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cortex-lab / phy

phy: interactive visualization and manual spike sorting of large-scale ephys data
BSD 3-Clause "New" or "Revised" License
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QMimeDatabase: Error loading internal MIME data An error has been encountered at line 1 of <internal MIME data>: Premature end of document.: #1212

Closed iamrameses closed 1 year ago

iamrameses commented 1 year ago

I set up a new conda environment following the instructions on the README page (except I specified Python version 3.9.16 and NumPy version 1.22.3). However, upon running phy on Kilosort2.5 data I received the error in the title of this issue. Thank you in advance!

(phy2) G:\Shared drives\Lab Name\Current Members\Username\Neuropixel recordings\T237ma\T237aa_g1\T237aa_g1_imec0>phy template-gui params.py --debug
11:41:24.269 [D] __init__:68          Start capturing exceptions.
11:41:24.375 [W] model:603            Unreferenced clusters found in templates (generally not a problem)
11:41:24.422 [D] model:619            Loading spike clusters.
11:41:24.454 [W] model:625            Unreferenced clusters found in spike_clusters (generally not a problem)
11:41:24.501 [D] model:569            No channel shank file found.
11:41:24.501 [D] model:692            Loading templates.
11:41:24.621 [D] model:724            Templates are dense.
11:41:24.621 [W] model:667            Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
11:41:24.621 [D] model:730            Loading the whitening matrix.
11:41:24.621 [D] model:737            Loading the inverse of the whitening matrix.
11:41:24.637 [W] model:55             2415/163216 values are nan in G:\Shared drives\Lab Name\Current Members\Username\Neuropixel recordings\T237ma\T237aa_g1\T237aa_g1_imec0\similar_templates.npy, replacing by zero.
11:41:24.643 [D] model:766            Loading features.
11:41:24.653 [D] model:781            Features are sparse.
11:41:24.653 [D] model:803            Loading template features.
11:41:24.653 [D] model:813            Template features are sparse.
11:41:24.653 [D] model:504            Load `cluster_KSLabel.tsv`.
11:41:24.669 [D] model:504            Load `cluster_ContamPct.tsv`.
11:41:24.669 [D] model:504            Load `cluster_Amplitude.tsv`.
11:41:24.669 [D] model:504            Load `cluster_group.tsv`.
11:41:25.061 [D] context:80           Create cache directory `G:\Shared drives\Lab Name\Current Members\Username\Neuropixel recordings\T237ma\T237aa_g1\T237aa_g1_imec0\.phy`.
11:41:25.187 [D] context:100          Initialize joblib cache dir at `G:\Shared drives\Lab Name\Current Members\Username\Neuropixel recordings\T237ma\T237aa_g1\T237aa_g1_imec0\.phy`.
11:41:25.187 [D] context:101          Reducing the size of the cache if needed.
11:41:25.187 [D] base:102             Add filter `high_pass`.
11:41:25.187 [D] config:31            Load config file `C:\Users\username\.phy\phy_config.py`.
11:41:25.187 [D] plugin:74            Scanning `C:\Users\username\phyllum\plugins`.
11:41:25.187 [D] plugin:78            Found plugin module `CerebellarLayerViewPlugin.py`.
11:41:25.187 [D] plugin:36            Register plugin `CerebellarLayerViewPlugin.CerebellarLayerViewPlugin`.
11:41:25.187 [D] plugin:78            Found plugin module `CerebellarNeuronViewPlugin.py`.
11:41:25.187 [D] plugin:36            Register plugin `CerebellarNeuronViewPlugin.CerebellarNeuronViewPlugin`.
11:41:25.187 [D] plugin:78            Found plugin module `ClusterMetricsPlugin.py`.
C:\Users\username\.conda\envs\phy2\lib\site-packages\umap\distances.py:1063: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
C:\Users\username\.conda\envs\phy2\lib\site-packages\umap\distances.py:1071: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
C:\Users\username\.conda\envs\phy2\lib\site-packages\umap\distances.py:1086: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
C:\Users\username\.conda\envs\phy2\lib\site-packages\umap\umap_.py:660: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
11:41:30.215 [D] plugin:36            Register plugin `ClusterMetricsPlugin.ClusterMetricsPlugin`.
11:41:30.215 [D] plugin:78            Found plugin module `CreateDatabase.py`.
11:41:30.215 [D] plugin:36            Register plugin `CreateDatabase.CreateDatabasePlugin`.
11:41:30.215 [D] plugin:78            Found plugin module `CrosscorrelogramAnalysis.py`.
11:41:30.215 [D] plugin:36            Register plugin `CrosscorrelogramAnalysis.crosscorrelogramAnalysisPlugin`.
11:41:30.215 [D] plugin:78            Found plugin module `CustomSimilarityPlugin.py`.
11:41:30.215 [D] plugin:36            Register plugin `CustomSimilarityPlugin.CustomSimilarityPlugin`.
11:41:30.215 [D] plugin:78            Found plugin module `CustomSplitPlugin.py`.
11:41:30.215 [D] plugin:36            Register plugin `CustomSplitPlugin.CustomSplitPlugin`.
11:41:30.230 [D] plugin:78            Found plugin module `CustomTraceViewPlugin.py`.
11:41:30.230 [D] plugin:36            Register plugin `CustomTraceViewPlugin.CustomTraceViewPlugin`.
11:41:30.230 [D] plugin:78            Found plugin module `MergePlugin.py`.
11:41:30.230 [D] plugin:36            Register plugin `MergePlugin.MergePlugin`.
11:41:30.230 [D] plugin:78            Found plugin module `MergePluginOriginal.py`.
11:41:30.230 [D] plugin:36            Register plugin `MergePluginOriginal.MergePluginOriginal`.
11:41:30.230 [D] plugin:78            Found plugin module `PlottingPlugin.py`.
11:41:30.230 [D] plugin:36            Register plugin `PlottingPlugin.PlottingPlugin`.
11:41:30.230 [D] plugin:78            Found plugin module `UMAPClusteringViewPlugin.py`.
11:41:30.230 [D] plugin:36            Register plugin `UMAPClusteringViewPlugin.UMAPClusteringViewPlugin`.
11:41:30.230 [D] plugin:78            Found plugin module `UMAPLayerClusteringViewPlugin.py`.
11:41:30.230 [D] plugin:36            Register plugin `UMAPLayerClusteringViewPlugin.UMAPLayerClusteringViewPlugin`.
11:41:30.230 [D] plugin:78            Found plugin module `WaveformRealignmentPlugin.py`.
11:41:30.230 [D] plugin:36            Register plugin `WaveformRealignmentPlugin.WaveformRealingnmentPlugin`.
11:41:30.230 [D] plugin:145           Loading 12 plugins.
11:41:30.230 [D] plugin:156           Attached plugin PlottingPlugin.
11:41:30.230 [D] plugin:156           Attached plugin CustomSimilarityPlugin.
11:41:30.246 [D] plugin:156           Attached plugin MergePlugin.
11:41:30.246 [D] plugin:156           Attached plugin CustomSplitPlugin.
PHYLLUM RUNNING: COMPUTING MULTIPLE METRICS FOR EACH CLUSTER. THIS PROCESS WILL TAKE SEVERAL MINUTES THE FIRST TIME THAT PHYLLUM IS EXECUTED OR AFTER THE PHY CACHE IS CLEANED WITH THE OPTION --clear-cache
11:41:41.737 [D] plugin:156           Attached plugin ClusterMetricsPlugin.
11:41:41.737 [D] plugin:156           Attached plugin CerebellarNeuronViewPlugin.
11:41:41.737 [D] plugin:156           Attached plugin CerebellarLayerViewPlugin.
11:41:41.737 [D] plugin:156           Attached plugin UMAPLayerClusteringViewPlugin.
11:41:41.737 [D] plugin:156           Attached plugin UMAPClusteringViewPlugin.
11:41:41.737 [D] plugin:156           Attached plugin CreateDatabase.
11:41:41.737 [D] plugin:156           Attached plugin CustomTraceViewPlugin.
11:41:41.737 [D] plugin:156           Attached plugin crosscorrelogramAnalysisPlugin.
11:41:41.791 [D] context:209          The file `G:\Shared drives\Lab Name\Current Members\Username\Neuropixel recordings\T237ma\T237aa_g1\T237aa_g1_imec0\.phy\new_cluster_id.pkl` doesn't exist.
11:41:41.791 [D] context:209          The file `G:\Shared drives\Lab Name\Current Members\Username\Neuropixel recordings\T237ma\T237aa_g1\T237aa_g1_imec0\.phy\spikes_per_cluster.pkl` doesn't exist.
11:41:41.806 [D] clustering:237       Recompute spikes_per_cluster manually: this might take a while.
11:41:41.963 [D] context:185          Save data to `G:\Shared drives\Lab Name\Current Members\Username\Neuropixel recordings\T237ma\T237aa_g1\T237aa_g1_imec0\.phy\spikes_per_cluster.pkl`.
11:41:42.077 [D] gui:463              Creating GUI.
11:41:42.089 [D] state:46             Load C:\Users\username\.phy\TemplateGUI\state.json for GUIState.
11:43:20.742 [D] gui:718              Add view ClusterView to GUI.
11:43:20.760 [D] gui:718              Add view SimilarityView to GUI.
11:43:20.804 [D] gui:718              Add view WaveformView to GUI.
11:43:20.808 [D] base:337             Set state for WaveformView.
11:43:20.821 [D] gui:718              Add view CorrelogramView to GUI.
11:43:20.824 [D] base:337             Set state for CorrelogramView.
11:43:20.848 [D] gui:718              Add view ISIView to GUI.
11:43:20.851 [D] base:337             Set state for ISIView.
11:43:20.864 [D] gui:718              Add view FeatureView to GUI.
11:43:20.866 [D] base:337             Set state for FeatureView.
11:43:20.890 [D] gui:718              Add view AmplitudeView to GUI.
11:43:20.892 [D] base:337             Set state for AmplitudeView.
11:43:20.914 [D] gui:718              Add view FiringRateView to GUI.
11:43:20.917 [D] base:337             Set state for FiringRateView.
11:43:21.640 [D] gui:718              Add view TraceView to GUI.
11:43:21.643 [D] base:337             Set state for TraceView.
11:43:21.644 [D] base:494             Set color scheme to random.
11:43:21.796 [D] base:1626            Adding default color schemes to TraceView.
11:43:22.701 [D] gui:718              Add view ProbeView to GUI.
11:43:22.704 [D] base:337             Set state for ProbeView.
11:43:22.725 [D] gui:718              Add view TemplateFeatureView to GUI.
11:43:22.727 [D] base:337             Set state for TemplateFeatureView.
11:43:22.752 [D] gui:718              Add view ClusterScatterView to GUI.
11:43:22.755 [D] base:337             Set state for ClusterScatterView.
11:43:22.755 [D] base:494             Set color scheme to random.
11:43:22.757 [D] base:1626            Adding default color schemes to ClusterScatterView.
11:43:22.978 [D] gui:519              Load the geometry state.
QMimeDatabase: Error loading internal MIME data
An error has been encountered at line 1 of <internal MIME data>: Premature end of document.:
iamrameses commented 1 year ago

I was able to resolve this issue by re-creating the environment from scratch (with no specified python or numpy version) and following the installation steps described in: https://github.com/cortex-lab/phy#developer-instructions