README

This repository contains the scripts needed to reproduce all the experiments/examples in the paper: SIMPA: An open-source toolkit for simulation and processing of photoacoustic images.

Installation

Please follow the installation instructions of the SIMPA package: https://github.com/IMSY-DKFZ/simpa#simpa-installation-instructions.

In order to make sure that all experiments run smoothly, all the external tools required by SIMPA have to be installed as well: https://github.com/IMSY-DKFZ/simpa#external-tools-installation-instructions. IMPORTANT: You have to build the MCX binary with all custom light sources from this GitHub fork: https://www.github.com/IMSY-DKFZ/mcx

After the successful installation of SIMPA, this package can be installed similarly:

1. git clone https://github.com/IMSY-DKFZ/simpa_paper_experiments.git
2. cd simpa_paper_experiments
3. git pull
4. pip install .

Make sure that you have your preferred virtual environment activated (tested with python 3.8.10) and run:

1. git clone https://github.com/IMSY-DKFZ/simpa.git
2. cd simpa
3. git checkout 7eee7bcbee7f652eb6bc3e57fd887c3cdb1cd5c2
4. pip install .
5. pip install memory-profiler matplotlib-scalebar

Run experiments

Make sure that your SIMPA path config file path_config.env contains the paths to MATLAB and the MCX binary and it is located according to: https://github.com/IMSY-DKFZ/simpa#path-management

There are two options for running all the experiments:

1. Execute bash run_all_experiments.sh located in simpa_paper_experiments/experiments.
2. Run each python script separately in the simpa_paper_experiments/experiments subdirectories. The memory and run time footprint experiment has to be executed separately. This means that the memory_footprint.py and evaluate_memory_footprint_resutls.py scripts are not meant to be executed by themselves. Change your directory to simpa_paper_experiments/experiments/pa_image_simulation Execute: bash run_memory_footprint_experiment.sh