Skip to main content

list manipulation - Finding Local Minima / Maxima in Noisy Data


I'm trying to find local minima / maxima in noisy data, consisting of data values taken at certain time intervals. Ideally, the function should take a pair of lists (one containing time values and one containing observed data values) and return the coordinates of the maxima and minima.


An example of the data is found below:


temptimelist = Range[200]/10;
tempvaluelist = Sinc[#] &@temptimelist + RandomReal[{-1, 1}, 200]*0.02;


While the questions here, here and here have a good range of answers, they don't fit with my requirements since (as far as I can see) they determine whether data is a local maximum / minimum by comparing it with the adjacent values. If I apply such an algorithm, my extrema will be identified as follows:


data with peaks identified


What I've done is to write the following code.


NoisyExtremaFinder = Function[{timeList, valueList, aroundRange},
(*NoisyExtremaFinder[] takes a pair of lists timeList_ and valueList_ and determines extrema in valueList_, returning a list containing the coordinates (as pairs of time_ and value_) of the minima as the first entry and the maxima as the second entry.

As the data is assumed to be noisy, we provide the option aroundRange_ to allow the user to determine the sensitivity of the search. Specifically, when aroundRange_=n, the function will compare each value with the preceding and subsequent n values to determine whether it is an extrema*)

extremaPosition =
Flatten@Position[

Map[#, Partition[valueList, 2*aroundRange + 1, 1, {-(1 + aroundRange), 1 + aroundRange}, {}]] - valueList, 0.] &;
(*extremaPosition[] is a custom function that determines the position of local Maxima or Minima in valueList_, with the sensitivity determined by the value of aroundRange. When aroundRange_=n, the function will compare each value with the preceding and subsequent n values to determine whether it is an extrema. You can either do extremaPosition[Max] or extremaPosition[Min] *)

extremaPoints =
Transpose@{timeList[[#]], valueList[[#]]} &@extremaPosition[#] &;
(*extremaPoints[] is a custom function that determines the coordinates of local Maxima or Minima in valueList_

Custom Functions Used: extremaPosition[]*)

{extremaPoints[Min], extremaPoints[Max]}];


Basically, instead of deciding whether a point is an extrema by comparing it only with adjacent terms, it decides whether the point is an extrema by comparing with the aroundRange preceeding and aroundRange subsequent points.


Then, by adding the following lines of code, we can see the final results:


NoisyExtremaFinder[temptimelist, tempvaluelist, 10]; (*parameter "10" chosen by estimating the distance from peak to peak*)
ListPlot[Transpose[{temptimelist, tempvaluelist}],
Epilog -> {PointSize[Medium], Red, Point[extremaPoints[Min]], Green,
Point[extremaPoints[Max]]}, ImageSize -> 700]

better peaks




Is there any better way to code to achieve the goal I have in mind of comparing a point with n preceeding and subsequent points?


I was also advised by rm-rf (in chat) to consider smoothing the noisy data first before trying to find the local minima / maxima. However, I was concerned that I could add unwanted artifacts into the data by the smoothing process. With regards to smoothing, is there an algorithm that is commonly used to filter experimental data? Filters that I have looked at include the Savitsky-Golay filter and the Low-Pass filter.



PS: My data sets have around 10,000 data points each.




Comments

Popular posts from this blog

functions - Get leading series expansion term?

Given a function f[x] , I would like to have a function leadingSeries that returns just the leading term in the series around x=0 . For example: leadingSeries[(1/x + 2)/(4 + 1/x^2 + x)] x and leadingSeries[(1/x + 2 + (1 - 1/x^3)/4)/(4 + x)] -(1/(16 x^3)) Is there such a function in Mathematica? Or maybe one can implement it efficiently? EDIT I finally went with the following implementation, based on Carl Woll 's answer: lds[ex_,x_]:=( (ex/.x->(x+O[x]^2))/.SeriesData[U_,Z_,L_List,Mi_,Ma_,De_]:>SeriesData[U,Z,{L[[1]]},Mi,Mi+1,De]//Quiet//Normal) The advantage is, that this one also properly works with functions whose leading term is a constant: lds[Exp[x],x] 1 Answer Update 1 Updated to eliminate SeriesData and to not return additional terms Perhaps you could use: leadingSeries[expr_, x_] := Normal[expr /. x->(x+O[x]^2) /. a_List :> Take[a, 1]] Then for your examples: leadingSeries[(1/x + 2)/(4 + 1/x^2 + x), x] leadingSeries[Exp[x], x] leadingSeries[(1/x + 2 + (1 - 1/x...

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...

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-...