Seabird-Processing

Execute Seabird Processing Toolbox functions with Python.

Installation

Pre-requisites

An installation of the Seabird Processing Suite is required to run these modules since they simply provide an abstraction of the command line tools provided by Seabird.

Install with pip

To install this tool in your current python environment do:

pip install seabird-processing

Configure the tool with the location of your Seabird Processing Suite installation by setting the SBE_BIN_DIR environment variable. For example, if you installed the software to C:\Program Files (x86)\Seabird\SBEDataProcessing-Win32 then you would set the environment variable SBE_BIN_DIR=C:\Program Files (x86)\Seabird\SBEDataProcessing-Win32\. By default, it is assumed that the software is installed to C:\Program Files (x86)\Seabird\SBEDataProcessing-Win32.

Usage

There are two ways to use this library. The first is to use individual functions which correspond one-to-one with the Searbird processing modules. The second is to use the Batch class which allows you to chain together multiple processing modules.

Command line functions

from seabird_processing import dat_cnv, filter_

xmlcon = './xmlcon/19-7467.xmlcon'

cnvfile = dat_cnv('./seabird_data_file.hex', './output/dir', xmlcon, './psa/DatCnv.psa')
# "filter" is a reserved keyword, so this function is called "filter_"
filtered = filter_(cnvfile, './output/dir', xmlcon, './psa/AlignCTD.psa')
# ...

Batch processing

from seabird_processing import Batch, configs

xmlcon = './path/to/xmlcon/12-3456.xmlcon'

# Create a batch executor and configure each step
batch = Batch([
    configs.DatCnvConfig(
        # `output_file_suffix` is optional
        output_dir="./datcnv", output_file_suffix="_datcnv",
        xmlcon=xmlcon, psa='./path/to/DatCnv.psa'),
    configs.FilterConfig(
        output_dir="./filter", output_file_suffix="_filter",
        xmlcon=xmlcon, psa='./path/to/Filter.psa'),
    configs.AlignCTDConfig(
        output_dir="./alignctd", output_file_suffix="_alignctd",
        xmlcon=xmlcon, psa='./path/to/AlignCTD.psa'),
    configs.CellTMConfig(
        output_dir="./celltm", output_file_suffix="_celltm",
        xmlcon=xmlcon, psa='./path/to/CellTM.psa'),
    configs.LoopEditConfig(
        output_dir="./loopedit", output_file_suffix="_loopedit",
        xmlcon=xmlcon, psa='./path/to/LoopEdit.psa'),
    configs.DeriveConfig(
        output_dir="./derive", output_file_suffix="_derive",
        xmlcon=xmlcon, psa='./path/to/Derive.psa'),
    configs.DeriveTEOS10Config(
        output_dir="./deriveteos10", output_file_suffix="_deriveteos10",
        xmlcon=xmlcon, psa='./path/to/DeriveTEOS_10.psa'),
    configs.BinAvgConfig(
        output_dir="./binavg", output_file_suffix="_binavg",
        xmlcon=xmlcon, psa='./path/to/BinAvg.psa'),
])

batch.run("./*.hex")

# You may also run an individual Config object
converter = configs.DatCnvConfig(
    output_dir="./datcnv", output_file_suffix="_datcnv",
    xmlcon=xmlcon, psa='./path/to/DatCnv.psa'
)
converter.run("./some/file.hex")

Copyright and Licensing Information

See LICENSE for details.

Bugs / Feature requests

Please file bug reports and feature requests on GitHub. We also welcome pull requests to add functionality or fix bugs!