source: branches/alma/src/MathUtils.cpp@ 3001

Last change on this file since 3001 was 1757, checked in by Kana Sugimoto, 14 years ago

New Development: Yes

JIRA Issue: Yes (CAS-2211)

Ready for Test: Yes

Interface Changes: Yes

What Interface Changed: ASAP 3.0.0 interface changes

Test Programs:

Put in Release Notes: Yes

Module(s): all the CASA sd tools and tasks are affected.

Description: Merged ATNF-ASAP 3.0.0 developments to CASA (alma) branch.

Note you also need to update casa/code/atnf.


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 7.8 KB
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1//#---------------------------------------------------------------------------
2//# MathUtilities.cc: General math operations
3//#---------------------------------------------------------------------------
4//# Copyright (C) 2004
5//# ATNF
6//#
7//# This program is free software; you can redistribute it and/or modify it
8//# under the terms of the GNU General Public License as published by the Free
9//# Software Foundation; either version 2 of the License, or (at your option)
10//# any later version.
11//#
12//# This program is distributed in the hope that it will be useful, but
13//# WITHOUT ANY WARRANTY; without even the implied warranty of
14//# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
15//# Public License for more details.
16//#
17//# You should have received a copy of the GNU General Public License along
18//# with this program; if not, write to the Free Software Foundation, Inc.,
19//# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
20//#
21//# Correspondence concerning this software should be addressed as follows:
22//# Internet email: Malte.Marquarding@csiro.au
23//# Postal address: Malte Marquarding,
24//# Australia Telescope National Facility,
25//# P.O. Box 76,
26//# Epping, NSW, 2121,
27//# AUSTRALIA
28//#
29//# $Id:
30//#---------------------------------------------------------------------------
31
32#include <casa/aips.h>
33#include <casa/Arrays/Vector.h>
34#include <casa/Arrays/Slice.h>
35#include <casa/Arrays/MaskedArray.h>
36#include <casa/Arrays/MaskArrMath.h>
37#include <casa/Arrays/VectorSTLIterator.h>
38#include <casa/BasicSL/String.h>
39#include <scimath/Mathematics/MedianSlider.h>
40#include <casa/Exceptions/Error.h>
41
42#include <scimath/Fitting/LinearFit.h>
43#include <scimath/Functionals/Polynomial.h>
44#include <scimath/Mathematics/AutoDiff.h>
45
46
47#include "MathUtils.h"
48
49using namespace casa;
50
51float mathutil::statistics(const String& which,
52 const MaskedArray<Float>& data)
53{
54 String str(which);
55 str.upcase();
56 if (str.matches(String("MIN"))) {
57 return min(data);
58 } else if (str.matches(String("MAX"))) {
59 return max(data);
60 } else if (str.matches(String("SUMSQ"))) {
61 return sumsquares(data);
62 } else if (str.matches(String("SUM"))) {
63 return sum(data);
64 } else if (str.matches(String("MEAN"))) {
65 return mean(data);
66 } else if (str.matches(String("VAR"))) {
67 return variance(data);
68 } else if (str.matches(String("STDDEV"))) {
69 return stddev(data);
70 } else if (str.matches(String("AVDEV"))) {
71 return avdev(data);
72 } else if (str.matches(String("RMS"))) {
73 uInt n = data.nelementsValid();
74 return sqrt(sumsquares(data)/n);
75 } else if (str.matches(String("MEDIAN"))) {
76 return median(data);
77 } else {
78 String msg = str + " is not a valid type of statistics";
79 throw(AipsError(msg));
80 }
81 return 0.0;
82}
83
84IPosition mathutil::minMaxPos(const String& which,
85 const MaskedArray<Float>& data)
86{
87 Float minVal, maxVal;
88 IPosition minPos(data.ndim(), 0), maxPos(data.ndim(), 0);
89 minMax(minVal, maxVal, minPos, maxPos, data);
90 String str(which);
91 str.upcase();
92 if (str.contains(String("MIN"))) {
93 return minPos;
94 } else if (str.contains(String("MAX"))) {
95 return maxPos;
96 } else {
97 String msg = str + " is not a valid type of statistics";
98 throw(AipsError(msg));
99 }
100 //return 0.0;
101}
102
103void mathutil::replaceMaskByZero(Vector<Float>& data, const Vector<Bool>& mask)
104{
105 for (uInt i=0; i<data.nelements(); i++) {
106 if (!mask[i]) data[i] = 0.0;
107 }
108}
109
110
111std::vector<std::string> mathutil::tovectorstring(const Vector<String>& in)
112{
113 std::vector<std::string> out;
114 out.reserve(in.nelements());
115 for (Array<String>::const_iterator it = in.begin(); it != in.end(); ++it) {
116 out.push_back(*it);
117 }
118 return out;
119}
120
121Vector<String> mathutil::toVectorString(const std::vector<std::string>& in)
122{
123 Vector<String> out(in.size());
124 Array<String>::iterator oit = out.begin();
125 for (std::vector<std::string>::const_iterator it=in.begin() ;
126 it != in.end(); ++it,++oit) {
127 *oit = *it;
128 }
129 return out;
130}
131
132void mathutil::hanning(Vector<Float>& out, Vector<Bool>& outmask,
133 const Vector<Float>& in, const Vector<Bool>& mask,
134 Bool relaxed, Bool ignoreOther) {
135 Vector< Vector<Float> > weights(8);
136 Vector<Float> vals(3);
137 vals = 0.0;weights[0] = vals;// FFF
138 vals[0] = 1.0; vals[1] = 0.0; vals[2] = 0.0; weights[1] = vals;// TFF
139 vals[0] = 0.0; vals[1] = 1.0; vals[2] = 0.0; weights[2] = vals;// FTF
140 vals[0] = 1.0/3.0; vals[1] = 2.0/3.0; vals[2] = 0.0; weights[3] = vals;// TTF
141 vals[0] = 0.0; vals[1] = 0.0; vals[2] = 1.0;weights[4] = vals;// FFT
142 vals[0] = 0.5; vals[1] = 0.0; vals[2] = 0.5; weights[5] = vals;// TFT
143 vals[0] = 0.0; vals[1] = 2.0/3.0; vals[2] = 1.0/3.0; weights[6] = vals;// FTT
144 vals[0] = 0.25; vals[1] = 0.5; vals[2] = 0.25; weights[7] = vals;// TTT
145 // Chris' case
146 Vector<Bool> weighted(8);
147 if (relaxed) {
148 weighted = False;
149 weighted[7] = True;
150
151 } else {
152 weighted = True;
153 weighted[0] = False;
154 }
155
156 out.resize(in.nelements());
157 outmask.resize(mask.nelements());
158 // make special case for first and last
159 /// ...here
160 // loop from 1..n-2
161 out.resize(in.nelements());
162 out[0] = in[0];out[out.nelements()-1] = in[in.nelements()-1];
163 outmask.resize(mask.nelements());
164 outmask = False;
165 uInt m;Vector<Float>* w;
166 for (uInt i=1; i < out.nelements()-1;++i) {
167 m = mask[i-1] + 2*mask[i] + 4*mask[i+1];
168 w = &(weights[m]);
169 if (weighted[m]) {
170 out[i] = (*w)[0]*in[i-1] + (*w)[1]*in[i] + (*w)[2]*in[i+1];
171 outmask[i] = True;
172 } else { // mask it
173 out[i] = in[i];//use arbitrary value
174 outmask[i] = False;
175 }
176 }
177}
178
179
180void mathutil::runningMedian(Vector<Float>& out, Vector<Bool>& outflag,
181 const Vector<Float>& in, const Vector<Bool>& flag,
182 float width)
183{
184 Int hwidth = Int(width+0.5);
185 Int fwidth = hwidth*2+1;
186 out.resize(in.nelements());
187 outflag.resize(flag.nelements());
188 MedianSlider ms(hwidth);
189 Slice sl(0, fwidth-1);
190 Float medval = ms.add(const_cast<Vector<Float>& >(in)(sl),
191 const_cast<Vector<Bool>& >(flag)(sl));
192 uInt n = in.nelements();
193 for (uInt i=hwidth; i<(n-hwidth); ++i) {
194 // add data value
195 out[i] = ms.add(in[i+hwidth], flag[i+hwidth]);
196 outflag[i] = (ms.nval() == 0);
197 }
198 // replicate edge values from first value with full width of values
199 for (uInt i=0;i<hwidth;++i) {
200 out[i] = out[hwidth];
201 outflag[i] = outflag[hwidth];
202 out[n-1-i] = out[n-1-hwidth];
203 outflag[n-1-i] = outflag[n-1-hwidth];
204 }
205}
206
207void mathutil::polyfit(Vector<Float>& out, Vector<Bool>& outmask,
208 const Vector<Float>& in, const Vector<Bool>& mask,
209 float width, int order)
210{
211 Int hwidth = Int(width+0.5);
212 Int fwidth = hwidth*2+1;
213 out.resize(in.nelements());
214 outmask.resize(mask.nelements());
215 LinearFit<Float> fitter;
216 Polynomial<Float> poly(order);
217 fitter.setFunction(poly);
218 Vector<Float> sigma(fwidth);
219 sigma = 1.0;
220 Vector<Float> parms;
221 Vector<Float> x(fwidth);
222 indgen(x);
223
224 uInt n = in.nelements();
225
226 for (uInt i=hwidth; i<(n-hwidth); ++i) {
227 // add data value
228 if (mask[i]) {
229 Slice sl(i-hwidth, fwidth);
230 const Vector<Float> &y = const_cast<Vector<Float>& >(in)(sl);
231 const Vector<Bool> &m = const_cast<Vector<Bool>& >(mask)(sl);
232 parms = fitter.fit(x, y, sigma, &m);
233
234 poly.setCoefficients(parms);
235 out[i] = poly(x[hwidth]);//cout << in[i] <<"->"<<out[i]<<endl;
236 } else {
237 out[i] = in[i];
238 }
239 outmask[i] = mask[i];
240 }
241 // replicate edge values from first value with full width of values
242 for (uInt i=0;i<hwidth;++i) {
243 out[i] = out[hwidth];
244 outmask[i] = outmask[hwidth];
245 out[n-1-i] = out[n-1-hwidth];
246 outmask[n-1-i] = outmask[n-1-hwidth];
247 }
248}
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