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BioSonics Time Series

Data products for BioSonics Echosounders are described here.

Revision History

  • 2011XXXX: Initial data products released in manufacturer DT4 and MATLab mat formats.

Formats

This data is available in DT4 and MAT formats. Content descriptions and example files are provided below.

To produce the file, the following requirements apply:

  • A new DT4 file is started at the beginning of each day (midnight UTC exactly), or when the driver is restarted (this should account for configuration changes, site changes, etc).
  • The instrument date/time field is replaced using the NEPTUNE timestamp at the beginning of the log file (since this timestamp is more accurate than the instrument clock).
  • Although each channel/frequency pings simultaneously, simultaneous ping packets will have slightly different time stamps, usually separated by 100 milliseconds. This means simultaneous ping packets may end up in different DT4 files if they occur on either side of midnight. The only way to sort this out is to look at the times in the MAT files.
DT4

This format is specific to the manufacturer, and consists of sections called tuples (e.g., channel descriptor, time and ping tuples). When using BioSonics data acquisition software, data is normally stored in this way. Although we use custom-built drivers to communicate with our instruments, we can use the raw data in the log file to produce the DT4 file which can be interpreted by BioSonics post-processing software (most recent version available from BioSonics website) in play-back mode, and commercial software like EchoView.

A new file is generated each day, and whenever the driver is restarted. The reference time in the time tuple and the ping time in the ping tuples correspond to the times the measurements were received at the NEPTUNE Canada shore station (in place of the internal instrument clock values).

The format and tuple contents are further described in the manufacturer's documentation. However, there are two tuples that are not described in this document, but are regularly included in DT4s.

  • pulse tuple (0X0013) - describes the pulse type of the data for each configuration 
    06 00 13 00 00 00 01 00 00 00 0C 00  indicates that configuration #1 is raw data pulse type
06 00 13 00 00 00 02 00 00 00 0C 00  indicates that configuration #2 is raw data pulse type
06 00 13 00 00 00 03 00 00 00 0C 00  indicates that configuration #3 is raw data pulse type
  • marker tuple (0X0010 and 0X0020) - used to indicate the start and end of the time & ping tuples 
    04 00 10 00 01 00 00 00 0A 00        signifies start of time/ping data
04 00 10 00 02 00 00 00 0A 00        signifies end of time/ping data
MAT

MAT files (v5) can be opened using MathWorks MATLAB 5.0 or later (7+ preferred). A new file a created every two hours from the start of the parent DT4 file. The file contains the following structures: meta, data, units.

meta: structure containing the following metadata fields, generated entirely from NEPTUNE's database.

  • deviceID: A unique identifier to represent the instrument within the NEPTUNE Canada network.
  • creationDate:Date and time (using ISO8601 format) that the data product was produced. This is a valuable indicator for comparing to other revisions of the same data product.
  • deviceName: A name given to the instrument.
  • deviceCode: A unique string for the instrument which is used to generate data product filenames.
  • deviceCategory: Device category to list under data search ('Echosounder').
  • lat: Obtained at time of deployment.
  • lon: Obtained at time of deployment.
  • depth: Obtained at time of deployment.
  • deviceHeading: Obtained at time of deployment.
  • siteName: Name corresponding to its latitude, longitude, depth position.
  • locationName: The node of the NEPTUNE Canada observatory. Each location contains many sites.
  • deploymentDateFrom: The date of the deployment on which the data was acquired
  • deploymentDateTo: The date of the end of the deployment on which the data was acquired
  • samplingPeriod: Sampling rate of the instrument in seconds.
  • searchID: The search ID from the data search details structure used to find this data (not applicable to post-processed MAT files)

data: structured array containing the BioSonics data (one structure per configuration in cycle), having the following fields which pertain to the dt4 contents (for details, refer to the manufacturer manual).

  • name: serial number
  • frequency: transducer frequency (Hz)
  • time: datenum vector, UTC timestamp (time source is NEPTUNE Canada shore station)
  • range: vector of distance to each bin
  • pingnum: ping number
  • vals: amplitude of return signal (AD Counts - main data matrix)
  • nsamps: number of samples in the ping tuples (read from the ping tuple)
  • env: structure containing environmental configuration values
    • absorb: configuration absorption coefficient
    • sv: configuration sound velocity
    • temperature: configuration temperature
    • salinity: configuration salinity
    • power: transmit power reduction factor
    • numChan: total number of frequencies/channels/configurations in the dt4 file
  • snd: structure containing details of the channel descriptor tuple
    • address: configuration number
    • npings: total number of pings in the dt4
    • npingsExtracted: total number of pings extracted from the dt4
    • sampperping: samples per ping (this is usually equal to max(data.nsamps) )
    • sampperiod: time between successive samples in a ping
    • pingperiod: number of seconds between successive pings
    • pulselen: duration of transmitted pulse
    • blank: initial blanking (number of samples skipped before data recording begins for each ping)
    • threshold: data collection threshold
    • rxee: receiver EEPROM image structure (can ignore split-beam options since that feature is not included in this instrument)
      • ssn: transducer SN
      • calDateNum: last calibration date (Matlab datenum)
      • calDateStr: last calibration date (datestring)
      • calTech: initials of technician performing calibration
      • sl: source level (0.1 dB)
      • rs: receiver sensitivity for main element (0.1 dB)
      • rsw: receiver sensitivity for wide-beam (0.1 dB)
      • pdpy: sign of split beam y-axis (zero=positive, nonzero=negative)
      • pdpx: sign of split beam x-axis (zero=positive, nonzero=negative)
      • noiseFloor: noise floor of transducer (AD Counts) due to system noise
      • transducerType: transducer hardware type (0 for single-beam, 3 for dual-beam, 4 for split-beam)
      • frequency: transducer frequency (Hz)
      • pdy: absolute value of the split-beam y-axis element separation (0.01 mm)
      • pdx: absolute value of the split-beam x-axis element separation (0.01 mm)
      • phpy: split-beam y-axis element polarity
      • phpx: split-beam x-axis element polarity
      • aoy: split-beam y-axis angle offset (0.01 degrees)
      • aox: split-beam x-axis angle offset (0.01 degrees)
      • bwy: y-axis -3dB one-way beam width for the main element (0.1 degrees)
      • bwx: x-axis -3dB one-way beam width for the main element (0.1 degrees)
      • sampleRate: sampling rate of the A/D converter (Hz), usually 41667.
      • bwwwy: y-axis -3dB one-way beam width for wide-beam or phase elements (0.1 degrees)
      • bwwx: x-axis -3dB one-way beam width for wide-beam or phase elements (0.1 degrees)
      • phy: split-beam y-axis phase aperture (0.1 degrees)
      • phx: split-beam x-axis phase aperture (0.1 degrees)
    • ccor: calibration correction
  • opmode: operating mode

units: structure containing unit of measure for fields in structures above. For instance, units.lat='degrees N'.

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