Can not read the trodes .rec file using spikeinterface.extractors.read_spikegadgets() #1810
Description
I'm using an HH128 and the MCU for tethered recording in Trodes. The signal looks good, and I can play back the .rec file within Trodes without issues.
However, when I try to load the .rec file into SpikeInterface using spikeinterface.extractors.read_spikegadgets(), I get an error stating that the file does not contain the channel mapping header.
Trodes version: 2.6.0
spikeinterface: 0.103
errors:
ZeroDivisionError Traceback (most recent call last)
Cell In[13], line 4
2 from probeinterface import generate_tetrode, ProbeGroup
3 # 1. Load the raw data (it will have NO geometry initially)
----> 4 recording = se.read_spikegadgets(r'C:\Users\gl_pc\Downloads\20260115_110218\20260115_110218\20260115_195453.rec/20260115_195453.rec')
5 recording
File c:\Users\gl_pc.conda\envs\si_trodes\Lib\site-packages\spikeinterface\extractors\neoextractors\spikegadgets.py:50, in SpikeGadgetsRecordingExtractor.init(self, file_path, stream_id, stream_name, all_annotations, use_names_as_ids)
41 def init(
42 self,
43 file_path,
(...) 47 use_names_as_ids: bool = False,
48 ):
49 neo_kwargs = self.map_to_neo_kwargs(file_path)
---> 50 NeoBaseRecordingExtractor.init(
51 self,
52 stream_id=stream_id,
53 stream_name=stream_name,
54 all_annotations=all_annotations,
55 use_names_as_ids=use_names_as_ids,
56 **neo_kwargs,
57 )
58 self._kwargs.update(dict(file_path=str(Path(file_path).absolute()), stream_id=stream_id))
60 probegroup = None # TODO remove once probeinterface is updated to 0.2.22 in the pyproject.toml
File c:\Users\gl_pc.conda\envs\si_trodes\Lib\site-packages\spikeinterface\extractors\neoextractors\neobaseextractor.py:188, in NeoBaseRecordingExtractor.init(self, stream_id, stream_name, block_index, all_annotations, use_names_as_ids, **neo_kwargs)
158 def init(
159 self,
160 stream_id: Optional[str] = None,
(...) 165 **neo_kwargs: Dict[str, Any],
166 ) -> None:
167 """
168 Initialize a NeoBaseRecordingExtractor instance.
169
(...) 185
186 """
--> 188 _NeoBaseExtractor.init(self, block_index, **neo_kwargs)
190 kwargs = dict(all_annotations=all_annotations)
191 if block_index is not None:
File c:\Users\gl_pc.conda\envs\si_trodes\Lib\site-packages\spikeinterface\extractors\neoextractors\neobaseextractor.py:27, in _NeoBaseExtractor.init(self, block_index, **neo_kwargs)
23 def init(self, block_index, **neo_kwargs):
24
25 # Avoids double initiation of the neo reader if it was already done in the init of the child class
26 if not hasattr(self, "neo_reader"):
---> 27 self.neo_reader = self.get_neo_io_reader(self.NeoRawIOClass, **neo_kwargs)
29 if self.neo_reader.block_count() > 1 and block_index is None:
30 raise Exception(
31 "This dataset is multi-block. Spikeinterface can load one block at a time. "
32 "Use 'block_index' to select the block to be loaded."
33 )
File c:\Users\gl_pc.conda\envs\si_trodes\Lib\site-packages\spikeinterface\extractors\neoextractors\neobaseextractor.py:66, in _NeoBaseExtractor.get_neo_io_reader(cls, raw_class, **neo_kwargs)
64 neoIOclass = getattr(rawio_module, raw_class)
65 neo_reader = neoIOclass(**neo_kwargs)
---> 66 neo_reader.parse_header()
68 return neo_reader
File c:\Users\gl_pc.conda\envs\si_trodes\Lib\site-packages\neo\rawio\baserawio.py:211, in BaseRawIO.parse_header(self)
197 """
198 Parses the header of the file(s) to allow for faster computations
199 for all other functions
200
201 """
202 # this must create
203 # self.header['nb_block']
204 # self.header['nb_segment']
(...) 208 # self.header['spike_channels']
209 # self.header['event_channels']
--> 211 self._parse_header()
212 self._check_stream_signal_channel_characteristics()
213 self.is_header_parsed = True
File c:\Users\gl_pc.conda\envs\si_trodes\Lib\site-packages\neo\rawio\spikegadgetsrawio.py:224, in SpikeGadgetsRawIO._parse_header(self)
220 self._mask_channels_bytes[stream_id] = []
222 # we can only produce these channels for a subset of spikegadgets setup. If this criteria isn't
223 # true then we should just use the raw_channel_ids and let the end user sort everything out
--> 224 if num_ephy_channels % num_chan_per_chip == 0:
225 all_hw_chans = [int(schan.attrib["hwChan"]) for trode in sconf for schan in trode]
226 missing_hw_chans = set(range(num_ephy_channels)) - set(all_hw_chans)
ZeroDivisionError: integer modulo by zero