catubc
commented
4 years ago Hi. It's not clear what the issue is, phy2 was released recently and we've had issues in the past generating data that could be safely loaded. I will post this error on the phy forum and see what Cyrille says.
Hi,
I have an error in my dataset and in the samples dataset.
I'm running yass and generating the phy files, and it works fine. Then, in phy/params.py I change the dat_path and add an additional '.' (since the data file is in the parent folder).
Then I try running 'phy template-gui params.py' (or 'phy template-gui phy/params.py', I tried both), and get the following error:
15:08:28.578 [W] model:397 There are 52572/59609 spikes after the end of the recording. 15:08:28.654 [E] init:62 An error has occurred (AssertionError): Traceback (most recent call last): File "/home/aurelien/dev/miniconda3/envs/phy2/bin/phy", line 11, in
load_entry_point('phy', 'console_scripts', 'phy')()
File "/home/aurelien/dev/miniconda3/envs/phy2/lib/python3.7/site-packages/click/core.py", line 829, in call
return self.main(args, kwargs)
File "/home/aurelien/dev/miniconda3/envs/phy2/lib/python3.7/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/aurelien/dev/miniconda3/envs/phy2/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/aurelien/dev/miniconda3/envs/phy2/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/home/aurelien/dev/miniconda3/envs/phy2/lib/python3.7/site-packages/click/core.py", line 610, in invoke
return callback(args, kwargs)
File "/home/aurelien/dev/miniconda3/envs/phy2/lib/python3.7/site-packages/click/decorators.py", line 21, in new_func
return f(get_current_context(), args, kwargs)
File "/home/aurelien/dev/phy/phy/apps/init.py", line 159, in cli_template_gui
template_gui(params_path, kwargs)
File "/home/aurelien/dev/phy/phy/apps/template/gui.py", line 199, in template_gui
gui = controller.create_gui()
File "/home/aurelien/dev/phy/phy/apps/base.py", line 1638, in create_gui
self.supervisor.attach(gui)
File "/home/aurelien/dev/phy/phy/cluster/supervisor.py", line 942, in attach
gui=gui, sort=gui.state.get('ClusterView', {}).get('current_sort', None))
File "/home/aurelien/dev/phy/phy/cluster/supervisor.py", line 760, in _create_views
gui, data=self.cluster_info, columns=self.columns, sort=sort)
File "/home/aurelien/dev/phy/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 "/home/aurelien/dev/phy/phy/cluster/supervisor.py", line 916, in
return [self.get_cluster_info(cluster_id) for cluster_id in self.clustering.cluster_ids]
File "/home/aurelien/dev/phy/phy/cluster/supervisor.py", line 745, in get_cluster_info
out[key] = func(cluster_id)
File "/home/aurelien/dev/phy/phy/apps/base.py", line 1150, in get_best_channel_label
return self._get_channel_labels([self.get_best_channel(cluster_id)])[0]
File "/home/aurelien/dev/phy/phy/utils/context.py", line 154, in memcached
out = f( args, kwargs)
File "/home/aurelien/dev/phy/phy/apps/base.py", line 1144, in get_best_channel
channel_ids = self.get_best_channels(cluster_id)
File "/home/aurelien/dev/phy/phy/utils/context.py", line 154, in memcached
out = f(*args, **kwargs)
File "/home/aurelien/dev/phy/phy/apps/template/gui.py", line 149, in get_best_channels
template = self.model.get_template(template_id)
File "/home/aurelien/dev/miniconda3/envs/phy2/lib/python3.7/site-packages/phylib/io/model.py", line 855, in get_template
return self._get_template_dense(template_id, channel_ids=channel_ids)
File "/home/aurelien/dev/miniconda3/envs/phy2/lib/python3.7/site-packages/phylib/io/model.py", line 796, in _get_template_dense
template = self._unwhiten(template_w).astype(np.float32)
File "/home/aurelien/dev/miniconda3/envs/phy2/lib/python3.7/site-packages/phylib/io/model.py", line 688, in _unwhiten
assert x.shape[1] == mat.shape[0]
AssertionError
This error is the one gotten with the samples data set provided by yass. The error is similar with my dataset. I'm using the newest version of phy2 (re-installed this morning) using the git clone method and pip install -e .