[2980] | 1 | //# SpectralEstimate.h: Get an initial estimate for spectral lines |
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| 2 | //# Copyright (C) 2001,2002,2003,2004 |
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| 3 | //# Associated Universities, Inc. Washington DC, USA. |
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| 4 | //# |
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| 5 | //# This library is free software; you can redistribute it and/or modify it |
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| 6 | //# under the terms of the GNU Library General Public License as published by |
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| 7 | //# the Free Software Foundation; either version 2 of the License, or (at your |
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| 8 | //# option) any later version. |
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| 9 | //# |
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| 10 | //# This library is distributed in the hope that it will be useful, but WITHOUT |
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| 11 | //# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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| 12 | //# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public |
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| 13 | //# License for more details. |
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| 14 | //# |
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| 15 | //# You should have received a copy of the GNU Library General Public License |
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| 16 | //# along with this library; if not, write to the Free Software Foundation, |
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| 17 | //# Inc., 675 Massachusetts Ave, Cambridge, MA 02139, USA. |
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| 18 | //# |
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| 19 | //# Correspondence concerning AIPS++ should be addressed as follows: |
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| 20 | //# Internet email: aips2-request@nrao.edu. |
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| 21 | //# Postal address: AIPS++ Project Office |
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| 22 | //# National Radio Astronomy Observatory |
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| 23 | //# 520 Edgemont Road |
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| 24 | //# Charlottesville, VA 22903-2475 USA |
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| 25 | //# |
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| 26 | //# |
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| 27 | //# $Id: SpectralEstimate.h 21229 2012-04-02 12:00:20Z gervandiepen $ |
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| 28 | |
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| 29 | #ifndef COMPONENTS_SPECTRALESTIMATE_H |
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| 30 | #define COMPONENTS_SPECTRALESTIMATE_H |
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| 31 | |
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| 32 | #include <casa/aips.h> |
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| 33 | #include <components/SpectralComponents/SpectralElement.h> |
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| 34 | #include <components/SpectralComponents/SpectralList.h> |
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| 35 | |
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| 36 | namespace casa { //# NAMESPACE CASA - BEGIN |
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| 37 | |
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| 38 | //# Forward Declarations |
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| 39 | class GaussianSpectralElement; |
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| 40 | template <class T> class Vector; |
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| 41 | |
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| 42 | // <summary> |
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| 43 | // Get an initial estimate for spectral lines |
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| 44 | // </summary> |
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| 45 | |
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| 46 | // <use visibility=export> |
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| 47 | |
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| 48 | // <reviewed reviewer="" date="yyyy/mm/dd" tests="tSpectralFit" demos=""> |
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| 49 | // </reviewed> |
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| 50 | |
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| 51 | // <prerequisite> |
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| 52 | // <li> <linkto class=SpectralFit>SpectralFit</linkto> class |
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| 53 | // </prerequisite> |
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| 54 | // |
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| 55 | // <etymology> |
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| 56 | // From spectral line and estimate |
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| 57 | // </etymology> |
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| 58 | // |
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| 59 | // <synopsis> |
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| 60 | // The SpectralEstimate class obtains an initial guess for spectral |
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| 61 | // components. The current implementation uses the entire |
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| 62 | // profile as signal region, or can set a window to be searched around |
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| 63 | // the highest peak automatically. A window can also be set manually. |
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| 64 | // The second derivative of |
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| 65 | // the profile in the signal region is calculated by fitting |
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| 66 | // a second degree polynomal. The smoothing parameter Q |
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| 67 | // determines the number of points used for this (=2*Q+1). |
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| 68 | // The gaussians can then be estimated as described by |
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| 69 | // Schwarz, 1968, Bull.Astr.Inst.Netherlands, Volume 19, 405. |
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| 70 | // |
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| 71 | // The elements guessed can be used in the |
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| 72 | // <linkto class=SpectralFit>SpectralFit</linkto> class. |
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| 73 | // |
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| 74 | // The default type found is a Gaussian, defined as: |
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| 75 | // <srcblock> |
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| 76 | // AMPL.exp[ -(x-CENTER)<sup>2</sup>/2 SIGMA<sup>2</sup>] |
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| 77 | // </srcblock> |
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| 78 | // |
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| 79 | // The parameter estimates are returned in units of zero-based |
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| 80 | // pixel indices. |
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| 81 | // </synopsis> |
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| 82 | // |
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| 83 | // <example> |
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| 84 | // </example> |
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| 85 | // |
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| 86 | // <motivation> |
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| 87 | // To have an automatic method to find spectral lines |
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| 88 | // </motivation> |
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| 89 | // |
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| 90 | // <todo asof="2001/02/14"> |
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| 91 | // <li> find a way to get to absorption lines as well |
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| 92 | // <li> add more estimation options |
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| 93 | // </todo> |
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| 94 | |
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| 95 | class SpectralEstimate { |
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| 96 | public: |
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| 97 | //# Constants |
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| 98 | // Default maximum number of components to be found |
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| 99 | static const uInt MAXPAR = 200; |
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| 100 | //# Enumerations |
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| 101 | //# Friends |
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| 102 | |
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| 103 | //# Constructors |
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| 104 | // Default constructor creates a default estimator (default max number |
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| 105 | // of components to be found is 200) with the given maximum number |
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| 106 | // of components that will be found. A value of zero will indicate |
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| 107 | // an unlimited number. |
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| 108 | explicit SpectralEstimate(const uInt maxpar=MAXPAR); |
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| 109 | // Create an estimator with the given maximum number of possible |
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| 110 | // elements. A value of zero will indicate an unlimited number. |
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| 111 | // Construct with a given rms in profiles, a cutoff for amplitudes |
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| 112 | // found, and a minimum width. Cutoff and minsigma default to 0.0, maximum |
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| 113 | // size of list produced to 200. |
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| 114 | explicit SpectralEstimate(const Double rms, |
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| 115 | const Double cutoff=0.0, const Double minsigma=0.0, |
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| 116 | const uInt maxpar=MAXPAR); |
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| 117 | // Copy constructor (deep copy) |
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| 118 | SpectralEstimate(const SpectralEstimate &other); |
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| 119 | |
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| 120 | //#Destructor |
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| 121 | // Destructor |
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| 122 | ~SpectralEstimate(); |
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| 123 | |
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| 124 | //# Operators |
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| 125 | // Assignment (copy semantics) |
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| 126 | SpectralEstimate &operator=(const SpectralEstimate &other); |
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| 127 | |
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| 128 | //# Member functions |
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| 129 | // Generate the estimates for a profile and return the |
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| 130 | // list found. The first function returns component parameters |
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| 131 | // in units of pixel indices. The second function calls the first |
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| 132 | // and then converts to the specified abcissa space (the supplied |
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| 133 | // vector must be monotonic); if the pixel-based center is out of range |
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| 134 | // of the supplied abcissa vector the conversion is done via extrapolation. |
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| 135 | // The der pointer is meant for debugging, and can return |
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| 136 | // the derivative profile. The second function throws an AipsError |
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| 137 | // if the vectors are not the same length. |
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| 138 | // <group> |
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| 139 | template <class MT> |
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| 140 | const SpectralList& estimate(const Vector<MT>& ordinate, |
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| 141 | Vector<MT> *der = 0); |
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| 142 | template <class MT> |
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| 143 | const SpectralList& estimate(const Vector<MT>& abcissa, |
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| 144 | const Vector<MT>& ordinate); |
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| 145 | // </group> |
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| 146 | |
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| 147 | // Return the list found. |
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| 148 | const SpectralList &list() const {return slist_p; }; |
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| 149 | |
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| 150 | // Set estimation parameters |
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| 151 | // <group> |
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| 152 | // Set the profile's estimated rms (forced to abs(rms)) |
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| 153 | void setRMS(const Double rms=0.0); |
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| 154 | // Set the amplitude cutoff for valid estimate (forced to max(0,cutoff)) |
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| 155 | void setCutoff(const Double cutoff=0.0); |
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| 156 | // Set the minimum width allowed (forced to max(0,minsigma)) |
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| 157 | void setMinSigma(const Double minsigma=0.0); |
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| 158 | // Set the number of points consider at each side of test point (i.e. a |
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| 159 | // width of 2q+1 is taken). Default internally is 2; max(1,q) taken. |
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| 160 | void setQ(const uInt q=2); |
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| 161 | // Set a region [lo,hi] over which to estimate. Lo and hi are given as |
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| 162 | // zero-based vector indices. |
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| 163 | void setRegion(const Int lo, const Int hi); |
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| 164 | // Do you want to look in an automatically determined window with signal? |
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| 165 | // Default is False, meaning the full (possibly regioned) profile. |
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| 166 | void setWindowing(const Bool win=False); |
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| 167 | // Set the maximum number of estimates to find (forced to >=1; 200 default) |
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| 168 | void setMaxN(const uInt maxpar=MAXPAR); |
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| 169 | // </group> |
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| 170 | |
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| 171 | private: |
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| 172 | //#Data |
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| 173 | // Use window search |
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| 174 | Bool useWindow_p; |
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| 175 | // rms estimate in profile |
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| 176 | Double rms_p; |
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| 177 | // Source cutoff amplitude |
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| 178 | Double cutoff_p; |
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| 179 | // Window low and end value |
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| 180 | // <group> |
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| 181 | Int windowLow_p; |
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| 182 | Int windowEnd_p; |
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| 183 | // </group> |
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| 184 | // Region low and high value |
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| 185 | // <group> |
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| 186 | Int regionLow_p; |
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| 187 | Int regionEnd_p; |
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| 188 | // </group> |
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| 189 | // Smoothing parameter. I.e. 2q+1 points are taken |
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| 190 | Int q_p; |
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| 191 | // Internal cashing of calculated values based on q |
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| 192 | // <group> |
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| 193 | Double a_p; |
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| 194 | Double b_p; |
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| 195 | // </group> |
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| 196 | // The minimum Gaussian width |
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| 197 | Double sigmin_p; |
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| 198 | // The second derivatives |
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| 199 | Double *deriv_p; |
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| 200 | // The list of components |
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| 201 | SpectralList slist_p; |
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| 202 | // The length of the current profile being estimated |
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| 203 | uInt lprof_p; |
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| 204 | |
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| 205 | //# Member functions |
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| 206 | // Get the window or the total spectrum |
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| 207 | template <class MT> |
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| 208 | uInt window(const Vector<MT> &prof); |
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| 209 | // Get the second derivatives |
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| 210 | template <class MT> |
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| 211 | void findc2(const Vector<MT> &prof); |
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| 212 | // Find the Gaussians |
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| 213 | template <class MT> |
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| 214 | void findga(const Vector<MT> &prof); |
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| 215 | // Convert the parameters of the components in the list from |
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| 216 | // pixel-based indices to the given abcissa-vector space. |
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| 217 | template <class MT> GaussianSpectralElement convertElement (const Vector<MT>& abcissa, |
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| 218 | const GaussianSpectralElement& el) const; |
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| 219 | }; |
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| 220 | |
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| 221 | |
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| 222 | } //# NAMESPACE CASA - END |
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| 223 | |
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| 224 | #ifndef CASACORE_NO_AUTO_TEMPLATES |
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| 225 | #include <components/SpectralComponents/Spectral2Estimate.tcc> |
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| 226 | #endif //# CASACORE_NO_AUTO_TEMPLATES |
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| 227 | #endif |
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