Add Frequency and Time to Pamguard Whistle Binaries

Description

Adds items freq and time to a Pamguard binary file from the Whistle & Moan Detector

Usage

contourToFreq(data, verbose = FALSE)

Arguments

Value

data with items freq and time added. These use the calculated FFT window length, hope size, and sample rate to compute the frequency and time values of the saved whistle contour

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Examples

# load example whistle file
wmFile <- system.file('extdata', 'WM.pgdf', package='PamBinaries')
wmData <- loadPamguardBinaryFile(wmFile)
# converts contour and FFT slice numbers to frequency and time values
wmData <- contourToFreq(wmData)
wmData$data[[1]]$contour
wmData$data[[1]]$freq
wmData$data[[1]]$time

Convert Pamguard Numeric Date to POSIXct

Description

a simple helper to convert Pamguard's numeric date to POSIXct format

Usage

convertPgDate(dateNum)

Arguments

Value

A POSIXct date in UTC

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Examples

# load the example click binary data, leaving date as numeric
clickFile <- system.file('extdata', 'Click.pgdf', package='PamBinaries')
clickData <- loadPamguardBinaryFile(clickFile, convertDate = FALSE)
# convert date to POSIXct
convertPgDate(clickData$data[[1]]$date)

Count Number of Active Channels

Description

Counts the number of active channels given a channel mapping

Usage

countChannels(channelMap)

Arguments

Value

The number of active channels (number of ones)

Note

Altered from original script to loop through 30 instead 32 because R stores only 32 bit integers. Should not ever have enough channels for this to matter.

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Convert Date Number to Milliseconds

Description

Converts numeric date to millisecond date.

Usage

dateNumToMillis(datenum)

Arguments

Value

Date as milliseconds

Note

Conversion to milliseconds to match how Java stores dates. Doesn't appear to ever be used.

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Load and Format Background Noise Data

Description

Reads and formats background noise data from Pamguard binary files or if not present in the original file will try to read the accompanying .pgnf noise file if it exists

Usage

loadBackgroundNoise(x)

plotBackgroundNoise(x)

combineBackgroundNoise(x, forPlot = FALSE)

Arguments

Value

A list with times storing the POSIXct time of each background measurement, and background a matrix of background values. For binary data based on spectrogram measurements, there will also be freq the frequency in Hertz for each column of background measurement

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Examples

# load the example click binary data, leaving date as numeric
gplFile <- system.file('extdata', 'GPL.pgdf', package='PamBinaries')
gplNoise <- loadBackgroundNoise(gplFile)
print(gplNoise)
plotBackgroundNoise(gplNoise)

Load Pamguard Binary File

Description

This function will load in the data from a Pamguard binary file. It will figure out the type of data being read based on the header of the file. All functions based on Matlab code written by Michael Oswald.

Usage

loadPamguardBinaryFile(
  fileName,
  skipLarge = FALSE,
  skipData = FALSE,
  debug = FALSE,
  keepUIDs = NULL,
  convertDate = FALSE,
  ...
)

Arguments

Value

This function returns a list containing two objects. Data contains all the binary data read. fileInfo contains metadata information for the file.

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Examples

# read example whistle data
wmFile <- system.file('extdata', 'WM.pgdf', package='PamBinaries')
whistleData <- loadPamguardBinaryFile(wmFile)
# works the same for different kinds of binary files
clickFile <- system.file('extdata', 'Click.pgdf', package='PamBinaries')
clickData <- loadPamguardBinaryFile(clickFile)
# convert date to POSIXct (default does not because it is faster)
clickPOSIX <- loadPamguardBinaryFile(clickFile, convertDate = TRUE)
clickData$data[[1]]$date
clickPOSIX$data[[1]]$date
# read only the fileInfo portion, has empty $data item
clickInfo <- loadPamguardBinaryFile(clickFile, skipData = TRUE)
# skip reading the large click waveforms, much faster if you dont need them
clickLess <- loadPamguardBinaryFile(clickFile, skipLarge = TRUE)
object.size(clickData)
object.size(clickLess)
# only read specific UID numbers
clickSpecific <- loadPamguardBinaryFile(clickFile, keepUIDs = c(4000006, 4000007))
names(clickSpecific$data)

Convert Java Millisecond Time to R

Description

Converts Java millisecond time into numeric time that R uses.

Usage

millisToDateNum(millis)

Arguments

Value

Numeric time used by R.

Note

Original function was more relevant as Matlab and Java use different time origins. Java & R both use 1970-01-01, but Java stores as milliseconds vs seconds in R.

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Pamguard Binary Data

Description

A wrapper for reading various types of binary data.

Usage

pamBinRead(
  fid,
  what = c("int8", "int16", "int32", "int64", "uint8", "uint16", "float", "double",
    "character"),
  n,
  seek = FALSE
)

Arguments

Value

Data of the type and number specified.

Note

R does not natively support 64-bit integers. Current implementation is to read an int64 as 8 separate 1-byte raw pieces. These are converted from hexidecimal, shifted by the appropriate power of 2, then summed. Currently cannot read more than one int64 at a time, shouldn't be necessary.

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Convert a PamBinary Object to Data Frame

Description

Converts a PamBinary object into a data frame. The data.frame will combine all of the data from the data part of the PamBinary object, but will not include annotations data, click waveforms, DIFAR demux data, or contours from the WMD detector. These are skipped because they are either inconsistent in their size, or are large objects. The function pbToDf is also called when as.data.frame is called on a PamBinary class object.

Usage

pbToDf(pb, templateNames = NULL)

Arguments

Value

a data.frame containing most of the binary data read in. Will not contain most annotation data, click waveforms, DIFAR demux data, or contour information from WMD detector. These are skipped because they are either incosistent in their size, or are large objects. Click template classifier information will be included if templateNames are supplied. If binary is from noise band monitor, noise data will be stored in columns noiseMean, noisePeak, and octaveBands, and the resulting dataframe will have a row for each separate octave band stored

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Examples

# load the data
clickFile <- system.file('extdata', 'Click.pgdf', package='PamBinaries')
clickData <- loadPamguardBinaryFile(clickFile)
# two methods two convert to a dataframe
head(pbToDf(clickData))
head(data.frame(clickData))

Plot Whistle Contour

Description

Plots the entire whistle contour saved in a Pamguard Whistle & Moan Detector binary file, highlighting the selected contour

Usage

plotWMD(data, id = 1, ...)

Arguments

Value

A ggplot object

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Examples

# load example whistle file
wmFile <- system.file('extdata', 'WM.pgdf', package='PamBinaries')
wmData <- loadPamguardBinaryFile(wmFile)
plotWMD(wmData, 1)
plotWMD(wmData, 2)

Read AIS Data

Description

Reads binary data stored by the AIS Processing module.

Usage

readAISData(fid, fileInfo, data, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Beam Former Annotation

Description

Reads binary data stored by beam former annotation module

Usage

readBeamFormerAnnotation(fid, fileInfo, anVersion, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Bearing Annotation

Description

Reads binary data stored by bearing annotation module

Usage

readBearingAnnotation(fid, fileInfo, anVersion, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Click Detector Background data

Description

Reads in the background data saved by the Click Detector

Usage

readClickBackground(fid, fileInfo, data)

Arguments

Value

a structure containing data from a single object

Author(s)

Michael Oswald taiki.sakai@noaa.gov

Read Click Classifier Annotation

Description

Reads binary data stored by Click Classifier annotations

Usage

readClickClsfrAnnotation(fid, fileInfo, debug = FALSE)

Arguments

Value

a vector of click classifiers, represented by the click type flag

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Click Data

Description

Reads binary data stored by the Click Detector module.

Usage

readClickData(
  fid,
  fileInfo,
  data,
  skipLarge = FALSE,
  debug = FALSE,
  getWave,
  onlyWave
)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Click Footer

Description

Reads module footer information for the Click Detector module. Note that sometimes there is no additional footer information, so check first whether or not the binaryLength variable is 0.

Usage

readClickFooter(file)

Arguments

Value

footer information for Click Detector module

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Click Trigger Level

Description

Reads binary data stored by the click detector trigger

Usage

readClickTriggerData(fid, fileInfo, data, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Click Trigger Header

Description

Reads file header information specific to the click trigger module

Usage

readClickTriggerHeader(file)

Arguments

Value

header information for the click trigger

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Clip Data

Description

Reads binary data stored by the Clip Generator module.

Usage

readClipData(fid, fileInfo, data, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Deep Learning Annotation

Description

Reads binary data stored by the DbHt module.

Usage

readDLAnnotation(fid, fileInfo, anVersion, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Deep Learning Detection Data

Description

Reads binary data stored by the DbHt module.

Usage

readDLDetData(fid, fileInfo, data, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Deep Learning Model Data

Description

Reads binary data stored by the Deep Learning Model module

Usage

readDLModelData(fid, fileInfo, data, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read DbHt Data

Description

Reads binary data stored by the DbHt module.

Usage

readDbHtData(fid, fileInfo, data, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Difar Data

Description

Reads binary data stored by the Difar Processing module.

Usage

readDifarData(fid, fileInfo, data, skipLarge = FALSE, debug = FALSE)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read File Footer

Description

Reads in the binary file footer. The input variable version is the file format read in from the file header. As of version 3, the file footer includes the lowest and highest UID values in the file.

Usage

readFileFooterInfo(fid, version)

Arguments

Value

footer information common to all files

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read File Header

Description

Reads file header information common to all files

Usage

readFileHeader(file, readExtra = FALSE)

Arguments

Value

header information common to all files

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read GPL Detections

Description

Reads binary data stored by the GPL Module.

Usage

readGPLDetections(fid, fileInfo, data, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Michael Oswald mo55@st-andrews.ac.uk

Read Java UTF-8 String

Description

Reads a Java UTF-8 string. The first 2 bytes are the length of the string, then the string itself.

Usage

readJavaUTFString(file)

Arguments

Value

the string and its length

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read LTSA Data

Description

Reads binary data stored by the LTSA module.

Usage

readLTSAData(fid, fileInfo, data, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read LTSA Header

Description

Reads file header information specific to the LTSA module

Usage

readLTSAHeader(file)

Arguments

Value

header information for the LTSA module

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Matched Classifier Annotation

Description

Reads annotations from the matched click classifier. The matched matched click classifier annotates click detections with a threshold, matchcorr and rejectcorr values. The threshold value is used in the binary classification process. If it exceeds a hard value then the click is classified with the set type. The matchcorr and rejectcorr values are simply the correlation values of the match and reject templates with the click.

Usage

readMatchClsfrAnnotation(fid, fileInfo, anVersion, debug = FALSE)

Arguments

Value

a vector with the threshold, matchcorr, and rejectcorr values. See description.

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Noise Band Data

Description

Reads binary data stored by the Noise Band Monitor.

Usage

readNoiseBandData(fid, fileInfo, data, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Noise Monitor Data

Description

Reads binary data stored by the Noise Monitor.

Usage

readNoiseMonData(fid, fileInfo, data, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Noise Monitor Header

Description

Reads file header information specific to the Noise Monitor module

Usage

readNoiseMonHeader(file)

Arguments

Value

header information for the Noise Monitor module

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Pamguard Data

Description

Reads in the object data that is common to all modules. This reads up to (but not including) the object binary length, and then calls a function to read the module-specific data.

Usage

readPamData(fid, fileInfo, skipLarge, debug = FALSE, keepUIDs, ...)

Arguments

Value

a structure containing data from a single object

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Right Whale Edge Detector Data

Description

Reads binary data stored by the Right Whale Edge Detector.

Usage

readRWEDetectorData(fid, fileInfo, data, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Spectral Background data

Description

Reads in the background data saved by various detectors (e.g WMD, Right Whale Edge Detector, etc) EXCEPT FOR the Click Detector

Usage

readSpectralBackground(fid, fileInfo, data)

Arguments

Value

a structure containing data from a single object

Author(s)

Michael Oswald taiki.sakai@noaa.gov

Read Standard Module Footer

Description

Reads the module footer information common to all modules. Differs from the legacy code in that it does not read in or skip any information specific to a module.

Usage

readStdModuleFooter(file)

Arguments

Value

footer information common to all modules

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Standard Module Header

Description

Reads the module header information common to all modules. Differs from the legacy code in that it does not read in or skip any information specific to a module.

Usage

readStdModuleHeader(file)

Arguments

Value

header information common to all modules

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read TDBL Annotation

Description

Reads binary data stored by TDBL annotation module

Usage

readTDBLAnnotation(fid, fileInfo, anVersion, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Target Motion Annotation

Description

Reads binary data stored by beam former annotation module

Usage

readTMAnnotation(fid, fileInfo, anVersion, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read a Tritech Track

Description

Reads binary data stored by the Gemini Tritech Module

Usage

readTritechTrack(fid, fileInfo, data, debug = FALSE, ...)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Benjamin Blundell bjb8@st-andrews.ac.uk

Read Whistle and Moan Data

Description

Reads binary data stored by the Whistle & Moan Detector

Usage

readWMDData(fid, fileInfo, data, skipLarge = FALSE, debug = FALSE)

Arguments

Value

a structure containing data from a single object, and a logical flag if an error has occurred

Author(s)

Taiki Sakai taiki.sakai@noaa.gov

Read Whistle & Moan Detector Header

Description

Reads file header information specific to the Whistle & Moan Detector module

Usage

readWMDHeader(file)

Arguments

Value

header information for the Whistle & Moan Detector module

Author(s)

Taiki Sakai taiki.sakai@noaa.gov