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-Fixed the error of the AUC ploting function
-Added a new plot function based on scans -Added an intensity threshold based on the histogram of the whole dataset -Minor fixes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,10 +1,11 @@ | ||
| # Generated by roxygen2: do not edit by hand | ||
| import(raster) | ||
| import(wavelets) | ||
| import(ggplot2) | ||
| import(sp) | ||
| import(flux) | ||
| export(DataInput.txt) | ||
| export(PlotAUCImage) | ||
| export(SmoothSpectra) | ||
|
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| # Generated by roxygen2: do not edit by hand | ||
| import(raster) | ||
| import(wavelets) | ||
| import(ggplot2) | ||
| import(sp) | ||
| import(flux) | ||
| export(DataInput.txt) | ||
| export(PlotAUCImage) | ||
| export(PlotScanImage) | ||
| export(SmoothSpectra) | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,131 +1,139 @@ | ||
| ######################################################################### | ||
| # rCRMI - R package for Confocal Raman Spectroscopy Imaging data processing and visualization | ||
| # Copyright (C) 2018 Lluc Sementé Fernàndez | ||
| # | ||
| # This program is free software: you can redistribute it and/or modify | ||
| # it under the terms of the GNU General Public License as published by | ||
| # the Free Software Foundation, either version 3 of the License, or | ||
| # (at your option) any later version. | ||
| # | ||
| # This program is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| ############################################################################ | ||
|
|
||
| #' DataInput.txt | ||
| #' | ||
| #' @param path full path to .txt file. | ||
| #' @param numBands Number of .txt files to process. | ||
| #' | ||
| #' @description Reads a .txt file containing Raman data from Reinshaw devices and convert it to an RamanR data object. | ||
| #' | ||
| #' @return a rCRSIObj data object. | ||
| #' @export | ||
| #' | ||
|
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| DataInput.txt <- function(path = NULL, numBands = 1) | ||
| { | ||
| writeLines("Select files...") | ||
|
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| #Data input read | ||
| PathToFile <- list() | ||
| for(i in 1:(numBands)) | ||
| { | ||
| if(is.null(path)) | ||
| { | ||
| PathToFile[[i]] <- file.choose() | ||
| }else | ||
| { | ||
| PathToFile[[i]] <- path[i] | ||
| } | ||
| } | ||
|
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||
|
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||
| writeLines("Starting the data structuring process...") | ||
|
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| rawData <- list() | ||
| for(i in 1:(numBands)) | ||
| { | ||
| tmp <- utils::read.table(file = PathToFile[[i]],header = FALSE) | ||
| if(i==1) | ||
| { | ||
| rawData <- tmp | ||
| } else | ||
| { | ||
| rawData <- cbind(rawData,tmp[,3:4]) | ||
| } | ||
| } | ||
|
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||
| #Raman Shift Axis, number of spectra & Raman band length | ||
| RamanShift <- array(dim = c(length(union(rawData[[3]],rawData[[3]])),numBands)) | ||
| for(i in 1:numBands) | ||
| { | ||
| p1 <- 3+(i-1)*2 | ||
| RamanShift[,i] <- union(rawData[[p1]],rawData[[p1]]) | ||
| } | ||
| BandLength <- (length(RamanShift)/numBands) | ||
|
|
||
| #Coordenates | ||
| X <- union(rawData[[1]],rawData[[1]]) | ||
| Y <- union(rawData[[2]],rawData[[2]]) | ||
| numPixels <- length(X)*length(Y) | ||
| Coords <- list(X = X, Y = Y) | ||
|
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||
| #Data Shaping | ||
| RamanData <- array(dim=c(numBands*numPixels,BandLength)) | ||
| for(i in 1:numBands) | ||
| { | ||
| p <- 2*i+2 | ||
| for(j in 1:numPixels) | ||
| { | ||
| RamanData[j+numPixels*(i-1),] <- rawData[[p]][((j-1)*BandLength+1):(j*BandLength)] | ||
| } | ||
| } | ||
|
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||
| writeLines("Data structuring complete...") | ||
| return(rCRMIObj(RamanData, numPixels, numBands, RamanShift, BandLength, Coords)) | ||
| } | ||
|
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|
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| rCRMIObj <- function(RamanData, numPixels, numBands = 1, RamanShift, BandsLenght, Coords) | ||
| { | ||
| rCRSIObj <- list() | ||
|
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||
| rCRSIObj$numPixels <- numPixels | ||
| rCRSIObj$numBands <- numBands | ||
| rCRSIObj$numSpectr <- numPixels*numBands | ||
| rCRSIObj$BandsLength <- BandsLenght | ||
| rCRSIObj$AbsCoords <- Coords | ||
| rCRSIObj$RelCoords <- list(X = 1:length(Coords$X), Y = 1:length(Coords$Y)) | ||
| rCRSIObj$PixelSize <- c(Coords$X[2]-Coords$X[1], Coords$Y[2]-Coords$Y[1]) | ||
| rCRSIObj$Data <- RamanData | ||
|
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||
| # ID <- gsub(x = as.character(Sys.time()),pattern = ("-"),replacement = "") | ||
| # ID <- gsub(x = ID,pattern = (":"),replacement = "") | ||
| # ID <- gsub(x = ID,pattern = (" "),replacement = "") | ||
| # rCRSIObj$ID <- ID | ||
| # | ||
| # if (numBands == 1 & BandsLenght > 391) | ||
| # { | ||
| # rCRSIObj$FullSpect <- TRUE | ||
| # } | ||
| # else rCRSIObj$FullSpect <- FALSE | ||
|
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| rCRSIObj$RamanShiftAxis <- RamanShift | ||
| rCRSIObj$AvrgSpectr <- RamanShift | ||
|
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||
| for (i in 1:numBands) | ||
| { | ||
| for (j in 1:numPixels) | ||
| { | ||
| rCRSIObj$AvrgSpectr[,i] <- 0 | ||
| } | ||
| } | ||
| rCRSIObj$AvrgSpectr <- AverageSpectrum(numBands, numPixels, rCRSIObj) | ||
| return (rCRSIObj) | ||
| } | ||
|
|
||
| ######################################################################### | ||
| # rCRMI - R package for Confocal Raman Spectroscopy Imaging data processing and visualization | ||
| # Copyright (C) 2018 Lluc Sementé Fernàndez | ||
| # | ||
| # This program is free software: you can redistribute it and/or modify | ||
| # it under the terms of the GNU General Public License as published by | ||
| # the Free Software Foundation, either version 3 of the License, or | ||
| # (at your option) any later version. | ||
| # | ||
| # This program is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| ############################################################################ | ||
|
|
||
| #' DataInput.txt | ||
| #' | ||
| #' @param path full path to .txt file. | ||
| #' @param numBands Number of .txt files to process. | ||
| #' | ||
| #' @description Reads a .txt file containing Raman data from Reinshaw devices and convert it to an RamanR data object. | ||
| #' | ||
| #' @return a rCRSIObj data object. | ||
| #' @export | ||
| #' | ||
|
|
||
| DataInput.txt <- function(path = NULL, numBands = 1, IntensityThreshold = T) | ||
| { | ||
| writeLines("Select files...") | ||
|
|
||
| #Data input read | ||
| PathToFile <- list() | ||
| for(i in 1:(numBands)) | ||
| { | ||
| if(is.null(path)) | ||
| { | ||
| PathToFile[[i]] <- file.choose() | ||
| }else | ||
| { | ||
| PathToFile[[i]] <- path[i] | ||
| } | ||
| } | ||
|
|
||
|
|
||
| writeLines("Starting the data structuring process...") | ||
|
|
||
| rawData <- list() | ||
| for(i in 1:(numBands)) | ||
| { | ||
| tmp <- utils::read.table(file = PathToFile[[i]],header = FALSE) | ||
| if(i==1) | ||
| { | ||
| rawData <- tmp | ||
| } else | ||
| { | ||
| rawData <- cbind(rawData,tmp[,3:4]) | ||
| } | ||
| } | ||
|
|
||
| #Raman Shift Axis, number of spectra & Raman band length | ||
| RamanShift <- array(dim = c(length(union(rawData[[3]],rawData[[3]])),numBands)) | ||
| for(i in 1:numBands) | ||
| { | ||
| p1 <- 3+(i-1)*2 | ||
| RamanShift[,i] <- union(rawData[[p1]],rawData[[p1]]) | ||
| } | ||
| BandLength <- (length(RamanShift)/numBands) | ||
|
|
||
| #Coordenates | ||
| X <- union(rawData[[1]],rawData[[1]]) | ||
| Y <- union(rawData[[2]],rawData[[2]]) | ||
| numPixels <- length(X)*length(Y) | ||
| Coords <- list(X = X, Y = Y) | ||
|
|
||
| #Data Shaping | ||
| RamanData <- array(dim=c(numBands*numPixels,BandLength)) | ||
| for(i in 1:numBands) | ||
| { | ||
| p <- 2*i+2 | ||
| for(j in 1:numPixels) | ||
| { | ||
| RamanData[j+numPixels*(i-1),] <- rawData[[p]][((j-1)*BandLength+1):(j*BandLength)] | ||
| } | ||
| } | ||
|
|
||
| return(rCRMIObj(RamanData, numPixels, numBands, RamanShift, BandLength, Coords, IntensityThreshold)) | ||
| } | ||
|
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||
|
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| rCRMIObj <- function(RamanData, numPixels, numBands = 1, RamanShift, BandsLenght, Coords, IntensityThreshold) | ||
| { | ||
| rCRSIObj <- list() | ||
|
|
||
| rCRSIObj$numPixels <- numPixels | ||
| rCRSIObj$numBands <- numBands | ||
| rCRSIObj$numSpectr <- numPixels*numBands | ||
| rCRSIObj$BandsLength <- BandsLenght | ||
| rCRSIObj$AbsCoords <- Coords | ||
| rCRSIObj$RelCoords <- list(X = 1:length(Coords$X), Y = 1:length(Coords$Y)) | ||
| rCRSIObj$PixelSize <- c(Coords$X[2]-Coords$X[1], Coords$Y[2]-Coords$Y[1]) | ||
| rCRSIObj$Data <- RamanData | ||
| rCRSIObj$RamanShiftAxis <- RamanShift | ||
| rCRSIObj$AvrgSpectr <- RamanShift | ||
|
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||
| for (i in 1:numBands) | ||
| { | ||
| for (j in 1:numPixels) | ||
| { | ||
| rCRSIObj$AvrgSpectr[,i] <- 0 | ||
| } | ||
| } | ||
|
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||
|
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| rCRSIObj$AvrgSpectr <- AverageSpectrum(numBands, numPixels, rCRSIObj) | ||
|
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| if(IntensityThreshold) | ||
| { | ||
| dens <- density(rCRSIObj$Data) | ||
| aucvec <- vector(length = (length(dens$x)-1)) | ||
| for(i in 2:length(dens$x)) | ||
| { | ||
| aucvec[i-1] <- flux::auc(x = dens$x[1:i], y = dens$y[1:i]) | ||
| } | ||
|
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| intThr <- dens$x[which(aucvec>0.99*max(aucvec))[1]] | ||
|
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| for(i in 1:rCRSIObj$BandsLength) | ||
| { | ||
| rCRSIObj$Data[which(rCRSIObj$Data[,i]>intThr),i] <- median(rCRSIObj$Data[,i]) | ||
| } | ||
| } | ||
|
|
||
| writeLines("Data structuring complete...") | ||
| return (rCRSIObj) | ||
| } | ||
|
|
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