1 | #include <iostream> |
---|
2 | #include <iomanip> |
---|
3 | #include <sstream> |
---|
4 | #include <fstream> |
---|
5 | #include <vector> |
---|
6 | #include <string> |
---|
7 | #include <cpgplot.h> |
---|
8 | #include <math.h> |
---|
9 | #include <unistd.h> |
---|
10 | #include <Detection/detection.hh> |
---|
11 | #include <Cubes/cubes.hh> |
---|
12 | #include <Utils/utils.hh> |
---|
13 | #include <ATrous/atrous.hh> |
---|
14 | |
---|
15 | using std::ofstream; |
---|
16 | using std::endl; |
---|
17 | |
---|
18 | Filter reconFilter; |
---|
19 | |
---|
20 | int main(int argc, char * argv[]) |
---|
21 | { |
---|
22 | |
---|
23 | string paramFile; |
---|
24 | string err_usage_msg("Usage:: Duchamp.x -p [parameter file]\n"); |
---|
25 | |
---|
26 | if(argc==1){ |
---|
27 | std::cout << err_usage_msg; |
---|
28 | exit(1); |
---|
29 | } |
---|
30 | else{ |
---|
31 | char c; |
---|
32 | while( ( c = getopt(argc,argv,"p:h") )!=-1){ |
---|
33 | switch(c) { |
---|
34 | case 'p': |
---|
35 | paramFile = optarg; |
---|
36 | break; |
---|
37 | case 'h': |
---|
38 | default : |
---|
39 | std::cout << err_usage_msg; |
---|
40 | exit(1); |
---|
41 | break; |
---|
42 | } |
---|
43 | } |
---|
44 | } |
---|
45 | |
---|
46 | Cube *cube = new Cube; |
---|
47 | cube->readParam(paramFile); |
---|
48 | if(cube->pars().getImageFile().empty()){ |
---|
49 | std::cerr << "Error: No input image has been given!"<<endl; |
---|
50 | std::cerr << "Use the imageFile parameter in "<< paramFile << " to specify the FITS file."<<endl; |
---|
51 | std::cerr << "Exiting..." << endl; |
---|
52 | exit(1); |
---|
53 | } |
---|
54 | |
---|
55 | // Filter needed for baseline removal and a trous reconstruction |
---|
56 | if(cube->pars().getFlagATrous() || cube->pars().getFlagBaseline()){ |
---|
57 | reconFilter.define(cube->pars().getFilterCode()); |
---|
58 | cube->pars().setFilterName(reconFilter.getName()); |
---|
59 | } |
---|
60 | |
---|
61 | string fname = cube->pars().getImageFile(); |
---|
62 | if(cube->pars().getFlagSubsection()){ |
---|
63 | cube->pars().parseSubsection(); |
---|
64 | fname+=cube->pars().getSubsection(); |
---|
65 | } |
---|
66 | std::cout << "Opening image: " << fname << endl; |
---|
67 | if( cube->getCube(fname) ){ |
---|
68 | std::cerr << "Error opening file : " << fname << endl; |
---|
69 | std::cerr << "Exiting..." << endl; |
---|
70 | exit(1); |
---|
71 | } |
---|
72 | else std::cout << "Opened successfully." << endl; |
---|
73 | if(!cube->isWCS()) std::cerr << "Warning! WCS is not good enough to be used.\n"; |
---|
74 | |
---|
75 | std::cout << cube->pars(); |
---|
76 | |
---|
77 | if(cube->pars().getFlagLog()){ |
---|
78 | ofstream logfile(cube->pars().getLogFile().c_str()); |
---|
79 | logfile << "New run of the Duchamp sourcefinder: "; |
---|
80 | logfile.close(); |
---|
81 | string syscall = "date >> " + cube->pars().getLogFile(); |
---|
82 | system(syscall.c_str()); |
---|
83 | logfile.open(cube->pars().getLogFile().c_str(),std::ios::app); |
---|
84 | logfile << cube->pars(); |
---|
85 | logfile.close(); |
---|
86 | } |
---|
87 | |
---|
88 | if(cube->pars().getFlagBlankPix()){ |
---|
89 | std::cout<<"Trimming the Blank Pixels from the edges... "<<std::flush; |
---|
90 | cube->trimCube(); |
---|
91 | std::cout<<"Done."<<endl; |
---|
92 | std::cout << "New dimensions: " << cube->getDimX(); |
---|
93 | if(cube->getNumDim()>1) std::cout << "x" << cube->getDimY(); |
---|
94 | if(cube->getNumDim()>2) std::cout << "x" << cube->getDimZ(); |
---|
95 | std::cout << endl; |
---|
96 | } |
---|
97 | |
---|
98 | if(cube->pars().getFlagMW()){ |
---|
99 | std::cout<<"Removing the Milky Way channels... "; |
---|
100 | cube->removeMW(); |
---|
101 | std::cout<<"Done."<<endl; |
---|
102 | } |
---|
103 | |
---|
104 | if(cube->pars().getFlagBaseline()){ |
---|
105 | std::cout<<"Removing the baselines... "<<std::flush; |
---|
106 | cube->removeBaseline(); |
---|
107 | std::cout<<" Done. "<<std::endl; |
---|
108 | } |
---|
109 | |
---|
110 | if(cube->getDimZ()==1) cube->pars().setMinChannels(0); // special case for 2D images. |
---|
111 | |
---|
112 | if(cube->pars().getFlagATrous()){ |
---|
113 | std::cout<<"Commencing search in reconstructed cube..."<<endl; |
---|
114 | cube->ReconSearch3D(); |
---|
115 | std::cout<<"Done. Found "<<cube->getNumObj()<<" objects."<<endl; |
---|
116 | } |
---|
117 | else{ |
---|
118 | std::cout<<"Commencing search in cube..."<<endl; |
---|
119 | cube->SimpleSearch3D(); |
---|
120 | std::cout<<"Done. Found "<<cube->getNumObj()<<" objects."<<endl; |
---|
121 | } |
---|
122 | |
---|
123 | std::cout<<"Merging lists... "<<std::flush; |
---|
124 | cube->ObjectMerger(); |
---|
125 | std::cout<<"Done. "<<endl; |
---|
126 | std::cout<<"Final object count = "<<cube->getNumObj()<<endl; |
---|
127 | |
---|
128 | cube->replaceBaseline(); |
---|
129 | |
---|
130 | if(cube->pars().getFlagCubeTrimmed()){ |
---|
131 | std::cout<<"Replacing the trimmed pixels on the edges... "<<std::flush; |
---|
132 | cube->unTrimCube(); |
---|
133 | std::cout<<"Done."<<endl; |
---|
134 | } |
---|
135 | |
---|
136 | if(cube->getNumObj()>0){ |
---|
137 | |
---|
138 | cube->calcObjectWCSparams(); |
---|
139 | |
---|
140 | cube->sortDetections(); |
---|
141 | |
---|
142 | cube->outputDetectionList(); |
---|
143 | } |
---|
144 | |
---|
145 | // cube->plotDetectionMap("/xs"); |
---|
146 | cube->plotMomentMap("/xs"); |
---|
147 | |
---|
148 | if(cube->pars().getFlagMaps()){ |
---|
149 | std::cout<<"Creating the maps... "<<std::flush; |
---|
150 | cube->plotMomentMap(cube->pars().getMomentMap()+"/vcps"); |
---|
151 | cube->plotDetectionMap(cube->pars().getDetectionMap()+"/vcps"); |
---|
152 | std::cout << "done.\n"; |
---|
153 | } |
---|
154 | |
---|
155 | if(cube->isWCS() && (cube->getNumObj()>0)){ |
---|
156 | std::cout << "Plotting the individual spectra... " << std::flush; |
---|
157 | cube->outputSpectra(); |
---|
158 | std::cout << "done.\n"; |
---|
159 | } |
---|
160 | else if(!(cube->isWCS())) std::cout << "Not plotting any spectra due to bad WCS.\n"; |
---|
161 | |
---|
162 | cpgend(); |
---|
163 | |
---|
164 | if(cube->pars().getFlagATrous()&& |
---|
165 | (cube->pars().getFlagOutputRecon()||cube->pars().getFlagOutputResid()) ){ |
---|
166 | std::cout << "Saving reconstructed cube... "<<std::flush; |
---|
167 | cube->saveReconstructedCube(); |
---|
168 | std::cout << "done.\n"; |
---|
169 | } |
---|
170 | |
---|
171 | if(cube->pars().getFlagLog() && (cube->getNumObj()>0)){ |
---|
172 | ofstream logfile(cube->pars().getLogFile().c_str(),std::ios::app); |
---|
173 | logfile << "=-=-=-=-=-=-=-\nCube summary\n=-=-=-=-=-=-=-\n"; |
---|
174 | logfile << *cube; |
---|
175 | logfile.close(); |
---|
176 | } |
---|
177 | |
---|
178 | if(cube->pars().getFlagVOT()){ |
---|
179 | ofstream votfile(cube->pars().getVOTFile().c_str()); |
---|
180 | cube->outputDetectionsVOTable(votfile); |
---|
181 | votfile.close(); |
---|
182 | } |
---|
183 | |
---|
184 | if(cube->pars().getFlagKarma()){ |
---|
185 | ofstream karmafile(cube->pars().getKarmaFile().c_str()); |
---|
186 | cube->outputDetectionsKarma(karmafile); |
---|
187 | karmafile.close(); |
---|
188 | } |
---|
189 | |
---|
190 | delete cube; |
---|
191 | |
---|
192 | return 0; |
---|
193 | } |
---|
194 | |
---|