Added Biocam NEO extractor

spikeinterface/extractors/extractorlist.py

@@ -18,7 +18,7 @@
     MaxwellRecordingExtractor, read_maxwell, MaxwellEventExtractor, read_maxwell_event,
     NixRecordingExtractor, read_nix,
     SpikeGadgetsRecordingExtractor, read_spikegadgets,
-
+    BiocamRecordingExtractor, read_biocam,
 )
 
 # NWB sorting/recording/event

spikeinterface/extractors/neoextractors/__init__.py

@@ -14,3 +14,4 @@
 from .maxwell import MaxwellRecordingExtractor, read_maxwell, MaxwellEventExtractor, read_maxwell_event
 from .nix import NixRecordingExtractor, read_nix
 from .spikegadgets import SpikeGadgetsRecordingExtractor, read_spikegadgets
+from .biocam import BiocamRecordingExtractor, read_biocam

spikeinterface/extractors/neoextractors/biocam.py

@@ -0,0 +1,47 @@
+import probeinterface as pi
+from .neobaseextractor import NeoBaseRecordingExtractor, NeoBaseSortingExtractor
+
+
+class BiocamRecordingExtractor(NeoBaseRecordingExtractor):
+    """
+    Class for reading data from a Biocam file from 3Brain.
+
+    Based on neo.rawio.BiocamRawIO
+
+    Parameters
+    ----------
+    file_path: str
+
+    stream_id: str or None
+
+    mea_pitch: float or None
+
+    electrode_width: float or None
+
+    """
+    mode = 'file'
+    NeoRawIOClass = 'BiocamRawIO'
+
+    def __init__(self, file_path, stream_id=None, mea_pitch=None, electrode_width=None):
+        neo_kwargs = {'filename': str(file_path)}
+        NeoBaseRecordingExtractor.__init__(self, stream_id=stream_id, **neo_kwargs)
+
+        # load probe from probeinterface
+        probe_kwargs = {}
+        if mea_pitch is not None:
+            probe_kwargs["mea_pitch"] = mea_pitch
+        if electrode_width is not None:
+            probe_kwargs["electrode_width"] = electrode_width
+        probe = pi.read_3brain(file_path, **probe_kwargs)
+        self.set_probe(probe, in_place=True)
+        self.set_property("row", self.get_property("contact_vector")["row"])
+        self.set_property("col", self.get_property("contact_vector")["col"])
+        self._kwargs = dict(file_path=str(file_path), stream_id=stream_id, mea_pitch=mea_pitch)
+
+
+def read_biocam(*args, **kwargs):
+    recording = BiocamRecordingExtractor(*args, **kwargs)
+    return recording
+
+
+read_biocam.__doc__ = BiocamRecordingExtractor.__doc__

spikeinterface/extractors/neoextractors/neobaseextractor.py

@@ -49,7 +49,6 @@ def __init__(self, stream_id=None, **neo_kwargs):
 
         # check channel groups
         chan_ids = signal_channels['id']
-        raw_dtypes = signal_channels['dtype']
 
         sampling_frequency = self.neo_reader.get_signal_sampling_rate(stream_index=self.stream_index)
         dtype = signal_channels['dtype'][0]
@@ -76,6 +75,7 @@ def __init__(self, stream_id=None, **neo_kwargs):
 
         self.set_property('gain_to_uV', final_gains)
         self.set_property('offset_to_uV', final_offsets)
+        self.set_property('channel_name', signal_channels["name"])
 
         nseg = self.neo_reader.segment_count(block_index=0)
         for segment_index in range(nseg):
@@ -160,7 +160,7 @@ def _auto_guess_sampling_frequency(self):
         that signal it do not make sens to have spikes at 50kHz sample
         when the sig is 10kHz.
         neo handle this but not spieinterface
-        
+
         In neo spikes can have diffrents sampling rate than signals so conversion from
         signals frames to times is format dependent
         """

spikeinterface/extractors/tests/test_neoextractors.py

@@ -167,6 +167,15 @@ class SpikeGadgetsRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ]
 
 
+@pytest.mark.skip(reason='Biocam not merged into neo yet')
+class BiocamRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
+    ExtractorClass = BiocamRecordingExtractor
+    downloads = ['biocam/biocam_hw3.0_fw1.6.brw']
+    entities = [
+        'biocam/biocam_hw3.0_fw1.6.brw'
+    ]
+
+
 if __name__ == '__main__':
     #~ test = MearecRecordingTest()
     # ~ test = MearecSortingTest()