1 | // ----------------------------------------------------------------------- |
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2 | // dataIO.cc: Read the data array from a FITS file into a Cube object. |
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3 | // ----------------------------------------------------------------------- |
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4 | // Copyright (C) 2006, Matthew Whiting, ATNF |
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5 | // |
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6 | // This program is free software; you can redistribute it and/or modify it |
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7 | // under the terms of the GNU General Public License as published by the |
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8 | // Free Software Foundation; either version 2 of the License, or (at your |
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9 | // option) any later version. |
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10 | // |
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11 | // Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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12 | // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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13 | // FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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14 | // for more details. |
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15 | // |
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16 | // You should have received a copy of the GNU General Public License |
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17 | // along with Duchamp; if not, write to the Free Software Foundation, |
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18 | // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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19 | // |
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20 | // Correspondence concerning Duchamp may be directed to: |
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21 | // Internet email: Matthew.Whiting [at] atnf.csiro.au |
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22 | // Postal address: Dr. Matthew Whiting |
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23 | // Australia Telescope National Facility, CSIRO |
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24 | // PO Box 76 |
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25 | // Epping NSW 1710 |
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26 | // AUSTRALIA |
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27 | // ----------------------------------------------------------------------- |
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28 | #include <iostream> |
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29 | #include <string> |
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30 | #define WCSLIB_GETWCSTAB // define this so that we don't try and redefine |
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31 | // wtbarr (this is a problem when using gcc v.4+ |
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32 | #include <fitsio.h> |
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33 | #include <math.h> |
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34 | #include <duchamp/duchamp.hh> |
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35 | #include <duchamp/param.hh> |
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36 | #include <duchamp/fitsHeader.hh> |
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37 | #include <duchamp/Cubes/cubes.hh> |
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38 | |
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39 | namespace duchamp |
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40 | { |
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41 | |
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42 | int Cube::getFITSdata(std::string fname) |
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43 | { |
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44 | /** |
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45 | * This function retrieves the data array from the FITS file at the |
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46 | * location given by the string argument. |
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47 | * Only the two spatial axes and the one spectral axis are stored in the |
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48 | * data array. These axes are given by the wcsprm variables wcs->lng, |
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49 | * wcs->lat and wcs->spec. |
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50 | * All other axes are just read by their first pixel, using the |
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51 | * fits_read_subsetnull_flt function |
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52 | */ |
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53 | |
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54 | int numAxes, status = 0; /* MUST initialize status */ |
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55 | fitsfile *fptr; |
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56 | |
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57 | // Open the FITS file |
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58 | status = 0; |
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59 | if( fits_open_file(&fptr,fname.c_str(),READONLY,&status) ){ |
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60 | fits_report_error(stderr, status); |
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61 | return FAILURE; |
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62 | } |
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63 | |
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64 | // Read the size of the FITS file -- number and sizes of the axes |
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65 | status = 0; |
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66 | if(fits_get_img_dim(fptr, &numAxes, &status)){ |
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67 | fits_report_error(stderr, status); |
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68 | return FAILURE; |
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69 | } |
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70 | |
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71 | long *dimAxes = new long[numAxes]; |
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72 | for(int i=0;i<numAxes;i++) dimAxes[i]=1; |
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73 | status = 0; |
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74 | if(fits_get_img_size(fptr, numAxes, dimAxes, &status)){ |
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75 | fits_report_error(stderr, status); |
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76 | return FAILURE; |
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77 | } |
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78 | |
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79 | // Identify which axes are the "interesting" ones |
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80 | int lng,lat,spc; |
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81 | if(this->head.isWCS()){ |
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82 | lng = this->head.WCS().lng; |
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83 | lat = this->head.WCS().lat; |
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84 | spc = this->head.WCS().spec; |
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85 | } |
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86 | else{ |
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87 | lng = 0; |
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88 | lat = 1; |
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89 | spc = 2; |
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90 | } |
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91 | |
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92 | int anynul; |
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93 | int npix = dimAxes[lng]; |
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94 | if(numAxes>1) npix *= dimAxes[lat]; |
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95 | if((spc>=0)&&(numAxes>spc)) npix *= dimAxes[spc]; |
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96 | |
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97 | float *pixarray = new float[npix];// the array of pixel values |
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98 | char *nullarray = new char[npix]; // the array of null pixels |
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99 | long *inc = new long[numAxes]; // the data-sampling increment |
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100 | |
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101 | // define the first and last pixels for each axis. |
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102 | // set both to 1 for the axes we don't want, and to the full |
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103 | // range for the ones we do. |
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104 | long *fpixel = new long[numAxes]; |
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105 | long *lpixel = new long[numAxes]; |
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106 | for(int i=0;i<numAxes;i++){ |
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107 | inc[i] = fpixel[i] = lpixel[i] = 1; |
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108 | } |
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109 | lpixel[lng] = dimAxes[lng]; |
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110 | if(numAxes>1) lpixel[lat] = dimAxes[lat]; |
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111 | if((spc>=0)&&(numAxes>spc)) lpixel[spc] = dimAxes[spc]; |
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112 | |
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113 | |
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114 | int colnum = 0; // want the first dataset in the FITS file |
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115 | |
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116 | // read the relevant subset, defined by the first & last pixel ranges |
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117 | status = 0; |
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118 | if(fits_read_subsetnull_flt(fptr, colnum, numAxes, dimAxes, |
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119 | fpixel, lpixel, inc, |
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120 | pixarray, nullarray, &anynul, &status)){ |
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121 | duchampError("Cube Reader", |
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122 | "There was an error reading in the data array:"); |
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123 | fits_report_error(stderr, status); |
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124 | return FAILURE; |
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125 | } |
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126 | |
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127 | delete [] fpixel; |
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128 | delete [] lpixel; |
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129 | delete [] inc; |
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130 | |
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131 | if(anynul==0){ |
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132 | // no blank pixels, so don't bother with any trimming or checking... |
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133 | if(this->par.getFlagTrim()) { |
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134 | // if user requested fixing, inform them of change. |
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135 | duchampWarning("Cube Reader", |
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136 | "No blank pixels, so setting flagTrim to false.\n"); |
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137 | } |
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138 | this->par.setFlagBlankPix(false); |
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139 | this->par.setFlagTrim(false); |
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140 | } |
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141 | |
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142 | this->initialiseCube(dimAxes); |
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143 | this->saveArray(pixarray,npix); |
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144 | delete [] pixarray; |
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145 | delete [] dimAxes; |
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146 | this->par.setOffsets(this->head.WCS()); |
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147 | |
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148 | //------------------------------------------------------------- |
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149 | // Once the array is saved, change the value of the blank pixels |
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150 | // from 0 (as they are set by fits_read_subsetnull_flt) to the |
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151 | // correct blank value as determined by the above code. |
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152 | for(int i=0; i<npix;i++){ |
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153 | if(nullarray[i]==1) this->array[i] = this->par.getBlankPixVal(); |
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154 | } |
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155 | |
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156 | delete [] nullarray; |
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157 | // Close the FITS file -- not needed any more in this function. |
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158 | status = 0; |
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159 | fits_close_file(fptr, &status); |
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160 | if (status){ |
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161 | duchampWarning("Cube Reader","Error closing file: "); |
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162 | fits_report_error(stderr, status); |
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163 | } |
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164 | |
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165 | return SUCCESS; |
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166 | |
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167 | } |
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168 | |
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169 | } |
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