seabird-processing 0.2.0rc1

Python interface for calling Seabird CTD processing commands

Seabird-Processing

Python bindings for executing Seabird SBE processing tools.

Description

This library contains an API for executing seabird SBE processing modules on Seabird data files (hex and cnv). The modules all accept text as input which allows for more convenient access to the command line functions which would normally require a file path as input. Under the hood, this library simply saves temporary files which are then processed through SBE, read into memory, and returned as in-memory text.

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_PROCESSING_PATH 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_PROCESSING_PATH=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 SBE processing modules. The second is to use the Pipeline 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')
# ...

Pipeline processing

from seabird_processing import Batch, configs

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

# Create a pipeline with some config files
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!