[3] | 1 | #include <iostream> |
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| 2 | #include <sstream> |
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| 3 | #include <fstream> |
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| 4 | #include <iomanip> |
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| 5 | #include <string> |
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| 6 | #include <Cubes/cubes.hh> |
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| 7 | #include <Utils/utils.hh> |
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| 8 | |
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| 9 | //using std::ofstream; |
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| 10 | using std::endl; |
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| 11 | using std::setw; |
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| 12 | using std::setprecision; |
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| 13 | |
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[20] | 14 | void Cube::outputDetectionsKarma(std::ostream &stream) |
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| 15 | { |
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| 16 | /** |
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| 17 | * outputDetectionsKarma |
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| 18 | * Prints to a stream (provided) the list of detected objects in the cube |
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| 19 | * in the format of an annotation file for the Karma suite of programs. |
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| 20 | * Annotation file draws a box enclosing the detection, and writes the ID number |
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| 21 | * of the detection to the right of the box. |
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| 22 | */ |
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| 23 | |
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| 24 | stream << "# Duchamp Source Finder results for cube " << this->par.getImageFile() << endl; |
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| 25 | stream << "COLOR RED" << endl; |
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| 26 | stream << "COORD W" << endl; |
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| 27 | for(int i=0;i<this->objectList.size();i++){ |
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[21] | 28 | float radius = this->objectList[i].getRAWidth()/120.; |
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| 29 | if(this->objectList[i].getDecWidth()/120.>radius) |
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| 30 | radius = this->objectList[i].getDecWidth()/120.; |
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| 31 | stream << "CIRCLE " |
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[20] | 32 | << this->objectList[i].getRA() << " " |
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| 33 | << this->objectList[i].getDec() << " " |
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[21] | 34 | << radius << endl; |
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[20] | 35 | stream << "TEXT " |
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[21] | 36 | << this->objectList[i].getRA() << " " |
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[20] | 37 | << this->objectList[i].getDec() << " " |
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| 38 | << this->objectList[i].getID() << endl; |
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| 39 | } |
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| 40 | |
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| 41 | } |
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| 42 | |
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[3] | 43 | void Cube::outputDetectionsVOTable(std::ostream &stream) |
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| 44 | { |
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| 45 | /** |
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| 46 | * outputDetectionsVOTable |
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| 47 | * Prints to a stream (provided) the list of detected objects in the cube |
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| 48 | * in a VOTable format. |
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| 49 | * Uses WCS information and assumes WCS parameters have been calculated for each |
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| 50 | * detected object. |
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| 51 | * If they have not (given by the isWCS() function), then those objects are not written... |
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| 52 | */ |
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| 53 | |
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| 54 | stream<<"<?xml version=\"1.0\"?>"<<endl; |
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| 55 | stream<<"<VOTABLE version=\"1.1\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\""<<endl; |
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| 56 | stream<<" xsi:noNamespaceSchemaLocation=\"http://www.ivoa.net/xml/VOTable/VOTable/v1.1\">"<<endl; |
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| 57 | |
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| 58 | stream<<" <COOSYS ID=\"J2000\" equinox=\"J2000.\" epoch=\"J2000.\" system=\"eq_FK5\"/>"<<endl; |
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| 59 | stream<<" <RESOURCE name=\"Duchamp Output\">"<<endl; |
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| 60 | stream<<" <TABLE name=\"Detections\">"<<endl; |
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| 61 | stream<<" <DESCRIPTION>Detected sources and parameters from running the Duchamp source finder.</DESCRIPTION>"<<endl; |
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| 62 | |
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| 63 | // PARAM section -- parts that are not entry-specific ie. apply to whole dataset |
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| 64 | stream<<" <PARAM name=\"FITS file\" datatype=\"char\" ucd=\"meta.file;meta.fits\" value=\"" << this->par.getImageFile() << "\"/>"<<endl; |
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| 65 | |
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| 66 | // FIELD section -- names, titles and info for each column. |
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| 67 | stream<<" <FIELD name=\"ID\" ID=\"col1\" ucd=\"meta.id\" datatype=\"int\" width=\"4\"/>"<<endl; |
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| 68 | stream<<" <FIELD name=\"Name\" ID=\"col2\" ucd=\"meta.id;meta.main\" datatype=\"char\" arraysize=\"14\"/>"<<endl; |
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| 69 | stream<<" <FIELD name=\"RA\" ID=\"col3\" ucd=\"pos.eq.ra;meta.main\" ref=\"J2000\" datatype=\"float\" width=\"10\" precision=\"6\" unit=\"deg\"/>"<<endl; |
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| 70 | stream<<" <FIELD name=\"Dec\" ID=\"col4\" ucd=\"pos.eq.dec;meta.main\" ref=\"J2000\" datatype=\"float\" width=\"10\" precision=\"6\" unit=\"deg\"/>"<<endl; |
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| 71 | stream<<" <FIELD name=\"w_RA\" ID=\"col3\" ucd=\"phys.angSize;pos.eq.ra\" ref=\"J2000\" datatype=\"float\" width=\"7\" precision=\"2\" unit=\"arcmin\"/>"<<endl; |
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| 72 | stream<<" <FIELD name=\"w_Dec\" ID=\"col4\" ucd=\"phys.angSize;pos.eq.dec\" ref=\"J2000\" datatype=\"float\" width=\"7\" precision=\"2\" unit=\"arcmin\"/>"<<endl; |
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| 73 | stream<<" <FIELD name=\"Vel\" ID=\"col4\" ucd=\"phys.veloc;src.dopplerVeloc\" datatype=\"float\" width=\"9\" precision=\"3\" unit=\"km/s\"/>"<<endl; |
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| 74 | stream<<" <FIELD name=\"w_Vel\" ID=\"col4\" ucd=\"phys.veloc;src.dopplerVeloc;spect.line.width\" datatype=\"float\" width=\"8\" precision=\"3\" unit=\"km/s\"/>"<<endl; |
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| 75 | stream<<" <FIELD name=\"Integrated_Flux\" ID=\"col4\" ucd=\"phys.flux;spect.line.intensity\" datatype=\"float\" width=\"10\" precision=\"4\" unit=\"km/s\"/>"<<endl; |
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| 76 | |
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| 77 | |
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| 78 | stream<<" <DATA>"<<endl |
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| 79 | <<" <TABLEDATA>"<<endl; |
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| 80 | |
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| 81 | stream.setf(std::ios::fixed); |
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| 82 | for(int i=0;i<this->objectList.size();i++){ |
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| 83 | if(this->objectList[i].isWCS()){ |
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| 84 | stream<<" <TR>"<<endl; |
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| 85 | stream<<" <TD>"<<setw(4)<<i+1<<"</TD>"; |
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| 86 | stream<<"<TD>" << setw(14) << this->objectList[i].getName() <<"</TD>"; |
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| 87 | stream<<setprecision(6); |
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| 88 | stream<<"<TD>" << setw(10) << this->objectList[i].getRA() <<"</TD>"; |
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| 89 | stream<<"<TD>" << setw(10) << this->objectList[i].getDec() <<"</TD>"; |
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| 90 | stream<<setprecision(2); |
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| 91 | stream<<"<TD>" << setw(7) << this->objectList[i].getRAWidth() <<"</TD>"; |
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| 92 | stream<<"<TD>" << setw(7) << this->objectList[i].getDecWidth() <<"</TD>"; |
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| 93 | stream<<setprecision(3); |
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| 94 | stream<<"<TD>" << setw(9) << this->objectList[i].getVel() <<"</TD>"; |
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| 95 | stream<<"<TD>" << setw(8) << this->objectList[i].getVelWidth() <<"</TD>"; |
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| 96 | stream<<setprecision(3); |
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| 97 | stream<<"<TD>" << setw(10) << this->objectList[i].getIntegFlux() <<"</TD>"; |
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| 98 | |
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| 99 | stream<<endl; |
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| 100 | stream<<" </TR>"<<endl; |
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| 101 | } |
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| 102 | } |
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| 103 | stream<<" </TABLEDATA>"<<endl; |
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| 104 | stream<<" </DATA>"<<endl; |
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| 105 | stream<<" </TABLE>"<<endl; |
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| 106 | stream<<" </RESOURCE>"<<endl; |
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| 107 | stream<<"</VOTABLE>"<<endl; |
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| 108 | resetiosflags(std::ios::fixed); |
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| 109 | |
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| 110 | } |
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| 111 | |
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| 112 | |
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| 113 | void Cube::outputDetectionList() |
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| 114 | { |
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| 115 | /** |
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| 116 | * outputDetectionList |
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| 117 | * A front-end to writing the full list of detected objects to a results file and to cout. |
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| 118 | * Uses outputDetectionTextWCS for each objects. |
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| 119 | * Leaves the testing of whether the WCS parameters for each object have been calculated |
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| 120 | * to outputDetectionTextWCS. |
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| 121 | */ |
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| 122 | |
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| 123 | int count=0; |
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| 124 | int flag; |
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| 125 | std::ofstream output(this->par.getOutFile().c_str()); |
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| 126 | output<<"Results of the Duchamp source finder: "; |
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| 127 | output.close(); |
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| 128 | string syscall = "date >> " + this->par.getOutFile(); |
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| 129 | system(syscall.c_str()); |
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| 130 | output.open(this->par.getOutFile().c_str(),std::ios::app); |
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| 131 | this->showParam(output); |
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| 132 | output<<"Total number of detections = "<<this->objectList.size()<<endl; |
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[19] | 133 | output<<"--------------------"<<endl; |
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[3] | 134 | if(flag=wcsset(wcs)){ |
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| 135 | std::cerr<<"outputDetectionList():: WCSSET failed! Code="<<flag <<": "<<wcs_errmsg[flag]<<endl; |
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| 136 | } |
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| 137 | outputDetectionTextWCSHeader(output,this->wcs); |
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| 138 | outputDetectionTextWCSHeader(std::cout,this->wcs); |
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| 139 | for(int i=0;i<this->objectList.size();i++){ |
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| 140 | this->objectList[i].outputDetectionTextWCS(output); |
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| 141 | this->objectList[i].outputDetectionTextWCS(std::cout); |
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| 142 | } |
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| 143 | } |
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| 144 | |
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| 145 | void Cube::logDetectionList() |
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| 146 | { |
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| 147 | /** |
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| 148 | * logDetectionList |
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| 149 | * A front-end to writing a list of detected objects to the log file. |
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| 150 | * Does not assume WCS, so uses outputDetectionText. |
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| 151 | * Designed to be used by searching routines before returning their final list. |
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| 152 | */ |
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| 153 | |
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| 154 | std::ofstream fout(this->par.getLogFile().c_str(),std::ios::app); |
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| 155 | outputDetectionTextHeader(fout); |
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| 156 | long pos; |
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| 157 | bool baselineFlag = this->par.getFlagBaseline(); |
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| 158 | for(int objCtr=0;objCtr<this->objectList.size();objCtr++){ |
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| 159 | Detection *obj = new Detection; |
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| 160 | *obj = objectList[objCtr]; |
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| 161 | if(this->par.getFlagCubeTrimmed()){ |
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| 162 | for(int pix=0;pix<obj->getSize();pix++){ |
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| 163 | // Need to correct the pixels first, as this hasn't been done yet. |
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| 164 | // Corrections needed for positions (to account for trimmed region) |
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| 165 | // and for the baseline removal, if it has happened. |
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| 166 | // Don't want to keep these changes, so just do it on a dummy variable. |
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| 167 | pos = obj->getX(pix) + obj->getY(pix)*this->axisDim[0] |
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| 168 | + obj->getZ(pix)*this->axisDim[0]*this->axisDim[1]; |
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| 169 | obj->setX(pix, obj->getX(pix) + this->par.getBorderLeft() ); |
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| 170 | obj->setY(pix, obj->getY(pix) + this->par.getBorderBottom() ); |
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| 171 | if(baselineFlag) obj->setF(pix, obj->getF(pix) + this->baseline[pos]); // add in baseline |
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| 172 | } |
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| 173 | obj->calcParams(); |
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| 174 | } |
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| 175 | obj->outputDetectionText(fout,objCtr); |
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| 176 | delete obj; |
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| 177 | } |
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| 178 | fout.close(); |
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| 179 | } |
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| 180 | |
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| 181 | void Cube::logDetection(Detection obj, int counter) |
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| 182 | { |
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| 183 | /** |
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| 184 | * logDetection |
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| 185 | * A front-end to writing a detected object to the log file. |
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| 186 | * Does not assume WCS, so uses outputDetectionText. |
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| 187 | * obj is passed by value, as we want to potentially change positions etc, but not for |
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| 188 | * object in the calling function. |
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| 189 | * Corrects for changes to positions of pixels and removal of baselines. |
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| 190 | * Designed to be used by searching routines before returning their final list. |
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| 191 | */ |
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| 192 | |
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| 193 | std::ofstream fout(this->par.getLogFile().c_str(),std::ios::app); |
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| 194 | bool baselineFlag = this->par.getFlagBaseline(); |
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| 195 | if(this->par.getFlagCubeTrimmed()){ |
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| 196 | for(int pix=0;pix<obj.getSize();pix++){ |
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| 197 | // Need to correct the pixels first, as this hasn't been done yet. |
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| 198 | // Corrections needed for positions (to account for trimmed region) |
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| 199 | // and for the baseline removal, if it has happened. |
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| 200 | // Don't want to keep these changes, so just do it on a dummy variable. |
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| 201 | long pos = obj.getX(pix) + obj.getY(pix)*this->axisDim[0] |
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| 202 | + obj.getZ(pix)*this->axisDim[0]*this->axisDim[1]; |
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| 203 | obj.setX(pix, obj.getX(pix) + this->par.getBorderLeft() ); |
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| 204 | obj.setY(pix, obj.getY(pix) + this->par.getBorderBottom() ); |
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| 205 | if(baselineFlag) obj.setF(pix, obj.getF(pix) + this->baseline[pos]); // add in baseline |
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| 206 | } |
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| 207 | obj.calcParams(); |
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| 208 | } |
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| 209 | obj.outputDetectionText(fout,counter); |
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| 210 | fout.close(); |
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| 211 | } |
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