DOPpy

Read binary files (.bdd) of DOP measurement devices.

The DOP measurement device series by Signal Processing implements the ultrasound Doppler velocimetry (UDV) measurement method to record velocity profiles in liquids. The measurement data can be saved in an ascii file (.ADD = ascii DOP data) or a binary file (.BDD = binary DOP data). While the ascii is human readable and relatively easy to import, it is generally larger than the binary format and does only contain the time, position and velocity information of the measurement. The binary format contains much more information (measurement parameters & settings) as well as having a more compact file-size. The downside is of course that the binary structure has to be decoded. The job of DOPpy is to read the binary data of a BDD-file and provide it for further analysis within a Python console or script.

Currently only files of the DOP2000 and DOP3000/3010 systems are supported. DOP4000 files are similar to the DOP3000 formats, but were not tested.

Requirements

DOPpy was written in Python 3.6 but should be compatible with Python 2.7. Required modules are numpy and matplotlib.

Installation

Just copy the the DOPpy.py file into the folder of your script or in any folder that is included in Python's PATH variable to access it from any script or a Python console.

Usage

This section is a quick overview of the features of DOPpy. For more information refer to the doc-strings of the respective functions.

Put the file DOPpy.py somwhere Python can find it (e.g. the folder of your script or a folder listed in the PATH variable). Call the function DOP(fname) from the module with the absolute or relative path to the BDD-file fname. The function determines which version (DOP2000 or 3000) the file is and returns a DOP2000 or DOP3000 instance, respectively.

import DOP from DOPpy
bdd = DOP('path/to/file.bdd')

Getting Parameters & Data

These classes have all available informations from the read file stored. They are subclasses of DOPBase. Every parameter of the file can be retrieved either by using the method bdd.getParam(param) or by treating the instance as a dictionary bdd[param], where param is a string with the name of the parameter. All available parameters can be retrieved with the bdd.keys() method. Since there can be a lot of parameters, a list of all parameters that contain a search string can be retrieved by calling bdd.keysSearch(searchterm). Channel-specific parameters are named with a prefix 'ch1_' followed by the name (e.g. 'ch2_prf' gives the pulse repetition frequency of channel 2). The available channel-specific parameter names can be retrieved with bdd.keysChannel(channel).

Additionally there are some predefined methods to retrieve often used data:

bdd.getChannels() returns the list of channels that were used in the measurement.
bdd.getProfileType(channel) returns the profile types that where recorded in a channel.
bdd.getTime(channel) returns the timestamps of the channel in seconds.
bdd.getDepth(channel) returns the gate depths of the channel in millimeter.
bdd.getVelocity(channel) returns the measured velocity of the channel in meter per second as a 2D numpy-array. The first dimension is the time, the second dimension the depth.
bdd.getEcho(channel) returns the echo amplitude of the channel as a 2D numpy-array. The first dimension is the time, the second dimension the depth.
bdd.getChannelParam(param, channel) returns the value of the channel-specific parameter given in param of the channel (see bdd.keysChannel).

For all these methods channel can be an integer or a list of integers. In the latter case a list of values is returned. If channel is omitted or set to None, it defaults to all recorded channels (see bdd.getChannels). These methods raise an error if the data is not available for at least one requested channel.

bdd.printSettings(channel) prints relevant operation parameters that were used during the measurement with the given channel. The mandatory argument channel is an integer.

Displaying Measurements

While DOPpy is primarily designed to import the data into python a couple of functions for quick visualisation of the measured data are available:

DOPBase.imshow(profile, channel) displays a color-plot of the profile with type profile for the specified channel over time and depth. See bdd.getChannels and bdd.getProfileType for available channels and their profile types, respectively.
bdd.replay(profile, channel) plots an animation of the profile-snapshots with type profile for the specified channel over the depth. See bdd.getChannels and bdd.getProfileType for available channels and their profile types, respectively.

For both methods channel can be an integer or a list of integers. They raise an error if the data is not available for at least one requested channel.

Notes / Known bugs

2D/3D-component measurements are currently not supported.
Very old DOP2000 file versions might not be read correctly. The script was tested with file version 'BINWDOPV4.06.1' .

Changelog

v2.13:

Implements the new DOPBase.imshow method for visualisation of the measured profiles over time and depth. It is the preferred method over DOPBase.contour to display data on an equidistant time and depth grid (faster, less memory intensive and no need for color levels).
Both DOPBase.imshow and DOPBase.contour show the channel number as the axes title and the profile name (without units) as the colorbar label.
If no velocity or echo is recorded, the respective maximum value is now set to NaN (channel parameters 'veloMax' and 'echoMax'). This avoids KeyError messages due to a missing data entry (e.g. in DOPBase.PrintSettings).
Improved error messages if a missing parameter is requested.

v2.12:

The DOPBase.printSettings method now also prints parameters resulting from the operation parameters (maximum velocity and depth). A spelling error in the output was corrected.

v2.11:

Corrected processing of the DOP3000 'aquisitionRate'-parameter.
The methods DOPBase._read and DOPBase._refine now raise an exception if they are called directly or are not redefined by a subclass.
Added the ability to replace parameter values from the file. See the DOP docstring for details.

v2.10:

Optimized code for reading the BDD-files (for DOP2000 and DOP3000), which is now less memory intensive. This allows larger files to be read faster and with less possibility of an Memory Error. The raw measurement data from the file are by default not saved any more. This behaviour can be changed by setting the saveMeas argument to True in the DOP-function.
Transformed certain parameters from their raw value to sensible ones used by the DOP-software. The raw parameter values are stored with an suffix '_file' to the parameter name. Examples: emitting power, TGC mode, sampling volume (DOP3000 only), spatial filter bandwidth, sensitivity.
Added the DOPBase.printSettings method to display important operation parameters used in the measurement.
Corrected axis labels in DOPBase.contour and DOPBase.replay and fixed handling of timerange and depthrange arguments in DOPBase.contour.
When decoding the comment string any character that does not fit the used codec is now ignored. This behaviour can be changed with the decode_errors keyword-argument for the function DOP.

v2.04:

Corrected time-calculation for DOP2000.

v2.03:

Imports true division from __future__ to avoid incompatibilities for use with Python 2.7 when dividing by integers.
Corrected a typo in keysChannel.

v2.02:

Fixed Doppler angle in velocity calculation of DOP3000 and added Doppler angle in velocity calculation of DOP2000.
Added DOPBase.removeAliasing to remove aliasing effects for smooth velocity data.
Added the option to plot custom horizontal and vertical lines in the DOPBase.replay method (see the Keyword-Argument section in the method's documentation).

v2.01:

Removed aliasing from echo-profile.
Added maxtimes argument to DOPBase.contour to avoid RAM overflow.

v2.00:

Initial "release"

License

pyZerrenner/DOPpy

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