00001 //# MomentWindow.h: 00002 //# Copyright (C) 1997,1999,2000,2001,2002 00003 //# Associated Universities, Inc. Washington DC, USA. 00004 //# 00005 //# This library is free software; you can redistribute it and/or modify it 00006 //# under the terms of the GNU Library General Public License as published by 00007 //# the Free Software Foundation; either version 2 of the License, or (at your 00008 //# option) any later version. 00009 //# 00010 //# This library is distributed in the hope that it will be useful, but WITHOUT 00011 //# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or 00012 //# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public 00013 //# License for more details. 00014 //# 00015 //# You should have received a copy of the GNU Library General Public License 00016 //# along with this library; if not, write to the Free Software Foundation, 00017 //# Inc., 675 Massachusetts Ave, Cambridge, MA 02139, USA. 00018 //# 00019 //# Correspondence concerning AIPS++ should be addressed as follows: 00020 //# Internet email: aips2-request@nrao.edu. 00021 //# Postal address: AIPS++ Project Office 00022 //# National Radio Astronomy Observatory 00023 //# 520 Edgemont Road 00024 //# Charlottesville, VA 22903-2475 USA 00025 //# 00026 //# $Id: MomentCalculator.h 20299 2008-04-03 05:56:44Z gervandiepen $ 00027 00028 #ifndef IMAGEANALYSIS_MOMENTWINDOW_H 00029 #define IMAGEANALYSIS_MOMENTWINDOW_H 00030 00031 #include <casa/aips.h> 00032 #include <coordinates/Coordinates/CoordinateSystem.h> 00033 #include <coordinates/Coordinates/SpectralCoordinate.h> 00034 #include <lattices/LatticeMath/LineCollapser.h> 00035 #include <scimath/Functionals/Gaussian1D.h> 00036 #include <scimath/Mathematics/NumericTraits.h> 00037 #include <casa/Arrays/Vector.h> 00038 #include <casa/Logging/LogIO.h> 00039 00040 namespace casa { 00041 00042 template <class T> class MomentsBase; 00043 00044 // <summary> Computes moments from a windowed profile </summary> 00045 // <use visibility=export> 00046 // 00047 // <reviewed reviewer="" date="yyyy/mm/dd" tests="" demos=""> 00048 // </reviewed> 00049 // 00050 // <prerequisite> 00051 // <li> <linkto class="MomentsBase">MomentsBase</linkto> 00052 // <li> <linkto class="ImageMoments">ImageMoments</linkto> 00053 // <li> <linkto class="MSMoments">MSMoments</linkto> 00054 // <li> <linkto class="LatticeApply">LatticeApply</linkto> 00055 // <li> <linkto class="MomentCalcBase">MomentCalcBase</linkto> 00056 // <li> <linkto class="LineCollapser">LineCollapser</linkto> 00057 // </prerequisite> 00058 // 00059 // <synopsis> 00060 // This concrete class is derived from the abstract base class MomentCalcBase 00061 // which provides an interface layer to the ImageMoments or MSMoments driver class. 00062 // ImageMoments or MSMoments creates a MomentWindow object and passes it to the LatticeApply 00063 // function lineMultiApply. This function iterates through a given lattice, 00064 // and invokes the <src>multiProcess</src> member function of MomentWindow on each profile 00065 // of pixels that it extracts from the input lattice. The <src>multiProcess</src> function 00066 // returns a vector of moments which are inserted into the output lattices also 00067 // supplied to the LatticeApply function. 00068 // 00069 // MomentWindow computes moments from a subset of the pixels selected from the 00070 // input profile. This subset is a simple index range, or window. The window is 00071 // selected, for each profile, that is thought to surround the spectral feature 00072 // of interest. This window can be found from the primary lattice, or from an 00073 // ancilliary lattice (ImageMoments or MSMoments offers a smoothed version of the primary 00074 // lattice as the ancilliary lattice). The moments are always computed from 00075 // primary lattice data. 00076 // 00077 // For each profile, the window can be found either interactively or automatically. 00078 // There are two interactive methods. Either you just mark the window with the 00079 // cursor, or you interactively fit a Gaussian to the profile and the +/- 3-sigma 00080 // window is returned. There are two automatic methods. Either Bosma's converging 00081 // mean algorithm is used, or an automatically fit Gaussian +/- 3-sigma window 00082 // is returned. 00083 // 00084 // The constructor takes an MomentsBase object that is actually an ImageMoments or 00085 // an MSMoments object; the one that is constructing 00086 // the MomentWindow object of course. There is much control information embodied 00087 // in the state of the ImageMoments or MSMoments object. This information is extracted by the 00088 // MomentCalcBase class and passed on to MomentWindow for consumption. 00089 // 00090 // Note that the ancilliary lattice is only accessed if the pointer to it 00091 // is non zero. 00092 // 00093 // See the <linkto class="MomentsBase">MomentsBase</linkto>, 00094 // <linkto class="ImageMoments">ImageMoments</linkto>, and 00095 // <linkto class="MSMoments">MSMoments</linkto> 00096 // for discussion about the moments that are available for computation. 00097 // 00098 // </synopsis> 00099 // 00100 // <example> 00101 // This example comes from ImageMoments. outPt is a pointer block holding 00102 // pointers to the output lattices. The ancilliary masking lattice is 00103 // just a smoothed version of the input lattice. os_P is a LogIO object. 00104 // 00105 // <srcBlock> 00106 // 00109 // 00110 // MomentCalcBase<T>* pMomentCalculator = 0; 00111 // if (clipMethod || smoothClipMethod) { 00112 // pMomentCalculator = new MomentClip<T>(pSmoothedImage, *this, os_p, outPt.nelements()); 00113 // } else if (windowMethod) { 00114 // pMomentCalculator = new MomentWindow<T>(pSmoothedImage, *this, os_p, outPt.nelements()); 00115 // } else if (fitMethod) { 00116 // pMomentCalculator = new MomentFit<T>(*this, os_p, outPt.nelements()); 00117 // } 00118 // 00120 // 00121 // LatticeApply<T>::lineMultiApply(outPt, *pInImage_p, *pMomentCalculator, 00122 // momentAxis_p, pProgressMeter); 00123 // delete pMomentCalculator; 00124 // 00125 // </srcBlock> 00126 // </example> 00127 // 00128 // <motivation> 00129 // </motivation> 00130 // 00131 // <note role=tip> 00132 // Note that there are is assignment operator or copy constructor. 00133 // Do not use the ones the system would generate either. 00134 // </note> 00135 // 00136 // <todo asof="yyyy/mm/dd"> 00137 // </todo> 00138 00139 00140 template <class T> class MomentWindow : public MomentCalcBase<T> 00141 { 00142 public: 00143 using AccumType = typename NumericTraits<T>::PrecisionType; 00144 using DataIterator = typename Vector<T>::const_iterator; 00145 using MaskIterator = Vector<Bool>::const_iterator; 00146 00147 // Constructor. The pointer is to a lattice containing the masking 00148 // lattice (created by ImageMoments or MSMoments). We also need the 00149 // ImageMoments or MSMoments object which is calling us, its logger, 00150 // and the number of output lattices it has created. 00151 MomentWindow(shared_ptr<Lattice<T>> pAncilliaryLattice, 00152 MomentsBase<T>& iMom, 00153 LogIO& os, 00154 const uInt nLatticeOut); 00155 00156 // Destructor (does nothing). 00157 ~MomentWindow(); 00158 00159 // This function is not implemented and throws an exception. 00160 virtual void process(T& out, 00161 Bool& outMask, 00162 const Vector<T>& in, 00163 const Vector<Bool>& inMask, 00164 const IPosition& pos); 00165 00166 // This function returns a vector of numbers from each input vector. 00167 // the output vector contains the moments known to the ImageMoments 00168 // or MSMoments object passed into the constructor. 00169 virtual void multiProcess(Vector<T>& out, 00170 Vector<Bool>& outMask, 00171 const Vector<T>& in, 00172 const Vector<Bool>& inMask, 00173 const IPosition& pos); 00174 00175 00176 private: 00177 00178 shared_ptr<Lattice<T>> _ancilliaryLattice; 00179 MomentsBase<T>& iMom_p; 00180 LogIO os_p; 00181 00182 const Vector<T>* pProfileSelect_p; 00183 Vector<T> ancilliarySliceRef_p; 00184 Vector<T> selectedData_p; 00185 T stdDeviation_p, peakSNR_p; 00186 Bool doFit_p; 00187 IPosition sliceShape_p; 00188 00189 // Automatically determine the spectral window 00190 Bool getAutoWindow(uInt& nFailed, 00191 Vector<Int>& window, 00192 const Vector<T>& x, 00193 const Vector<T>& y, 00194 const Vector<Bool>& mask, 00195 const T peakSNR, 00196 const T stdDeviation, 00197 const Bool doFit) const; 00198 00199 // Automatically determine the spectral window via Bosma's algorithm 00200 Bool _getBosmaWindow ( 00201 Vector<Int>& window, const Vector<T>& y, 00202 const Vector<Bool>& mask, const T peakSNR, 00203 const T stdDeviation 00204 ) const; 00205 00206 // Take the fitted Gaussian parameters and set an N-sigma window. 00207 // If the window is too small return a Fail condition. 00208 Bool setNSigmaWindow(Vector<Int>& window, 00209 const T pos, 00210 const T width, 00211 const Int nPts, 00212 const Int N) const; 00213 00214 00215 //# Make members of parent class known. 00216 protected: 00217 using MomentCalcBase<T>::constructorCheck; 00218 using MomentCalcBase<T>::setPosLabel; 00219 //using MomentCalcBase<T>::convertF; 00220 using MomentCalcBase<T>::selectMoments_p; 00221 using MomentCalcBase<T>::calcMoments_p; 00222 using MomentCalcBase<T>::calcMomentsMask_p; 00223 using MomentCalcBase<T>::doMedianI_p; 00224 using MomentCalcBase<T>::doMedianV_p; 00225 using MomentCalcBase<T>::doAbsDev_p; 00226 using MomentCalcBase<T>::cSys_p; 00227 using MomentCalcBase<T>::doCoordProfile_p; 00228 using MomentCalcBase<T>::doCoordRandom_p; 00229 using MomentCalcBase<T>::pixelIn_p; 00230 using MomentCalcBase<T>::worldOut_p; 00231 using MomentCalcBase<T>::sepWorldCoord_p; 00232 using MomentCalcBase<T>::integratedScaleFactor_p; 00233 using MomentCalcBase<T>::momAxisType_p; 00234 using MomentCalcBase<T>::nFailed_p; 00235 using MomentCalcBase<T>::abcissa_p; 00236 }; 00237 00238 } 00239 00240 #ifndef CASACORE_NO_AUTO_TEMPLATES 00241 #include <imageanalysis/ImageAnalysis/MomentWindow.tcc> 00242 #endif 00243 #endif