[3] | 1 | #include <iostream> |
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| 2 | #include <iomanip> |
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| 3 | #include <vector> |
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| 4 | #include <string> |
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| 5 | #include <wcs.h> |
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| 6 | #include <param.hh> |
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| 7 | #include <Detection/detection.hh> |
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| 8 | |
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| 9 | using std::setw; |
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| 10 | using std::setprecision; |
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| 11 | using std::endl; |
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| 12 | |
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| 13 | std::ostream& operator<< ( std::ostream& theStream, Voxel& vox) |
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| 14 | { |
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| 15 | /** |
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| 16 | * << operator for Voxel class |
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| 17 | * A convenient way of printing the coordinate & flux values of a voxel. |
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| 18 | */ |
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| 19 | |
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| 20 | theStream << setw(4) << vox.itsX ; |
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| 21 | theStream << " " << setw(4) << vox.itsY; |
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| 22 | theStream << " " << setw(4) << vox.itsZ; |
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| 23 | theStream << setprecision(4); |
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| 24 | theStream << " " << vox.itsF; |
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| 25 | |
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| 26 | } |
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| 27 | |
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| 28 | |
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| 29 | void Detection::calcParams() |
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| 30 | { |
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| 31 | /** |
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| 32 | * Detection::calcParams() |
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| 33 | * A function that calculates centroid positions, minima & maxima of coordinates, |
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| 34 | * and total & peak fluxes for a detection. |
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| 35 | */ |
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| 36 | |
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| 37 | this->xcentre = 0; |
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| 38 | this->ycentre = 0; |
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| 39 | this->zcentre = 0; |
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| 40 | this->totalFlux = 0; |
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| 41 | this->peakFlux = 0; |
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| 42 | this->xmin = 0; |
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| 43 | this->xmax = 0; |
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| 44 | this->ymin = 0; |
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| 45 | this->ymax = 0; |
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| 46 | this->zmin = 0; |
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| 47 | this->zmax = 0; |
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| 48 | int *ctr = new int; |
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| 49 | for((*ctr)=0;(*ctr)<this->pix.size();(*ctr)++){ |
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| 50 | this->xcentre += this->pix[*ctr].itsX; |
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| 51 | this->ycentre += this->pix[*ctr].itsY; |
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| 52 | this->zcentre += this->pix[*ctr].itsZ; |
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| 53 | this->totalFlux += this->pix[*ctr].itsF; |
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| 54 | if(((*ctr)==0)||(this->pix[*ctr].itsX<this->xmin)) this->xmin = this->pix[*ctr].itsX; |
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| 55 | if(((*ctr)==0)||(this->pix[*ctr].itsX>this->xmax)) this->xmax = this->pix[*ctr].itsX; |
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| 56 | if(((*ctr)==0)||(this->pix[*ctr].itsY<this->ymin)) this->ymin = this->pix[*ctr].itsY; |
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| 57 | if(((*ctr)==0)||(this->pix[*ctr].itsY>this->ymax)) this->ymax = this->pix[*ctr].itsY; |
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| 58 | if(((*ctr)==0)||(this->pix[*ctr].itsZ<this->zmin)) this->zmin = this->pix[*ctr].itsZ; |
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| 59 | if(((*ctr)==0)||(this->pix[*ctr].itsZ>this->zmax)) this->zmax = this->pix[*ctr].itsZ; |
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| 60 | if(((*ctr)==0)||(this->pix[*ctr].itsF>this->peakFlux)) this->peakFlux = this->pix[*ctr].itsF; |
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| 61 | } |
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| 62 | delete ctr; |
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| 63 | this->xcentre /= this->pix.size(); |
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| 64 | this->ycentre /= this->pix.size(); |
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| 65 | this->zcentre /= this->pix.size(); |
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| 66 | } |
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| 67 | |
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| 68 | void Detection::calcWCSparams(wcsprm *wcs) |
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| 69 | { |
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| 70 | /** |
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| 71 | * Detection::calcWCSParams(wcsprm *) |
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| 72 | * Use the input wcs to calculate the position and velocity information for the Detection. |
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| 73 | * Makes no judgement as to whether the WCS is good -- this needs to be done beforehand. |
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| 74 | * Quantities calculated: |
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[22] | 75 | * RA: ra [deg], ra (string), ra width. |
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| 76 | * Dec: dec [deg], dec (string), dec width. |
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| 77 | * Vel: vel [km/s], min & max vel, vel width. |
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| 78 | * Other: coord type for all three axes, nuRest, name (IAU-style, in equatorial or Galactic) |
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| 79 | * Uses getIntegFlux to calculate the integrated flux in (say) [Jy km/s] |
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[3] | 80 | */ |
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| 81 | |
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| 82 | double *pixcrd = new double[15]; |
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| 83 | double *world = new double[15]; |
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| 84 | /* |
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| 85 | define a five-point array in 3D: |
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| 86 | (x,y,z), (x,y,z1), (x,y,z2), (x1,y1,z), (x2,y2,z) |
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| 87 | note x = central point, x1 = minimum x, x2 = maximum x etc. |
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| 88 | */ |
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| 89 | pixcrd[0] = pixcrd[3] = pixcrd[6] = this->xcentre; |
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| 90 | pixcrd[9] = this->xmin-0.5; |
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| 91 | pixcrd[12] = this->xmax+0.5; |
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| 92 | pixcrd[1] = pixcrd[4] = pixcrd[7] = this->ycentre; |
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| 93 | pixcrd[10] = this->ymin-0.5; |
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| 94 | pixcrd[13] = this->ymax+0.5; |
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| 95 | pixcrd[2] = pixcrd[11] = pixcrd[14] = this->zcentre; |
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| 96 | pixcrd[5] = this->zmin; |
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| 97 | pixcrd[8] = this->zmax; |
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[22] | 98 | int flag = pixToWCSMulti(wcs, pixcrd, world, 5); |
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[3] | 99 | delete [] pixcrd; |
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| 100 | |
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[22] | 101 | // world now has the WCS coords for the five points -- use this to work out WCS params. |
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| 102 | |
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[3] | 103 | this->lngtype = wcs->lngtyp; |
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| 104 | this->lattype = wcs->lattyp; |
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| 105 | this->ztype = wcs->ctype[2]; |
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| 106 | this->nuRest = wcs->restfrq; |
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| 107 | this->ra = world[0]; |
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| 108 | this->dec = world[1]; |
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[38] | 109 | this->raS = decToDMS(this->ra,this->lngtype); |
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| 110 | this->decS = decToDMS(this->dec,this->lattype); |
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[3] | 111 | this->raWidth = angularSeparation(world[9],world[1],world[12],world[1]) * 60.; |
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| 112 | this->decWidth = angularSeparation(world[0],world[10],world[0],world[13]) * 60.; |
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[42] | 113 | if(this->lngtype=="RA") this->name = getIAUNameEQ(this->ra,this->dec,wcs->equinox); |
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| 114 | else this->name = getIAUNameGAL(this->ra,this->dec); |
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[22] | 115 | this->vel = setVel_kms(wcs, world[2]); |
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| 116 | this->velMin = setVel_kms(wcs, world[5]); |
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| 117 | this->velMax = setVel_kms(wcs, world[8]); |
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| 118 | this->velWidth = fabs(this->velMax - this->velMin); |
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[3] | 119 | |
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| 120 | this->getIntegFlux(wcs); |
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| 121 | |
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| 122 | this->flagWCS = true; |
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| 123 | |
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| 124 | delete [] world; |
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| 125 | |
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| 126 | } |
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| 127 | |
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| 128 | float Detection::getIntegFlux(wcsprm *wcs) |
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| 129 | { |
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| 130 | /** |
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| 131 | * Detection::getIntegFlux(wcsprm *) |
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| 132 | * Uses the input wcs to calculate the velocity-integrated flux, |
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| 133 | * putting velocity in units of km/s. |
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| 134 | * Integrates over full spatial and velocity range as given by extrema calculated |
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| 135 | * by calcWCSparams. |
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| 136 | * Units are (Jy/beam) . km/s (no correction for the beam is made here...) |
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| 137 | */ |
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| 138 | |
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| 139 | // include one pixel either side in each direction |
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| 140 | int xsize = (this->xmax-this->xmin+3); |
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| 141 | int ysize = (this->ymax-this->ymin+3); |
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| 142 | int zsize = (this->zmax-this->zmin+3); |
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| 143 | vector <bool> isObj(xsize*ysize*zsize,false); |
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| 144 | vector <float> fluxArray(xsize*ysize*zsize,0.); |
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[22] | 145 | // work out which pixels are object pixels |
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[3] | 146 | for(int p=0;p<this->pix.size();p++){ |
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| 147 | int pos = (this->pix[p].getX()-this->xmin+1) + (this->pix[p].getY()-this->ymin+1)*xsize + |
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| 148 | (this->pix[p].getZ()-this->zmin+1)*xsize*ysize; |
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| 149 | fluxArray[pos] = this->pix[p].getF(); |
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| 150 | isObj[pos] = true; |
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| 151 | } |
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[22] | 152 | |
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| 153 | // work out the WCS coords for each pixel |
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| 154 | double *world = new double[xsize*ysize*zsize*3]; |
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| 155 | double *pix = new double[xsize*ysize*zsize*3]; |
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[3] | 156 | for(int i=0;i<xsize*ysize*zsize;i++){ |
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[22] | 157 | pix[i*3+0] = this->xmin -1 + i%xsize; |
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| 158 | pix[i*3+1] = this->ymin -1 + (i/xsize)%ysize; |
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| 159 | pix[i*3+2] = this->zmin -1 + i/(xsize*ysize); |
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[3] | 160 | } |
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[22] | 161 | int flag = pixToWCSMulti(wcs, pix, world, xsize*ysize*zsize); |
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| 162 | delete [] pix; |
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[3] | 163 | |
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[22] | 164 | // put velocity coords into km/s |
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| 165 | for(int i=0;i<xsize*ysize*zsize;i++) |
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| 166 | world[3*i+2] = setVel_kms(wcs,world[3*i+2]); |
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[3] | 167 | |
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| 168 | this->intFlux = 0.; |
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| 169 | for(int pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
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| 170 | for(int z=0; z<zsize; z++){ |
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| 171 | int pos = z*xsize*ysize + pix; |
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| 172 | if(isObj[pos]){ // if it's an object pixel... |
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| 173 | float deltaVel = (world[3*(pos+xsize*ysize)+2] - world[ 3*(pos-xsize*ysize)+2 ]) / 2.; |
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| 174 | this->intFlux += fluxArray[pos] * fabsf(deltaVel); |
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| 175 | } |
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| 176 | } |
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| 177 | } |
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| 178 | delete [] world; |
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| 179 | } |
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| 180 | |
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| 181 | |
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| 182 | // void Detection::addAnObject(Detection &toAdd) |
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| 183 | // { |
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| 184 | /** |
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| 185 | * Detection::addAnObject(Detection &) |
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| 186 | * Combines two objects by adding all the pixels of the argument to the instigator. |
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| 187 | * All pixel & flux parameters are recalculated (so that calcParams does not need to be |
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| 188 | * called a second time), but WCS parameters are not. |
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| 189 | */ |
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| 190 | /* |
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| 191 | int *ctr = new int; |
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| 192 | this->xcentre *= this->pix.size(); |
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| 193 | this->ycentre *= this->pix.size(); |
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| 194 | this->zcentre *= this->pix.size(); |
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| 195 | for((*ctr)=0;(*ctr)<toAdd.getSize();(*ctr)++){ |
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| 196 | this->pix.push_back(toAdd.getPixel(*ctr)); |
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| 197 | this->xcentre += toAdd.getX(*ctr); |
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| 198 | this->ycentre += toAdd.getY(*ctr); |
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| 199 | this->zcentre += toAdd.getZ(*ctr); |
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| 200 | this->totalFlux += toAdd.getF(*ctr); |
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| 201 | if(toAdd.getX(*ctr)<this->xmin) this->xmin=toAdd.getX(*ctr); |
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| 202 | if(toAdd.getX(*ctr)>this->xmax) this->xmax=toAdd.getX(*ctr); |
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| 203 | if(toAdd.getY(*ctr)<this->ymin) this->ymin=toAdd.getY(*ctr); |
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| 204 | if(toAdd.getY(*ctr)>this->ymax) this->ymax=toAdd.getY(*ctr); |
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| 205 | if(toAdd.getZ(*ctr)<this->zmin) this->zmin=toAdd.getZ(*ctr); |
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| 206 | if(toAdd.getZ(*ctr)>this->zmax) this->zmax=toAdd.getZ(*ctr); |
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| 207 | if(toAdd.getF(*ctr)>this->peakFlux) this->peakFlux=toAdd.getF(*ctr); |
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| 208 | } |
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| 209 | this->xcentre /= this->pix.size(); |
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| 210 | this->ycentre /= this->pix.size(); |
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| 211 | this->zcentre /= this->pix.size(); |
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| 212 | |
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| 213 | delete ctr; |
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| 214 | |
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| 215 | } |
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| 216 | */ |
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| 217 | |
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| 218 | |
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| 219 | void Detection::addAnObject(Detection &toAdd) |
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| 220 | { |
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| 221 | /** |
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| 222 | * Detection::addAnObject(Detection &) |
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| 223 | * Combines two objects by adding all the pixels of the argument to the instigator. |
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| 224 | * All pixel & flux parameters are recalculated (so that calcParams does not need to be |
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| 225 | * called a second time), but WCS parameters are not. |
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| 226 | */ |
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| 227 | |
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| 228 | int *ctr = new int; |
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| 229 | int *ctr2 = new int; |
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| 230 | bool *isNewPix = new bool; |
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| 231 | this->xcentre *= this->pix.size(); |
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| 232 | this->ycentre *= this->pix.size(); |
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| 233 | this->zcentre *= this->pix.size(); |
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| 234 | for((*ctr)=0;(*ctr)<toAdd.getSize();(*ctr)++){ |
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| 235 | // For each pixel in the new object, test to see if it already appears in the object |
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| 236 | long *x = new long; |
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| 237 | *x = toAdd.getX(*ctr); |
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| 238 | long *y = new long; |
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| 239 | *y = toAdd.getY(*ctr); |
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| 240 | long *z = new long; |
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| 241 | *z = toAdd.getZ(*ctr); |
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| 242 | float *f = new float; |
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| 243 | *f = toAdd.getF(*ctr); |
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| 244 | *isNewPix = true; |
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| 245 | *ctr2 = 0; |
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| 246 | while( *isNewPix && (*ctr2<this->pix.size()) ){ |
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| 247 | *isNewPix = *isNewPix && (( this->pix[*ctr2].itsX != *x ) || |
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| 248 | ( this->pix[*ctr2].itsY != *y ) || |
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| 249 | ( this->pix[*ctr2].itsZ != *z ) ); |
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| 250 | *ctr2 += 1; |
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| 251 | } |
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| 252 | if(*isNewPix){ |
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| 253 | // If the pixel is new, add it to the object and re-calculate the parameters. |
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| 254 | this->pix.push_back(toAdd.getPixel(*ctr)); |
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| 255 | this->xcentre += *x; |
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| 256 | this->ycentre += *y; |
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| 257 | this->zcentre += *z; |
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| 258 | this->totalFlux += *f; |
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| 259 | if(*x<this->xmin) this->xmin=*x; |
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| 260 | if(*x>this->xmax) this->xmax=*x; |
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| 261 | if(*y<this->ymin) this->ymin=*y; |
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| 262 | if(*y>this->ymax) this->ymax=*y; |
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| 263 | if(*z<this->zmin) this->zmin=*z; |
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| 264 | if(*z>this->zmax) this->zmax=*z; |
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| 265 | if(*f>this->peakFlux) this->peakFlux=*f; |
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| 266 | } |
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| 267 | delete x,y,z,f; |
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| 268 | } |
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| 269 | this->xcentre /= this->pix.size(); |
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| 270 | this->ycentre /= this->pix.size(); |
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| 271 | this->zcentre /= this->pix.size(); |
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| 272 | |
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| 273 | delete ctr; |
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| 274 | delete ctr2; |
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| 275 | delete isNewPix; |
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| 276 | } |
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| 277 | |
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| 278 | |
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| 279 | void Detection::addOffsets(Param &par) |
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| 280 | { |
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| 281 | this->xSubOffset = par.getXOffset(); |
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| 282 | this->ySubOffset = par.getYOffset(); |
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| 283 | this->zSubOffset = par.getZOffset(); |
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| 284 | } |
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| 285 | |
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| 286 | bool Detection::hasEnoughChannels(int minNumber) |
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| 287 | { |
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| 288 | /** |
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| 289 | * bool hasEnoughChannels(int) |
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| 290 | * A function to determine if the Detection has enough |
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| 291 | * contiguous channels to meet the minimum requirement |
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| 292 | * given as the argument. |
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| 293 | * Needs to have at least one occurence of minNumber consecutive |
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| 294 | * channels present to return true. Otherwise returns false. |
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| 295 | */ |
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| 296 | |
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| 297 | // Original requirement -- based on total span |
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| 298 | // int numChannels = this->getZmax() - this->getZmin() + 1; |
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| 299 | |
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| 300 | // Alternative -- number of distinct channels detected |
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| 301 | // int numChannels = 0; |
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| 302 | // this->SortByZ(); |
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| 303 | // if(this->getSize()>0) numChannels++; |
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| 304 | // for(int i=1;i<this->getSize();i++) |
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| 305 | // if(this->getZ(i)>this->getZ(i-1)) numChannels++; |
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| 306 | // return (numChannels < minNumber); |
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| 307 | |
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| 308 | // Preferred method -- need a set of minNumber consecutive channels present. |
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| 309 | this->SortByZ(); |
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| 310 | int numChannels = 0; |
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| 311 | bool result = false; |
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| 312 | if(this->getSize()>0) numChannels++; |
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| 313 | for(int i=1;i<this->getSize();i++) { |
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| 314 | if( (this->getZ(i) - this->getZ(i-1)) == 1) numChannels++; |
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| 315 | else if( (this->getZ(i) - this->getZ(i-1)) >= 2) numChannels = 1; |
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| 316 | |
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| 317 | if( numChannels == minNumber) result = true; |
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| 318 | } |
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| 319 | return result; |
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| 320 | |
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| 321 | } |
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| 322 | |
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[16] | 323 | int Detection::getSpatialSize() |
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| 324 | { |
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| 325 | /** |
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| 326 | * int getSpatialSize() |
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| 327 | * A function that returns the number of distinct spatial |
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| 328 | * pixels in a Detection. |
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| 329 | */ |
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| 330 | |
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| 331 | vector<Pixel> spatialPix; |
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| 332 | Pixel newpix; |
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| 333 | bool addThisOne; |
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| 334 | newpix.setXY(this->getX(0),this->getY(0)); |
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| 335 | spatialPix.push_back(newpix); |
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| 336 | for(int i=1;i<this->pix.size();i++){ |
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| 337 | newpix.setXY(this->getX(i),this->getY(i)); |
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| 338 | addThisOne = true; |
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| 339 | for(int j=0;(j<spatialPix.size())&&addThisOne;j++) { |
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| 340 | // do whole list or until addThisOne=false |
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| 341 | addThisOne = ( (newpix.getX()!=spatialPix[j].getX()) || |
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| 342 | (newpix.getY()!=spatialPix[j].getY()) ); |
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| 343 | // ie. if one of X or Y is different, addThisOne is true. |
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| 344 | } |
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| 345 | if(addThisOne) spatialPix.push_back(newpix); |
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| 346 | } |
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| 347 | return spatialPix.size(); |
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| 348 | } |
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| 349 | |
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[3] | 350 | std::ostream& operator<< ( std::ostream& theStream, Detection& obj) |
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| 351 | { |
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| 352 | /** |
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| 353 | * << operator for Detection class |
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| 354 | * A convenient way of printing the coordinate & flux |
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| 355 | * values for each pixel in the Detection |
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| 356 | */ |
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| 357 | |
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| 358 | for(int i=0;i<obj.pix.size();i++) theStream << obj.pix[i] << endl; |
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| 359 | theStream<<"---"<<endl; |
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| 360 | } |
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| 361 | |
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| 362 | Detection combineObjects(Detection &first, Detection &second) |
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| 363 | { |
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| 364 | // make the new object |
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| 365 | int *ctr = new int; |
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| 366 | Detection *newObject = new Detection; |
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| 367 | for(*ctr=0;(*ctr)<first.getSize();(*ctr)++){ |
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| 368 | newObject->addPixel(first.getPixel(*ctr)); |
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| 369 | } |
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| 370 | for(*ctr=0;(*ctr)<second.getSize();(*ctr)++){ |
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| 371 | newObject->addPixel(second.getPixel(*ctr)); |
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| 372 | } |
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| 373 | delete ctr; |
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| 374 | newObject->calcParams(); |
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| 375 | return *newObject; |
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| 376 | } |
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| 377 | |
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| 378 | vector <Detection> combineLists(vector <Detection> &first, vector <Detection> &second) |
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| 379 | { |
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| 380 | // make the new object |
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| 381 | vector <Detection> newList(first.size()+second.size()); |
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| 382 | for(int i=0;i<first.size();i++) newList[i] = first[i]; |
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| 383 | for(int i=0;i<second.size();i++) newList[i+first.size()] = second[i]; |
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| 384 | |
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| 385 | return newList; |
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| 386 | } |
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| 387 | |
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