Error starting template-gui

[jaredluckas]

Hi,

I'm having issues starting up phy, but only on certain computers. I'm currently running miniconda3 on Windows 10. Each time I try to use template-gui, I run into an error that says

TypeError: sequence item 0: expected str instance, VertexShader found

Note that I do not run into this issue on a different computer where I have set up phy identically (though I cannot use that computer to process the data due to low RAM). As far as I know, there should be no difference between the two computers set-up wise, yet I am still getting this error. I've tried reinstalling everything only to continually get this error. Does anyone know what it might mean?

Thanks

[rossant]

If you run phy with the --debug option on the command line, do you get a more complete error message/traceback?

[JannaAarse]

Hi,

I have the same problem, I was running it with --debug and this is the error message I get :

(phy) C:\Temp_sorting\VR32\20190722-kilosort\New folder>phy template-gui params.py --debug 15:38:45 [D] config:46 Load config file C:\Users\jma18\.phy\phy_config.py. 15:38:46 [D] plugin:35 Register plugin phycontrib.kwik_gui.gui.KwikGUIPlugin. 15:38:46 [D] plugin:35 Register plugin phycontrib.template.gui.TemplateGUIPlugin. 15:38:46 [D] plugin:35 Register plugin phycontrib.utils.precache.PrecachePlugin. 15:38:46 [D] plugin:35 Register plugin phycontrib.utils.saveprompt.SavePromptPlugin. 15:38:46 [D] cli:107 Attach plugin phycontrib.kwik_gui.gui.KwikGUIPlugin to CLI. 15:38:46 [D] cli:107 Attach plugin phycontrib.template.gui.TemplateGUIPlugin to CLI. 15:38:46 [D] gui:253 Loading traces at 20190722_JAVR32_Light_session_13.bin. 15:38:46 [D] gui:268 Loading amplitudes. 15:38:46 [D] gui:277 Loading 31098 spike clusters. 15:38:46 [D] gui:283 Loading spike templates. 15:38:46 [D] gui:289 Loading spike samples. 15:38:46 [D] gui:293 Loading templates. 15:38:46 [D] gui:299 Loading the whitening matrix. 15:38:46 [D] gui:303 Loading unwhitened templates. 15:38:46 [D] gui:321 Loading similar templates. 15:38:46 [D] gui:326 Loading channel mapping. 15:38:46 [D] gui:334 Loading channel positions. 15:38:46 [D] gui:339 Loading features. 15:38:46 [D] gui:370 Loading template features. 15:38:46 [D] gui:424 HP filtering the data for waveforms 15:38:46 [D] gui:453 Loading the cluster groups. 15:38:46 [D] context:56 Initialize joblib cache dir at C:\Temp_sorting\VR32\20190722-kilosort\New folder\.phy. 15:38:46 [D] context:80 Load memcache for phy.cluster.manual.controller.get_mean_masks. 15:38:46 [D] context:80 Load memcache for phy.cluster.manual.controller.get_mean_features. 15:38:46 [D] context:80 Load memcache for phy.cluster.manual.controller.get_mean_waveforms. 15:38:46 [D] context:80 Load memcache for phycontrib.template.gui.get_waveforms_amplitude. 15:38:46 [D] context:80 Load memcache for phycontrib.template.gui.get_waveform_lims. 15:38:46 [D] context:80 Load memcache for phy.cluster.manual.controller.get_feature_lim. 15:38:46 [D] context:80 Load memcache for phy.cluster.manual.controller.get_trace_lim. 15:38:46 [D] context:80 Load memcache for phy.cluster.manual.controller.get_close_clusters. 15:38:46 [D] context:80 Load memcache for phy.cluster.manual.controller.get_probe_depth. 15:38:46 [D] context:80 Load memcache for phy.cluster.manual.controller.get_correlograms. 15:38:46 [D] context:80 Load memcache for phy.cluster.manual.controller.spikes_per_cluster. 15:38:46 [D] context:80 Load memcache for phycontrib.template.gui.get_amplitudes. 15:38:46 [D] context:80 Load memcache for phycontrib.template.gui.get_cluster_templates. 15:38:46 [D] context:80 Load memcache for phycontrib.template.gui.get_cluster_pair_features. 15:38:46 [D] context:80 Load memcache for phycontrib.template.gui._cluster_template_similarities. 15:38:46 [D] context:80 Load memcache for phycontrib.template.gui._sim_ij. 15:38:46 [D] context:128 The file C:\Temp_sorting\VR32\20190722-kilosort\New folder\.phy\new_cluster_id.json doesn't exist. 15:38:46 [D] config:46 Load config file C:\Users\jma18\.phy\phy_config.py. 15:38:46 [D] gui:428 Load the GUI state from C:\Users\jma18\.phy\TemplateGUI\state.json. 15:38:46 [D] utils:51 Get box size for 25 points. 15:38:46 [E] cli:39 An error has occurred (TypeError): sequence item 0: expected str instance, VertexShader found 15:38:46 [D] cli:42 Traceback (most recent call last): File "c:\users\jma18.conda\envs\phy\lib\runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "c:\users\jma18.conda\envs\phy\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File "C:\Users\jma18.conda\envs\phy\Scripts\phy.exe__main.py", line 9, in sys.exit(phy()) File "c:\users\jma18.conda\envs\phy\lib\site-packages\click\core.py", line 764, in call return self.main(args, kwargs) File "c:\users\jma18.conda\envs\phy\lib\site-packages\click\core.py", line 717, in main rv = self.invoke(ctx) File "c:\users\jma18.conda\envs\phy\lib\site-packages\click\core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "c:\users\jma18.conda\envs\phy\lib\site-packages\click\core.py", line 956, in invoke return ctx.invoke(self.callback, ctx.params) File "c:\users\jma18.conda\envs\phy\lib\site-packages\click\core.py", line 555, in invoke return callback(args, *kwargs) File "c:\users\jma18.conda\envs\phy\lib\site-packages\click\decorators.py", line 17, in new_func return f(get_current_context(), args, **kwargs) File "c:\users\jma18.conda\envs\phy\lib\site-packages\phycontrib\template\gui.py", line 814, in cluster_manual _run_cmd('_run(params)', ctx, globals(), locals()) File "c:\users\jma18.conda\envs\phy\lib\site-packages\phy\utils\cli.py", line 76, in _runcmd return exec(cmd, glob, loc) File "", line 1, in File "c:\users\jma18.conda\envs\phy\lib\site-packages\phycontrib\template\gui.py", line 787, in _run gui = controller.create_gui() File "c:\users\jma18.conda\envs\phy\lib\site-packages\phycontrib\template\gui.py", line 727, in create_gui config_dir=config_dir, File "c:\users\jma18.conda\envs\phy\lib\site-packages\phy\cluster\manual\controller.py", line 457, in create_gui self.add_trace_view(gui) File "c:\users\jma18.conda\envs\phy\lib\site-packages\phy\cluster\manual\controller.py", line 407, in add_trace_view channel_order=self.channel_order, File "c:\users\jma18.conda\envs\phy\lib\site-packages\phy\cluster\manual\views.py", line 681, in init__ self.go_to(duration / 2.) File "c:\users\jma18.conda\envs\phy\lib\site-packages\phy\cluster\manual\views.py", line 897, in go_to self.set_interval((time - half_dur, time + half_dur)) File "c:\users\jma18.conda\envs\phy\lib\site-packages\phy\cluster\manual\views.py", line 817, in set_interval self.build() File "c:\users\jma18.conda\envs\phy\lib\site-packages\phy\plot\plot.py", line 193, in build self.add_visual(visual) File "c:\users\jma18.conda\envs\phy\lib\site-packages\phy\plot\base.py", line 283, in add_visual visual.on_resize(self.size) File "c:\users\jma18.conda\envs\phy\lib\site-packages\phy\plot\base.py", line 81, in on_resize s = '\n'.join(self.program.shaders) TypeError: sequence item 0: expected str instance, VertexShader found

Thanks for the help, Janna

[rossant]

This is with phy1, right? Could you try with phy2 in a new conda environment?

[jaredluckas]

Yes, this issue was with phy1. I was not able to resolve the problem, so I installed phy2 and it seems to run normally, with no errors.

[JannaAarse]

How do I install phy2 ? I was running --upgrade but I get this Requirement already up-to-date: phy in c:\users\jma18.conda\envs\phy\lib\site-packages (1.0.9) Requirement already up-to-date: phycontrib in c:\users\jma18.conda\envs\phy\lib\site-packages (1.0.15)

[rossant]

you'll find instructions here: https://phy.readthedocs.io/en/latest/installation/

[JannaAarse]

Thanks for the instructions, I tried it and got this error message from that moment on

(phy2) C:\Temp_sorting\VR32\20190722-kilosort\New folder>phy template-gui params.py 'phy' is not recognized as an internal or external command, operable program or batch file.

I deleted everything I had from Phy and Anaconda, reinstalled everything and still get this error message.

[JannaAarse]

I also tried everything from message #855 , running pip install for everything that I could find under pip in the environment file, but that just lead to another error message (phy2) C:\Temp_sorting\VR32\20190723\kilosort data>phy template-gui params.py Usage: phy [OPTIONS] COMMAND [ARGS]...

Error: No such command "template-gui".

I am really sorry for bothering, I am completely new to anaconda and phyton, I only know a tiny bit in matlab, we are using phy on another computers in the lab, we never had this problem before. I am not sure what I am doing wrong.

[jaredluckas]

Yeah I was having this problem at first for phy2 as well. I found that you will have to download and install git from here -> https://git-scm.com/ Then, you have to add the git.exe (which you will find wherever git has installed onto your computer, for example mine was in C:\Users\jluckas\AppData\Local\Programs\Git\bin\git.exe) into your PATH environment variable. If your problem was the same as mine, you couldn't get the last pip dependency phylib. You can fix this by using pip install git+https://github.com/cortex-lab/phylib.git in the phy2 environment once you've installed git and added it to your PATH.

[Yliew6-gt]

This is with phy1, right? Could you try with phy2 in a new conda environment?

Hi, I have this exact same issue when running phy1. I have installed phy2 on my computer but I wanted to view some old dataset that I have previously curated with phy1. However the template-gui will not open properly and I got about identical error posted above. Is there a way to use the phy1 while having phy2 installed? Thanks.

[TypeError: sequence item 0: expected str instance, VertexShader found]