Merge branch 'main' of github.com:SpikeInterface/spikeinterface into fix-pca-multiprocessing

Author: alejoe91

src/spikeinterface/core/sortinganalyzer.py

@@ -232,6 +232,8 @@ def __repr__(self) -> str:
             txt += " - sparse"
         if self.has_recording():
             txt += " - has recording"
+        if self.has_temporary_recording():
+            txt += " - has temporary recording"
         ext_txt = f"Loaded {len(self.extensions)} extensions: " + ", ".join(self.extensions.keys())
         txt += "\n" + ext_txt
         return txt
@@ -350,7 +352,7 @@ def create_memory(cls, sorting, recording, sparsity, return_scaled, rec_attribut
     def create_binary_folder(cls, folder, sorting, recording, sparsity, return_scaled, rec_attributes):
         # used by create and save_as
 
-        assert recording is not None, "To create a SortingAnalyzer you need recording not None"
+        assert recording is not None, "To create a SortingAnalyzer you need to specify the recording"
 
         folder = Path(folder)
         if folder.is_dir():
@@ -1221,7 +1223,7 @@ def compute(self, input, save=True, extension_params=None, verbose=False, **kwar
                     extensions[ext_name] = ext_params
             self.compute_several_extensions(extensions=extensions, save=save, verbose=verbose, **job_kwargs)
         else:
-            raise ValueError("SortingAnalyzer.compute() need str, dict or list")
+            raise ValueError("SortingAnalyzer.compute() needs a str, dict or list")
 
     def compute_one_extension(self, extension_name, save=True, verbose=False, **kwargs) -> "AnalyzerExtension":
         """
@@ -1355,7 +1357,9 @@ def compute_several_extensions(self, extensions, save=True, verbose=False, **job
 
             for extension_name, extension_params in extensions_with_pipeline.items():
                 extension_class = get_extension_class(extension_name)
-                assert self.has_recording(), f"Extension {extension_name} need the recording"
+                assert (
+                    self.has_recording() or self.has_temporary_recording()
+                ), f"Extension {extension_name} requires the recording"
 
                 for variable_name in extension_class.nodepipeline_variables:
                     result_routage.append((extension_name, variable_name))
@@ -1603,17 +1607,17 @@ def _sort_extensions_by_dependency(extensions):
 def _get_children_dependencies(extension_name):
     """
     Extension classes have a `depend_on` attribute to declare on which class they
-    depend. For instance "templates" depend on "waveforms". "waveforms depends on "random_spikes".
+    depend on. For instance "templates" depends on "waveforms". "waveforms" depends on "random_spikes".
 
-    This function is making the reverse way : get all children that depend of a
+    This function is going the opposite way: it finds all children that depend on a
     particular extension.
 
-    This is recursive so this includes : children and so grand children and great grand children
+    The implementation is recursive so that the output includes children, grand children, great grand children, etc.
 
-    This function is usefull for deleting on recompute.
-    For instance recompute the "waveforms" need to delete "template"
-    This make sens if "ms_before" is change in "waveforms" because the template also depends
-    on this parameters.
+    This function is useful for deleting existing extensions on recompute.
+    For instance, recomputing the "waveforms" needs to delete the "templates", since the latter depends on the former.
+    For this particular example, if we change the "ms_before" parameter of the "waveforms", also the "templates" will
+    require recomputation as this parameter is inherited.
     """
     names = []
     children = _extension_children[extension_name]

src/spikeinterface/postprocessing/principal_component.py

@@ -363,12 +363,12 @@ def run_for_all_spikes(self, file_path=None, verbose=False, **job_kwargs):
 
         job_kwargs = fix_job_kwargs(job_kwargs)
         p = self.params
-        we = self.sorting_analyzer
-        sorting = we.sorting
+        sorting_analyzer = self.sorting_analyzer
+        sorting = sorting_analyzer.sorting
         assert (
-            we.has_recording()
-        ), "To compute PCA projections for all spikes, the waveform extractor needs the recording"
-        recording = we.recording
+            sorting_analyzer.has_recording() or sorting_analyzer.has_temporary_recording()
+        ), "To compute PCA projections for all spikes, the sorting analyzer needs the recording"
+        recording = sorting_analyzer.recording
 
         # assert sorting.get_num_segments() == 1
         assert p["mode"] in ("by_channel_local", "by_channel_global")
@@ -378,8 +378,9 @@ def run_for_all_spikes(self, file_path=None, verbose=False, **job_kwargs):
 
         sparsity = self.sorting_analyzer.sparsity
         if sparsity is None:
-            sparse_channels_indices = {unit_id: np.arange(we.get_num_channels()) for unit_id in we.unit_ids}
-            max_channels_per_template = we.get_num_channels()
+            num_channels = recording.get_num_channels()
+            sparse_channels_indices = {unit_id: np.arange(num_channels) for unit_id in sorting_analyzer.unit_ids}
+            max_channels_per_template = num_channels
         else:
             sparse_channels_indices = sparsity.unit_id_to_channel_indices
             max_channels_per_template = max([chan_inds.size for chan_inds in sparse_channels_indices.values()])
@@ -462,9 +463,7 @@ def _fit_by_channel_local(self, n_jobs, progress_bar, max_threads_per_process, m
         return pca_models
 
     def _fit_by_channel_global(self, progress_bar):
-        # we = self.sorting_analyzer
         p = self.params
-        # unit_ids = we.unit_ids
         unit_ids = self.sorting_analyzer.unit_ids
 
         # there is one unique PCA accross channels