source: trunk/src/FitsIO/wcsIO.cc @ 864

// -----------------------------------------------------------------------
// wcsIO.cc: Get the World Coordinate System for a particular FITS file.
// -----------------------------------------------------------------------
// Copyright (C) 2006, Matthew Whiting, ATNF
//
// This program is free software; you can redistribute it and/or modify it
// under the terms of the GNU General Public License as published by the
// Free Software Foundation; either version 2 of the License, or (at your
// option) any later version.
//
// Duchamp is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
// FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
// for more details.
//
// You should have received a copy of the GNU General Public License
// along with Duchamp; if not, write to the Free Software Foundation,
// Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA
//
// Correspondence concerning Duchamp may be directed to:
//    Internet email: Matthew.Whiting [at] atnf.csiro.au
//    Postal address: Dr. Matthew Whiting
//                    Australia Telescope National Facility, CSIRO
//                    PO Box 76
//                    Epping NSW 1710
//                    AUSTRALIA
// -----------------------------------------------------------------------
#include <iostream>
#include <string>
#include <string.h>
#include <stdlib.h>
#include <wcslib/wcs.h>
#include <wcslib/wcshdr.h>
#include <wcslib/fitshdr.h>
#include <wcslib/wcsfix.h>
#include <wcslib/wcsunits.h>
#define WCSLIB_GETWCSTAB // define this so that we don't try and redefine 
                         //  wtbarr (this is a problem when using gcc v.4+
#include <fitsio.h>
#include <math.h>
#include <duchamp/duchamp.hh>
#include <duchamp/fitsHeader.hh>
#include <duchamp/Cubes/cubes.hh>

namespace duchamp
{

  OUTCOME FitsHeader::defineWCS(std::string fname, Param &par)
  {
    ///   A function that reads the WCS header information from the 
    ///    FITS file given by fname
    ///   It will also sort out the spectral axis, and covert to the correct 
    ///    velocity type, or frequency type if need be.
    ///   It calls FitsHeader::readBUNIT so that the Integrated Flux units can
    ///    be calculated by FitsHeader::fixUnits.
    /// \param fname Fits file to read.
    /// \param par Param set to help fix the units with.

    fitsfile *fptr;
    int numAxes;
    int noComments = 1; //so that fits_hdr2str will ignore COMMENT, HISTORY etc
    int nExc = 0,nkeys;
    char *hdr;

    // Open the FITS file
    int status = 0;
    if( fits_open_file(&fptr,fname.c_str(),READONLY,&status) ){
      fits_report_error(stderr, status);
      return FAILURE;
    }

    // Get the dimensions of the FITS file -- number of axes and size of each.
    status = 0;
    if(fits_get_img_dim(fptr, &numAxes, &status)){
      fits_report_error(stderr, status);
      return FAILURE;
    }
    long *dimAxes = new long[numAxes];
    for(int i=0;i<numAxes;i++) dimAxes[i]=1;
    status = 0;
    if(fits_get_img_size(fptr, numAxes, dimAxes, &status)){
      fits_report_error(stderr, status);
      return FAILURE;
    }

    // Read in the entire PHU of the FITS file to a std::string.
    // This will be read by the wcslib functions to extract the WCS.
    status = 0;
    fits_hdr2str(fptr, noComments, NULL, nExc, &hdr, &nkeys, &status);
    if( status ){
      duchampWarning("Cube Reader",
                     "Error whilst reading FITS header to string: ");
      fits_report_error(stderr, status);
      return FAILURE;
    }

    // Close the FITS file -- not needed any more in this function.
    status = 0;
    fits_close_file(fptr, &status);
    if (status){
      duchampWarning("Cube Reader","Error closing file: ");
      fits_report_error(stderr, status);
    }
  
    // Define a temporary, local version of the WCS
    struct wcsprm *localwcs;
    localwcs = (struct wcsprm *)calloc(1,sizeof(struct wcsprm));
    localwcs->flag=-1;

    // Initialise this temporary wcsprm structure
    status = wcsini(true, numAxes, localwcs);
    if(status){
      std::stringstream errmsg;
      errmsg << "wcsini failed! Code=" << status
             << ": " << wcs_errmsg[status] << std::endl;
      duchampError("Cube Reader",errmsg.str());
      return FAILURE;
    }

    this->naxis=0;
    for(int i=0;i<numAxes;i++)
      if(dimAxes[i]>1) this->naxis++;

    int relax=1; // for wcspih -- admit all recognised informal WCS extensions
    int ctrl=2;  // for wcspih -- report each rejected card and its reason for rejection
    int localnwcs, nreject;
    // Parse the FITS header to fill in the wcsprm structure
    status=wcspih(hdr, nkeys, relax, ctrl, &nreject, &localnwcs, &localwcs);
    if(status){
      // if here, something went wrong -- report what.
      std::stringstream errmsg;
      errmsg << "wcspih failed!\nWCSLIB error code=" << status
             << ": " << wcs_errmsg[status] << std::endl;
      duchampWarning("Cube Reader",errmsg.str());
    }
    else{  
      int stat[NWCSFIX];
      // Applies all necessary corrections to the wcsprm structure
      //  (missing cards, non-standard units or spectral types, ...)
      status = wcsfix(1, (const int*)dimAxes, localwcs, stat);
      if(status) {
        std::stringstream errmsg;
        errmsg << "wcsfix failed:\n";
        errmsg << "Function status returns are:\n";
        for(int i=0; i<NWCSFIX; i++)
          if (stat[i] > 0) 
            errmsg << i+1 << ": WCSFIX error code=" << stat[i] << ": "
                   << wcsfix_errmsg[stat[i]] << std::endl;
        duchampWarning("Cube Reader", errmsg.str() );
      }
      // Set up the wcsprm struct. Report if something goes wrong.
      status = wcsset(localwcs);
      if(status){
        std::stringstream errmsg;
        errmsg<<"wcsset failed!\n"
              <<"WCSLIB error code=" << status 
              <<": "<<wcs_errmsg[status] << std::endl;
        duchampWarning("Cube Reader",errmsg.str());
      }
      else{

        int stat[NWCSFIX];
        // Re-do the corrections to account for things like NCP projections
        status = wcsfix(1, (const int*)dimAxes, localwcs, stat);
        if(status) {
          std::stringstream errmsg;
          errmsg << "wcsfix failed:\n";
          errmsg << "Function status returns are:\n";
          for(int i=0; i<NWCSFIX; i++)
            if (stat[i] > 0) 
              errmsg << i+1 << ": WCSFIX error code=" << stat[i] << ": "
                     << wcsfix_errmsg[stat[i]] << std::endl;
          duchampWarning("Cube Reader", errmsg.str() );
        }

        if(localwcs->spec>=0){ //if there is a spectral axis

          int index = localwcs->spec;
          std::string desiredType="",specType = localwcs->ctype[index];
          std::string shortType = specType.substr(0,4);
          if(shortType=="VELO" || shortType=="VOPT" || shortType=="ZOPT" 
             || shortType=="VRAD" || shortType=="BETA"){
            if(localwcs->restfrq != 0){
              // Set the spectral axis to a standard specification: VELO-F2V
              desiredType = duchampVelocityType;
              if(localwcs->restwav == 0) 
                localwcs->restwav = 299792458.0 /  localwcs->restfrq;
              this->spectralDescription = duchampSpectralDescription[VELOCITY];
            }
            else{
              // No rest frequency defined, so just use given specification
              desiredType = specType;
              this->spectralDescription = duchampSpectralDescription[VELOCITY];
            }
          }
          else if (shortType=="FREQ" && localwcs->restfrq!=0){
            // No rest frequency defined, so put spectral dimension in frequency. 
            // Set the spectral axis to a standard specification: FREQ
            duchampWarning("Cube Reader",
                           "No rest frequency defined. Using frequency units in spectral axis.\n");
            desiredType = duchampFrequencyType;
            par.setSpectralUnits("MHz");
            if(strcmp(localwcs->cunit[index],"")==0){
              duchampWarning("Cube Reader",
                             "No frequency unit given. Assuming frequency axis is in Hz.\n");
              strcpy(localwcs->cunit[index],"Hz");
            }
            this->spectralDescription = duchampSpectralDescription[FREQUENCY];
          }
          else {
            desiredType = duchampFrequencyType;
            par.setSpectralUnits("MHz");
            if(strcmp(localwcs->cunit[index],"")==0){
              duchampWarning("Cube Reader",
                             "No frequency unit given. Assuming frequency axis is in Hz.\n");
              strcpy(localwcs->cunit[index],"Hz");
            }
            this->spectralDescription = duchampSpectralDescription[FREQUENCY];
          }     

          // Now we need to make sure the spectral axis has the correct setup.
          //  We use wcssptr to translate it if it is not of the desired type,
          //  or if the spectral units are not defined.

          bool needToTranslate = false;

          if(strncmp(specType.c_str(),desiredType.c_str(),4)!=0) 
            needToTranslate = true;

          std::string blankstring = "";
          if(strcmp(localwcs->cunit[localwcs->spec],blankstring.c_str())==0)
            needToTranslate = true;

          if(needToTranslate){

            if(strcmp(localwcs->ctype[localwcs->spec],"VELO")==0)
              strcpy(localwcs->ctype[localwcs->spec],"VELO-F2V");

            index = localwcs->spec;
        
            status = wcssptr(localwcs, &index, (char *)desiredType.c_str());
            if(status){
              std::stringstream errmsg;
              errmsg<< "WCSSPTR failed! Code=" << status << ": "
                    << wcs_errmsg[status] << std::endl
                    << "(wanted to convert from type \"" << specType
                    << "\" to type \"" << desiredType << "\")\n";
              duchampWarning("Cube Reader",errmsg.str());

            }

          }
    
        } // end of if(localwcs->spec>=0)
        else if(localwcs->naxis>2){

          par.setSpectralUnits( wcs->cunit[2] );
          this->spectralDescription = wcs->ctype[2];

        }
          
        // Save the wcs to the FitsHeader class that is running this function
        this->setWCS(localwcs);
        this->setNWCS(localnwcs);
 
        // Now that the WCS is defined, use it to set the offsets in the Param set
        par.setOffsets(localwcs);

      }
    }

    // work out whether the array is 2dimensional
    if(localwcs->naxis==2) this->flag2D = true;
    else{
      int numDim=0;
      for(int i=0;i<numAxes;i++) if(dimAxes[i]>1) numDim++;
      this->flag2D = (numDim<=2);
    }

    // clean up allocated memory
    wcsvfree(&localnwcs,&localwcs);
    wcsfree(localwcs);
    free(localwcs);
    free(hdr);
    delete [] dimAxes;

    return SUCCESS;

  }

}