R/read.EEM.R

In RichardLaBrie/paRafac_correction: Corrects EEM all at once before using Matlab for PARAFAC

#'@title Reads CSV file of EEMs produced by the Cary Eclipe fluorometer
#'
#'@description This function reads a CSV file produced by the Cary Eclipe fluorometer
#'
#'@param excitation is a vector of three variables of the scanning setup (min, max, interval).
#'Default is c(220, 450, 5)
#'@param emission is a vector of three variables of the scanning setup (min, max, interval).
#'Default is c(230, 600, 2)
#'@param EMCOL is a logical parameter indicating whether or not the emission are
#'stored as column in the csv file. Default is FALSE.
#'@param samplepercsv is a parameter which indicates the number of sample
#'@param split is a parameter to define the symbol between your samples name if samplepercsv > 1.
#'Default is "_"
#'@param dot.number is a paramater for the number of . in CDOM file name. Default is 1 (.txt or .csv)
#'@param fluorometer is a paramater for the fluorometer model. Default is "Cary Eclipse".
#'Other model supported: "Shimadzu"
#'@param EEMskip is a parameter to skip lines in EEM file before data. Default is 1
#'
#'@seealso \code{\link{plot.EEM.go}}
#'
#'@export
#'
#'
#

read.EEM <- function(filename, excitation = c(220, 450, 5), emission = c(230, 600, 2),
                     EMCOL = FALSE, samplepercsv = 1, split = "_", dot.number = 1,
                     fluorometer = "Cary Eclipse", EEMskip, data.file = "data", subfolder)
{

  # define wavelenght vectors and matrix
  wlex = seq(excitation[1], excitation[2], excitation[3])
  wlem = seq(emission[1], emission[2], emission[3])

  nex = length(wlex)
  nem = length(wlem)

  if(fluorometer == "Shimadzu")
  {
    data = read.csv(paste0("./",data.file, subfolder, filename), skip = EEMskip)
    Ex = rep(wlex,each=nem)
    data = cbind(Ex, data)
    colnames(data) = c("Ex", "Em", "Fluo")
    eem = reshape(data, idvar = "Ex", timevar = "Em", direction = "wide")
    eem = eem[,-1]
    rownames(eem) = wlex
    colnames(eem) = wlem
  }
  
  
  
  if(fluorometer == "Cary Eclipse")
  {
    data = read.csv(paste0("./",data.file, subfolder, filename), skip = EEMskip)
    eem = matrix(nrow = nex, ncol = nem)
    eem2 = matrix(nrow = nex, ncol = nem)
    eem3 = matrix(nrow = nex, ncol = nem)
    eem4 = matrix(nrow = nex, ncol = nem)
    data = as.matrix(data)
    # lopp on either nem or nex
	  if (EMCOL)
  	{
  	x = 1
  	if (samplepercsv == 1)
  		{
  		for (i in seq(2, (2 * nem), 2))
  			{
    		eem[, x] = data[, i]
  			x = x + 1
	  		}
    	}
    	else
	    {
	      if(samplepercsv == 2)
	      {
	      	x = 1
	  	  	for (i in seq(2, (2 * samplepercsv * nem), 4))
	  	  	{
	  	  		eem[, x] = data[, i]
	  		  	x = x + 1
	  		  }
	  	  	x = 1
	  	  	for (j in seq(4, (2 * samplepercsv * nem), 4))
	  	  	{
	  	  		eem2[, x] = data[, j]
	  	  		x = x + 1
	  	  	}
	  	  }
	     	else
	    	{
	    		if(samplepercsv == 3)
	    		{
	    			x = 1
	    			for (i in seq(2, (2 * samplepercsv * nem), 6))
	    			{
	    				eem[, x] = data[, i]
	    				x = x + 1
	    			}
	    			x = 1
	    			for (j in seq(4, (2 * samplepercsv * nem), 6))
	    			{
	    				eem2[, x] = data[, j]
	    				x = x + 1
	    			}
	    			x = 1
	    			for (k in seq(6, (2 * samplepercsv * nem), 6))
	 	  			{
	    				eem3[, x] = data[, k]
	    				x = x + 1
	 	  			}	
  	  		}
  	  		else
		  		{
	  	  		x = 1
		    		for (i in seq(2, (2 * samplepercsv * nem), 8))
			  		{
		    			eem[, x] = data[, i]
		    			x = x + 1
			  		}
		    		x = 1
		    		for (j in seq(4, (2 * samplepercsv * nem), 8))
			  		{
		    			eem2[, x] = data[, j]
		    			x = x + 1
			  		}
		    		x = 1
			     	for (k in seq(6, (2 * samplepercsv * nem), 8))
			  		{
		    			eem3[, x] = data[, k]
		    			x = x + 1
			  		}
		    		x = 1
		    		for (l in seq(8, (2 * samplepercsv * nem), 8))
			  		{
			     		eem4[, x] = data[, l]
  	  				x = x + 1
  					}
  				}
  			}
  		}
	  }
    else 
  	{
  		x = 1
  		if (samplepercsv == 1)
  		{
     		for (i in seq(2, (2 * nex), 2))
	  		{
	   	  	eem[x, ] = data[, i]
	     		x = x + 1
	   		}
		  }
     	else
	  	{
    		x = 1
    		if(samplepercsv == 2)
    		{
    			for (i in seq(2, (2 * samplepercsv * nex), 4))
    			{
	  	  		eem[x, ] = data[, i]
	  	  		x = x + 1
	  			}
    			x = 1
    			for (j in seq(4, (2 * samplepercsv * nex), 4))
	  			{
	     			eem2[x, ] = data[, j]
	     			x = x + 1
		  		}
		  	}
	    	else
		  	{
		    	if(samplepercsv == 3)
  	  		{
  	  			x = 1
  	  			for (i in seq(2, (2 * samplepercsv * nex), 6))
  	  			{
  	  				eem[x, ] = data[, i]
  	  				x = x + 1
  	  			}
  	  			x = 1
  	  			for (j in seq(4, (2 * samplepercsv * nex), 6))
  	  			{
  	  				eem2[x, ] = data[, j]
  	  				x = x + 1
  	  			}
  	  			x = 1
  	  			for (k in seq(6, (2 * samplepercsv * nex), 6))
  	  			{
  	  				eem3[x, ] = data[, k]
  	  				x = x + 1
  	  			}	
  	  		}
  	  		else
	    		{
	    			for (i in seq(2, (2 * samplepercsv * nex), 8))
	    			{
	    				eem[x, ] = data[, i]
	    				x = x + 1
	    			}
	    			x = 1
	    			for (j in seq(4, (2 * samplepercsv * nex), 8))
	    			{
	    				eem2[x, ] = data[, j]
	    				x = x + 1
	    			}
	    			x = 1
	    			for (k in seq(6, (2 * samplepercsv * nex), 8))
	    			{
	    				eem3[x, ] = data[, k]
	    				x = x + 1
	    			}
	    			x = 1
	    			for (l in seq(8, (2 * samplepercsv * nex), 8))
	    			{
	    				eem4[x, ] = data[, l]
	    				x = x + 1
	    			}
	    		}
	    	}
  	  }
	  }
	}
	
	 # extract file name
 if (.Platform$OS.type == "unix")
 {
  if(samplepercsv == 1)
  {
  x = unlist(strsplit(filename, '/'))
  ix = length(x)
  z = unlist(strsplit(x[ix], ".", fixed = T))[dot.number] 
  }
  else
  {
  x = unlist(strsplit(filename, "/"))
  ix = length(x)
  y = unlist(strsplit(x[ix], ".", fixed = T))[dot.number] 
  z = unlist(strsplit(y, split))
  }
 }
 else
 {
  if(samplepercsv == 1)
  {
  x = unlist(strsplit(filename, "\\", fixed = T))
  ix = length(x)
  z = unlist(strsplit(x[ix], ".", fixed = T))[dot.number] 
  }
  else
  {
  x = unlist(strsplit(filename, "\\", fixed = T))
  ix = length(x)
  y = unlist(strsplit(x[ix], ".", fixed = T))[dot.number] 
  z = unlist(strsplit(y, split))
  }
 }
	
	 if(samplepercsv == 1)
		{
		 data = list(EEM.name = list(name1 = z), EEM.list = list(eem = eem), wlex = wlex, wlem = wlem)
		}
	 else
		{
		 if(samplepercsv == 2)
			{
			 data = list(EEM.name = list(name1 = z[1], name2 = z[2]), EEM.list = list(eem = eem, eem2 = eem2), wlex = wlex, wlem = wlem)
			}
		 else
			{
			 if(samplepercsv == 3)
			 {
			 data = list(EEM.name = list(name1 = z[1], name2 = z[2], name3 = z[3]), EEM.list = list(eem = eem, eem2 = eem2, eem3 = eem3), wlex = wlex, wlem = wlem)
			 }
			 else
		 {
				 data = list(EEM.name = list(name1 = z[1], name2 = z[2], name3 = z[3], name4 = z[4]), EEM.list = list(eem = eem, eem2 = eem2, eem3 = eem3, eem4 = eem4), wlex = wlex, wlem = wlem)
			 }
			}
		}
	 return(data)

}