--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_preprocessing/Int_Funct.R	Mon Jul 30 10:33:03 2018 -0400
@@ -0,0 +1,236 @@
+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))
+}
+
+binarySearch <- function(a, target, lower = TRUE) {
+  # search the index i in a such that a[i] == target 
+  # if it doesn't exists and lower, it searches the closer a[i] such that a[i] < target
+  # if !lower, it seraches the closer a[i] such that a[i] > target 
+  # a should be monotone but can be increasing or decreasing
+  
+  # if a is increasing INVARIANT: a[amin] < target < a[amax]
+  N <- length(a)
+  if ((a[N] - target) * (a[N] - a[1]) <= 0) {
+    return(N)
+  }
+  if ((a[1] - target) * (a[N] - a[1]) >= 0) {
+    return(1)
+  }
+  amin <- 1
+  amax <- N
+  while (amin + 1 < amax) {
+    amid <- floor((amin + amax)/2)
+    if ((a[amid] - target) * (a[amax] - a[amid]) < 0) {
+      amin <- amid
+    } else if ((a[amid] - target) * (a[amax] - a[amid]) > 0) {
+      amax <- amid
+    } else {
+      # a[amid] == a[amax] or a[amid] == target In both cases, a[amid] ==
+      # target
+      return(amid)
+    }
+  }
+  if (xor(lower, a[amin] > a[amax])) {
+    # (lower && a[amin] < a[amax]) || (!lower && a[min] > a[max]) 
+    # If increasing and we want the lower, we take amin 
+    # If decreasing and we want the bigger, we take amin too
+    return(amin)
+  } else {
+    return(amax)
+  }
+}
+
+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]], ".")
+      }
+    }
+  }
+}
+
+endTreatment <- function(name, begin_info, Signal_data) {
+  
+  # begin_info: object outputted from beginTreatment
+  
+  
+  # Formatting the entries and printing process time -----------------------
+  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 the formatted data and metadata entries --------------------
+  return(Signal_data)
+}
+
+Interpol <- function(t, y) {
+  # y: sample
+  # t : warping function
+  
+  m <- length(y)
+  # t <= m-1
+  # because if t > m-1, y[ti+1] will be NA when we compute g
+  valid <- 1 <= t & t <= m-1 # FIXME it was '<' in Bubble v2
+  s <- (1:m)[valid]
+  ti <- floor(t[s])
+  tr <- t[s] - ti
+  g <- y[ti + 1] - y[ti]
+  f <- y[ti] + tr * g
+  list(f=f, s=s, g=g)
+}
+
+vec2mat <- function(vec) {
+  
+  return(matrix(vec, nrow = 1, dimnames = list(c(1), names(vec)))) 
+  
+}
+
+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)
+}
+
+binarySearch <- function(a, target, lower = TRUE) {
+  # search the index i in a such that a[i] == target 
+  # if it doesn't exists and lower, it searches the closer a[i] such that a[i] < target
+  # if !lower, it seraches the closer a[i] such that a[i] > target 
+  # a should be monotone but can be increasing or decreasing
+  
+  # if a is increasing INVARIANT: a[amin] < target < a[amax]
+  N <- length(a)
+  if ((a[N] - target) * (a[N] - a[1]) <= 0) {
+    return(N)
+  }
+  if ((a[1] - target) * (a[N] - a[1]) >= 0) {
+    return(1)
+  }
+  amin <- 1
+  amax <- N
+  while (amin + 1 < amax) {
+    amid <- floor((amin + amax)/2)
+    if ((a[amid] - target) * (a[amax] - a[amid]) < 0) {
+      amin <- amid
+    } else if ((a[amid] - target) * (a[amax] - a[amid]) > 0) {
+      amax <- amid
+    } else {
+      # a[amid] == a[amax] or a[amid] == target In both cases, a[amid] ==
+      # target
+      return(amid)
+    }
+  }
+  if (xor(lower, a[amin] > a[amax])) {
+    # (lower && a[amin] < a[amax]) || (!lower && a[min] > a[max]) 
+    # If increasing and we want the lower, we take amin 
+    # If decreasing and we want the bigger, we take amin too
+    return(amin)
+  } else {
+    return(amax)
+  }
+}
+
+# returns the discrete borders of the interval for a numeric vector a
+
+indexInterval <- function (a, from, to, inclusive=TRUE) {
+  # If inclusive and from <= to, we need to take the lower
+  # If not inclusive and from > to, we need to take the lower too
+  lowerFrom <- xor(inclusive, from > to)
+  fromIndex <- binarySearch(a, from, lowerFrom)
+  toIndex <- binarySearch(a, to, !lowerFrom)
+  return(fromIndex:toIndex)
+}