Refactor metrics into its own module (#4183)

Author: alejoe91

.github/scripts/determine_testing_environment.py

@@ -20,7 +20,7 @@
 plexon2_changed = False
 preprocessing_changed = False
 postprocessing_changed = False
-qualitymetrics_changed = False
+metrics_changed = False
 sorters_changed = False
 sorters_external_changed = False
 sorters_internal_changed = False
@@ -58,8 +58,8 @@
         preprocessing_changed = True
     elif "postprocessing" in changed_file.parts:
         postprocessing_changed = True
-    elif "qualitymetrics" in changed_file.parts:
-        qualitymetrics_changed = True
+    elif "metrics" in changed_file.parts:
+        metrics_changed = True
     elif "comparison" in changed_file.parts:
         comparison_changed = True
     elif "curation" in changed_file.parts:
@@ -89,12 +89,12 @@
 run_extractor_tests = run_everything or extractors_changed or plexon2_changed
 run_preprocessing_tests = run_everything or preprocessing_changed
 run_postprocessing_tests = run_everything or postprocessing_changed
-run_qualitymetrics_tests = run_everything or qualitymetrics_changed
+run_metrics_tests = run_everything or metrics_changed
 run_curation_tests = run_everything or curation_changed
 run_sortingcomponents_tests = run_everything or sortingcomponents_changed
 
 run_comparison_test = run_everything or run_generation_tests or comparison_changed
-run_widgets_test = run_everything or run_qualitymetrics_tests or run_preprocessing_tests or widgets_changed
+run_widgets_test = run_everything or run_metrics_tests or run_preprocessing_tests or widgets_changed
 run_exporters_test = run_everything or run_widgets_test or exporters_changed
 
 run_sorters_test = run_everything or sorters_changed
@@ -109,7 +109,7 @@
     "RUN_EXTRACTORS_TESTS": run_extractor_tests,
     "RUN_PREPROCESSING_TESTS": run_preprocessing_tests,
     "RUN_POSTPROCESSING_TESTS": run_postprocessing_tests,
-    "RUN_QUALITYMETRICS_TESTS": run_qualitymetrics_tests,
+    "RUN_METRICS_TESTS": run_metrics_tests,
     "RUN_CURATION_TESTS": run_curation_tests,
     "RUN_SORTINGCOMPONENTS_TESTS": run_sortingcomponents_tests,
     "RUN_GENERATION_TESTS": run_generation_tests,

.github/scripts/import_test.py

@@ -5,7 +5,7 @@
     "import spikeinterface",
     "import spikeinterface.core",
     "import spikeinterface.extractors",
-    "import spikeinterface.qualitymetrics",
+    "import spikeinterface.metrics",
     "import spikeinterface.preprocessing",
     "import spikeinterface.comparison",
     "import spikeinterface.postprocessing",

.github/workflows/all-tests.yml

@@ -69,7 +69,7 @@ jobs:
           echo "RUN_EXTRACTORS_TESTS=${RUN_EXTRACTORS_TESTS}"
           echo "RUN_PREPROCESSING_TESTS=${RUN_PREPROCESSING_TESTS}"
           echo "RUN_POSTPROCESSING_TESTS=${RUN_POSTPROCESSING_TESTS}"
-          echo "RUN_QUALITYMETRICS_TESTS=${RUN_QUALITYMETRICS_TESTS}"
+          echo "RUN_METRICS_TESTS=${RUN_METRICS_TESTS}"
           echo "RUN_CURATION_TESTS=${RUN_CURATION_TESTS}"
           echo "RUN_SORTINGCOMPONENTS_TESTS=${RUN_SORTINGCOMPONENTS_TESTS}"
           echo "RUN_GENERATION_TESTS=${RUN_GENERATION_TESTS}"
@@ -175,13 +175,13 @@ jobs:
           pip list
           ./.github/run_tests.sh postprocessing --no-virtual-env
 
-      - name: Test quality metrics
+      - name: Test metrics
         shell: bash
-        if: env.RUN_QUALITYMETRICS_TESTS == 'true'
+        if: env.RUN_METRICS_TESTS == 'true'
         run: |
-          pip install -e .[qualitymetrics]
+          pip install -e .[metrics]
           pip list
-          ./.github/run_tests.sh qualitymetrics --no-virtual-env
+          ./.github/run_tests.sh metrics --no-virtual-env
 
       - name: Test comparison
         shell: bash

doc/api.rst

@@ -226,19 +226,31 @@ spikeinterface.postprocessing
     .. autofunction:: compute_correlograms
     .. autofunction:: compute_acgs_3d
     .. autofunction:: compute_isi_histograms
-    .. autofunction:: get_template_metric_names
     .. autofunction:: align_sorting
 
 
-spikeinterface.qualitymetrics
------------------------------
+spikeinterface.metrics
+----------------------
 
-.. automodule:: spikeinterface.qualitymetrics
+.. automodule:: spikeinterface.metrics.quality
 
     .. autofunction:: compute_quality_metrics
     .. autofunction:: get_quality_metric_list
     .. autofunction:: get_quality_pca_metric_list
-    .. autofunction:: get_default_qm_params
+    .. autofunction:: get_default_quality_metrics_params
+
+.. automodule:: spikeinterface.metrics.template
+
+    .. autofunction:: compute_template_metrics
+    .. autofunction:: get_template_metric_list
+    .. autofunction:: get_default_template_metrics_params
+    .. autofunction:: get_single_channel_template_metric_names
+    .. autofunction:: get_multi_channel_template_metric_names
+
+.. automodule:: spikeinterface.metrics.spiketrain
+
+    .. autofunction:: get_spiketrain_metric_list
+    .. autofunction:: get_default_spiketrain_metrics_params
 
 
 spikeinterface.sorters
@@ -419,7 +431,7 @@ Drift
 ~~~~~
 
 .. automodule:: spikeinterface.generation
-    :no-index:
+    :noindex:
 
     .. autofunction:: generate_drifting_recording
     .. autofunction:: generate_displacement_vector
@@ -434,7 +446,7 @@ Hybrid
 ~~~~~~
 
 .. automodule:: spikeinterface.generation
-    :no-index:
+    :noindex:
 
     .. autofunction:: generate_hybrid_recording
     .. autofunction:: estimate_templates_from_recording
@@ -451,7 +463,6 @@ Noise
 ~~~~~
 
 .. automodule:: spikeinterface.generation
-    :no-index:
 
     .. autofunction:: generate_noise
 
@@ -508,9 +519,6 @@ spikeinterface.benchmark
 .. automodule:: spikeinterface.benchmark.benchmark_peak_localization
 
     .. autoclass:: PeakLocalizationStudy
-
-.. automodule:: spikeinterface.benchmark.benchmark_peak_localization
-
     .. autoclass:: UnitLocalizationStudy
 
 .. automodule:: spikeinterface.benchmark.benchmark_motion_estimation

doc/conf.py

@@ -35,8 +35,8 @@
     '../examples/tutorials/core/analyzer_some_units',
     '../examples/tutorials/core/analyzer.zarr',
     '../examples/tutorials/curation/my_folder',
-    '../examples/tutorials/qualitymetrics/curated_sorting',
-    '../examples/tutorials/qualitymetrics/clean_analyzer.zarr',
+    '../examples/tutorials/metrics/curated_sorting',
+    '../examples/tutorials/metrics/clean_analyzer.zarr',
     '../examples/tutorials/widgets/waveforms_mearec',
 
 ]
@@ -129,7 +129,7 @@
                                        '../examples/tutorials/core',
                                        '../examples/tutorials/extractors',
                                        '../examples/tutorials/curation',
-                                       '../examples/tutorials/qualitymetrics',
+                                       '../examples/tutorials/metrics',
                                        '../examples/tutorials/comparison',
                                        '../examples/tutorials/widgets',
                                        '../examples/tutorials/forhowto',

doc/get_started/import.rst

@@ -26,10 +26,10 @@ to import the :code:`core` module followed by:
     import spikeinterface.extractors as se
     import spikeinterface.preprocessing as spre
     import spikeinterface.sorters as ss
-    import spikinterface.postprocessing as spost
-    import spikeinterface.qualitymetrics as sqm
+    import spikeinterface.postprocessing as spost
+    import spikeinterface.metrics as sm
     import spikeinterface.exporters as sexp
-    import spikeinterface.comparsion as scmp
+    import spikeinterface.comparison as scmp
     import spikeinterface.curation as scur
     import spikeinterface.sortingcomponents as sc
     import spikeinterface.widgets as sw

doc/get_started/quickstart.rst

@@ -42,7 +42,7 @@ We need to import one by one different submodules separately
     import spikeinterface.preprocessing as spre
     import spikeinterface.sorters as ss
     import spikeinterface.postprocessing as spost
-    import spikeinterface.qualitymetrics as sqm
+    import spikeinterface.metrics.quality as sqm
     import spikeinterface.comparison as sc
     import spikeinterface.exporters as sexp
     import spikeinterface.curation as scur
@@ -627,7 +627,7 @@ compute quality metrics (some quality metrics require certain extensions
 
 .. code:: ipython3
 
-    qm_params = sqm.get_default_qm_params()
+    qm_params = sqm.get_default_quality_metrics_params()
     pprint(qm_params)
 
 

doc/how_to/analyze_neuropixels.rst

@@ -699,15 +699,14 @@ make a copy of the analyzer and all computed extensions.
 Quality metrics
 ---------------
 
-We have a single function ``compute_quality_metrics(SortingAnalyzer)``
-that returns a ``pandas.Dataframe`` with the desired metrics.
+The ``analyzer.compute("quality_metrics").get_data()`` returns a ``pandas.Dataframe`` with the desired metrics.
 
 Note that this function is also an extension and so can be saved. And so
-this is equivalent to do :
+this is equivalent to do:
 ``metrics = analyzer.compute("quality_metrics").get_data()``
 
 Please visit the `metrics
-documentation <https://spikeinterface.readthedocs.io/en/latest/modules/qualitymetrics.html>`__
+documentation <https://spikeinterface.readthedocs.io/en/latest/modules/metrics/quality.html>`__
 for more information and a list of all supported metrics.
 
 Some metrics are based on PCA (like
@@ -721,20 +720,12 @@ PCA for their computation. This can be achieved with:
     metric_names=['firing_rate', 'presence_ratio', 'snr', 'isi_violation', 'amplitude_cutoff']
 
 
-    # metrics = analyzer.compute("quality_metrics").get_data()
-    # equivalent to
-    metrics = si.compute_quality_metrics(analyzer, metric_names=metric_names)
+    metrics_ext = analyzer.compute("quality_metrics", metric_names=metric_names)
+    metrics = metrics_ext.get_data()
 
     metrics
 
 
-.. parsed-literal::
-
-    /home/samuel.garcia/Documents/SpikeInterface/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")
-
-
-
 
 .. raw:: html
 

doc/images/overview.png

@@ -9,7 +9,7 @@ Modules documentation
     preprocessing
     sorters
     postprocessing
-    qualitymetrics
+    metrics
     comparison
     exporters
     widgets