#!/usr/bin/perl
#
# Perl script to convert CSV output from glucometer into graphs, using gnuplot.
#
# Author: Timothy Allen <tim@treehouse.org.za>
# License: MIT
#
# TODO Convert to python (see # https://www.physicsforums.com/threads/gnuplot-how-to-find-the-area-under-a-curve-integrate.382070/
# )

use strict;
use warnings;
use Getopt::Long;
use IPC::Open3;
use Time::Piece;
use Time::Seconds;
use Data::Dumper;

$Data::Dumper::Sortkeys = 1;

my $error = "Usage: $0 --input <CSV file> --output <output PDF> [--max <n.n>] [--low <n.n>] [--high <n.n>]\n";
my @filelines;
my @sortedlines;
my @data;
my @avg_data;
my $intervals;
my %seen_days; 
my %seen_weeks; 
my $page_size;
my $gnuplot_data;
my $total_day_graphs;
my $total_week_graphs;
my $count_graphs = 0; 
my $page_number  = 0;
my $interval     = 15; # The number of minutes to average points for the area range graph

my $input        = '';
my $output       = '';
# set these values either in mmol/L or mg/dL (don't mix them)
my $max_glucose  = 8;
my $min_glucose  = 4;
my $graph_max    = 21;
my $units        = '';
my $page         = 'a4';
my $graphs_per_page = 2;
GetOptions ("input=s"    => \$input,          # The name of the CSV file from which to read values
            "output=s"   => \$output,         # The name of the PDF file to output
            "high:f"     => \$max_glucose,    # The high end of your target blood glucose level
            "low:f"      => \$min_glucose,    # The low end of your target blood glucose level
            "max:i"      => \$graph_max,      # The highest displayed glucose level on each graph
            "units:s"    => \$units,          # mmol/L or mg/dL
            "pagesize:s" => \$page,           # size of page to print
            "graphs:i"   => \$graphs_per_page)  # The number of days printed on each page
    or die $error;



# Calculate the max and min glucose values for each time interval
# Takes an array ref of lines; returns a hash of intervals by time and min/max
sub calculate_max_min {
    my %opts   = @_;
    my $lines  = $opts{lines};
    my $fmt    = $opts{format} || qq("%Y-%m-%d %H:%M:%S");
    my %intervals;
    foreach my $row ( @{$lines} ) {
        my ( $key, $value ) = split /,/, $row;
        $value =~ s#"(.*)"#$1#;
        my $date  = Time::Piece->strptime( $key, $fmt );
        my ( $hour, $minute ) = ( $date->hour, $date->min );
        my $time = sprintf( "%02d:%02d:00", $hour, int($minute/$interval)*$interval );
    
        # Override the current minimum values for this interval if it
        # exists; otherwise, set it
        if ( exists ( $intervals{$time}{min} ) ) {
            if ( $intervals{$time}{min} < $value ) {
                $intervals{$time}{min} = $value;
            }
        } else { 
            $intervals{$time}{min} = $value;
        }
        # Override the current maximum values for this interval if it
        # exists; otherwise, set it
        if ( exists ( $intervals{$time}{max} ) ) {
            if ( $intervals{$time}{max} > $value ) {
                $intervals{$time}{max} = $value;
            }
        } else { 
            $intervals{$time}{max} = $value;
        }
    }
    return \%intervals;
}



open( my $ifh, '<:encoding(UTF-8)', $input ) 
    or die "Could not open file '$input' $!";
 
while ( my $row = <$ifh> ) {
    chomp( $row );
    push @filelines, $row;
}

close( $ifh )
    or warn "close failed: $!";

if ( $page =~ /a4/i ) {
    $page_size = "29.7cm,21.0cm";
} elsif ( $page =~ /letter/i ) {
    $page_size = "11in,8.5in";
} elsif ( $page =~ /\d+(cm|in),\d+/ ) {
    $page_size = $page;
} else { 
    # A4 size default
    $page_size = "29.7cm,21.0cm";
}

# Standardise units for gnuplot's A1C calculations 
if ( $units =~ /mg/i ) {
    $units = 'mg/dL';
} elsif ( $units =~ /mmol/i ) {
    $units = 'mmol/L';
} else {
    $units = '';
}

# Get the list of days for which to produce graphs
foreach my $row ( @filelines ) {
    if ( $row =~ m#^"((\d{4})-(\d{2})-(\d{2}))#ms ) { 
        my ( $date,$year,$month,$day ) = ( $1, split /-/, $1 ); 
        my $time  = Time::Piece->strptime( $date, "%Y-%m-%d" );
        my $week = $time->strftime("%W");
        $seen_weeks{$year}{$week}++;
        $seen_days{$date}++; 
    }
}
$total_day_graphs = scalar keys %seen_days;
$total_week_graphs = scalar keys %seen_weeks;

$intervals = calculate_max_min( 'lines' => \@filelines, 'format' => '"%Y-%m-%d %H:%M:%S"' );

# Set up basic gnuplot output options
push @data, qq(
set terminal pdf size $page_size enhanced font 'Calibri,14' linewidth 1 
#set output '$output'
);

# Read each line into a $Data variable for use by gnuplot
foreach my $d ( sort keys %seen_days ) { 
    my $label = "$1$2$3" if ( $d =~ m#(\d{4})-(\d{2})-(\d{2})# );
    push @data, qq(
\$Data$label << EOD
"timestamp","blood glucose","meal","method","comment");
    @sortedlines = ();
    foreach my $row (@filelines) {
        if ( $row =~ m#^"$d .*$# ) {
            push @sortedlines, qq($row);
        }
    }
#    @sortedlines = map { "    $_" } @sortedlines; # indent data structure
    push @data, join "\n", sort @sortedlines;
    push @data, qq(EOD);
}

# Output data averages by hour of the day
push @data, qq(
\$DataAvg << EOD
"timestamp","blood glucose","meal","method","comment");
@sortedlines = ();
foreach my $row (@filelines) {
    if ( $row =~ m#^(")\d{4}-\d{2}-\d{2} (.*)$# ) {
        push @sortedlines, qq($1$2);
    }
}
#@sortedlines = map { "    $_" } @sortedlines; # indent data structure
push @data, join "\n", sort @sortedlines;
push @data, qq(EOD);

# Output the max and min glucose values for each $interval time period
push @data, qq(
\$DataMaxMin << EOD
"timestamp","max","min");
@sortedlines = ();
foreach my $time  ( sort keys %$intervals ) {
    push @sortedlines, qq("$time","$intervals->{$time}->{max}","$intervals->{$time}->{min}");
}
#@sortedlines = map { "    $_" } @sortedlines; # indent data structure
push @data, join "\n", sort @sortedlines;
push @data, qq(EOD);


# Output weekly data averages by hour of the day
foreach my $year ( sort keys %seen_weeks ) { 
    foreach my $week ( sort keys %{$seen_weeks{$year}} ) { 
        my $time  = Time::Piece->strptime( $year, "%Y" );
        my $mon = $time + ( ONE_WEEK * ( $week - 1 ) );
        my $sun = $time + ( ONE_WEEK * ( $week - 1 ) ) + ( ONE_DAY * 6 );
        my $label = $mon->strftime("%Y%m%d");

        # Select data from the week in question
        my @weeklines;
        foreach my $row (@filelines) {
            foreach my $dow ( 0 .. 7 ) {
                my $day = $mon + ( ONE_DAY * $dow );
                my $d   = $day->strftime("%Y-%m-%d");
                if ( $row =~ m#^"$d .*$#ms ) {
                    push @weeklines, $row;
                }
            }
        }

        push @data, qq(
\$DataWeek$label << EOD
"timestamp","blood glucose","meal","method","comment");
        @sortedlines = ();
        foreach my $row (@weeklines) {
	    if ($row =~  m#^(")\d{4}-\d{2}-\d{2} (.*)$# ) {
                push @sortedlines, qq($1$2);
            }
        }
#        @sortedlines = map { "    $_" } @sortedlines; # indent data structure
        push @data, join "\n", sort @sortedlines;
        push @data, qq(EOD);
    

        push @data, qq(
\$DataWeekAvg$label << EOD
"timestamp","blood glucose","meal","method","comment");
        @sortedlines = ();
        foreach my $row (@weeklines) {
	    if ($row =~  m#^(")\d{4}-\d{2}-\d{2} (.*)$# ) {
                push @sortedlines, qq($1$2);
            }
        }
        my $week_intervals = calculate_max_min( 'lines' => \@sortedlines, 'format' => '"%H:%M:%S"' );
#        @sortedlines = map { "    $_" } @sortedlines; # indent data structure
        push @data, join "\n", sort @sortedlines;
        push @data, qq(EOD);


        push @data, qq(
\$DataMaxMin$label << EOD
"timestamp","max","min");
        @sortedlines = ();
        foreach my $time  ( sort keys %{$week_intervals} ) {
            push @sortedlines, qq("$time","$intervals->{$time}->{max}","$intervals->{$time}->{min}");
        }
#        @sortedlines = map { "    $_" } @sortedlines; # indent data structure
        push @data, sort @sortedlines;
        push @data, qq(EOD);
    }
}


# Sample each day's values into a smoothed plot, and store each plot in a new table
push @data, qq(
set datafile separator ","

# Read the CSV time format
set timefmt "%Y-%m-%d %H:%M:%S"
# Store in table in seconds, as the value must be a number
set format x "%s" timedate
set format y "%.2f" numeric 

);
foreach my $d ( sort keys %seen_days ) { 
    my $label = "$1$2$3" if ( $d =~ m#(\d{4})-(\d{2})-(\d{2})# );
    push @data, qq(
set samples 10000

set xdata
stats \$Data$label using 2
Mean$label = STATS_mean

set xdata time
set table \$SmoothData$label
plot \$Data$label using 1:2 smooth mcsplines
unset table
set table 'SmoothData$label'
plot \$Data$label using 1:2 smooth mcsplines
unset table
);
}

# Sample the average $interval values into a smoothed plot, and store in a new table
push @data, qq(
set datafile separator ","

# Read the CSV time format
set timefmt "%H:%M:%S"
# Store in table in seconds, as the value must be a number
set format x "%s" timedate
set format y "%.2f" numeric 

set samples 10000

set xdata
stats \$DataAvg using 2
MeanTotal = STATS_mean

set xdata time

set table \$DataAvgTable
plot \$DataAvg using 1:2 smooth mcsplines
unset table

set table \$SmoothDataAvg
plot \$DataAvg using 1:2 smooth bezier
unset table


# Convert DataMaxMin from CSV to table
set table \$DataMaxMinTable
plot \$DataMaxMin using 1:2:3 with table
unset table
);



















# Set up output options for gnuplot.
# We don't bother to do this at the start, since the CSV needs a comma separator
# and the new $SmoothData, which contains a table, needs a whitespace separator
push @data, qq(
# ensure separator handles tables
#reset
set datafile separator whitespace

set key off
set style data lines
set xdata time
set timefmt "%H:%M:%S"
set format x "%H:%M" timedate
set format y "%.0f" numeric 
# If extended to 23:59, the x grid overlaps with the border
set xrange ["00:00":"23:58"]
set yrange [0:$graph_max]

set style line 100 dt 3 lw 1 lc rgb "#202020"
set style line 101 dt 1 lw 1 lc rgb "#202020"
set linetype 110 lc rgb "red"

set lmargin 12
set rmargin 10
set tmargin 5
set bmargin 5

set multiplot title layout $graphs_per_page,1 

);

# For each day, generate a graph with some fancy options
foreach my $d ( sort keys %seen_days ) { 
    my $label = "$1$2$3" if ( $d =~ m#(\d{4})-(\d{2})-(\d{2})# );
    my $time  = Time::Piece->strptime( $d, "%Y-%m-%d" );
    #my $title = $time->strftime("%a %d %b %Y");
    my $title = $time->strftime("%A, %d %B %Y");

    $count_graphs++;

    push @data, qq(
set title "Daily Glucose Summary for $title" font "Calibri,18"
set xlabel "Time" offset 0,-0.25
set ylabel "Blood glucose" 
set xtics left tc rgb "#000000"
set ytics 2    tc rgb "#000000"
set grid ytics ls 100 front

set object 1 rect from graph 0, first $min_glucose to graph 1,first $max_glucose fc ls 6 fs solid 0.2 back

AVG = Mean$label
AVG_LABEL = gprintf("Average glucose: %.2f", AVG) 
set object 2 rect at graph 0.9, graph 0.9 fc ls 2 fs transparent solid 0.5 front size char strlen(AVG_LABEL), char 3
set label 2 AVG_LABEL at graph 0.9, graph 0.9 front center

plot \$SmoothData$label using (strftime("%H:%M:%S", \$1)):2:( \$2 > $max_glucose || \$2 < $min_glucose ? 110 : 1 ) with lines lw 3 lc variable 

# Add an x grid
set multiplot previous
set title "  "
set xlabel " " offset 0,-0.25
set ylabel " " 
set xtics tc rgb "#ffffff00" 
set ytics tc rgb "#ffffff00"
unset grid
unset object 1
set grid xtics ls 101
plot 1/0
);

    if ( $count_graphs % $graphs_per_page == 0 && $count_graphs < $total_day_graphs ) {
        push @data, qq(unset multiplot);
        push @data, qq(set multiplot layout $graphs_per_page,1);
        $page_number++;
    }

}
# End daily graph plot

# Plot and display a graph with the average glucose values for every $interval for all recorded days
push @data, qq(
unset multiplot

# ensure separator handles tables
set datafile separator whitespace

set key off
set style data lines
set xdata time
set timefmt "%H:%M:%S"
set format x "%H:%M" timedate
set format y "%.0f" numeric 
# If extended to 23:59, the x grid overlaps with the border
set xrange ["00:00":"23:58"]
set yrange [0:$graph_max]

set style line 100 dt 3 lw 1 lc rgb "#202020"
set style line 101 dt 1 lw 1 lc rgb "#202020"
set linetype 110 lc rgb "red"
set linetype 111 lc rgb "#B0B0B0"
set style fill transparent solid 0.5 noborder

set lmargin 12
set rmargin 10
set tmargin 5
set bmargin 5

set multiplot title layout $graphs_per_page,1 

set title "Overall Average Daily Glucose" font "Calibri,18"
set xlabel "Time" offset 0,-0.25
set ylabel "Blood glucose" 
set xtics left tc rgb "#000000"
set ytics 2    tc rgb "#000000"
set grid ytics ls 100 front

set object 1 rect from graph 0, first $min_glucose to graph 1,first $max_glucose fc ls 6 fs solid 0.05 back

AVG = MeanTotal
AVG_LABEL = gprintf("Average glucose: %.2f", AVG) 
set object 2 rect at graph 0.9, graph 0.9 fc ls 2 fs transparent solid 0.5 front size char strlen(AVG_LABEL), char 3
set label 2 AVG_LABEL at graph 0.9, graph 0.9 front center

A1C = 0
if (A1C == 0 && '$units' eq 'mg/dL') {
    A1C = (MeanTotal + 46.7) / 28.7
}
if (A1C == 0 && '$units' eq 'mmol/L') {
    A1C = (MeanTotal + 2.59) / 1.59
}
# mg/dL numbers tend to be higher than 35
if (A1C == 0 && MeanTotal >= 35) { 
    A1C = (MeanTotal + 46.7) / 28.7
}
# mmol/L numbers tend to be lower than 35
if (A1C == 0 && MeanTotal < 35) { 
    A1C = (MeanTotal + 2.59) / 1.59
}

A1C_LABEL = gprintf("Average A1c: %.1f", A1C) 
set object 3 rect at graph 0.07, graph 0.9 fc ls 4 fs transparent solid 0.5 front size char strlen(A1C_LABEL), char 3
set label 3 A1C_LABEL at graph 0.07, graph 0.9 front center

plot \$DataMaxMinTable using (strftime("%H:%M:%S", \$1)):2:3 with filledcurves lc 111, \$SmoothDataAvg using (strftime("%H:%M:%S", \$1)):2:( \$2 > $max_glucose || \$2 < $min_glucose ? 110 : 1 ) with lines lw 3 lc variable 

# Add an x grid
set multiplot previous
set title "  "
set xlabel " " offset 0,-0.25
set ylabel " " 
set xtics tc rgb "#ffffff00" 
set ytics tc rgb "#ffffff00"
unset grid
unset object 1
set grid xtics ls 101
plot 1/0
);
# End overall average plot





=cut

foreach my $year ( sort keys %seen_weeks ) { 
    foreach my $week ( sort keys %{$seen_weeks{$year}} ) { 
        my $time  = Time::Piece->strptime( "$year", "%Y" );
        my $mon = $time + ( ONE_WEEK * ( $week - 1 ) );
        my $sun = $time + ( ONE_WEEK * ( $week - 1 ) ) + ( ONE_DAY * 6 );
        my $label = $mon->strftime("%Y-%m-%d");
        my $title = $mon->strftime("%Y-%m-%d") . " to " . $sun->strftime("%Y-%m-%d");
        push @data, qq(
#reset
set datafile separator ","

set timefmt "%H:%M:%S"
set format x "%s" timedate
set format y "%.2f" numeric 
set samples 10000
set xdata
stats \$DataAvg using 2
MeanTotal = STATS_mean

set xdata time

set table \$DataAvgTable
plot \$DataAvg using 1:2 smooth mcsplines
unset table

set table \$SmoothDataAvg
plot \$DataAvg using 1:2 smooth bezier
unset table

# Convert DataMaxMin from CSV to table
set table \$DataMaxMinTable
plot \$DataMaxMin using 1:2:3 with table
unset table

reset
set datafile separator whitespace

set key off
set style data lines
set xdata time
set timefmt "%H:%M:%S"
set format x "%H:%M" timedate
set format y "%.0f" numeric 
# If extended to 23:59, the x grid overlaps with the border
set xrange ["00:00":"23:58"]
set yrange [0:$graph_max]

set style line 100 dt 3 lw 1 lc rgb "#202020"
set style line 101 dt 1 lw 1 lc rgb "#202020"
set linetype 110 lc rgb "red"
set linetype 111 lc rgb "#B0B0B0"
set style fill transparent solid 0.5 noborder

set lmargin 12
set rmargin 10
set tmargin 5
set bmargin 5

set multiplot title layout $graphs_per_page,1 

set title "Average Daily Glucose from $title" font "Calibri,18"
set xlabel "Time" offset 0,-0.25
set ylabel "Blood glucose" 
set xtics left tc rgb "#000000"
set ytics 2    tc rgb "#000000"
set grid ytics ls 100 front

set object 1 rect from graph 0, first $min_glucose to graph 1,first $max_glucose fc ls 6 fs solid 0.05 back

AVG = MeanTotal
AVG_LABEL = gprintf("Average glucose: %.2f", AVG) 
set object 2 rect at graph 0.9, graph 0.9 fc ls 2 fs transparent solid 0.5 front size char strlen(AVG_LABEL), char 3
set label 2 AVG_LABEL at graph 0.9, graph 0.9 front center

A1C = 0
if (A1C == 0 && '$units' eq 'mg/dL') {
    A1C = (MeanTotal + 46.7) / 28.7
}
if (A1C == 0 && '$units' eq 'mmol/L') {
    A1C = (MeanTotal + 2.59) / 1.59
}
# mg/dL numbers tend to be higher than 35
if (A1C == 0 && MeanTotal >= 35) { 
    A1C = (MeanTotal + 46.7) / 28.7
}
# mmol/L numbers tend to be lower than 35
if (A1C == 0 && MeanTotal < 35) { 
    A1C = (MeanTotal + 2.59) / 1.59
}

A1C_LABEL = gprintf("Average A1c: %.1f", A1C) 
set object 3 rect at graph 0.07, graph 0.9 fc ls 4 fs transparent solid 0.5 front size char strlen(A1C_LABEL), char 3
set label 3 A1C_LABEL at graph 0.07, graph 0.9 front center

plot \$DataMaxMinTable using (strftime("%H:%M:%S", \$1)):2:3 with filledcurves lc 111, \$SmoothDataAvg using (strftime("%H:%M:%S", \$1)):2:( \$2 > $max_glucose || \$2 < $min_glucose ? 110 : 1 ) with lines lw 3 lc variable 

# Add an x grid
set multiplot previous
set title "  "
set xlabel " " offset 0,-0.25
set ylabel " " 
set xtics tc rgb "#ffffff00" 
set ytics tc rgb "#ffffff00"
unset grid
unset object 1
set grid xtics ls 101
plot 1/0

);
        if ( $count_graphs % $graphs_per_page == 0 && $count_graphs < $total_day_graphs ) {
            push @data, qq(unset multiplot);
            push @data, qq(set multiplot layout $graphs_per_page,1);
            $page_number++;
        }
    }
}
=cut

push @data, qq(
unset multiplot
test
);

# Cleanup stored variables
foreach my $d ( sort keys %seen_days ) { 
    my $label = "$1$2$3" if ( $d =~ m#(\d{4})-(\d{2})-(\d{2})# );
    push @data, qq(undefine \$Data$label);
    push @data, qq(undefine \$SmoothData$label);
}

push @data, qq(
undefine \$DataAvg
undefine \$DataAvgTable
undefine \$SmoothDataAvg
undefine \$DataMaxMin
undefine \$DataMaxMinTable
);


# run the data through gnuplot
$gnuplot_data = join "\n", @data;
print $gnuplot_data;

open( my $ofh, '>', $output ) 
    or die "Could not open file '$output' $!";

my ( $pid, $stdin, $stdout, $stderr );
use Symbol 'gensym'; 
$stderr = gensym;

$pid = open3( $stdin, $stdout, $stderr, 'gnuplot' );

print $stdin $gnuplot_data;
close( $stdin );

while ( <$stdout> ) {
    print $ofh "$_";
}

while ( <$stderr> ) {
    warn $_;
}

close($stdout);
close($stderr);

waitpid( $pid, 0 );
my $child_exit_status = $? >> 8;

close( $ofh )
    or warn "close failed: $!";

#open(GNUPLOT, "|gnuplot");
#print GNUPLOT $gnuplot_data;
#close(GNUPLOT); 


# vim : set expandtab shiftwidth=4 softtabstop=4 tw=1000 :