source: trunk/src/FitsIO/wcsIO.cc @ 356

// -----------------------------------------------------------------------
// 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 <stdlib.h>
#include <wcs.h>
#include <wcshdr.h>
#include <fitshdr.h>
#include <wcsfix.h>
#include <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.hh>
#include <fitsHeader.hh>
#include <Cubes/cubes.hh>

int 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());
    }

    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 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.

      std::cerr << specType << "\n";

      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)
    
    // Save the wcs to the FitsHeader class that is running this function
    this->setWCS(localwcs);
    this->setNWCS(localnwcs);

  }

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

  // Get the brightness unit, so that we can set the units for the 
  //  integrated flux when we go to fixUnits.
  this->readBUNIT(fname);

  if(localwcs->spec>=0) this->fixUnits(par);

  return SUCCESS;

}