R/preprocess.R

In pnojai/rwalk: Random Walk Model of Neurotransmitter Release and Uptake

calculate_time_correction <- function(coord, dat_fn, sample_rate, stim_period) {
        tolerance <- .001
        
        dat <- read_experiment_csv(dat_fn, sr = sample_rate)
        
        igor_time_max_stim_1 <- as.numeric(coord[1, 1])
        igor_start_stim_1 <- as.numeric(coord[1, 2])
        time_cutoff_stim_1 <- igor_start_stim_1 + stim_period
        
        dat_stim_1 <- dat[dat$time_sec <= time_cutoff_stim_1, ]
        
        electrode_max <- max(dat_stim_1[dat_stim_1$time_sec <= time_cutoff_stim_1, "electrode"])
        # Take the minimum time for electrode_max. It might have lasted for multiple measurements.
        actual_time_max_stim_1 <- min(dat_stim_1[dat_stim_1$electrode == electrode_max, "time_sec"])
        
        time_correction <- actual_time_max_stim_1 - igor_time_max_stim_1
        
        if (abs(time_correction) < tolerance) {
                result <- 0
        } else {
                result <- time_correction
        }
        
        result
}

preprocess_coord_file <- function(coord_fn, dat_fn, input_dir, output_dir, sample_rate,
                                  stim_period) {
        
        # Split coordinate file name.
        
        # Read the coordinate file
        coord <- data.table::fread(paste(input_dir, coord_fn, sep = "/"))

        # Igor times sometimes are displaced due to a bug.
        # Correct them.
        time_correction <- calculate_time_correction(coord = coord, dat_fn = dat_fn,
                                                     sample_rate = sample_rate,
                                                     stim_period = stim_period)
        
        if (time_correction != 0) {
                coord <- coord + time_correction
        }
        
        # Append column for toggling inclusion of a stimulus
        coord <- cbind(coord, include = TRUE)
        
        print(head(coord))
        
        1
        
}

preprocess_rename_files <- function(mapdoc, input_dir, output_dir) {
        # print(mapdoc)
        # print(input_dir)
        # print(output_dir)

        
        1
        
}

validate_input_in_mapdoc <- function(mapdoc, input_dir) {
        scrub_log <- data.table::fread(mapdoc)
        input_queue <- dir(input_dir)
        # print(scrub_log[[1]])
        # print(input_queue)
        
        # REMEMBER!
        # Data frames are lists of vectors.
        # If you want the %in% operator to work, the table of values scanned must
        # be a vector, and for a column in a data frame to be a vector, you must
        # reference it with list addressing, i.e. double brackets.
        input_queue_not_in_log <- sum(!(input_queue %in% scrub_log[[1]]))
        
        if (input_queue_not_in_log) {
                print("Error: input file not in map")
                print(paste0("Map: ", mapdoc))
        }
        
        if (input_queue_not_in_log) {
                result <- FALSE
        } else {
                result <- TRUE
        }
        
        result
}