--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_preprocessing/ReadFids_script.R	Mon Jul 30 10:33:03 2018 -0400
@@ -0,0 +1,404 @@
+################################################################################################
+#
+#   Read FIDs in Bruker format
+#
+#
+################################################################################################
+
+
+# vec2mat ==============================================================================
+vec2mat <- function(vec) {
+  return(matrix(vec, nrow = 1, dimnames = list(c(1), names(vec)))) 
+}
+
+
+# ReadFid ==============================================================================
+ReadFid <- function(path) {
+  
+  # Read 1D FID using Bruker XWinNMR and TopSpin format.  It is inspired of the
+  # matNMR matlab library which deals with 2D FID and also other formats
+  # Read also the parameters in the acqus file
+  
+  paramFile <- file.path(path, "acqus")
+  # BYTEORDA: 0 -> Little Endian 1 -> Big Endian
+  params <- readParams(paramFile, c("TD", "BYTORDA", "DIGMOD", "DECIM", "DSPFVS", 
+                                    "SW_h", "SW", "O1"))
+  
+  if (params[["DSPFVS"]] >= 20) {
+    # The group delay first order phase correction is given directly from version 20
+    grpdly <- readParams(paramFile, c("GRPDLY"))
+    params[["GRPDLY"]] <- grpdly[["GRPDLY"]]
+  }
+  TD <- params[["TD"]]
+  endianness <- if (params$BYTORDA) 
+    "big" else "little"
+  if (TD%%2 != 0) {
+    stop(paste("Only even numbers are allowed for size in TD because it is complex 
+               data with the real and imaginary part for each element.", 
+               "The TD value is in the", paramFile, "file"))
+  }
+  
+  # Interpret params Dwell Time, time between 2 data points in the FID
+  params[["DT"]] <- 1/(2 * params[["SW_h"]])
+  
+  # Read fid
+  fidFile <- file.path(path, "fid")
+  fidOnDisk <- readBin(fidFile, what = "int", n = TD, size = 4L, endian = endianness)
+  
+  # Real size that is on disk (it should be equal to TD2, except for TopSpin/Bruker
+  # (which is our case) according to matNMR as just discussed
+  TDOnDisk <- length(fidOnDisk)
+  if (TDOnDisk < TD) {
+    warning("Size is smaller than expected, the rest is filled with zero so the size is the same for every fid")
+    fidGoodSize <- sapply(vector("list", length = TD), function(x) 0)
+    fidGoodSize[1:TDOnDisk] <- fidOnDisk
+    
+  } else if (TDOnDisk > TD) {
+    warning("Size is bigger than expected, the rest ignored so the size is the same for every fid")
+    fidGoodSize <- fidOnDisk(1:TD)
+    
+  } else {
+    fidGoodSize <- fidOnDisk
+  }
+  
+  fidRePart <- fidGoodSize[seq(from = 1, to = TD, by = 2)]
+  fidImPart <- fidGoodSize[seq(from = 2, to = TD, by = 2)]
+  fid <- complex(real = fidRePart, imaginary = fidImPart)
+  
+  return(list(fid = fid, params = params))
+}
+
+
+
+
+# getDirsContainingFid ==============================================================================
+getDirsContainingFid <- function(path) {
+  subdirs <- dir(path, full.names = TRUE)
+  if (length(subdirs) > 0) {
+    cond <- sapply(subdirs, function(x)  {
+      content <- dir(x)
+      # subdirs must contain fid, acqu and acqus files
+      return("fid" %in% content && "acqu" %in% content && "acqus" %in% content)
+    })
+    subdirs <- subdirs[cond]
+  }
+  return(subdirs)
+}
+
+
+
+
+
+
+# beginTreatment ==============================================================================
+
+beginTreatment <- function(name, Signal_data = NULL, Signal_info = NULL, 
+                           force.real = FALSE) {
+  
+  cat("Begin", name, "\n")
+  
+  
+  # Formatting the Signal_data and Signal_info -----------------------
+  
+  vec <- is.vector(Signal_data)
+  if (vec) {
+    Signal_data <- vec2mat(Signal_data)
+  }
+  if (is.vector(Signal_info)) {
+    Signal_info <- vec2mat(Signal_info)
+  }
+  if (!is.null(Signal_data)) {
+    if (!is.matrix(Signal_data)) {
+      stop("Signal_data is not a matrix.")
+    }
+    if (!is.complex(Signal_data) && !is.numeric(Signal_data)) {
+      stop("Signal_data contains non-numerical values.")
+    }
+  }
+  if (!is.null(Signal_info) && !is.matrix(Signal_info)) {
+    stop("Signal_info is not a matrix.")
+  }
+  
+  
+  Original_data <- Signal_data
+  
+  # Extract the real part of the spectrum ---------------------------
+  
+  if (force.real) {
+    if (is.complex(Signal_data)) {
+      Signal_data <- Re(Signal_data)
+    } else {
+      # The signal is numeric Im(Signal_data) is zero anyway so let's avoid
+      # using complex(real=...,imaginary=0) which would give a complex signal
+      # in endTreatment()
+      force.real <- FALSE
+    }
+  }
+  
+  
+  # Return the formatted data and metadata entries --------------------
+  
+  return(list(start = proc.time(), vec = vec, force.real = force.real, 
+              Original_data = Original_data, Signal_data = Signal_data, Signal_info = Signal_info))
+}
+
+
+# endTreatment ==============================================================================
+
+endTreatment <- function(name, begin_info, Signal_data) {
+  end_time = proc.time() # record it as soon as possible
+  start_time = begin_info[["start"]]
+  delta_time = end_time - start_time
+  delta = delta_time[]
+  cat("End", name, "\n")
+  cat("It lasted",
+      round(delta["user.self"], 3), "s user time,",
+      round(delta["sys.self"] , 3), "s system time and",
+      round(delta["elapsed"]  , 3), "s elapsed time.\n")
+  if (begin_info[["force.real"]]) {
+    # The imaginary part is left untouched
+    i <- complex(real=0, imaginary=1)
+    Signal_data = Signal_data + i * Im(begin_info[["Original_data"]])
+  }
+  if (begin_info[["vec"]]) {
+    Signal_data = Signal_data[1,]
+  }
+  return(Signal_data)
+}
+
+
+# checkArg ==============================================================================
+
+checkArg <- function(arg, checks, can.be.null=FALSE) {
+  check.list <- list(bool=c(is.logical, "a boolean"),
+                     int =c(function(x){x%%1==0}, "an integer"),
+                     num =c(is.numeric, "a numeric"),
+                     str =c(is.character, "a string"),
+                     pos =c(function(x){x>0}, "positive"),
+                     pos0=c(function(x){x>=0}, "positive or zero"),
+                     l1 =c(function(x){length(x)==1}, "of length 1")
+  )
+  if (is.null(arg)) {
+    if (!can.be.null) {
+      stop(deparse(substitute(arg)), " is null.")
+    }
+  } else {
+    if (is.matrix(arg)) {
+      stop(deparse(substitute(arg)), " is not scalar.")
+    }
+    for (c in checks) {
+      if (!check.list[[c]][[1]](arg)) {
+        stop(deparse(substitute(arg)), " is not ", check.list[[c]][[2]], ".")
+      }
+    }
+  }
+}
+
+
+# getArg ==============================================================================
+
+getArg <- function(arg, info, argname, can.be.absent=FALSE) {
+  if (is.null(arg)) {
+    start <- paste("impossible to get argument", argname, "it was not given directly and");
+    if (!is.matrix(info)) {
+      stop(paste(start, "the info matrix was not given"))
+    }
+    if (!(argname %in% colnames(info))) {
+      if (can.be.absent) {
+        return(NULL)
+      } else {
+        stop(paste(start, "is not in the info matrix"))
+      }
+    }
+    if (nrow(info) < 1) {
+      stop(paste(start, "the info matrix has no row"))
+    }
+    arg <- info[1,argname]
+    if (is.na(arg)) {
+      stop(paste(start, "it is NA in the info matrix"))
+    }
+  }
+  return(arg)
+}
+
+
+
+# getTitle ==============================================================================
+
+# Get the name of the signal from the title file or fromt the name of the subdirectory
+# Get the name of the signal from the title file or fromt the name of the subdirectory
+
+getTitle <- function(path, l, subdirs) {
+  title <- NULL
+  title_file <- file.path(file.path(file.path(path, "pdata"), "1"), "title")
+  if (file.exists(title_file)) {
+    lines <- readLines(title_file, warn = FALSE)
+    if (length(lines) >= 1)  {
+      first_line <- gsub("^\\s+|\\s+$", "", lines[l])
+      if (nchar(first_line) >= 1)  {
+        title <- first_line
+      } else {
+        warning(paste("The", l ,"line of the title file is blank for directory ", 
+                      path, "and the (sub)dirs names are used instead"))
+      }
+    } else {
+      warning(paste("The title file is empty for directory ", path, "and the (sub)dirs names are used instead"))
+    }
+  } else {
+    warning(paste("Title file doesn't exists for directory ", path, "\n the (sub)dirs names are  used instead"))
+  }
+  if (is.null(title)) {
+    if(subdirs) {
+      separator <- .Platform$file.sep
+      path_elem <- strsplit(path,separator)[[1]]
+      title <- paste(path_elem[length(path_elem)-1], path_elem[length(path_elem)], sep = "_")
+    } else{title <- basename(path)} 
+  }
+  return(title)
+}
+
+
+
+
+# readParams ==============================================================================
+# Read parameter values for Fid_info in the ReadFids function
+
+readParams <- function(file, paramsName) {
+  
+  isDigit <- function(c) {
+    return(suppressWarnings(!is.na(as.numeric(c))))
+  }
+  lines <- readLines(file)
+  params <- sapply(paramsName, function(x) NULL)
+  
+  for (paramName in paramsName)  {
+    # Find the line with the parameter I add a '$' '=' in the pattern so that for
+    # example 'TD0' is not found where I look for 'TD' and LOCSW and WBSW when I look
+    # for 'SW'
+    pattern <- paste("\\$", paramName, "=", sep = "")
+    occurences <- grep(pattern, lines)
+    if (length(occurences) == 0L)  {
+      stop(paste(file, "has no field", pattern))
+    }
+    if (length(occurences) > 1L) {
+      warning(paste(file, "has more that one field", pattern, " I take the first one"))
+    }
+    line <- lines[occurences[1]]
+    
+    # Cut beginning and end of the line '##$TD= 65536' -> '65536'
+    igual = as.numeric(regexpr("=", line))
+    
+    first <- igual
+    while (first <= nchar(line) & !isDigit(substr(line, first, first))) {
+      first <- first + 1
+    }
+    last <- nchar(line)
+    while (last > 0 & !isDigit(substr(line, last, last)))  {
+      last <- last - 1
+    }
+    params[paramName] <- as.numeric(substr(line, first, last))
+  }
+  return(params)
+}
+
+
+
+# ReadFids ==============================================================================
+
+ReadFids <- function(path, l = 1, subdirs = FALSE, dirs.names = FALSE) {
+  
+  # Data initialisation and checks ----------------------------------------------
+  begin_info <- beginTreatment("ReadFids")
+  checkArg(path, c("str"))
+  checkArg(l, c("pos"))
+  if (file.exists(path) == FALSE) {
+    stop(paste("Invalid path:", path))
+  }
+  
+  
+  # Extract the FIDs and their info ----------------------------------------------
+  
+  if (subdirs == FALSE) {
+    fidDirs <- getDirsContainingFid(path)
+    n <- length(fidDirs)
+    if (n == 0L)  {
+      stop(paste("No valid fid in", path))
+    }
+    if (dirs.names) {
+      separator <- .Platform$file.sep
+      path_elem <- strsplit(fidDirs,separator)
+      fidNames <- sapply(path_elem, function(x) x[[length(path_elem[[1]])]])
+    }else {fidNames <- sapply(X = fidDirs, FUN = getTitle, l = l, subdirs = subdirs,  USE.NAMES = F)}
+    
+    for (i in 1:n)  {
+      fidList <- ReadFid(fidDirs[i])
+      fid <- fidList[["fid"]]
+      info <- fidList[["params"]]
+      m <- length(fid)
+      if (i == 1)  {
+        Fid_data <- matrix(nrow = n, ncol = m, dimnames = list(fidNames, 
+                                                               info[["DT"]] * (0:(m - 1))))
+        Fid_info <- matrix(nrow = n, ncol = length(info), dimnames = list(fidNames, 
+                                                                          names(info)))
+      }
+      Fid_data[i, ] <- fid
+      Fid_info[i, ] <- unlist(info)
+    }
+    
+  } else  {
+    maindirs <- dir(path, full.names = TRUE) # subdirectories
+    Fid_data <- numeric()
+    Fid_info <- numeric()
+    
+    fidDirs <- c()
+    for (j in maindirs) {
+      fd <- getDirsContainingFid(j) # recoved FIDs from subdirectories
+      n <- length(fd)
+      if (n > 0L)  {
+        fidDirs <- c(fidDirs, fd)
+      } else {warning(paste("No valid fid in",j ))}
+    }
+    
+    if (dirs.names==TRUE) {
+      if (length(fidDirs)!= length(dir(path))) { # at least one subdir contains more than 1 FID
+        separator <- .Platform$file.sep
+        path_elem <- strsplit(fidDirs,separator)
+        fidNames <- sapply(path_elem, function(x) paste(x[[length(path_elem[[1]])-1]],
+                                                        x[[length(path_elem[[1]])]], sep = "_"))
+      }else {fidNames <- dir(path)}
+      
+    } else {fidNames <- sapply(X = fidDirs, FUN = getTitle, l = l, subdirs = subdirs, USE.NAMES = F)}
+    
+    for (i in 1:length(fidNames))  {
+      fidList <- ReadFid(fidDirs[i])
+      fid <- fidList[["fid"]]
+      info <- fidList[["params"]]
+      m <- length(fid)
+      if (i == 1)  {
+        Fid_data <- matrix(nrow = length(fidNames), ncol = m, dimnames = list(fidNames, 
+                                                                              info[["DT"]] * (0:(m - 1))))
+        Fid_info <- matrix(nrow = length(fidNames), ncol = length(info), dimnames = list(fidNames, 
+                                                                                         names(info)))
+      }
+      Fid_data[i, ] <- fid
+      Fid_info[i, ] <- unlist(info)
+    }
+    
+    
+  }
+  
+  # Check for non-unique IDs ----------------------------------------------
+  NonnuniqueIds <- sum(duplicated(row.names(Fid_data)))
+  cat("dim Fid_data: ", dim(Fid_data), "\n")
+  cat("IDs: ", rownames(Fid_data), "\n")
+  cat("non-unique IDs?", NonnuniqueIds, "\n")
+  if (NonnuniqueIds > 0) {
+    warning("There are duplicated IDs: ", Fid_data[duplicated(Fid_data)])
+  }
+  
+  
+  # Return the results ----------------------------------------------
+  return(list(Fid_data = endTreatment("ReadFids", begin_info, Fid_data), Fid_info = Fid_info))
+  
+}
+