--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_preprocessing/ptw.R	Mon Jul 30 10:33:03 2018 -0400
@@ -0,0 +1,98 @@
+ptw <- function (ref, samp, selected.traces, init.coef = c(0, 1, 0), 
+          try = FALSE, warp.type = c("individual", "global"), optim.crit = c("WCC", 
+                                                                             "RMS"), mode = c("forward", "backward"), smooth.param = ifelse(try, 
+                                                                                                                                            0, 1e+05), trwdth = 20, trwdth.res = trwdth, verbose = FALSE, 
+          ...) 
+{
+  optim.crit <- match.arg(optim.crit)
+  warp.type <- match.arg(warp.type)
+  mode <- match.arg(mode)
+  if (is.vector(ref)) 
+    ref <- matrix(ref, nrow = 1)
+  if (is.vector(samp)) 
+    samp <- matrix(samp, nrow = 1)
+  if (nrow(ref) > 1 && nrow(ref) != nrow(samp)) 
+    stop("The number of references does not equal the number of samples")
+  if (length(dim(ref)) > 2) 
+    stop("Reference cannot be an array")
+  if (length(dim(samp)) > 2) 
+    stop("Sample cannot be an array")
+  if (nrow(samp) == 1) 
+    warp.type <- "individual"
+  r <- nrow(samp)
+  if (!missing(selected.traces)) {
+    samp <- samp[selected.traces, , drop = FALSE]
+    if (nrow(ref) > 1) 
+      ref <- ref[selected.traces, , drop = FALSE]
+  }
+  if (is.vector(init.coef)) 
+    init.coef <- matrix(init.coef, nrow = 1)
+  if (warp.type == "global") {
+    if (nrow(init.coef) != 1) 
+      stop("Only one warping function is allowed with global alignment.")
+  }
+  else {
+    if (nrow(init.coef) != nrow(samp)) 
+      if (nrow(init.coef) == 1) {
+        init.coef <- matrix(init.coef, byrow = TRUE, 
+                            nrow = nrow(samp), ncol = length(init.coef))
+      }
+    else {
+      stop("The number of warping functions does not match the number of samples")
+    }
+  }
+  if (warp.type == "individual") {
+    w <- matrix(0, nrow(samp), ncol(ref))
+    a <- matrix(0, nrow(samp), ncol(init.coef))
+    v <- rep(0, nrow(samp))
+    warped.sample <- matrix(NA, nrow = nrow(samp), ncol = ncol(samp))
+    for (i in 1:nrow(samp)) {
+      if (verbose & nrow(samp) > 1) 
+        cat(ifelse(nrow(ref) == 1, paste("Warping sample", 
+                                         i, "with the reference \n"), paste("Warping sample", 
+                                                                            i, "with reference \n", i)))
+      if (nrow(ref) == 1) {
+        rfrnc <- ref
+      }
+      else {
+        rfrnc <- ref[i, , drop = FALSE]
+      }
+      quad.res <- pmwarp(rfrnc, samp[i, , drop = FALSE], 
+                         optim.crit, init.coef[i, ], try = try, mode = mode, 
+                         smooth.param = smooth.param, trwdth = trwdth, 
+                         trwdth.res = trwdth.res, ...)
+      w[i, ] <- quad.res$w
+      a[i, ] <- quad.res$a
+      v[i] <- quad.res$v
+      warped.sample[i, ] <- c(warp.sample(samp[i, , drop = FALSE], 
+                                          w[i, ], mode = mode))
+    }
+  }
+  else {
+    if (nrow(ref) == 1) 
+      ref <- matrix(ref, nrow = nrow(samp), ncol = ncol(ref), 
+                    byrow = TRUE)
+    if (verbose) {
+      if (nrow(ref) == 1) {
+        cat("Simultaneous warping of samples with reference... \n")
+      }
+      else {
+        cat("Simultaneous warping of samples with references... \n")
+      }
+    }
+    quad.res <- pmwarp(ref, samp, optim.crit, c(init.coef), 
+                       try = try, mode = mode, smooth.param = smooth.param, 
+                       trwdth = trwdth, trwdth.res = trwdth.res, ...)
+    w <- t(as.matrix(quad.res$w))
+    a <- t(as.matrix(quad.res$a))
+    v <- quad.res$v
+    warped.sample <- t(warp.sample(samp, w, mode))
+  }
+  if (verbose) 
+    cat("\nFinished.\n")
+  result <- list(reference = ref, sample = samp, warped.sample = warped.sample, 
+                 warp.coef = a, warp.fun = w, crit.value = v, optim.crit = optim.crit, 
+                 mode = mode, warp.type = warp.type)
+  class(result) <- "ptw"
+  result
+}
\ No newline at end of file