No state set to SimilarityView and WaveformView when starting gui
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Description
I am using the sample data (https://github.com/kwikteam/phy-data) and am trying to see it in the phy template gui. Starting it with phy template-gui params.py --debug I see that no state is set to SimilarityView and WaveformView. In the gui, I see blank windows for both. How can I solve this? I get the same error using my own data output from Kilosort2.
Output:
10:03:39.569 [D] init:68 Start capturing exceptions.
10:03:39.634 [W] model:591 Unreferenced clusters found in templates (generally not a problem)
10:03:39.637 [D] model:607 Loading spike clusters.
10:03:39.641 [W] model:613 Unreferenced clusters found in spike_clusters (generally not a problem)
10:03:39.669 [D] model:680 Loading templates.
10:03:39.695 [D] model:708 Templates are sparse.
10:03:39.697 [W] model:655 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
10:03:39.698 [D] model:718 Loading the whitening matrix.
10:03:39.715 [D] model:725 Loading the inverse of the whitening matrix.
10:03:39.752 [D] model:754 Loading features.
10:03:39.761 [D] model:769 Features are sparse.
10:03:39.766 [D] model:791 Loading template features.
10:03:39.791 [D] model:801 Template features are sparse.
10:03:39.800 [D] model:492 Load cluster_group.tsv.
10:03:40.244 [D] context:101 Reducing the size of the cache if needed.
10:03:40.266 [D] base:102 Add filter high_pass.
10:03:40.272 [D] plugin:145 Loading 0 plugins.
10:03:40.317 [D] gui:463 Creating GUI.
10:03:40.734 [D] gui:718 Add view ClusterView to GUI.
10:03:40.761 [D] gui:718 Add view SimilarityView to GUI.
10:03:40.803 [D] gui:718 Add view WaveformView to GUI.
10:03:40.810 [D] base:337 Set state for WaveformView.
10:03:40.827 [D] gui:718 Add view CorrelogramView to GUI.
10:03:40.833 [D] base:337 Set state for CorrelogramView.
10:03:40.867 [D] gui:718 Add view ISIView to GUI.
10:03:40.874 [D] base:337 Set state for ISIView.
10:03:40.909 [D] gui:718 Add view FeatureView to GUI.
10:03:40.915 [D] base:337 Set state for FeatureView.
10:03:40.951 [D] gui:718 Add view AmplitudeView to GUI.
10:03:40.956 [D] base:337 Set state for AmplitudeView.
10:03:40.987 [D] gui:718 Add view FiringRateView to GUI.
10:03:40.992 [D] base:337 Set state for FiringRateView.
10:03:41.064 [D] gui:718 Add view TraceView to GUI.
10:03:41.072 [D] base:337 Set state for TraceView.
10:03:41.074 [D] base:494 Set color scheme to depth.
10:03:41.092 [D] base:1623 Adding default color schemes to TraceView.
10:03:41.130 [D] gui:718 Add view ProbeView to GUI.
10:03:41.138 [D] base:337 Set state for ProbeView.
10:03:41.164 [D] gui:718 Add view TemplateFeatureView to GUI.
10:03:41.172 [D] base:337 Set state for TemplateFeatureView.
10:03:41.205 [D] gui:718 Add view ClusterScatterView to GUI.
10:03:41.212 [D] base:337 Set state for ClusterScatterView.
10:03:41.214 [D] base:494 Set color scheme to firing_rate.
10:03:41.217 [D] base:1623 Adding default color schemes to ClusterScatterView.
10:03:41.435 [D] gui:519 Load the geometry state.
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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 from the phy template-gui params.py --debug entry point and compare the logged initialization of SimilarityView and WaveformView with the views that receive state. Reproduce the blank windows using the linked sample data and determine what state setup is missing; done means both views initialize with visible data.
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
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 38/100