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Convert an Innovasea Vemco VRL file to a VUE CSV file

Source: R/util-vue.r
vue_convert.Rd

Use Innovasea's command line program VUE.exe (distributed with VUE software) to make a CSV file containing detection data from a VRL file (receiver event data are not supported).

Usage

vue_convert(
  src,
  out_dir = NULL,
  overwrite = FALSE,
  recursive = FALSE,
  vue_exe_path = NULL,
  skip_pattern = "-RLD_",
  show_progress = TRUE,
  diagn = FALSE
)

Arguments

src

Character string with path and name of a detection file (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.

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 files in all subdirectories of src will be converted. Default is FALSE. Ignored if src is a not directory.

vue_exe_path

The full path to VUE.exe. If NULL (default) then the path to VUE.exe must be in the PATH environment variable of the system. See check_vue.

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 vue.exe) should be displayed (default = FALSE).

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).

Details

If src is a directory, then all source files in that directory (including all subdirectories if recursive = TRUE) with supported extension ("vrl") will be converted to CSV. Otherwise, only those files specified in src will be converted. Each output CSV file will have same name as its source file, except extension will be csv.

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

Note

Tested on VUE 2.8.1.

Only detection records are written. Receiver event data are not exported because that functionality was not supported by the VUE system command at time of writing. See vue_convert to extract detection and event data.

VUE does not automatically correct timestamps for clock skew. To create a CSV file with corrected timestamps using VUE's linear time correction method, first time-correct each file using the VRL editor in VUE (under Tools menu). To speed up that process, uncheck the "Import" checkbox next to each filename, then run vue_convert to create a CSV for each edited (e.g. time-corrected) VRL.

Output

A comma-separated-values (CSV) text file in Innovasea's default VUE Export format for each input VRL file. Each CSV is named the same (except for extension) as the source file (e.g., VR2W_109924_20110718_1.csv).

Author

C. Holbrook (cholbrook@glfc.org)

Examples

if (FALSE) { # \dontrun{

# Check vue.exe
check_vue()

# all examples below assume path to VUE.exe is in system PATH environment
# variable. If not (you get an error), add input argument 'vue_exe_path'
# with path directory with VUE.exe.
# e.g.,
# vue_convert(vrl_files,
#            vue_exe_path = "C:/Program Files (x86)/Vemco/VUE")

# 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 VUE.exe; default args
vue_convert(vrl_files2)

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

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


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

# write to new directory
vue_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)
vue_convert(vrl_files3)

# same but use input dir only and overwrite = TRUE
vue_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)

vue_convert(vrl_files3, out_dir = new_dir3)

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