Peakfind and Release Notes Version 6 7: Difference between pages

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===Purpose===


Automated identification of peaks.
Version 6.7 of PLS_Toolbox and Solo was released in March, 2012.


===Synopsis===
For general product information, see [http://www.eigenvector.com/software/pls_toolbox.htm PLS_Toolbox Product Page]. For information on Solo, see [http://www.eigenvector.com/software/solo.htm Solo Product Page].


:[i0,iw] = peakfind(x,width,tolfac,w,options)
(back to [[Release Notes PLS Toolbox and Solo]])
:[i0,iw] = peakfind(x,width,options)


===Description===
==NEW FEATURES==


Given a set of measured traces (x) PEAKFIND attempts to find the location of the peaks. Different algorithms are available and each is discussed in the Algorithm Section.
===Design Of Experients (DOE) Tools===
* bla


====Inputs====
===Other Method Improvements===
* bla
 
===Preprocessing===
* bla
 
===Import / Export===
* bla
 
===DataSet Editor===
* bla


* '''x''' =  matrix of measured traces. Each  row of (x) is an individual trace with potential peaks.
===Plot Controls===
* Selectable plot themes. [[Image:Figbg_color.gif|thumb|| ]]
* bla


* '''width''' = number of points in Savitzky-Golay filter.
===[[AnalysisWindow_Layout|Analysis Window]]===
* Show CV results for confusion table when available.
* Improved [[modelcache]] performance and string handling.


====Optional Inputs====
===[[WorkspaceBrowser_Layout|Workspace Browser]] ===
* Drag Drop - Enable dragging and dropping of system files onto the Browser window as well as to Analysis window. Enhanced highlighting of drop location.


* '''tolfac''' = tolerance on the estimated residuals, peaks heights are estimated to be > tolfac\*residuals {default: tolfac = 3}.
===Command-line Tool Changes===
* bla


* '''w''' = odd scalar window width for determining local maxima {default: w = 3} (see LOCALMAXIMA).


* '''options''' = discussed below in the Options Section.
==NEW FUNCTIONS AND FILES==


====Outputs====
*''Full Support for Matlab R2012a''


* '''i0''' =   cell array with each cell containing the indices of the location of the major peaks for each of the  traces.
===Misc New Functions===
:[[autoexport]] - Exports a DataSet object to a file of the specified format.
:[[classsummary]] - List class and axisscale distributions for a DataSet.
:[[figuretheme]] - Resets a figure background and axes to a specified color.
:[[meantrimmed]] - Trimmed mean.
:[[mediantrimmed]] - Trimmed median.
:[[windowfilter]] - Spectral filtering.


* '''iw''' =   cell array with each cell containing the indices of the location of the windows containing each peak in (i0). (If not included in the output argument list, it is not calculated and the algorithm is slightly faster.) .
===Design of Analysis Tools===
:[[anovadoe]]        - Function to perform ANOVA for 2^k factorial model X, Y data


===Algorithm===
===Other Changes===


Each peak finding algorithm uses the smoothed and second derivative data (see SAVGOL) and an estimate of the residuals. The smoothed and second derivative are estimated as:
:[[crossval]] - improved display of classification results, improved integration with model input
 
:d0 = savgol(x,width,2,0);
 
:d2 = savgol(x,width,2,2);
 
The residuals are defined for the  row/trace as
 
:residuals = sqrt(mean((x(i,:)-d0(i,:)).\^2));
 
For options.algorithm = 'd0', locates a candidate set of peaks (pks) by identifying local maxima (within the specified window size) in the smoothed data:
 
:pks = localmaxima(d0(i,:),w);
 
Next, the input (tolfac) is used to estimate two thresholds (tol0) and (tol2) using the smoothed and second derivative data:
 
:tol0 = tolfac\*sqrt(mean((x(i,:)-d0(i,:)).\^2));
 
:tol2 = tol0\*(max(d2(i,:))-min(d2(i,:)))/ ...
 
:            (max(d0(i,:))-min(d0(i,:)));
 
Finally, the set of major peaks are selected from the initial candidate set of peaks . To be accepted, the value of d0 and d2 at the peak location must surpass the estimated noise level of both d0 and d2 by the tolerance factor (tolfac).
 
:i0{i} = pks(d0(i,pks)>tol0 & d2(i,pks)<-tol2);
 
For options.algorithm = 'd2', the algorithm operates similarly to what is described for d0 except that it locates candidate peaks as the local maxima on the second derivative data and to be accepted, a peak must only surpass the estimated noise level of d2 by the tolerance factor. That is, d0 is not considered at all in the calculation except to estimate the noise level.
 
For options.algorithm = 'd2r', as with 'd2', 'd2r' locates peaks in the second derivative data, d2, but selects the final set as those peaks which have a "relative" height (difference between closest d2 peak valley and d2 peak top) which surpasses the estimated noise level of d2 by the tolerance factor, tolfac.
 
===Options===
 
*'''options'''  = structure array with the following fields:
 
* '''name''': 'options', name indicating that this is an options structure.
 
* '''algorithm''': [ {'d0'} | 'd2' | 'd2r' ] selects an algorithm used to identify peak location. These algorithms are complimentary and may work differently in the presense of backgrounds and other peak shape effects.
 
*  ''''d0'''' : locates a candidate set of peaks by identifying local maxima (within the specified window size) in the smoothed data (d0). Next, a threshold on d0 and the second derivative (d2) is used to select a final set of peaks from this candidate set. To be accepted, the value of d0 and d2 at the peak location must surpass the estimated noise level of both d0 and d2 by the tolerance factor (tolfac).
 
*  ''''d2'''' : locates candidate peaks as local maxima in the smoothed 2nd derivative data (d2) and selects a final set of peaks as those candidate peaks which surpass (by the tolerance factor, tolfac) the estimated noise level of d2. d0 position or value is not considered in any part of the selection except to estimate the noise level.
 
*  ''''d2r'''' : as with 'd2', 'd2r' locates peaks in d2, but selects the final set as those peaks which have a "relative" height (difference between closest d2 peak valley and d2 peak top) which surpasses (by the tolerance factor, tolfac) the estimated noise level of d2.
 
* '''npeaks''':  The maximum number of peaks to find.
 
*  '''{'all'}''' chooses all peaks that are > tolfac.
 
*  '''1,2,3,''' ... integer maximum number of peaks.
 
===See Also===
 
[[fitpeaks]], [[localmaxima]]

Revision as of 10:36, 7 March 2012


Version 6.7 of PLS_Toolbox and Solo was released in March, 2012.

For general product information, see PLS_Toolbox Product Page. For information on Solo, see Solo Product Page.

(back to Release Notes PLS Toolbox and Solo)

NEW FEATURES

Design Of Experients (DOE) Tools

  • bla

Other Method Improvements

  • bla

Preprocessing

  • bla

Import / Export

  • bla

DataSet Editor

  • bla

Plot Controls

Analysis Window

  • Show CV results for confusion table when available.
  • Improved modelcache performance and string handling.

Workspace Browser

  • Drag Drop - Enable dragging and dropping of system files onto the Browser window as well as to Analysis window. Enhanced highlighting of drop location.

Command-line Tool Changes

  • bla


NEW FUNCTIONS AND FILES

  • Full Support for Matlab R2012a

Misc New Functions

autoexport - Exports a DataSet object to a file of the specified format.
classsummary - List class and axisscale distributions for a DataSet.
figuretheme - Resets a figure background and axes to a specified color.
meantrimmed - Trimmed mean.
mediantrimmed - Trimmed median.
windowfilter - Spectral filtering.

Design of Analysis Tools

anovadoe - Function to perform ANOVA for 2^k factorial model X, Y data

Other Changes

crossval - improved display of classification results, improved integration with model input
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