A package to run sim reconstructions including parameter estimation.
Project description
pyFairSIM
python version of the fast sim project
install
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 explaining texts to the values you need.
run parameter estimation
To run a parameter estimation for a given sim-stack use
python -m pyfairsim.parameter_estimation -f <path-to-image> -s <path-to-settings> -o <path-to-save-settings>
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 pyfairsim.reconstruction -f <path-to-image> -s <path-to-settings> -o <path-to-save-reconstructed-image>
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 pyfairsim.batch_reconstruction
run absolute phase estimation
Runs a non-iterative phase estimation based on auto-correlation by Wicker et al. For it to work parameter estimation needs to be executed first.
python -m pyfairsim.phase_estimation -f <path-to-image> -s <path-to-settings> -o <path-to-save-settings>
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