1 | // ----------------------------------------------------------------------- |
---|
2 | // detection.cc : Member functions for the Detection class. |
---|
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 <iomanip> |
---|
30 | #include <vector> |
---|
31 | #include <map> |
---|
32 | #include <string> |
---|
33 | #include <wcslib/wcs.h> |
---|
34 | #include <math.h> |
---|
35 | #include <duchamp/duchamp.hh> |
---|
36 | #include <duchamp/param.hh> |
---|
37 | #include <duchamp/fitsHeader.hh> |
---|
38 | #include <duchamp/Utils/utils.hh> |
---|
39 | #include <duchamp/PixelMap/Voxel.hh> |
---|
40 | #include <duchamp/PixelMap/Object3D.hh> |
---|
41 | #include <duchamp/Detection/detection.hh> |
---|
42 | #include <duchamp/Cubes/cubeUtils.hh> |
---|
43 | #include <duchamp/Outputs/columns.hh> |
---|
44 | |
---|
45 | using namespace PixelInfo; |
---|
46 | |
---|
47 | namespace duchamp |
---|
48 | { |
---|
49 | |
---|
50 | void Detection::defaultDetection() |
---|
51 | { |
---|
52 | this->xSubOffset = 0; |
---|
53 | this->ySubOffset = 0; |
---|
54 | this->zSubOffset = 0; |
---|
55 | this->haveParams = false; |
---|
56 | this->totalFlux = 0.; |
---|
57 | this->eTotalFlux = 0.; |
---|
58 | this->peakFlux = 0.; |
---|
59 | this->intFlux = 0.; |
---|
60 | this->eIntFlux = 0.; |
---|
61 | this->xpeak = 0; |
---|
62 | this->ypeak = 0; |
---|
63 | this->zpeak = 0; |
---|
64 | this->peakSNR = 0.; |
---|
65 | this->xCentroid = 0.; |
---|
66 | this->yCentroid = 0.; |
---|
67 | this->zCentroid = 0.; |
---|
68 | this->centreType="centroid"; |
---|
69 | this->negSource = false; |
---|
70 | this->flagText=""; |
---|
71 | this->id = -1; |
---|
72 | this->name = ""; |
---|
73 | this->flagWCS=false; |
---|
74 | this->specOK = true; |
---|
75 | this->raS = ""; |
---|
76 | this->decS = ""; |
---|
77 | this->ra = 0.; |
---|
78 | this->dec = 0.; |
---|
79 | this->raWidth = 0.; |
---|
80 | this->decWidth = 0.; |
---|
81 | this->majorAxis = 0.; |
---|
82 | this->minorAxis = 0.; |
---|
83 | this->posang = 0.; |
---|
84 | this->specUnits = ""; |
---|
85 | this->specType = ""; |
---|
86 | this->fluxUnits = ""; |
---|
87 | this->intFluxUnits = ""; |
---|
88 | this->lngtype = "RA"; |
---|
89 | this->lattype = "DEC"; |
---|
90 | this->vel = 0.; |
---|
91 | this->velWidth = 0.; |
---|
92 | this->velMin = 0.; |
---|
93 | this->velMax = 0.; |
---|
94 | this->w20 = 0.; |
---|
95 | this->v20min = 0.; |
---|
96 | this->v20max = 0.; |
---|
97 | this->w50 = 0.; |
---|
98 | this->v50min = 0.; |
---|
99 | this->v50max = 0.; |
---|
100 | this->posPrec = Catalogues::prPOS; |
---|
101 | this->xyzPrec = Catalogues::prXYZ; |
---|
102 | this->fintPrec = Catalogues::prFLUX; |
---|
103 | this->fpeakPrec = Catalogues::prFLUX; |
---|
104 | this->velPrec = Catalogues::prVEL; |
---|
105 | this->snrPrec = Catalogues::prSNR; |
---|
106 | } |
---|
107 | |
---|
108 | Detection::Detection(): |
---|
109 | Object3D() |
---|
110 | { |
---|
111 | this->defaultDetection(); |
---|
112 | } |
---|
113 | |
---|
114 | Detection::Detection(const Object3D& o): |
---|
115 | Object3D(o) |
---|
116 | { |
---|
117 | this->defaultDetection(); |
---|
118 | } |
---|
119 | |
---|
120 | Detection::Detection(const Detection& d): |
---|
121 | Object3D(d) |
---|
122 | { |
---|
123 | operator=(d); |
---|
124 | } |
---|
125 | |
---|
126 | Detection& Detection::operator= (const Detection& d) |
---|
127 | { |
---|
128 | ((Object3D &) *this) = d; |
---|
129 | this->xSubOffset = d.xSubOffset; |
---|
130 | this->ySubOffset = d.ySubOffset; |
---|
131 | this->zSubOffset = d.zSubOffset; |
---|
132 | this->haveParams = d.haveParams; |
---|
133 | this->totalFlux = d.totalFlux; |
---|
134 | this->eTotalFlux = d.eTotalFlux; |
---|
135 | this->intFlux = d.intFlux; |
---|
136 | this->eIntFlux = d.eIntFlux; |
---|
137 | this->peakFlux = d.peakFlux; |
---|
138 | this->xpeak = d.xpeak; |
---|
139 | this->ypeak = d.ypeak; |
---|
140 | this->zpeak = d.zpeak; |
---|
141 | this->peakSNR = d.peakSNR; |
---|
142 | this->xCentroid = d.xCentroid; |
---|
143 | this->yCentroid = d.yCentroid; |
---|
144 | this->zCentroid = d.zCentroid; |
---|
145 | this->centreType = d.centreType; |
---|
146 | this->negSource = d.negSource; |
---|
147 | this->flagText = d.flagText; |
---|
148 | this->id = d.id; |
---|
149 | this->name = d.name; |
---|
150 | this->flagWCS = d.flagWCS; |
---|
151 | this->specOK = d.specOK; |
---|
152 | this->raS = d.raS; |
---|
153 | this->decS = d.decS; |
---|
154 | this->ra = d.ra; |
---|
155 | this->dec = d.dec; |
---|
156 | this->raWidth = d.raWidth; |
---|
157 | this->decWidth = d.decWidth; |
---|
158 | this->majorAxis = d.majorAxis; |
---|
159 | this->minorAxis = d.minorAxis; |
---|
160 | this->posang = d.posang; |
---|
161 | this->specUnits = d.specUnits; |
---|
162 | this->specType = d.specType; |
---|
163 | this->fluxUnits = d.fluxUnits; |
---|
164 | this->intFluxUnits = d.intFluxUnits; |
---|
165 | this->lngtype = d.lngtype; |
---|
166 | this->lattype = d.lattype; |
---|
167 | this->vel = d.vel; |
---|
168 | this->velWidth = d.velWidth; |
---|
169 | this->velMin = d.velMin; |
---|
170 | this->velMax = d.velMax; |
---|
171 | this->w20 = d.w20; |
---|
172 | this->v20min = d.v20min; |
---|
173 | this->v20max = d.v20max; |
---|
174 | this->w50 = d.w50; |
---|
175 | this->v50min = d.v50min; |
---|
176 | this->v50max = d.v50max; |
---|
177 | this->posPrec = d.posPrec; |
---|
178 | this->xyzPrec = d.xyzPrec; |
---|
179 | this->fintPrec = d.fintPrec; |
---|
180 | this->fpeakPrec = d.fpeakPrec; |
---|
181 | this->velPrec = d.velPrec; |
---|
182 | this->snrPrec = d.snrPrec; |
---|
183 | return *this; |
---|
184 | } |
---|
185 | |
---|
186 | //-------------------------------------------------------------------- |
---|
187 | float Detection::getXcentre() |
---|
188 | { |
---|
189 | if(this->centreType=="peak") return this->xpeak; |
---|
190 | else if(this->centreType=="average") return this->getXaverage(); |
---|
191 | else return this->xCentroid; |
---|
192 | } |
---|
193 | |
---|
194 | float Detection::getYcentre() |
---|
195 | { |
---|
196 | if(this->centreType=="peak") return this->ypeak; |
---|
197 | else if(this->centreType=="average") return this->getYaverage(); |
---|
198 | else return this->yCentroid; |
---|
199 | } |
---|
200 | |
---|
201 | float Detection::getZcentre() |
---|
202 | { |
---|
203 | if(this->centreType=="peak") return this->zpeak; |
---|
204 | else if(this->centreType=="average") return this->getZaverage(); |
---|
205 | else return this->zCentroid; |
---|
206 | } |
---|
207 | |
---|
208 | //-------------------------------------------------------------------- |
---|
209 | |
---|
210 | bool Detection::voxelListsMatch(std::vector<Voxel> voxelList) |
---|
211 | { |
---|
212 | /// @details |
---|
213 | /// A test to see whether there is a 1-1 correspondence between |
---|
214 | /// the given list of Voxels and the voxel positions contained in |
---|
215 | /// this Detection's pixel list. No testing of the fluxes of the |
---|
216 | /// Voxels is done. |
---|
217 | /// |
---|
218 | /// \param voxelList The std::vector list of Voxels to be tested. |
---|
219 | |
---|
220 | bool listsMatch = true; |
---|
221 | // compare sizes |
---|
222 | listsMatch = listsMatch && (voxelList.size() == this->getSize()); |
---|
223 | if(!listsMatch) return listsMatch; |
---|
224 | |
---|
225 | // make sure all Detection pixels are in voxel list |
---|
226 | listsMatch = listsMatch && this->voxelListCovered(voxelList); |
---|
227 | |
---|
228 | // make sure all voxels are in Detection |
---|
229 | std::vector<Voxel>::iterator vox; |
---|
230 | for(vox=voxelList.begin();vox<voxelList.end();vox++) |
---|
231 | listsMatch = listsMatch && this->isInObject(*vox); |
---|
232 | |
---|
233 | return listsMatch; |
---|
234 | |
---|
235 | } |
---|
236 | //-------------------------------------------------------------------- |
---|
237 | |
---|
238 | bool Detection::voxelListCovered(std::vector<Voxel> voxelList) |
---|
239 | { |
---|
240 | /// @details |
---|
241 | /// A test to see whether the given list of Voxels contains each |
---|
242 | /// position in this Detection's pixel list. It does not look for |
---|
243 | /// a 1-1 correspondence: the given list can be a super-set of the |
---|
244 | /// Detection. No testing of the fluxes of the Voxels is done. |
---|
245 | /// |
---|
246 | /// \param voxelList The std::vector list of Voxels to be tested. |
---|
247 | |
---|
248 | bool listsMatch = true; |
---|
249 | |
---|
250 | // make sure all Detection pixels are in voxel list |
---|
251 | size_t v1=0; |
---|
252 | std::vector<Voxel> detpixlist = this->getPixelSet(); |
---|
253 | while(listsMatch && v1<detpixlist.size()){ |
---|
254 | bool inList = false; |
---|
255 | size_t v2=0; |
---|
256 | while(!inList && v2<voxelList.size()){ |
---|
257 | inList = inList || detpixlist[v1].match(voxelList[v2]); |
---|
258 | v2++; |
---|
259 | } |
---|
260 | listsMatch = listsMatch && inList; |
---|
261 | v1++; |
---|
262 | } |
---|
263 | |
---|
264 | return listsMatch; |
---|
265 | |
---|
266 | } |
---|
267 | //-------------------------------------------------------------------- |
---|
268 | |
---|
269 | void Detection::invert() |
---|
270 | { |
---|
271 | /// @details |
---|
272 | /// A front-end to simplify the inversion that is done at the Cube level. |
---|
273 | /// The fluxes are made negative, and the negSource flag is flipped. |
---|
274 | /// This can be used at any time - it doesn't matter which way the inversion is happening. |
---|
275 | |
---|
276 | this->negSource = !this->negSource; |
---|
277 | this->totalFlux = -1. * this->totalFlux; |
---|
278 | this->intFlux = -1. * this->intFlux; |
---|
279 | this->peakFlux = -1. * this->peakFlux; |
---|
280 | |
---|
281 | } |
---|
282 | |
---|
283 | //-------------------------------------------------------------------- |
---|
284 | |
---|
285 | void Detection::calcFluxes(std::vector<Voxel> voxelList) |
---|
286 | { |
---|
287 | /// @details |
---|
288 | /// A function that calculates total & peak fluxes (and the location |
---|
289 | /// of the peak flux) for a Detection. |
---|
290 | /// |
---|
291 | /// \param fluxArray The array of flux values to calculate the |
---|
292 | /// flux parameters from. |
---|
293 | /// \param dim The dimensions of the flux array. |
---|
294 | |
---|
295 | // this->haveParams = true; |
---|
296 | |
---|
297 | this->totalFlux = this->peakFlux = 0; |
---|
298 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
---|
299 | |
---|
300 | // first check that the voxel list and the Detection's pixel list |
---|
301 | // have a 1-1 correspondence |
---|
302 | |
---|
303 | if(!this->voxelListCovered(voxelList)){ |
---|
304 | DUCHAMPERROR("Detection::calcFluxes","Voxel list provided does not match"); |
---|
305 | return; |
---|
306 | } |
---|
307 | |
---|
308 | std::vector<Voxel>::iterator vox; |
---|
309 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
310 | if(this->isInObject(*vox)){ |
---|
311 | long x = vox->getX(); |
---|
312 | long y = vox->getY(); |
---|
313 | long z = vox->getZ(); |
---|
314 | float f = vox->getF(); |
---|
315 | this->totalFlux += f; |
---|
316 | this->xCentroid += x*f; |
---|
317 | this->yCentroid += y*f; |
---|
318 | this->zCentroid += z*f; |
---|
319 | if( (vox==voxelList.begin()) || //first time round |
---|
320 | (this->negSource&&(f<this->peakFlux)) || |
---|
321 | (!this->negSource&&(f>this->peakFlux)) ) |
---|
322 | { |
---|
323 | this->peakFlux = f; |
---|
324 | this->xpeak = x; |
---|
325 | this->ypeak = y; |
---|
326 | this->zpeak = z; |
---|
327 | } |
---|
328 | } |
---|
329 | } |
---|
330 | |
---|
331 | this->xCentroid /= this->totalFlux; |
---|
332 | this->yCentroid /= this->totalFlux; |
---|
333 | this->zCentroid /= this->totalFlux; |
---|
334 | } |
---|
335 | //-------------------------------------------------------------------- |
---|
336 | |
---|
337 | void Detection::calcFluxes(std::map<Voxel,float> &voxelMap) |
---|
338 | { |
---|
339 | /// @details |
---|
340 | /// A function that calculates total & peak fluxes (and the location |
---|
341 | /// of the peak flux) for a Detection. |
---|
342 | /// |
---|
343 | /// \param fluxArray The array of flux values to calculate the |
---|
344 | /// flux parameters from. |
---|
345 | /// \param dim The dimensions of the flux array. |
---|
346 | |
---|
347 | // this->haveParams = true; |
---|
348 | |
---|
349 | this->totalFlux = this->peakFlux = 0; |
---|
350 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
---|
351 | |
---|
352 | std::vector<Voxel> voxelList = this->getPixelSet(); |
---|
353 | std::vector<Voxel>::iterator vox; |
---|
354 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
355 | if(voxelMap.find(*vox) == voxelMap.end()){ |
---|
356 | DUCHAMPERROR("Detection::calcFluxes","Voxel list provided does not match"); |
---|
357 | return; |
---|
358 | } |
---|
359 | else { |
---|
360 | long x = vox->getX(); |
---|
361 | long y = vox->getY(); |
---|
362 | long z = vox->getZ(); |
---|
363 | float f = voxelMap[*vox]; |
---|
364 | this->totalFlux += f; |
---|
365 | this->xCentroid += x*f; |
---|
366 | this->yCentroid += y*f; |
---|
367 | this->zCentroid += z*f; |
---|
368 | if( (vox==voxelList.begin()) || //first time round |
---|
369 | (this->negSource&&(f<this->peakFlux)) || |
---|
370 | (!this->negSource&&(f>this->peakFlux)) ) |
---|
371 | { |
---|
372 | this->peakFlux = f; |
---|
373 | this->xpeak = x; |
---|
374 | this->ypeak = y; |
---|
375 | this->zpeak = z; |
---|
376 | } |
---|
377 | } |
---|
378 | } |
---|
379 | |
---|
380 | this->xCentroid /= this->totalFlux; |
---|
381 | this->yCentroid /= this->totalFlux; |
---|
382 | this->zCentroid /= this->totalFlux; |
---|
383 | } |
---|
384 | //-------------------------------------------------------------------- |
---|
385 | |
---|
386 | void Detection::calcFluxes(float *fluxArray, size_t *dim) |
---|
387 | { |
---|
388 | /// @details |
---|
389 | /// A function that calculates total & peak fluxes (and the location |
---|
390 | /// of the peak flux) for a Detection. |
---|
391 | /// |
---|
392 | /// \param fluxArray The array of flux values to calculate the |
---|
393 | /// flux parameters from. |
---|
394 | /// \param dim The dimensions of the flux array. |
---|
395 | |
---|
396 | // this->haveParams = true; |
---|
397 | |
---|
398 | this->totalFlux = this->peakFlux = 0; |
---|
399 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
---|
400 | |
---|
401 | std::vector<Voxel> voxList = this->getPixelSet(); |
---|
402 | std::vector<Voxel>::iterator vox=voxList.begin(); |
---|
403 | for(;vox<voxList.end();vox++){ |
---|
404 | |
---|
405 | long x=vox->getX(); |
---|
406 | long y=vox->getY(); |
---|
407 | long z=vox->getZ(); |
---|
408 | size_t ind = vox->arrayIndex(dim); |
---|
409 | float f = fluxArray[ind]; |
---|
410 | this->totalFlux += f; |
---|
411 | this->xCentroid += x*f; |
---|
412 | this->yCentroid += y*f; |
---|
413 | this->zCentroid += z*f; |
---|
414 | if( (vox==voxList.begin()) || |
---|
415 | (this->negSource&&(f<this->peakFlux)) || |
---|
416 | (!this->negSource&&(f>this->peakFlux)) ) |
---|
417 | { |
---|
418 | this->peakFlux = f; |
---|
419 | this->xpeak = x; |
---|
420 | this->ypeak = y; |
---|
421 | this->zpeak = z; |
---|
422 | } |
---|
423 | |
---|
424 | } |
---|
425 | |
---|
426 | this->xCentroid /= this->totalFlux; |
---|
427 | this->yCentroid /= this->totalFlux; |
---|
428 | this->zCentroid /= this->totalFlux; |
---|
429 | } |
---|
430 | //-------------------------------------------------------------------- |
---|
431 | |
---|
432 | void Detection::calcWCSparams(FitsHeader &head) |
---|
433 | { |
---|
434 | /// @details |
---|
435 | /// Use the input wcs to calculate the position and velocity |
---|
436 | /// information for the Detection. |
---|
437 | /// Quantities calculated: |
---|
438 | /// <ul><li> RA: ra [deg], ra (string), ra width. |
---|
439 | /// <li> Dec: dec [deg], dec (string), dec width. |
---|
440 | /// <li> Vel: vel [km/s], min & max vel, vel width. |
---|
441 | /// <li> coord type for all three axes, nuRest, |
---|
442 | /// <li> name (IAU-style, in equatorial or Galactic) |
---|
443 | /// </ul> |
---|
444 | /// |
---|
445 | /// Note that the regular parameters are NOT recalculated! |
---|
446 | /// |
---|
447 | /// \param head FitsHeader object that contains the WCS information. |
---|
448 | |
---|
449 | if(head.isWCS()){ |
---|
450 | |
---|
451 | double *pixcrd = new double[15]; |
---|
452 | double *world = new double[15]; |
---|
453 | /* |
---|
454 | define a five-point array in 3D: |
---|
455 | (x,y,z), (x,y,z1), (x,y,z2), (x1,y1,z), (x2,y2,z) |
---|
456 | [note: x = central point, x1 = minimum x, x2 = maximum x etc.] |
---|
457 | and convert to world coordinates. |
---|
458 | */ |
---|
459 | pixcrd[0] = pixcrd[3] = pixcrd[6] = this->getXcentre(); |
---|
460 | pixcrd[9] = this->getXmin()-0.5; |
---|
461 | pixcrd[12] = this->getXmax()+0.5; |
---|
462 | pixcrd[1] = pixcrd[4] = pixcrd[7] = this->getYcentre(); |
---|
463 | pixcrd[10] = this->getYmin()-0.5; |
---|
464 | pixcrd[13] = this->getYmax()+0.5; |
---|
465 | pixcrd[2] = pixcrd[11] = pixcrd[14] = this->getZcentre(); |
---|
466 | pixcrd[5] = this->getZmin(); |
---|
467 | pixcrd[8] = this->getZmax(); |
---|
468 | int flag = head.pixToWCS(pixcrd, world, 5); |
---|
469 | delete [] pixcrd; |
---|
470 | if(flag!=0) { |
---|
471 | DUCHAMPERROR("calcWCSparams", "Error in calculating the WCS for this object."); |
---|
472 | } |
---|
473 | else{ |
---|
474 | |
---|
475 | // world now has the WCS coords for the five points |
---|
476 | // -- use this to work out WCS params |
---|
477 | |
---|
478 | this->haveParams = true; |
---|
479 | |
---|
480 | this->specOK = head.canUseThirdAxis(); |
---|
481 | this->lngtype = head.lngtype(); |
---|
482 | this->lattype = head.lattype(); |
---|
483 | this->specUnits = head.getSpectralUnits(); |
---|
484 | this->specType = head.getSpectralType(); |
---|
485 | this->fluxUnits = head.getFluxUnits(); |
---|
486 | // if fluxUnits are eg. Jy/beam, make intFluxUnits = Jy km/s |
---|
487 | this->intFluxUnits = head.getIntFluxUnits(); |
---|
488 | this->ra = world[0]; |
---|
489 | this->dec = world[1]; |
---|
490 | int precision = -int(log10(fabs(head.WCS().cdelt[head.WCS().lng]*3600./10.))); |
---|
491 | this->raS = decToDMS(this->ra, this->lngtype,precision); |
---|
492 | this->decS = decToDMS(this->dec,this->lattype,precision); |
---|
493 | this->raWidth = angularSeparation(world[9],world[1], |
---|
494 | world[12],world[1]) * 60.; |
---|
495 | this->decWidth = angularSeparation(world[0],world[10], |
---|
496 | world[0],world[13]) * 60.; |
---|
497 | |
---|
498 | this->name = head.getIAUName(this->ra, this->dec); |
---|
499 | this->vel = head.specToVel(world[2]); |
---|
500 | this->velMin = head.specToVel(world[5]); |
---|
501 | this->velMax = head.specToVel(world[8]); |
---|
502 | this->velWidth = fabs(this->velMax - this->velMin); |
---|
503 | |
---|
504 | this->flagWCS = true; |
---|
505 | } |
---|
506 | delete [] world; |
---|
507 | |
---|
508 | } |
---|
509 | else { |
---|
510 | double x=this->getXcentre(),y=this->getYcentre(),z=this->getZmin(); |
---|
511 | this->velMin = head.pixToVel(x,y,z); |
---|
512 | z=this->getZmax(); |
---|
513 | this->velMax = head.pixToVel(x,y,z); |
---|
514 | this->velWidth = fabs(this->velMax - this->velMin); |
---|
515 | } |
---|
516 | |
---|
517 | |
---|
518 | } |
---|
519 | //-------------------------------------------------------------------- |
---|
520 | |
---|
521 | void Detection::calcIntegFlux(size_t zdim, std::vector<Voxel> voxelList, FitsHeader &head) |
---|
522 | { |
---|
523 | /// @details |
---|
524 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
525 | /// putting velocity in units of km/s. |
---|
526 | /// The fluxes used are taken from the Voxels, rather than an |
---|
527 | /// array of flux values. |
---|
528 | /// Integrates over full spatial and velocity range as given |
---|
529 | /// by the extrema calculated by calcWCSparams. |
---|
530 | /// |
---|
531 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
532 | /// corrected by the beam size (in pixels). This is done by |
---|
533 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
534 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
535 | /// pix/beam --> Jy) |
---|
536 | /// |
---|
537 | /// \param zdim The size of the spectral axis (needed to find the velocity widths) |
---|
538 | /// \param voxelList The list of Voxels with flux information |
---|
539 | /// \param head FitsHeader object that contains the WCS information. |
---|
540 | |
---|
541 | if(!this->voxelListCovered(voxelList)){ |
---|
542 | DUCHAMPERROR("Detection::calcIntegFlux","Voxel list provided does not match"); |
---|
543 | return; |
---|
544 | } |
---|
545 | |
---|
546 | if(!head.is2D()){ |
---|
547 | |
---|
548 | this->haveParams = true; |
---|
549 | |
---|
550 | const int border = 1; // include one pixel either side in each direction |
---|
551 | size_t xsize = size_t(this->xmax-this->xmin+2*border+1); |
---|
552 | size_t ysize = size_t(this->ymax-this->ymin+2*border+1); |
---|
553 | size_t zsize = size_t(this->zmax-this->zmin+2*border+1); |
---|
554 | size_t xzero = size_t(std::max(0L,this->xmin-border)); |
---|
555 | size_t yzero = size_t(std::max(0L,this->ymin-border)); |
---|
556 | size_t zzero = size_t(std::max(0L,this->zmin-border)); |
---|
557 | size_t spatsize=xsize*ysize; |
---|
558 | size_t size = xsize*ysize*zsize; |
---|
559 | std::vector <bool> isObj(size,false); |
---|
560 | double *localFlux = new double[size]; |
---|
561 | for(size_t i=0;i<size;i++) localFlux[i]=0.; |
---|
562 | |
---|
563 | std::vector<Voxel>::iterator vox; |
---|
564 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
565 | if(this->isInObject(*vox)){ |
---|
566 | size_t pos=(vox->getX()-xzero) + (vox->getY()-yzero)*xsize + (vox->getZ()-zzero)*spatsize; |
---|
567 | localFlux[pos] = vox->getF(); |
---|
568 | isObj[pos] = true; |
---|
569 | } |
---|
570 | } |
---|
571 | |
---|
572 | // work out the WCS coords for each pixel |
---|
573 | double *world = new double[size]; |
---|
574 | double xpt,ypt,zpt; |
---|
575 | for(size_t i=0;i<size;i++){ |
---|
576 | xpt = double( this->getXmin() - border + i%xsize ); |
---|
577 | ypt = double( this->getYmin() - border + (i/xsize)%ysize ); |
---|
578 | zpt = double( this->getZmin() - border + i/(xsize*ysize) ); |
---|
579 | world[i] = head.pixToVel(xpt,ypt,zpt); |
---|
580 | } |
---|
581 | |
---|
582 | double integrated = 0.; |
---|
583 | for(size_t pix=0; pix<spatsize; pix++){ // loop over each spatial pixel. |
---|
584 | for(size_t z=0; z<zsize; z++){ |
---|
585 | size_t pos = z*xsize*ysize + pix; |
---|
586 | if(isObj[pos]){ // if it's an object pixel... |
---|
587 | double deltaVel; |
---|
588 | if(z==0) |
---|
589 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
590 | else if(z==(zsize-1)) |
---|
591 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
592 | else |
---|
593 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
594 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
595 | } |
---|
596 | } |
---|
597 | } |
---|
598 | this->intFlux = integrated; |
---|
599 | |
---|
600 | delete [] world; |
---|
601 | delete [] localFlux; |
---|
602 | |
---|
603 | calcVelWidths(zdim,voxelList,head); |
---|
604 | |
---|
605 | } |
---|
606 | else // in this case there is just a 2D image. |
---|
607 | this->intFlux = this->totalFlux; |
---|
608 | |
---|
609 | if(head.isWCS()){ |
---|
610 | // correct for the beam size if the flux units string ends in "/beam" |
---|
611 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
612 | } |
---|
613 | |
---|
614 | } |
---|
615 | //-------------------------------------------------------------------- |
---|
616 | |
---|
617 | void Detection::calcIntegFlux(size_t zdim, std::map<Voxel,float> voxelMap, FitsHeader &head) |
---|
618 | { |
---|
619 | /// @details |
---|
620 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
621 | /// putting velocity in units of km/s. |
---|
622 | /// The fluxes used are taken from the Voxels, rather than an |
---|
623 | /// array of flux values. |
---|
624 | /// Integrates over full spatial and velocity range as given |
---|
625 | /// by the extrema calculated by calcWCSparams. |
---|
626 | /// |
---|
627 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
628 | /// corrected by the beam size (in pixels). This is done by |
---|
629 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
630 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
631 | /// pix/beam --> Jy) |
---|
632 | /// |
---|
633 | /// \param zdim The size of the spectral axis (needed to find the velocity widths) |
---|
634 | /// \param voxelList The list of Voxels with flux information |
---|
635 | /// \param head FitsHeader object that contains the WCS information. |
---|
636 | |
---|
637 | if(!head.is2D()){ |
---|
638 | |
---|
639 | this->haveParams = true; |
---|
640 | |
---|
641 | const int border = 1; // include one pixel either side in each direction |
---|
642 | size_t xsize = size_t(this->xmax-this->xmin+2*border+1); |
---|
643 | size_t ysize = size_t(this->ymax-this->ymin+2*border+1); |
---|
644 | size_t zsize = size_t(this->zmax-this->zmin+2*border+1); |
---|
645 | size_t xzero = size_t(std::max(0L,this->xmin-border)); |
---|
646 | size_t yzero = size_t(std::max(0L,this->ymin-border)); |
---|
647 | size_t zzero = size_t(std::max(0L,this->zmin-border)); |
---|
648 | size_t spatsize=xsize*ysize; |
---|
649 | size_t size = xsize*ysize*zsize; |
---|
650 | |
---|
651 | this->intFlux = 0.; |
---|
652 | std::vector<Voxel> voxelList = this->getPixelSet(); |
---|
653 | std::vector<Voxel>::iterator vox; |
---|
654 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
655 | if(voxelMap.find(*vox) == voxelMap.end()){ |
---|
656 | DUCHAMPERROR("Detection::calcIntegFlux","Voxel list provided does not match"); |
---|
657 | return; |
---|
658 | } |
---|
659 | else { |
---|
660 | this->intFlux += voxelMap[*vox]; |
---|
661 | } |
---|
662 | } |
---|
663 | this->intFlux *= fabs(head.WCS().cdelt[head.WCS().spec]); |
---|
664 | |
---|
665 | calcVelWidths(zdim,voxelMap,head); |
---|
666 | |
---|
667 | } |
---|
668 | else // in this case there is just a 2D image. |
---|
669 | this->intFlux = this->totalFlux; |
---|
670 | |
---|
671 | if(head.isWCS()){ |
---|
672 | // correct for the beam size if the flux units string ends in "/beam" |
---|
673 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
674 | } |
---|
675 | |
---|
676 | } |
---|
677 | //-------------------------------------------------------------------- |
---|
678 | |
---|
679 | void Detection::calcIntegFlux(float *fluxArray, size_t *dim, FitsHeader &head, Param &par) |
---|
680 | { |
---|
681 | /// @details |
---|
682 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
683 | /// putting velocity in units of km/s. |
---|
684 | /// Integrates over full spatial and velocity range as given |
---|
685 | /// by the extrema calculated by calcWCSparams. |
---|
686 | /// |
---|
687 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
688 | /// corrected by the beam size (in pixels). This is done by |
---|
689 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
690 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
691 | /// pix/beam --> Jy) |
---|
692 | /// |
---|
693 | /// \param fluxArray The array of flux values. |
---|
694 | /// \param dim The dimensions of the flux array. |
---|
695 | /// \param head FitsHeader object that contains the WCS information. |
---|
696 | |
---|
697 | this->haveParams = true; |
---|
698 | |
---|
699 | const int border=1; // include one pixel either side in each direction |
---|
700 | size_t xsize = std::min(size_t(this->xmax-this->xmin+2*border+1),dim[0]); |
---|
701 | size_t ysize = std::min(size_t(this->ymax-this->ymin+2*border+1),dim[1]); |
---|
702 | size_t zsize = std::min(size_t(this->zmax-this->zmin+2*border+1),dim[2]); |
---|
703 | size_t xzero = size_t(std::max(0L,this->xmin-border)); |
---|
704 | size_t yzero = size_t(std::max(0L,this->ymin-border)); |
---|
705 | size_t zzero = size_t(std::max(0L,this->zmin-border)); |
---|
706 | size_t spatsize = xsize*ysize; |
---|
707 | size_t size = xsize*ysize*zsize; |
---|
708 | std::vector <bool> isObj(size,false); |
---|
709 | double *localFlux = new double[size]; |
---|
710 | for(size_t i=0;i<size;i++) localFlux[i]=0.; |
---|
711 | float *momMap = new float[spatsize]; |
---|
712 | for(size_t i=0;i<spatsize;i++) momMap[i]=0.; |
---|
713 | // work out which pixels are object pixels |
---|
714 | std::vector<Voxel> voxlist = this->getPixelSet(); |
---|
715 | for(std::vector<Voxel>::iterator v=voxlist.begin();v<voxlist.end();v++){ |
---|
716 | size_t spatpos=(v->getX()-xzero) + (v->getY()-yzero)*xsize; |
---|
717 | size_t pos= spatpos + (v->getZ()-zzero)*spatsize; |
---|
718 | localFlux[pos] = fluxArray[v->arrayIndex(dim)]; |
---|
719 | momMap[spatpos] += fluxArray[v->arrayIndex(dim)]*head.WCS().cdelt[head.WCS().spec]; |
---|
720 | isObj[pos] = true; |
---|
721 | } |
---|
722 | |
---|
723 | if(!head.is2D()){ |
---|
724 | |
---|
725 | // work out the WCS coords for each pixel |
---|
726 | double *world = new double[size]; |
---|
727 | double xpt,ypt,zpt; |
---|
728 | size_t i=0; |
---|
729 | for(size_t z=zzero;z<zzero+zsize;z++){ |
---|
730 | for(size_t y=yzero;y<yzero+ysize;y++){ |
---|
731 | for(size_t x=xzero;x<xzero+xsize;x++){ |
---|
732 | xpt=double(x); |
---|
733 | ypt=double(y); |
---|
734 | zpt=double(z); |
---|
735 | world[i++] = head.pixToVel(xpt,ypt,zpt); |
---|
736 | } |
---|
737 | } |
---|
738 | } |
---|
739 | |
---|
740 | double integrated = 0.; |
---|
741 | for(size_t pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
---|
742 | for(size_t z=0; z<zsize; z++){ |
---|
743 | size_t pos = z*xsize*ysize + pix; |
---|
744 | if(isObj[pos]){ // if it's an object pixel... |
---|
745 | double deltaVel; |
---|
746 | if(z==0) |
---|
747 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
748 | else if(z==(zsize-1)) |
---|
749 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
750 | else |
---|
751 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
752 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
753 | } |
---|
754 | } |
---|
755 | } |
---|
756 | |
---|
757 | delete [] world; |
---|
758 | |
---|
759 | this->intFlux = integrated; |
---|
760 | |
---|
761 | calcVelWidths(fluxArray, dim, head, par); |
---|
762 | |
---|
763 | } |
---|
764 | else // in this case there is just a 2D image. |
---|
765 | this->intFlux = this->totalFlux; |
---|
766 | |
---|
767 | delete [] localFlux; |
---|
768 | delete [] momMap; |
---|
769 | |
---|
770 | |
---|
771 | if(head.isWCS()){ |
---|
772 | // correct for the beam size if the flux units string ends in "/beam" and we have beam info |
---|
773 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
774 | } |
---|
775 | |
---|
776 | } |
---|
777 | //-------------------------------------------------------------------- |
---|
778 | |
---|
779 | void Detection::findShape(const float *fluxArray, const size_t *dim, FitsHeader &head) |
---|
780 | { |
---|
781 | const long border=1; // include one pixel either side in each direction |
---|
782 | size_t x1 = size_t(std::max(long(0),this->xmin-border)); |
---|
783 | size_t y1 = size_t(std::max(long(0),this->ymin-border)); |
---|
784 | size_t x2 = size_t(std::min(long(dim[0])-1,this->xmax+border)); |
---|
785 | size_t y2 = size_t(std::min(long(dim[1])-1,this->ymax+border)); |
---|
786 | size_t xsize = x2-x1+1; |
---|
787 | size_t ysize = y2-y1+1; |
---|
788 | size_t spatsize = xsize*ysize; |
---|
789 | |
---|
790 | float *momentMap = new float[spatsize]; |
---|
791 | for(size_t i=0;i<spatsize;i++) momentMap[i]=0.; |
---|
792 | // work out which pixels are object pixels |
---|
793 | std::vector<Voxel> voxlist = this->getPixelSet(); |
---|
794 | float delta = (head.isWCS() && head.getWCS()->spec>=0) ? fabs(head.WCS().cdelt[head.WCS().spec]) : 1.; |
---|
795 | float sign = this->negSource ? -1. : 1.; |
---|
796 | for(std::vector<Voxel>::iterator v=voxlist.begin();v<voxlist.end();v++){ |
---|
797 | size_t spatpos=(v->getX()-x1) + (v->getY()-y1)*xsize; |
---|
798 | if(spatpos<spatsize) |
---|
799 | momentMap[spatpos] += fluxArray[v->arrayIndex(dim)] * delta * sign; |
---|
800 | else DUCHAMPTHROW("findShape","Memory overflow - accessing spatpos="<<spatpos<<" when spatsize="<<spatsize <<". Pixel is (x,y)=("<<v->getX() <<","<<v->getY()<<") and (x1,y1)="<<x1<<","<<y1<<"), (x2,y2)="<<x2<<","<<y2<<"), xsize="<<xsize); |
---|
801 | } |
---|
802 | |
---|
803 | size_t smldim[2]; smldim[0]=xsize; smldim[1]=ysize; |
---|
804 | Image *smlIm = new Image(smldim); |
---|
805 | smlIm->saveArray(momentMap,spatsize); |
---|
806 | smlIm->setMinSize(1); |
---|
807 | float max = *std::max_element(momentMap,momentMap+spatsize); |
---|
808 | smlIm->stats().setThreshold(max/2.); |
---|
809 | std::vector<Object2D> objlist=smlIm->findSources2D(); |
---|
810 | |
---|
811 | Object2D combined; |
---|
812 | for(size_t i=0;i<objlist.size();i++) combined = combined + objlist[i]; |
---|
813 | std::string extraFlag=""; |
---|
814 | bool ellipseGood = combined.findEllipse(true, momentMap, xsize, ysize, 0,0, this->getXcentre()-x1, this->getYcentre()-y1); // try first by weighting the pixels by their flux |
---|
815 | if(!ellipseGood) { |
---|
816 | ellipseGood = combined.findEllipse(false, momentMap, xsize, ysize, 0,0, this->getXcentre()-x1, this->getYcentre()-y1); // if that fails, remove the flux weighting |
---|
817 | extraFlag="W"; |
---|
818 | } |
---|
819 | float scale=head.getShapeScale(); |
---|
820 | if(ellipseGood){ |
---|
821 | // multiply axes by 2 to go from semi-major to FWHM... |
---|
822 | this->majorAxis = combined.major() * head.getAvPixScale() * 2. * scale; |
---|
823 | this->minorAxis = combined.minor() * head.getAvPixScale() * 2. * scale; |
---|
824 | this->posang = combined.posAng() * 180. / M_PI; |
---|
825 | // std::cerr << "*** " << combined.getSize()<< " " << majorAxis<<" " << minorAxis << " " << posang<< " " << scale <<"\n"; |
---|
826 | } |
---|
827 | else { |
---|
828 | extraFlag="w"; |
---|
829 | std::pair<double,double> axes = combined.getPrincipalAxes(); |
---|
830 | this->majorAxis = std::max(axes.first,axes.second) * head.getAvPixScale() * scale; |
---|
831 | this->minorAxis = std::min(axes.first,axes.second) * head.getAvPixScale() * scale; |
---|
832 | this->posang = combined.getPositionAngle() * 180. / M_PI; |
---|
833 | // std::cerr << "** " << combined.getSize()<< " " << majorAxis<<" " << minorAxis << " " << posang<< " " << scale <<"\n"; |
---|
834 | } |
---|
835 | this->flagText += extraFlag; |
---|
836 | |
---|
837 | |
---|
838 | delete smlIm; |
---|
839 | delete [] momentMap; |
---|
840 | } |
---|
841 | |
---|
842 | //-------------------------------------------------------------------- |
---|
843 | |
---|
844 | void Detection::calcVelWidths(size_t zdim, std::vector<Voxel> voxelList, FitsHeader &head) |
---|
845 | { |
---|
846 | /// @details |
---|
847 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
848 | /// peak integrated flux. The procedure is as follows: first |
---|
849 | /// generate an integrated flux spectrum (using all given voxels |
---|
850 | /// that lie in the object's spatial map); find the peak; starting |
---|
851 | /// at the spectral edges of the detection, move in or out until |
---|
852 | /// you reach the 20% or 50% peak flux level. Linear interpolation |
---|
853 | /// between points is done. |
---|
854 | /// |
---|
855 | /// \param zdim The size of the spectral axis in the cube |
---|
856 | /// \param voxelList The list of Voxels with flux information |
---|
857 | /// \param head FitsHeader object that contains the WCS information. |
---|
858 | |
---|
859 | float *intSpec = new float[zdim]; |
---|
860 | for(size_t i=0;i<zdim;i++) intSpec[i]=0; |
---|
861 | |
---|
862 | Object2D spatMap = this->getSpatialMap(); |
---|
863 | for(int s=0;s<spatMap.getNumScan();s++){ |
---|
864 | std::vector<Voxel>::iterator vox; |
---|
865 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
866 | if(spatMap.isInObject(*vox)){ |
---|
867 | intSpec[vox->getZ()] += vox->getF(); |
---|
868 | } |
---|
869 | } |
---|
870 | } |
---|
871 | |
---|
872 | calcVelWidths(zdim, intSpec, head); |
---|
873 | |
---|
874 | delete [] intSpec; |
---|
875 | |
---|
876 | } |
---|
877 | |
---|
878 | //-------------------------------------------------------------------- |
---|
879 | |
---|
880 | void Detection::calcVelWidths(size_t zdim, std::map<Voxel,float> voxelMap, FitsHeader &head) |
---|
881 | { |
---|
882 | /// @details |
---|
883 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
884 | /// peak integrated flux. The procedure is as follows: first |
---|
885 | /// generate an integrated flux spectrum (using all given voxels |
---|
886 | /// that lie in the object's spatial map); find the peak; starting |
---|
887 | /// at the spectral edges of the detection, move in or out until |
---|
888 | /// you reach the 20% or 50% peak flux level. Linear interpolation |
---|
889 | /// between points is done. |
---|
890 | /// |
---|
891 | /// \param zdim The size of the spectral axis in the cube |
---|
892 | /// \param voxelList The list of Voxels with flux information |
---|
893 | /// \param head FitsHeader object that contains the WCS information. |
---|
894 | |
---|
895 | float *intSpec = new float[zdim]; |
---|
896 | for(size_t i=0;i<zdim;i++) intSpec[i]=0; |
---|
897 | |
---|
898 | std::vector<Voxel> voxelList = this->getPixelSet(); |
---|
899 | std::vector<Voxel>::iterator vox; |
---|
900 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
901 | if(voxelMap.find(*vox) == voxelMap.end()){ |
---|
902 | DUCHAMPERROR("Detection::calcVelWidths","Voxel list provided does not match"); |
---|
903 | return; |
---|
904 | } |
---|
905 | else { |
---|
906 | intSpec[vox->getZ()] += voxelMap[*vox]; |
---|
907 | } |
---|
908 | } |
---|
909 | |
---|
910 | calcVelWidths(zdim, intSpec, head); |
---|
911 | |
---|
912 | delete [] intSpec; |
---|
913 | |
---|
914 | } |
---|
915 | |
---|
916 | //-------------------------------------------------------------------- |
---|
917 | |
---|
918 | void Detection::calcVelWidths(size_t zdim, float *intSpec, FitsHeader &head) |
---|
919 | { |
---|
920 | |
---|
921 | // finding the 20% & 50% points. Start at the velmin & velmax |
---|
922 | // points. Then, if the int flux there is above the 20%/50% |
---|
923 | // limit, go out, otherwise go in. This is to deal with the |
---|
924 | // problems from double- (or multi-) peaked sources. |
---|
925 | |
---|
926 | this->haveParams = true; |
---|
927 | |
---|
928 | double zpt,xpt=double(this->getXcentre()),ypt=double(this->getYcentre()); |
---|
929 | bool goLeft; |
---|
930 | |
---|
931 | if(this->negSource){ |
---|
932 | // if we've inverted the source, need to make the feature |
---|
933 | // positive for the interpolation/extrapolation to work |
---|
934 | for(size_t i=0;i<zdim;i++) intSpec[i] *= -1.; |
---|
935 | } |
---|
936 | |
---|
937 | float peak=0.; |
---|
938 | size_t peakLoc=0; |
---|
939 | for(size_t z=this->getZmin();z<=size_t(this->getZmax());z++) { |
---|
940 | if(z==0 || peak<intSpec[z]){ |
---|
941 | peak = intSpec[z]; |
---|
942 | peakLoc = z; |
---|
943 | } |
---|
944 | } |
---|
945 | |
---|
946 | size_t z=this->getZmin(); |
---|
947 | goLeft = intSpec[z]>peak*0.5; |
---|
948 | if(goLeft) while(z>0 && intSpec[z]>peak*0.5) z--; |
---|
949 | else while(z<peakLoc && intSpec[z]<peak*0.5) z++; |
---|
950 | if(z==0) this->v50min = this->velMin; |
---|
951 | else{ |
---|
952 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
953 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
954 | this->v50min = head.pixToVel(xpt,ypt,zpt); |
---|
955 | } |
---|
956 | z=this->getZmax(); |
---|
957 | goLeft = intSpec[z]<peak*0.5; |
---|
958 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.5) z--; |
---|
959 | else while(z<zdim && intSpec[z]>peak*0.5) z++; |
---|
960 | if(z==zdim) this->v50max = this->velMax; |
---|
961 | else{ |
---|
962 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
963 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
964 | this->v50max = head.pixToVel(xpt,ypt,zpt); |
---|
965 | } |
---|
966 | z=this->getZmin(); |
---|
967 | goLeft = intSpec[z]>peak*0.2; |
---|
968 | if(goLeft) while(z>0 && intSpec[z]>peak*0.2) z--; |
---|
969 | else while(z<peakLoc && intSpec[z]<peak*0.2) z++; |
---|
970 | if(z==0) this->v20min = this->velMin; |
---|
971 | else{ |
---|
972 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
973 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
974 | this->v20min = head.pixToVel(xpt,ypt,zpt); |
---|
975 | } |
---|
976 | z=this->getZmax(); |
---|
977 | goLeft = intSpec[z]<peak*0.2; |
---|
978 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.2) z--; |
---|
979 | else while(z<zdim && intSpec[z]>peak*0.2) z++; |
---|
980 | if(z==zdim) this->v20max = this->velMax; |
---|
981 | else{ |
---|
982 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
983 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
984 | this->v20max = head.pixToVel(xpt,ypt,zpt); |
---|
985 | } |
---|
986 | |
---|
987 | this->w20 = fabs(this->v20min - this->v20max); |
---|
988 | this->w50 = fabs(this->v50min - this->v50max); |
---|
989 | |
---|
990 | if(this->negSource){ |
---|
991 | // un-do the inversion, in case intSpec is needed elsewhere |
---|
992 | for(size_t i=0;i<zdim;i++) intSpec[i] *= -1.; |
---|
993 | } |
---|
994 | |
---|
995 | |
---|
996 | } |
---|
997 | //-------------------------------------------------------------------- |
---|
998 | |
---|
999 | void Detection::calcVelWidths(float *fluxArray, size_t *dim, FitsHeader &head, Param &par) |
---|
1000 | { |
---|
1001 | /// @details |
---|
1002 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
1003 | /// peak integrated flux. The procedure is as follows: first |
---|
1004 | /// generate an integrated flux spectrum (summing each spatial |
---|
1005 | /// pixel's spectrum); find the peak; starting at the spectral |
---|
1006 | /// edges of the detection, move in or out until you reach the 20% |
---|
1007 | /// or 50% peak flux level. Linear interpolation between points is |
---|
1008 | /// done. |
---|
1009 | /// |
---|
1010 | /// \param fluxArray The array of flux values. |
---|
1011 | /// \param dim The dimensions of the flux array. |
---|
1012 | /// \param head FitsHeader object that contains the WCS information. |
---|
1013 | |
---|
1014 | if(dim[2] > 2){ |
---|
1015 | |
---|
1016 | float *intSpec = new float[dim[2]]; |
---|
1017 | size_t size=dim[0]*dim[1]*dim[2]; |
---|
1018 | bool *mask = par.makeBlankMask(fluxArray,size); |
---|
1019 | getIntSpec(*this,fluxArray,dim,mask,1.,intSpec); |
---|
1020 | |
---|
1021 | this->calcVelWidths(dim[2],intSpec,head); |
---|
1022 | |
---|
1023 | delete [] intSpec; |
---|
1024 | |
---|
1025 | } |
---|
1026 | else{ |
---|
1027 | this->v50min = this->v20min = this->velMin; |
---|
1028 | this->v50max = this->v20max = this->velMax; |
---|
1029 | this->w20 = fabs(this->v20min - this->v20max); |
---|
1030 | this->w50 = fabs(this->v50min - this->v50max); |
---|
1031 | } |
---|
1032 | |
---|
1033 | } |
---|
1034 | //-------------------------------------------------------------------- |
---|
1035 | |
---|
1036 | void Detection::setOffsets(Param &par) |
---|
1037 | { |
---|
1038 | /// @details |
---|
1039 | /// This function stores the values of the offsets for each cube axis. |
---|
1040 | /// The offsets are the starting values of the cube axes that may differ from |
---|
1041 | /// the default value of 0 (for instance, if a subsection is being used). |
---|
1042 | /// The values will be used when the detection is outputted. |
---|
1043 | |
---|
1044 | this->xSubOffset = par.getXOffset(); |
---|
1045 | this->ySubOffset = par.getYOffset(); |
---|
1046 | this->zSubOffset = par.getZOffset(); |
---|
1047 | } |
---|
1048 | //-------------------------------------------------------------------- |
---|
1049 | |
---|
1050 | bool Detection::hasEnoughChannels(int minNumber) |
---|
1051 | { |
---|
1052 | /// @details |
---|
1053 | /// A function to determine if the Detection has enough |
---|
1054 | /// contiguous channels to meet the minimum requirement |
---|
1055 | /// given as the argument. |
---|
1056 | /// \param minNumber How many channels is the minimum acceptable number? |
---|
1057 | /// \return True if there is at least one occurence of minNumber consecutive |
---|
1058 | /// channels present to return true. False otherwise. |
---|
1059 | |
---|
1060 | // Preferred method -- need a set of minNumber consecutive channels present. |
---|
1061 | |
---|
1062 | int numChan = this->getMaxAdjacentChannels(); |
---|
1063 | bool result = (numChan >= minNumber); |
---|
1064 | |
---|
1065 | return result; |
---|
1066 | |
---|
1067 | } |
---|
1068 | //-------------------------------------------------------------------- |
---|
1069 | |
---|
1070 | void Detection::drawBorders(int xoffset, int yoffset) |
---|
1071 | { |
---|
1072 | /// @details |
---|
1073 | /// For a given object, draw borders around the spatial extent of the object. |
---|
1074 | /// \param xoffset The offset from 0 of the x-axis of the plotting window |
---|
1075 | /// \param yoffset The offset from 0 of the y-axis of the plotting window |
---|
1076 | |
---|
1077 | if(!cpgtest()){ |
---|
1078 | DUCHAMPERROR("Draw Borders","There is no PGPlot device open."); |
---|
1079 | } |
---|
1080 | else{ |
---|
1081 | |
---|
1082 | float x1,x2,y1,y2; |
---|
1083 | cpgqwin(&x1,&x2,&y1,&y2); |
---|
1084 | int xsize = int(x2 - x1) + 1; |
---|
1085 | int ysize = int(y2 - y1) + 1; |
---|
1086 | |
---|
1087 | cpgswin(0,xsize-1,0,ysize-1); |
---|
1088 | |
---|
1089 | std::vector<std::vector<Voxel> > vertexSets = this->getVertexSet(); |
---|
1090 | |
---|
1091 | for(size_t n=0;n<vertexSets.size();n++){ |
---|
1092 | // for each set of vertices |
---|
1093 | |
---|
1094 | cpgmove(vertexSets[n][0].getX()-xoffset,vertexSets[n][0].getY()-yoffset); |
---|
1095 | for(size_t i=1;i<vertexSets[n].size();i++) |
---|
1096 | cpgdraw(vertexSets[n][i].getX()-xoffset,vertexSets[n][i].getY()-yoffset); |
---|
1097 | |
---|
1098 | } |
---|
1099 | |
---|
1100 | cpgswin(x1,x2,y1,y2); |
---|
1101 | |
---|
1102 | } |
---|
1103 | |
---|
1104 | } |
---|
1105 | |
---|
1106 | |
---|
1107 | void Detection::addDetection(Detection &other) |
---|
1108 | { |
---|
1109 | for(std::map<long, Object2D>::iterator it = other.chanlist.begin(); it!=other.chanlist.end();it++) |
---|
1110 | // this->addChannel(*it); |
---|
1111 | this->addChannel(it->first, it->second); |
---|
1112 | this->haveParams = false; // make it appear as if the parameters haven't been calculated, so that we can re-calculate them |
---|
1113 | } |
---|
1114 | |
---|
1115 | Detection operator+ (Detection &lhs, Detection &rhs) |
---|
1116 | { |
---|
1117 | Detection output = lhs; |
---|
1118 | for(std::map<long, Object2D>::iterator it = rhs.chanlist.begin(); it!=rhs.chanlist.end();it++) |
---|
1119 | output.addChannel(it->first, it->second); |
---|
1120 | output.haveParams = false; // make it appear as if the parameters haven't been calculated, so that we can re-calculate them |
---|
1121 | return output; |
---|
1122 | } |
---|
1123 | |
---|
1124 | |
---|
1125 | bool Detection::canMerge(Detection &other, Param &par) |
---|
1126 | { |
---|
1127 | bool near = this->isNear(other,par); |
---|
1128 | if(near) return this->isClose(other,par); |
---|
1129 | else return near; |
---|
1130 | } |
---|
1131 | |
---|
1132 | bool Detection::isNear(Detection &other, Param &par) |
---|
1133 | { |
---|
1134 | |
---|
1135 | bool flagAdj = par.getFlagAdjacent(); |
---|
1136 | float threshS = par.getThreshS(); |
---|
1137 | float threshV = par.getThreshV(); |
---|
1138 | |
---|
1139 | long gap; |
---|
1140 | if(flagAdj) gap = 1; |
---|
1141 | else gap = long( ceil(threshS) ); |
---|
1142 | |
---|
1143 | bool areNear; |
---|
1144 | // Test X ranges |
---|
1145 | if((this->xmin-gap)<other.xmin) areNear=((this->xmax+gap)>=other.xmin); |
---|
1146 | else areNear=(other.xmax>=(this->xmin-gap)); |
---|
1147 | // Test Y ranges |
---|
1148 | if(areNear){ |
---|
1149 | if((this->ymin-gap)<other.ymin) areNear=areNear&&((this->ymax+gap)>=other.ymin); |
---|
1150 | else areNear=areNear&&(other.ymax>=(this->ymin-gap)); |
---|
1151 | } |
---|
1152 | // Test Z ranges |
---|
1153 | if(areNear){ |
---|
1154 | gap = long(ceil(threshV)); |
---|
1155 | if((this->zmin-gap)<other.zmin) areNear=areNear&&((this->zmax+gap)>=other.zmin); |
---|
1156 | else areNear=areNear&&(other.zmax>=(this->zmin-gap)); |
---|
1157 | } |
---|
1158 | |
---|
1159 | return areNear; |
---|
1160 | |
---|
1161 | } |
---|
1162 | |
---|
1163 | bool Detection::isClose(Detection &other, Param &par) |
---|
1164 | { |
---|
1165 | bool close = false; // this will be the value returned |
---|
1166 | |
---|
1167 | bool flagAdj = par.getFlagAdjacent(); |
---|
1168 | float threshS = par.getThreshS(); |
---|
1169 | float threshV = par.getThreshV(); |
---|
1170 | |
---|
1171 | // |
---|
1172 | // If we get to here, the pixel ranges overlap -- so we do a |
---|
1173 | // pixel-by-pixel comparison to make sure they are actually |
---|
1174 | // "close" according to the thresholds. Otherwise, close=false, |
---|
1175 | // and so don't need to do anything else before returning. |
---|
1176 | // |
---|
1177 | |
---|
1178 | std::vector<long> zlist1 = this->getChannelList(); |
---|
1179 | std::vector<long> zlist2 = other.getChannelList(); |
---|
1180 | Scan test1,test2; |
---|
1181 | |
---|
1182 | for(size_t ct1=0; (!close && (ct1<zlist1.size())); ct1++){ |
---|
1183 | for(size_t ct2=0; (!close && (ct2<zlist2.size())); ct2++){ |
---|
1184 | |
---|
1185 | if(abs(zlist1[ct1]-zlist2[ct2])<=threshV){ |
---|
1186 | |
---|
1187 | Object2D temp1 = this->getChanMap(zlist1[ct1]); |
---|
1188 | Object2D temp2 = other.getChanMap(zlist2[ct2]); |
---|
1189 | |
---|
1190 | close = temp1.canMerge(temp2,threshS,flagAdj); |
---|
1191 | |
---|
1192 | } |
---|
1193 | |
---|
1194 | } |
---|
1195 | } |
---|
1196 | |
---|
1197 | return close; |
---|
1198 | |
---|
1199 | } |
---|
1200 | |
---|
1201 | |
---|
1202 | |
---|
1203 | } |
---|