| 1 | //#---------------------------------------------------------------------------
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| 2 | //# SDLineFinder.h: A class for automated spectral line search
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| 3 | //#---------------------------------------------------------------------------
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| 4 | //# Copyright (C) 2004
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| 5 | //# ATNF
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| 6 | //#
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| 7 | //# This program is free software; you can redistribute it and/or modify it
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| 8 | //# under the terms of the GNU General Public License as published by the Free
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| 9 | //# Software Foundation; either version 2 of the License, or (at your option)
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| 10 | //# any later version.
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| 11 | //#
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| 12 | //# This program is distributed in the hope that it will be useful, but
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| 13 | //# WITHOUT ANY WARRANTY; without even the implied warranty of
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| 14 | //# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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| 15 | //# Public License for more details.
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| 16 | //#
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| 17 | //# You should have received a copy of the GNU General Public License along
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| 18 | //# with this program; if not, write to the Free Software Foundation, Inc.,
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| 19 | //# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
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| 20 | //#
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| 21 | //# Correspondence concerning this software should be addressed as follows:
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| 22 | //# Internet email: Malte.Marquarding@csiro.au
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| 23 | //# Postal address: Malte Marquarding,
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| 24 | //# Australia Telescope National Facility,
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| 25 | //# P.O. Box 76,
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| 26 | //# Epping, NSW, 2121,
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| 27 | //# AUSTRALIA
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| 28 | //#
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| 29 | //# $Id:
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| 30 | //#---------------------------------------------------------------------------
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| 31 | #ifndef SDLINEFINDER_H
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| 32 | #define SDLINEFINDER_H
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| 33 |
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| 34 | // STL
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| 35 | #include <vector>
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| 36 | #include <list>
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| 37 | #include <utility>
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| 38 | #include <exception>
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| 39 |
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| 40 | // boost
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| 41 | #include <boost/python.hpp>
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| 42 |
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| 43 | // AIPS++
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| 44 | #include <casa/aips.h>
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| 45 | #include <casa/Exceptions/Error.h>
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| 46 | #include <casa/Arrays/Vector.h>
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| 47 | #include <casa/Utilities/Assert.h>
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| 48 | #include <casa/Utilities/CountedPtr.h>
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| 49 |
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| 50 | // ASAP
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| 51 | #include "SDMemTableWrapper.h"
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| 52 | #include "SDMemTable.h"
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| 53 |
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| 54 | namespace asap {
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| 55 |
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| 56 | // SDLineFinder - a class for automated spectral line search
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| 57 | struct SDLineFinder {
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| 58 | SDLineFinder() throw();
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| 59 | virtual ~SDLineFinder() throw(casa::AipsError);
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| 60 |
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| 61 | // set the scan to work with (in_scan parameter), associated mask (in_mask
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| 62 | // parameter) and the edge channel rejection (in_edge parameter)
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| 63 | // if in_edge has zero length, all channels chosen by mask will be used
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| 64 | // if in_edge has one element only, it represents the number of
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| 65 | // channels to drop from both sides of the spectrum
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| 66 | // in_edge is introduced for convinience, although all functionality
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| 67 | // can be achieved using a spectrum mask only
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| 68 | void setScan(const SDMemTableWrapper &in_scan,
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| 69 | const std::vector<bool> &in_mask,
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| 70 | const boost::python::tuple &in_edge) throw(casa::AipsError);
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| 71 |
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| 72 | // search for spectral lines. Number of lines found is returned
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| 73 | int findLines() throw(casa::AipsError);
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| 74 |
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| 75 | // get the mask to mask out all lines that have been found (default)
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| 76 | // if invert=true, only channels belong to lines will be unmasked
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| 77 | // Note: all channels originally masked by the input mask (in_mask
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| 78 | // in setScan) or dropped out by the edge parameter (in_edge
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| 79 | // in setScan) are still excluded regardless on the invert option
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| 80 | std::vector<bool> getMask(bool invert=false) const throw(casa::AipsError);
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| 81 |
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| 82 | // get range for all lines found. If defunits is true (default), the
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| 83 | // same units as used in the scan will be returned (e.g. velocity
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| 84 | // instead of channels). If defunits is false, channels will be returned
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| 85 | std::vector<int> getLineRanges(bool defunits=true)
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| 86 | const throw(casa::AipsError);
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| 87 | protected:
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| 88 | // concatenate two lists preserving the order. If two lines appear to
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| 89 | // be adjacent, they are joined into the new one
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| 90 | void addNewSearchResult(const std::list<std::pair<int, int> > &newlines)
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| 91 | throw(casa::AipsError);
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| 92 | private:
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| 93 | casa::CountedConstPtr<SDMemTable> scan; // the scan to work with
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| 94 | casa::Vector<casa::Bool> mask; // associated mask
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| 95 | std::pair<int,int> edge; // start and stop+1 channels
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| 96 | // to work with
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| 97 | casa::Float threshold; // detection threshold - the
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| 98 | // minimal signal to noise ratio
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| 99 | casa::Double box_size; // size of the box for running
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| 100 | // mean calculations, specified as
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| 101 | // a fraction of the whole spectrum
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| 102 | int min_nchan; // A minimum number of consequtive
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| 103 | // channels, which should satisfy
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| 104 | // the detection criterion, to be
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| 105 | // a detection
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| 106 | std::list<std::pair<int, int> > lines; // container of start and stop+1
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| 107 | // channels of the spectral lines
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| 108 | // a buffer for the spectrum
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| 109 | mutable casa::Vector<casa::Float> spectrum;
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| 110 |
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| 111 | };
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| 112 | } // namespace asap
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| 113 | #endif // #ifndef SDLINEFINDER_H
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