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I need to create a parameter file that can be managed across a Python 3.7 and a C code base. This file needs to be modifiable either by the C or the Python program with the changes being taking effect on the other software (an update function will handle reading the updated file). It's best if the file is not human readable, as it contains information that is better left obfuscated.
**Is there a recommended method to do so? **
I could create separate python and C files, but the set of parameters will change over time (for code maintenance), and the values would be changed by these programs. The list would also be very long. It would be a hassle to maintain two different files and update them over time. Also, the file may need to be exchanged between users, such that a version modified by the software ran by user1 needs to be readable by the software run by user2. The idea is that other parts of both codes could access parts of the parameter list without knowing the full contents of the list.
To clarify the example, I could have a parameter.h file containing:
struct {
double par1 =1.1;
int par 2 =2;
} par_list
And I could have a parameter.py with:
class par_list:
def(__self__):
self.par1 = double(1.1)
self.par2 = int(2)
Then, by doing a import in Python or a include in C, I could initialize the parameter list. But in this case the parameters are being read on different files.
I'm considering using some kind of binary file to keep the values, and create a script that writes both the Python and C code that reads and updates the values. I'm concerned because the binary file would need to be interchangeable between ARM architecture running Linux, and x86 architecture running Windows.
Here is an example working with numpy:
C code:
#include <stdio.h>
#include <stdint.h>
struct Struct_format{
uint8_t the_unsigned_int8;
int32_t the_signed_int32[2];
double the_double;
};
typedef struct Struct_format upperStruct;
//Use separate file to define default value:
void printStruct(upperStruct test_struct){
printf("test_struct.the_unsigned_int8 = %d\n", test_struct.the_unsigned_int8);
printf("test_struct.the_signed_int32[0] = %d\n", test_struct.the_signed_int32[0]);
printf("test_struct.the_signed_int32[1] = %d\n", test_struct.the_signed_int32[1]);
printf("test_struct.the_double = %f\n", test_struct.the_double);
}
void main(){
//Define a "default" value:
upperStruct fromC2Python = {4U,{-3,-1},2.1};
printf("Printing fromC2Python\n");
printStruct(fromC2Python);
//Save this default in a file:
FILE * fid = fopen("fromC2Python.bin","w");
fwrite((void *)&fromC2Python, sizeof(fromC2Python) ,1, fid);
fclose(fid);
//Now load the file created by Python:
upperStruct fromPython2C;
FILE * fid_py = fopen("fromPython2C.bin","r");
fread(&fromPython2C, sizeof(fromPython2C) ,1, fid_py);
fclose(fid_py);
printf("Printing fromPython2C\n");
printStruct(fromPython2C);
}
Python code:
import numpy
datatype = numpy.dtype([('potato',
[('time', numpy.uint8),
('sec', numpy.int32, 2)]),
('temp', numpy.float64)],
align=True)
fromPython2C = numpy.array([((5, (-6, -7)), 61.55)], dtype=datatype)
print(fromPython2C)
fromPython2C.tofile("fromPython2C.bin", sep="")
fromC2Python = numpy.fromfile("fromC2Python.bin", dtype=datatype, count=-1, sep="")
print(fromC2Python)
print(fromC2Python['potato'])
print(fromC2Python['potato']['time'])
print(fromC2Python['temp'])
The ideia is that numpy allows reading and writing to structured binary files. Hence, it suffices to create the dtype specification with a text parser.
I want to reproduce an ODE solver created using Mathematica with GSL.
Here is the Mathematica code which uses NDSolve:
result[r_] := NDSolve[{
s'[t] == theta - (mu*s[t]) - ((betaA1*IA1[t] + betaA2*IA2[t] + betaB1*IB1[t] + betaB2*IB2[t]) +
(betaA1T*TA1[t] + betaA2T*TA2[t] + betaB1T*TB1[t] + betaB2T*TB2[t])) * s[t] -
((gammaA1*IA1[t] + gammaA2*IA2[t] + gammaB1*IB1[t] + gammaB2*IB2[t]) +
(gammaA1T*TA1[t] + gammaA2T*TA2[t] + gammaB1T*TB1[t] + gammaB2T*TB2[t])),
//... Some other equations
s[0] = sinit,IA1[0] = IA1init,IA2[0] = IA2init,
IB1[0] = IB1init,IB2[0] = IB2init,TA1[0] = TA1init,
TA2[0] = TA2init,TB1[0] = TB1init,TB2[0] = TB2init},
{s,IA1,IA2,IB1,IB2,TA1,TA2,TB1,TB2},{t,0,tmax},
MaxSteps->100000, StartingStepSize->0.1, Method->{"ExplicitRungeKutta"}];
Trying to get the exact equivalent using GSL:
int run_simulation() {
gsl_odeiv_evolve* e = gsl_odeiv_evolve_alloc(nbins);
gsl_odeiv_control* c = gsl_odeiv_control_y_new(1e-17, 0);
gsl_odeiv_step* s = gsl_odeiv_step_alloc(gsl_odeiv_step_rkf45, nbins);
gsl_odeiv_system sys = {function, NULL, nbins, this };
while (_t < _tmax) { //convergence check here
int status = gsl_odeiv_evolve_apply(e, c, s, &sys, &_t, _tmax, &_h, y);
if (status != GSL_SUCCESS) { return status; }
}
return 0;
}
Where nbins is the number of equations given to the solver and _h the current step size.
I don't provide the equations themselves here, but the only way I found to limit the number of steps (as done with MaxSteps->100000 under Mathematica), is to adapt the first argument of the gsl_odeiv_control_y_new control feature. Here 1e-17 gives me something around 140000 steps...
Does anyone know a way to force the GSL's ODE solver to use a given maximum number of steps? As you probably understood, it is important to me to have results that I can really compare between those two tools.
Thanks for the help.
MaxSteps in Mathematica is only important when RK (Runge Kutta) gets stuck, and consequently fail to proper evolve your system. It does not fix the number of steps you want to take or the accuracy you need. Of course, higher accuracy demands lower step size which will imply more steps in a fixed interval. But my point is, unless you have a weird system where RK gets stuck and fails (and you would clear see the Mathematica error message in this case) or you set maxsteps to be ridiculous small, MaxSteps won't help you to proper compare mathematica and GSL.
To make a proper comparison you need to setup the same accuracy demands and control function in both programs. In fact, you can setup an arbitrary control function in GSL, besides the standard options, trough the API gsl_odeiv2_control_alloc and gsl_odeiv2_control_hadjust functions. You also must check what is the exactly stopping condition used in your Mathematica code.
Another option is to use a non-adaptive fixed step RK in both programs (in gsl you can call evolve the system with fix steps by calling gsl_odeiv2_driver_apply_fixed_step).
Last thing. 1e-17 seems to be an insane relative accuracy demand. Remember that roundoff errors usually does not allow RK to reach this level of accuracy. Actually roundoff errors is one of the things that can make RK to get stuck and/or make Mathematica/GSL to disagree with each other!!!! You should set accuracy to be > 1e-10.
I would like to, within my own compiled C++ code, check to see if a library package is loaded in R (if not, load it), call a function from that library and get the results back to in my C++ code.
Could someone point me in the right direction? There seems to be a plethora of info on R and different ways of calling R from C++ and vis versa, but I have not come across exactly what I am wanting to do.
Thanks.
Dirk's probably right that RInside makes life easier. But for the die-hards... The essence comes from Writing R Extensions sections 8.1 and 8.2, and from the examples distributed with R. The material below covers constructing and evaluating the call; dealing with the return value is a different (and in some sense easier) topic.
Setup
Let's suppose a Linux / Mac platform. The first thing is that R must have been compiled to allow linking, either to a shared or static R library. I work with an svn copy of R's source, in the directory ~/src/R-devel. I switch to some other directory, call it ~/bin/R-devel, and then
~/src/R-devel/configure --enable-R-shlib
make -j
this generates ~/bin/R-devel/lib/libR.so; perhaps whatever distribution you're using already has this? The -j flag runs make in parallel, which greatly speeds the build.
Examples for embedding are in ~/src/R-devel/tests/Embedding, and they can be made with cd ~/bin/R-devel/tests/Embedding && make. Obviously, the source code for these examples is extremely instructive.
Code
To illustrate, create a file embed.cpp. Start by including the header that defines R data structures, and the R embedding interface; these are located in bin/R-devel/include, and serve as the primary documentation. We also have a prototype for the function that will do all the work
#include <Rembedded.h>
#include <Rdefines.h>
static void doSplinesExample();
The work flow is to start R, do the work, and end R:
int
main(int argc, char *argv[])
{
Rf_initEmbeddedR(argc, argv);
doSplinesExample();
Rf_endEmbeddedR(0);
return 0;
}
The examples under Embedding include one that calls library(splines), sets a named option, then runs a function example("ns"). Here's the routine that does this
static void
doSplinesExample()
{
SEXP e, result;
int errorOccurred;
// create and evaluate 'library(splines)'
PROTECT(e = lang2(install("library"), mkString("splines")));
R_tryEval(e, R_GlobalEnv, &errorOccurred);
if (errorOccurred) {
// handle error
}
UNPROTECT(1);
// 'options(FALSE)' ...
PROTECT(e = lang2(install("options"), ScalarLogical(0)));
// ... modified to 'options(example.ask=FALSE)' (this is obscure)
SET_TAG(CDR(e), install("example.ask"));
R_tryEval(e, R_GlobalEnv, NULL);
UNPROTECT(1);
// 'example("ns")'
PROTECT(e = lang2(install("example"), mkString("ns")));
R_tryEval(e, R_GlobalEnv, &errorOccurred);
UNPROTECT(1);
}
Compile and run
We're now ready to put everything together. The compiler needs to know where the headers and libraries are
g++ -I/home/user/bin/R-devel/include -L/home/user/bin/R-devel/lib -lR embed.cpp
The compiled application needs to be run in the correct environment, e.g., with R_HOME set correctly; this can be arranged easily (obviously a deployed app would want to take a more extensive approach) with
R CMD ./a.out
Depending on your ambitions, some parts of section 8 of Writing R Extensions are not relevant, e.g., callbacks are needed to implement a GUI on top of R, but not to evaluate simple code chunks.
Some detail
Running through that in a bit of detail... An SEXP (S-expression) is a data structure fundamental to R's representation of basic types (integer, logical, language calls, etc.). The line
PROTECT(e = lang2(install("library"), mkString("splines")));
makes a symbol library and a string "splines", and places them into a language construct consisting of two elements. This constructs an unevaluated language object, approximately equivalent to quote(library("splines")) in R. lang2 returns an SEXP that has been allocated from R's memory pool, and it needs to be PROTECTed from garbage collection. PROTECT adds the address pointed to by e to a protection stack, when the memory no longer needs to be protected, the address is popped from the stack (with UNPROTECT(1), a few lines down). The line
R_tryEval(e, R_GlobalEnv, &errorOccurred);
tries to evaluate e in R's global environment. errorOccurred is set to non-0 if an error occurs. R_tryEval returns an SEXP representing the result of the function, but we ignore it here. Because we no longer need the memory allocated to store library("splines"), we tell R that it is no longer PROTECT'ed.
The next chunk of code is similar, evaluating options(example.ask=FALSE), but the construction of the call is more complicated. The S-expression created by lang2 is a pair list, conceptually with a node, a left pointer (CAR) and a right pointer (CDR). The left pointer of e points to the symbol options. The right pointer of e points to another node in the pair list, whose left pointer is FALSE (the right pointer is R_NilValue, indicating the end of the language expression). Each node of a pair list can have a TAG, the meaning of which depends on the role played by the node. Here we attach an argument name.
SET_TAG(CDR(e), install("example.ask"));
The next line evaluates the expression that we have constructed (options(example.ask=FALSE)), using NULL to indicate that we'll ignore the success or failure of the function's evaluation. A different way of constructing and evaluating this call is illustrated in R-devel/tests/Embedding/RParseEval.c, adapted here as
PROTECT(tmp = mkString("options(example.ask=FALSE)"));
PROTECT(e = R_ParseVector(tmp, 1, &status, R_NilValue));
R_tryEval(VECTOR_ELT(e, 0), R_GlobalEnv, NULL);
UNPROTECT(2);
but this doesn't seem like a good strategy in general, as it mixes R and C code and does not allow computed arguments to be used in R functions. Instead write and manage R code in R (e.g., creating a package with functions that perform complicated series of R manipulations) that your C code uses.
The final block of code above constructs and evaluates example("ns"). Rf_tryEval returns the result of the function call, so
SEXP result;
PROTECT(result = Rf_tryEval(e, R_GlobalEnv, &errorOccurred));
// ...
UNPROTECT(1);
would capture that for subsequent processing.
There is Rcpp which allows you to easily extend R with C++ code, and also have that C++ code call back to R. There are examples included in the package which show that.
But maybe what you really want is to keep your C++ program (i.e. you own main()) and call out to R? That can be done most easily with
RInside which allows you to very easily embed R inside your C++ application---and the test for library, load if needed and function call are then extremely easy to do, and the (more than a dozen) included examples show you how to. And Rcpp still helps you to get results back and forth.
Edit: As Martin was kind enough to show things the official way I cannot help and contrast it with one of the examples shipping with RInside. It is something I once wrote quickly to help someone who had asked on r-help about how to load (a portfolio optimisation) library and use it. It meets your requirements: load a library, accesses some data in pass a weights vector down from C++ to R, deploy R and get the result back.
// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; tab-width: 8; -*-
//
// Simple example for the repeated r-devel mails by Abhijit Bera
//
// Copyright (C) 2009 Dirk Eddelbuettel
// Copyright (C) 2010 - 2011 Dirk Eddelbuettel and Romain Francois
#include <RInside.h> // for the embedded R via RInside
int main(int argc, char *argv[]) {
try {
RInside R(argc, argv); // create an embedded R instance
std::string txt = "suppressMessages(library(fPortfolio))";
R.parseEvalQ(txt); // load library, no return value
txt = "M <- as.matrix(SWX.RET); print(head(M)); M";
// assign mat. M to NumericMatrix
Rcpp::NumericMatrix M = R.parseEval(txt);
std::cout << "M has "
<< M.nrow() << " rows and "
<< M.ncol() << " cols" << std::endl;
txt = "colnames(M)"; // assign columns names of M to ans and
// into string vector cnames
Rcpp::CharacterVector cnames = R.parseEval(txt);
for (int i=0; i<M.ncol(); i++) {
std::cout << "Column " << cnames[i]
<< " in row 42 has " << M(42,i) << std::endl;
}
} catch(std::exception& ex) {
std::cerr << "Exception caught: " << ex.what() << std::endl;
} catch(...) {
std::cerr << "Unknown exception caught" << std::endl;
}
exit(0);
}
This rinside_sample2.cpp, and there are lots more examples in the package. To build it, you just say 'make rinside_sample2' as the supplied Makefile is set up to find R, Rcpp and RInside.
Hello I am studying for a test for an intro to C programming class and yesterday I was trying to write this program to print out the even prime numbers between 2 and whatever number the user enters and I spent about 2 hours trying to write it properly and eventually I did it. I have 2 pictures I uploaded below. One of which displays the correct code and the correct output. The other shows one of my first attempts at the problem which didn't work correctly, I went back and made it as similar to the working code as I could without directly copying and pasting everything.
unfortunately new users aren't allowed to post pictures hopefully these links below will work.
This fails, it doesn't print all numbers in range with natural square root:
for (i = 2; i <= x; i++)
{
//non relevant line
a = sqrt(i);
aa = a * a;
if (aa == i);
printf("%d ",i);
}
source: http://i.imgur.com/WGG6n.jpg
While this succeeds, and prints even numbers with natural sqaure root
for (i = 2; i <= x; i++)
{
a = sqrt(i);
aa = a * a;
if (aa == i && ((i/2) *2) == i)
printf("%d ", i);
}
source: http://i.imgur.com/Kpvpq.jpg
Hopefully you can see and read the screen shots I have here. I know that the 'incorrect code' picture does not have the (i/2)*2 == i part but I figured that it would still print just the odd and even numbers, it also has the code to calculate "sqrd" but that shouldn't affect the output. Please correct me if I'm wrong on that last part though.
And Yes I am using Dev-C++ which I've read is kinda crappy of a program but I initally did this on code::blocks and it did the same thing...
Please I would very much appreciate any advice or suggestions as to what I did wrong 2 hours prior to actually getting the darn code to work for me.
Thank you,
Adam
your code in 'that' includes:
if (aa == i);
// ^
printf(...);
[note the ; at the end of the if condition]
Thus, if aa == i - an empty statement happens, and the print always occures, because it is out of the scope of the if statement.
To avoid this issue in the future, you might want to use explicit scoping1 [using {, } after control flow statements] - at least during your first steps of programming the language.
1: spartan programmers will probably hate this statement
Such errors are common. I use "step Over", "Step Into", "Break Points" and "watch window" to debug my program. Using these options, you can execute your program line by line and keep track of the variables used in each line. This way, u'll know which line is not getting executed in the desired way.
I have written a program which writes a list of data to a '.dat' file with the intention of then plotting it separately using gnuplot. Is there a way of making my code plot it automatically? My output is of the form:
x-coord analytic approximation
x-coord analytic approximation
x-coord analytic approximation
x-coord analytic approximation
x-coord analytic approximation
....
Ideally, when I run the code the graph would also be printed with an x-label, y-label and title (which could be changed from my C code). Many thanks.
I came across this while searching for something else regarding gnuplot. Even though it's an old question, I thought I'd contribute some sample code. I use this for a program of mine, and I think it does a pretty tidy job. AFAIK, this PIPEing only works on Unix systems (see the edit below for Windows users). My gnuplot installation is the default install from the Ubuntu repository.
#include <stdlib.h>
#include <stdio.h>
#define NUM_POINTS 5
#define NUM_COMMANDS 2
int main()
{
char * commandsForGnuplot[] = {"set title \"TITLEEEEE\"", "plot 'data.temp'"};
double xvals[NUM_POINTS] = {1.0, 2.0, 3.0, 4.0, 5.0};
double yvals[NUM_POINTS] = {5.0 ,3.0, 1.0, 3.0, 5.0};
FILE * temp = fopen("data.temp", "w");
/*Opens an interface that one can use to send commands as if they were typing into the
* gnuplot command line. "The -persistent" keeps the plot open even after your
* C program terminates.
*/
FILE * gnuplotPipe = popen ("gnuplot -persistent", "w");
int i;
for (i=0; i < NUM_POINTS; i++)
{
fprintf(temp, "%lf %lf \n", xvals[i], yvals[i]); //Write the data to a temporary file
}
for (i=0; i < NUM_COMMANDS; i++)
{
fprintf(gnuplotPipe, "%s \n", commandsForGnuplot[i]); //Send commands to gnuplot one by one.
}
return 0;
}
EDIT
In my application, I also ran into the problem that the plot doesn't appear until the calling program is closed. To get around this, add a fflush(gnuplotPipe) after you've used fprintf to send it your final command.
I've also seen that Windows users may use _popen in place of popen -- however I can't confirm this as I don't have Windows installed.
EDIT 2
One can avoid having to write to a file by sending gnuplot the plot '-' command followed by data points followed by the letter "e".
e.g.
fprintf(gnuplotPipe, "plot '-' \n");
int i;
for (int i = 0; i < NUM_POINTS; i++)
{
fprintf(gnuplotPipe, "%lf %lf\n", xvals[i], yvals[i]);
}
fprintf(gnuplotPipe, "e");
You can either create a gnuplot script and spawn a process running gnuplot to plot this script from the commandline, or you may use one of the provided interfaces. For C, there is a POSIX pipe-based interface from Nicolas Devillard available here:
http://ndevilla.free.fr/gnuplot/
...and an iostream-based C++ version is available via git (see: http://www.stahlke.org/dan/gnuplot-iostream/ )
The most portable and probably the easiest way would still be calling gnuplot to plot a script, though. As sje397 mentioned, check your documentation for the system() call in stdlib.h.
On a sidenote, there is also GNU plotutils, which offers libplot, a library for plotting datasets, which you could use in your application. See: http://www.gnu.org/software/plotutils/
Although I've seen a lot of ways of doing this, the most simplest way of doing this would be by using the system() (from stdlib.h) function in C.
First make a gnuplot script and save it as "name.gp" (neither the name nor the extension matter).
A simple script would be,
plot 'Output.dat' with lines
After saving this script file, just add
system("gnuplot -p name.gp");
at the end of your code.
It's as simple as that.
Make sure to add gnuplot path to the Windows System Path variables.
I've adapted the accepted answer to plot a float array while avoiding the use of a temporary file. In it, float* data_ is the array and size_t size_ its size. Hopefully it is helpful for someone!
Cheers,
Andres
void plot(const char* name="FloatSignal"){
// open persistent gnuplot window
FILE* gnuplot_pipe = popen ("gnuplot -persistent", "w");
// basic settings
fprintf(gnuplot_pipe, "set title '%s'\n", name);
// fill it with data
fprintf(gnuplot_pipe, "plot '-'\n");
for(size_t i=0; i<size_; ++i){
fprintf(gnuplot_pipe, "%zu %f\n", i, data_[i]);
}
fprintf(gnuplot_pipe, "e\n");
// refresh can probably be omitted
fprintf(gnuplot_pipe, "refresh\n");
}
I know it's too late, but answering if it may help someone.
fputs really does the job, you want. first you need to print the data you want to plot in a temporary file data.temp.
FILE *pipe_gp = popen("gnuplot -p", "w");
fputs("set terminal png \n",pipe_gp);
fputs("set output 'abc.png' \n",pipe_gp);
fputs("set xlabel 'f' \n",pipe_gp);
fputs("set xrange [0:100] \n",pipe_gp);
fputs("set yrange [0:100] \n",pipe_gp);
fputs("plot 'data.temp' u 1:2 w circles lc rgb 'pink' notitle \n",pipe_gp);
pclose(pipe_gp);