[299] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // getImage.cc: Read in a FITS file to 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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[3] | 28 | #include <iostream> |
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| 29 | #include <string> |
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[142] | 30 | #include <string.h> |
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[394] | 31 | #include <wcslib/wcs.h> |
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| 32 | #include <wcslib/wcshdr.h> |
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[400] | 33 | #include <wcslib/fitshdr.h> |
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[394] | 34 | #include <wcslib/wcsfix.h> |
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| 35 | #include <wcslib/wcsunits.h> |
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[142] | 36 | #define WCSLIB_GETWCSTAB // define this so that we don't try and redefine |
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[321] | 37 | // wtbarr (this is a problem when using gcc v.4+) |
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[66] | 38 | #include <fitsio.h> |
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[69] | 39 | #include <math.h> |
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[393] | 40 | #include <duchamp/duchamp.hh> |
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| 41 | #include <duchamp/param.hh> |
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| 42 | #include <duchamp/fitsHeader.hh> |
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| 43 | #include <duchamp/Cubes/cubes.hh> |
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[3] | 44 | |
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[378] | 45 | namespace duchamp |
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[3] | 46 | { |
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| 47 | |
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[378] | 48 | std::string imageType[4] = {"point", "spectrum", "image", "cube"}; |
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[3] | 49 | |
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[698] | 50 | OUTCOME Cube::getMetadata() |
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[528] | 51 | { |
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| 52 | /// @details |
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| 53 | /// A front-end to the Cube::getMetadata() function, that does |
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| 54 | /// subsection checks. Does the flux unit conversion if the user |
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| 55 | /// has requested it. Assumes the Param is set up properly. |
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| 56 | |
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[910] | 57 | // int exists; |
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| 58 | // fits_file_exists(fname.c_str(),&exists,&status); |
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| 59 | // if(exists<=0){ |
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| 60 | // fits_report_error(stderr, status); |
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[913] | 61 | // DUCHAMPERROR("Cube Reader", Requested image (" << fname << ") does not exist!); |
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[910] | 62 | // return FAILURE; |
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| 63 | // } |
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| 64 | if(this->par.checkImageExists() == FAILURE) return FAILURE; |
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| 65 | |
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[442] | 66 | std::string fname = par.getImageFile(); |
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| 67 | if(par.getFlagSubsection()) fname+=par.getSubsection(); |
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[443] | 68 | |
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[971] | 69 | this->head.openFITS(fname); |
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| 70 | |
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[698] | 71 | OUTCOME result = getMetadata(fname); |
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[443] | 72 | |
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| 73 | if(result==SUCCESS){ |
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| 74 | // Convert the flux Units if the user has so requested |
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[899] | 75 | this->convertFluxUnits(this->head.getFluxUnits(),this->par.getNewFluxUnits()); |
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[443] | 76 | } |
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| 77 | |
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[971] | 78 | this->head.closeFITS(); |
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| 79 | |
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[443] | 80 | return result; |
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[442] | 81 | } |
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| 82 | //-------------------------------------------------------------------- |
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| 83 | |
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[698] | 84 | OUTCOME Cube::getMetadata(std::string fname) |
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[378] | 85 | { |
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[528] | 86 | /// @details |
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| 87 | /// Read in the metadata associated with the cube from the file |
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| 88 | /// fname (assumed to be in FITS format). Function is a front end |
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| 89 | /// to the I/O functions in the FitsIO/ directory. This function |
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| 90 | /// will check that the file exists, report the dimensions and |
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| 91 | /// then get other functions to read the WCS and necessary header |
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| 92 | /// keywords. This function does not read in the data array -- |
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| 93 | /// that is done by Cube::getCube(). Note that no conversion of |
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| 94 | /// flux units is done -- you need to call Cube::getMetadata() or |
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| 95 | /// do it separately. |
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| 96 | /// \param fname A std::string with name of FITS file. |
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| 97 | /// \return SUCCESS or FAILURE. |
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[168] | 98 | |
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[378] | 99 | int numAxes, status = 0; /* MUST initialize status */ |
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| 100 | |
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| 101 | // Read the size information -- number and lengths of all axes. |
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| 102 | // Just use this for reporting purposes. |
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| 103 | status = 0; |
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[971] | 104 | if(fits_get_img_dim(this->head.FPTR(), &numAxes, &status)){ |
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[378] | 105 | fits_report_error(stderr, status); |
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| 106 | return FAILURE; |
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| 107 | } |
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[973] | 108 | |
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[944] | 109 | this->head.setNumAxes(numAxes); |
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[378] | 110 | long *dimAxes = new long[numAxes]; |
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| 111 | for(int i=0;i<numAxes;i++) dimAxes[i]=1; |
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| 112 | status = 0; |
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[971] | 113 | if(fits_get_img_size(this->head.FPTR(), numAxes, dimAxes, &status)){ |
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[378] | 114 | fits_report_error(stderr, status); |
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| 115 | return FAILURE; |
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| 116 | } |
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[443] | 117 | |
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[378] | 118 | // Report the size of the FITS file |
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| 119 | if(this->par.isVerbose()){ |
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| 120 | std::cout << "Dimensions of FITS file: "; |
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| 121 | int dim = 0; |
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| 122 | std::cout << dimAxes[dim]; |
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| 123 | while(dim+1<numAxes) std::cout << "x" << dimAxes[++dim]; |
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| 124 | std::cout << std::endl; |
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| 125 | } |
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[103] | 126 | |
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[570] | 127 | |
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[378] | 128 | // Get the WCS information |
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[971] | 129 | if(this->head.defineWCS(this->par) == FAILURE) return FAILURE; |
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[103] | 130 | |
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[795] | 131 | // Read the necessary header information, and copy some of it into the Param. |
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[971] | 132 | if(this->head.readHeaderInfo(this->par) == FAILURE){ |
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| 133 | DUCHAMPWARN("Cube Reader", "Problems with metadata, but will press on..."); |
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[945] | 134 | } |
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[795] | 135 | |
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[378] | 136 | if(!this->head.isWCS()) |
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[913] | 137 | DUCHAMPWARN("Cube Reader","WCS is not good enough to be used.\n"); |
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[3] | 138 | |
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[508] | 139 | // allocate the dimension array in the Cube. |
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[700] | 140 | if(this->initialiseCube(dimAxes,false) == FAILURE) return FAILURE; |
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[508] | 141 | |
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| 142 | delete [] dimAxes; |
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| 143 | |
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[442] | 144 | return SUCCESS; |
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| 145 | |
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| 146 | } |
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| 147 | //-------------------------------------------------------------------- |
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| 148 | |
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| 149 | |
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[698] | 150 | OUTCOME Cube::getCube(std::string fname) |
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[442] | 151 | { |
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[528] | 152 | /// @details |
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| 153 | /// Read in a cube from the file fname (assumed to be in FITS |
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| 154 | /// format). Function is a front end to the data I/O function in |
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| 155 | /// the FitsIO/ directory. This function calls the getMetadata() |
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| 156 | /// function, then reads in the actual data array. |
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| 157 | /// \param fname A std::string with name of FITS file. |
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| 158 | /// \return SUCCESS or FAILURE. |
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[442] | 159 | |
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[971] | 160 | this->head.openFITS(fname); |
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| 161 | |
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[700] | 162 | if(this->getMetadata(fname) == FAILURE) return FAILURE; |
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[442] | 163 | |
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[378] | 164 | // Get the data array from the FITS file. |
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| 165 | // Report the dimensions of the data array that was read (this can be |
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| 166 | // different to the full FITS array). |
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| 167 | if(this->par.isVerbose()) std::cout << "Reading data ... "<<std::flush; |
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[971] | 168 | if(this->getFITSdata() == FAILURE) return FAILURE; |
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[443] | 169 | |
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[378] | 170 | if(this->par.isVerbose()){ |
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| 171 | std::cout << "Done. Data array has dimensions: "; |
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| 172 | std::cout << this->axisDim[0]; |
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[978] | 173 | std::cout <<"x"<< this->axisDim[1]; |
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[378] | 174 | if(this->axisDim[2]>1) std::cout <<"x"<< this->axisDim[2]; |
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| 175 | std::cout << "\n"; |
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| 176 | } |
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[46] | 177 | |
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[434] | 178 | // Convert the flux Units if the user has so requested |
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[899] | 179 | this->convertFluxUnits(this->head.getFluxUnits(),this->par.getNewFluxUnits(),ARRAY); |
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[434] | 180 | |
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[971] | 181 | this->head.closeFITS(); |
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| 182 | |
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[442] | 183 | return SUCCESS; |
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[3] | 184 | |
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[378] | 185 | } |
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[442] | 186 | //-------------------------------------------------------------------- |
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[378] | 187 | |
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[434] | 188 | |
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[899] | 189 | void Cube::convertFluxUnits(std::string oldUnit, std::string newUnit, ARRAYREF whichArray) |
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[434] | 190 | { |
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[528] | 191 | /// @details |
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| 192 | /// If the user has requested new flux units (via the input |
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| 193 | /// parameter newFluxUnits), this function converts the units |
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| 194 | /// given by BUNIT to those given by newFluxUnits. If no simple |
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| 195 | /// conversion can be found (by using wcsunits()) then nothing is |
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| 196 | /// done and the user is informed, otherwise the |
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| 197 | /// FitsHeader::fluxUnits parameter is updated and the pixel array |
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| 198 | /// is converted accordingly. |
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[434] | 199 | |
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[899] | 200 | if(newUnit!=""){ |
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[434] | 201 | |
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[443] | 202 | if(oldUnit != newUnit){ |
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[434] | 203 | |
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[443] | 204 | if(this->par.isVerbose()){ |
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| 205 | std::cout << "Converting flux units from " << oldUnit << " to " << newUnit << "... "; |
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| 206 | std::cout << std::flush; |
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| 207 | } |
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[434] | 208 | |
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[443] | 209 | double scale,offset,power; |
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| 210 | int status = wcsunits(oldUnit.c_str(), newUnit.c_str(), &scale, &offset, &power); |
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| 211 | |
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| 212 | if(status==0){ |
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[434] | 213 | |
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[443] | 214 | this->head.setFluxUnits( newUnit ); |
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| 215 | this->head.setIntFluxUnits(); |
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[434] | 216 | |
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[899] | 217 | if(whichArray == ARRAY){ |
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| 218 | if(this->arrayAllocated){ |
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| 219 | for(size_t i=0;i<this->numPixels;i++) |
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| 220 | if(!this->isBlank(i)) this->array[i] = pow(scale * this->array[i] + offset, power); |
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| 221 | } |
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[496] | 222 | } |
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[899] | 223 | else if(whichArray==RECON){ |
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| 224 | if(this->reconAllocated){ |
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| 225 | for(size_t i=0;i<this->numPixels;i++) |
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| 226 | if(!this->isBlank(i)) this->recon[i] = pow(scale * this->recon[i] + offset, power); |
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| 227 | } |
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| 228 | } |
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| 229 | else if(whichArray==BASELINE){ |
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| 230 | if(this->baselineAllocated){ |
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| 231 | for(size_t i=0;i<this->numPixels;i++) |
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| 232 | if(!this->isBlank(i)) this->baseline[i] = pow(scale * this->baseline[i] + offset, power); |
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| 233 | } |
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| 234 | } |
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[443] | 235 | if(this->par.isVerbose()) { |
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| 236 | std::cout << " Done.\n"; |
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| 237 | } |
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[434] | 238 | } |
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[443] | 239 | else{ |
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| 240 | if(this->par.isVerbose()) std::cout << "\n"; |
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[913] | 241 | DUCHAMPWARN("convertFluxUnits", "Could not convert units from " << oldUnit << " to " << newUnit << ". Leaving BUNIT as " << oldUnit); |
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[443] | 242 | } |
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[434] | 243 | } |
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| 244 | } |
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| 245 | |
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| 246 | } |
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| 247 | |
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| 248 | |
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[3] | 249 | } |
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