//#---------------------------------------------------------------------------
//# SDFITSImageWriter.cc: ASAP class to write out single dish spectra as FITS images
//#---------------------------------------------------------------------------
//# Copyright (C) 2004
//# 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.
//#
//# This program 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 this program; if not, write to the Free Software Foundation, Inc.,
//# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
//#
//# Correspondence concerning this software should be addressed as follows:
//#        Internet email: Malte.Marquarding@csiro.au
//#        Postal address: Malte Marquarding,
//#                        Australia Telescope National Facility,
//#                        P.O. Box 76,
//#                        Epping, NSW, 2121,
//#                        AUSTRALIA
//#
//# $Id: SDFITSImageWriter.cc 901 2006-03-10 02:29:22Z mar637 $
//#---------------------------------------------------------------------------

#include "SDFITSImageWriter.h"

#include <casa/aips.h>
#include <casa/Arrays/Array.h>
#include <casa/Arrays/Vector.h>
#include <casa/Arrays/VectorIter.h>
#include <casa/Utilities/CountedPtr.h>
#include <casa/OS/Directory.h>

#include <coordinates/Coordinates/CoordinateUtil.h>
#include <coordinates/Coordinates/CoordinateSystem.h>
#include <coordinates/Coordinates/SpectralCoordinate.h>
#include <coordinates/Coordinates/DirectionCoordinate.h>
#include <coordinates/Coordinates/StokesCoordinate.h>
#include <coordinates/Coordinates/ObsInfo.h>

#include <images/Images/ImageFITSConverter.h>
#include <images/Images/TempImage.h>

#include <lattices/Lattices/ArrayLattice.h>

#include <measures/Measures/MEpoch.h>
#include <measures/Measures/Stokes.h>

#include <tables/Tables/Table.h>
#include <tables/Tables/ScalarColumn.h>
#include <tables/Tables/ArrayColumn.h>

#include "STDefs.h"
#include "STHeader.h"
#include "SDMemTable.h"
#include "SDPol.h"

using namespace casa;
using namespace asap;


SDFITSImageWriter::SDFITSImageWriter()
{;}

SDFITSImageWriter::~SDFITSImageWriter()
{;}


Bool SDFITSImageWriter::write(const SDMemTable& sdTable, 
                              const String& dirName, Bool toStokes,
                              Bool verbose)
{

// Get global Header from Table

   STHeader header = sdTable.getSTHeader();
   MEpoch::Ref timeRef(sdTable.getTimeReference());
   MDirection::Types dirRef = sdTable.getDirectionReference();

// Prepare initial ObsInfo

   ObsInfo oi;
   oi.setTelescope(String(header.antennaname));
   oi.setObserver(String(header.observer));

// Column keywords

   Table tab = sdTable.table();
   ROArrayColumn<Double> dirCol(tab, String("DIRECTION"));
   ROScalarColumn<Double> timeCol(tab, "TIME");
   ROArrayColumn<uInt> freqidCol(tab, "FREQID");
   ROArrayColumn<uInt> restfreqidCol(tab, "RESTFREQID");
   ROScalarColumn<String> srcCol(tab, "SRCNAME");

// Output Image Shape; spectral axis to be updated

   IPosition shapeOut(4,1);                 // spectral, direction (2), stokes

// Axes (should be in header)

   const uInt beamAxis = asap::BeamAxis;
   const uInt ifAxis = asap::IFAxis;
   const uInt stokesAxis = asap::PolAxis;
   const uInt chanAxis = asap::ChanAxis;
   const Unit RAD(String("rad"));

// Output Directory

   String dirName2(dirName);
   if (dirName.length()==0) {
      dirName2 = String("asap_FITS");
   }
   Directory dir(dirName2);
   dir.create(True);
   ostringstream oss;
   oss << "Created directory '" << dirName2 << "' for output files";

   // Temps

   Vector<Int> whichStokes(1,1);
   Array<Double> whichDir;
   Vector<Double> lonLat(2);
   IPosition posDir(2,0);
   Projection proj(Projection::SIN);                   // What should we use ?
   Matrix<Double> xForm(2,2);
   xForm = 0.0; xForm.diagonal() = 1.0;
   Vector<Double> incLonLat(2,0.0);
   Vector<Double> refPixLonLat(2,0.0);

// Do we have linear or circular ?  No way to know yet...

   Bool linear = True;

// Loop over rows

   uInt maxMem = 128;
   Bool preferVelocity = False;
   Bool opticalVelocity = False;
   Int bitPix = -32;                     // FLoating point
   Float minPix = 1.0;
   Float maxPix = -1.0;
   Bool overWrite = True;
   Bool degLast = False;
   Bool reallyVerbose = False;
//
   String errMsg;
   const uInt nRows = sdTable.nRow();
   for (uInt iRow=0; iRow<nRows; iRow++) {

// Get data converted to Stokes

      const MaskedArray<Float>& dataIn(sdTable.rowAsMaskedArray(iRow,toStokes));
      const Array<Float>& values = dataIn.getArray();
      const Array<Bool>& mask = dataIn.getMask();
      const IPosition& shapeIn = dataIn.shape();
      shapeOut(0) = shapeIn(chanAxis);
      TiledShape tShapeOut(shapeOut);

// Update ObsInfo (time changes per integration)

      Double dTmp;
      timeCol.get(iRow, dTmp);
      MVEpoch tmp2(Quantum<Double>(dTmp, Unit(String("d"))));
      MEpoch epoch(tmp2, timeRef);
      oi.setObsDate(epoch);

// Iterate through data in this row by spectra

      ReadOnlyVectorIterator<Float> itData(values, chanAxis);
      ReadOnlyVectorIterator<Bool> itMask(mask, chanAxis);
      while (!itData.pastEnd()) {
         const IPosition& pos = itData.pos();

// Form SpectralCoordinate 

         Vector<uInt> iTmp;
         freqidCol.get(iRow, iTmp);
         uInt freqID = iTmp(pos(ifAxis));
//
         restfreqidCol.get(iRow, iTmp);
         uInt restFreqID = iTmp(pos(ifAxis));
//
         SpectralCoordinate sC = sdTable.getSpectralCoordinate(freqID, restFreqID, iRow);

// Form DirectionCoordinate
 
         dirCol.get(iRow, whichDir);
         posDir(0) = pos(beamAxis);
         posDir(1) = 0;
         lonLat[0] = whichDir(posDir);
//
         posDir(0) = pos(beamAxis);
         posDir(1) = 1;
         lonLat[1] = whichDir(posDir);
         DirectionCoordinate dC(dirRef, proj, lonLat[0], lonLat[1],
                               incLonLat[0], incLonLat[1], xForm, 
                               refPixLonLat[0], refPixLonLat[1]);

// Form Stokes Coordinate (Stokes info still sketchy);

         Stokes::StokesTypes stokes = SDPolUtil::convertStokes(pos(stokesAxis), toStokes, linear);
         String stokesName = Stokes::name(stokes);
         whichStokes(0) = Int(stokes);
         StokesCoordinate stC(whichStokes);

// Create CoordinateSystem

         CoordinateSystem cSys;
         cSys.addCoordinate(sC);
         cSys.addCoordinate(dC);
         cSys.addCoordinate(stC);
         cSys.setObsInfo(oi);

// Reform data into correct shape for output

         Array<Float> t1(itData.array().reform(shapeOut));
         Array<Bool> m1(itMask.array().reform(shapeOut));

// Create aips++ Image

         TempImage<Float> tIm(tShapeOut, cSys);
         tIm.put(t1);
//
         ArrayLattice<Bool> latMask(m1);
         tIm.attachMask(latMask);

// Write out as FITS Image file

         ostringstream oss2;
         oss2 << "row" << iRow << "_beam" << pos(0) << "_if" 
	     << pos(1) << "_" << stokesName  << "_" << srcCol(iRow) << ".fits";
         String tS(oss2);
         String fileName = dirName2 + String("/") + tS;
         if (verbose) oss << endl << "Writing row " << iRow 
			   << " into file '" << tS << "'";
//
         Bool ok = ImageFITSConverter::ImageToFITS(errMsg, tIm, fileName, 
						   maxMem, preferVelocity,
						   opticalVelocity, bitPix, 
						   minPix, maxPix, overWrite,
						   degLast, reallyVerbose);
         if (!ok) {
	   oss << endl<< "Error writing fits - " << errMsg;
         }

// Next spectrum

         itData.next();
         itMask.next();
      }
   }
//
   if (!verbose) {
     oss << endl<< "Wrote " << nRows << " into individual FITS files";
   }
   pushLog(String(oss));
   return True;
}