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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7 | #include <math.h> |
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8 | #include <wcs.h> |
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9 | #include <wcshdr.h> |
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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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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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21 | class Param |
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22 | { |
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23 | public: |
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24 | Param(); |
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25 | virtual ~Param(){if(sizeOffsets>0) delete [] offsets;}; |
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26 | Param(const Param& p); |
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27 | Param& operator= (const Param& p); |
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28 | int verifySubsection(); // in FitsIO/subsection.cc |
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29 | void setOffsets(struct wcsprm *wcs); // in FitsIO/subsection.cc |
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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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33 | bool isInMW(int z){return ( flagMW && (z>=minMW) && (z<=maxMW) );}; |
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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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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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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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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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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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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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59 | // |
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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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68 | bool getFlagOutputSmooth(){return flagOutputSmooth;}; |
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69 | void setFlagOutputSmooth(bool flag){flagOutputSmooth=flag;}; |
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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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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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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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88 | bool getFlagXOutput(){return flagXOutput;}; |
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89 | void setFlagXOutput(bool b){flagXOutput=b;}; |
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90 | // |
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91 | bool getFlagNegative(){return flagNegative;}; |
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92 | void setFlagNegative(bool flag){flagNegative=flag;}; |
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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 | bool getFlagUsingBlank(){return flagUsingBlank;}; |
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104 | void setFlagUsingBlank(bool b){flagUsingBlank=b;}; |
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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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113 | bool getFlagUsingBeam(){return flagUsingBeam;}; |
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114 | void setFlagUsingBeam(bool b){flagUsingBeam=b;}; |
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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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152 | float getThreshold(){return threshold;}; |
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153 | void setThreshold(float f){threshold=f;}; |
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154 | bool getFlagUserThreshold(){return flagUserThreshold;}; |
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155 | void setFlagUserThreshold(bool b){flagUserThreshold=b;}; |
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156 | // |
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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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162 | bool getFlagATrous(){return flagATrous;}; |
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163 | void setFlagATrous(bool flag){flagATrous=flag;}; |
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164 | int getReconDim(){return reconDim;}; |
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165 | void setReconDim(int i){reconDim=i;}; |
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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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184 | string getSpectralMethod(){return spectralMethod;}; |
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185 | void setSpectralMethod(string s){spectralMethod=s;}; |
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186 | string getSpectralUnits(){return spectralUnits;}; |
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187 | void setSpectralUnits(string s){spectralUnits=s;}; |
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188 | bool drawBorders(){return borders;}; |
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189 | void setDrawBorders(bool f){borders=f;}; |
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190 | bool drawBlankEdge(){return blankEdge;}; |
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191 | void setDrawBlankEdge(bool f){blankEdge=f;}; |
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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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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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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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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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206 | |
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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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212 | bool flagOutputSmooth;// Should the Hanning-smoothed cube be written? |
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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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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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219 | bool flagMaps; // Should we produce detection and moment maps |
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220 | // in postscript form? |
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221 | string detectionMap; // The name of the detection map (ps file). |
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222 | string momentMap; // The name of the 0th moment map (ps file). |
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223 | bool flagXOutput; // Should there be an xwindows output of the |
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224 | // detection map? |
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225 | |
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226 | // Cube related parameters |
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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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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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235 | bool flagUsingBlank; // If true, we are using the blankPixValue keyword, |
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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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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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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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244 | // Trim-related |
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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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252 | // Subsection offsets |
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253 | long *offsets; // The array of offsets for each FITS axis. |
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254 | long sizeOffsets; // The size of the offsets array. |
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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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259 | bool flagBaseline; // Whether to do baseline subtraction before |
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260 | // reconstruction and/or searching. |
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261 | // Detection-related |
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262 | int minPix; // Minimum number of pixels for a detected object |
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263 | // to be counted |
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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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270 | // Basic detection |
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271 | float snrCut; // How many sigma above mean is a detection |
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272 | // when sigma-clipping |
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273 | float threshold; // What the threshold is (when sigma-clipping). |
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274 | bool flagUserThreshold;// Whether the user has defined a threshold of |
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275 | // their own. |
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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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279 | // A trous reconstruction parameters |
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280 | bool flagATrous; // Are we using the a trous reconstruction? |
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281 | int reconDim; // How many dimensions to use for the reconstruction? |
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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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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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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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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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302 | bool borders; // Whether to draw a border around the individual |
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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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308 | |
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309 | }; |
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310 | |
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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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319 | |
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320 | public: |
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321 | FitsHeader(); |
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322 | virtual ~FitsHeader(){wcsvfree(&nwcs,&wcs);}; |
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323 | FitsHeader(const FitsHeader& h); |
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324 | FitsHeader& operator= (const FitsHeader& h); |
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325 | |
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326 | struct wcsprm *getWCS(); // in param.cc |
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327 | void setWCS(struct wcsprm *w); // in param.cc |
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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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331 | int readHeaderInfo(string fname, Param &par); |
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332 | int defineWCS(string fname, Param &par); |
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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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336 | string getSpectralUnits(){return spectralUnits;}; |
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337 | void setSpectralUnits(string s){spectralUnits=s;}; |
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338 | string getSpectralDescription(){return spectralDescription;}; |
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339 | void setSpectralDescription(string s){spectralDescription=s;}; |
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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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350 | int getBlankKeyword(){return blankKeyword;}; |
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351 | void setBlankKeyword(int f){blankKeyword=f;}; |
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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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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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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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375 | struct wcsprm *wcs; // The WCS parameters for the cube in a |
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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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394 | }; |
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395 | |
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396 | string makelower( string s ); |
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397 | |
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398 | #endif |
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