Plotting an input curve and its FFT using gnuplot in C++

Question

I'm currently working on a project¹ which will result in millions of FFTs being solved time and time again. I have a finished prototype in Python (using numpy, scipy, and the pyfftw3 package), but there are significant bottlenecks in calculation speed. I have been writing a GPU version using arrayfire, but there's still a large amount of number crunching which can't be done in parallel. I'm hoping that translating the project to C++, either the entire thing or just the compute-intensive parts, will provide an extra boost over Python where the GPU isn't appropriate.

As a starting point, I have written a very basic C++ script which defines a Gaussian curve, takes the FFT using the FFTW3 library, and plots the input curve with its FFT using gnuplot. As this is my first script in C++ (neglecting 'hello world') I'd like to make sure I'm not wandering severely off track when it comes to optimizing efficiency and speed. I haven't benchmarked this yet, but was hoping that someone with more experience in using these libraries and the language could scan over it and point out any howlers.

The code:

#include "gnuplot-iostream.h"
#include <iostream>
#include <vector>
#include <cmath>
#include <fftw3.h>
#include <complex>

typedef std::complex<double> doubleComp;

int main()
{
    Gnuplot gp;

    doubleComp i;
    i = -1;
    i = sqrt(i);

    int gridOrder = 9;
    int nPoints = pow(2, gridOrder);
    int halfPoints = pow(2, gridOrder-1);
    float tau = 18;
    float inTemp, outTemp;

    fftw_complex in[nPoints], out[nPoints], pArr1[nPoints], pArr2[nPoints];
    fftw_plan p;

    for (int idx=0; idx<nPoints; idx++) {
        in[idx][0] = exp(-pow((idx-halfPoints)/tau, 2));
        in[idx][1] = 0;
    }

    p = fftw_plan_dft_1d(nPoints, pArr1, pArr2, FFTW_FORWARD, FFTW_MEASURE);
    fftw_execute_dft(p, in, out);

    for (int idx=0; idx<nPoints; idx++) {
        out[idx][0] *= (1/double(nPoints));
        out[idx][1] *= (1/double(nPoints));
    }

    std::vector<std::pair<double, double> >inPlot;
    std::vector<std::pair<double, double> >outPlot;
    for (int idx=0; idx<nPoints; idx++) {
        inTemp = std::abs(in[idx][0] + i*in[idx][1]);

        // Deal with fftshifts needed for visuals:
        if (idx > halfPoints)
            outTemp = std::abs(out[idx-halfPoints][0] +
                                i*out[idx-halfPoints][1]);
        if (idx < halfPoints)
            outTemp = std::abs(out[idx+halfPoints][0] +
                                i*out[idx+halfPoints][1]);

        inPlot.push_back(std::make_pair(idx-halfPoints, inTemp));
        outPlot.push_back(std::make_pair(idx-halfPoints, outTemp));
    }

    gp << "set xlabel 'Grid points' font 'Helvetica, 12'\n" << 
        "set ylabel 'Intensity' font 'Helvetica, 12'" << std::endl;
    gp << "set tics font 'Helvetica, 10'" << std::endl;
    gp << "set title 'Gaussian pulse example' font 'Helvetica, 13'" << std::endl;
    gp << "set grid xtics lt 0 lw 1 lc 'gray'\n" << 
        "set grid ytics lt 0 lw 2 lc 'gray'" << std::endl;

    gp << "set term wxt '0'" << std::endl;
    gp << "plot '-' lt 1 lw 2 linecolor 'blue' with line title 'Time domain'\n";
    gp.send1d(inPlot);

    gp << "set term wxt '1'" << std::endl;
    gp << "plot '-' lt 11 lw 2 with line title"
        "'Spectral domain'\n";
    gp.send1d(outPlot);

    fftw_destroy_plan(p);

    return 0;
}

To compile (Ubuntu 16.04):

g++ -O3 GaussianPulseDefinition.cpp -o GaussianPulseDefinition -lboost_system -lboost_iostreams -lboost_filesystem -lfftw3 -lm

¹ For those who like to know the application: The project is basically a coupled PDE solver (with Qt GUI) aimed at simulating the nonlinear dynamics of optical pulse propagation in optical fibre, fibre laser systems, optical amplifiers, etc.

Ha! Lucky enough to have come across an excellent tutorial which I've been reading religiously. Also, the packages I'm using here have nearly direct counterparts in python and MATLAB, which I use daily. Even so, this would take 15mins for me in python, but took >2 weeks in c++... — FeeJF, Feb 7 at 14:07

ternonlerwen · Accepted Answer · 2017-02-07 18:33:59Z

Firstly, does the program give correct results?

If so, how do you know?

Without going into extensive unit testing, checking your results against a Matlab prototype/your Python implementation is probably good enough for now.

I can't comment on the Gnuplot functions as I don't have it installed, also but some general C++ tips are...

std::vectors are your friend! Try use them instead of C-style arrays. They 'know' their size and accessing out-of-bounds values are a major problem with C-style arrays and definitely for fiddly calculations like FFT. (You can use my_vector.data() to pass it into C-style functions).
Reduce reliance on a 'global' nPoints constant by using the vectors .size() member. (Unfortunately this outputs an unsigned integer size_t so there are some casts in the code to silence the compiler warnings). This is so that if nPoints goes out of sync with the size of the array/vector, you're not going to access an out-of-bounds value.
Always try to define a variable's value as soon as you declare it. Undefined variables are a major problem as C++ doesn't (usually) auto-define say, a double to zero. (double x; would refer to some garbage value in memory).
Always try to define variables when you need them i.e. as late as possible (see code for examples)
Try get into the habit of spitting out little functions right from the get-go, instead of one big block of code. It will break the problem up and be easier to debug. Also this will limit some variables scope so its easier to see what parts of the program change what variables.
For FFTs probably best to stick to doubles all round for the extra precision (removed the floats)
Use C++11 if you can and turn up the compiler warning level g++ -std=c++11 -Wall ...

Hopefully a bit to get you started!

I whole heartedly recommend this book if you're coming from Python, it's a short in length but really comprehensive and does a much better job than I could at explaining how to write good C++, and by the man himself - Stroustrup's "A Tour Of C++"

//#include "gnuplot-iostream.h"
#include <iostream>
#include <vector>
#include <cmath>
#include <fftw3.h>
#include <complex>
#include <cassert>

using doublePairs = std::vector<std::pair<double, double> >; // using (instead of typedef) for long named vector of pairs 

void makeGaussian(std::vector<fftw_complex>& v, double tau) { // pass-by-reference indicates v is going to be altered
    for (size_t idx=0; idx<v.size(); idx++) {   // in.size() so we don't go out of range
        const int halfPoints = v.size() / 2;
        v[idx][0] = exp(-pow((idx-halfPoints)/tau, 2));
        v[idx][1] = 0;
    }
}

void performFft(std::vector<fftw_complex>& in,
                std::vector<fftw_complex>& out) {

    fftw_plan p;

    assert(in.size() == out.size()); // test same sizes
    const int nPoints = static_cast<int> (in.size());

    std::vector<fftw_complex> pArr1 (nPoints);
    std::vector<fftw_complex> pArr2 (nPoints);
    p = fftw_plan_dft_1d(nPoints, pArr1.data(), pArr2.data(), FFTW_FORWARD, FFTW_MEASURE);
    fftw_execute_dft(p, in.data(), out.data()); // access raw pointers to vectors for c-style function call

    fftw_destroy_plan(p);

    for (auto& n : out) {                           // nicer c++11 range based for loop
        n[0] *= (1/static_cast<double> (nPoints));  // static_cast<T> is preferred to c-style casts
        n[1] *= (1/static_cast<double> (nPoints));
    }
}

void makePlotPairArrays(const std::vector<fftw_complex>& in,
                        const std::vector<fftw_complex>& out,
                        doublePairs& inPlot, 
                        doublePairs& outPlot) {

    assert(in.size() == out.size()); // test same sizes
    const std::complex<double> i {std::sqrt(-1)}; // typedef not necessary? (it's only used once)
    const int halfPoints = in.size() / 2;

    for (size_t idx=0; idx<in.size(); idx++) {
        // these Temps should be doubles?? since it's a pair of doubles not floats?
        // would lead to less precise FFTs
        double inTemp = std::abs(in[idx][0] + i*in[idx][1]); // keep these local to the loop scope

        // Deal with fftshifts needed for visuals:
        double outTemp {0};

        const int idx_ = static_cast<int> (idx); // for signed/unsigned compiler warnings
        if (idx_ > halfPoints)                              // what about when idx == halfPoints ???
            outTemp = std::abs(out[idx-halfPoints][0] +     // try make this an if/else statement so
                                i*out[idx-halfPoints][1]);  // at least one branch is always touched
        if (idx_ < halfPoints)
            outTemp = std::abs(out[idx+halfPoints][0] +
                                i*out[idx+halfPoints][1]);

        inPlot.push_back(std::make_pair(idx-halfPoints, inTemp));
        outPlot.push_back(std::make_pair(idx-halfPoints, outTemp));
    }
}

int main()
{
    constexpr int gridOrder = 9;
    constexpr int nPoints = std::pow(2, gridOrder);
    constexpr double tau = 18;
    // 'halfPoints' not needed here by declaring in function's scope
    // std::pow(2, gridOrder-1); BTW pow is heavy why not nPoints / 2?

    // our fft arrays
    std::vector<fftw_complex> in (nPoints);
    std::vector<fftw_complex> out (nPoints);

    makeGaussian(in, tau);

    performFft(in, out);

    doublePairs inPlot;
    doublePairs outPlot;
    makePlotPairArrays (in, out, inPlot, outPlot);

    // ... do the GnuPlotting

    return 0;
}

Great! Thanks a lot for taking the time to go through this. I've not had enough time to fully digest your edits (or even test the code you've given), but will be doing over the next couple of days. — FeeJF, Feb 7 at 19:31
No problem! I meant to spend 15 mins but ended up being over an hour! I hope someone else can add some more info on the FFTW usage (I do DSP but haven't used that library because of licensing). TBH Python is very nice for plotting (and you're comfortable with it) so maybe you could write your FFT stuff as C++ functions and hook into them with Boost.Python? Or I presume you've already tried pypi.python.org/pypi/pyFFTW ? — ternonlerwen, Feb 7 at 22:56
No! I hadn't tried boost.python! Will definitely look into it. My other plan was to just save everything to file then use matplotlib, but would much prefer to use the convenience of something like gnuplot if it works out. I've tried the python fftw library extensively and it's fantastic, just experimenting mainly to see if c++ will give me any speed benefits, and also just out of curiosity :-D thanks for spending the time going through it. — FeeJF, Feb 7 at 23:15
One thing I'm not sure about: Why is it recommended that variables are declared when needed (as late as possible)? From a readability perspective I personally prefer to have declarations in one block early on, at the start of each function and organised by type. Is there a particular reason why this is considered bad practise? — FeeJF, Feb 22 at 10:39
@FeeJF it's probably okay to declare constants at the head of a scope (use const or C++11 constexpr). Especially if these are sort of 'parameters' for you to tweak things as you're testing. But the reason is for errors/debugging. It's good to declare in as small a scope as possible. Declaring in a small scope means that only things in that scope can change the variable. If you must have variables in larger scopes then declaring as late as possible means only things after that declaration can change the variable. — ternonlerwen, Feb 25 at 9:26

FeeJF · Answer 2 · 2017-02-13 13:19:59Z

Using the excellent suggestions from ternonlerwen this code is hugely improved. Here are some minor tweaks that I have made to ternonlerwen's version:

const int idx_ = static_cast<int> (idx) missing from makeGaussian(), which is now added. Using idx-halfPoints, with idx having type size_t results in unexpected values as halfPoints is an integer constant.
I have separated the transform plan creation, execution, and plan destruction. The plan only needs to be calculated once for vectors of a given size, so there is no need to create and destroy a plan with every call to FFTW if more than one FFT is needed for a given data set (as is the case for my application).
For me, defining the imaginary unit i requires two lines. Simply having std::complex<double> i = std::sqrt(-1); returns nan.
idx and idx_ were mixed up in the fftshift part of makePlotPairArrays(), causing a similar problem as point 1. I have also made the suggested changes to the part of makePlotPairArrays() which does the fftshift, as I had overlooked the idx=halfPoints case in my first post.
I have passed nPoints as an argument to functions where it is needed, rather than recalculating it each time.
Additional code for saving the plots has been included at the bottom.

And I think that's pretty much it.

Code:

#include "gnuplot-iostream.h"
#include <iostream>
#include <vector>
#include <cmath>
#include <fftw3.h>
#include <complex>
#include <cassert>

using doublePairs = std::vector<std::pair<double, double> >;

void makeGaussian(std::vector<fftw_complex>& v,
                  double tau) {
    for (size_t idx=0; idx<v.size(); idx++) {
        const int halfPoints = v.size() / 2;
        const int idx_ = static_cast<int> (idx);
        v[idx][0] = exp(-pow((idx_-halfPoints)/tau, 2));
        v[idx][1] = 0;
    }
}

void planForwardFFT(fftw_plan& p,
                    int nPoints) {
    std::vector<fftw_complex> pArr1 (nPoints);
    std::vector<fftw_complex> pArr2 (nPoints);
    p = fftw_plan_dft_1d(nPoints, pArr1.data(), pArr2.data(),
                        FFTW_FORWARD, FFTW_MEASURE);
}

void performFFT(std::vector<fftw_complex>& in,
                std::vector<fftw_complex>& out,
                fftw_plan p,
                int nPoints) {
    assert(in.size() == out.size());
    fftw_execute_dft(p, in.data(), out.data());

    for (auto& n : out) {
        n[0] *= (1/static_cast<double> (nPoints));
        n[1] *= (1/static_cast<double> (nPoints));
    }
}

void makePlotPairArrays(const std::vector<fftw_complex>& in,
                        const std::vector<fftw_complex>& out,
                        doublePairs& inPlot, 
                        doublePairs& outPlot) {

    assert(in.size() == out.size());

    std::complex<double> i=-1;
    i = sqrt(i);

    const int halfPoints = in.size() / 2;

    for (size_t idx=0; idx<in.size(); idx++) {
        double inTemp = std::abs(in[idx][0] + i*in[idx][1]);

        /*
        Deal with fftshifts needed for visuals:
        The method used here may not be the fastest -- Time-domain
        approach is often implemented.
        */
        double outTemp {0};
        const int idx_ = static_cast<int> (idx);
        if (idx_ >= halfPoints)
            outTemp = std::abs(out[idx_-halfPoints][0] +
                                i*out[idx_-halfPoints][1]);
        else
            outTemp = std::abs(out[idx_+halfPoints][0] +
                                i*out[idx_+halfPoints][1]);

        inPlot.push_back(std::make_pair(idx_-halfPoints, inTemp));
        outPlot.push_back(std::make_pair(idx_-halfPoints, outTemp));
    }
}

int main() {
    Gnuplot gp;
    constexpr int gridOrder = 9;
    constexpr int nPoints = std::pow(2, gridOrder);
    constexpr double tau = 18;

    std::vector<fftw_complex> in (nPoints);
    std::vector<fftw_complex> out (nPoints);

    makeGaussian(in, tau);

    fftw_plan p;

    planForwardFFT(p, nPoints);
    performFFT(in, out, p, nPoints);

    doublePairs inPlot;
    doublePairs outPlot;
    makePlotPairArrays (in, out, inPlot, outPlot);

    // ... do the GnuPlotting
    gp << "set xlabel 'Grid points' font 'Helvetica, 12'\n" << 
        "set ylabel 'Intensity' font 'Helvetica, 12'" << std::endl;
    gp << "set tics font 'Helvetica, 10'" << std::endl;
    gp << "set title 'Gaussian pulse example' font 'Helvetica, 13'" << std::endl;
    gp << "set grid xtics lt 0 lw 1 lc 'gray'\n" << 
        "set grid ytics lt 0 lw 2 lc 'gray'" << std::endl;

    gp << "set term wxt '0'" << std::endl;
    gp << "plot '-' lt 1 lw 2 linecolor 'blue' with line title 'Time domain'\n";
    gp.send1d(inPlot);

    gp << "set term wxt '1'" << std::endl;
    gp << "plot '-' lt 11 lw 2 with line title"
        "'Spectral domain'\n";
    gp.send1d(outPlot);

    fftw_destroy_plan(p);

    return 0;
}

Compiling:

g++ -std=c++11 -Wall -O3 GaussianPulseDefinition_rev1.cpp -o GaussianPulseDefinition_rev1 -lboost_system -lboost_iostreams -lboost_filesystem -lfftw3 -lm

Saving the plots:

Replace the lines under // ... do the GnuPlotting with the following (unix only, I think):

gp << "set xlabel 'Grid points' font 'Helvetica, 12'\n" << 
    "set ylabel 'Intensity' font 'Helvetica, 12'" << std::endl;
gp << "set tics font 'Helvetica, 10'" << std::endl;
gp << "set title 'Gaussian pulse example' font 'Helvetica, 13'" << std::endl;
gp << "set grid xtics lt 0 lw 1 lc 'gray'\n" << 
    "set grid ytics lt 0 lw 2 lc 'gray'" << std::endl;

gp << "set term png" << std::endl;
gp << "set output 'Time.png'" << std::endl;
gp << "plot '-' lt 1 lw 2 linecolor 'blue' with line title 'Time domain'\n";
gp.send1d(inPlot);
gp << "set term x11" << std::endl;

gp << "set term png" << std::endl;
gp << "set output 'Spectrum.png'" << std::endl;
gp << "plot '-' lt 11 lw 2 with line title"
    "'Spectral domain'\n";
gp.send1d(outPlot);
gp << "set term x11" << std::endl;

This will save two .png files of the plots (Time.png and Spectrum.png).

Looks great! And do you know how it's doing for speed vs. python? Without getting into benchmarking, a very crude quick test could just be a loop of performing 1000 FFTs in both C++ and Python, + a stopwatch. — ternonlerwen, Feb 25 at 9:37
Not had chance to benchmark it properly yet, but will put the results here when I finally do. — FeeJF, Mar 1 at 9:12

asked	5 months ago
viewed	283 times
active	4 months ago

current community

your communities

more stack exchange communities

Plotting an input curve and its FFT using gnuplot in C++

2 Answers 2

Your Answer

Not the answer you're looking for? Browse other questions tagged c++ performance beginner data-visualization signal-processing or ask your own question.

Hot Network Questions

current community

your communities

more stack exchange communities

Plotting an input curve and its FFT using gnuplot in C++

2 Answers 2

Your Answer

Sign up or log in

Post as a guest

Not the answer you're looking for? Browse other questions tagged c++ performance beginner data-visualization signal-processing or ask your own question.

Related

Hot Network Questions