1 | #include <iostream> |
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2 | #include <string> |
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3 | #define WCSLIB_GETWCSTAB // define this so that we don't try and redefine |
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4 | // wtbarr (this is a problem when using gcc v.4+ |
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5 | #include <fitsio.h> |
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6 | #include <math.h> |
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7 | #include <duchamp.hh> |
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8 | #include <Cubes/cubes.hh> |
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9 | |
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10 | int Cube::getFITSdata(string fname) |
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11 | { |
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12 | /** |
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13 | * This function retrieves the data array from the FITS file at the |
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14 | * location given by the string argument. |
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15 | * Only the two spatial axes and the one spectral axis are stored in the |
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16 | * data array. These axes are given by the wcsprm variables wcs->lng, |
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17 | * wcs->lat and wcs->spec. |
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18 | * All other axes are just read by their first pixel, using the |
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19 | * fits_read_subsetnull_ functions |
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20 | */ |
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21 | |
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22 | long nelements; |
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23 | int bitpix,numAxes; |
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24 | int status = 0, nkeys; /* MUST initialize status */ |
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25 | fitsfile *fptr; |
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26 | |
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27 | // Open the FITS file |
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28 | status = 0; |
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29 | if( fits_open_file(&fptr,fname.c_str(),READONLY,&status) ){ |
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30 | fits_report_error(stderr, status); |
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31 | return FAILURE; |
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32 | } |
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33 | |
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34 | // Read the size of the FITS file -- number and sizes of the axes |
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35 | status = 0; |
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36 | if(fits_get_img_dim(fptr, &numAxes, &status)){ |
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37 | fits_report_error(stderr, status); |
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38 | return FAILURE; |
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39 | } |
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40 | long *dimAxes = new long[numAxes]; |
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41 | for(int i=0;i<numAxes;i++) dimAxes[i]=1; |
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42 | status = 0; |
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43 | if(fits_get_img_size(fptr, numAxes, dimAxes, &status)){ |
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44 | fits_report_error(stderr, status); |
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45 | return FAILURE; |
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46 | } |
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47 | |
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48 | // Identify which axes are the "interesting" ones |
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49 | int lng,lat,spc; |
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50 | if(this->head.isWCS()){ |
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51 | lng = this->head.getWCS()->lng; |
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52 | lat = this->head.getWCS()->lat; |
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53 | spc = this->head.getWCS()->spec; |
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54 | } |
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55 | else{ |
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56 | lng = 0; |
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57 | lat = 1; |
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58 | spc = 2; |
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59 | } |
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60 | |
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61 | |
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62 | int anynul; |
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63 | int npix = dimAxes[lng]*dimAxes[lat]*dimAxes[spc]; |
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64 | |
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65 | float *pixarray = new float[npix];// the array of pixel values |
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66 | char *nullarray = new char[npix]; // the array of null pixels |
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67 | long *inc = new long[numAxes]; // the data-sampling increment |
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68 | |
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69 | // define the first and last pixels for each axis. |
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70 | // set both to 1 for the axes we don't want, and to the full |
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71 | // range for the ones we do. |
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72 | long *fpixel = new long[numAxes]; |
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73 | long *lpixel = new long[numAxes]; |
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74 | for(int i=0;i<numAxes;i++){ |
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75 | inc[i] = fpixel[i] = lpixel[i] = 1; |
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76 | } |
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77 | lpixel[lng] = dimAxes[lng]; |
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78 | lpixel[lat] = dimAxes[lat]; |
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79 | lpixel[spc] = dimAxes[spc]; |
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80 | |
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81 | int colnum = 0; // want the first dataset in the FITS file |
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82 | |
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83 | // prepare the Cube's pixel array -- so that we don't have to use saveArray; |
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84 | // if(this->numPixels>0) delete [] array; |
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85 | // this->array = new float[npix]; |
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86 | // this->numPixels = npix; |
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87 | // read the relevant subset, defined by the first & last pixel ranges |
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88 | status = 0; |
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89 | if(fits_read_subsetnull_flt(fptr, colnum, numAxes, dimAxes, |
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90 | fpixel, lpixel, inc, |
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91 | // this->array, nullarray, &anynul, &status)){ |
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92 | pixarray, nullarray, &anynul, &status)){ |
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93 | duchampError("getFITSdata", |
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94 | "There was an error reading in the data array:"); |
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95 | fits_report_error(stderr, status); |
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96 | return FAILURE; |
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97 | } |
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98 | |
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99 | delete [] fpixel; |
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100 | delete [] lpixel; |
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101 | delete [] inc; |
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102 | |
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103 | if(anynul==0){ |
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104 | // no blank pixels, so don't bother with any trimming or checking... |
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105 | if(this->par.getFlagBlankPix()) { |
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106 | // if user requested fixing, inform them of change. |
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107 | duchampWarning("getFITSdata", |
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108 | "No blank pixels, so setting flagBlankPix to false.\n"); |
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109 | } |
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110 | this->par.setFlagBlankPix(false); |
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111 | } |
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112 | |
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113 | this->initialiseCube(dimAxes); |
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114 | this->saveArray(pixarray,npix); |
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115 | delete [] pixarray; |
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116 | delete [] dimAxes; |
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117 | this->par.setOffsets(this->head.getWCS()); |
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118 | //------------------------------------------------------------- |
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119 | // Once the array is saved, change the value of the blank pixels from |
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120 | // 0 (as they are set by fits_read_pixnull) to the correct blank value |
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121 | // as determined by the above code. |
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122 | for(int i=0; i<npix;i++){ |
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123 | // if(nullarray[i]==1) this->array[i] = blank*bscale + bzero; |
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124 | // if(isnan(array[i])) this->array[i] = par.getBlankPixVal(); |
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125 | if(nullarray[i]==1) this->array[i] = this->par.getBlankPixVal(); |
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126 | } |
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127 | |
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128 | delete [] nullarray; |
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129 | // Close the FITS file -- not needed any more in this function. |
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130 | status = 0; |
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131 | fits_close_file(fptr, &status); |
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132 | if (status){ |
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133 | duchampWarning("defineWCS","Error closing file: "); |
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134 | fits_report_error(stderr, status); |
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135 | } |
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136 | |
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137 | return SUCCESS; |
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138 | |
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139 | } |
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