FeatureView doesn't work.

[Youmin7025]

Hello, I have a problem when using the TemplateGUI: all works well (no error, all subviews works well), but the FeatureView displays nothing.

I downloaded the template data in the tutorial (https://codeload.github.com/kwikteam/phy-data/zip/master) and run "phy template-gui params.py" in the data path. The same problem occurred for my own data sorted by Kilosort4.

I wish to see something in the FeatureView when I:
1. selected two clusters in the ClusterView
2. selected one in the ClusterView and another in the SimilarityView

FYI, the spikeinterface-gui (https://github.com/SpikeInterface/spikeinterface-gui) can show the FeatureView (ndscatter in its window) for the same data (the data were stored in .zarr before the "export_to_phy").

Wish to get your help.

Thanks.

[fabioladuarte]

I am running into the same problem. I get a long output of errors/warning messages that look like the ones in issue #1358 . Additionally, when I try to split any clusters, the gui freezes, and I get the following message:
12:45:15.530 [W] actions:213 Error when executing action Split.

I tried re-installing the packages with the latest environment,yml file, but still got the same problem so not sure it's a compatibility issue.

Any help is greatly appreciated!

[Youmin7025]

I am running into the same problem. I get a long output of errors/warning messages that look like the ones in issue #1358 . Additionally, when I try to split any clusters, the gui freezes, and I get the following message: 12:45:15.530 [W] actions:213 Error when executing action Split.

I tried re-installing the packages with the latest environment,yml file, but still got the same problem so not sure it's a compatibility issue.

Any help is greatly appreciated!

In my case, the 'split' actions works well in the AmplitudeView.
FYI, the environment was built totally following the instructions in the readme file of phy.

[JesusJBallesteros]

Hello all,
I've been having issues with new installations (since last week) from the environment file provided in the git. The issues are related to FeatureView, AmplitudeView, etc., either not being populated or not being created at all.
I could not find any obvious explanation on why this happens, and because I had an older phy2 environment installed somewhere else, I just cloned and installed it on the new machines. This gave me a flawless working phy2.
I'm sharing the cloned environment here, in case it helps:
phy2_local.yml
Hopefully someone can compare packages and check the root of the problem?
Cheers.

[Youmin7025]

Many thanks to you!
The environment you provided fix my problems in the Windows platform.

However, the main mechanics in my lab use Ubuntu. This environment file cannot be loaded directly in Ubuntu platform. I'm going to find another way to fix it.

Again, thank you very much!

[Darilbii]

I'm experiencing the same issue on Ubuntu

[Darilbii]

In my case there is a repeating error whenever I select a unit. Here is the read out

Traceback (most recent call last):
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/gui/qt.py", line 547, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/cluster/views/base.py", line 175, in _worker
    self.on_select(cluster_ids=cluster_ids, **kwargs)
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/cluster/views/base.py", line 143, in on_select
    self.plot(**kwargs)
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/cluster/views/feature.py", line 362, in plot
    background = self.features(channel_ids=self.channel_ids)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/joblib/memory.py", line 577, in __call__
    return self._cached_call(args, kwargs, shelving=False)[0]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/joblib/memory.py", line 532, in _cached_call
    return self._call(call_id, args, kwargs, shelving)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/joblib/memory.py", line 771, in _call
    output = self.func(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/apps/base.py", line 386, in _get_features
    return self._get_spike_features(spike_ids, channel_ids)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/apps/base.py", line 367, in _get_spike_features
    data = self.model.get_features(spike_ids, channel_ids)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phylib/io/model.py", line 1037, in get_features
    features = from_sparse(features, cols, channel_ids)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phylib/io/model.py", line 94, in from_sparse
    assert np.all(np.isin(c, np.r_[channel_ids.astype(np.int32), -1]))
                                   ^^^^^^^^^^^^^^^^^^
AttributeError: 'list' object has no attribute 'astype'

[Youmin7025]

In my case there is a repeating error whenever I select a unit. Here is the read out

Traceback (most recent call last):
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/gui/qt.py", line 547, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/cluster/views/base.py", line 175, in _worker
    self.on_select(cluster_ids=cluster_ids, **kwargs)
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/cluster/views/base.py", line 143, in on_select
    self.plot(**kwargs)
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/cluster/views/feature.py", line 362, in plot
    background = self.features(channel_ids=self.channel_ids)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/joblib/memory.py", line 577, in __call__
    return self._cached_call(args, kwargs, shelving=False)[0]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/joblib/memory.py", line 532, in _cached_call
    return self._call(call_id, args, kwargs, shelving)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/joblib/memory.py", line 771, in _call
    output = self.func(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/apps/base.py", line 386, in _get_features
    return self._get_spike_features(spike_ids, channel_ids)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/apps/base.py", line 367, in _get_spike_features
    data = self.model.get_features(spike_ids, channel_ids)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phylib/io/model.py", line 1037, in get_features
    features = from_sparse(features, cols, channel_ids)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darilbii/anaconda3/envs/phy2/lib/python3.11/site-packages/phylib/io/model.py", line 94, in from_sparse
    assert np.all(np.isin(c, np.r_[channel_ids.astype(np.int32), -1]))
                                   ^^^^^^^^^^^^^^^^^^
AttributeError: 'list' object has no attribute 'astype'

I have the same error with you when launch the gui.

[Daruum]

Hey, I don’t know if this will help, but in my case, I modified 'anaconda3\envs\phy2\Lib\site-packages\phylib\io\model.py'.

Original function:

def from_sparse(data, cols, channel_ids):

"""Convert a sparse structure into a dense one.

Parameters
----------

data : array-like
    A (n_spikes, n_channels_loc, ...) array with the data.
cols : array-like
    A (n_spikes, n_channels_loc) array with the channel indices of
    every row in data.
channel_ids : array-like
    List of requested channel ids (columns).

"""
# The axis in the data that contains the channels.
if len(channel_ids) != len(np.unique(channel_ids)):
    raise NotImplementedError("Multiple identical requested channels " "in from_sparse().")
channel_axis = 1
...

Fixe:

 def from_sparse(data, cols, channel_ids):

"""Convert a sparse structure into a dense one.

Parameters
----------

data : array-like
    A (n_spikes, n_channels_loc, ...) array with the data.
cols : array-like
    A (n_spikes, n_channels_loc) array with the channel indices of
    every row in data.
channel_ids : array-like
    List of requested channel ids (columns).

"""
# --- FIXE ---
channel_ids = np.array(channel_ids)
# ------------------------------

# The axis in the data that contains the channels.
if len(channel_ids) != len(np.unique(channel_ids)):
    raise NotImplementedError("Multiple identical requested channels " "in from_sparse().")
channel_axis = 1
...

It seems that this fixed the problem of the Feature View not being displayed.