R/plot.png.overview.R

In mruessler/rephys: Analyse electrophysiological data

#' plot.png.overview
#'
#' This file is part of the rephys package.
#'
#' Copyright(c) Martin Rüßler
#'
#' This file may be licensed under the terms of of the
#' GNU General Public License Version 3 (the ``GPL''),
#' or (at your option) any later version.
#'
#' Software distributed under the License is distributed
#' on an ``AS IS'' basis, WITHOUT WARRANTY OF ANY KIND, either
#' express or implied. See the GPL for the specific language
#' governing rights and limitations.
#'
#' You should have received a copy of the GPL along with this
#' program. If not, go to http://www.gnu.org/licenses/gpl.html
#' or write to the Free Software Foundation, Inc.,
#' 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#'
#' The development of this software was supported by the
#' Excellence Cluster EXC 277 Cognitive Interaction Technology.
#' The Excellence Cluster EXC 277 is a grant of the Deutsche
#' Forschungsgemeinschaft (DFG) in the context of the German
#' Excellence Initiative.
#'
#' @description \code{plot.png.overview} A function to create png overviews of ephys log files
#' @param wd character working directory where the data is. It is required to use the folder containing the data, meta, and png subfolders as input
#' @param maxchunk numeric add a maximum number of files to be processed at once
#' @export
#'
plot.png.overview <- function(wd = NA, maxchunk = 100) {
	# check whether a working directory was specified
	if (is.na(wd) == TRUE) {
		wd <- readline(prompt = "Please enter a folder path! ")
	}
	dd <- paste0(wd, "/data")
	# get the files from folder
	storage <- dir(dd, pattern = ".csv")
	writeLines(paste(length(storage), "files to process."))
	# only do chunks of maxchunk at maximum (due to memory limitations)
	while (length(storage) > 0) {
		if (length(storage) >= maxchunk) {
			files <- storage[1:maxchunk]
		}
		else {
			files <- storage
		}
		# get the data from the files
		data <- read.ephysdata(files, folder = dd, mc = TRUE)
		# plot the data from the files
		writeLines("Writing png files.")
		for (i in 1:length(files)) {
			# dual recordings
			if (ncol(data) == 2 * length(files)) {
				tsdata <- ts(data = data[((i * 2) - 1):(i * 2)], start = 1/25000, end = 10, deltat = 1/25000)
				png(width = 960, filename = sub(pattern = ".csv", replacement = "--raw.png", x = paste0(wd, "/png/", files)[i]))
				par(mfrow = c(2, 1), bty = "n", omi = c(rep(0.5, 4)), mai = c(0.1, 0.1, 0.2, 0.1))
				plot(tsdata[, 1], ylim = c(-0.2, 0.15), xlab = "", ylab = "Amplitude", xaxt = "n", main = files[i])
				plot(tsdata[, 2], ylim = c(-0.2, 0.15), xlab = "Time (s)", ylab = "Amplitude")
				dev.off()
			}
			# single recordings
			else {
				tsdata <- ts(data = data[i], start = 1/25000, end = 10, deltat = 1/25000)
				png(width = 960, filename = sub(pattern = ".csv", replacement = "--raw.png", x = paste0(wd, "/png/", files)[i]))
				plot(tsdata, ylim = c(-0.2, 0.15), xlab = "Time (s)", ylab = "Amplitude", main = files[i])
				dev.off()
			}
		}
		writeLines("Finished writing png files.")
		storage <- storage[-(1:maxchunk)]
		# remove NA from storage if introduced
		storage <- storage[!is.na(storage)]
		if (length(storage) > 0) {
			writeLines(paste0(length(storage), " files left."))
		}
	}
}