To get an introduction into Spatial NCDE-based training and inference, as well as setting up the repository correctly please walk through the interactive notebook train_spatial_ncde.ipnyb
To run the training with a given parameterfile run:
python train_spatialNCDE.py --parameterfile "path/to/parameterfile"
The path should be relative from the directory from where the script is being run (inside the NeuralCDE-QMRI directory).
In order to generate parameter maps from a trained model run:
python parameter_maps_new.py --parameterfile "path/to/parameterfile"
The path should again be relative from the run directory.
For visualizing the generated parametermaps run:
python vis_dash.py --parameterfile "path/to/parameterfile"
The path should again be relative from the run directory. NOTE: Visualization is currently not yet feature complete, can only show parametermaps as of now.