add better spa file reading, fix duplicate metadata name issue, add test

R/as_OpenSpecy.R

@@ -322,7 +322,22 @@ as_OpenSpecy.default <- function(x, spectra,
       stop("inconsistent input for 'metadata'", call. = F)
     }
   }
-
+
+  if(any(duplicated(names(obj$metadata)))){
+      message("Duplicate column names found, adding a unique numeric ID to the end.")
+      nms <- names(obj$metadata)
+      # Identify all names that are duplicated
+      dups <- duplicated(nms) | duplicated(nms, fromLast = TRUE)
+      # Initialize a vector to hold the counts
+      counts <- rep(NA, length(nms))
+      # For duplicated names, generate sequence numbers starting from 0
+      counts[dups] <- ave(seq_along(nms)[dups], nms[dups], FUN = function(x) seq_along(x) - 0)
+      # Create new names by appending counts to duplicated names
+      new_nms <- nms
+      new_nms[dups] <- paste0(nms[dups], "_", counts[dups] - 1)
+      # Update the names in os$metadata
+      names(obj$metadata) <- new_nms
+  }
   return(obj)
 }
 

R/read_ext.R

@@ -204,36 +204,43 @@ read_spa <- function(file,
   if (!grepl("\\.spa$", ignore.case = T, file))
     stop("file type should be 'spa'", call. = F)
 
-  trb <- file.path(file) |> file(open = "rb", ...)
-
-  seek(trb, 576, origin = "start")
-  spr <- readBin(trb, "numeric", n = 2, size = 4)
-
-  if (!all(spr >= 0 & spr <= 15000 & spr[1] > spr[2]))
-    stop("unknown spectral range", call. = F)
-
-  # Read the start offset
-  seek(trb, 386, origin = "start")
-  startOffset <- readBin(trb, "int", n = 1, size = 2)
-  # Read the length
-  seek(trb, 390, origin = "start")
-  readLength <- readBin(trb, "int", n = 1, size = 2)
-
-  # seek to the start
-  seek(trb, startOffset, origin = "start")
-
-  # we'll read four byte chunks
-  floatCount <- readLength / 4
-
-  # read all our floats
-  floatData <- c(readBin(trb, "double", floatCount, size = 4))
-
-  close(trb)
-
-  x <- seq(spr[1], spr[2], length = length(floatData))
-  y <- floatData
-
-  os <- as_OpenSpecy(x, data.table(intensity = y), metadata = metadata,
+    # Read a *.spa file
+    # Returns:
+    #   A list containing Spectra, Wavelengths (nm), and Titles
+    # Converted to r from https://github.com/lerkoah/spa-on-python/blob/master/LoadSpectrum.py
+    con <- file(file, "rb", ...) # Open the file in binary mode
+    on.exit(close(con)) # Ensure the file is closed
+
+    seek(con, where = 564, rw = "r")
+    Spectrum_Pts <- readBin(con, integer(), size = 4, n = 1, endian = "little")
+
+    seek(con, where = 30, rw = "r")
+    SpectraTitlesRaw <- readBin(con, raw(), n = 255)
+    SpectraTitles <- rawToChar(SpectraTitlesRaw[SpectraTitlesRaw != as.raw(0)])
+
+    seek(con, where = 576, rw = "r")
+    Max_Wavenum <- readBin(con, numeric(), size = 4, n = 1, endian = "little")
+    Min_Wavenum <- readBin(con, numeric(), size = 4, n = 1, endian = "little")
+
+    # Generate wavenumbers
+    Wavenumbers <- rev(seq(Min_Wavenum, Max_Wavenum, length.out = Spectrum_Pts))
+
+    seek(con, where = 288, rw = "r")
+
+    Flag <- 0
+    while (Flag != 3) {
+        Flag <- readBin(con, integer(), size = 2, n = 1, endian = "little")
+    }
+
+    DataPosition <- readBin(con, integer(), size = 2, n = 1, endian = "little")
+    seek(con, where = DataPosition, rw = "r")
+
+    Spectra <- readBin(con, numeric(), size = 4, n = Spectrum_Pts, endian = "little")
+
+    # Return the results
+    metadata$title <- SpectraTitles
+
+    os <- as_OpenSpecy(Wavenumbers, data.table(intensity = Spectra), metadata,
                      session_id = T)
 
   return(os)

tests/testthat/test-as_OpenSpecy.R

@@ -10,6 +10,16 @@ test_that("as_OpenSpecy() handles errors correctly", {
                                          intensity = df$intensity)) |>
     expect_error()
 
+  as_OpenSpecy(df, metadata = list(file_name = "test", 
+                                   file_name = "test", 
+                                   fun_val = "t", 
+                                   check = "c",
+                                   check = "a",
+                                   check = "a")) |>
+      check_OpenSpecy() |>
+      expect_true() |>
+      expect_message() 
+
   as_OpenSpecy(data.frame(x = df$wavenumber, abs = df$intensity)) |>
     expect_message()
   as_OpenSpecy(data.frame(wav = df$wavenumber, y = df$intensity)) |>