From 0f376efcbff637618ccb631f4489bf14f7e6b476 Mon Sep 17 00:00:00 2001
From: hugomflavio <hmflavio92@gmail.com>
Date: Mon, 1 Jul 2024 19:21:00 -0400
Subject: [PATCH] new processFile function for updated innovasea format (#97)

---
 DESCRIPTION                 |  2 +-
 NEWS.md                     |  3 ++-
 R/load.R                    | 44 +++++++++++++++++++++++++++++++++++++
 man/processInnovaseaFile.Rd | 18 +++++++++++++++
 4 files changed, 65 insertions(+), 2 deletions(-)
 create mode 100644 man/processInnovaseaFile.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index ed1a568..1d0312b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: actel
 Title: Acoustic Telemetry Data Analysis
-Version: 1.3.0.9005
+Version: 1.3.0.9006
 Authors@R: person("Hugo", "Flávio", role = c("aut", "cre"), email = "hflavio@wlu.ca", comment = c(ORCID = "0000-0002-5174-1197"))
 Description: Designed for studies where animals tagged with acoustic tags are expected
     to move through receiver arrays. This package combines the advantages of automatic sorting and checking 
diff --git a/NEWS.md b/NEWS.md
index fd2314c..515cfd6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -11,7 +11,8 @@ Fixes:
 Enhancements:
   * Improve timestamp handling when importing data through `preload()` (issue [#94](https://github.com/hugomflavio/actel/issues/94)).
   * Improve column name checks to avoid accidentally matching anything to the dot wildcard.
-  * Add new "first to first" method to speed calculations (issue [#94](https://github.com/hugomflavio/actel/issues/96))
+  * Add new "first to first" method to speed calculations (issue [#96](https://github.com/hugomflavio/actel/issues/96))
+  * New `processInnovaseaFile()` function to handle updated innovasea detection file format (issue [#97](https://github.com/hugomflavio/actel/issues/97)).
 
 ## actel 1.3.0
 
diff --git a/R/load.R b/R/load.R
index faa2e8e..ba58d83 100644
--- a/R/load.R
+++ b/R/load.R
@@ -1333,6 +1333,13 @@ compileDetections <- function(path = "detections", start.time = NULL, stop.time
             })
           unknown.file <- FALSE
         }
+        if (unknown.file && all(!is.na(match(c("Device Time (UTC)", "Full ID", "Serial Number"), colnames(aux))))) {
+          appendTo("debug", paste0("File '", i, "' matches an Innovasea log."))
+          output <- tryCatch(processInnovaseaFile(input = aux), error = function(e) {
+              stopAndReport("Something went wrong when processing file '", i, "'. If you are absolutely sure this file is ok, contact the developer.\nOriginal error:", sub("^Error:", "", e))
+            })
+          unknown.file <- FALSE
+        }
         if (unknown.file) {
           appendTo(c("Screen", "Report", "Warning"),
             paste0("File '", i, "' does not match to any of the supported hydrophone file formats!\n         If your file corresponds to a hydrophone log and actel did not recognize it, please get in contact through www.github.com/hugomflavio/actel/issues/new"))
@@ -1549,6 +1556,43 @@ processVemcoFile <- function(input) {
   return(input)
 }
 
+#' Innovasea files
+#'
+#' Processes Innovasea ALS files
+#'
+#' @param input the detections data frame.
+#'
+#' @return A data frame of standardized detections from the input file.
+#'
+#' @keywords internal
+#'
+processInnovaseaFile <- function(input) {
+  appendTo("Debug", "Running processInnovaseaFile.")
+
+  colnames(input) <- gsub(" ", ".", colnames(input))
+
+  transmitter_aux <- strsplit(input$Full.ID, "-", fixed = TRUE)
+  input$CodeSpace <- unlist(lapply(transmitter_aux, function(x) paste(x[1:2], collapse = "-"))) # Rejoin code space
+  input$Signal <- unlist(lapply(transmitter_aux, function(x) x[3])) # extract only signal
+  input$Receiver <- input$Serial.Number
+  input$Timestamp <- input$`Device.Time.(UTC)`
+  input$Sensor.Value <- input$Raw.Data
+  input$Sensor.Unit <- rep(NA_character_, nrow(input))
+
+  input <- input[, c("Timestamp", "Receiver", "CodeSpace", "Signal", "Sensor.Value", "Sensor.Unit")]
+  input$Timestamp <- fasttime::fastPOSIXct(as.character(input$Timestamp), tz = "UTC")
+  
+  if (any(is.na(input$Timestamp)))
+    stop("Importing timestamps failed", call. = FALSE)
+  if (any(is.na(input$Receiver)))
+    stop("Importing receivers failed", call. = FALSE)
+  if (any(is.na(input$Signal)))
+    stop("Importing code space failed", call. = FALSE)
+  if (any(is.na(input$Receiver)))
+    stop("Importing signals failed", call. = FALSE)
+  return(input)
+}
+
 #' Convert code spaces
 #'
 #' Unifies CodeSpace names, to avoid having different names depending on ALS vendor.
diff --git a/man/processInnovaseaFile.Rd b/man/processInnovaseaFile.Rd
new file mode 100644
index 0000000..eaae781
--- /dev/null
+++ b/man/processInnovaseaFile.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/load.R
+\name{processInnovaseaFile}
+\alias{processInnovaseaFile}
+\title{Innovasea files}
+\usage{
+processInnovaseaFile(input)
+}
+\arguments{
+\item{input}{the detections data frame.}
+}
+\value{
+A data frame of standardized detections from the input file.
+}
+\description{
+Processes Innovasea ALS files
+}
+\keyword{internal}