seismogram-pipeline

Directory structure

• lib/ the meat of the repo: image processing scripts and utilities
• / command line entry points for the various scripts in lib/
• /in sample input files

Dependencies

The python scripts are written for Python 2.7. An easy way to install most of the dependencies is with Anaconda.

You'll also need geojson:

pip install geojson

and docopt:

pip install docopt==0.6.1

There may eventually be Netlogo, MATLAB, or javascript files in this repository.

Use

All the scripts in the / directory are runnable from a command line like so:

python name_of_script.py

Running a script with no arguments (like in the above example) will output a usage message that explains what arguments are required and what arguments are optional. For example, running python get_all_metadata.py outputs:

Usage:
  pipeline.py --image <filename> --output <directory> [--scale <scale>] [--debug <directory>]
  pipeline.py -h | --help

Arguments in [square brackets] are optional, whereas unbracketed arguments are required.

python get_all_metadata.py -h or --help outputs a more detailed help message:

Description:
  Generate all metadata (ROI, meanlines, intersections, and segments as of 6/10/2015)
  for a single seismogram.

Usage:
  pipeline.py --image <filename> --output <directory> [--scale <scale>] [--debug <directory>]
  pipeline.py -h | --help

Options:
  -h --help             Show this screen.
  --image <filename>    Filename of seismogram.
  --output <directory>  Save metadata in <directory>.
  --scale <scale>       1 for a full-size seismogram, 0.25 for quarter-size, etc. [default: 1]
  --debug <directory>   Save intermediate steps as images for inspection in <directory>.

The repository comes with a sample quarter-size seismogram in the in/ directory. The command to generate all metadata for this image would be:

python get_all_metadata.py --image in/dummy-seismo-small.png --output some-directory --scale 0.25

And if you want to see images of the intermediate processing steps, use the --debug argument: --debug some-debug-directory.