Waveforms view only show mean waveforms
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Description
Hi all,
I have an issue using the waveforms view. I can only display the mean waveform view and the button "toggle mean waveforms" does not have any effect.
Here is my phy folder : https://instituteicm-my.sharepoint.com/:f:/g/personal/anthony_pinto_icm-institute_org/EjKkyzBR4O5OvbYDfxM1R9sBHFJO2Mmn3hOWhgyv42xfYg?e=jwBj4v
Here is the log file if you want to have a quick look at it before downloading all the data.
[90m16:13:31.396 [D] context:80 Create cache directory `\\l2export\iss02.charpier\analyses\anthony.pinto\git_lustre\priam\data\1_2_postprocessed\multi_v2.0\02711_2019-04-19_10-00\curation\mHaT2\phy\.phy`.[0m
[90m16:13:31.396 [D] context:80 Create cache directory `\\l2export\iss02.charpier\analyses\anthony.pinto\git_lustre\priam\data\1_2_postprocessed\multi_v2.0\02711_2019-04-19_10-00\curation\mHaT2\phy\.phy`.[0m
[90m16:13:31.806 [D] context:100 Initialize joblib cache dir at `\\l2export\iss02.charpier\analyses\anthony.pinto\git_lustre\priam\data\1_2_postprocessed\multi_v2.0\02711_2019-04-19_10-00\curation\mHaT2\phy\.phy`.[0m
[90m16:13:31.806 [D] context:100 Initialize joblib cache dir at `\\l2export\iss02.charpier\analyses\anthony.pinto\git_lustre\priam\data\1_2_postprocessed\multi_v2.0\02711_2019-04-19_10-00\curation\mHaT2\phy\.phy`.[0m
[90m16:13:31.826 [D] context:101 Reducing the size of the cache if needed.[0m
[90m16:13:31.826 [D] context:101 Reducing the size of the cache if needed.[0m
[90m16:13:32.017 [D] base:102 Add filter `high_pass`.[0m
[90m16:13:32.017 [D] base:102 Add filter `high_pass`.[0m
[90m16:13:32.101 [D] config:31 Load config file `C:\Users\anthony.pinto\.phy\phy_config.py`.[0m
[90m16:13:32.101 [D] config:31 Load config file `C:\Users\anthony.pinto\.phy\phy_config.py`.[0m
[90m16:13:32.189 [D] plugin:145 Loading 0 plugins.[0m
[90m16:13:32.189 [D] plugin:145 Loading 0 plugins.[0m
[90m16:13:32.866 [D] context:209 The file `\\l2export\iss02.charpier\analyses\anthony.pinto\git_lustre\priam\data\1_2_postprocessed\multi_v2.0\02711_2019-04-19_10-00\curation\mHaT2\phy\.phy\new_cluster_id.pkl` doesn't exist.[0m
[90m16:13:32.866 [D] context:209 The file `\\l2export\iss02.charpier\analyses\anthony.pinto\git_lustre\priam\data\1_2_postprocessed\multi_v2.0\02711_2019-04-19_10-00\curation\mHaT2\phy\.phy\new_cluster_id.pkl` doesn't exist.[0m
[90m16:13:32.888 [D] context:209 The file `\\l2export\iss02.charpier\analyses\anthony.pinto\git_lustre\priam\data\1_2_postprocessed\multi_v2.0\02711_2019-04-19_10-00\curation\mHaT2\phy\.phy\spikes_per_cluster.pkl` doesn't exist.[0m
[90m16:13:32.888 [D] context:209 The file `\\l2export\iss02.charpier\analyses\anthony.pinto\git_lustre\priam\data\1_2_postprocessed\multi_v2.0\02711_2019-04-19_10-00\curation\mHaT2\phy\.phy\spikes_per_cluster.pkl` doesn't exist.[0m
[90m16:13:32.901 [D] clustering:237 Recompute spikes_per_cluster manually: this might take a while.[0m
[90m16:13:32.901 [D] clustering:237 Recompute spikes_per_cluster manually: this might take a while.[0m
[90m16:13:32.974 [D] context:185 Save data to `\\l2export\iss02.charpier\analyses\anthony.pinto\git_lustre\priam\data\1_2_postprocessed\multi_v2.0\02711_2019-04-19_10-00\curation\mHaT2\phy\.phy\spikes_per_cluster.pkl`.[0m
[90m16:13:32.974 [D] context:185 Save data to `\\l2export\iss02.charpier\analyses\anthony.pinto\git_lustre\priam\data\1_2_postprocessed\multi_v2.0\02711_2019-04-19_10-00\curation\mHaT2\phy\.phy\spikes_per_cluster.pkl`.[0m
[90m16:13:33.257 [D] gui:463 Creating GUI.[0m
[90m16:13:33.257 [D] gui:463 Creating GUI.[0m
[90m16:13:33.333 [D] state:46 Load C:\Users\anthony.pinto\.phy\TemplateGUI\state.json for GUIState.[0m
[90m16:13:33.333 [D] state:46 Load C:\Users\anthony.pinto\.phy\TemplateGUI\state.json for GUIState.[0m
[90m16:13:34.035 [D] gui:718 Add view ClusterView to GUI.[0m
[90m16:13:34.035 [D] gui:718 Add view ClusterView to GUI.[0m
[90m16:13:34.186 [D] gui:718 Add view SimilarityView to GUI.[0m
[90m16:13:34.186 [D] gui:718 Add view SimilarityView to GUI.[0m
[90m16:13:34.293 [D] gui:718 Add view WaveformView to GUI.[0m
[90m16:13:34.293 [D] gui:718 Add view WaveformView to GUI.[0m
[90m16:13:34.372 [D] base:337 Set state for WaveformView.[0m
[90m16:13:34.372 [D] base:337 Set state for WaveformView.[0m
[90m16:13:34.465 [D] gui:718 Add view CorrelogramView to GUI.[0m
[90m16:13:34.465 [D] gui:718 Add view CorrelogramView to GUI.[0m
[90m16:13:34.536 [D] base:337 Set state for CorrelogramView.[0m
[90m16:13:34.536 [D] base:337 Set state for CorrelogramView.[0m
[90m16:13:34.623 [D] gui:718 Add view ISIView to GUI.[0m
[90m16:13:34.623 [D] gui:718 Add view ISIView to GUI.[0m
[90m16:13:34.693 [D] base:337 Set state for ISIView.[0m
[90m16:13:34.693 [D] base:337 Set state for ISIView.[0m
[90m16:13:34.784 [D] gui:718 Add view FeatureView to GUI.[0m
[90m16:13:34.784 [D] gui:718 Add view FeatureView to GUI.[0m
[90m16:13:34.856 [D] base:337 Set state for FeatureView.[0m
[90m16:13:34.856 [D] base:337 Set state for FeatureView.[0m
[90m16:13:34.954 [D] gui:718 Add view AmplitudeView to GUI.[0m
[90m16:13:34.954 [D] gui:718 Add view AmplitudeView to GUI.[0m
[90m16:13:35.074 [D] base:337 Set state for AmplitudeView.[0m
[90m16:13:35.074 [D] base:337 Set state for AmplitudeView.[0m
[90m16:13:35.111 [D] gui:718 Add view FiringRateView to GUI.[0m
[90m16:13:35.111 [D] gui:718 Add view FiringRateView to GUI.[0m
[90m16:13:35.125 [D] base:337 Set state for FiringRateView.[0m
[90m16:13:35.125 [D] base:337 Set state for FiringRateView.[0m
[90m16:13:35.444 [D] gui:519 Load the geometry state.[0m
[90m16:13:35.444 [D] gui:519 Load the geometry state.[0m
[90m16:13:38.599 [D] supervisor:817 Clusters selected: [13] (20)[0m
[90m16:13:38.599 [D] supervisor:817 Clusters selected: [13] (20)[0m
[90m16:16:12.074 [D] state:171 Update GUI state for ClusterView[0m
[90m16:16:12.074 [D] state:171 Update GUI state for ClusterView[0m
[90m16:16:12.139 [D] state:171 Update GUI state for WaveformView[0m
[90m16:16:12.139 [D] state:171 Update GUI state for WaveformView[0m
[90m16:16:12.205 [D] state:171 Update GUI state for CorrelogramView[0m
[90m16:16:12.205 [D] state:171 Update GUI state for CorrelogramView[0m
[90m16:16:12.268 [D] state:171 Update GUI state for ISIView[0m
[90m16:16:12.268 [D] state:171 Update GUI state for ISIView[0m
[90m16:16:12.387 [D] state:171 Update GUI state for FeatureView[0m
[90m16:16:12.387 [D] state:171 Update GUI state for FeatureView[0m
[90m16:16:12.428 [D] state:171 Update GUI state for AmplitudeView[0m
[90m16:16:12.428 [D] state:171 Update GUI state for AmplitudeView[0m
[90m16:16:12.448 [D] state:171 Update GUI state for FiringRateView[0m
[90m16:16:12.448 [D] state:171 Update GUI state for FiringRateView[0m
[90m16:16:12.455 [D] context:138 Save memcache for `phy.apps.base._get_mean_waveforms`.[0m
[90m16:16:12.455 [D] context:138 Save memcache for `phy.apps.base._get_mean_waveforms`.[0m
[90m16:16:12.494 [D] context:138 Save memcache for `phy.apps.base._get_template_waveforms`.[0m
[90m16:16:12.494 [D] context:138 Save memcache for `phy.apps.base._get_template_waveforms`.[0m
[90m16:16:12.527 [D] context:138 Save memcache for `phy.apps.base.get_mean_spike_template_amplitudes`.[0m
[90m16:16:12.527 [D] context:138 Save memcache for `phy.apps.base.get_mean_spike_template_amplitudes`.[0m
[90m16:16:12.562 [D] context:138 Save memcache for `phy.apps.base.get_template_counts`.[0m
[90m16:16:12.562 [D] context:138 Save memcache for `phy.apps.base.get_template_counts`.[0m
[90m16:16:12.601 [D] context:138 Save memcache for `phy.apps.base.get_template_for_cluster`.[0m
[90m16:16:12.601 [D] context:138 Save memcache for `phy.apps.base.get_template_for_cluster`.[0m
[90m16:16:12.634 [D] context:138 Save memcache for `phy.apps.template.gui.get_template_amplitude`.[0m
[90m16:16:12.634 [D] context:138 Save memcache for `phy.apps.template.gui.get_template_amplitude`.[0m
[90m16:16:12.742 [D] context:138 Save memcache for `phy.apps.base.get_cluster_amplitude`.[0m
[90m16:16:12.742 [D] context:138 Save memcache for `phy.apps.base.get_cluster_amplitude`.[0m
[90m16:16:12.837 [D] context:138 Save memcache for `phy.apps.base.get_mean_firing_rate`.[0m
[90m16:16:12.837 [D] context:138 Save memcache for `phy.apps.base.get_mean_firing_rate`.[0m
[90m16:16:12.912 [D] context:138 Save memcache for `phy.apps.base.get_best_channel`.[0m
[90m16:16:12.912 [D] context:138 Save memcache for `phy.apps.base.get_best_channel`.[0m
[90m16:16:12.967 [D] context:138 Save memcache for `phy.apps.template.gui.get_best_channels`.[0m
[90m16:16:12.967 [D] context:138 Save memcache for `phy.apps.template.gui.get_best_channels`.[0m
[90m16:16:13.030 [D] context:138 Save memcache for `phy.apps.base.get_channel_shank`.[0m
[90m16:16:13.030 [D] context:138 Save memcache for `phy.apps.base.get_channel_shank`.[0m
[90m16:16:13.084 [D] context:138 Save memcache for `phy.apps.base.get_probe_depth`.[0m
[90m16:16:13.084 [D] context:138 Save memcache for `phy.apps.base.get_probe_depth`.[0m
[90m16:16:13.139 [D] context:138 Save memcache for `phy.apps.base.peak_channel_similarity`.[0m
[90m16:16:13.139 [D] context:138 Save memcache for `phy.apps.base.peak_channel_similarity`.[0m
[90m16:16:13.229 [D] gui:600 Save the geometry state.[0m
[90m16:16:13.229 [D] gui:600 Save the geometry state.[0m
[90m16:16:13.240 [D] state:218 Save global GUI state to `C:\Users\anthony.pinto\.phy\TemplateGUI\state.json`.[0m
[90m16:16:13.240 [D] state:218 Save global GUI state to `C:\Users\anthony.pinto\.phy\TemplateGUI\state.json`.[0m
[90m16:16:13.256 [D] state:232 Save local GUI state to `\\l2export\iss02.charpier\analyses\anthony.pinto\git_lustre\priam\data\1_2_postprocessed\multi_v2.0\02711_2019-04-19_10-00\curation\mHaT2\phy\.phy\state.json`.[0m
[90m16:16:13.256 [D] state:232 Save local GUI state to `\\l2export\iss02.charpier\analyses\anthony.pinto\git_lustre\priam\data\1_2_postprocessed\multi_v2.0\02711_2019-04-19_10-00\curation\mHaT2\phy\.phy\state.json`.[0m
I am a bit confused about the exact reason of this issue. I exported the data using the function from spikeinterface like that:
sexp.export_to_phy(
waveform_extractor=waveforms,
output_folder=os.path.join(output_folder, 'phy'),
compute_pc_features=True,
compute_amplitudes=True,
copy_binary=True,
peak_sign='neg',
remove_if_exists=True,
verbose=True,
)
To add a bit more context, my folder is located at a very long path and it was the origin of a problem with the waveforms a few weeks ago as mentionned here https://github.com/cortex-lab/phy/issues/1219#issue-1880538192 but I found a workaround by doing that : https://www.howtogeek.com/266621/how-to-make-windows-10-accept-file-paths-over-260-characters/ so I avoided the windows limit of 260 characters. I though it solved my issue because with the previous issue the waveforms were not displaying at all and now I can see them.
I would like to find a workaround because I would like to avoid to move the location of the phy folder if possible.
Cheers,
Anthony
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the issue with the exported phy folder and the provided spikeinterface export_to_phy call. Inspect the WaveformView behavior around the “toggle mean waveforms” control and compare it with the logged waveform-loading steps. Done means the control visibly switches between mean and non-mean waveforms for a reproducible dataset.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100