[299] | 1 | // ----------------------------------------------------------------------- |
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[474] | 2 | // mainSelavy: Selavy is a program to re-analyse detected objects from |
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| 3 | // a Duchamp run. |
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[299] | 4 | // ----------------------------------------------------------------------- |
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| 5 | // Copyright (C) 2006, Matthew Whiting, ATNF |
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| 6 | // |
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| 7 | // This program is free software; you can redistribute it and/or modify it |
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| 8 | // under the terms of the GNU General Public License as published by the |
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| 9 | // Free Software Foundation; either version 2 of the License, or (at your |
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| 10 | // option) any later version. |
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| 11 | // |
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| 12 | // Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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| 13 | // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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| 14 | // FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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| 15 | // for more details. |
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| 16 | // |
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| 17 | // You should have received a copy of the GNU General Public License |
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| 18 | // along with Duchamp; if not, write to the Free Software Foundation, |
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| 19 | // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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| 20 | // |
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| 21 | // Correspondence concerning Duchamp may be directed to: |
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| 22 | // Internet email: Matthew.Whiting [at] atnf.csiro.au |
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| 23 | // Postal address: Dr. Matthew Whiting |
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| 24 | // Australia Telescope National Facility, CSIRO |
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| 25 | // PO Box 76 |
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| 26 | // Epping NSW 1710 |
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| 27 | // AUSTRALIA |
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| 28 | // ----------------------------------------------------------------------- |
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[218] | 29 | #include <iostream> |
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| 30 | #include <fstream> |
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| 31 | #include <string> |
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| 32 | #include <cpgplot.h> |
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| 33 | #include <math.h> |
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| 34 | #include <unistd.h> |
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| 35 | #include <time.h> |
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| 36 | |
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[393] | 37 | #include <duchamp/duchamp.hh> |
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| 38 | #include <duchamp/param.hh> |
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| 39 | #include <duchamp/PixelMap/Voxel.hh> |
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| 40 | #include <duchamp/Detection/detection.hh> |
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| 41 | #include <duchamp/Cubes/cubes.hh> |
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| 42 | #include <duchamp/Utils/utils.hh> |
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| 43 | #include <duchamp/ATrous/atrous.hh> |
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[218] | 44 | |
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[258] | 45 | using namespace PixelInfo; |
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[474] | 46 | using namespace duchamp; |
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[258] | 47 | |
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[218] | 48 | int main(int argc, char * argv[]) |
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| 49 | { |
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| 50 | |
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[232] | 51 | std::string paramFile,fitsfile,temp; |
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[218] | 52 | Cube *cube = new Cube; |
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| 53 | |
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[474] | 54 | if(cube->getopts(argc,argv,"Selavy")==FAILURE) return FAILURE; |
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[218] | 55 | |
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[474] | 56 | std::vector<int> plotObject = getObjectRequest(argc,argv); |
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| 57 | |
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[218] | 58 | if(cube->pars().getImageFile().empty()){ |
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| 59 | std::stringstream errmsg; |
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| 60 | errmsg << "No input image has been given!\n" |
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| 61 | << "Use the imageFile parameter in " |
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| 62 | << paramFile << " to specify the FITS file.\nExiting...\n"; |
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[474] | 63 | duchampError("Selavy", errmsg.str()); |
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[218] | 64 | return FAILURE; |
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| 65 | } |
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| 66 | |
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| 67 | if(cube->pars().getFlagSubsection()){ |
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| 68 | // make sure the subsection is OK. |
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| 69 | if(cube->pars().verifySubsection() == FAILURE){ |
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[474] | 70 | duchampError("Selavy", |
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[218] | 71 | "Unable to use the subsection provided.\nExiting...\n"); |
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| 72 | return FAILURE; |
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| 73 | } |
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| 74 | } |
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| 75 | |
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| 76 | std::cout << "Opening image: " |
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| 77 | << cube->pars().getFullImageFile() << std::endl; |
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| 78 | |
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| 79 | if( cube->getCube() == FAILURE){ |
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| 80 | std::stringstream errmsg; |
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| 81 | errmsg << "Unable to open image file " |
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| 82 | << cube->pars().getFullImageFile() |
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| 83 | << "\nExiting...\n"; |
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[474] | 84 | duchampError("Selavy", errmsg.str()); |
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[218] | 85 | return FAILURE; |
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| 86 | } |
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| 87 | else std::cout << "Opened successfully." << std::endl; |
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| 88 | |
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| 89 | // Read in any saved arrays that are in FITS files on disk. |
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| 90 | cube->readSavedArrays(); |
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| 91 | |
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| 92 | |
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[232] | 93 | std::ifstream logfile(cube->pars().getLogFile().c_str()); |
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[218] | 94 | |
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| 95 | if(!logfile.is_open()){ |
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| 96 | std::cerr << "\aUnable to open file " |
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| 97 | << cube->pars().getLogFile() << "\nExiting...\n"; |
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| 98 | return 1; |
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| 99 | } |
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| 100 | |
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| 101 | // read down until first Detection # line |
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| 102 | cube->setCubeStats(); |
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| 103 | std::cerr << "Reading from logfile : " << cube->pars().getLogFile() << "\n"; |
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| 104 | while(getline(logfile,temp), temp.substr(0,11)!="Detection #"){ } |
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[474] | 105 | int x1,x2, ypix, zpix; |
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[218] | 106 | while(!logfile.eof()){ |
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| 107 | Detection obj; |
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| 108 | while(getline(logfile,temp), temp.substr(0,3)!="---"){ |
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[474] | 109 | for(int i=0;i<temp.size();i++) |
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| 110 | if(temp[i]=='-' || temp[i]==',') temp[i] = ' '; |
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[218] | 111 | std::stringstream ss; |
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| 112 | ss.str(temp); |
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[474] | 113 | ss >> x1 >> x2 >> ypix >> zpix; |
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| 114 | Scan scn(ypix,x1,x2-x1+1); |
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| 115 | obj.pixels().addScan(scn,zpix); |
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[218] | 116 | } |
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[221] | 117 | obj.setOffsets(cube->pars()); |
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[218] | 118 | obj.calcParams(); |
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[474] | 119 | std::cerr << obj << "\n"; |
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[218] | 120 | if(obj.getSize()>0) cube->addObject(obj); |
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| 121 | getline(logfile,temp); // reads next line -- should be Detection #... |
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[474] | 122 | if(temp.substr(0,11)!="Detection #"){ |
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| 123 | // if it is, then read two lines to finish off the file. This should trigger the eof flag above. |
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| 124 | getline(logfile,temp); |
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| 125 | getline(logfile,temp); |
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| 126 | } |
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[218] | 127 | } |
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| 128 | |
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| 129 | std::cout<<"Final object count = "<<cube->getNumObj()<<std::endl; |
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[474] | 130 | |
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| 131 | cube->prepareOutputFile(); |
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[218] | 132 | |
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| 133 | cube->calcObjectWCSparams(); |
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| 134 | cube->setObjectFlags(); |
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[474] | 135 | cube->sortDetections(); |
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[218] | 136 | |
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[474] | 137 | cube->outputDetectionList(); |
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| 138 | |
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[218] | 139 | if((cube->getDimZ()>1) && (cube->getNumObj()>0)){ |
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| 140 | std::cout << "Plotting the individual spectra... " << std::flush; |
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| 141 | cube->outputSpectra(); |
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| 142 | std::cout << "done.\n"; |
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| 143 | } |
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| 144 | |
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| 145 | } |
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