346 lines
9.3 KiB
Perl
346 lines
9.3 KiB
Perl
#!/usr/bin/perl
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#
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# Perl script to convert CSV output from glucometer into graphs, using gnuplot.
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#
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# Author: Timothy Allen <tim@treehouse.org.za>
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# License: MIT
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#
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use strict;
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use warnings;
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use Getopt::Long;
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use IPC::Open3;
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use Time::Piece;
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my $error = "Usage: $0 --input <CSV file> --output <output PDF> [--max <n.n>] [--low <n.n>] [--high <n.n>]\n";
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my @lines;
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my %seen;
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my @data;
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my @avg_data;
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my $a1c_calc;
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my $gnuplot_data;
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my $total_graphs;
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my $count_graphs = 0;
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my $page_number = 0;
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my $input = "";
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my $output = "";
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# set these values either in mmol/L or mg/dL (don't mix them)
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my $max_glucose = 8;
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my $min_glucose = 4;
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my $graph_max = 21;
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my $units = 'mmol/L';
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my $days_per_page = 2;
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GetOptions ("input=s" => \$input, # The name of the CSV file from which to read values
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"output=s" => \$output, # The name of the PDF file to output
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"high:f" => \$max_glucose, # The high end of your target blood glucose level
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"low:f" => \$min_glucose, # The low end of your target blood glucose level
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"max:i" => \$graph_max, # The highest displayed glucose level on each graph
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"units:s" => \$units, # mmol/L or mg/dL
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"graphs:i" => \$days_per_page) # The number of days printed on each page
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or die $error;
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open( my $ifh, '<:encoding(UTF-8)', $input )
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or die "Could not open file '$input' $!";
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while ( my $row = <$ifh> ) {
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chomp( $row );
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push @lines, $row;
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}
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close( $ifh )
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or warn "close failed: $!";
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# Set up basic gnuplot options for reading the CSV data
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push @data, qq(
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set terminal pdf size 29.7cm,21.0cm enhanced font 'Calibri,14' linewidth 1
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#set output '$output'
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);
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# Get the list of days for which to produce graphs
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foreach my $row ( @lines ) {
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if ( $row =~ m#^"(\d{4}-\d{2}-\d{2})#ms ) {
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my $day = $1;
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$seen{$day}++;
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}
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}
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$total_graphs = scalar keys %seen;
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# Read each line into a $Data variable for use by gnuplot
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# Then sample into a smoothed plot for each day, and store each smoothed line in a new $SmoothData$date variable
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foreach my $d ( sort keys %seen ) {
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my $label = "$1$2$3" if ( $d =~ m#(\d{4})-(\d{2})-(\d{2})# );
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push @data, qq(
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\$Data$label << EOD
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"timestamp","blood glucose","meal","method","comment");
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foreach my $row (@lines) {
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if ( $row =~ s#^"($d )#"$1#ms ) {
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push @data, $row;
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}
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}
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push @data, qq(EOD);
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push @data, qq(
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set datafile separator ","
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set timefmt "%Y-%m-%d %H:%M:%S"
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set format x "%s" timedate
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set format y "%.2f" numeric
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set samples 10000
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set xdata
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stats \$Data$label using 2
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Mean$label = STATS_mean
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set xdata time
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set table \$SmoothData$label
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#plot \$Data$label using "timestamp":"blood glucose"
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#plot \$Data$label using "timestamp":"blood glucose" smooth frequency
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plot \$Data$label using "timestamp":"blood glucose" smooth mcsplines
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#plot \$Data$label using "timestamp":"blood glucose" smooth bezier
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unset table
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undefine \$Data$label
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);
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}
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# Set up output options for gnuplot.
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# We don't bother to do this at the start, since the CSV needs a comma separator
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# and the new $SmoothData, which contains a table, needs a whitespace separator
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push @data, qq(
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# change separator from CSV to table
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reset
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set datafile separator whitespace
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set key off
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set style data lines
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set xdata time
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set timefmt "%H:%M:%S"
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set format x "%H:%M" timedate
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set format y "%.0f" numeric
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set yrange [0:$graph_max]
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# If extended to 23:59, the x grid overlaps with the border
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set xrange ["00:00":"23:58"]
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set style line 100 dt 3 lw 1 lc rgb "#202020"
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set style line 101 dt 1 lw 1 lc rgb "#202020"
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set linetype 110 lc rgb "red"
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set lmargin 12
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set rmargin 10
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set tmargin 5
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set bmargin 5
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set multiplot title layout $days_per_page,1
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);
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# For each day, generate a graph with some fancy options
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foreach my $d ( sort keys %seen ) {
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my $label = "$1$2$3" if ( $d =~ m#(\d{4})-(\d{2})-(\d{2})# );
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my $time = Time::Piece->strptime ( $d, "%Y-%m-%d" );
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#my $title = $time->strftime("%a %d %b %Y");
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my $title = $time->strftime("%A, %d %B %Y");
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$count_graphs++;
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# Algorithms for calculating HbA1c
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if ( $units =~ /mg/i ) {
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$a1c_calc = "(AVG + 46.7) / 28.7";
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} else { # Assume mmol/L
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$a1c_calc = "(AVG + 2.59) / 1.59";
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}
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push @data, qq(
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set title "Daily Glucose Summary for $title" font "Calibri,18"
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set xlabel "Time" offset 0,-0.25
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set ylabel "Blood glucose"
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set xtics left tc rgb "#000000"
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set ytics 2 tc rgb "#000000"
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set grid ytics ls 100 front
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#set arrow from graph 0,first $min_glucose to graph 1,first $min_glucose ls 6 lw 2 nohead
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#set arrow from graph 0,first $max_glucose to graph 1,first $max_glucose ls 6 lw 2 nohead
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set object 1 rect from graph 0, first $min_glucose to graph 1,first $max_glucose fc ls 6 fs solid 0.2 back
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AVG = Mean$label
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AVG_LABEL = gprintf("Average glucose: %.2f", AVG)
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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
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set label 2 AVG_LABEL at graph 0.9, graph 0.9 front center
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#A1C = $a1c_calc
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#A1C_LABEL = gprintf("Average A1c: %.1f", A1C)
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#set object 3 rect at graph 0.07, graph 0.9 fc ls 5 fs transparent solid 0.5 front size char strlen(A1C_LABEL), char 3
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#set label 3 A1C_LABEL at graph 0.07, graph 0.9 front center
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#plot \$SmoothData$label using 1:2:( \$2 > $max_glucose || \$2 < $min_glucose ? 110 : $count_graphs ) with linespoints ls 120 lc variable
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plot \$SmoothData$label using (strftime("%H:%M:%S", \$1)):2:( \$2 > $max_glucose || \$2 < $min_glucose ? 110 : 1 ) with lines lw 3 lc variable
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undefine \$SmoothData$label
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# Add an x grid
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set multiplot previous
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set title " "
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set xlabel " " offset 0,-0.25
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set ylabel " "
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set xtics tc rgb "#ffffff00"
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set ytics tc rgb "#ffffff00"
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unset grid
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unset object 1
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set grid xtics ls 101
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plot 1/0
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);
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if ( $count_graphs % $days_per_page == 0 && $count_graphs < $total_graphs ) {
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push @data, qq(unset multiplot);
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push @data, qq(set multiplot layout $days_per_page,1);
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$page_number++;
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}
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}
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# Output data averages by hour of the day
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push @data, qq(
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\$DataAvg << EOD
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"timestamp","blood glucose","meal","method","comment");
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my @sorted_rows;
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foreach my $row (@lines) {
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if ( $row =~ s#^"\d{4}-\d{2}-\d{2} #"#ms ) {
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push @sorted_rows, $row;
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}
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}
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push @data, sort @sorted_rows;
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push @data, qq(EOD);
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push @data, qq(
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reset
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set datafile separator ","
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set timefmt "%H:%M:%S"
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set format x "%s" timedate
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set format y "%.2f" numeric
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set samples 10000
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set xdata
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stats \$DataAvg using 2
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MeanTotal = STATS_mean
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set xdata time
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set table \$SmoothDataAvg
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plot \$DataAvg using 1:2 smooth bezier
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unset table
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set table \$TableDataAvg
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plot \$DataAvg using 1:2 smooth mcsplines
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unset table
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undefine \$DataAvg
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reset
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set datafile separator whitespace
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set key off
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set style data lines
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set xdata time
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set timefmt "%H:%M:%S"
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set format x "%H:%M" timedate
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set format y "%.0f" numeric
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set yrange [0:$graph_max]
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# If extended to 23:59, the x grid overlaps with the border
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set xrange ["00:00":"23:58"]
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set style line 100 dt 3 lw 1 lc rgb "#202020"
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set style line 101 dt 1 lw 1 lc rgb "#202020"
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set linetype 110 lc rgb "red"
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set lmargin 12
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set rmargin 10
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set tmargin 5
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set bmargin 5
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set multiplot title layout $days_per_page,1
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set title "Average Daily Glucose" font "Calibri,18"
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set xlabel "Time" offset 0,-0.25
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set ylabel "Blood glucose"
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set xtics left tc rgb "#000000"
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set ytics 2 tc rgb "#000000"
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set grid ytics ls 100 front
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set object 1 rect from graph 0, first $min_glucose to graph 1,first $max_glucose fc ls 6 fs solid 0.2 back
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AVG = MeanTotal
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AVG_LABEL = gprintf("Average glucose: %.2f", AVG)
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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
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set label 2 AVG_LABEL at graph 0.9, graph 0.9 front center
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A1C = $a1c_calc
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A1C_LABEL = gprintf("Average A1c: %.1f", A1C)
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set object 3 rect at graph 0.07, graph 0.9 fc ls 5 fs transparent solid 0.5 front size char strlen(A1C_LABEL), char 3
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set label 3 A1C_LABEL at graph 0.07, graph 0.9 front center
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plot \$SmoothDataAvg using ( strftime("%H:%M:%S", \$1) ):2:( \$2 > $max_glucose || \$2 < $min_glucose ? 110 : 1 ) with lines lw 3 lc variable
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#plot \$TableDataAvg using (strftime("%H:%M:%S", \$1)):2 with lines lw 1 lc 5, \$SmoothDataAvg using (strftime("%H:%M:%S", \$1)):2:( \$2 > $max_glucose || \$2 < $min_glucose ? 110 : 1 ) with lines lw 3 lc variable
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undefine \$DataAvg
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undefine \$SmoothDataAvg
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undefine \$TableDataAvg
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# Add an x grid
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set multiplot previous
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set title " "
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set xlabel " " offset 0,-0.25
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set ylabel " "
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set xtics tc rgb "#ffffff00"
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set ytics tc rgb "#ffffff00"
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unset grid
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unset object 1
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set grid xtics ls 101
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plot 1/0
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);
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push @data, qq(
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unset multiplot
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#test
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);
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# run the data through gnuplot
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$gnuplot_data = join "\n", @data;
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print $gnuplot_data;
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open( my $ofh, '>', $output )
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or die "Could not open file '$output' $!";
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my ( $pid, $stdin, $stdout, $stderr );
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use Symbol 'gensym';
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$stderr = gensym;
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$pid = open3( $stdin, $stdout, $stderr, 'gnuplot' );
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print $stdin $gnuplot_data;
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close( $stdin );
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while ( <$stdout> ) {
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print $ofh "$_";
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}
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while ( <$stderr> ) {
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warn $_;
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}
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close($stdout);
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close($stderr);
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waitpid( $pid, 0 );
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my $child_exit_status = $? >> 8;
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close( $ofh )
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or warn "close failed: $!";
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#open(GNUPLOT, "|gnuplot");
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#print GNUPLOT $gnuplot_data;
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#close(GNUPLOT);
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# vim: set expandtab shiftwidth=4 softtabstop=4 :
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