Renumbers the particle indices in a motive list, either sequentially or in a way that preserves particle indices while still making sure there are no duplicates in the list of indices.
This MOTL manipulation script uses one MATLAB compiled scripts below:
../functions/subtom_renumber_motl
- scratch_dir
Absolute path to the folder with the input to be processed. Other paths are relative to this one.
- mcr_cache_dir
Absolute path to MCR directory for the processing.
- exec_dir
Directory for executables
- renumber_motl_exec
Renumber motive list executable
- input_motl_fn
Relative path and name of the input MOTL file to be renumbered.
- output_motl_fn
Relative path and name of the output MOTL file.
- sort_row
If you want to have the output MOTL file sorted by a particular field before renumbering then specify it here.
- do_sequential
If the following is 1, particles will be completely renumbered from 1 to the number of particles in the motive list. If it is 0, particles will be renumbered in a way that preserves the original index while still removing any duplicate indices. As a guide you probably want to renumber sequentially after cleaning from initial oversampled coordinates, but do not want to renumber sequentially in other cases.
scratch_dir="${PWD}"
mcr_cache_dir="${scratch_dir}/mcr"
exec_dir="/net/dstore2/teraraid/dmorado/software/subTOM/bin"
renumber_motl_exec="${exec_dir}/MOTL/subtom_renumber_motl"
input_motl_fn="combinedmotl/allmotl_1.em"
output_motl_fn="combinedmotl/allmotl_unique_1.em"
sort_row="4"
do_sequential="0"