From 8f8dd470041c347214dbcfd5464d1d88595c2a29 Mon Sep 17 00:00:00 2001
From: "Win Cowger, PhD" <wincowger@gmail.com>
Date: Thu, 4 Jan 2024 10:11:31 -0800
Subject: [PATCH] add new function for calculating points from wavenumber
 windows.

---
 NAMESPACE                           |  3 +++
 R/smooth_intens.R                   | 37 +++++++++++++++++++++++++++--
 man/smooth_intens.Rd                |  8 +++++++
 tests/testthat/test-smooth_intens.R |  7 ++++++
 4 files changed, 53 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index eaa3a0d6..b1fc4ab7 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,6 +14,8 @@ S3method(as_OpenSpecy,list)
 S3method(c_spec,OpenSpecy)
 S3method(c_spec,default)
 S3method(c_spec,list)
+S3method(calc_window_points,OpenSpecy)
+S3method(calc_window_points,default)
 S3method(collapse_spec,OpenSpecy)
 S3method(collapse_spec,default)
 S3method(conform_spec,OpenSpecy)
@@ -71,6 +73,7 @@ export(ai_classify)
 export(as_OpenSpecy)
 export(as_hyperSpec)
 export(c_spec)
+export(calc_window_points)
 export(check_OpenSpecy)
 export(check_lib)
 export(collapse_spec)
diff --git a/R/smooth_intens.R b/R/smooth_intens.R
index a2c4a58c..ed065cf2 100644
--- a/R/smooth_intens.R
+++ b/R/smooth_intens.R
@@ -16,6 +16,7 @@
 #' @param polynomial polynomial order for the filter
 #' @param window number of data points in the window, filter length (must be
 #' odd).
+#' @param wavenum_width the width of the window you want in wavenumbers. 
 #' @param derivative the derivative order if you want to calculate the
 #' derivative. Zero (default) is no derivative.
 #' @param abs logical; whether you want to calculate the absolute value of the
@@ -26,11 +27,17 @@
 #'
 #' @return
 #' \code{smooth_intens()} returns an \code{OpenSpecy} object.
-#'
+#' 
+#' \code{calc_window_points()} returns a single numberic vector object of the 
+#' number of points needed to fill the window and can be passed to \code{smooth_intens()}.
+#' For many applications, this is more reusable than specifying a static number of points. 
+#' 
 #' @examples
 #' data("raman_hdpe")
 #'
 #' smooth_intens(raman_hdpe)
+#' 
+#' smooth_intens(raman_hdpe, window = calc_window_points(x = raman_hdpe, wavenum_width = 70))
 #'
 #' @author
 #' Win Cowger, Zacharias Steinmetz
@@ -59,7 +66,8 @@ smooth_intens.default <- function(x, ...) {
 #' @rdname smooth_intens
 #'
 #' @export
-smooth_intens.OpenSpecy <- function(x, polynomial = 3, window = 11,
+smooth_intens.OpenSpecy <- function(x, polynomial = 3, 
+                                    window = 11,
                                     derivative = 1, abs = TRUE,
                                     make_rel = TRUE, ...) {
   filt <- x$spectra[, lapply(.SD, .sgfilt, p = polynomial, n = window,
@@ -70,6 +78,31 @@ smooth_intens.OpenSpecy <- function(x, polynomial = 3, window = 11,
   return(x)
 }
 
+#' @export
+calc_window_points <- function(x, ...) {
+    UseMethod("calc_window_points")
+}
+
+#'
+#' @export
+calc_window_points.default <- function(x, ...) {
+    stop("object 'x' needs to be of class 'OpenSpecy'")
+}
+
+#'
+#' @export
+calc_window_points.OpenSpecy <- function(x, wavenum_width = 70){
+    raw_points <- floor(wavenum_width/spec_res(x))
+    if(raw_points %% 2 == 0){
+        raw_points <- raw_points - 1
+    }
+    if(raw_points > length(x$wavenumber)){
+        stop("The wavenum_width must be shorter than the full spectrum.")
+    }
+    return(raw_points)
+}
+
+
 #' @importFrom signal filter sgolay
 .sgfilt <- function(y, p, n, m, abs = F, ...) {
   out <- signal::filter(filt = sgolay(p = p, n = n, m = m, ...), x = y)
diff --git a/man/smooth_intens.Rd b/man/smooth_intens.Rd
index 2d2fc55f..a4585d87 100644
--- a/man/smooth_intens.Rd
+++ b/man/smooth_intens.Rd
@@ -37,10 +37,16 @@ resulting output.}
 \item{make_rel}{logical; if \code{TRUE} spectra are automatically normalized
 with \code{\link{make_rel}()}.}
 
+\item{wavenum_width}{the width of the window you want in wavenumbers.}
+
 \item{\ldots}{further arguments passed to \code{\link[signal]{sgolay}()}.}
 }
 \value{
 \code{smooth_intens()} returns an \code{OpenSpecy} object.
+
+\code{calc_window_points()} returns a single numberic vector object of the
+number of points needed to fill the window and can be passed to \code{smooth_intens()}.
+For many applications, this is more reusable than specifying a static number of points.
 }
 \description{
 This smoother can enhance the signal to noise ratio of the data and uses a
@@ -58,6 +64,8 @@ data("raman_hdpe")
 
 smooth_intens(raman_hdpe)
 
+smooth_intens(raman_hdpe, window = calc_window_points(x = raman_hdpe, wavenum_width = 70))
+
 }
 \references{
 Savitzky A, Golay MJ (1964). “Smoothing and Differentiation of Data by
diff --git a/tests/testthat/test-smooth_intens.R b/tests/testthat/test-smooth_intens.R
index 4f88636b..f34074c9 100644
--- a/tests/testthat/test-smooth_intens.R
+++ b/tests/testthat/test-smooth_intens.R
@@ -4,6 +4,13 @@ test_that("smooth_intens() handles input errors correctly", {
   smooth_intens(1:1000) |> expect_error()
 })
 
+test_that("calc_window_points() will return consistent values", {
+    calc_window_points(raman_hdpe, 70) |> expect_equal(27)
+    calc_window_points(raman_hdpe, 50) |> expect_equal(19)
+    calc_window_points(raman_hdpe, 140) |> expect_equal(55)
+    calc_window_points(raman_hdpe, 10000) |> expect_error()
+})
+
 test_that("smooth_intens() works as expected", {
   smt <- smooth_intens(raman_hdpe, polynomial = 3) |> expect_silent()