cortex-lab
All windows blank in Phy
After upgrading to Ubuntu 22 I can open Phy but all windows are black.
(base) ella@fishfish:~$ cd /media/probeX/intanData/ela/analyzedData/ela_0023
(base) ella@fishfish:/media/probeX/intanData/ela/analyzedData/ela_0023$ conda activate phy
(phy) ella@fishfish:/media/probeX/intanData/ela/analyzedData/ela_0023$ phy template-gui params.py --debug
15:54:14.605 [D] init:68 Start capturing exceptions.
15:54:15.479 [W] model:592 Unreferenced clusters found in templates (generally not a problem)
15:54:15.881 [D] model:607 Loading spike clusters.
15:54:16.368 [W] model:614 Unreferenced clusters found in spike_clusters (generally not a problem)
15:54:16.790 [D] model:557 No channel shank file found.
15:54:16.792 [D] model:680 Loading templates.
15:54:16.971 [D] model:712 Templates are dense.
15:54:16.971 [W] model:656 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
15:54:16.971 [D] model:718 Loading the whitening matrix.
15:54:16.974 [D] model:725 Loading the inverse of the whitening matrix.
15:54:16.992 [D] model:754 Loading features.
15:54:16.994 [D] model:769 Features are sparse.
15:54:16.994 [D] model:791 Loading template features.
15:54:16.996 [D] model:801 Template features are sparse.
15:54:16.997 [D] model:492 Load cluster_Amplitude.tsv.
15:54:17.005 [D] model:492 Load cluster_KSLabel.tsv.
15:54:17.014 [D] model:492 Load cluster_group.tsv.
15:54:17.023 [D] model:492 Load cluster_ContamPct.tsv.
Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
15:54:17.833 [D] context:100 Initialize joblib cache dir at /media/probeX/intanData/ela/analyzedData/ela_0023/.phy.
15:54:17.839 [D] context:101 Reducing the size of the cache if needed.
15:54:18.758 [D] base:102 Add filter high_pass.
15:54:18.758 [D] config:31 Load config file /home/ella/.phy/phy_config.py.
15:54:18.759 [D] plugin:145 Loading 0 plugins.
15:54:18.759 [D] context:126 Load memcache for phy.apps.base._get_mean_waveforms.
15:54:18.760 [D] context:126 Load memcache for phy.apps.base._get_mean_waveforms.
15:54:18.760 [D] context:126 Load memcache for phy.apps.base._get_template_waveforms.
15:54:18.809 [D] context:126 Load memcache for phy.apps.base.get_mean_spike_template_amplitudes.
15:54:18.809 [D] context:126 Load memcache for phy.apps.base.get_template_counts.
15:54:18.836 [D] context:126 Load memcache for phy.apps.base.get_template_for_cluster.
15:54:18.838 [D] context:126 Load memcache for phy.apps.template.gui.get_template_amplitude.
15:54:18.839 [D] context:126 Load memcache for phy.apps.base.get_cluster_amplitude.
15:54:18.840 [D] context:126 Load memcache for phy.apps.base.get_mean_firing_rate.
15:54:18.840 [D] context:126 Load memcache for phy.apps.base.get_best_channel.
15:54:18.843 [D] context:126 Load memcache for phy.apps.template.gui.get_best_channels.
15:54:18.847 [D] context:126 Load memcache for phy.apps.base.get_channel_shank.
15:54:18.847 [D] context:126 Load memcache for phy.apps.base.get_probe_depth.
15:54:18.848 [D] context:126 Load memcache for phy.apps.base.peak_channel_similarity.
15:54:19.196 [D] context:185 Save data to /media/probeX/intanData/ela/analyzedData/ela_0023/.phy/spikes_per_cluster.pkl.
15:54:19.776 [D] gui:463 Creating GUI.
15:54:19.784 [D] state:46 Load /home/ella/.phy/TemplateGUI/state.json for GUIState.
15:54:19.785 [D] state:46 Load /media/probeX/intanData/ela/analyzedData/ela_0023/.phy/state.json for GUIState.
15:54:20.150 [D] gui:718 Add view ClusterView to GUI.
15:54:20.178 [D] gui:718 Add view SimilarityView to GUI.
15:54:20.236 [D] gui:718 Add view WaveformView to GUI.
15:54:20.244 [D] base:337 Set state for WaveformView.
15:54:20.264 [D] gui:718 Add view CorrelogramView to GUI.
15:54:20.266 [D] base:337 Set state for CorrelogramView.
15:54:20.304 [D] gui:718 Add view ISIView to GUI.
15:54:20.307 [D] base:337 Set state for ISIView.
15:54:20.342 [D] gui:718 Add view AmplitudeView to GUI.
15:54:20.345 [D] base:337 Set state for AmplitudeView.
15:54:20.381 [D] gui:718 Add view FiringRateView to GUI.
15:54:20.384 [D] base:337 Set state for FiringRateView.
15:54:21.232 [D] gui:718 Add view TraceView to GUI.
15:54:21.234 [D] base:337 Set state for TraceView.
15:54:21.235 [D] base:494 Set color scheme to random.
15:54:24.198 [D] base:1623 Adding default color schemes to TraceView.
15:54:27.957 [D] gui:718 Add view ProbeView to GUI.
15:54:27.961 [D] base:337 Set state for ProbeView.
15:54:27.987 [D] gui:718 Add view TemplateFeatureView to GUI.
15:54:27.989 [D] base:337 Set state for TemplateFeatureView.
15:54:28.022 [D] gui:718 Add view ClusterScatterView to GUI.
15:54:28.024 [D] base:337 Set state for ClusterScatterView.
15:54:28.024 [D] base:494 Set color scheme to random.
15:54:28.027 [D] base:1623 Adding default color schemes to ClusterScatterView.
15:54:28.210 [D] gui:718 Add view TemplateView to GUI.
15:54:28.214 [D] base:337 Set state for TemplateView.
15:54:28.215 [D] base:494 Set color scheme to random.
15:54:28.217 [D] base:1623 Adding default color schemes to TemplateView.
15:54:28.324 [D] gui:519 Load the geometry state.
15:54:28.568 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.623 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.674 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.724 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.754 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.786 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.817 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.849 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.854 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.856 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.856 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.857 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.858 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.858 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.859 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.860 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.887 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.888 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.889 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.889 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.890 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.891 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.892 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.892 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.893 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.894 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.895 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.895 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.896 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.896 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.897 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.898 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.997 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:28.999 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:29.000 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:29.000 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:29.001 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:29.002 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:29.003 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.882 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.885 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.886 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.887 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.888 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.889 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.890 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.891 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.892 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.893 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.894 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.895 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.896 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.898 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
15:54:34.899 [D] base:702 Exception in paintGL: Attempt to retrieve context when no valid context
Same issue on linux
Using pyqt version 5.13.1 but tried 5.12.1 as well. Python version 3.7.0
I believe I'm having a similar issue on mac 13.4.1, python 3.11.3. I am getting the following errors (excerpt below, but it just continues on with paintGL initializetGL errors):
phy template-gui params.py --debug
22:32:02.120 [D] init:68 Start capturing exceptions.
22:32:02.128 [W] model:603 Unreferenced clusters found in templates (generally not a problem)
22:32:02.129 [D] model:619 Loading spike clusters.
22:32:02.131 [W] model:625 Unreferenced clusters found in spike_clusters (generally not a problem)
22:32:02.136 [D] model:692 Loading templates.
22:32:02.162 [D] model:720 Templates are sparse.
22:32:02.162 [W] model:667 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
22:32:02.162 [D] model:730 Loading the whitening matrix.
22:32:02.164 [D] model:737 Loading the inverse of the whitening matrix.
22:32:02.192 [D] model:766 Loading features.
22:32:02.266 [D] model:781 Features are sparse.
22:32:02.267 [D] model:803 Loading template features.
22:32:02.289 [D] model:813 Template features are sparse.
22:32:02.291 [D] model:504 Load cluster_group.tsv.
22:32:02.929 [D] context:100 Initialize joblib cache dir at /Users/maorloff/Downloads/phy-data-master/template/.phy.
22:32:02.930 [D] context:101 Reducing the size of the cache if needed.
22:32:02.959 [D] base:102 Add filter high_pass.
22:32:02.959 [D] config:31 Load config file /Users/maorloff/.phy/phy_config.py.
22:32:02.961 [D] plugin:145 Loading 0 plugins.
22:32:02.961 [D] context:126 Load memcache for phy.apps.base._get_mean_waveforms.
22:32:02.961 [D] context:126 Load memcache for phy.apps.base._get_mean_waveforms.
22:32:02.962 [D] context:126 Load memcache for phy.apps.base._get_template_waveforms.
22:32:02.962 [D] context:126 Load memcache for phy.apps.base.get_mean_spike_template_amplitudes.
22:32:02.963 [D] context:126 Load memcache for phy.apps.base.get_template_counts.
22:32:02.963 [D] context:126 Load memcache for phy.apps.base.get_template_for_cluster.
22:32:02.964 [D] context:126 Load memcache for phy.apps.template.gui.get_template_amplitude.
22:32:02.965 [D] context:126 Load memcache for phy.apps.base.get_cluster_amplitude.
22:32:02.965 [D] context:126 Load memcache for phy.apps.base.get_mean_firing_rate.
22:32:02.966 [D] context:126 Load memcache for phy.apps.base.get_best_channel.
22:32:02.966 [D] context:126 Load memcache for phy.apps.template.gui.get_best_channels.
22:32:02.967 [D] context:126 Load memcache for phy.apps.base.get_channel_shank.
22:32:02.968 [D] context:126 Load memcache for phy.apps.base.get_probe_depth.
22:32:02.968 [D] context:126 Load memcache for phy.apps.base.peak_channel_similarity.
22:32:02.969 [D] context:209 The file /Users/maorloff/Downloads/phy-data-master/template/.phy/new_cluster_id.pkl doesn't exist.
22:32:02.975 [D] context:185 Save data to /Users/maorloff/Downloads/phy-data-master/template/.phy/spikes_per_cluster.pkl.
22:32:02.986 [D] gui:463 Creating GUI.
22:32:03.058 [D] state:46 Load /Users/maorloff/.phy/TemplateGUI/state.json for GUIState.
22:32:03.059 [D] state:46 Load /Users/maorloff/Downloads/phy-data-master/template/.phy/state.json for GUIState.
22:32:03.315 [D] gui:718 Add view ClusterView to GUI.
22:32:03.379 [D] gui:718 Add view SimilarityView to GUI.
22:32:03.445 [D] gui:718 Add view WaveformView to GUI.
22:32:03.506 [D] base:337 Set state for WaveformView.
22:32:03.522 [D] gui:718 Add view CorrelogramView to GUI.
22:32:03.525 [D] base:337 Set state for CorrelogramView.
22:32:03.554 [D] gui:718 Add view ISIView to GUI.
22:32:03.559 [D] base:337 Set state for ISIView.
22:32:03.579 [D] gui:718 Add view FeatureView to GUI.
22:32:03.582 [D] base:337 Set state for FeatureView.
22:32:03.612 [D] gui:718 Add view AmplitudeView to GUI.
22:32:03.616 [D] base:337 Set state for AmplitudeView.
22:32:03.644 [D] gui:718 Add view FiringRateView to GUI.
22:32:03.647 [D] base:337 Set state for FiringRateView.
22:32:03.741 [D] gui:718 Add view TraceView to GUI.
22:32:03.744 [D] base:337 Set state for TraceView.
22:32:03.745 [D] base:494 Set color scheme to random.
22:32:03.769 [D] base:1626 Adding default color schemes to TraceView.
22:32:03.808 [D] gui:718 Add view ProbeView to GUI.
22:32:03.811 [D] base:337 Set state for ProbeView.
22:32:03.837 [D] gui:718 Add view ClusterScatterView to GUI.
22:32:03.840 [D] base:337 Set state for ClusterScatterView.
22:32:03.840 [D] base:494 Set color scheme to random.
22:32:03.841 [D] base:1626 Adding default color schemes to ClusterScatterView.
22:32:04.007 [D] gui:519 Load the geometry state.
22:32:04.244 [D] base:675 Exception in initializetGL: GLError(
err = 1280,
description = b'invalid enumerant',
baseOperation = glEnable,
cArguments = (GL_POINT_SPRITE,)
)
Error in Vertex shader 847 (
000 #define GLUMPY__VERTEX_SHADER_ 001 // --- Snippets code : start --- // 002 // --- Snippets code : end --- // ...
Error in Vertex shader 847 (
000 #define GLUMPY__VERTEX_SHADER_ 001 // --- Snippets code : start --- // 002 // --- Snippets code : end --- // 003 varying vec2 v_pos_tmp; ...
Error in Vertex shader 847 (
... 001 // --- Snippets code : start --- // 002 // --- Snippets code : end --- // 003 varying vec2 v_pos_tmp; 004 005 uniform vec2 u_window_size; 006 uniform vec2 u_pan; ...
22:32:04.256 [D] base:702 Exception in paintGL: Shader compilation error
22:32:04.261 [D] base:675 Exception in initializetGL: GLError(
err = 1280,
description = b'invalid enumerant',
baseOperation = glEnable,
cArguments = (GL_POINT_SPRITE,)
)
Error in Vertex shader 716 (
000 #define GLUMPY__VERTEX_SHADER_ 001 // --- Snippets code : start --- // 002 // --- Snippets code : end --- // ...
Error in Vertex shader 716 (
000 #define GLUMPY__VERTEX_SHADER_ 001 // --- Snippets code : start --- // 002 // --- Snippets code : end --- // 003 varying vec2 v_pos_tmp; ...
Error in Vertex shader 716 (
... 001 // --- Snippets code : start --- // 002 // --- Snippets code : end --- // 003 varying vec2 v_pos_tmp; 004 005 uniform vec2 u_window_size; 006 uniform vec2 u_pan; ...
Identical issue on Mac 13.0, Apple M2.
In phy.log many repetitions of:
12:12:59.211 [D] base:675 Exception in initializetGL: GLError(
err = 1280,
description = b'invalid enumerant',
baseOperation = glEnable,
cArguments = (GL_POINT_SPRITE,)
)
12:12:59.211 [D] base:675 Exception in initializetGL: GLError(
err = 1280,
description = b'invalid enumerant',
baseOperation = glEnable,
cArguments = (GL_POINT_SPRITE,)
)
And in stoud while running the program:
Error in Vertex shader 210 (<string>)
-> 'varying' : syntax error: syntax error
...
001 // --- Snippets code : start --- //
002 // --- Snippets code : end --- //
003 varying vec2 v_pos_tmp;
004
005 uniform vec2 u_window_size;
...
Error in Vertex shader 91 (<string>)
-> '' : version '120' is not supported
000 #define _GLUMPY__VERTEX_SHADER__
001 // --- Snippets code : start --- //
002 // --- Snippets code : end --- //
