Package: dbdreader
DBDREADERChange logVersion 0.5.5Makes MultiDBD’s get_CTD_sync method compatible with RBR CTD data.Version 0.5.4Adds support for reading compressed data files for windows platform.Improved building environmentVersion 0.5.1Adds support for reading compressed data filesdbdrename.py now accepts -x and -X options to rename compressed data files as uncompressed data filesVersion 0.4.15Modifies sorting key algorithm to the DBDList class. This fixes a
bug when glider data filenames are composed of a glider name that
contains a dash. For example, filenames such as hereon-amadeus-2019-3-1.sbd
would fail, but are valid now.Version 0.4.14Adds a new option to the get() method of the MultiDBD class, where
if the keyword include_sources=True, for each parameter an
additional list is returned that has for each data point a reference
to the DBD instance that produced the data point. This allows to
query the source of a specific data point.This merges the (modified) pull request #14 by MCazaly.Version 0.4.13Modifies behaviour when the user requests a parameter that has no
data. If the requested parameter is not a valid glider sensor name,
assume a user-error and raise an exception, otherwise return an
empty array.This behaviour fixes a bug for MultiDBD:
each file opened with MultiDBD would fail to produce any data if one or
more parameters that are asked for, are not present in the file.New behaviour returns data for the exisiting parameters (only); empty
array for the missing parameters (or nans if return_nans=True)Concludes pull request #16 by jklymak.Version 0.4.12PatternSelect now accepts the option of a non-standard cache
directory.
Thanks to hawesie.MultiDBD’s get_sync() now returns nan’s for those parameters for
which no data exist, provided that at least one of the requested
parameters contains data.Version 0.4.11Version 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 0.4.10Includes 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 0.4.9Bug 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 0.4.8Support 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 0.4.7Bug fix for reading dbd files on Windows.a wheel provided for CPython 3.9 on Windows 64 bit.Version 0.4.6Added  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 0.4.5dbdreader now ignores the first line of data in each binary filedbdreader checks whether the value of the parameters read are finite, ignoring them if they are not.SynopsisSlocum 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
moduledbdreaderprovides the utilities to extract the data from the
binary files, so that they can be further analysed.Installation (linux)The python moduledbdreadercan 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 dosudo dnf installpython3-devel, orsudoapt-getinstallpython3-devon
Ubuntu.Furthermore, as of version 0.5, which adds support for reading
compressed files, a dependency on the lz4 library is introduced. If
available, the system-wide library will be used (recommended
approach). Alternatively, the lz4.[ch] files from the original source
(https://github.com/lz4/lz4), and included in this package, will be
compiled into the C-extension. To install the system-wide lz4 library
on Fedora you would dosudo dnf installlz4-devellz4-libs. On
Ubuntu this can be achieved bysudoapt-getinstallliblz4-devliblz4-1.Alternatively, dbdreader can also be installed from PyPi, usingpip3 install dbdreader.Installation on WindowsIf 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 boxpython developmentduring the setup. Once installed
dbdreader can be installed, and the C-extension should be compiled
automatically.Installiation using pip, for example as inpy-mpip install dbdreaderalso 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: dbdreaderDocumentationComprehensive documentation is provided athttps://dbdreader.readthedocs.io/en/latest/Quick-startFor 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.ExamplesTo 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 2Python 2.7 is not supported anymore. However, you should be able to
make the code able to run on python2.7 using thefuturepackage.pip install futurepasteurize dbdreader.For details seehttp://python-future.org/pasteurize.html.