[3] | 1 | #ifndef PARAM_H |
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| 2 | #define PARAM_H |
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| 3 | |
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| 4 | #include <iostream> |
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| 5 | #include <string> |
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| 6 | #include <vector> |
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[170] | 7 | #include <math.h> |
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[103] | 8 | #include <wcs.h> |
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[204] | 9 | #include <wcshdr.h> |
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[3] | 10 | |
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| 11 | using std::string; |
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| 12 | using std::vector; |
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| 13 | |
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| 14 | /** |
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| 15 | * Param class. |
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| 16 | * Used for storing parameters used by all functions. |
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| 17 | */ |
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[112] | 18 | |
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| 19 | class FitsHeader; // foreshadow this so that Param knows it exists |
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| 20 | |
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[3] | 21 | class Param |
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| 22 | { |
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| 23 | public: |
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| 24 | Param(); |
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[204] | 25 | virtual ~Param(){if(sizeOffsets>0) delete [] offsets;}; |
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| 26 | Param(const Param& p); |
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[137] | 27 | Param& operator= (const Param& p); |
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[164] | 28 | int verifySubsection(); // in FitsIO/subsection.cc |
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[204] | 29 | void setOffsets(struct wcsprm *wcs); // in FitsIO/subsection.cc |
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[164] | 30 | int readParams(string paramfile); // in param.cc |
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| 31 | void copyHeaderInfo(FitsHeader &head);// in param.cc |
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| 32 | bool isBlank(float &value); // in param.cc |
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[187] | 33 | bool isInMW(int z){return ( flagMW && (z>=minMW) && (z<=maxMW) );}; |
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[208] | 34 | string outputSmoothFile(); // in param.cc |
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| 35 | string outputReconFile(); // in param.cc |
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| 36 | string outputResidFile(); // in param.cc |
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[3] | 37 | friend std::ostream& operator<< ( std::ostream& theStream, Param& par); |
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| 38 | friend class Image; |
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| 39 | |
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| 40 | // |
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| 41 | string getImageFile(){return imageFile;}; |
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| 42 | void setImageFile(string fname){imageFile = fname;}; |
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[106] | 43 | string getFullImageFile(){ |
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| 44 | if(flagSubsection) return imageFile+subsection; |
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| 45 | else return imageFile; |
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| 46 | }; |
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[3] | 47 | bool getFlagSubsection(){return flagSubsection;}; |
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| 48 | void setFlagSubsection(bool flag){flagSubsection=flag;}; |
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| 49 | string getSubsection(){return subsection;}; |
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| 50 | void setSubsection(string range){subsection = range;}; |
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[71] | 51 | bool getFlagReconExists(){return flagReconExists;}; |
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| 52 | void setFlagReconExists(bool flag){flagReconExists=flag;}; |
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| 53 | string getReconFile(){return reconFile;}; |
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| 54 | void setReconFile(string file){reconFile = file;}; |
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[208] | 55 | bool getFlagSmoothExists(){return flagSmoothExists;}; |
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| 56 | void setFlagSmoothExists(bool flag){flagSmoothExists=flag;}; |
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| 57 | string getSmoothFile(){return smoothFile;}; |
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| 58 | void setSmoothFile(string file){smoothFile = file;}; |
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[71] | 59 | // |
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[3] | 60 | bool getFlagLog(){return flagLog;}; |
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| 61 | void setFlagLog(bool flag){flagLog=flag;}; |
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| 62 | string getLogFile(){return logFile;}; |
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| 63 | void setLogFile(string fname){logFile = fname;}; |
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| 64 | string getOutFile(){return outFile;}; |
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| 65 | void setOutFile(string fname){outFile = fname;}; |
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| 66 | string getSpectraFile(){return spectraFile;}; |
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| 67 | void setSpectraFile(string fname){spectraFile = fname;}; |
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[208] | 68 | bool getFlagOutputSmooth(){return flagOutputSmooth;}; |
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| 69 | void setFlagOutputSmooth(bool flag){flagOutputSmooth=flag;}; |
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[3] | 70 | bool getFlagOutputRecon(){return flagOutputRecon;}; |
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| 71 | void setFlagOutputRecon(bool flag){flagOutputRecon=flag;}; |
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| 72 | bool getFlagOutputResid(){return flagOutputResid;}; |
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| 73 | void setFlagOutputResid(bool flag){flagOutputResid=flag;}; |
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| 74 | bool getFlagVOT(){return flagVOT;}; |
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| 75 | void setFlagVOT(bool flag){flagVOT=flag;}; |
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| 76 | string getVOTFile(){return votFile;}; |
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| 77 | void setVOTFile(string fname){votFile = fname;}; |
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[20] | 78 | bool getFlagKarma(){return flagKarma;}; |
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| 79 | void setFlagKarma(bool flag){flagKarma=flag;}; |
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| 80 | string getKarmaFile(){return karmaFile;}; |
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| 81 | void setKarmaFile(string fname){karmaFile = fname;}; |
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[3] | 82 | bool getFlagMaps(){return flagMaps;}; |
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| 83 | void setFlagMaps(bool flag){flagMaps=flag;}; |
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| 84 | string getDetectionMap(){return detectionMap;}; |
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| 85 | void setDetectionMap(string fname){detectionMap = fname;}; |
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| 86 | string getMomentMap(){return momentMap;}; |
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| 87 | void setMomentMap(string fname){momentMap = fname;}; |
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[195] | 88 | bool getFlagXOutput(){return flagXOutput;}; |
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| 89 | void setFlagXOutput(bool b){flagXOutput=b;}; |
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[3] | 90 | // |
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[60] | 91 | bool getFlagNegative(){return flagNegative;}; |
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| 92 | void setFlagNegative(bool flag){flagNegative=flag;}; |
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[3] | 93 | bool getFlagBlankPix(){return flagBlankPix;}; |
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| 94 | void setFlagBlankPix(bool flag){flagBlankPix=flag;}; |
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| 95 | float getBlankPixVal(){return blankPixValue;}; |
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| 96 | void setBlankPixVal(float v){blankPixValue=v;}; |
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| 97 | int getBlankKeyword(){return blankKeyword;}; |
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| 98 | void setBlankKeyword(int v){blankKeyword=v;}; |
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| 99 | float getBscaleKeyword(){return bscaleKeyword;}; |
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| 100 | void setBscaleKeyword(float v){bscaleKeyword=v;}; |
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| 101 | float getBzeroKeyword(){return bzeroKeyword;}; |
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| 102 | void setBzeroKeyword(float v){bzeroKeyword=v;}; |
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[103] | 103 | bool getFlagUsingBlank(){return flagUsingBlank;}; |
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| 104 | void setFlagUsingBlank(bool b){flagUsingBlank=b;}; |
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[3] | 105 | bool getFlagMW(){return flagMW;}; |
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| 106 | bool setFlagMW(bool flag){flagMW=flag;}; |
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| 107 | int getMaxMW(){return maxMW;}; |
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| 108 | void setMaxMW(int m){maxMW=m;}; |
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| 109 | int getMinMW(){return minMW;}; |
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| 110 | void setMinMW(int m){minMW=m;}; |
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| 111 | void setBeamSize(float s){numPixBeam = s;}; |
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| 112 | float getBeamSize(){return numPixBeam;}; |
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[172] | 113 | bool getFlagUsingBeam(){return flagUsingBeam;}; |
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| 114 | void setFlagUsingBeam(bool b){flagUsingBeam=b;}; |
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[3] | 115 | // |
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| 116 | bool getFlagCubeTrimmed(){return flagTrimmed;}; |
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| 117 | void setFlagCubeTrimmed(bool flag){flagTrimmed = flag;}; |
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| 118 | long getBorderLeft(){return borderLeft;}; |
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| 119 | void setBorderLeft(long b){borderLeft = b;}; |
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| 120 | long getBorderRight(){return borderRight;}; |
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| 121 | void setBorderRight(long b){borderRight = b;}; |
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| 122 | long getBorderBottom(){return borderBottom;}; |
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| 123 | void setBorderBottom(long b){borderBottom = b;}; |
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| 124 | long getBorderTop(){return borderTop;}; |
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| 125 | void setBorderTop(long b){borderTop = b;}; |
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| 126 | // |
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| 127 | long getXOffset(){return xSubOffset;}; |
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| 128 | void setXOffset(long o){xSubOffset = o;}; |
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| 129 | long getYOffset(){return ySubOffset;}; |
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| 130 | void setYOffset(long o){ySubOffset = o;}; |
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| 131 | long getZOffset(){return zSubOffset;}; |
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| 132 | void setZOffset(long o){zSubOffset = o;}; |
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| 133 | // |
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| 134 | int getMinPix(){return minPix;}; |
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| 135 | void setMinPix(int m){minPix=m;}; |
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| 136 | // |
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| 137 | bool getFlagGrowth(){return flagGrowth;}; |
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| 138 | void setFlagGrowth(bool flag){flagGrowth=flag;}; |
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| 139 | float getGrowthCut(){return growthCut;}; |
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| 140 | void setGrowthCut(float c){growthCut=c;}; |
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| 141 | // |
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| 142 | bool getFlagFDR(){return flagFDR;}; |
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| 143 | void setFlagFDR(bool flag){flagFDR=flag;}; |
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| 144 | float getAlpha(){return alphaFDR;}; |
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| 145 | void setAlpha(float a){alphaFDR=a;}; |
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| 146 | // |
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| 147 | bool getFlagBaseline(){return flagBaseline;}; |
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| 148 | void setFlagBaseline(bool flag){flagBaseline = flag;}; |
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| 149 | // |
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| 150 | float getCut(){return snrCut;}; |
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| 151 | void setCut(float c){snrCut=c;}; |
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[189] | 152 | float getThreshold(){return threshold;}; |
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| 153 | void setThreshold(float f){threshold=f;}; |
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[190] | 154 | bool getFlagUserThreshold(){return flagUserThreshold;}; |
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| 155 | void setFlagUserThreshold(bool b){flagUserThreshold=b;}; |
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[3] | 156 | // |
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[201] | 157 | bool getFlagSmooth(){return flagSmooth;}; |
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| 158 | void setFlagSmooth(bool b){flagSmooth=b;}; |
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| 159 | int getHanningWidth(){return hanningWidth;}; |
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| 160 | void setHanningWidth(int f){hanningWidth=f;}; |
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| 161 | // |
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[3] | 162 | bool getFlagATrous(){return flagATrous;}; |
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| 163 | void setFlagATrous(bool flag){flagATrous=flag;}; |
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[103] | 164 | int getReconDim(){return reconDim;}; |
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| 165 | void setReconDim(int i){reconDim=i;}; |
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[3] | 166 | int getMinScale(){return scaleMin;}; |
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| 167 | void setMinScale(int s){scaleMin=s;}; |
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| 168 | float getAtrousCut(){return snrRecon;}; |
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| 169 | void setAtrousCut(float c){snrRecon=c;}; |
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| 170 | int getFilterCode(){return filterCode;}; |
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| 171 | void setFilterCode(int c){filterCode=c;}; |
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| 172 | string getFilterName(){return filterName;}; |
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| 173 | void setFilterName(string s){filterName=s;}; |
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| 174 | // |
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| 175 | bool getFlagAdjacent(){return flagAdjacent;}; |
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| 176 | void setFlagAdjacent(bool flag){flagAdjacent=flag;}; |
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| 177 | float getThreshS(){return threshSpatial;}; |
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| 178 | void setThreshS(float t){threshSpatial=t;}; |
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| 179 | float getThreshV(){return threshVelocity;}; |
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| 180 | void setThreshV(float t){threshVelocity=t;}; |
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| 181 | int getMinChannels(){return minChannels;}; |
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| 182 | void setMinChannels(int n){minChannels=n;}; |
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| 183 | // |
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[45] | 184 | string getSpectralMethod(){return spectralMethod;}; |
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| 185 | void setSpectralMethod(string s){spectralMethod=s;}; |
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[103] | 186 | string getSpectralUnits(){return spectralUnits;}; |
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| 187 | void setSpectralUnits(string s){spectralUnits=s;}; |
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[3] | 188 | bool drawBorders(){return borders;}; |
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| 189 | void setDrawBorders(bool f){borders=f;}; |
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[142] | 190 | bool drawBlankEdge(){return blankEdge;}; |
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| 191 | void setDrawBlankEdge(bool f){blankEdge=f;}; |
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[3] | 192 | bool isVerbose(){return verbose;}; |
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| 193 | void setVerbosity(bool f){verbose=f;}; |
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| 194 | |
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| 195 | private: |
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| 196 | // Input files |
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| 197 | string imageFile; // The image to be analysed. |
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| 198 | bool flagSubsection; // Whether we just want a subsection of the image |
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[142] | 199 | string subsection; // The subsection requested, taking the form |
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| 200 | // [x1:x2,y1:y2,z1:z2] |
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| 201 | // If you want the full range of one index, use * |
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[71] | 202 | bool flagReconExists; // The reconstructed array is in a FITS file on disk. |
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| 203 | string reconFile; // The FITS file containing the reconstructed array. |
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[208] | 204 | bool flagSmoothExists;// The Hanning-smoothed array is in a FITS file. |
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| 205 | string smoothFile; // The FITS file containing the smoothed array. |
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[71] | 206 | |
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[3] | 207 | // Output files |
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| 208 | bool flagLog; // Should we do the intermediate logging? |
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| 209 | string logFile; // Where the intermediate logging goes. |
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| 210 | string outFile; // Where the final results get put. |
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| 211 | string spectraFile; // Where the spectra are displayed |
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[208] | 212 | bool flagOutputSmooth;// Should the Hanning-smoothed cube be written? |
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[3] | 213 | bool flagOutputRecon; // Should the reconstructed cube be written? |
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| 214 | bool flagOutputResid; // Should the reconstructed cube be written? |
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| 215 | bool flagVOT; // Should we save results in VOTable format? |
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| 216 | string votFile; // Where the VOTable goes. |
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[20] | 217 | bool flagKarma; // Should we save results in Karma annotation format? |
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| 218 | string karmaFile; // Where the Karma annotation file goes. |
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[142] | 219 | bool flagMaps; // Should we produce detection and moment maps |
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| 220 | // in postscript form? |
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[3] | 221 | string detectionMap; // The name of the detection map (ps file). |
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[17] | 222 | string momentMap; // The name of the 0th moment map (ps file). |
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[195] | 223 | bool flagXOutput; // Should there be an xwindows output of the |
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| 224 | // detection map? |
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[3] | 225 | |
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| 226 | // Cube related parameters |
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[120] | 227 | bool flagNegative; // Are we going to search for negative features? |
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| 228 | bool flagBlankPix; // A flag that indicates whether there are pixels |
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| 229 | // defined as BLANK and whether we need to remove |
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| 230 | // & ignore them in processing. |
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[3] | 231 | float blankPixValue; // Pixel value that is considered BLANK. |
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| 232 | int blankKeyword; // The FITS header keyword BLANK. |
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| 233 | float bscaleKeyword; // The FITS header keyword BSCALE. |
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| 234 | float bzeroKeyword; // The FITS header keyword BZERO. |
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[112] | 235 | bool flagUsingBlank; // If true, we are using the blankPixValue keyword, |
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[142] | 236 | // otherwise we use the value in the FITS header. |
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| 237 | bool flagMW; // A flag that indicates whether to ignore the |
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| 238 | // Milky Way channels. |
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[3] | 239 | int maxMW; // Last Galactic velocity plane for HIPASS cubes |
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| 240 | int minMW; // First Galactic velocity plane for HIPASS cubes |
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| 241 | float numPixBeam; // Size (area) of the beam in pixels. |
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[172] | 242 | bool flagUsingBeam; // If true, we are using the numPixBeam parameter, |
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| 243 | // otherwise we use the value in the FITS header. |
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[3] | 244 | // Trim-related |
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[142] | 245 | bool flagTrimmed; // Has the cube been trimmed of excess BLANKs |
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| 246 | // around the edge? |
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| 247 | long borderLeft; // The number of BLANK pixels trimmed from the |
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| 248 | // Left of the cube; |
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| 249 | long borderRight; // The number trimmed from the Right of the cube; |
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| 250 | long borderBottom; // The number trimmed from the Bottom of the cube; |
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| 251 | long borderTop; // The number trimmed from the Top of the cube; |
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[3] | 252 | // Subsection offsets |
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[164] | 253 | long *offsets; // The array of offsets for each FITS axis. |
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[204] | 254 | long sizeOffsets; // The size of the offsets array. |
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[3] | 255 | long xSubOffset; // The offset in the x-direction from the subsection |
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| 256 | long ySubOffset; // The offset in the y-direction from the subsection |
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| 257 | long zSubOffset; // The offset in the z-direction from the subsection |
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| 258 | // Baseline related; |
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[142] | 259 | bool flagBaseline; // Whether to do baseline subtraction before |
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| 260 | // reconstruction and/or searching. |
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[3] | 261 | // Detection-related |
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[142] | 262 | int minPix; // Minimum number of pixels for a detected object |
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| 263 | // to be counted |
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[3] | 264 | // Object growth |
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| 265 | bool flagGrowth; // Are we growing objects once they are found? |
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| 266 | float growthCut; // The SNR that we are growing objects down to. |
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| 267 | // FDR analysis |
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| 268 | bool flagFDR; // Should the FDR method be used? |
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| 269 | float alphaFDR; // Alpha value for FDR detection algorithm |
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[189] | 270 | // Basic detection |
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[142] | 271 | float snrCut; // How many sigma above mean is a detection |
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| 272 | // when sigma-clipping |
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[189] | 273 | float threshold; // What the threshold is (when sigma-clipping). |
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[190] | 274 | bool flagUserThreshold;// Whether the user has defined a threshold of |
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| 275 | // their own. |
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[201] | 276 | // Smoothing of the cube |
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| 277 | bool flagSmooth; // Should the cube be smoothed before searching? |
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| 278 | int hanningWidth; // Width for hanning smoothing. |
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[3] | 279 | // A trous reconstruction parameters |
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| 280 | bool flagATrous; // Are we using the a trous reconstruction? |
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[103] | 281 | int reconDim; // How many dimensions to use for the reconstruction? |
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[3] | 282 | int scaleMin; // Min scale used in a trous reconstruction |
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| 283 | float snrRecon; // SNR cutoff used in a trous reconstruction |
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[142] | 284 | // (only wavelet coefficients that survive this |
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| 285 | // threshold are kept) |
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| 286 | int filterCode; // The code number for the filter to be used |
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| 287 | // (saves having to parse names) |
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| 288 | string filterName; // The code number converted into a name, |
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| 289 | // for outputting purposes. |
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[3] | 290 | |
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| 291 | // Volume-merging parameters |
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| 292 | bool flagAdjacent; // Whether to use the adjacent criterion for |
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| 293 | // judging if objects are to be merged. |
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| 294 | float threshSpatial; // Maximum spatial separation between objects |
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| 295 | float threshVelocity; // Maximum channels separation between objects |
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| 296 | int minChannels; // Minimum no. of channels to make an object |
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| 297 | // Input-Output related |
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[142] | 298 | string spectralMethod; // A string indicating choice of spectral plotting |
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| 299 | // method: choices are "peak" (default) or "sum" |
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| 300 | string spectralUnits; // A string indicating what units the spectral |
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| 301 | // axis should be quoted in. |
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[3] | 302 | bool borders; // Whether to draw a border around the individual |
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[142] | 303 | // pixels of a detection in the spectral display |
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| 304 | bool blankEdge; // Whether to draw a border around the BLANK pixel |
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| 305 | // region in the moment maps and cutout images |
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| 306 | bool verbose; // Whether to use maximum verbosity -- use progress |
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| 307 | // indicators in the reconstruction & merging steps. |
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[3] | 308 | |
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| 309 | }; |
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| 310 | |
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[103] | 311 | class FitsHeader |
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| 312 | { |
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| 313 | /** |
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| 314 | * FitsHeader Class |
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| 315 | * |
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| 316 | * Stores information from a FITS header, including WCS information |
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| 317 | * in the form of a wcsprm struct, as well as various keywords. |
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| 318 | */ |
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[3] | 319 | |
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[103] | 320 | public: |
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| 321 | FitsHeader(); |
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[204] | 322 | virtual ~FitsHeader(){wcsvfree(&nwcs,&wcs);}; |
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[103] | 323 | FitsHeader(const FitsHeader& h); |
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| 324 | FitsHeader& operator= (const FitsHeader& h); |
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| 325 | |
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[204] | 326 | struct wcsprm *getWCS(); // in param.cc |
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| 327 | void setWCS(struct wcsprm *w); // in param.cc |
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[103] | 328 | bool isWCS(){return wcsIsGood;}; |
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| 329 | int getNWCS(){return nwcs;}; |
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| 330 | void setNWCS(int i){nwcs=i;}; |
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[159] | 331 | int readHeaderInfo(string fname, Param &par); |
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| 332 | int defineWCS(string fname, Param &par); |
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[192] | 333 | int readBUNIT(string fname); |
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| 334 | int readBLANKinfo(string fname, Param &par); |
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| 335 | int readBeamInfo(string fname, Param &par); |
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[103] | 336 | string getSpectralUnits(){return spectralUnits;}; |
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| 337 | void setSpectralUnits(string s){spectralUnits=s;}; |
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[186] | 338 | string getSpectralDescription(){return spectralDescription;}; |
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| 339 | void setSpectralDescription(string s){spectralDescription=s;}; |
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[103] | 340 | string getFluxUnits(){return fluxUnits;}; |
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| 341 | void setFluxUnits(string s){fluxUnits=s;}; |
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| 342 | string getIntFluxUnits(){return intFluxUnits;}; |
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| 343 | void setIntFluxUnits(string s){intFluxUnits=s;}; |
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| 344 | float getBeamSize(){return beamSize;}; |
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| 345 | void setBeamSize(float f){beamSize=f;}; |
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| 346 | float getBmajKeyword(){return bmajKeyword;}; |
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| 347 | void setBmajKeyword(float f){bmajKeyword=f;}; |
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| 348 | float getBminKeyword(){return bminKeyword;}; |
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| 349 | void setBminKeyword(float f){bminKeyword=f;}; |
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[112] | 350 | int getBlankKeyword(){return blankKeyword;}; |
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| 351 | void setBlankKeyword(int f){blankKeyword=f;}; |
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[103] | 352 | float getBzeroKeyword(){return bzeroKeyword;}; |
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| 353 | void setBzeroKeyword(float f){bzeroKeyword=f;}; |
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| 354 | float getBscaleKeyword(){return bscaleKeyword;}; |
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| 355 | void setBscaleKeyword(float f){bscaleKeyword=f;}; |
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[145] | 356 | float getAvPixScale(){ |
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| 357 | return sqrt( fabs ( (wcs->pc[0]*wcs->cdelt[0])* |
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| 358 | (wcs->pc[wcs->naxis+1]*wcs->cdelt[1]))); |
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| 359 | }; |
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[103] | 360 | |
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| 361 | // front ends to WCS functions |
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| 362 | int wcsToPix(const double *world, double *pix); |
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| 363 | int pixToWCS(const double *pix, double *world); |
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| 364 | int wcsToPix(const double *world, double *pix, const int npts); |
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| 365 | int pixToWCS(const double *pix, double *world, const int npts); |
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| 366 | double pixToVel(double &x, double &y, double &z); |
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| 367 | double *pixToVel(double &x, double &y, double *zarray, int size); |
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| 368 | double specToVel(const double &z); |
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| 369 | double velToSpec(const float &vel); |
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| 370 | string getIAUName(double ra, double dec); |
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| 371 | |
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| 372 | void fixUnits(Param &par); |
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| 373 | |
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| 374 | private: |
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[204] | 375 | struct wcsprm *wcs; // The WCS parameters for the cube in a |
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[186] | 376 | // struct from the wcslib library. |
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| 377 | int nwcs; // The number of WCS parameters |
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| 378 | bool wcsIsGood; // A flag indicating whether there is a |
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| 379 | // valid WCS present. |
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| 380 | string spectralUnits; // The units of the spectral dimension |
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| 381 | string spectralDescription; // The description of the spectral dimension |
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| 382 | // (Frequency, Velocity, ...) |
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| 383 | string fluxUnits; // The units of pixel flux (from header) |
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| 384 | string intFluxUnits; // The units of pixel flux (from header) |
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| 385 | float beamSize; // The calculated beam size in pixels. |
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| 386 | float bmajKeyword; // The FITS header keyword BMAJ. |
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| 387 | float bminKeyword; // The FITS header keyword BMIN. |
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| 388 | int blankKeyword; // The FITS header keyword BLANK. |
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| 389 | float bzeroKeyword; // The FITS header keyword BZERO. |
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| 390 | float bscaleKeyword; // The FITS header keyword BSCALE. |
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| 391 | double scale; // scale param for converting spectral coords |
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| 392 | double offset; // offset param for converting spectral coords |
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| 393 | double power; // power param for converting spectral coords |
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[103] | 394 | }; |
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| 395 | |
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| 396 | string makelower( string s ); |
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| 397 | |
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[3] | 398 | #endif |
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