Skip to main content

numerics - Does Mathematica reuse previous computations?


I am doing an analysis of experimental results in which I need to repeat the same GaussianFilter hundred of times on different data. As explained in the documentation, GaussianFilter just convolves the data with a Gaussian kernel. Does it recompute the kernel every time I call the function, or will it somehow preserve and reuse the previous kernel? Would it be more efficient computationally for me to precompute the kernel (which I could do easily by applying GaussianFilter to a KroneckerDelta array), then do hundreds of ListConvolves instead of hundreds of GaussianFilters?



Answer



Here I implemented three different versions of Gaussian filtering (for periodic data). It took me a while to adjust the constants and still some of them might be wrong.


Prepare the Gaussian kernel


n = 200000;

σ = .1;
t = Subdivide[-1. Pi, 1. Pi, n - 1];
ker = 1/Sqrt[2 Pi]/ σ Exp[-(t/σ)^2/2];
ker = Join[ker[[Quotient[n,2] + 1 ;;]], ker[[;; Quotient[n,2]]]];

Generate noisy function


u = Sin[t] + Cos[2 t] + 1.5 Cos[3 t] + .5 RandomReal[{-1, 1}, Length[t]];

The three methods with their timings. As Niki Estner pointed out, GaussianFilter with the option Method -> "Gaussian" performs much batter than GaussianFilter with the default emthod.


kerhat = 2 Pi/Sqrt[N@n] Fourier[ker];

vConvolve = (2. Pi/n) ListConvolve[ker, u, {-1, -1}]; // RepeatedTiming // First
vFFT = Re[Fourier[InverseFourier[u] kerhat]]; // RepeatedTiming // First
vFilter = GaussianFilter[u, 1./(Pi) σ n, Padding -> "Periodic"]; // RepeatedTiming // First
vGaussian = GaussianFilter[u, 1./(Pi) σ n, Padding -> "Periodic", Method -> "Gaussian"]; // RepeatedTiming // First


0.0038


0.0058


0.055


0.0072




ListLinePlot[{u, vFFT, vFilter, vConvolve}]

enter image description here


From further experiments with different values for n, GaussianFilter seems to be slower by a factor 10-20 over a wide range of n (from n = 1000 to n = 1000000). So it seems that it does use some FFT-based method (because it has the same speed asymptotics) but maybe some crucial part of the algorithm is not compiled (the factor 10 is somewhat an indicator for that) or does not use the fastest FFT implementation possible. A bit weird.


So, to my own surprise, your idea of computing the kernel once does help but for quite unexpected reasons.


Comments

Popular posts from this blog

front end - keyboard shortcut to invoke Insert new matrix

I frequently need to type in some matrices, and the menu command Insert > Table/Matrix > New... allows matrices with lines drawn between columns and rows, which is very helpful. I would like to make a keyboard shortcut for it, but cannot find the relevant frontend token command (4209405) for it. Since the FullForm[] and InputForm[] of matrices with lines drawn between rows and columns is the same as those without lines, it's hard to do this via 3rd party system-wide text expanders (e.g. autohotkey or atext on mac). How does one assign a keyboard shortcut for the menu item Insert > Table/Matrix > New... , preferably using only mathematica? Thanks! Answer In the MenuSetup.tr (for linux located in the $InstallationDirectory/SystemFiles/FrontEnd/TextResources/X/ directory), I changed the line MenuItem["&New...", "CreateGridBoxDialog"] to read MenuItem["&New...", "CreateGridBoxDialog", MenuKey["m", Modifiers-...

How to thread a list

I have data in format data = {{a1, a2}, {b1, b2}, {c1, c2}, {d1, d2}} Tableform: I want to thread it to : tdata = {{{a1, b1}, {a2, b2}}, {{a1, c1}, {a2, c2}}, {{a1, d1}, {a2, d2}}} Tableform: And I would like to do better then pseudofunction[n_] := Transpose[{data2[[1]], data2[[n]]}]; SetAttributes[pseudofunction, Listable]; Range[2, 4] // pseudofunction Here is my benchmark data, where data3 is normal sample of real data. data3 = Drop[ExcelWorkBook[[Column1 ;; Column4]], None, 1]; data2 = {a #, b #, c #, d #} & /@ Range[1, 10^5]; data = RandomReal[{0, 1}, {10^6, 4}]; Here is my benchmark code kptnw[list_] := Transpose[{Table[First@#, {Length@# - 1}], Rest@#}, {3, 1, 2}] &@list kptnw2[list_] := Transpose[{ConstantArray[First@#, Length@# - 1], Rest@#}, {3, 1, 2}] &@list OleksandrR[list_] := Flatten[Outer[List, List@First[list], Rest[list], 1], {{2}, {1, 4}}] paradox2[list_] := Partition[Riffle[list[[1]], #], 2] & /@ Drop[list, 1] RM[list_] := FoldList[Transpose[{First@li...

plotting - How to draw lines between specified dots on ListPlot?

I would like to create a plot where I have unconnected dots and some connected. So far, I have figured out how to draw the dots. My code is the following: ListPlot[{{1, 1}, {2, 2}, {3, 3}, {4, 4}, {1, 4}, {2, 5}, {3, 6}, {4, 7}, {1, 7}, {2, 8}, {3, 9}, {4, 10}, {1, 10}, {2, 11}, {3, 12}, {4,13}, {2.5, 7}}, Ticks -> {{1, 2, 3, 4}, None}, AxesStyle -> Thin, TicksStyle -> Directive[Black, Bold, 12], Mesh -> Full] I have thought using ListLinePlot command, but I don't know how to specify to the command to draw only selected lines between the dots. Do have any suggestions/hints on how to do that? Thank you. Answer One possibility would be to use Epilog with Line : ListPlot[ {{1, 1}, {2, 2}, {3, 3}, {4, 4}, {1, 4}, {2, 5}, {3, 6}, {4, 7}, {1, 7}, {2, 8}, {3, 9}, {4, 10}, {1, 10}, {2, 11}, {3, 12}, {4, 13}, {2.5, 7}}, Ticks -> {{1, 2, 3, 4}, None}, AxesStyle -> Thin, TicksStyle -> Directive[Black, Bold, 12], Mesh -> Full, Epilog -> { Line[ ...