Phy failure to launch

[verocg]

Hello,

I am having issues getting Phy operational. Kilosort is working fine, and generates all the correct files (.npy). However, when I try to launch Phy, I get a list of error messages. I am new to coding, and have no experience with Python, so even opening these files I haven't been able to figure out the issue.

The output from trying to launch "phy template-gui params.py" is below:

←[33m18:30:00.081 [W] model:545 Unreferenced clusters found in templates (generally not a problem)←[0m ←[33m18:30:00.084 [W] model:567 Unreferenced clusters found in spike_clusters (generally not a problem)←[0m ←[33m18:30:00.090 [W] model:54 104/225 values are nan in C:\Users\TDT\Documents\DATA\Dingo\02022021\RFmap_1\similar_templates.npy, replacing by zero.←[0m ←[0m18:30:00.187 [I] state:180 Copied c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\apps\template\static\state.json to C:\Users\TDT.phy\TemplateGUI\state.json.←[0m ←[31m18:30:00.318 [E] init:62 An error has occurred (AssertionError): Traceback (most recent call last): File "c:\users\tdt\anaconda3\envs\phy2\lib\runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "c:\users\tdt\anaconda3\envs\phy2\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File "C:\Users\TDT\anaconda3\envs\phy2\Scripts\phy.exe__main.py", line 7, in sys.exit(phycli()) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\click\core.py", line 1025, in call__ return self.main(args, kwargs) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\click\core.py", line 955, in main rv = self.invoke(ctx) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\click\core.py", line 1517, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\click\core.py", line 1279, in invoke return ctx.invoke(self.callback, ctx.params) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\click\core.py", line 710, in invoke return callback(args, kwargs) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\click\decorators.py", line 18, in new_func return f(get_current_context(), args, kwargs) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\apps__init__.py", line 159, in cli_template_gui template_gui(params_path, kwargs) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\apps\template\gui.py", line 199, in template_gui gui = controller.create_gui() File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\apps\base.py", line 1638, in create_gui self.supervisor.attach(gui) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\cluster\supervisor.py", line 942, in attach gui=gui, sort=gui.state.get('ClusterView', {}).get('current_sort', None)) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\cluster\supervisor.py", line 760, in _create_views gui, data=self.cluster_info, columns=self.columns, sort=sort) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\cluster\supervisor.py", line 916, in cluster_info return [self.get_cluster_info(cluster_id) for cluster_id in self.clustering.cluster_ids] File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\cluster\supervisor.py", line 916, in return [self.get_cluster_info(cluster_id) for cluster_id in self.clustering.cluster_ids] File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\cluster\supervisor.py", line 745, in get_cluster_info out[key] = func(cluster_id) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\apps\base.py", line 1150, in get_best_channel_label return self._get_channel_labels([self.get_best_channel(cluster_id)])[0] File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\utils\context.py", line 154, in memcached out = f(args, kwargs) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\apps\base.py", line 1144, in get_best_channel channel_ids = self.get_best_channels(cluster_id) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\utils\context.py", line 154, in memcached out = f(*args, **kwargs) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phy\apps\template\gui.py", line 149, in get_best_channels template = self.model.get_template(template_id) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phylib\io\model.py", line 855, in get_template return self._get_template_dense(template_id, channel_ids=channel_ids) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phylib\io\model.py", line 798, in _get_template_dense channelids, amplitude, best_channel = self._find_best_channels(template) File "c:\users\tdt\anaconda3\envs\phy2\lib\site-packages\phylib\io\model.py", line 787, in _find_best_channels assert best_channel in channel_ids AssertionError ←[0m

[neurvanna]

I'm having the same issue, could you please share how you've solved this? Thanks!

[verocg]

I think my issue was due to kilosort not saving all the output files correctly due to access issues to my output folder. When I changed the output directory to a different folder with full write access this issue with phy went away. Hope this helps if you haven't already resolved your issue!