New analysis code development

My personal repo for Adesnik Lab data analysis. General warning: Lots of monsters and untested code within!! Use at your own peril... Subject to code breaking changes at any time.

Installation

• Use mamba to manage the environment (you can use conda, it's just slower) (mamba easily installs on top of conda)

• Clone repo from GitHub

• Change to holofun directory

• Create environment with mamba env create -f environment.yml

• Install analysis package with pip install -e .

• To install OASIS, clone repo and build according to their instructions.

• To get it to install on windows install C++ build tools.

  • There might be other ways to get it to install via conda listed compilers, but I have not tried that.

• env2.yml is the alternate build from conda-forge. These packages are tpyically more up to date. You will not get a MKL numpy build (might not matter for basic analysis unless you start doing lots of FFTs, matmul, dots, etc.). Be sure to comment out jax[cpu] if you are on windows (will not build).

Other useful conda/mamba tips

• To force a clean reinstall (recommended if you are making significant changes to more complicated libraries or want to install dask, numba, or jax)

  mamba env create --file environment.yml --force
  
  # alternatively, for update from the yml
  mamba env update --file environment.yml  --prune
  

  • Note that --file environment.yml can be left out of command if you are in the directory with that file (and it is named as such)

Modules

• .tiffs -> SItiff, a decently well tested class for loading ScanImage tiffs
• .daq -> SetupDaqFile, a mostly working class for setupdaq data files
• .s2p -> Suite2pData, a still in-development class for loading python s2p data
• .analysis -> generic tools for trace manipulation and processing