1 | #include <iostream> |
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2 | #include <string> |
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3 | #include <wcs.h> |
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4 | #include <wcshdr.h> |
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5 | #include <fitshdr.h> |
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6 | #include <wcsfix.h> |
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7 | #include <fitsio.h> |
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8 | #include <math.h> |
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9 | #include <duchamp.hh> |
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10 | #include <Cubes/cubes.hh> |
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11 | |
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12 | #ifdef NAN |
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13 | float nanValue = NAN; |
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14 | #endif |
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15 | |
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16 | using std::endl; |
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17 | |
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18 | string imageType[4] = {"point", "spectrum", "image", "cube"}; |
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19 | |
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20 | int Cube::getCube(string fname) |
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21 | { |
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22 | /** |
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23 | * Cube::getCube(string ) |
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24 | * Read in a cube from the file fname (assumed to be in FITS format). |
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25 | * Function reads in the following: |
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26 | * - axis dimensions |
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27 | * - pixel array |
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28 | * - WCS information (in form of WCSLIB wcsprm structure) |
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29 | * - Header keywords: BUNIT (brightness unit), |
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30 | * BLANK, BZERO, BSCALE (to determine blank pixel value) |
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31 | * BMAJ, BMIN, CDELT1, CDELT2 (to determine beam size) |
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32 | */ |
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33 | |
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34 | |
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35 | short int maxdim=3; |
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36 | long *fpixel = new long[maxdim]; |
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37 | for(int i=0;i<maxdim;i++) fpixel[i]=1; |
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38 | long *dimAxes = new long[maxdim]; |
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39 | for(int i=0;i<maxdim;i++) dimAxes[i]=1; |
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40 | long nelements; |
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41 | int bitpix,numAxes; |
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42 | int status = 0, nkeys; /* MUST initialize status */ |
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43 | fitsfile *fptr; |
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44 | |
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45 | if( fits_open_file(&fptr,fname.c_str(),READONLY,&status) ){ |
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46 | fits_report_error(stderr, status); |
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47 | return FAILURE; |
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48 | } |
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49 | |
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50 | status = 0; |
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51 | fits_get_img_param(fptr, maxdim, &bitpix, &numAxes, dimAxes, &status); |
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52 | if(status){ |
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53 | fits_report_error(stderr, status); |
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54 | return FAILURE; |
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55 | } |
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56 | |
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57 | if(numAxes<=3) std::cout << "Dimensions of " << imageType[numAxes] << ": " << dimAxes[0]; |
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58 | else std::cout << "Dimensions of " << imageType[3] << ": " << dimAxes[0]; |
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59 | if(numAxes>1) std::cout << "x" << dimAxes[1]; |
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60 | if(numAxes>2) std::cout << "x" << dimAxes[2]; |
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61 | std::cout << endl; |
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62 | |
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63 | int npix = dimAxes[0]*dimAxes[1]*dimAxes[2]; |
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64 | float *array = new float[npix]; |
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65 | int anynul; |
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66 | char *nullarray = new char[npix]; |
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67 | for(int i=0;i<npix;i++) nullarray[i] = 0; |
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68 | |
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69 | //------------------------------------------------------------- |
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70 | // Reading in the pixel array. |
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71 | // The location of any blank pixels (as determined by the header keywords) is stored |
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72 | // in nullarray (set to 1). Also anynul will be set to 1 to indicate the presence of |
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73 | // blank pixels. If anynul==1 then all pixels are non-blank. |
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74 | |
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75 | status = 0; |
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76 | fits_read_pixnull(fptr, TFLOAT, fpixel, npix, array, nullarray, &anynul, &status); |
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77 | // fits_read_pix(fptr, TFLOAT, fpixel, npix, NULL, array, &anynul, &status); |
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78 | if(status){ |
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79 | fits_report_error(stderr, status); |
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80 | return FAILURE; |
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81 | } |
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82 | |
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83 | if(anynul==0){ // no blank pixels, so don't bother with any trimming or checking... |
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84 | if(this->par.getFlagBlankPix()) // if user requested fixing, inform them of change. |
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85 | std::cerr << "WARNING <getCube> : No blank pixels, so setting flagBlankPix to false...\n"; |
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86 | this->par.setFlagBlankPix(false); |
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87 | } |
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88 | |
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89 | //------------------------------------------------------------- |
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90 | // Read the header in preparation for WCS and BUNIT/BLANK/etc extraction. |
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91 | char *hdr = new char; |
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92 | int noComments = 1; //so that fits_hdr2str will not write out COMMENT, HISTORY etc |
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93 | int nExc = 0; |
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94 | status = 0; |
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95 | fits_hdr2str(fptr, noComments, NULL, nExc, &hdr, &nkeys, &status); |
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96 | if( status ){ |
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97 | std::cerr << "WARNING <getCube> : Error reading in header to string: "; |
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98 | fits_report_error(stderr, status); |
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99 | } |
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100 | |
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101 | //------------------------------------------------------------- |
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102 | // Read the BUNIT header keyword, to store the brightness unit. |
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103 | int blank; |
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104 | float bscale, bzero; |
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105 | char *comment = new char[80]; |
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106 | char *bunit = new char[80]; |
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107 | status = 0; |
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108 | fits_read_key(fptr, TSTRING, "BUNIT", bunit, comment, &status); |
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109 | if (status){ |
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110 | std::cerr << "WARNING <getCube> : Error reading BUNIT keyword: "; |
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111 | fits_report_error(stderr, status); |
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112 | } |
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113 | else this->setBUnit(bunit); |
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114 | |
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115 | //------------------------------------------------------------- |
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116 | // Reading in the Blank pixel value keywords. |
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117 | // If the BLANK keyword is in the header, use that and store the relevant values. |
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118 | // If not, use the default value (either the default from param.cc or from the param file) |
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119 | // and assume simple values for the keywords --> the scale keyword is the same as the |
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120 | // blank value, the blank keyword (which is an int) is 1 and the bzero (offset) is 0. |
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121 | status = 0; |
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122 | if(this->par.getFlagBlankPix()){ |
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123 | if( !fits_read_key(fptr, TINT32BIT, "BLANK", &blank, comment, &status) ){ |
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124 | fits_read_key(fptr, TFLOAT, "BZERO", &bzero, comment, &status); |
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125 | fits_read_key(fptr, TFLOAT, "BSCALE", &bscale, comment, &status); |
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126 | this->par.setBlankPixVal(blank*bscale+bzero); |
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127 | this->par.setBlankKeyword(blank); |
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128 | this->par.setBscaleKeyword(bscale); |
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129 | this->par.setBzeroKeyword(bzero); |
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130 | } |
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131 | if (status){ |
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132 | std::cerr << "WARNING <getCube> : Error reading BLANK keyword: "; |
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133 | fits_report_error(stderr, status); |
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134 | std::cerr << "Using default BLANK (physical) value (" << this->par.getBlankPixVal() << ")." << endl; |
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135 | for(int i=0;i<npix;i++) if(isnan(array[i])) array[i] = this->par.getBlankPixVal(); |
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136 | this->par.setBlankKeyword(1); |
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137 | this->par.setBscaleKeyword(this->par.getBlankPixVal()); |
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138 | this->par.setBzeroKeyword(0.); |
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139 | } |
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140 | } |
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141 | |
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142 | //------------------------------------------------------------- |
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143 | // Reading in the beam parameters from the header. |
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144 | // Use these, plus the basic WCS parameters to calculate the size of the beam in pixels. |
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145 | float bmaj,bmin,cdelt1,cdelt2; |
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146 | status = 0; |
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147 | if( !fits_read_key(fptr, TFLOAT, "BMAJ", &bmaj, comment, &status) ){ |
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148 | fits_read_key(fptr, TFLOAT, "BMIN", &bmin, comment, &status); |
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149 | fits_read_key(fptr, TFLOAT, "CDELT1", &cdelt1, comment, &status); |
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150 | fits_read_key(fptr, TFLOAT, "CDELT2", &cdelt2, comment, &status); |
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151 | this->par.setBeamSize( M_PI * (bmaj/2.) * (bmin/2.) / fabsf(cdelt1*cdelt2) ); |
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152 | } |
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153 | if (status){ |
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154 | std::cerr << |
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155 | "WARNING <getCube> : No beam information in header. Setting size to nominal 10 pixels.\n"; |
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156 | this->par.setBeamSize(10.); |
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157 | } |
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158 | |
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159 | status = 0; |
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160 | fits_close_file(fptr, &status); |
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161 | if (status){ |
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162 | std::cerr << "WARNING <getCube> : Error closing file: "; |
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163 | fits_report_error(stderr, status); |
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164 | } |
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165 | |
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166 | this->initialiseCube(dimAxes); |
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167 | this->saveArray(array,npix); |
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168 | //------------------------------------------------------------- |
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169 | // Once the array is saved, change the value of the blank pixels from |
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170 | // 0 (as they are set by fits_read_pixnull) to the correct blank value |
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171 | // as determined by the above code. |
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172 | for(int i=0; i<npix;i++){ |
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173 | if(nullarray[i]==1) this->array[i] = blank*bscale + bzero; |
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174 | } |
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175 | |
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176 | //------------------------------------------------------------- |
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177 | // Now convert the FITS header to a WCS structure, using the WCSLIB functions. |
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178 | int relax=1, ctrl=2, nwcs, nreject; |
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179 | wcsprm *wcs = new wcsprm; |
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180 | wcsini(true,numAxes,wcs); |
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181 | wcs->flag=-1; |
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182 | int flag; |
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183 | if(flag = wcspih(hdr, nkeys, relax, ctrl, &nreject, &nwcs, &wcs)) { |
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184 | std::cerr<<"WARNING <getCube> : WCSPIH failed! Code="<<flag<<": "<<wcs_errmsg[flag]<<endl; |
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185 | } |
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186 | else{ |
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187 | int stat[6],axes[3]={dimAxes[0],dimAxes[1],dimAxes[2]}; |
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188 | if(flag=wcsfix(1,axes,wcs,stat)) { |
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189 | std::cerr<<"WARNING <getCube> : WCSFIX failed!"<<endl; |
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190 | for(int i=0; i<NWCSFIX; i++) |
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191 | if (stat[i] > 0) std::cerr<<"wcsfix ERROR "<<flag<<": "<< wcsfix_errmsg[stat[i]] <<endl; |
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192 | } |
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193 | if(flag=wcsset(wcs)){ |
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194 | std::cerr<<"WARNING <getCube> : WCSSET failed! Code="<<flag <<": "<<wcs_errmsg[flag]<<endl; |
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195 | } |
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196 | |
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197 | this->setWCS(wcs); |
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198 | this->setNWCS(nwcs); |
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199 | } |
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200 | wcsfree(wcs); |
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201 | |
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202 | if(!this->flagWCS) std::cerr << "WARNING <getCube> : WCS is not good enough to be used.\n"; |
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203 | |
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204 | delete hdr; |
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205 | delete [] array; |
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206 | delete [] fpixel; |
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207 | delete [] dimAxes; |
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208 | |
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209 | return SUCCESS; |
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210 | |
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211 | } |
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212 | |
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213 | Cube getCube(string fname, Param par) |
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214 | { |
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215 | short int maxdim=3; |
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216 | long *fpixel = new long[maxdim]; |
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217 | for(int i=0;i<maxdim;i++) fpixel[i]=1; |
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218 | long *dimAxes = new long[maxdim]; |
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219 | for(int i=0;i<maxdim;i++) dimAxes[i]=1; |
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220 | long nelements; |
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221 | int bitpix,numAxes,anynul; |
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222 | int status = 0, nkeys; /* MUST initialize status */ |
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223 | fitsfile *fptr; |
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224 | |
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225 | if( fits_open_file(&fptr,fname.c_str(),READONLY,&status) ){ |
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226 | fits_report_error(stderr, status); |
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227 | return 1; |
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228 | } |
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229 | |
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230 | fits_get_img_param(fptr, maxdim, &bitpix, &numAxes, dimAxes, &status); |
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231 | int npix = dimAxes[0]*dimAxes[1]*dimAxes[2]; |
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232 | float *array = new float[npix]; |
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233 | fits_read_pix(fptr, TFLOAT, fpixel, npix, NULL, array, &anynul, &status); |
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234 | |
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235 | // Read the header |
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236 | char *hdr = new char; |
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237 | int noComments = 1; //fits_hdr2str will not write out COMMENT, HISTORY etc |
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238 | int nExc = 0; |
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239 | if( fits_hdr2str(fptr, noComments, NULL, nExc, &hdr, &nkeys, &status) ){ |
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240 | fits_report_error(stderr, status); |
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241 | return 1; |
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242 | } |
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243 | |
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244 | float blank, bscale, bzero; |
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245 | char *comment = new char[80]; |
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246 | // if( fits_movabs_hdu(fptr, 1, IMAGE_HDU, &status)) fits_report_error(stderr, status); |
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247 | if( !fits_read_key(fptr, TFLOAT, "BLANK", &blank, comment, &status) ){ |
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248 | fits_read_key(fptr, TFLOAT, "BZERO", &bzero, comment, &status); |
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249 | fits_read_key(fptr, TFLOAT, "BSCALE", &bscale, comment, &status); |
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250 | par.setBlankPixVal(blank*bscale+bzero); |
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251 | } |
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252 | if (status) fits_report_error(stderr, status); |
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253 | char *bunit = new char[80]; |
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254 | fits_read_key(fptr, TSTRING, "BUNIT", bunit, comment, &status); |
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255 | if (status) fits_report_error(stderr, status); |
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256 | |
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257 | fits_close_file(fptr, &status); |
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258 | if (status) fits_report_error(stderr, status); |
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259 | |
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260 | int relax=1, ctrl=2, nwcs, nreject; |
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261 | wcsprm *wcs = new wcsprm; |
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262 | wcsini(true,numAxes,wcs); |
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263 | wcs->flag=-1; |
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264 | int flag; |
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265 | if(flag = wcspih(hdr, nkeys, relax, ctrl, &nreject, &nwcs, &wcs)) { |
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266 | std::cerr<<"getImage.cc:: WCSPIH failed! Code="<<flag<<": "<<wcs_errmsg[flag]<<endl; |
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267 | return 1; |
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268 | } |
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269 | |
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270 | int stat[6],axes[3]={dimAxes[0],dimAxes[1],dimAxes[2]}; |
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271 | if(flag=wcsfix(1,axes,wcs,stat)) { |
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272 | std::cerr<<"getImage.cc:: WCSFIX failed!"<<endl; |
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273 | for(int i=0; i<NWCSFIX; i++) |
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274 | if (stat[i] > 0) std::cerr<<"wcsfix ERROR "<<flag<<": "<< wcsfix_errmsg[stat[i]] <<endl; |
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275 | return 1; |
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276 | } |
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277 | if(flag=wcsset(wcs)){ |
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278 | std::cerr<<"getImage.cc:: WCSSET failed! Code="<<flag <<": "<<wcs_errmsg[flag]<<endl; |
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279 | return 1; |
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280 | } |
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281 | |
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282 | Cube *data = new Cube(dimAxes); |
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283 | data->saveArray(array,npix); |
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284 | data->setWCS(wcs); |
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285 | data->setNWCS(nwcs); |
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286 | data->setBUnit(bunit); |
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287 | |
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288 | wcsfree(wcs); |
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289 | delete hdr; |
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290 | delete [] array; |
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291 | delete [] fpixel; |
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292 | delete [] dimAxes; |
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293 | |
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294 | |
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295 | return *data; |
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296 | } |
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297 | |
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298 | Image getImage(string fname) |
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299 | { |
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300 | int maxdim=2; |
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301 | long *fpixel = new long[maxdim]; |
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302 | for(int i=0;i<maxdim;i++) fpixel[i]=1; |
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303 | long *dimAxes = new long[maxdim]; |
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304 | for(int i=0;i<maxdim;i++) dimAxes[i]=1; |
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305 | long nelements; |
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306 | int bitpix,numAxes,anynul; |
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307 | int status = 0, nkeys; /* MUST initialize status */ |
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308 | fitsfile *fptr; |
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309 | |
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310 | std::cerr << fname.c_str() << endl; |
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311 | |
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312 | fits_open_file(&fptr,fname.c_str(),READONLY,&status); |
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313 | if (status) fits_report_error(stderr, status); |
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314 | fits_get_img_param(fptr, maxdim, &bitpix, &numAxes, dimAxes, &status); |
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315 | int npix = dimAxes[0]*dimAxes[1]; |
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316 | float *cube = new float[npix]; |
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317 | fits_read_pix(fptr, TFLOAT, fpixel, npix, NULL, cube, &anynul, &status); |
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318 | fits_close_file(fptr, &status); |
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319 | if (status) fits_report_error(stderr, status); |
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320 | |
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321 | Image data(dimAxes); |
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322 | data.saveArray(cube,npix); |
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323 | |
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324 | delete [] cube; |
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325 | delete [] fpixel; |
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326 | delete [] dimAxes; |
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327 | |
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328 | // std::cerr << data.getSize()<<" "<<data.getDimX()<<" "<<data.getDimY()<<endl; |
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329 | |
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330 | return data; |
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331 | } |
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332 | |
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333 | DataArray getImage(string fname, short int maxdim) |
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334 | { |
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335 | long *fpixel = new long[maxdim]; |
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336 | for(int i=0;i<maxdim;i++) fpixel[i]=1; |
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337 | long *dimAxes = new long[maxdim]; |
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338 | for(int i=0;i<maxdim;i++) dimAxes[i]=1; |
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339 | long nelements; |
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340 | int bitpix,numAxes,anynul; |
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341 | int status = 0, nkeys; /* MUST initialize status */ |
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342 | fitsfile *fptr; |
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343 | |
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344 | std::cerr << fname.c_str() << endl; |
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345 | |
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346 | fits_open_file(&fptr,fname.c_str(),READONLY,&status); |
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347 | if (status) fits_report_error(stderr, status); |
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348 | fits_get_img_param(fptr, maxdim, &bitpix, &numAxes, dimAxes, &status); |
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349 | int npix = dimAxes[0]; |
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350 | for(int i=1;i<numAxes;i++) npix *= dimAxes[i]; |
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351 | float *cube = new float[npix]; |
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352 | fits_read_pix(fptr, TFLOAT, fpixel, npix, NULL, cube, &anynul, &status); |
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353 | fits_close_file(fptr, &status); |
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354 | if (status) fits_report_error(stderr, status); |
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355 | |
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356 | DataArray data(numAxes,dimAxes); |
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357 | data.saveArray(cube,npix); |
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358 | |
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359 | delete [] cube; |
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360 | delete [] fpixel; |
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361 | delete [] dimAxes; |
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362 | |
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363 | return data; |
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364 | } |
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365 | |
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