collectfish

Collect data generated by thunderfish in a wavefish and a pulsefish table.

Command line arguments

collectfish --help

returns

usage: collectfish [-h] [--version] [-v] [-t {wave,pulse}] [-c] [-m N]
                   [-p N:M] [-w N] [-r COLUMN] [-s] [-i FILE:REC:TEMP]
                   [-q Q10] [-S] [-n NAME] [-o PATH]
                   [-f {dat,ascii,csv,rtai,md,tex,html,same}]
                   file [file ...]

Collect data generated by thunderfish in a wavefish and a pulsefish table.

positional arguments:
  file                  a *-wavefish.* or *-pulsefish.* file as generated by
                        thunderfish

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  -v                    verbosity level: -v for meta data coverage, -vv for
                        additional info on discarded recordings.
  -t {wave,pulse}       wave-type or pulse-type fish
  -c                    remove initial common directories from input files
  -m N                  maximum number of fish to be taken from each recording
  -p N:M                add properties of peak N to M of pulse-type EODs to
                        the table
  -w N                  add properties of first N harmonics of wave-type EODs
                        to the table
  -r COLUMN             columns to be removed from output table
  -s                    also write table with statistics
  -i FILE:REC:TEMP      insert rows from metadata table in FILE matching
                        recording in colum REC. The optional TEMP specifies a
                        column with temperatures to which EOD frequencies
                        should be adjusted
  -q Q10                Q10 value for adjusting EOD frequencies to a common
                        temperature
  -S                    skip recordings that are not contained in metadata
                        table
  -n NAME               name for summary files that is appended to "wavefish"
                        or "pulsefish"
  -o PATH               path where to store summary tables
  -f {dat,ascii,csv,rtai,md,tex,html,same}
                        file format used for saving summary tables ("same"
                        uses same format as input files)

version 1.9.3 by Benda-Lab (2019-2020)