Problem reading Maxwell two datasets

[sofiapuvogelvittini]

Hello, I am getting the following error while trying to read a Maxwell two dataset:

"KeyError Traceback (most recent call last) Cell In[9], line 1 ----> 1 se.read_maxwell(h5_data,rec_name=rec_si, stream_id=well_si)

File ~/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/extractors/neoextractors/maxwell.py:62, in MaxwellRecordingExtractor.init(self, file_path, stream_id, stream_name, block_index, all_annotations, rec_name, install_maxwell_plugin, use_names_as_ids) 59 self.install_maxwell_plugin() 61 neo_kwargs = self.map_to_neo_kwargs(file_path, rec_name) ---> 62 NeoBaseRecordingExtractor.init( 63 self, 64 stream_id=stream_id, 65 stream_name=stream_name, 66 block_index=block_index, 67 all_annotations=all_annotations, 68 use_names_as_ids=use_names_as_ids, 69 **neo_kwargs, 70 ) 72 self.extra_requirements.append("h5py") 74 # well_name is stream_id

File ~/anaconda3/envs/si_env/lib/python3.11/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 ~/anaconda3/envs/si_env/lib/python3.11/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 ~/anaconda3/envs/si_env/lib/python3.11/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 ~/anaconda3/envs/si_env/lib/python3.11/site-packages/neo/rawio/baserawio.py:185, in BaseRawIO.parse_header(self) 172 def parse_header(self): 173 """ 174 This must parse the file header to get all stuff for fast use later on. 175 (...) 183 184 """ --> 185 self._parse_header() 186 self._check_stream_signal_channel_characteristics() 187 self.is_header_parsed = True

File ~/anaconda3/envs/si_env/lib/python3.11/site-packages/neo/rawio/maxwellrawio.py:145, in MaxwellRawIO._parse_header(self) 143 gain_uV = 3.3 / (1024 gain) 1e6 144 mapping = settings["mapping"] --> 145 sigs = h5file["wells"][stream_id][self.rec_name]["groups"]["routed"]["raw"] 147 channel_ids = np.array(mapping["channel"]) 148 electrode_ids = np.array(mapping["electrode"])

File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()

File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()

File ~/anaconda3/envs/si_env/lib/python3.11/site-packages/h5py/_hl/group.py:357, in Group.getitem(self, name) 355 raise ValueError("Invalid HDF5 object reference") 356 elif isinstance(name, (bytes, str)): --> 357 oid = h5o.open(self.id, self._e(name), lapl=self._lapl) 358 else: 359 raise TypeError("Accessing a group is done with bytes or str, " 360 "not {}".format(type(name)))

File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()

File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()

File h5py/h5o.pyx:189, in h5py.h5o.open()

KeyError: "Unable to synchronously open object (object 'routed' doesn't exist)""

Not very sure what it means, and is interesting that for othe recordings, same setup, I dont get any error.

here you can find the respective dataset and the jupyter notebook I am using "SC2_all_wells_latest.ipynb": https://drive.google.com/drive/folders/1CoqJTnrn4_qIQEU_rZEc3MuNhaxgHln3?usp=sharing

I've also added another folder, 'data_that_works', which contains a recording of the same plate at a later time point. This one can be read

Could you please help me figure out what may be going wrong here? Thanks a lot!

[alejoe91]

@sofiapuvogelvittini the problem with the dataset is that for some well*** fields there are no signals associated to them.

I made a PR with a fix here #1579 . Can you test it out?

[sofiapuvogelvittini]

I am still encountering the same error after switching to the branch :/

[alejoe91]

Weird! I was able to open both dataset with the fix. How did you install from the PR branch? Make sure you restart the notebook!

[sofiapuvogelvittini]

I am sorry, I think I was not installing it properly. I have now managed to install it correctly, and it’s working with both datasets! Thank you for your help!