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Merge pull request #125 from wincowgerDEV/manage_spec-v1.0
Functions for managing spectra for v1.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| #' @rdname conform_spec | ||
| #' | ||
| #' @title Conform spectra | ||
| #' | ||
| #' @description | ||
| #' | ||
| #' | ||
| #' @details | ||
| #' Many of | ||
| #' | ||
| #' @param x a list object of class \code{OpenSpecy}. | ||
| #' @param res spectral resolution adjusted to. | ||
| #' | ||
| #' @return | ||
| #' \code{adj_intens()} returns a data frame containing two columns | ||
| #' named \code{"wavenumber"} and \code{"intensity"}. | ||
| #' | ||
| #' @examples | ||
| #' data("raman_hdpe") | ||
| #' | ||
| #' adj_intens(raman_hdpe) | ||
| #' | ||
| #' @author | ||
| #' Win Cowger, Zacharias Steinmetz | ||
| #' | ||
| #' @seealso | ||
| #' \code{\link{subtr_bg}()} for spectral background correction; | ||
| #' \code{\link{match_spec}()} matches spectra with the Open Specy or other | ||
| #' reference libraries | ||
| #' | ||
| #' @importFrom magrittr %>% | ||
| #' @importFrom data.table .SD | ||
| #' @export | ||
| conform_spec <- function(x, res = 5) { | ||
| UseMethod("conform_spec") | ||
| } | ||
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| #' @rdname conform_spec | ||
| #' | ||
| #' @export | ||
| conform_spec.default <- function(x, res = 5) { | ||
| stop("object 'x' needs to be of class 'OpenSpecy'", call. = F) | ||
| } | ||
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| #' @rdname conform_spec | ||
| #' | ||
| #' @export | ||
| conform_spec.OpenSpecy <- function(x, res = 5) { | ||
| wn <- conform_res(x$wavenumber, res = res) | ||
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| spec <- x$spectra[, lapply(.SD, .conform_intens, | ||
| x = x$wavenumber, | ||
| xout = wn)] | ||
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| x$wavenumber <- wn | ||
| x$spectra <- spec | ||
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| return(x) | ||
| } | ||
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| .conform_intens <- function(...) { | ||
| approx(...)$y | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,141 @@ | ||
| #' @rdname manage_spec | ||
| #' | ||
| #' @title Manage spectral objects | ||
| #' | ||
| #' @description | ||
| #' Functions for | ||
| #' | ||
| #' @details | ||
| #' details | ||
| #' | ||
| #' @param x a list object of class \code{OpenSpecy}. | ||
| #' @param file file to be read from or written to. | ||
| #' @param share defaults to \code{NULL}; needed to share spectra with the | ||
| #' Open Specy community; see \code{\link{share_spec}()} for details. | ||
| #' @param method submethod to be used for reading text files; defaults to | ||
| #' \code{\link[data.table]{fread}()} but \code{\link[utils]{read.csv}()} works | ||
| #' as well. | ||
| #' @param \ldots further arguments passed to the submethods. | ||
| #' | ||
| #' @return | ||
| #' All \code{read_*()} functions return data frames containing two columns | ||
| #' named \code{"wavenumber"} and \code{"intensity"}. | ||
| #' | ||
| #' @examples | ||
| #' c() | ||
| #' | ||
| #' @author | ||
| #' Zacharias Steinmetz, Win Cowger | ||
| #' | ||
| #' @seealso | ||
| #' \code{\link[hyperSpec]{read.jdx}()}; | ||
| #' | ||
| #' @importFrom magrittr %>% | ||
| #' @importFrom data.table data.table as.data.table fread | ||
| #' @export | ||
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| #' @rdname data_norm | ||
| #' | ||
| #' @export | ||
| c_spec <- function(..., wavenumbers = NULL, res = NULL, coords = NULL){ | ||
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| if(!is.list(files)) { | ||
| lof <- lapply(files, read_spec, coords = NULL) | ||
| } | ||
| else{ | ||
| lof <- files | ||
| } | ||
|
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| if(!is.null(wavenumbers)){ | ||
| if(wavenumbers == "first"){ | ||
| lof <- lapply(lof, function(x) { | ||
| conform_spectra(data = x, | ||
| xout = {if(!is.null(res)) conform_res(lof[[1]]$wavenumber, res = res) else lof[[1]]$wavenumber}, | ||
| coords = NULL) | ||
| }) | ||
| } | ||
| if(wavenumbers == "max_range"){ | ||
| all = unique(unlist(lapply(lof, function(x) x$wavenumber))) | ||
| lof <- lapply(lof, function(x) { | ||
| conform_spectra(data = x, | ||
| xout = {if(!is.null(res)) conform_res(all, res = res) else all}, | ||
| coords = NULL)}) | ||
| } | ||
| if(wavenumbers == "min_range"){ | ||
| smallest_range = which.min(vapply(lof, function(x) length(x$wavenumber), FUN.VALUE = numeric(1))) | ||
| lof <- lapply(lof, function(x) { | ||
| conform_spectra(data = x, | ||
| xout = {if(!is.null(res)) conform_res(lof[[smallest_range]]$wavenumber, res = res) else lof[[smallest_range]]$wavenumber}, | ||
| coords = NULL)}) | ||
| } | ||
| if(wavenumbers == "most_common_range"){ | ||
| wavenumbers = table(unlist(lapply(lof, function(x) x$wavenumber))) | ||
| common_range = as.numeric(names(wavenumbers)[wavenumbers == max(wavenumbers)]) | ||
| lof <- lapply(lof, function(x) { | ||
| conform_spectra(data = x, | ||
| xout = {if(!is.null(res)) conform_res(lof[[common_range]]$wavenumber, res = res) else lof[[common_range]]$wavenumber}, | ||
| coords = NULL)}) | ||
| } | ||
| } | ||
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| unlisted <- unlist(lof, recursive = F) | ||
|
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| list <- tapply(unlisted, names(unlisted), FUN = function(x) unname((x))) | ||
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| if(length(unique(vapply(list$wavenumber, length, FUN.VALUE = numeric(1)))) > 1 & is.null(wavenumbers)){ | ||
| stop("Wavenumbers are not the same between spectra, you need to specify how the wavenumbers should be merged.", call. = F) | ||
| } | ||
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| as_OpenSpecy( | ||
| x = list$wavenumber[[1]], | ||
| spectra = as.data.table(list$spectra), | ||
| metadata = rbindlist(list$metadata, fill = T) | ||
| ) | ||
| } | ||
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| #' @rdname manage_spec | ||
| #' | ||
| #' @importFrom data.table rbindlist | ||
| #' @export | ||
| # c_spec <- function(...) { | ||
| # cin <- c(...) | ||
| # | ||
| # lst <- tapply(cin, names(cin), FUN = function(x) unname((x))) | ||
| # | ||
| # as_OpenSpecy( | ||
| # x = lst$wavenumber[[1]], | ||
| # # TODO: Probably should add a check to make sure all the wavenumbers are | ||
| # # aligned before doing this. | ||
| # spectra = as.data.table(lst$spectra), | ||
| # metadata = rbindlist(lst$metadata, fill = T) | ||
| # ) | ||
| # } | ||
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| c_spec <- function(...) { | ||
| UseMethod("conform_spec") | ||
| } | ||
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| #' @rdname conform_spec | ||
| #' | ||
| #' @export | ||
| conform_spec.default <- function(...) { | ||
| stop("'...' items need to be of class 'OpenSpecy'", call. = F) | ||
| } | ||
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| #' @rdname conform_spec | ||
| #' | ||
| #' @export | ||
| conform_spec.list <- function(...) { | ||
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| } | ||
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| #' @rdname conform_spec | ||
| #' | ||
| #' @export | ||
| conform_spec.OpenSpecy <- function(...) { | ||
| lst <- list(...) | ||
|
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| do.call | ||
| } |
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