#!/usr/bin/perl -w
use strict;
no warnings "recursion";

my %ISFET_currents;
my $searchdir;
my $outfile;

unless(defined($ARGV[0]) && defined($ARGV[1])) {
    print "Parsing ISFET-2007 transconductance IV curve data files\
    \tsearches in folders recursively starting from specified \"root\" folder\
    \tFoldername => must be ISFET number (device was marked)\
    \tOutput file => to write parsed data\n\
    Data processing:\n\
    \t-find current values at Ugs = 5V\
    \t-find out about the pH of buffer in filename(if recorded)\
    \t-check wheather channel currents meet 350..650 uA range\
    \t-find difference between currents in channels\
    \t-say OK for using if remained ISFETS meet less than 60 uA difference\n\n";

    print "Usage:\t./current_script  searchdir  output_filename\n\n";
    exit;
}
chomp($searchdir = $ARGV[0]);

chomp($outfile = $ARGV[1]);

open(DATA_FILE, ">>$outfile") ||
die "Can't open $outfile: $!";

parse_dir($searchdir);

foreach my $ISFET (sort keys %ISFET_currents) {

    if(($ISFET_currents{$ISFET}) < 60 ) {
        print DATA_FILE "\nISFET #$ISFET Current diff = $ISFET_currents{$ISFET}";
        print DATA_FILE " OK";

    }
}
close(DATA_FILE);

sub parse_dir {

    my $searchdir = shift;

    my $ISFET_num = $searchdir;
    $ISFET_num    =~  s{.*/}{};

    opendir(DIR, $searchdir) ||
    die "\nCan't open $searchdir: $!";

    my @files = readdir(DIR);
    closedir(DIR);

    foreach my $current_file (@files) {
        next if $current_file =~ m/^\.\.?$/;

        if ( $current_file =~ m/ugs/i ) {

            my $pH_data;

            if( $current_file =~ m/pH((\d+)[_.]?(\d+))/gi ) {
                $pH_data = 'pH' . $1;
            }

            open(CUR_FILE, "<$searchdir/$current_file") ||
            die "Can't open $current_file: $!";

            my @iv_lines= <CUR_FILE>;

            my($Ugs, $Uds, $I0, $I1) = iv_check(@iv_lines);
            my $I_diff = abs($I0 - $I1);
            $I_diff =~ s/(.\d\d)\d+/$1/g;

                if(($I0 < 350 || $I0 > 650 ) ||
                   ($I1 < 350 || $I1 > 650 ))   {

                    print DATA_FILE "\n=============================\
                    \nFile: $current_file\
                    \nISFET = $ISFET_num\
                    \nChannel current is not in range 350..650 uA\
                    \nChannel currents I = $I0, $I1 uA
                    \nVoltage Ugs = $Ugs\n\
                    $pH_data\n";
                } else {

                    $ISFET_currents{$ISFET_num} = $I_diff;
                    print DATA_FILE"\n===============================\
                    \nFile: $current_file\
                    \nISFET = $ISFET_num\
                    \nVoltages:\
                    \n\tUgs = -$Ugs\
                    \n\tUds = -$Uds\
                    \nCurrents:\
                    \n\tI0 = $I0\
                    \n\tI1 = $I1\
                    \n\tDifference = $I_diff\n";
                }
            close(CUR_FILE);
        }

        if ( -d "$searchdir/$current_file" ) {
            parse_dir("$searchdir/$current_file");
        }
    }
}

sub iv_check {

    my @lines = @_;
    my @iv_checked;
    foreach my $line (@lines) {

        next unless $line =~ m/^(\d\.\d{2})
                                (?>\s+)
                                (\d\.\d{2})
                                (?>\s+)
                                (\d+\.\d{2})
                                (?>\s+)
                                (\d+\.\d{2})
                              /xgi;
        my $Ugs = $1;
        my $Uds = $2;
        my $I0  = $3;
        my $I1  = $4;

            if( $Ugs > 4.90 && $Ugs < 5.20) {

                push @iv_checked, $Ugs, $Uds, $I0, $I1;
                return @iv_checked;
            }

    }
}