vdat_convert: Convert an Innovasea VRL or VDAT file to a Fathom CSV file

In ocean-tracking-network/glatos: A package for the Great Lakes Acoustic Telemetry Observation System

Convert an Innovasea VRL or VDAT file to a Fathom CSV file

Description

Use Innovasea's VDAT command line program VDAT.exe (distributed with Fathom Connect software) to make a CSV file containing data from a VRL or VDAT file in Fathom CSV format.

Usage

vdat_convert(
  src,
  out_dir = NULL,
  output_format = "csv.fathom",
  overwrite = FALSE,
  recursive = FALSE,
  vdat_exe_path = NULL,
  skip_pattern = "-RLD_",
  show_progress = TRUE,
  diagn = FALSE,
  export_settings = NULL
)

Arguments

src	Character string with path and name of a detection file (VDAT or VRL), a vector of file names, or a directory containing files. If only file name is given, then the file must be located in the working directory.
out_dir	Optional character string with directory where CSV files will be written. If NULL (default) then each file will be written to the same directory as its source file.
output_format	Character string with output format. Options are: "csv.fathom" (default) writes a single CSV file (for each input file) with multiple record types interleaved; "csv.fathom.split" writes a folder (for each input file) containing a separate CSV for each record type.
overwrite	Logical. If TRUE, output CSV file(s) will overwrite existing CSV file(s) with same name in out_dir. If FALSE (default), any output files that already exist in out_dir will be skipped, with warning.
recursive	Logical. If TRUE and src is a directory, then all VRL/VDAT files in all subdirectories of src will be converted. Default is FALSE. Ignored if src is a not directory.
vdat_exe_path	The full path to VDAT.exe. If NULL (default) then the path to VDAT.exe must be in the PATH environment variable of the system. See check_vdat.
skip_pattern	A regular expression used to exclude files from processing. Default value "-RLD_" will exclude "RAW LOG" files. Ignored if src contains file names.
show_progress	Logical. Indicates if progress bar should be shown.
diagn	Logical. Indicates if errors or warnings message (from vdat.exe) should be displayed (default = FALSE).
export_settings	(NOT YET IMPLEMENTED). Placeholder for future specification of other options available via Fathom Data Export app. (E.g., 'Data Types to Include', 'Data Filter', 'Filename Suffix', 'Time Offset in Hours', 'Split CSV by UTC Day'.)

Details

If src is a directory, then all source files in that directory (including all subdirectories if recursive = TRUE) with supported extensions (currently "vrl" and "vdat") will be converted to CSV. Otherwise, only those files specified in src will be converted.

Conversion is done by system call to the Innovasea program VDAT.exe (included with Innovasea's Fathom Connect software; available at https://support.fishtracking.innovasea.com/s/downloads). VDAT.exe must be available at the location specified by vdat_exe_path or via system PATH environment variable. See also check_vdat.

Value

A character string or vector with the full path and name of each output file, including files that were skipped (when output file exists and overwrite = FALSE).

Output

Output depends on output_format:

If output_format = "csv.fathom": A comma-separated-values (CSV) text file in Innovasea's Fathom CSV format for each input VRL/VDAT file. Each CSV is named the same (except for extension) as the source file (e.g., VR2W_109924_20110718_1.csv).

If output_format = "csv.fathom.split": A directory containing a set of CSV files for each input VRL/VDAT file. Each CSV file contains data for one record type in Innovasea's Fathom CSV format and each file name matches the corresponding record type (e.g, BATTERY.csv, DET.csv, HEALTH_VR2W.csv). Each directory is named the same (except for extension) as the source file (e.g., VR2W_109924_20110718_1.csv-fathom-split).

Note

Tested on VDAT version vdat-10.6.0-20240716-1903df-release

Author(s)

C. Holbrook, [e-mail]

Examples

## Not run: 

# Check vdat.exe
check_vdat()

# all examples below assume path to VDAT.exe is in system PATH environment
# variable. If not (you get an error), add input argument 'vdat_exe_path'
# with path directory with VDAT.exe.
# e.g.,
# vdat_convert(vrl_files,
#             vdat_exe_path = "C:/Program Files/Innovasea/Fathom")

# get path to example VRL files in glatos
vrl_files <- system.file("extdata", "detection_files_raw",
  c(
    "VR2W_109924_20110718_1.vrl",
    "VR2W180_302187_20180629_1.vrl",
    "VR2AR_546310_20190613_1.vrl",
    "VR2Tx_480022_20190613_1.vrl"
  ),
  package = "glatos"
)

# copy to temp_dir
temp_dir <- tempdir()
vrl_files2 <- file.path(temp_dir, basename(vrl_files))
file.copy(vrl_files, vrl_files2)

# uncomment to open in file browser
# utils::browseURL(temp_dir)

# call VDAT.exe; default args
vdat_convert(vrl_files2)

# run again and overwrite
vdat_convert(vrl_files2, overwrite = TRUE)

# run again without progress bars
vdat_convert(vrl_files2, overwrite = TRUE, show_progress = FALSE)

# use split output format
vdat_convert(vrl_files2, output_format = "csv.fathom.split")

# change output directory
new_dir <- file.path(temp_dir, "testdir")
if (!dir.exists(new_dir)) dir.create(new_dir)

# write to new directory
vdat_convert(vrl_files2, out_dir = new_dir)


# multiple source folders
# make new folder for each vrl file inside temp directory
new_dir2 <- file.path(
  temp_dir,
  "testdir2",
  seq_along(vrl_files2)
)
for (i in 1:length(new_dir2)) {
  if (!dir.exists(new_dir2[i])) dir.create(new_dir2[i], recursive = TRUE)
}

# redistribute files
vrl_files3 <- file.path(new_dir2, basename(vrl_files2))
file.copy(vrl_files2, vrl_files3)

# write each CSV file to same location as corresponding VRL (full path input)
vdat_convert(vrl_files3)

# same but use input dir only and overwrite = TRUE
vdat_convert(dirname(vrl_files3), overwrite = TRUE)

# same but write all CSV files to new location
new_dir3 <- file.path(temp_dir, "testdir3")
if (!dir.exists(new_dir3)) dir.create(new_dir3)

vdat_convert(vrl_files3, out_dir = new_dir3)

# same but use input dir only and recursive = TRUE
vdat_convert(
  src = file.path(temp_dir, "testdir2"),
  out_dir = new_dir3,
  overwrite = TRUE,
  recursive = TRUE
)

## End(Not run)

ocean-tracking-network/glatos documentation built on April 17, 2025, 10:38 p.m.