SpHEAR/findpeaks.m

## Copyright (c) 2012 Juan Pablo Carbajal <carbajal@ifi.uzh.ch>
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 3 of the License, or
## (at your option) any later version.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this program; if not, see <http://www.gnu.org/licenses/>.

## -*- texinfo -*-
## @deftypefn  {Function File} {[@var{pks}, @var{loc}, @var{extra}] =} findpeaks (@var{data})
## @deftypefnx {Function File} {@dots{} =} findpeaks (@dots{}, @var{property}, @var{value})
## @deftypefnx {Function File} {@dots{} =} findpeaks (@dots{}, @asis{"DoubleSided"})
## Finds peaks on @var{data}.
##
## Peaks of a positive array of data are defined as local maxima. For
## double-sided data, they are maxima of the positive part and minima of
## the negative part. @var{data} is expected to be a single column
## vector.
##
## The function returns the value of @var{data} at the peaks in
## @var{pks}. The index indicating their position is returned in
## @var{loc}.
##
## The third output argument is a structure with additional information:
##
## @table @asis
## @item "parabol"
## A structure containing the parabola fitted to each returned peak. The
## structure has two fields, @asis{"x"} and @asis{"pp"}. The field
## @asis{"pp"} contains the coefficients of the 2nd degree polynomial
## and @asis{"x"} the extrema of the intercal here it was fitted.
##
## @item "height"
## The estimated height of the returned peaks (in units of @var{data}).
##
## @item "baseline"
## The height at which the roots of the returned peaks were calculated
## (in units of @var{data}).
##
## @item "roots"
## The abscissa values (in index units) at which the parabola fitted to
## each of the returned peaks crosses the @asis{"baseline"} value. The
## width of the peak is calculated by @command{diff(roots)}.
## @end table
##
## This function accepts property-value pair given in the list below:
##
## @table @asis
##
## @item "MinPeakHeight"
## Minimum peak height (positive scalar). Only peaks that exceed this
## value will be returned. For data taking positive and negative values
## use the option "DoubleSided". Default value @code{2*std (abs (detrend
## (data,0)))}.
##
## @item "MinPeakDistance"
## Minimum separation between (positive integer). Peaks separated by
## less than this distance are considered a single peak. This distance
## is also used to fit a second order polynomial to the peaks to
## estimate their width, therefore it acts as a smoothing parameter.
## Default value 4.
##
## @item "MinPeakWidth"
## Minimum width of peaks (positive integer). The width of the peaks is
## estimated using a parabola fitted to the neighborhood of each peak.
## The neighborhood size is equal to the value of
## @asis{"MinPeakDistance"}. The width is evaluated at the half height
## of the peak with baseline at "MinPeakHeight". Default value 2.
##
## @item "DoubleSided"
## Tells the function that data takes positive and negative values. The
## base-line for the peaks is taken as the mean value of the function.
## This is equivalent as passing the absolute value of the data after
## removing the mean.
## @end table
##
## Run @command{demo findpeaks} to see some examples.
## @end deftypefn

function [pks idx varargout] = findpeaks (data, varargin)

  ## --- Parse arguments --- #
  __data__ = abs (detrend (data,0));

  posscal = @(x)isscalar (x) && x >= 0;

  parser = inputParser ();
  parser.FunctionName = "findpeaks";
  parser = addParamValue (parser,"MinPeakHeight", 2*std (__data__),posscal);
  parser = addParamValue (parser,"MinPeakDistance",4,posscal);
  parser = addParamValue (parser,"MinPeakWidth",2,posscal);
  parser = addSwitch (parser,"DoubleSided");

  parser = parse(parser,varargin{:});

  minH      = parser.Results.MinPeakHeight;
  minD      = parser.Results.MinPeakDistance;
  minW      = parser.Results.MinPeakWidth;
  dSided    = parser.Results.DoubleSided;

  clear parser posscal
  ## ------ #

  if dSided
    [data __data__] = deal (__data__, data);
  elseif min(data)<0
    error ("findpeaks:InvalidArgument",
           'Data contains negative values. You may want to "DoubleSided" option');
  endif

  ## Rough estimates of first and second derivative
  df1 = diff (data,1)([1; (1:end)']);
  df2 = diff (data,2)([1; 1; (1:end)']);

  ## check for changes of sign of 1st derivative and negativity of 2nd
  ## derivative.
  idx = find (df1.*[df1(2:end); 0]<0 & [df2(2:end); 0]<0);

  ## Get peaks that are beyond given height
  tf  = data(idx) > minH;
  idx = idx(tf);

  ## sort according to magnitude
  [~,tmp] = sort(data(idx),"descend");
  idx_s = idx(tmp);

  ## Treat peaks separated less than minD as one
  # http://savannah.gnu.org/bugs/?43691
  # D = abs (idx_s - idx_s');
  D = bsxfun (@minus, idx_s, idx_s');
  if any(D(:) < minD)

    i = 1;
    peak = cell ();
    node2visit = 1:size(D,1);
    visited = [];
    idx_pruned = idx_s;

    ## debug
##    h = plot(1:length(data),data,"-",idx_s,data(idx_s),'.r',idx_s,data(idx_s),'.g');
##    set(h(3),"visible","off");

    while ~isempty (node2visit)

      d = D(node2visit(1),:);

      visited = [visited node2visit(1)];
      node2visit(1) = [];

      neighs  = setdiff (find (d < minD), visited);
      if ~isempty (neighs)
        ## debug
##        set(h(3),"xdata",idx_s(neighs),"ydata",data(idx_s(neighs)),"visible","on")
##        pause(0.2)
##        set(h(3),"visible","off");

        idx_pruned   = setdiff (idx_pruned,idx_s(neighs));

        visited    = [visited neighs];
        node2visit = setdiff (node2visit,visited);

        ## debug
##        set(h(2),"xdata",idx_pruned,"ydata",data(idx_pruned))
##        pause
      endif

    endwhile
    idx = idx_pruned;
  endif

  ## Estimate widths of peaks and filter for:
  ## width smaller than given.
  ## wrong concavity.
  ## not high enough
  ## data at peak is lower than parabola by 1%
  if minW > 0
    ## debug
##    h = plot(1:length(data),data,"-",idx,data(idx),'.r',...
##          idx,data(idx),'og',idx,data(idx),'-m');
##    set(h(4),"linewidth",2)
##    set(h(3:4),"visible","off");

    idx_pruned = idx;
    n  = length(idx);
    np = length(data);
    struct_count = 0;
    for i=1:n
      ind = (round (max(idx(i)-minD/2,1)) : ...
             round (min(idx(i)+minD/2,np)))';
      pp = polyfit (ind,data(ind),2);
      H  = pp(3) - pp(2)^2/(4*pp(1));

      ## debug
##      x = linspace(ind(1)-1,ind(end)+1,10);
##      set(h(4),"xdata",x,"ydata",polyval(pp,x),"visible","on")
##      set(h(3),"xdata",ind,"ydata",data(ind),"visible","on")
##      pause(0.2)
##      set(h(3:4),"visible","off");

      rz = roots ([pp(1:2) pp(3)-mean([H,minH])]);
      width = abs (diff (rz));
      if width < minW || pp(1) > 0 || H < minH || data(idx(i)) < 0.99*H
        idx_pruned = setdiff (idx_pruned, idx(i));
      elseif nargout > 2
        struct_count++;
        extra.parabol(struct_count).x  = ind([1 end]);
        extra.parabol(struct_count).pp = pp;

        extra.roots(struct_count,1:2)    = rz;
        extra.height(struct_count)   = H;
        extra.baseline(struct_count) = mean([H,minH]);
      endif

      ## debug
##      set(h(2),"xdata",idx_pruned,"ydata",data(idx_pruned))
##      pause(0.2)

    endfor
  idx = idx_pruned;
  endif


  if dSided
    pks = __data__(idx);
  else
    pks = data(idx);
  endif

  if nargout()>2
    varargout{1} = extra;
  endif

endfunction

%!demo
%! t = 2*pi*linspace(0,1,1024)';
%! y = sin(3.14*t) + 0.5*cos(6.09*t) + 0.1*sin(10.11*t+1/6) + 0.1*sin(15.3*t+1/3);
%!
%! data1 = abs(y); # Positive values
%! [pks idx] = findpeaks(data1);
%!
%! data2 = y; # Double-sided
%! [pks2 idx2] = findpeaks(data2,"DoubleSided");
%! [pks3 idx3] = findpeaks(data2,"DoubleSided","MinPeakHeight",0.5);
%!
%! subplot(1,2,1)
%! plot(t,data1,t(idx),data1(idx),'.m')
%! subplot(1,2,2)
%! plot(t,data2,t(idx2),data2(idx2),".m;>2*std;",t(idx3),data2(idx3),"or;>0.1;")
%! legend("Location","NorthOutside","Orientation","horizontal")
%!
%! #----------------------------------------------------------------------------
%! # Finding the peaks of smooth data is not a big deal!

%!demo
%! t = 2*pi*linspace(0,1,1024)';
%! y = sin(3.14*t) + 0.5*cos(6.09*t) + 0.1*sin(10.11*t+1/6) + 0.1*sin(15.3*t+1/3);
%!
%! data = abs(y + 0.1*randn(length(y),1)); # Positive values + noise
%! [pks idx] = findpeaks(data,"MinPeakHeight",1);
%!
%! dt = t(2)-t(1);
%! [pks2 idx2] = findpeaks(data,"MinPeakHeight",1,...
%!                              "MinPeakDistance",round(0.5/dt));
%!
%! subplot(1,2,1)
%! plot(t,data,t(idx),data(idx),'.r')
%! subplot(1,2,2)
%! plot(t,data,t(idx2),data(idx2),'.r')
%!
%! #----------------------------------------------------------------------------
%! # Noisy data may need tunning of the parameters. In the 2nd example,
%! # MinPeakDistance is used as a smoother of the peaks.