adapt binary OPUS file reader function to differering block position structures in OPUS files of ALPHA spectrometers at ETH Zuerich and ICRAF. Redefine offsets for upper and lower frequencies, number of points, and spectral information offsets for sample spectra.

R/load-spectra.R

@@ -64,23 +64,27 @@ read_opus_bin <- function(file.name){
       re <- grepRaw("RES", pr, all = TRUE)[1] + 5
       snm <- grepRaw("SNM", pr, all = TRUE)[1] + 7
       lwn <- grepRaw("LWN", pr, all = TRUE)[1] + 7
-      fx <- grepRaw("FXV", pr, all = TRUE)[3] + 7
-      lx <- grepRaw("LXV", pr, all = TRUE)[1] + 7 # changed for ETH spectra !!! -> before: [3] + 7
-      npt0 <- grepRaw("NPT", pr, all = TRUE)[2] + 3
-      npt1 <- grepRaw("NPT", pr, all = TRUE)[3] + 7
       mxy <- grepRaw("MXY", pr, all = TRUE)[1] + 7
       mny <- grepRaw("MNY", pr, all = TRUE)[3] + 7
       end <- grepRaw("END", pr, all = TRUE) + 11
       dat <- grepRaw( "DAT", pr, all = TRUE)[1] + 7
       tim <- grepRaw("TIM", pr, all = TRUE) + 11
-      # calculate end and start of each block
-      offs <- end[5:10]
-      # for ICRAF spectra:
-      if (offs[1] > 50000) {
-        lx <- grepRaw("LXV", pr, all = TRUE)[4] + 7
+      # Select matching positions based on file structure
+      # Calculate how many number of points blocks are present in file
+      npt_length <- length(grepRaw("NPT", pr, all = TRUE))
+      # If spectra are from ETH Alpha
+      if (npt_length < 9) {
+        fx_sample <- grepRaw("FXV", pr, all = TRUE)[1] + 7
+        lx_sample <- grepRaw("LXV", pr, all = TRUE)[1] + 7
+        npt_sample <- grepRaw("NPT", pr, all = TRUE)[1] + 7
+      # If spectra are from ICRAF Alpha
+      } else {
+        fx_sample <- grepRaw("FXV", pr, all = TRUE)[3] + 7
+        lx_sample <- grepRaw("LXV", pr, all = TRUE)[3] + 7
+        npt_sample <- grepRaw("NPT", pr, all = TRUE)[3] + 7
       }
 
-      byts <- diff(offs)
+      # byts <- diff(offs)
       ZFF <- hexView::readRaw(file.name, offset = z, nbytes = 4,
         human = "int", size = 2)[[5]][1]
       RES <- hexView::readRaw(file.name, offset = re, nbytes = 4,
@@ -136,58 +140,46 @@ read_opus_bin <- function(file.name){
       # Combine the above parameters
       spectrum.meta <- c(SSN, Material, Scandate, ZFF, RES, LWN)
       # Get number of data points for each spectra data block
-      NPT0 <- hexView::readRaw(
-        file.name, offset = npt0, nbytes = 12,
-        human = "int", size = 4)[[5]][2]
-      NPT1 <- hexView::readRaw(
-        file.name, offset = npt1, nbytes = 4,
+      NPT_sample <- hexView::readRaw(
+        file.name, offset = npt_sample, nbytes = 12,
         human = "int", size = 4)[[5]][1]
+      # Add extra step for spectrum "CI_tb_05_soil_cal.2" measured at ETH
+      if(NPT_sample > 10000) {
+        npt_sample <- grepRaw("NPT", pr, all = TRUE)[2] + 7
+        NPT_sample <- hexView::readRaw(
+          file.name, offset = npt_sample, nbytes = 12,
+          human = "int", size = 4)[[5]][1]
+      }
       # fxv:	Frequency of first point
-      fxv <- hexView::readRaw(
-        file.name, offset = fx, nbytes = 16,
+      fxv_sample <- hexView::readRaw(
+        file.name, offset = fx_sample, nbytes = 16,
         human = "real", size = 8)[[5]][1]
       # lxv:	Frequency of last point
-      lxv <- hexView::readRaw(
-        file.name, offset = lx, nbytes = 16,
+      lxv_sample <- hexView::readRaw(
+        file.name, offset = lx_sample, nbytes = 16,
         human = "real", size = 8)[[5]][1]
       # Read all through all the data blocks inside the OPUS file
-      nbytes1 <- NPT0 * 4 # initial parameters
-      smxa <- c()
-      smna <- c()
-      nbytes.f <- NPT1 * 4
-      # return(offs[1]) -> check offset of different spectral files
+      nbytes_spc_sample <- NPT_sample * 4
 
-      ## Calculate wavenumbers
-      wavenumbers <- rev(seq(lxv, fxv, (fxv - lxv)/(NPT1 - 1)))
+      # Offsets (start) of sample spectra
+      if (length(end) == 17) {
+      offs_spc_sample <- end[16]
+      }
+      if (length(end) == 16) {
+        offs_spc_sample <- end[15]
+      } else {
+        offs_spc_sample <- end[7]
+      }
 
-      if (offs[1] < 2000) {
-        offs.f <- offs[3]
-          nbytes.f <- NPT1 * 4
-          wavenumbers <- rev(seq(lxv, fxv, (fxv - lxv)/(NPT1 - 1)))
-        }
-      else if (offs[1] > 20000) {
-        offs.f <- offs[3]
-        nbytes.f <- NPT1 * 4
-        wavenumbers <- rev(seq(lxv, fxv, (fxv - lxv)/(NPT1 - 1))) }
-      else if (offs[1] < 10000) {  # added!
-        offs.f <- offs[1]
-        nbytes.f <- NPT0 * 4
-        wavenumbers <- rev(seq(lxv, fxv, (fxv - lxv)/(NPT0 - 1)))
-      } else {  # for vert-MIR
-        offs.f <- 7188
-        nbytes.f <- NPT0 * 4
-        lxv <- hexView::readRaw(
-          file.name, offset = 8768, nbytes = 16,
-          human = "real", size = 8)[[5]][1]
-        fxv <- hexView::readRaw(
-          file.name, offset = 8752, nbytes = 16,
-          human = "real", size = 8)[[5]][1]
-        wavenumbers <- rev(seq(lxv, fxv, (fxv - lxv)/(NPT0 - 1)))
-        }
+      ## Calculate wavenumbers
+      wavenumbers <- rev(seq(lxv_sample, fxv_sample,
+        (fxv_sample - lxv_sample)/(NPT_sample - 1)))
 
-        spectra <- hexView::readRaw(file.name, width = NULL,
-          offset = offs.f - 4, nbytes = nbytes.f, human = "real", # needs to be -4 according to soil.spec function
-          size = 4, endian = "little")[[5]]
+      # Read spectra
+      spectra <- hexView::readRaw(file.name, width = NULL,
+        offset = offs_spc_sample, nbytes = nbytes_spc_sample,
+        human = "real",
+        size = 4, endian = "little")[[5]]
 
       # File name
       file_name <- sub(".+/(.+)", "\\1", file.name)