[WIP] Feature/add spectravista: reading spectral data from SVC *.sig

.Rbuildignore

@@ -1,3 +1,4 @@
 .git
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,62 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+
+          - {os: ubuntu-latest,   r: 'release'}
+#         - {os: macos-latest,   r: 'release'}
+#         - {os: windows-latest, r: 'release'}
+#         - {os: ubuntu-latest,   r: 'oldrel-1'}
+#         - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      PKG_SYSREQS: false
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+          extra-repositories: https://pecanproject.r-universe.dev
+
+      - name: dependencies on Linux
+        if: runner.os == 'Linux'
+        run: sudo apt-get install -y make pandoc git libssl-dev libgdal-dev gdal-bin libgeos-dev libproj-dev libsqlite3-dev libicu-dev libudunits2-dev librdf0-dev libxml2-dev libfreetype6-dev libjpeg-dev libpng-dev libtiff-dev libfontconfig1-dev libfribidi-dev libharfbuzz-dev libcurl4-gnutls-dev pkg-config
+
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck, testthat, PEcAnRTM, rjags
+          needs: check
+          dependencies: '"hard"'
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          error-on: '"error"'
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.gitignore

@@ -5,4 +5,4 @@
 settings.xml~
 *.RData
 *.Rdata
-
+R-FieldSpectra.Rproj

DESCRIPTION

@@ -27,11 +27,13 @@ Suggests:
     spectrolab
 Depends:
     R (>= 2.10)
+Remotes: 
+    meireles/spectrolab
 NeedsCompilation: no
 SystemRequirements: OS_type: unix, mac
 License: GNU GENERAL PUBLIC LICENSE Version 3
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2

NAMESPACE

@@ -7,5 +7,6 @@ export(convolve.spectra)
 export(extract.metadata)
 export(jump.correction)
 export(read.asd)
+export(read.sig)
 export(settings)
 export(smooth.spectra)

R/read.sig.R

@@ -0,0 +1,104 @@
+#--------------------------------------------------------------------------------------------------------------#
+##' Function to read .sig files and extract spectral data
+##'
+##'This function will read ".sig" files and extract the speczral data. The resulting data frame will
+##'have the option for all data as well as selected data , which can be obtained by providing the
+##'boolean parameter.
+##'
+##' @name read.sig
+##' @title read .sig files from SVC
+##'
+##' @param path A character string specifying the path to the directory or a single sig file.
+##' @param default A logical value indicating whether to include all columns from the `.sig` files
+#'            (`TRUE`) or only selected columns (`FALSE`). Default is `TRUE`.
+#'
+##'
+##' @return A data data frame with the following columns :
+##' \describe{
+##' \item{Wavelengths(nm)}{Numeric vector representing the wavelengths in nanometers.}
+##' \item{file}{gives information on the file name}
+##' \item{Reflectance(\%)}{Numeric vector of reflectance percentages.}
+##' \item{Target Values (optional)}{Provides the targer values}
+##' \item{Reference Values (optional)}{Provides information on the reference values}
+##' }
+##'
+##' @details
+##' The function can read a single file or multiple files in a directory.
+##' The file is then read line by line and the spectral data is extracted from the line after "data=".
+##' The extracted data is then converted into a data frame with appropriate names.
+##'
+##'@examples
+##'\dontrun{
+##'path <- "/path/to/your/file.sig"
+##'data <- read.sig(path, default = FALSE)
+##'print(head(data))
+##'}
+##'
+##'@export
+##'
+##'@author Methun George, Steffen Neumann
+##'
+
+
+
+
+
+read.sig <- function(path, default = TRUE) {
+  # Check if the path exists
+  if (!file.exists(path)) {
+    stop("The path does not exist: ", path)
+  }
+
+  # Check if the path is a directory or a single file
+  path_info <- file.info(path)
+  if (path_info$isdir) {
+    sig_files <- list.files(path = path, pattern = "\\.sig$", full.names = TRUE)
+  } else {
+    sig_files <- path
+  }
+
+  # An empty list to store the data frames
+  all_data <- list()
+
+  # Read each file and then combine the data
+  for (file in sig_files) {
+    file_content <- readLines(file)
+    data_start <- grep("^data=", file_content)
+    data_lines <- file_content[(data_start + 1):length(file_content)]
+    data <- read.table(text = data_lines, header = FALSE, fill = TRUE)
+
+    # Add the filename
+    name_line <- grep("^name=", file_content, value = TRUE)
+    if (length(name_line) > 0) {
+      file_name <- sub("^name=", "", name_line)
+    } else {
+      file_name <- basename(file)  # Default to file name if not found in metadata
+    }
+
+    if (default) {
+      # If parameter,'all' is TRUE, include all columns with original column names
+      data$file_name <- file_name
+      if (ncol(data) >= 4) {
+        colnames(data) <- c("Wavelengths(nm)", "Reference Values", "Target Values", "Reflectance(%)", "file_name")
+      }
+      } else {
+      # If 'all' is FALSE, only select the wavelength and reflectance columns
+      if (ncol(data) >= 4) {
+        data <- data[, c(1, 4), drop = FALSE]
+        colnames(data) <- c("Wavelengths(nm)", "Reflectance(%)")
+      } else {
+        stop("Data does not have enough columns to extract the required columns!!!")
+      }
+      data$file_name <- file_name
+    }
+
+    # Store the data frame in the list
+    all_data[[length(all_data) + 1]] <- data
+  }
+
+  # Combine all data frames
+  combined_data <- do.call(rbind, all_data)
+  return(combined_data)
+}
+
+

README.md

@@ -1,3 +1,7 @@
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/georgejr45/R-FieldSpectra/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/georgejr45/R-FieldSpectra/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
 # R-FieldSpectra
 R library for importing and processing field spectroscopy data collected with ASD, Spectra Vista, and Spectral Evolution instruments
 

tests/testthat/test_openASD.R

@@ -1,9 +1,19 @@
 context("opening spectra files")
 
-test_that("open ASD spectra file", {
+test_that("open single ASD spectra file", {
 
   file.dir <- system.file("extdata/PM01_TIAM_B_LC_REFL00005.asd",package="FieldSpectra")
   spec <- read.asd(file.dir, out.dir=file.path('~'), start.wave=350, end.wave=2500, step.size=1)
   expect_equal(round(sum(spec$Spectra)), 517)
 
-})
+})
+
+# test_that("open multiple ASD spectra file", {
+#   
+#   file.dir <- system.file("extdata/",package="FieldSpectra")
+#   spec <- read.asd(file.dir, out.dir=file.path('~'), start.wave=350, end.wave=2500, step.size=1)
+#   expect_equal(round(sum(spec$Spectra)), 517)
+#   
+# })
+# 
+

tests/testthat/test_openSIG.R

@@ -0,0 +1,33 @@
+# Create test
+test_that("read.sig function works correctly with default parameter", {
+  # Create a temporary directory and file for testing
+  temp_dir <- tempdir()
+  temp_file <- file.path(temp_dir, "test.sig")
+
+  # Create a mock .sig file with some sample data
+  writeLines(c(
+    "name=test_file.sig",
+    "data=",
+    "400 1 2 10",
+    "500 1 2 20",
+    "600 1 2 30",
+    "700 1 2 40"
+  ), temp_file)
+
+  filepath <- system.file("extdata/gr070214_003.sig",package="FieldSpectra")
+
+  # Test with default = TRUE (all columns)
+  data_all <- read.sig(filepath, default = TRUE)
+  expect_equal(ncol(data_all), 5)  # Should have 5 columns
+  expect_equal(colnames(data_all), c("Wavelengths(nm)", "Reference Values", "Target Values", "Reflectance(%)", "file_name"))
+
+  # Test with default = FALSE (selected columns)
+  data_selected <- read.sig(filepath, default = FALSE)
+  expect_equal(ncol(data_selected), 3)  # Should have 3 columns: Wavelengths(nm), Reflectance(%), file_name
+  expect_equal(colnames(data_selected), c("Wavelengths(nm)", "Reflectance(%)", "file_name"))
+
+  # Clean up
+  unlink(temp_file)
+})
+
+