Cleanups.
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@ -5,39 +5,48 @@
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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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# TODO Convert to python (see # https://www.physicsforums.com/threads/gnuplot-how-to-find-the-area-under-a-curve-integrate.382070/
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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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use Data::Dumper;
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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 @sorted_lines;
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my @data;
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my @avg_data;
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my %intervals;
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my %seen;
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my $a1c_calc;
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my $page_size;
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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 $interval = 15; # The number of minutes to average points for the area range graph
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my $input = "";
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my $output = "";
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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 $units = '';
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my $page = 'a4';
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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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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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"pagesize:s" => \$page, # size of page to print
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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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@ -51,9 +60,20 @@ while ( my $row = <$ifh> ) {
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close( $ifh )
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or warn "close failed: $!";
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if ( $page =~ /a4/i ) {
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$page_size = "29.7cm,21.0cm";
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} elsif ( $page =~ /letter/i ) {
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$page_size = "11in,8.5in";
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} elsif ( $page =~ /\d+(cm|in),\d+/ ) {
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$page_size = $page;
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} else {
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# A4 size default
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$page_size = "29.7cm,21.0cm";
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}
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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 terminal pdf size $page_size enhanced font 'Calibri,14' linewidth 1
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#set output '$output'
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);
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@ -144,13 +164,6 @@ foreach my $d ( sort keys %seen ) {
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$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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@ -168,11 +181,6 @@ 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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@ -200,18 +208,66 @@ plot 1/0
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}
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# Output data averages by hour of the day
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@sorted_lines = ();
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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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push @sorted_lines, $row;
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}
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}
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push @data, sort @sorted_rows;
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push @data, sort @sorted_lines;
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push @data, qq(EOD);
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# Output min/max for each time interval
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foreach my $row ( @sorted_lines ) {
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$row =~ s/"//g;
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my ( $time, $value ) = split /,/, $row;
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my ( $hour, $minute, $second ) = split /:/, $time;
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$time = sprintf( "%02d:%02d:00", $hour, int($minute/$interval)*$interval );
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# Override the current minimum values for this interval if it
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# exists; otherwise, set it
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if ( exists ( $intervals{$time}{min} ) ) {
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if ( $intervals{$time}{min} < $value ) {
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$intervals{$time}{min} = $value;
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}
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} else {
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$intervals{$time}{min} = $value;
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}
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# Override the current maximum values for this interval if it
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# exists; otherwise, set it
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if ( exists ( $intervals{$time}{max} ) ) {
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if ( $intervals{$time}{max} > $value ) {
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$intervals{$time}{max} = $value;
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}
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} else {
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$intervals{$time}{max} = $value;
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}
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}
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$Data::Dumper::Sortkeys = 1;
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#die Dumper(\%intervals);
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push @data, qq(
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\$DataMaxMin << EOD
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"timestamp","max","min");
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foreach my $time ( sort keys %intervals ) {
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warn $time;
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push @data, qq("$time","$intervals{$time}{max}","$intervals{$time}{min}");
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}
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push @data, qq(EOD);
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# Standardise units for gnuplot's A1C calculations
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if ( $units =~ /mg/i ) {
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$units = 'mg/dL';
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} elsif ( $units =~ /mmol/i ) {
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$units = 'mmol/L';
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} else {
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$units = '';
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}
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push @data, qq(
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reset
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set datafile separator ","
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@ -225,16 +281,41 @@ stats \$DataAvg using 2
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MeanTotal = STATS_mean
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set xdata time
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set table \$DataAvgTable
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#avg(x) = g
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#min(x) = x<g
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#max(x) = x>g
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#f(x) = g
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#fit f(x) \$DataAvg using 1:(\$2>MeanTotal?\$2:'') via t, g
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#plot f(x) smooth mcsplines
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#plot \$DataAvg using 1:(\$2>MeanTotal?\$2:'') every $count_graphs/2 lc 2, \$DataAvg using 1:(\$2<MeanTotal?\$2:'') every $count_graphs/2 lc 1
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#samples(x) = \$0 > 4 ? 5 : (\$0+1)
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#avg5(x) = (shift5(x), (back1+back2+back3+back4+back5)/samples(\$0))
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#shift5(x) = (back5 = back4, back4 = back3, back3 = back2, back2 = back1, back1 = x)
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## Initialize a running sum
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#init(x) = (back1 = back2 = back3 = back4 = back5 = sum = 0)
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#plot sum = init(0), \$DataAvg using 1:2 title 'data' lw 2 lc rgb 'forest-green', '' using 1:(avg5(\$2)) pt 7 ps 0.5 lw 1 lc rgb "blue"
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plot \$DataAvg using 1:2 smooth mcsplines
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unset table
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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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# Convert DataMaxMin from CSV to table
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set table \$DataMaxMinTable
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plot \$DataMaxMin using 1:2:3 with table
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unset table
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reset
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set datafile separator whitespace
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@ -252,6 +333,8 @@ 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 linetype 111 lc rgb "#B0B0B0"
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set style fill transparent solid 0.5 noborder
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set lmargin 12
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set rmargin 10
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@ -267,24 +350,43 @@ 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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set object 1 rect from graph 0, first $min_glucose to graph 1,first $max_glucose fc ls 6 fs solid 0.05 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 = $a1c_calc
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A1C = 0
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if (A1C == 0 && '$units' eq 'mg/dL') {
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A1C = (MeanTotal + 46.7) / 28.7
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}
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if (A1C == 0 && '$units' eq 'mmol/L') {
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A1C = (MeanTotal + 2.59) / 1.59
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}
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# mg/dL numbers tend to be higher than 35
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if (A1C == 0 && MeanTotal >= 35) {
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A1C = (MeanTotal + 46.7) / 28.7
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}
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# mmol/L numbers tend to be lower than 35
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if (A1C == 0 && MeanTotal < 35) {
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A1C = (MeanTotal + 2.59) / 1.59
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}
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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 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
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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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#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 \$DataAvgTable using (strftime("%H:%M:%S", \$1)):2 with points lc 5 ps 0.5 pt 37, \$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 \$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
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undefine \$DataAvg
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undefine \$DataMaxMin
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undefine \$DataMaxMinTable
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undefine \$SmoothDataAvg
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undefine \$TableDataAvg
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undefine \$DataAvgTable
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# Add an x grid
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set multiplot previous
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@ -302,7 +404,7 @@ plot 1/0
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push @data, qq(
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unset multiplot
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#test
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test
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);
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# run the data through gnuplot
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@ -342,4 +444,4 @@ close( $ofh )
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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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# vim : set expandtab shiftwidth=4 softtabstop=4 tw=1000 :
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