Cannot open TemplateFeatureView

[florian6973]

Hi!

I am opening an issue about the Template Feature View, because I try to export a WaveformExtractor from spikeinterface (0.100.8) to phy, but then I cannot open the Template Feature View (it does not appear). I saw there are a few issues opened about this issue but they only focus on KS3 and not through the spikeinterface export. I would be very grateful if you have any ideas of why it is happening and potentially how to solve it. Thanks :)

Log:

(phy2) C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy>phy template-gui params.py --debug
14:31:24.320 [D] init:68 Start capturing exceptions.
14:31:24.320 [W] model:1408 File None does not exist.
14:31:24.320 [D] model:619 Loading spike clusters.
14:31:24.335 [D] model:569 No channel shank file found.
14:31:24.336 [D] model:692 Loading templates.
14:31:24.337 [D] model:724 Templates are dense.
14:31:24.337 [W] model:667 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
14:31:24.337 [D] model:730 Loading the whitening matrix.
14:31:24.337 [D] model:434 Whitening matrix file not found.
14:31:24.342 [D] model:737 Loading the inverse of the whitening matrix.
14:31:24.342 [D] model:440 Whitening matrix inverse file not found, computing it.
14:31:24.342 [D] model:744 Inversing the whitening matrix (46, 46).
14:31:24.404 [W] traces:462 File C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy\None does not exist.
14:31:24.404 [W] traces:462 File C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy\None does not exist.
14:31:24.404 [D] model:766 Loading features.
14:31:24.404 [D] model:788 Features are dense.
14:31:24.404 [D] model:803 Loading template features.
14:31:24.902 [D] context:80 Create cache directory C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy\.phy.
14:31:25.002 [D] context:100 Initialize joblib cache dir at C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy\.phy.
14:31:25.018 [D] context:101 Reducing the size of the cache if needed.
14:31:25.021 [D] base:102 Add filter high_pass.
14:31:25.024 [D] config:31 Load config file C:\Users\guoyu\.phy\phy_config.py.
14:31:25.024 [D] plugin:145 Loading 0 plugins.
14:31:25.037 [D] context:209 The file C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy\.phy\new_cluster_id.pkl doesn't exist.
14:31:25.043 [D] context:209 The file C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy\.phy\spikes_per_cluster.pkl doesn't exist.
14:31:25.043 [D] clustering:237 Recompute spikes_per_cluster manually: this might take a while.
14:31:25.043 [D] context:185 Save data to C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy\.phy\spikes_per_cluster.pkl.
14:31:25.052 [D] gui:463 Creating GUI.
14:31:25.119 [D] state:46 Load C:\Users\guoyu.phy\TemplateGUI\state.json for GUIState.
14:31:27.195 [D] gui:718 Add view ClusterView to GUI.
14:31:27.246 [D] gui:718 Add view SimilarityView to GUI.
14:31:27.317 [D] gui:718 Add view WaveformView to GUI.
14:31:27.336 [D] base:337 Set state for WaveformView.
14:31:27.355 [D] gui:718 Add view CorrelogramView to GUI.
14:31:27.360 [D] base:337 Set state for CorrelogramView.
14:31:27.396 [D] gui:718 Add view ISIView to GUI.
14:31:27.398 [D] base:337 Set state for ISIView.
14:31:27.426 [D] gui:718 Add view FeatureView to GUI.
14:31:27.429 [D] base:337 Set state for FeatureView.
14:31:27.475 [D] gui:718 Add view AmplitudeView to GUI.
14:31:27.477 [D] base:337 Set state for AmplitudeView.
14:31:27.509 [D] gui:718 Add view FiringRateView to GUI.
14:31:27.512 [D] base:337 Set state for FiringRateView.
14:31:27.514 [W] gui:671 Could not create view TraceView.
14:31:27.539 [D] gui:718 Add view ProbeView to GUI.
14:31:27.542 [D] base:337 Set state for ProbeView.
14:31:27.543 [W] gui:671 Could not create view TemplateFeatureView.
14:31:27.573 [D] gui:718 Add view ClusterScatterView to GUI.
14:31:27.577 [D] base:337 Set state for ClusterScatterView.
14:31:27.577 [D] base:494 Set color scheme to firing_rate.
14:31:27.579 [D] base:1626 Adding default color schemes to ClusterScatterView.
14:31:28.231 [D] gui:519 Load the geometry state.
QMimeDatabase: Error loading internal MIME data
An error has been encountered at line 1 of : Premature end of document.:
14:31:35.778 [W] gui:671 Could not create view TemplateFeatureView.

Folder:

[zm711]

Hey Florent,

How did you install Phy? You have the QMimeDatabase error which is often due to some install problems.

[florian6973]

Hi Zach!

Thanks for your reply! I strictly followed the current readme, creating a conda environment with python 3.11, then pip install from git and finally opening phy...

[zm711]

I think there might be an issue with conda-forge for one of the packages. I haven't diagnosed which one yet.

could you make do the following (after cloning the repo. You'll either need to edit the requirements.txt to numpy<2.0 or go from my recent PR #1289.

conda create -n phy2_test python=3.11
cd phy
pip install -e .

And see if that works. I'm still trying to diagnose why installing purely with the conda instructions doesn't seem to be working since NumPy 2.0 came out.

[florian6973]

Thanks for your reply!
After following this new installation workflow, it still does not work unfortunately (without the MIME error though now):

16:17:34.280 [D] init:68 Start capturing exceptions.
16:17:34.280 [W] model:1415 File None does not exist.
16:17:34.296 [D] model:619 Loading spike clusters.
16:17:34.296 [D] model:569 No channel shank file found.
16:17:34.296 [D] model:692 Loading templates.
16:17:34.296 [D] model:724 Templates are dense.
16:17:34.296 [W] model:667 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
16:17:34.296 [D] model:730 Loading the whitening matrix.
16:17:34.296 [D] model:434 Whitening matrix file not found.
16:17:34.296 [D] model:737 Loading the inverse of the whitening matrix.
16:17:34.296 [W] traces:462 File C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy\None does not exist.
16:17:34.296 [W] traces:462 File C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy\None does not exist.
16:17:34.296 [D] model:766 Loading features.
16:17:34.312 [D] model:788 Features are dense.
16:17:34.312 [D] model:803 Loading template features.
16:17:34.878 [D] context:100 Initialize joblib cache dir at C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy\.phy.
16:17:34.878 [D] context:101 Reducing the size of the cache if needed.
16:17:34.894 [D] base:102 Add filter high_pass.
16:17:34.894 [D] config:31 Load config file C:\Users\guoyu\.phy\phy_config.py.
16:17:34.894 [D] plugin:146 Loading 0 plugins.
16:17:34.894 [D] context:126 Load memcache for phy.apps.base._get_mean_waveforms.
16:17:34.894 [D] context:126 Load memcache for phy.apps.base._get_mean_waveforms.
16:17:34.894 [D] context:126 Load memcache for phy.apps.base._get_template_waveforms.
16:17:34.894 [D] context:126 Load memcache for phy.apps.base.get_mean_spike_template_amplitudes.
16:17:34.894 [D] context:126 Load memcache for phy.apps.base.get_template_counts.
16:17:34.894 [D] context:126 Load memcache for phy.apps.base.get_template_for_cluster.
16:17:34.894 [D] context:126 Load memcache for phy.apps.template.gui.get_template_amplitude.
16:17:34.894 [D] context:126 Load memcache for phy.apps.base.get_cluster_amplitude.
16:17:34.894 [D] context:126 Load memcache for phy.apps.base.get_mean_firing_rate.
16:17:34.894 [D] context:126 Load memcache for phy.apps.base.get_best_channel.
16:17:34.894 [D] context:126 Load memcache for phy.apps.template.gui.get_best_channels.
16:17:34.894 [D] context:126 Load memcache for phy.apps.base.get_channel_shank.
16:17:34.909 [D] context:126 Load memcache for phy.apps.base.get_probe_depth.
16:17:34.911 [D] context:126 Load memcache for phy.apps.base.peak_channel_similarity.
16:17:34.912 [D] context:209 The file C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy\.phy\new_cluster_id.pkl doesn't exist.
16:17:34.925 [D] context:185 Save data to C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy\.phy\spikes_per_cluster.pkl.
16:17:34.928 [D] gui:463 Creating GUI.
16:17:34.988 [D] state:46 Load C:\Users\guoyu.phy\TemplateGUI\state.json for GUIState.
16:17:34.988 [D] state:46 Load C:\Users\guoyu\OneDrive\Documents\Florent\SpikeSorting\ms5-phy\phy.phy\state.json for GUIState.
16:17:36.326 [D] gui:718 Add view ClusterView to GUI.
16:17:36.360 [D] gui:718 Add view SimilarityView to GUI.
16:17:36.482 [D] gui:718 Add view WaveformView to GUI.
16:17:36.496 [D] base:337 Set state for WaveformView.
16:17:36.514 [D] gui:718 Add view CorrelogramView to GUI.
16:17:36.517 [D] base:337 Set state for CorrelogramView.
16:17:36.539 [D] gui:718 Add view ISIView to GUI.
16:17:36.541 [D] base:337 Set state for ISIView.
16:17:36.602 [D] gui:718 Add view FeatureView to GUI.
16:17:36.606 [D] base:337 Set state for FeatureView.
16:17:36.648 [D] gui:718 Add view AmplitudeView to GUI.
16:17:36.651 [D] base:337 Set state for AmplitudeView.
16:17:36.672 [D] gui:718 Add view FiringRateView to GUI.
16:17:36.674 [D] base:337 Set state for FiringRateView.
16:17:36.691 [D] gui:718 Add view ProbeView to GUI.
16:17:36.694 [D] base:337 Set state for ProbeView.
16:17:36.720 [D] gui:718 Add view ClusterScatterView to GUI.
16:17:36.722 [D] base:337 Set state for ClusterScatterView.
16:17:36.722 [D] base:494 Set color scheme to random.
16:17:36.723 [D] base:1626 Adding default color schemes to ClusterScatterView.
16:17:37.454 [D] gui:519 Load the geometry state.
16:17:39.273 [D] supervisor:817 Clusters selected: [6] (5)
16:17:43.619 [W] gui:671 Could not create view TemplateFeatureView.

[zm711]

Why is your file None?

16:17:34.280 [W] model:1415 File None does not exist.

[florian6973]

I exported to phy with these options to minimize the size: si.export_to_phy(waveform_extractor, output_folder='phy', verbose=True, use_relative_path=True, copy_binary=False) Since the PC features were properly showing (see below), I did think it would be the same for the template features.

So I exported again with copy_binary=True (now phy can access the recording), but the TemplateFeatureView still does not show up:

(phy2_test) C:\Users\guoyu\Downloads\phy2>phy template-gui params.py --debug
08:02:30.897 [D] init:68 Start capturing exceptions.
08:02:30.944 [D] model:619 Loading spike clusters.
08:02:30.991 [D] model:569 No channel shank file found.
08:02:30.991 [D] model:692 Loading templates.
08:02:30.991 [D] model:724 Templates are dense.
08:02:31.007 [W] model:667 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
08:02:31.007 [D] model:730 Loading the whitening matrix.
08:02:31.007 [D] model:434 Whitening matrix file not found.
08:02:31.007 [D] model:737 Loading the inverse of the whitening matrix.
08:02:31.007 [D] model:440 Whitening matrix inverse file not found, computing it.
08:02:31.007 [D] model:744 Inversing the whitening matrix (1, 1).
08:02:31.024 [D] model:766 Loading features.
08:02:31.043 [D] model:781 Features are sparse.
08:02:31.043 [D] model:803 Loading template features.
08:02:31.043 [D] model:504 Load cluster_amplitude_cutoff.tsv.
08:02:31.053 [D] model:504 Load cluster_amplitude_cv_median.tsv.
08:02:31.060 [D] model:504 Load cluster_amplitude_cv_range.tsv.
08:02:31.071 [D] model:504 Load cluster_amplitude_median.tsv.
08:02:31.071 [D] model:504 Load cluster_channel_group.tsv.
08:02:31.086 [D] model:504 Load cluster_firing_range.tsv.
08:02:31.101 [D] model:504 Load cluster_group.tsv.
08:02:31.109 [D] model:504 Load cluster_isi_violations_count.tsv.
08:02:31.117 [D] model:504 Load cluster_isi_violations_ratio.tsv.
08:02:31.133 [D] model:504 Load cluster_presence_ratio.tsv.
08:02:31.143 [D] model:504 Load cluster_rp_contamination.tsv.
08:02:31.157 [D] model:504 Load cluster_rp_violations.tsv.
08:02:31.165 [D] model:504 Load cluster_sd_ratio.tsv.
08:02:31.182 [D] model:504 Load cluster_si_unit_ids.tsv.
08:02:31.192 [D] model:504 Load cluster_sliding_rp_violation.tsv.
08:02:31.197 [D] model:504 Load cluster_snr.tsv.
08:02:31.213 [D] model:504 Load cluster_sync_spike_2.tsv.
08:02:31.213 [D] model:504 Load cluster_sync_spike_4.tsv.
08:02:31.229 [D] model:504 Load cluster_sync_spike_8.tsv.
08:02:31.711 [D] context:80 Create cache directory C:\Users\guoyu\Downloads\phy2\.phy.
08:02:31.792 [D] context:100 Initialize joblib cache dir at C:\Users\guoyu\Downloads\phy2\.phy.
08:02:31.792 [D] context:101 Reducing the size of the cache if needed.
08:02:31.792 [D] base:102 Add filter high_pass.
08:02:31.792 [D] config:31 Load config file C:\Users\guoyu\.phy\phy_config.py.
08:02:31.810 [D] plugin:146 Loading 0 plugins.
08:02:31.822 [D] context:209 The file C:\Users\guoyu\Downloads\phy2\.phy\new_cluster_id.pkl doesn't exist.
08:02:31.822 [D] context:209 The file C:\Users\guoyu\Downloads\phy2\.phy\spikes_per_cluster.pkl doesn't exist.
08:02:31.822 [D] clustering:237 Recompute spikes_per_cluster manually: this might take a while.
08:02:31.822 [D] context:185 Save data to C:\Users\guoyu\Downloads\phy2\.phy\spikes_per_cluster.pkl.
08:02:31.822 [D] gui:463 Creating GUI.
08:02:31.869 [D] state:46 Load C:\Users\guoyu.phy\TemplateGUI\state.json for GUIState.
08:02:33.456 [D] gui:718 Add view ClusterView to GUI.
08:02:33.490 [D] gui:718 Add view SimilarityView to GUI.
08:02:33.702 [D] gui:718 Add view WaveformView to GUI.
08:02:33.718 [D] base:337 Set state for WaveformView.
08:02:33.749 [D] gui:718 Add view CorrelogramView to GUI.
08:02:33.753 [D] base:337 Set state for CorrelogramView.
08:02:33.803 [D] gui:718 Add view ISIView to GUI.
08:02:33.809 [D] base:337 Set state for ISIView.
08:02:33.882 [D] gui:718 Add view FeatureView to GUI.
08:02:33.888 [D] base:337 Set state for FeatureView.
08:02:33.950 [D] gui:718 Add view AmplitudeView to GUI.
08:02:33.955 [D] base:337 Set state for AmplitudeView.
08:02:33.999 [D] gui:718 Add view FiringRateView to GUI.
08:02:34.002 [D] base:337 Set state for FiringRateView.
08:02:34.020 [D] gui:718 Add view ProbeView to GUI.
08:02:34.022 [D] base:337 Set state for ProbeView.
08:02:34.061 [D] gui:718 Add view ClusterScatterView to GUI.
08:02:34.066 [D] base:337 Set state for ClusterScatterView.
08:02:34.067 [D] base:494 Set color scheme to random.
08:02:34.068 [D] base:1626 Adding default color schemes to ClusterScatterView.
08:02:34.113 [D] gui:718 Add view TemplateView to GUI.
08:02:34.116 [D] base:337 Set state for TemplateView.
08:02:34.117 [D] base:494 Set color scheme to random.
08:02:34.118 [D] base:1626 Adding default color schemes to TemplateView.
08:02:34.155 [D] gui:718 Add view TemplateView to GUI.
08:02:34.160 [D] base:337 Set state for TemplateView (1).
08:02:34.161 [D] base:494 Set color scheme to random.
08:02:34.163 [D] base:1626 Adding default color schemes to TemplateView (1).
08:02:34.912 [D] gui:519 Load the geometry state.
08:02:39.395 [D] base:276 Close view TemplateView (1).
08:02:39.395 [D] state:171 Update GUI state for TemplateView (1)
08:02:40.870 [D] supervisor:817 Clusters selected: [0] (4)
08:02:41.856 [D] supervisor:839 Similar clusters selected: [7] (4)
08:02:45.576 [W] gui:671 Could not create view TemplateFeatureView.

[zm711]

Hey Florent, could you list all files in the folder. Either as a full picture or just as a list. This could be that the export_to_phy function is missing something. We've added some additional features to it with the 0.101.0 release coming soon, but I know you're trying to stay on 0.100.x for now. Which sorter were you using?

[florian6973]

For this one I was using MountainSort5, here are all the files in the folder:

Folder PATH listing for volume Windows-SSD
Volume serial number is 340B-6FD7
C:.
│ amplitudes.npy
│ channel_groups.npy
│ channel_map.npy
│ channel_map_si.npy
│ channel_positions.npy
│ cluster_amplitude_cutoff.tsv
│ cluster_amplitude_cv_median.tsv
│ cluster_amplitude_cv_range.tsv
│ cluster_amplitude_median.tsv
│ cluster_channel_group.tsv
│ cluster_firing_range.tsv
│ cluster_group.tsv
│ cluster_isi_violations_count.tsv
│ cluster_isi_violations_ratio.tsv
│ cluster_presence_ratio.tsv
│ cluster_rp_contamination.tsv
│ cluster_rp_violations.tsv
│ cluster_sd_ratio.tsv
│ cluster_si_unit_ids.tsv
│ cluster_sliding_rp_violation.tsv
│ cluster_snr.tsv
│ cluster_sync_spike_2.tsv
│ cluster_sync_spike_4.tsv
│ cluster_sync_spike_8.tsv
│ params.py
│ pc_features.npy
│ pc_feature_ind.npy
│ phy.log
│ recording.dat
│ similar_templates.npy
│ spike_clusters.npy
│ spike_templates.npy
│ spike_times.npy
│ templates.npy
│ whitening_mat_inv.npy
│
└───.phy
│ spikes_per_cluster.pkl
│ state.json
│
├───memcache
│ phy.apps.base.get_best_channel.pkl
│ phy.apps.base.get_channel_shank.pkl
│ phy.apps.base.get_cluster_amplitude.pkl
│ phy.apps.base.get_mean_firing_rate.pkl
│ phy.apps.base.get_mean_spike_template_amplitudes.pkl
│ phy.apps.base.get_probe_depth.pkl
│ phy.apps.base.get_template_counts.pkl
│ phy.apps.base.get_template_for_cluster.pkl
│ phy.apps.base.peak_channel_similarity.pkl
│ phy.apps.base._get_mean_waveforms.pkl
│ phy.apps.base._get_template_waveforms.pkl
│ phy.apps.template.gui.get_best_channels.pkl
│ phy.apps.template.gui.get_template_amplitude.pkl
│
└───phy
└───apps
└───base
├───BaseController
│ ├───_get_correlograms
│ │ │ func_code.py
│ │ │
│ │ ├───9440f18609f2fb2f54002db34d535c28
│ │ │ metadata.json
│ │ │ output.pkl
│ │ │
│ │ └───e9380640d7a1fce9450e896212c3c529
│ │ metadata.json
│ │ output.pkl
│ │
│ └───_get_correlograms_rate
│ │ func_code.py
│ │
│ ├───21c011882470d608d668678de26c8a58
│ │ metadata.json
│ │ output.pkl
│ │
│ └───78ac1302226b9c5bf26c5633cab6fb29
│ metadata.json
│ output.pkl
│
├───FeatureMixin
│ ├───get_spike_feature_amplitudes
│ └───_get_features
│ │ func_code.py
│ │
│ ├───24e3400218971593519fa9a3675b4ec8
│ │ metadata.json
│ │ output.pkl
│ │
│ ├───7a48f028123fd49893a06fc6ef2129f3
│ │ metadata.json
│ │ output.pkl
│ │
│ └───e8f9fb7c0b150b4269a23168aca1e0be
│ metadata.json
│ output.pkl
│
├───TemplateMixin
│ ├───get_amplitudes
│ ├───get_spike_template_amplitudes
│ │ │ func_code.py
│ │ │
│ │ ├───0fe0be0053102709521f1c4d56c35e9b
│ │ │ metadata.json
│ │ │ output.pkl
│ │ │
│ │ ├───60d8a3e5695717826d97c51421f4c9aa
│ │ │ metadata.json
│ │ │ output.pkl
│ │ │
│ │ ├───a887b0a772bdda52b283dffbc81cf48e
│ │ │ metadata.json
│ │ │ output.pkl
│ │ │
│ │ └───adbdce6361b9abc70d4b39502596cdbd
│ │ metadata.json
│ │ output.pkl
│ │
│ └───get_spike_template_features
└───WaveformMixin
└───_get_waveforms_with_n_spikes

If you think it should be solved with 0.101.0, I can test it as well, and if so it will strongly motivate a faster transition to this new version...

[florian6973]

Just tested 0.101.0rc0, and I get the same error unfortunately:

rec_si, _ = si.read_mearec(path)
sort_ms = si.run_sorter("mountainsort5", rec_si, remove_existing_folder=True)
sa = si.create_sorting_analyzer(sort_ms, rec_si)
sa.compute(['random_spikes'])
sa.compute(['waveforms'])
sa.compute(['templates'])
si.export_to_phy(
    sorting_analyzer=sa,
    output_folder='phy_test_2',
    use_relative_path=True,    
)

10:02:22.629 [D] init:68 Start capturing exceptions.
10:02:22.636 [D] model:619 Loading spike clusters.
10:02:22.641 [D] model:569 No channel shank file found.
10:02:22.643 [D] model:692 Loading templates.
10:02:22.647 [D] model:720 Templates are sparse.
10:02:22.648 [W] model:667 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
10:02:22.649 [D] model:730 Loading the whitening matrix.
10:02:22.649 [D] model:434 Whitening matrix file not found.
10:02:22.649 [D] model:737 Loading the inverse of the whitening matrix.
10:02:22.652 [D] model:766 Loading features.
10:02:22.653 [D] model:781 Features are sparse.
10:02:22.653 [D] model:803 Loading template features.
10:02:22.654 [D] model:504 Load cluster_channel_group.tsv.
10:02:22.655 [D] model:504 Load cluster_group.tsv.
10:02:22.656 [D] model:504 Load cluster_si_unit_ids.tsv.
10:02:23.128 [D] context:100 Initialize joblib cache dir at C:\Users\guoyu\Downloads\phy_test_2\.phy.
10:02:23.128 [D] context:101 Reducing the size of the cache if needed.
10:02:23.141 [D] base:102 Add filter high_pass.
10:02:23.144 [D] config:31 Load config file C:\Users\guoyu\.phy\phy_config.py.
10:02:23.146 [D] plugin:146 Loading 0 plugins.
10:02:23.147 [D] context:126 Load memcache for phy.apps.base._get_mean_waveforms.
10:02:23.148 [D] context:126 Load memcache for phy.apps.base._get_mean_waveforms.
10:02:23.150 [D] context:126 Load memcache for phy.apps.base._get_template_waveforms.
10:02:23.152 [D] context:126 Load memcache for phy.apps.base.get_mean_spike_template_amplitudes.
10:02:23.153 [D] context:126 Load memcache for phy.apps.base.get_template_counts.
10:02:23.154 [D] context:126 Load memcache for phy.apps.base.get_template_for_cluster.
10:02:23.155 [D] context:126 Load memcache for phy.apps.template.gui.get_template_amplitude.
10:02:23.156 [D] context:126 Load memcache for phy.apps.base.get_cluster_amplitude.
10:02:23.159 [D] context:126 Load memcache for phy.apps.base.get_mean_firing_rate.
10:02:23.161 [D] context:126 Load memcache for phy.apps.base.get_best_channel.
10:02:23.161 [D] context:126 Load memcache for phy.apps.template.gui.get_best_channels.
10:02:23.163 [D] context:126 Load memcache for phy.apps.base.get_channel_shank.
10:02:23.164 [D] context:126 Load memcache for phy.apps.base.get_probe_depth.
10:02:23.166 [D] context:126 Load memcache for phy.apps.base.peak_channel_similarity.
10:02:23.169 [D] context:209 The file C:\Users\guoyu\Downloads\phy_test_2\.phy\new_cluster_id.pkl doesn't exist.
10:02:23.186 [D] context:185 Save data to C:\Users\guoyu\Downloads\phy_test_2\.phy\spikes_per_cluster.pkl.
10:02:23.196 [D] gui:463 Creating GUI.
10:02:23.245 [D] state:46 Load C:\Users\guoyu.phy\TemplateGUI\state.json for GUIState.
10:02:23.248 [D] state:46 Load C:\Users\guoyu\Downloads\phy_test_2.phy\state.json for GUIState.
10:02:24.529 [D] gui:718 Add view ClusterView to GUI.
10:02:24.561 [D] gui:718 Add view SimilarityView to GUI.
10:02:24.682 [D] gui:718 Add view WaveformView to GUI.
10:02:24.696 [D] base:337 Set state for WaveformView.
10:02:24.726 [D] gui:718 Add view CorrelogramView to GUI.
10:02:24.732 [D] base:337 Set state for CorrelogramView.
10:02:24.788 [D] gui:718 Add view ISIView to GUI.
10:02:24.798 [D] base:337 Set state for ISIView.
10:02:24.828 [D] gui:718 Add view FeatureView to GUI.
10:02:24.831 [D] base:337 Set state for FeatureView.
10:02:24.879 [D] gui:718 Add view AmplitudeView to GUI.
10:02:24.884 [D] base:337 Set state for AmplitudeView.
10:02:24.931 [D] gui:718 Add view FiringRateView to GUI.
10:02:24.938 [D] base:337 Set state for FiringRateView.
10:02:24.971 [D] gui:718 Add view ProbeView to GUI.
10:02:24.979 [D] base:337 Set state for ProbeView.
10:02:25.018 [D] gui:718 Add view ClusterScatterView to GUI.
10:02:25.023 [D] base:337 Set state for ClusterScatterView.
10:02:25.023 [D] base:494 Set color scheme to random.
10:02:25.030 [D] base:1626 Adding default color schemes to ClusterScatterView.
10:02:25.083 [D] gui:718 Add view TemplateView to GUI.
10:02:25.087 [D] base:337 Set state for TemplateView.
10:02:25.087 [D] base:494 Set color scheme to random.
10:02:25.088 [D] base:1626 Adding default color schemes to TemplateView.
10:02:26.188 [D] gui:519 Load the geometry state.
10:02:28.457 [D] supervisor:817 Clusters selected: [6] (8)
10:02:30.592 [W] gui:671 Could not create view TemplateFeatureView.
10:03:23.504 [D] supervisor:839 Similar clusters selected: [3] (7)

I also heard that Sam plans to release spikeinterface-gui with curation features, do you think it is as mature as phy regarding functionalities please? Thanks

[zm711]

It looks like you are missing template_feature_ind and templates_features. Could you check for those? This could be a problem with our export to phy function in si. If it is a problem over there then we need to check with Sam and Alessio to see if there is a reason we can't generate those files (ie we can't make the whitening matrix because not every sorter does whitening) or we just haven't yet.

[florian6973]

Thanks for your reply! I checked but I could not find them unfortunately. It seems these files are not created in https://github.com/SpikeInterface/spikeinterface/blob/1197aad12b7170432eec8b887e24b9bc29921eab/src/spikeinterface/exporters/to_phy.py ... Should I open a spikeinterface issue then?

[zm711]

Yeah I would open the issue there. That way you can ask if it was intentional not to make those files :)