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!