source: trunk/src/SDLineFinder.h @ 352

//#---------------------------------------------------------------------------
//# SDLineFinder.h: A class for automated spectral line search
//#---------------------------------------------------------------------------
//# Copyright (C) 2004
//# ATNF
//#
//# 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 2 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, write to the Free Software Foundation, Inc.,
//# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
//#
//# Correspondence concerning this software should be addressed as follows:
//#        Internet email: Malte.Marquarding@csiro.au
//#        Postal address: Malte Marquarding,
//#                        Australia Telescope National Facility,
//#                        P.O. Box 76,
//#                        Epping, NSW, 2121,
//#                        AUSTRALIA
//#
//# $Id:
//#---------------------------------------------------------------------------
#ifndef SDLINEFINDER_H
#define SDLINEFINDER_H

// STL
#include <vector>
#include <list>
#include <utility>
#include <exception>

// boost
#include <boost/python.hpp>

// AIPS++
#include <casa/aips.h>
#include <casa/Exceptions/Error.h>
#include <casa/Arrays/Vector.h>
#include <casa/Utilities/Assert.h>
#include <casa/Utilities/CountedPtr.h>

// ASAP
#include "SDMemTableWrapper.h"
#include "SDMemTable.h"

namespace asap {

///////////////////////////////////////////////////////////////////////////////
//
// LFLineListOperations - a class incapsulating  operations with line lists
//                        The LF prefix stands for Line Finder
//

struct  LFLineListOperations {
   // concatenate two lists preserving the order. If two lines appear to
   // be adjacent or have a non-void intersection, they are joined into 
   // the new line
   static void addNewSearchResult(const std::list<std::pair<int, int> >
                  &newlines, std::list<std::pair<int, int> > &lines_list)
                           throw(casa::AipsError);

   // extend all line ranges to the point where a value stored in the
   // specified vector changes (e.g. value-mean change its sign)
   // This operation is necessary to include line wings, which are below
   // the detection threshold. If lines becomes adjacent, they are
   // merged together. Any masked channel stops the extension
   static void searchForWings(std::list<std::pair<int, int> > &newlines,
                       const casa::Vector<casa::Int> &signs,
                       const casa::Vector<casa::Bool> &mask,
                       const std::pair<int,int> &edge)
                           throw(casa::AipsError);
protected:
           
   // An auxiliary object function to test whether two lines have a non-void
   // intersection
   class IntersectsWith : public std::unary_function<pair<int,int>, bool> {
       std::pair<int,int> line1;           // range of the first line
                                           // start channel and stop+1
   public:
        IntersectsWith(const std::pair<int,int> &in_line1);
        // return true if line2 intersects with line1 with at least one
        // common channel, and false otherwise
        bool operator()(const std::pair<int,int> &line2) const throw();
   };

   // An auxiliary object function to build a union of several lines
   // to account for a possibility of merging the nearby lines
   class BuildUnion {
       std::pair<int,int> temp_line;       // range of the first line
                                           // start channel and stop+1
   public:
        BuildUnion(const std::pair<int,int> &line1);
        // update temp_line with a union of temp_line and new_line
        // provided there is no gap between the lines
        void operator()(const std::pair<int,int> &new_line) throw();
        // return the result (temp_line)
        const std::pair<int,int>& result() const throw();
   };
   
   // An auxiliary object function to test whether a specified line
   // is at lower spectral channels (to preserve the order in the line list)
   class LaterThan : public std::unary_function<pair<int,int>, bool> {
       std::pair<int,int> line1;           // range of the first line
                                           // start channel and stop+1
   public:
        LaterThan(const std::pair<int,int> &in_line1);

        // return true if line2 should be placed later than line1
        // in the ordered list (so, it is at greater channel numbers)
        bool operator()(const std::pair<int,int> &line2) const throw();
   }; 
   
   
};

//
///////////////////////////////////////////////////////////////////////////////

///////////////////////////////////////////////////////////////////////////////
//
// SDLineFinder  -  a class for automated spectral line search
//
//

struct SDLineFinder : protected LFLineListOperations {
   SDLineFinder() throw();
   virtual ~SDLineFinder() throw(casa::AipsError);

   // set the scan to work with (in_scan parameter), associated mask (in_mask
   // parameter) and the edge channel rejection (in_edge parameter)
   //   if in_edge has zero length, all channels chosen by mask will be used
   //   if in_edge has one element only, it represents the number of
   //      channels to drop from both sides of the spectrum
   //   in_edge is introduced for convinience, although all functionality
   //   can be achieved using a spectrum mask only   
   void setScan(const SDMemTableWrapper &in_scan,
                const std::vector<bool> &in_mask,
                const boost::python::tuple &in_edge) throw(casa::AipsError);

   // search for spectral lines. Number of lines found is returned
   int findLines() throw(casa::AipsError);

   // get the mask to mask out all lines that have been found (default)
   // if invert=true, only channels belong to lines will be unmasked
   // Note: all channels originally masked by the input mask (in_mask
   //       in setScan) or dropped out by the edge parameter (in_edge
   //       in setScan) are still excluded regardless on the invert option
   std::vector<bool> getMask(bool invert=false) const throw(casa::AipsError);

   // get range for all lines found. If defunits is true (default), the
   // same units as used in the scan will be returned (e.g. velocity
   // instead of channels). If defunits is false, channels will be returned
   std::vector<int>   getLineRanges(bool defunits=true)
                                const throw(casa::AipsError);
private:
   casa::CountedConstPtr<SDMemTable> scan; // the scan to work with
   casa::Vector<casa::Bool> mask;          // associated mask
   std::pair<int,int> edge;                // start and stop+1 channels
                                           // to work with
   casa::Float threshold;                  // detection threshold - the 
                                           // minimal signal to noise ratio
   casa::Double box_size;                  // size of the box for running
                                           // mean calculations, specified as
                                           // a fraction of the whole spectrum
   int  min_nchan;                         // A minimum number of consequtive
                                           // channels, which should satisfy
                                           // the detection criterion, to be
                                           // a detection
   std::list<std::pair<int, int> > lines;  // container of start and stop+1
                                           // channels of the spectral lines
   // a buffer for the spectrum
   mutable casa::Vector<casa::Float>  spectrum;
};

//
///////////////////////////////////////////////////////////////////////////////

} // namespace asap
#endif // #ifndef SDLINEFINDER_H