phy works better on computers with sufficient RAM, a recent graphics card, and an SSD to store data files.
Main dependencies are NumPy, SciPy, PyQt5, pyopengl, joblib. The full list of dependencies is available in the
Upgrading from phy 1 to phy 2
- Never install phy 1 and phy 2 in the same conda environment.
- It is recommended to delete
Minimal installation instructions (to be completed):
Open a terminal and type:
conda create -n phy2 python pip numpy matplotlib scipy h5py pyqt cython -y conda activate phy2 pip install colorcet pyopengl qtconsole requests traitlets tqdm joblib click mkdocs pip install git+https://github.com/cortex-lab/phy.git@dev pip install git+https://github.com/cortex-lab/phylib.git
- Phy should now be installed. Open the GUI on a dataset as follows (the phy2 environment should still be activated):
cd path/to/my/spikesorting/output phy template-gui params.py
- 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
How to reset the GUI configuration
This might be useful if the organization of the views in the GUI is incorrect.
phy with the
--clear-state option. Alternatively, delete both files:
- Global GUI state:
~/.phy/TemplateGUI/state.json(common to all datasets)
- Local GUI state:
.phy/state.json(within your data directory)