Here are a few tips if something goes wrong.
Look at existing GitHub issues to see if someone else had the same problem. If not, feel free to open a new issue by giving a descriptive title and a comprehensive description of the problem, including screenshots if needed.
When calling the phy GUI from the command-line interface, append the
--debug option to the command to get more complete error messages, e.g.
phy template-gui params.py --debug
Please copy and paste the full console output to the GitHub issue if requested.
Sending your dataset to the main developer
In some cases, the main phy developer will ask you to send him your dataset in order to identify and fix the problem. You should compress the whole folder, excluding:
.physubdirectory, not needed, and
- the raw data if it is too big.
If you don't include the raw data in the compressed archive, please let the developer know the exact filename and file size (in bytes) of the raw data file(s).
Use a service like Dropbox, Google Drive, or Transfernow to send the archive to the developer.
Graphic issue on Windows 10
Several users have reported display issues on Windows 10, especially on computers with a dual graphics chipset (e.g. integrated Intel GPU, and discrete NVIDIA GPU). phy works best on NVIDIA GPUs. If you have this problem:
- Check that your screen is connected to your NVIDIA GPU and not the integrated one.
- Enable the discrete NVIDIA GPU (see this user's advice)
Issues with the GUI layout or the views
phy saves the GUI layout and view options (called GUI state) in two directories:
- Global GUI state:
~/.phy/TemplateGUI/state.jsonfor the Template GUI (common to all datasets)
- Local GUI state:
.phy/state.json(within your data directory)
If you want to reset the default GUI layout and view options, delete these two files, or run the GUI with the
--clear-state option which will delete these files for you:
phy template-gui params.py --clear-state
You can also safely delete the
.phy subdirectory which only contain the local GUI state and the data-specific cache, or use the
--clear-cache option which will delete this directory for you:
phy template-gui params.py --clear-cache
.phy: subdirectory inside the data directory. This subdirectory contains the cache that is used to make phy faster. You can always safely delete it: the cache will be automatically reconstructed the next time you launch the GUI. The only drawback is that performance will be a bit worse when you first select clusters in the GUI.
~is your home directory) this directory contains your custom plugins and user preferences for the GUI. If you delete it, you will lose the layout configuration of the GUI (which will be automatically reset the next time you open the GUI) and your user preferences. More specifically, the GUI parameters are found in
~/.phy/TemplateGUI/state.jsonfor the Template GUI, and so on.
Scaling discrepancy between templates and waveforms
There seems to be a scaling factor in the templates exported by KiloSort. Until this is fixed properly, a work-around is to add the following line to
template_scaling = 20.0 # or any other scaling factor
Error "No module named PyQt5.sip"
If you receive the error:
No module named PyQt5.sip, try to run the following commands in your conda environment (solution found by Claire Ward):
pip uninstall pyqt5 pyqt5-tools pip install pyqt5 pyqt5-tools pyqt5.sip