pyfairsim 0.0.1

A package to run sim reconstructions including parameter estimation.

pyFairSIM

python version of the fast sim project

install

download repo. Run pip install .\pyFairSIM.

settings

All settings and physical parameters are read from a json file. To get an example file run python -m create_example_settings.py and change all the explaning texts to the values you need.

run parameter estimation

To run a parameter estimation for a given sim-stack use python -m parameter_estimation.py -f -s -o . For help use python -m parameter_estimation.py -h. Settings and save settings path can be the same then the obtained values overwrite the old values.

run reconstruction

To run a reconstruction for a given sim-stack use python -m reconstruction.py -f -s -o . For help use python -m reconstruction.py -h

run batch reconstruction

Runs a parameter estimation and then a reconstruction on all .tiff/.tif files in given folder and all subfolders. Command: python -m batch_reconstruction.py

run absolute phase estimation

not working properly at the moment.