterface/src/spikeinterface/qualitymetrics/misc_metrics.py:999: UserWarning: The recording is too short given the specified 'interval_s' and 'min_num_bins'. Drift metrics will be set to NaN
+      warnings.warn(
+    /home/nolanlab/Chris/Developing/spikeinterface/src/spikeinterface/qualitymetrics/misc_metrics.py:147: UserWarning: Bin duration of 60s is larger than recording duration. Presence ratios are set to NaN.
+      warnings.warn(
+
+
+
+
 .. raw:: html
 
     <div>
@@ -719,7 +785,7 @@ in the same way as earlier
           <td>0.0</td>
           <td>1.536918</td>
           <td>NaN</td>
-          <td>27.140698</td>
+          <td>27.449127</td>
           <td>0.0</td>
           <td>0.0</td>
           <td>0.0</td>
@@ -743,7 +809,7 @@ in the same way as earlier
           <td>0.0</td>
           <td>1.311148</td>
           <td>NaN</td>
-          <td>24.059540</td>
+          <td>24.363658</td>
           <td>0.0</td>
           <td>0.0</td>
           <td>0.0</td>
@@ -767,7 +833,7 @@ in the same way as earlier
           <td>0.0</td>
           <td>2.016703</td>
           <td>NaN</td>
-          <td>24.387525</td>
+          <td>24.339651</td>
           <td>0.0</td>
           <td>0.0</td>
           <td>0.0</td>
@@ -791,7 +857,7 @@ in the same way as earlier
           <td>0.0</td>
           <td>2.011083</td>
           <td>NaN</td>
-          <td>26.948630</td>
+          <td>26.662774</td>
           <td>0.0</td>
           <td>0.0</td>
           <td>0.0</td>
@@ -815,7 +881,7 @@ in the same way as earlier
           <td>0.0</td>
           <td>0.680199</td>
           <td>NaN</td>
-          <td>9.585650</td>
+          <td>9.632134</td>
           <td>0.0</td>
           <td>0.0</td>
           <td>0.0</td>
@@ -839,7 +905,7 @@ in the same way as earlier
           <td>0.0</td>
           <td>0.965515</td>
           <td>NaN</td>
-          <td>13.196613</td>
+          <td>13.269441</td>
           <td>0.0</td>
           <td>0.0</td>
           <td>0.0</td>
@@ -863,7 +929,7 @@ in the same way as earlier
           <td>0.0</td>
           <td>1.177009</td>
           <td>NaN</td>
-          <td>8.193233</td>
+          <td>8.206179</td>
           <td>0.0</td>
           <td>0.0</td>
           <td>0.0</td>
@@ -885,9 +951,9 @@ in the same way as earlier
           <td>NaN</td>
           <td>0.0</td>
           <td>0.0</td>
-          <td>0.973417</td>
+          <td>0.974259</td>
           <td>0.155</td>
-          <td>8.808388</td>
+          <td>8.791409</td>
           <td>0.0</td>
           <td>0.0</td>
           <td>0.0</td>
@@ -911,7 +977,7 @@ in the same way as earlier
           <td>0.0</td>
           <td>0.949695</td>
           <td>0.310</td>
-          <td>11.125336</td>
+          <td>11.190016</td>
           <td>0.0</td>
           <td>0.0</td>
           <td>0.0</td>
@@ -933,9 +999,9 @@ in the same way as earlier
           <td>NaN</td>
           <td>0.0</td>
           <td>0.0</td>
-          <td>1.021080</td>
+          <td>1.027925</td>
           <td>0.270</td>
-          <td>8.281832</td>
+          <td>8.340747</td>
           <td>0.0</td>
           <td>0.0</td>
           <td>0.0</td>
@@ -963,15 +1029,16 @@ web-based visualization. For this to work you need to install
 
     w1 = sw.plot_quality_metrics(analyzer_TDC, display=False, backend="sortingview")
 
-https://figurl.org/f?v=npm://@fi-sci/figurl-sortingview@12/dist&d=sha1://c0312bc14387471531af9913147098b94cc640cf
+
+https://figurl.org/f?v=npm://@fi-sci/figurl-sortingview@12/dist&d=sha1://25075d7e8810c6239e2be02f288285091283c283
 
 
 .. code:: ipython3
 
     w2 = sw.plot_sorting_summary(analyzer_TDC, display=False, curation=True, backend="sortingview")
 
 
-https://figurl.org/f?v=npm://@fi-sci/figurl-sortingview@12/dist&d=sha1://688cd7a233857847b5663e565dbf3f2807887013
+https://figurl.org/f?v=npm://@fi-sci/figurl-sortingview@12/dist&d=sha1://588f5c77f7f1f445addcc219c648213d5324b123
 
 
 The sorting summary plot can also be used for manual labeling and
@@ -1112,11 +1179,11 @@ performance and plot a confusion matrix
 
 
 
-.. image:: get_started_files/get_started_84_1.png
+.. image:: get_started_files/get_started_87_1.png
 
 
 
-.. image:: get_started_files/get_started_84_2.png
+.. image:: get_started_files/get_started_87_2.png
 
 
 When comparing two sorters (2.), we can see the matching of units
@@ -1133,14 +1200,14 @@ between sorters. Units which are not matched have -1 as their unit id:
 
     0    0.0
     1    1.0
-    2    8.0
-    3    2.0
-    4    5.0
-    5    4.0
-    6    7.0
+    2    2.0
+    3    3.0
+    4   -1.0
+    5   -1.0
+    6    4.0
     7    6.0
-    8    9.0
-    9    3.0
+    8    7.0
+    9    5.0
     dtype: float64
 
 
@@ -1158,14 +1225,12 @@ or the reverse:
 
     0    0.0
     1    1.0
-    2    3.0
-    3    9.0
-    4    5.0
-    5    4.0
+    2    2.0
+    3    3.0
+    4    6.0
+    5    9.0
     6    7.0
-    7    6.0
-    8    2.0
-    9    8.0
+    7    8.0
     dtype: float64
 
 
@@ -1190,11 +1255,11 @@ graph showing how the units are matched between the sorters.
 
 
 
-.. image:: get_started_files/get_started_90_1.png
+.. image:: get_started_files/get_started_93_1.png
 
 
 
-.. image:: get_started_files/get_started_90_2.png
+.. image:: get_started_files/get_started_93_2.png
 
 
 We see that 10 unit were found by all sorters (note that this simulated