Instead of running PreprocessImageData.m in runprediction.sh instead have the code call:
def_datapackages.m
this also writes a textfile in the same folder (where the de_augmentation matlab file is stored),
which you could use to tell the wrapper how many z-stacks and how many x/y packages are to be done.
Then in the loop in preprocess_package.m must called for every z stack and every datapackage to create the augmented images.
preprocess_package.m <indir> <outdir> <xy_package> <z_stack> <augmentation speed>
% Example: preprocess_package ~/EMdata1/ ~/AugmentedEMData/ 15 2 1fm 10
%
% Speed: supported values 1,2,4 or 10
% speeds up processing potentially with a negative effect on accuracy (speed of 1 equals highest accuracy)
Instead of running PreprocessImageData.m in runprediction.sh instead have the code call: def_datapackages.m
this also writes a textfile in the same folder (where the de_augmentation matlab file is stored), which you could use to tell the wrapper how many z-stacks and how many x/y packages are to be done.
Then in the loop in preprocess_package.m must called for every z stack and every datapackage to create the augmented images.