Plotting

gsl.pl

@@ -41,6 +41,7 @@ write_gsl(Options) :-
   write_jacobian(Options),
   write_initial_values(Options),
   write_initial_parameter_values(Options),
+  write_print_headers(Options),
   write_print(Options).
 
 write_headers(Options) :-
@@ -228,6 +229,35 @@ initial_parameter_values(double p[])
 ').
 
 
+write_print_headers(Options) :-
+  (
+    memberchk(headers: Headers, Options)
+  ->
+    write('
+void
+print_headers(FILE *csv)
+{
+  fprintf(csv, "#Time'),
+    \+ (
+      member(Header, Headers),
+      \+ (
+        format(',\\"~a\\"', [Header])
+      )
+    ),
+    write('\\n"'),
+    write(');
+}
+')
+  ;
+    write('
+void
+print_headers(FILE *csv)
+{
+}
+')
+  ).
+
+
 write_print(Options) :-
   memberchk(equations: Equations, Options),
   length(Equations, VariableCount),

library/gsl_solver.c

@@ -22,6 +22,7 @@ main(void)
     double x[VARIABLE_COUNT];
     initial_values(x);
     initial_parameter_values(parameters);
+    print_headers(csv);
     while (t < TIME_FINAL) {
         int status = gsl_odeiv2_evolve_apply(
             e, c, s, &sys, &t, TIME_FINAL, &h, x);

numerical_simulation.pl

@@ -28,10 +28,12 @@ make_ode_system :-
 
 
 solve :-
+  gather_headers(Headers),
   gather_equations(Equations),
   gather_initial_values(InitialValues),
   gather_initial_parameter_values(InitialParameterValues),
   Options = [
+    headers: Headers,
     equations: Equations,
     initial_values: InitialValues,
     initial_parameter_values: InitialParameterValues,
@@ -46,6 +48,20 @@ solve :-
   add_trace('numerical_simulation', Table).
 
 
+gather_headers(Headers) :-
+  peek_count(variable_counter, VariableCount),
+  VariableMax is VariableCount - 1,
+  findall(
+    Header,
+    (
+      between(0, VariableMax, VariableIndex),
+      variable(Molecule, VariableIndex),
+      format(atom(Header), '[~a]', [Molecule])
+    ),
+    Headers
+  ).
+
+
 gather_equations(Equations) :-
   peek_count(variable_counter, VariableCount),
   VariableMax is VariableCount - 1,
@@ -96,6 +112,7 @@ enumerate_variables :-
   \+ (
     ode(Molecule, _),
     \+ (
+      atom(Molecule),
       count(variable_counter, VariableIndex),
       assertz(variable(Molecule, VariableIndex))
     )

ode.pl

@@ -20,8 +20,8 @@ list_ODE :-
 compute_ode :-
   retractall(ode(_, _)),
   \+ (
-    item([model: current_model, kind: rule, item: Item]),
-    rule(Item, Kinetics, Reactants, Products),
+    item([model: current_model, kind: reaction, item: Item]),
+    reaction(Item, Kinetics, Reactants, Products),
     \+ (
       kinetics(Kinetics, Reactants, KineticsExpression),
       add_molecules(Reactants, -KineticsExpression),

plot.pl

+:- module(
+  plot,
+  [
+    plot/0,
+    export_plot/1
+  ]
+).
+
+
+plot :-
+  biocham_command,
+  doc('plots the current trace.'),
+  export_plot(plot),
+  process_create(path(gnuplot), ['-persist', 'plot.plot'], []).
+
+
+export_plot(FileTemplate) :-
+  biocham_command,
+  doc('
+    saves the numerical trace of the last simulation into two files:
+    \\argument{FileTemplate}\\texttt{.csv} and \\texttt{.plot}.
+  '),
+  format(atom(PlotFile), '~a.plot', [FileTemplate]),
+  format(atom(CsvFile), '~a.csv', [FileTemplate]),
+  export_trace(CsvFile),
+  setup_call_cleanup(
+    open(PlotFile, write, Stream),
+    export_plot_stream(Stream, CsvFile),
+    close(Stream)
+  ).
+
+export_plot_stream(Stream, CsvFile) :-
+  format(Stream, '\c
+set style data lines
+set format y "%g"
+set xrange [*:*]
+set yrange [*:*]
+set ytics nomirror autofreq
+set xtics nomirror
+set mxtics default
+set key outside Left reverse
+set datafile separator ","
+plot "~a"
+', [CsvFile]).

toc.org

@@ -55,6 +55,8 @@
 - numerical_simulation.pl
 *** Traces
 - traces.pl
+*** Plotting the result of simulations
+- plot.pl
 * Index
 + index
 * Bibliography

toplevel.pl

@@ -139,7 +139,7 @@ command(Command) :-
       Command = (_ for _)
     )
   ->
-    add_reaction(Command)
+    command(add_reaction(Command))
   ;
     throw(error(unknown_command(Functor/Arity)))
   ).