OpenMS
2.8.0

Computes the SavitzkyGolay filter coefficients using QR decomposition. More...
#include <OpenMS/FILTERING/SMOOTHING/SavitzkyGolayFilter.h>
Public Member Functions  
SavitzkyGolayFilter ()  
Constructor. More...  
~SavitzkyGolayFilter () override  
Destructor. More...  
template<class InputIt , class OutputIt >  
void  filter (InputIt first, InputIt last, OutputIt d_first) 
void  filter (MSSpectrum &spectrum) 
Removed the noise from an MSSpectrum containing profile data. More...  
void  filter (MSChromatogram &chromatogram) 
Removed the noise from an MSChromatogram. More...  
void  filterExperiment (PeakMap &map) 
Removed the noise from an MSExperiment containing profile data. More...  
Public Member Functions inherited from ProgressLogger  
ProgressLogger ()  
Constructor. More...  
virtual  ~ProgressLogger () 
Destructor. More...  
ProgressLogger (const ProgressLogger &other)  
Copy constructor. More...  
ProgressLogger &  operator= (const ProgressLogger &other) 
Assignment Operator. More...  
void  setLogType (LogType type) const 
Sets the progress log that should be used. The default type is NONE! More...  
LogType  getLogType () const 
Returns the type of progress log being used. More...  
void  startProgress (SignedSize begin, SignedSize end, const String &label) const 
Initializes the progress display. More...  
void  setProgress (SignedSize value) const 
Sets the current progress. More...  
void  endProgress () const 
Ends the progress display. More...  
void  nextProgress () const 
increment progress by 1 (according to range beginend) More...  
Public Member Functions inherited from DefaultParamHandler  
DefaultParamHandler (const String &name)  
Constructor with name that is displayed in error messages. More...  
DefaultParamHandler (const DefaultParamHandler &rhs)  
Copy constructor. More...  
virtual  ~DefaultParamHandler () 
Destructor. More...  
virtual DefaultParamHandler &  operator= (const DefaultParamHandler &rhs) 
Assignment operator. More...  
virtual bool  operator== (const DefaultParamHandler &rhs) const 
Equality operator. More...  
void  setParameters (const Param ¶m) 
Sets the parameters. More...  
const Param &  getParameters () const 
Nonmutable access to the parameters. More...  
const Param &  getDefaults () const 
Nonmutable access to the default parameters. More...  
const String &  getName () const 
Nonmutable access to the name. More...  
void  setName (const String &name) 
Mutable access to the name. More...  
const std::vector< String > &  getSubsections () const 
Nonmutable access to the registered subsections. More...  
Protected Member Functions  
void  updateMembers_ () override 
This method is used to update extra member variables at the end of the setParameters() method. More...  
Protected Member Functions inherited from DefaultParamHandler  
void  defaultsToParam_ () 
Updates the parameters after the defaults have been set in the constructor. More...  
Protected Attributes  
std::vector< double >  coeffs_ 
Coefficients. More...  
UInt  frame_size_ 
UInt of the filter kernel (number of pretabulated coefficients) More...  
UInt  order_ 
The order of the smoothing polynomial. More...  
Protected Attributes inherited from ProgressLogger  
LogType  type_ 
time_t  last_invoke_ 
ProgressLoggerImpl *  current_logger_ 
Protected Attributes inherited from DefaultParamHandler  
Param  param_ 
Container for current parameters. More...  
Param  defaults_ 
Container for default parameters. This member should be filled in the constructor of derived classes! More...  
std::vector< String >  subsections_ 
Container for registered subsections. This member should be filled in the constructor of derived classes! More...  
String  error_name_ 
Name that is displayed in error messages during the parameter checking. More...  
bool  check_defaults_ 
If this member is set to false no checking if parameters in done;. More...  
bool  warn_empty_defaults_ 
If this member is set to false no warning is emitted when defaults are empty;. More...  
Additional Inherited Members  
Public Types inherited from ProgressLogger  
enum  LogType { CMD , GUI , NONE } 
Possible log types. More...  
Static Public Member Functions inherited from DefaultParamHandler  
static void  writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") 
Writes all parameters to meta values. More...  
Static Protected Member Functions inherited from ProgressLogger  
static String  logTypeToFactoryName_ (LogType type) 
Return the name of the factory product used for this log type. More...  
Static Protected Attributes inherited from ProgressLogger  
static int  recursion_depth_ 
Computes the SavitzkyGolay filter coefficients using QR decomposition.
This class represents a SavitzkyGolay lowpassfilter. The idea of the SavitzkyGolay filter is to find filtercoefficients that preserve higher moments, which means to approximate the underlying function within the moving window by a polynomial of higher order (typically quadratic or quartic). Therefore we leastsquares fit for each data point a polynomial to all points in the window and set to be the value of that polynomial at position . This method is superior to adjacent averaging because it tends to preserve features of the data such as peak height and width, which are usually 'washed out' by adjacent averaging.
Because of the linearity of the problem, we can reduce the work computing by fitting in advance, for fictious data consisting of all zeros except for a singe 1 and then do the fits on the real data just by taking linear combinations. There are a particular sets of filter coefficients which accomplish the process of polynomial leastsquares fit inside a moving window. To get the symmetric coefficientmatrix with
The first (last) rows of we need to smooth the first (last) data points of the signal. So we use for the smoothing of the first data point the data point itself and the next future points. For the second point we take the first datapoint, the data point itself and of rightward data points... . We compute the Matrix by solving the underlying leastsquares problems with the singular value decomposition. Here we demonstrate the computation of the first row of a coefficientmatrix for a SavitzkyGolay Filter of order=3 and frameSize=5: The designmatrix for the leastsquares fit of a linear combination of 3 basis functions to 5 data points is:
To smooth the first data point we have to create a designmatrix with . Now we have to solve the overdetermined set of linear equations
where represents the fictious data. Therefore we solve the normal equations of the leastsquares problem
Now, it is possible to get
with . Because we only need one row of the inverse matrix, it is possible to use LU decomposition with only a single backsubstitution. The vector represents the wanted coefficients. Note that the solution of a leastsquares problem directly from the normal equations is faster than the singular value decomposition but rather susceptible to roundoff error!
Name  Type  Default  Restrictions  Description 

frame_length  int  11  The number of subsequent data points used for smoothing. This number has to be uneven. If it is not, 1 will be added. 

polynomial_order  int  4  Order or the polynomial that is fitted. 
Constructor.

override 
Destructor.

inline 

inline 
Removed the noise from an MSChromatogram.

inline 
Removed the noise from an MSSpectrum containing profile data.

inline 
Removed the noise from an MSExperiment containing profile data.
References MSExperiment::getChromatogram(), MSExperiment::getChromatograms(), and MSExperiment::size().

overrideprotectedvirtual 
This method is used to update extra member variables at the end of the setParameters() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.

protected 
Coefficients.

protected 
UInt of the filter kernel (number of pretabulated coefficients)

protected 
The order of the smoothing polynomial.