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cortex-lab
Waveforms view only show mean waveforms
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
@Antho2422,
Hey Anthony, happy we got through one issue hopefully we can figure this out. It looks like we are missing the beginning of the log since it should say when it is loading files. (It should say whether templates are sparse or dense etc). Could you include that in the log as well. Did you run
phy template-gui params.py --debug
I just want to make sure we have the full log, so we can see why it is doing the mean only and not raw. Unfortunately I'm pretty busy for the next week, but I'm happy to troubleshoot more next week.
@zm711
Thank you for your answer. I will run the debug mode asap but I'm pretty sure the issue is the same as the last one. It happens only when the path to my phy folder is really long. I was wondering if maybe we can allow relative path.
Would be very usefull because I'm using phy in a pipeline where the architecture of folders is organized in a certain way to run multiple experiment and facilitate the user usage and I would like to keep it like that. I would like to be able to launch phy from a folder without having to move the folder before opening it.
If we find a solution for that I would be more than happy 👍
Thank you very much ! Cheers
@Antho2422,
After you last issue I added that option to Spikeinterface :)
Do:
exp.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,
use_relative_path=True # here is the new argument
)
It will require the newest version of the SpikeInterface (0.99.1 with pip install or install from source). Give it a try and let me know if that helps. Zach
@zm711
Oh I did not notice that thank you ! I will check as soon as possible
Hi! I have the same problem, in WaveformView the raw display works only, I am not able to switch to "Toggle Mean Waveforms" either using "M" or the drop-down menu with the mouse.
Have you found a solution for this? I don't have as long path names so that part should be OK. Thanks in advance!
