#########################################################################
# rCRSI - R package for Confocal Raman Spectroscopy Imaging data processing and visualization
# Copyright (C) 2018 Lluc Sementé Fernà ndez
#
# 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/>.
############################################################################
AverageSpectrum <- function(numBands, numPixels, rCRSIObj, plot = T)
{
temp<- array(dim =(c(rCRSIObj$BandsLength,numBands)))
for (i in 1:numBands)
{
for (j in 1:rCRSIObj$BandsLength)
{
temp[j,i] <- 0
}
}
for (i in 1:numBands)
{
for (j in 1:numPixels)
{
temp[,i] <- temp[,i] + rCRSIObj$Data[(j+(numPixels*(i-1))),]
}
temp[,i] <- temp[,i] / numPixels
}
if(plot)
{
for (i in 1:numBands)
{
g <- ggplot2::ggplot(mapping = ggplot2::aes(y = temp[,i], x = rCRSIObj$RamanShiftAxis[,i])) + ggplot2::geom_line(colour = "red") +
ggplot2::ylim(c(min(temp[,i]), max(temp[,i]))) + ggplot2::ggtitle(label = "Average Spectrum") + ggplot2::labs(x ="Raman Shift", y = "Counts") +
ggplot2::theme_bw() + ggplot2::scale_x_continuous(breaks = trunc(seq(from = min(rCRSIObj$RamanShiftAxis[,i]), to = max(rCRSIObj$RamanShiftAxis[,i]),length.out = 30)),minor_breaks = ggplot2::waiver())
print(g)
}
}
return(temp)
}
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