Merge remote-tracking branch 'origin/develop' into job_queues

Author: juhuntenburg

brainbox/io/one.py

@@ -941,17 +941,18 @@ def _get_spike_sorting_collection(self, spike_sorter='pykilosort', revision=None
         _logger.debug(f"selecting: {collection} to load amongst candidates: {self.collections}")
         return collection
 
-    def download_spike_sorting_object(self, obj, spike_sorter='pykilosort', dataset_types=None):
+    def download_spike_sorting_object(self, obj, spike_sorter='pykilosort', dataset_types=None, collection=None):
         """
         Downloads an ALF object
         :param obj: object name, str between 'spikes', 'clusters' or 'channels'
         :param spike_sorter: (defaults to 'pykilosort')
-        :param dataset_types: list of extra dataset types
+        :param dataset_types: list of extra dataset types, for example ['spikes.samples']
+        :param collection: string specifiying the collection, for example 'alf/probe01/pykilosort'
         :return:
         """
         if len(self.collections) == 0:
             return {}, {}, {}
-        self.collection = self._get_spike_sorting_collection(spike_sorter=spike_sorter)
+        self.collection = collection or self._get_spike_sorting_collection(spike_sorter=spike_sorter)
         _logger.debug(f"loading spike sorting from {self.collection}")
         spike_attributes, cluster_attributes = self._get_attributes(dataset_types)
         attributes = {'spikes': spike_attributes, 'clusters': cluster_attributes, 'channels': None,

ibllib/dsp/voltage.py

@@ -218,8 +218,8 @@ def interpolate_bad_channels(data, channel_labels=None, h=None, p=1.3, kriging_d
             data[i, :] = 0
             continue
         data[i, :] = np.matmul(weights[imult], data[imult, :])
-    # from easyqc.gui import viewseis
-    # f = viewseis(data.T, si=1/30, h=h, title='interp2', taxis=0)
+    # from viewephys.gui import viewephys
+    # f = viewephys(data.T, fs=1/30, h=h, title='interp2')
     return data
 
 

release_notes.md

@@ -1,4 +1,6 @@
 ## Release Note 2.10
+## unreleased
+- brainbox.io.one.SpikeSortingLoader: option to load using `collection` argument
 
 ## Release Note 2.10.6 2022-03-15
 - Allow parent tasks to be 'Incomplete' to run task on local server