dbdreader 0.4.11

A python module to access binary data files generated by Teledyne WebbResearch gliders

DBDREADER

Change log

Version 0.4.11

• Version 0.4.9 introduced a bug that in some rare circumstances caused segmentation faults. This has been fixed.

• Merged pull request by roje-bodc with improved error handling in case of missing cache files. If a DbdError occurs due to a missing cache file, detailed information can be obtained from the .data property of the exception instance.

Version 0.4.10

• Includes pull request by jklymak, which allows dbdreader to deal with empty files, and files capitalised file extensions, as well as a check on the encoding version.

• Includes a bug fix when raising an exception when handling a prior exception in case of reading problematic files.

• Assumes that if the first parameter given to MultiDBD is a string, the user did not mean to provide a list of filename strings, but a pattern. An error is raised if pattern is specified explicitly when filenames is given as a string.

Version 0.4.9

• Bug fix for handling inf values correctly (issue #8). Thanks to jr3cermak for spotting this bug.

• Bug fix for incorrect behaviour when reading the time parameter explicitly for example xxx.get(“m_present_time”).

Version 0.4.8

• Support for reading {demnst}bd files from G3S gliders (issue #6). (Thanks to Owain Jones)

• Bug fix for correctly throwing an exception when cache file is missing(issue #5)

Version 0.4.7

• Bug fix for reading dbd files on Windows.

• a wheel provided for CPython 3.9 on Windows 64 bit.

Version 0.4.6

• Added get_CTD_sync, a convenience method to retrieve CTD data, and other parameters mapped on the CTD time stamps. Also ensures time stamps are monotonically increasing.

• Adds bounds to what values of latitude and longitude are considered valid.

Version 0.4.5

• dbdreader now ignores the first line of data in each binary file

• dbdreader checks whether the value of the parameters read are finite, ignoring them if they are not.

Synopsis

Slocum ocean gliders are autonomous underwater vehicles, used for making oceanographic measurements. The data that these devices and their sensors collect, are stored in binary data files. The python module dbdreader provides the utilities to extract the data from the binary files, so that they can be further analysed.

Installation

The python module dbdreader can be installed from source, using the standard method to install python code. Note that this method requires an C-extension to be build. (The actual reading from files is done in C for speed.) In order to build the extension successfully, you would need a C-compiler. On Linux, this can be gcc, with supporting development/header files for python. On Fedora you would do sudo dnf install python3-devel.

Alternatively, dbdreader can also be installed from PyPi, using pip3 install dbdreader.

Installation on Windows

If you want to install dbdreader from source, you will need a C compiler as well to compile the C-extension. Besides the Python environment you will need to install the Microsoft Visual Studio Compiler. The community edition will do. When installing MVSC, make sure you tick the box python development during the setup. Once installed dbdreader can be installed, and the C-extension should be compiled automatically.

Installiation using pip, for example as in py -m pip install dbdreader also requires the C compiler. For Python version 3.9, however, a wheel is provided, which can be installed adding the option --only-binary :all: to the pip command:

$ pip install --only-binary :all: dbdreader

Documentation

Comprehensive documentation is provided at https://dbdreader.readthedocs.io/en/latest/

Quick-start

For the impatient…

The dbdreader module implements a class DBD() which provides the machinery to read a single dbd file. The most commonly used methods are:

• get(parametername)

• get_sync(parametername, *other_parameternames)

The first method returs a tuple with time and values for requested parameter. The second method, returns a tuple with time and values of the first parameter requested, and of all further listed parameters, all interpolated on the time base of the first parameter.

Mostly, it is not one file that is required to be processed, but a number of them. This interface is implemented by the MultiDBD class. Files can either be specified as a list of filenames, or as a pattern using wildcards.

Examples

To read a single file:

>>> dbd = DBD("00010010.dbd")
>>> t, pitch = dbd.get("m_pitch")
>>> t, hdg, ptch, roll = dbd.get_sync("m_heading", "m_pitch", "m_roll)

Or, doing the same, but using both dbd and ebd files:

>>> dbd = DBD(pattern="00010010.[de]bd")
>>> t, pitch = dbd.get("m_pitch")
>>> t, hdg, ptch, roll = dbd.get_sync("m_heading", "m_pitch", "m_roll")
>>> t, p_ctd, p_nav = dbd.get_sync("sci_water_pressure", "m_water_pressure")

Python 2

Python 2.7 is not supported anymore. However, you should be able to make the code able to run on python2.7 using the future package.

• pip install future

• pasteurize dbdreader.

For details see http://python-future.org/pasteurize.html.