SpikeInterface
Exception: There are no channel locations
Getting the error message "Exception: There are no channel locations." Running sorting on kilosort2, through the kilosort GUI/MATLAB, sorting seems to work fine so evidently channel locations do exist on their end. Below is the error message;
ss.Kilosort2Sorter.set_kilosort2_path(r"C:\Users\lab-admin\Desktop\AnthonySpikeInterface\Kilosort-2.0")
sorting = ss.run_sorter(sorter_name='kilosort2',recording=recording,remove_existing_folder=True,output_folder='D:\\results_test2',verbose=True)
printf('Found', len(sorting.get_unit_ids()),'units')
---------------------------------------------------------------------------
Exception Traceback (most recent call last)
Cell In[21], line 2
1 # run spike sorting on entire recording
----> 2 sorting_KS25 = si.run_sorter('kilosort2', recording,remove_existing_folder=True,output_folder='D:\\results_test2', verbose=True)
File ~\AppData\Roaming\Python\Python311\site-packages\spikeinterface\sorters\runsorter.py:147, in run_sorter(sorter_name, recording, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, docker_image, singularity_image, delete_container_files, with_output, **sorter_params)
140 container_image = singularity_image
141 return run_sorter_container(
142 container_image=container_image,
143 mode=mode,
144 **common_kwargs,
145 )
--> 147 return run_sorter_local(**common_kwargs)
File ~\AppData\Roaming\Python\Python311\site-packages\spikeinterface\sorters\runsorter.py:172, in run_sorter_local(sorter_name, recording, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, with_output, **sorter_params)
170 output_folder = SorterClass.initialize_folder(recording, output_folder, verbose, remove_existing_folder)
171 SorterClass.set_params_to_folder(recording, output_folder, sorter_params, verbose)
--> 172 SorterClass.setup_recording(recording, output_folder, verbose=verbose)
173 SorterClass.run_from_folder(output_folder, raise_error, verbose)
174 if with_output:
File ~\AppData\Roaming\Python\Python311\site-packages\spikeinterface\sorters\basesorter.py:226, in BaseSorter.setup_recording(cls, recording, output_folder, verbose)
224 all_params = json.load(f)
225 sorter_params = all_params["sorter_params"]
--> 226 cls._setup_recording(recording, sorter_output_folder, sorter_params, verbose)
File ~\AppData\Roaming\Python\Python311\site-packages\spikeinterface\sorters\external\kilosortbase.py:123, in KilosortBase._setup_recording(cls, recording, sorter_output_folder, params, verbose)
121 @classmethod
122 def _setup_recording(cls, recording, sorter_output_folder, params, verbose):
--> 123 cls._generate_channel_map_file(recording, sorter_output_folder)
125 skip_kilosort_preprocessing = params.get("skip_kilosort_preprocessing", False)
127 if (
128 recording.binary_compatible_with(dtype="int16", time_axis=0, file_paths_lenght=1)
129 and not skip_kilosort_preprocessing
130 ):
131 # no copy
File ~\AppData\Roaming\Python\Python311\site-packages\spikeinterface\sorters\external\kilosortbase.py:45, in KilosortBase._generate_channel_map_file(recording, sorter_output_folder)
43 # prepare electrode positions for this group (only one group, the split is done in basesorter)
44 groups = [1] * recording.get_num_channels()
---> 45 positions = np.array(recording.get_channel_locations())
46 if positions.shape[1] != 2:
47 raise RuntimeError("3D 'location' are not supported. Set 2D locations instead")
File ~\AppData\Roaming\Python\Python311\site-packages\spikeinterface\core\baserecordingsnippets.py:345, in BaseRecordingSnippets.get_channel_locations(self, channel_ids, axes)
343 locations = self.get_property("location")
344 if locations is None:
--> 345 raise Exception("There are no channel locations")
346 locations = np.asarray(locations)[channel_indices]
347 return select_axes(locations, axes)
Exception: There are no channel locations
SpikeInterface version: 0.99.1
My recording data is as follows:
BinaryRecordingExtractor: 384 channels - 20.0kHz - 1 segments - 108,036,352 samples
5,401.82s (1.50 hours) - int16 dtype - 77.27 GiB
file_paths: ['D:\\2023recording\\2023-12-31_1333_WT-female-adult\\2023-12-31_15-21-08\\Record Node 101\\experiment1\\recording1\\continuous\\Neuropix-PXI-100.ProbeA-AP\\continuous.dat']
Thank you in advance.
Hi,
How do you load the recording? Can you print(recording.get_channel_locations())
I think you loaded the dat file directly as a binary file. That doesn't load channel locations. You should use the read_openephys function:
recording = se.read_openephys("path-to-2023-12-31_15-21-08")
This worked perfectly with experiment_names! and stream_name Thank you for the swift response.
However, I am unsure of how to perform spike sorting now. I understand that with most multi segmented recordings, you can concatenate them all together into "one recording." However, in my case the segments are all separate recordings. My following recording looks like this:
recording = se.read_openephys(recording2,experiment_names="experiment1",stream_name="Record_Node_101#Neuropix-PXI-100.ProbeA-AP")
13,728.15s (3.81 hours) - int16 dtype - 294.57 GiB
Segments:
Samples: 108,036,352 | 105,753,348 | 53,943,552 | 71,952,720 | 72,158,448
Durations: 3,601.21s (1.00 hours) | 3,525.11s (58.75 minutes) | 1,798.12s (29.97 minutes) | 2,398.42s (39.97 minutes) | 2,405.28s (40.09 minutes)
Memory: 77.27 GiB | 75.64 GiB | 38.58 GiB | 51.46 GiB | 51.61 GiB
Is there a way to simply set recording to one of these segments? Calling "segment_index" does not work for kilosort2:
# run spike sorting on entire recording
sorting_KS25 = si.run_sorter('kilosort2', recording,remove_existing_folder=True,output_folder='D:\\results_test2', verbose=True,segment_index=1)
ValueError: This sorter kilosort2 does not handle multi-segment recordings, use si.concatenate_recordings(...)
Maybe I am not understandings the arguments for read_openephys. The following is my folder archecture:
**...\Record_Node_101\experiment1**
recording1
recording2
recording3
recording4
recording5
**...\Record_Node_101\experiment1\recording1**
continuous
events
**...\Record_Node_101\experiment1\recording1\continuous**
Neuropix-PXI-100.ProbeA-AP
Neuropix-PXI-100.ProbeA-LFP
**...\Record_Node_101\experiment1\recording1\continuous**
continuous.dat
Nevermind, there is a function called "select_segment_recording" in the core module that I missed. Thanks for the help!