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cortex-lab / phy

phy: interactive visualization and manual spike sorting of large-scale ephys data
BSD 3-Clause "New" or "Revised" License
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Assertion issue, problem to load file with one electrode per group #1066

Closed Clementp69 closed 3 months ago

Clementp69 commented 3 years ago

Hi everyone,

I am using SpikeInterface to sort spikes from my 16 channel recordings (200µm space between contact).

I've configured my probe file in order to have one channel per group.

This doing 16 sortings, one per channel. My sorting is okay but when I wanted to export it on phy with these commands :

st.postprocessing.export_to_phy(recording, sorting_IRON, output_folder='sorter140121', grouping_property='group') !phy template-gui sorter140121/params.py

I have this error :

11:58:55.853 [E] init:62 An error has occurred (AssertionError): Traceback (most recent call last): File "c:\program files\anaconda3\lib\runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "c:\program files\anaconda3\lib\runpy.py", line 85, in run_code exec(code, run_globals) File "C:\Program Files\Anaconda3\Scripts\phy.exe_main.py", line 7, in sys.exit(phycli()) File "c:\program files\anaconda3\lib\site-packages\click\core.py", line 764, in call return self.main(args, kwargs) File "c:\program files\anaconda3\lib\site-packages\click\core.py", line 717, in main rv = self.invoke(ctx) File "c:\program files\anaconda3\lib\site-packages\click\core.py", line 1137, in invoke return process_result(sub_ctx.command.invoke(sub_ctx)) File "c:\program files\anaconda3\lib\site-packages\click\core.py", line 956, in invoke return ctx.invoke(self.callback, ctx.params) File "c:\program files\anaconda3\lib\site-packages\click\core.py", line 555, in invoke return callback(args, *kwargs) File "c:\program files\anaconda3\lib\site-packages\click\decorators.py", line 17, in new_func return f(get_current_context(), args, kwargs) File "c:\program files\anaconda3\lib\site-packages\phy\apps_init.py", line 159, in cli_template_gui template_gui(params_path, kwargs) File "c:\program files\anaconda3\lib\site-packages\phy\apps\template\gui.py", line 198, in template_gui controller = TemplateController(model=load_model(params_path), dir_path=dir_path, kwargs) File "c:\program files\anaconda3\lib\site-packages\phylib\io\model.py", line 1178, in load_model return TemplateModel(get_template_params(params_path)) File "c:\program files\anaconda3\lib\site-packages\phylib\io\model.py", line 297, in init self._load_data() File "c:\program files\anaconda3\lib\site-packages\phylib\io\model.py", line 356, in _load_data self.sparse_templates = self._load_templates() File "c:\program files\anaconda3\lib\site-packages\phylib\io\model.py", line 652, in _load_templates assert cols.shape == (n_templates, n_channels_loc) AssertionError

Does someone have a solution to this? Is it possible in Phy to load file with one channel per group ?

Thanks in advance, Clément G

luciano-censoni commented 3 years ago

Commenting because I have an identical issue.

zm711 commented 3 months ago

We have worked on the phy exporter in spikeinterface. If this is still an issue I would considering opening an issue in spikeinterface and opening a new issue here (linked) so we can track this.