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To get started, given a HDF5 file with let's say 192 frames lightfield data:

• First, in workflow-utils, let's use pose-extract (to be moved to here?) to extract backbone information:

  for i in `seq 0 192`; do echo $i;
    ./pose-extract-lf.py punc31_gCAMP5_td_video32_global_gfpfilter.hdf5 $i
      | ./tsv2json.sh >../../nemashow/meteor/data/punc31_gCAMP5_td_video32_global_gfpfilter.hdf5-$i-backbone.json;
  done
  

If you have nemashow checked out in the respective directory, this will also store the backbone files in such a way that nemashow will display the backbone curve.

• Then, in sigextract, let's produce straightened images in the 's/' subdirectory:

  for i in `seq 169 192`; do echo $i;
    ./straighten.py punc31_gCAMP5_td_video32_global_gfpfilter.hdf5 $i \
      ../nemashow/meteor/data/punc31_gCAMP5_td_video32_global_gfpfilter.hdf5-$i-backbone.json \
      s/punc31_gCAMP5_td_video32_global_gfpfilter.hdf5-$(printf '%03d' $i)-s.png;
  done