1 | // ----------------------------------------------------------------------- |
---|
2 | // spectraUtils.cc: Utility functions to obtain & manipulate spectra |
---|
3 | // ----------------------------------------------------------------------- |
---|
4 | // Copyright (C) 2006, Matthew Whiting, ATNF |
---|
5 | // |
---|
6 | // This program is free software; you can redistribute it and/or modify it |
---|
7 | // under the terms of the GNU General Public License as published by the |
---|
8 | // Free Software Foundation; either version 2 of the License, or (at your |
---|
9 | // option) any later version. |
---|
10 | // |
---|
11 | // Duchamp is distributed in the hope that it will be useful, but WITHOUT |
---|
12 | // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
---|
13 | // FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
---|
14 | // for more details. |
---|
15 | // |
---|
16 | // You should have received a copy of the GNU General Public License |
---|
17 | // along with Duchamp; if not, write to the Free Software Foundation, |
---|
18 | // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
---|
19 | // |
---|
20 | // Correspondence concerning Duchamp may be directed to: |
---|
21 | // Internet email: Matthew.Whiting [at] atnf.csiro.au |
---|
22 | // Postal address: Dr. Matthew Whiting |
---|
23 | // Australia Telescope National Facility, CSIRO |
---|
24 | // PO Box 76 |
---|
25 | // Epping NSW 1710 |
---|
26 | // AUSTRALIA |
---|
27 | // ----------------------------------------------------------------------- |
---|
28 | #include <iostream> |
---|
29 | #include <fstream> |
---|
30 | #include <iomanip> |
---|
31 | #include <sstream> |
---|
32 | #include <string> |
---|
33 | #include <vector> |
---|
34 | #include <math.h> |
---|
35 | #include <wcslib/wcs.h> |
---|
36 | #include <duchamp/Cubes/cubeUtils.hh> |
---|
37 | #include <duchamp/param.hh> |
---|
38 | #include <duchamp/duchamp.hh> |
---|
39 | #include <duchamp/fitsHeader.hh> |
---|
40 | #include <duchamp/PixelMap/Object3D.hh> |
---|
41 | #include <duchamp/Cubes/cubes.hh> |
---|
42 | #include <duchamp/Cubes/plots.hh> |
---|
43 | #include <duchamp/Utils/utils.hh> |
---|
44 | |
---|
45 | using namespace PixelInfo; |
---|
46 | |
---|
47 | namespace duchamp |
---|
48 | { |
---|
49 | |
---|
50 | void getSpecAbscissae(Detection &object, FitsHeader &head, size_t zdim, float *abscissae) |
---|
51 | { |
---|
52 | /// @details |
---|
53 | /// A function that returns an array of |
---|
54 | /// frequency/velocity/channel/etc values (that can be used as the |
---|
55 | /// abscissae on the spectral plot). |
---|
56 | /// \param object The object on which our spectrum is centered (in |
---|
57 | /// case the spectral value changes with x & y |
---|
58 | /// \param head The FitsHeader set of parameters that determine the coordinate transformation. |
---|
59 | /// \param zdim The length of the spectral axis |
---|
60 | /// \param abscissae The array of spectral values -- must be allocated first |
---|
61 | |
---|
62 | getSpecAbscissae(head,object.getXcentre(),object.getYcentre(),zdim, abscissae); |
---|
63 | } |
---|
64 | |
---|
65 | void getSpecAbscissae(FitsHeader &head, float xpt, float ypt, size_t zdim, float *abscissae) |
---|
66 | { |
---|
67 | /// @details |
---|
68 | /// A function that returns an array of |
---|
69 | /// frequency/velocity/channel/etc values (that can be used as the |
---|
70 | /// horizontal axis on the spectral plot). |
---|
71 | /// \param head The FitsHeader set of parameters that determine the coordinate transformation. |
---|
72 | /// \param xpt The x-value of the spatial position on which our spectrum is centred. |
---|
73 | /// \param ypt The y-value of the spatial position on which our spectrum is centred. |
---|
74 | /// \param zdim The length of the spectral axis |
---|
75 | /// \param abscissae The array of spectral values -- must be allocated first. |
---|
76 | |
---|
77 | if(head.isWCS()){ |
---|
78 | double xval = double(xpt); |
---|
79 | double yval = double(ypt); |
---|
80 | for(double zval=0;zval<zdim;zval++) |
---|
81 | abscissae[int(zval)] = head.pixToVel(xval,yval,zval); |
---|
82 | } |
---|
83 | else |
---|
84 | for(double zval=0;zval<zdim;zval++) abscissae[int(zval)] = zval; |
---|
85 | |
---|
86 | } |
---|
87 | //-------------------------------------------------------------------- |
---|
88 | |
---|
89 | void getIntSpec(Detection &object, float *fluxArray, size_t *dimArray, std::vector<bool> mask, |
---|
90 | float beamCorrection, float *spec) |
---|
91 | { |
---|
92 | /// @details |
---|
93 | /// The base function that extracts an integrated spectrum for a |
---|
94 | /// given object from a pixel array. The spectrum is returned as |
---|
95 | /// the integrated flux, corrected for the beam using the given |
---|
96 | /// correction factor. |
---|
97 | /// \param object The Detection in question |
---|
98 | /// \param fluxArray The full array of pixel values. |
---|
99 | /// \param dimArray The axis dimensions for the fluxArray |
---|
100 | /// \param mask A mask array indicating whether given pixels are valid |
---|
101 | /// \param beamCorrection How much to divide the summed spectrum |
---|
102 | /// by to return the integrated flux. |
---|
103 | /// \param spec The integrated spectrum for the object -- must be allocated first. |
---|
104 | |
---|
105 | for(size_t i=0;i<dimArray[2];i++) spec[i] = 0.; |
---|
106 | size_t xySize = dimArray[0]*dimArray[1]; |
---|
107 | bool *done = new bool[xySize]; |
---|
108 | for(size_t i=0;i<xySize;i++) done[i]=false; |
---|
109 | std::vector<Voxel> voxlist = object.getPixelSet(); |
---|
110 | std::vector<Voxel>::iterator vox; |
---|
111 | for(vox=voxlist.begin();vox<voxlist.end();vox++){ |
---|
112 | size_t pos = vox->getX() + dimArray[0] * vox->getY(); |
---|
113 | if(!done[pos]){ |
---|
114 | done[pos] = true; |
---|
115 | for(size_t z=0;z<dimArray[2];z++){ |
---|
116 | if(mask[pos+z*xySize]){ |
---|
117 | spec[z] += fluxArray[pos + z*xySize] / beamCorrection; |
---|
118 | } |
---|
119 | } |
---|
120 | } |
---|
121 | } |
---|
122 | delete [] done; |
---|
123 | |
---|
124 | } |
---|
125 | //-------------------------------------------------------------------- |
---|
126 | |
---|
127 | void getPeakSpec(Detection &object, float *fluxArray, size_t *dimArray, bool *mask, float *spec) |
---|
128 | { |
---|
129 | /// @details |
---|
130 | /// The base function that extracts an peak spectrum for a |
---|
131 | /// given object from a pixel array. The spectrum is returned as |
---|
132 | /// the integrated flux, corrected for the beam using the given |
---|
133 | /// correction factor. |
---|
134 | /// \param object The Detection in question |
---|
135 | /// \param fluxArray The full array of pixel values. |
---|
136 | /// \param dimArray The axis dimensions for the fluxArray |
---|
137 | /// \param mask A mask array indicating whether given pixels are valid |
---|
138 | /// \param spec The peak spectrum for the object -- must be allocated first |
---|
139 | |
---|
140 | if((object.getXPeak()<0 || object.getXPeak()>=int(dimArray[0])) || (object.getYPeak()<0 || object.getYPeak()>=int(dimArray[1]))){ |
---|
141 | DUCHAMPWARN("getPeakSpec","Object peak outside array boundaries"); |
---|
142 | for (size_t z=0;z<dimArray[2];z++) spec[z]=0.; |
---|
143 | } |
---|
144 | else{ |
---|
145 | size_t xySize = dimArray[0]*dimArray[1]; |
---|
146 | size_t pos = object.getXPeak() + dimArray[0]*object.getYPeak(); |
---|
147 | for(size_t z=0;z<dimArray[2];z++){ |
---|
148 | if(mask[pos + z*xySize]) |
---|
149 | spec[z] = fluxArray[pos + z*xySize]; |
---|
150 | } |
---|
151 | } |
---|
152 | } |
---|
153 | //-------------------------------------------------------------------- |
---|
154 | |
---|
155 | |
---|
156 | void Cube::getSpectralArrays(int objNum, float *specx, float *specy, |
---|
157 | float *specRecon, float *specBase) |
---|
158 | { |
---|
159 | /// @details |
---|
160 | /// A utility function that goes and calculates, for a given |
---|
161 | /// Detection, the spectral arrays, according to whether we want |
---|
162 | /// the peak or integrated flux. The arrays can be used by |
---|
163 | /// Cube::plotSpectrum() and Cube::writeSpectralData(). The arrays |
---|
164 | /// calculated are listed below. Their length is given by the |
---|
165 | /// length of the Cube's spectral dimension. |
---|
166 | /// |
---|
167 | /// Note that the arrays need to be allocated prior to calling |
---|
168 | /// this function. |
---|
169 | /// |
---|
170 | /// \param objNum The number of the object under |
---|
171 | /// consideration. If negative, we extract the single |
---|
172 | /// spectrum at (x,y)=(0,0) (useful for the 1D case). |
---|
173 | /// \param specx The array of frequency/velocity/channel/etc |
---|
174 | /// values (the x-axis on the spectral plot). |
---|
175 | /// \param specy The array of flux values, matching the specx |
---|
176 | /// array. |
---|
177 | /// \param specRecon The reconstructed or smoothed array, done in |
---|
178 | /// the same way as specy. |
---|
179 | /// \param specBase The fitted baseline values, done in the same |
---|
180 | /// way as specy. |
---|
181 | |
---|
182 | size_t xdim = this->axisDim[0]; |
---|
183 | size_t ydim = this->axisDim[1]; |
---|
184 | size_t zdim = this->axisDim[2]; |
---|
185 | |
---|
186 | for(size_t i=0;i<zdim;i++){ |
---|
187 | specy[i] = 0.; |
---|
188 | specRecon[i] = 0.; |
---|
189 | specBase[i] = 0.; |
---|
190 | } |
---|
191 | |
---|
192 | double xloc,yloc; |
---|
193 | size_t spatpos=0; |
---|
194 | std::vector<Voxel> voxlist; |
---|
195 | if(objNum>=0){ |
---|
196 | if(this->par.getSpectralMethod()=="sum"){ |
---|
197 | xloc=double(this->objectList->at(objNum).getXcentre()); |
---|
198 | yloc=double(this->objectList->at(objNum).getYcentre()); |
---|
199 | voxlist = this->objectList->at(objNum).getPixelSet(); |
---|
200 | } |
---|
201 | else{ |
---|
202 | spatpos = this->objectList->at(objNum).getXPeak() + |
---|
203 | xdim*this->objectList->at(objNum).getYPeak(); |
---|
204 | } |
---|
205 | } |
---|
206 | |
---|
207 | if(this->head.isWCS()){ |
---|
208 | // double xval = double(this->objectList->at(objNum).getXcentre()); |
---|
209 | // double yval = double(this->objectList->at(objNum).getYcentre()); |
---|
210 | // for(double zval=0;zval<zdim;zval++) |
---|
211 | // specx[int(zval)] = this->head.pixToVel(xval,yval,zval); |
---|
212 | for(double zval=0;zval<zdim;zval++) |
---|
213 | specx[int(zval)] = this->head.pixToVel(xloc,yloc,zval); |
---|
214 | } |
---|
215 | else |
---|
216 | for(double zval=0;zval<zdim;zval++) specx[int(zval)] = zval; |
---|
217 | |
---|
218 | float beamCorrection; |
---|
219 | if(this->header().needBeamSize()) |
---|
220 | beamCorrection = this->head.beam().area(); |
---|
221 | else beamCorrection = 1.; |
---|
222 | |
---|
223 | if(objNum>=0 && this->par.getSpectralMethod()=="sum"){ |
---|
224 | bool *done = new bool[xdim*ydim]; |
---|
225 | for(size_t i=0;i<xdim*ydim;i++) done[i]=false; |
---|
226 | // std::vector<Voxel> voxlist = this->objectList->at(objNum).getPixelSet(); |
---|
227 | std::vector<Voxel>::iterator vox; |
---|
228 | for(vox=voxlist.begin();vox<voxlist.end();vox++){ |
---|
229 | spatpos = vox->getX() + xdim * vox->getY(); |
---|
230 | if(!done[spatpos]){ |
---|
231 | done[spatpos] = true; |
---|
232 | for(size_t z=0;z<zdim;z++){ |
---|
233 | if(!(this->isBlank(spatpos+z*xdim*ydim))){ |
---|
234 | specy[z] += this->array[spatpos + z*xdim*ydim] / beamCorrection; |
---|
235 | if(this->reconExists) |
---|
236 | specRecon[z] += this->recon[spatpos + z*xdim*ydim] / beamCorrection; |
---|
237 | if(this->par.getFlagBaseline()) |
---|
238 | specBase[z] += this->baseline[spatpos + z*xdim*ydim] / beamCorrection; |
---|
239 | } |
---|
240 | } |
---|
241 | } |
---|
242 | } |
---|
243 | delete [] done; |
---|
244 | } |
---|
245 | else {// if(par.getSpectralMethod()=="peak"){ |
---|
246 | // size_t spatpos = this->objectList->at(objNum).getXPeak() + |
---|
247 | // xdim*this->objectList->at(objNum).getYPeak(); |
---|
248 | for(size_t z=0;z<zdim;z++){ |
---|
249 | specy[z] = this->array[spatpos + z*xdim*ydim]; |
---|
250 | if(this->reconExists) |
---|
251 | specRecon[z] = this->recon[spatpos + z*xdim*ydim]; |
---|
252 | if(this->par.getFlagBaseline()) |
---|
253 | specBase[z] = this->baseline[spatpos + z*xdim*ydim]; |
---|
254 | } |
---|
255 | } |
---|
256 | |
---|
257 | } |
---|
258 | //-------------------------------------------------------------------- |
---|
259 | |
---|
260 | void getSmallVelRange(Detection &obj, FitsHeader &head, |
---|
261 | double *minvel, double *maxvel) |
---|
262 | { |
---|
263 | /// @details |
---|
264 | /// Routine to calculate the velocity range for the zoomed-in region. |
---|
265 | /// This range should be the maximum of 20 pixels, or 3x the wdith of |
---|
266 | /// the detection. |
---|
267 | /// Need to : |
---|
268 | /// Calculate pixel width of a 3x-detection-width region. |
---|
269 | /// If smaller than 20, calculate velocities of central vel +- 10 pixels |
---|
270 | /// If not, use the 3x-detection-width |
---|
271 | /// Range returned via "minvel" and "maxvel" parameters. |
---|
272 | /// \param obj Detection under examination. |
---|
273 | /// \param head FitsHeader, containing the WCS information. |
---|
274 | /// \param minvel Returned value of minimum velocity |
---|
275 | /// \param maxvel Returned value of maximum velocity |
---|
276 | |
---|
277 | double *pixcrd = new double[3]; |
---|
278 | double *world = new double[3]; |
---|
279 | float minpix,maxpix; |
---|
280 | // define new velocity extrema |
---|
281 | // -- make it 3x wider than the width of the detection. |
---|
282 | *minvel = 0.5*(obj.getVelMin()+obj.getVelMax()) - 1.5*obj.getVelWidth(); |
---|
283 | *maxvel = 0.5*(obj.getVelMin()+obj.getVelMax()) + 1.5*obj.getVelWidth(); |
---|
284 | // Find velocity range in number of pixels: |
---|
285 | world[0] = obj.getRA(); |
---|
286 | world[1] = obj.getDec(); |
---|
287 | world[2] = head.velToSpec(*minvel); |
---|
288 | head.wcsToPix(world,pixcrd); |
---|
289 | minpix = pixcrd[2]; |
---|
290 | world[2] = head.velToSpec(*maxvel); |
---|
291 | head.wcsToPix(world,pixcrd); |
---|
292 | maxpix = pixcrd[2]; |
---|
293 | if(maxpix<minpix) std::swap(maxpix,minpix); |
---|
294 | |
---|
295 | if((maxpix - minpix + 1) < 20){ |
---|
296 | pixcrd[0] = double(obj.getXcentre()); |
---|
297 | pixcrd[1] = double(obj.getYcentre()); |
---|
298 | pixcrd[2] = obj.getZcentre() - 10.; |
---|
299 | head.pixToWCS(pixcrd,world); |
---|
300 | // *minvel = setVel_kms(wcs,world[2]); |
---|
301 | *minvel = head.specToVel(world[2]); |
---|
302 | pixcrd[2] = obj.getZcentre() + 10.; |
---|
303 | head.pixToWCS(pixcrd,world); |
---|
304 | // *maxvel = setVel_kms(wcs,world[2]); |
---|
305 | *maxvel = head.specToVel(world[2]); |
---|
306 | if(*maxvel<*minvel) std::swap(*maxvel,*minvel); |
---|
307 | } |
---|
308 | delete [] pixcrd; |
---|
309 | delete [] world; |
---|
310 | |
---|
311 | } |
---|
312 | //-------------------------------------------------------------------- |
---|
313 | |
---|
314 | void getSmallZRange(Detection &obj, double *minz, double *maxz) |
---|
315 | { |
---|
316 | /// @details |
---|
317 | /// Routine to calculate the pixel range for the zoomed-in spectrum. |
---|
318 | /// This range should be the maximum of 20 pixels, or 3x the width |
---|
319 | /// of the detection. |
---|
320 | /// Need to : |
---|
321 | /// Calculate pixel width of a 3x-detection-width region. |
---|
322 | /// If smaller than 20, use central pixel +- 10 pixels |
---|
323 | /// Range returned via "minz" and "maxz" parameters. |
---|
324 | /// \param obj Detection under examination. |
---|
325 | /// \param minz Returned value of minimum z-pixel coordinate |
---|
326 | /// \param maxz Returned value of maximum z-pixel coordinate |
---|
327 | |
---|
328 | *minz = 2.*obj.getZmin() - obj.getZmax(); |
---|
329 | *maxz = 2.*obj.getZmax() - obj.getZmin(); |
---|
330 | |
---|
331 | if((*maxz - *minz + 1) < 20){ |
---|
332 | *minz = obj.getZcentre() - 10.; |
---|
333 | *maxz = obj.getZcentre() + 10.; |
---|
334 | } |
---|
335 | |
---|
336 | } |
---|
337 | //-------------------------------------------------------------------- |
---|
338 | |
---|
339 | } |
---|