Custom process chunk, new lsd scripts, new command line options #5
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…oesn't have an effect
…p tensorflow scripts
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This pull requests adds the capability of defining a custom
process_chunkfunction in the model config scripts that will be used to do custom chunk processing. This is useful if wanting to run multiple models on a single chunk (seetensorflow_acrlsd.py) or for postprocessing, or anywhere custom handling of chunk is desired.Also added in this PR are two example tensorflow model scripts for predicting local shape descriptors (lsds) and affinities based on https://github.com/funkelab/lsd.
tensorflow_lsd.pytakes in the raw data as input, rescales it and predicts 10 lsds as output. The second script,tensorflow_acrlsd.py, runs the aforementioned model first, and uses its output plus the rescaled raw as input to another model to produce 3 affinities as output.Instructions have also been added to the readme for tensorflow installation
Command line options have also been added to define the gpu queue and chargeback group.
@stuarteberg