jcesardasilva / optscan

Optmization of scan grid for scanning microscopy using a solver for the travelling salesman program implemented in Google OR-Tools

optscan

Optmization of scan grid for scanning microscopy using a solver for the travelling salesman program implemented in Google OR-Tools https://developers.google.com/optimization/routing/tsp

The implementation here is published here [1] and code has the following DOI in Zenodo:

We will be happy with your citation if you use it.

Installation

Installation should be as simple as :

sudo python3 setup.py install

or, for local installation, using the flag --user :

python3 setup.py install --user

Running examples

You can edit the file round_roi_optim.py and run:

python3 examples/round_roi_optim.py

Dependencies

Optscan depends on standard python packages:

• numpy
• matplotlib
• ortools
• python >=3.6

Credits

Based on a code snippet originally posted here https://developers.google.com/optimization/routing/tsp

And also here https://github.com/google/or-tools/blob/stable/ortools/constraint_solver/samples/tsp_cities.py

References

[1]: da Silva, J.C., Guilloud, C., Hignette, O., Jarnias, C., Ponchut, C., Ruat, M., Labiche, J.-C., Pacureanu, A., Yang, Y., Salome, M. et al. (2019). J. Synchrotron Rad. 26, https://doi.org/10.1107/S1600577519006301