MSFitsInput.h

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//# MSFitsInput:  simple uvfits (random group) to MeasurementSet conversion
//# Copyright (C) 1996,1997,1998,1999,2000,2001,2002,2003
//# Associated Universities, Inc. Washington DC, USA.
//#
//# 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 Mass Ave, Cambridge, MA 02139, USA.
//#
//# Correspondence concerning AIPS++ should be addressed as follows:
//#        Internet email: aips2-request@nrao.edu.
//#        Postal address: AIPS++ Project Office
//#                        National Radio Astronomy Observatory
//#                        520 Edgemont Road
//#                        Charlottesville, VA 22903-2475 USA
//#
//# $Id: MSFitsInput.h 21531 2014-12-24 11:46:02Z gervandiepen $

#ifndef MS_MSFITSINPUT_H
#define MS_MSFITSINPUT_H

#include <casacore/casa/aips.h>
#include <casacore/casa/Arrays/Matrix.h>
#include <casacore/casa/Arrays/Vector.h>
#include <casacore/casa/Containers/Block.h>
#include <casacore/casa/Containers/Record.h>
#include <casacore/fits/FITS/fits.h>
#include <casacore/fits/FITS/hdu.h>
#include <casacore/casa/Logging/LogIO.h>
#include <casacore/ms/MeasurementSets/MeasurementSet.h>
#include <casacore/measures/Measures/MDirection.h>
#include <casacore/measures/Measures/MFrequency.h>
#include <casacore/casa/BasicSL/String.h>
#include <casacore/ms/MeasurementSets/MSTileLayout.h>
#include <casacore/tables/Tables/BaseTable.h>

namespace casacore { //# NAMESPACE CASACORE - BEGIN

class FitsInput;
class BinaryTable;
class MSColumns;

// <summary>
// A helper class for MSFitsInput
// </summary>
// <use visibility=local>
// <etymology>
// This class can hold a primary array of several datatypes
// </etymology>
// <synopsis>
// This is a helper class to avoid cumbersome switch statements on the
// template type of the primary array 
// It forwards all the PrimaryArray member functions we need in the filler.
// </synopsis>
class MSPrimaryTableHolder
{
  // This is a helper class to avoid cumbersome switch statements on the
  // template type of the primary array
  // It forwards all the PrimaryTable member function we need in the filler.
public:
  // Construct an empty holder, used to attach to later
  MSPrimaryTableHolder();

  // Construct from an input file containing a FITS primary group hdu.
  // Throws an exception if the datatype is not Short, FitsLong or Float
  MSPrimaryTableHolder(FitsInput& infile);

  ~MSPrimaryTableHolder();

  // Attach to the input file, create the appropriate PrimaryArray.
  // Throws an exception if the datatype is not Short, FitsLong or Float
  void attach(FitsInput& infile);

  // Detach from the input file
  void detach();

  //# forwarding functions

  // Number of dimensions
  Int dims()
  {return hdu_p->dims();}

  // Length of i'th axis
  Int dim(Int i)
  {return hdu_p->dim(i);}

  // Coordinate type
  Char* ctype(Int i)
  { return pf ? pf->ctype(i) : (pl ? pl->ctype(i) : ps->ctype(i));}

  // Coordinate reference value
  Double crval(Int i)
  { return pf ? pf->crval(i) : (pl ? pl->crval(i) : ps->crval(i));}

  // Coordinate reference pixel
  Double crpix(Int i)
  { return pf ? pf->crpix(i) : (pl ? pl->crpix(i) : ps->crpix(i));}

  // Coordinate delta
  Double cdelt(Int i)
  { return pf ? pf->cdelt(i) : (pl ? pl->cdelt(i) : ps->cdelt(i));}

  // Keyword of given type
  const FitsKeyword* kw(const FITS::ReservedName& n)
  { return hdu_p->kw(n);}

  // All keywords
  ConstFitsKeywordList& kwlist()
  { return hdu_p->kwlist();}

  // Advance to next keyword
  const FitsKeyword* nextkw()
  { return hdu_p->nextkw();}

  // Read the next group
  Int read() {
     if (pf) return pf->read(); 
     else if (pl) return pl->read(); 
     else if (ps) return ps->read(); 
     else if (pb) return pb->read(); 
     else cout << "can not read the table" << endl;
     return 0;
  }

private:
  HeaderDataUnit* hdu_p;
  PrimaryTable<Short>* ps;
  PrimaryTable<FitsLong>* pl;
  PrimaryTable<Float>* pf;
  PrimaryTable<uChar>* pb;
};

// <summary>
// A helper class for MSFitsInput
// </summary>
// <use visibility=local>
// <etymology>
// This class can hold a primary group of several datatypes
// </etymology>
// <synopsis>
// This is a helper class to avoid cumbersome switch statements on the
// template type of the primary group
// It forwards all the PrimaryGroup member functions we need in the filler.
// </synopsis>
class MSPrimaryGroupHolder
{
  // This is a helper class to avoid cumbersome switch statements on the
  // template type of the primary group
  // It forwards all the PrimaryGroup member function we need in the filler.
public:
  // Construct an empty holder, used to attach to later
  MSPrimaryGroupHolder();

  // Construct from an input file containing a FITS primary group hdu.
  // Throws an exception if the datatype is not Short, FitsLong or Float
  MSPrimaryGroupHolder(FitsInput& infile);

  ~MSPrimaryGroupHolder();

  // Attach to the input file, create the appropriate PrimaryGroup.
  // Throws an exception if the datatype is not Short, FitsLong or Float
  void attach(FitsInput& infile);

  // Detach from the input file
  void detach();

  //# forwarding functions

  // Number of dimensions
  Int dims()
  {return hdu_p->dims();}

  // Length of i'th axis
  Int dim(Int i)
  {return hdu_p->dim(i);}

  // Coordinate type
  Char* ctype(Int i)
  { return pf ? pf->ctype(i) : (pl ? pl->ctype(i) : ps->ctype(i));}

  // Coordinate reference value
  Double crval(Int i)
  { return pf ? pf->crval(i) : (pl ? pl->crval(i) : ps->crval(i));}

  // Coordinate reference pixel
  Double crpix(Int i)
  { return pf ? pf->crpix(i) : (pl ? pl->crpix(i) : ps->crpix(i));}

  // Coordinate delta
  Double cdelt(Int i)
  { return pf ? pf->cdelt(i) : (pl ? pl->cdelt(i) : ps->cdelt(i));}

  // Keyword of given type
  const FitsKeyword* kw(const FITS::ReservedName& n)
  { return hdu_p->kw(n);}

  // All keywords
  ConstFitsKeywordList& kwlist()
  { return hdu_p->kwlist();}

  // Advance to next keyword
  const FitsKeyword* nextkw()
  { return hdu_p->nextkw();}

  // Number of groups
  Int gcount() const
  { return pf ? pf->gcount() : ( pl ? pl->gcount() : ps->gcount());}

  // Number of parameters
  Int pcount() const
  { return pf ? pf->pcount() : ( pl ? pl->pcount() : ps->pcount());}

  // Parameter type
  Char* ptype(Int i) const
  { return pf ? pf->ptype(i) : ( pl ? pl->ptype(i) : ps->ptype(i));}

  // Read the next group
  Int read()
  { return pf ? pf->read() : ( pl ? pl->read() : ps->read());}

  // Get i'th parameter
  Double parm(Int i)
  { return pf ? pf->parm(i) : ( pl ? pl->parm(i) : ps->parm(i));}

  // Get group data with index i, scaled and converted to Double
  Double operator () (Int i) const
  { return pf ? (*pf)(i) : ( pl ? (*pl)(i) : (*ps)(i));}

private:
  HeaderDataUnit* hdu_p;
  PrimaryGroup<Short>* ps;
  PrimaryGroup<FitsLong>* pl;
  PrimaryGroup<Float>* pf;
};

// <summary>
// UV FITS to MeasurementSet filler
// </summary>

// <use visibility=export>

// <prerequisite>
//   <li> MeasurementSet
//   <li> FITS classes
// </prerequisite>
//
// <etymology>
// MSFitsInput handles the conversion of FITS files to MeasurementSets
// </etymology>
//
// <synopsis>
// UV FITS to MeasurementSet filler. This can handle single source fits and
// multi source fits as written by classic AIPS. Also copes with multiple
// arrays (i.e. multiple AN tables) but doesn't correct for 5 day offsets
// introduced by DBCON.
// </synopsis>

class MSFitsInput
{
  // This is an implementation helper class used to store 'local' data
  // during the filling process.
public:
  // Create from output and input file names. This function opens the input
  // file, and checks the output file is writable.
  MSFitsInput(const String& msFile, const String& fitsFile, const Bool NewNameStyle=False);

  // The destructor is fairly trivial.
  ~MSFitsInput();

  // Read all the data from the FITS file and create the MeasurementSet. Throws
  // an exception when it has severe trouble interpreting the FITS file.
  // 
  void readFitsFile(Int obsType = MSTileLayout::Standard);

  // A simultaneous change to MSFitsOutput means that no longer are
  // antenna positions being rotated when written to UVFITS. Calling
  // this method with b=True will perform the reverse of a rotation
  // when converting from uvfits to MS for relevant UVFITS files which
  // were written prior to this change. Else no rotation of antenna
  // positions is done.
  void rotateAntennaPositions(Bool b) {
      _rotateAnts = b;
  }

protected:

  // Check that the input is a UV fits file with required contents.
  // Returns False if not ok.
  Bool checkInput(FitsInput& infile);

  // Read the axis info of the primary group, throws an exception if required
  // axes are missing.
  void getPrimaryGroupAxisInfo();

  // Set up the MeasurementSet, including StorageManagers and fixed columns.
  // If useTSM is True, the Tiled Storage Manager will be used to store
  // DATA, FLAG and WEIGHT_SPECTRUM. Use obsType to choose the tiling
  // scheme.
  void setupMeasurementSet(const String& MSFileName, Bool useTSM=True,
               Int obsType = MSTileLayout::Standard);

  // Read a binary table extension of type AIPS AN and create an antenna table
  void fillAntennaTable(BinaryTable& bt);

  // Read a binary table extension and update history table
  void fillHistoryTable(ConstFitsKeywordList& kwl);

  // Read a binary table extension and update history table
  void fillObservationTable(ConstFitsKeywordList& kwl);

  //extract axis information
  void getAxisInfo(ConstFitsKeywordList&);

  //extract axis information
  void sortPolarizations();

  void fillPolarizationTable();

  //verify that the fits contains visibility data
  void checkRequiredAxis();

  void fillSpectralWindowTable(BinaryTable& bt);

  // fill Field table 
  void fillFieldTable(BinaryTable& bt);
  void fillFieldTable(double, double, String);

  void fillMSMainTable(BinaryTable& bt);

  void fillPointingTable();

  void fillSourceTable();

  // fill the Feed table with minimal info needed for synthesis processing
  void fillFeedTable();

  // Fill the Observation and ObsLog tables
  void fillObsTables();

  // Fill the main table from the Primary group data
  // if we have enough memory try to do it in mem
  void fillMSMainTableColWise(Int& nField, Int& nSpW);
  //else do it row by row
  void fillMSMainTable(Int& nField, Int& nSpW);

  // fill spectralwindow table from FITS FQ table + header info
  void fillSpectralWindowTable(BinaryTable& bt, Int nSpW);

  // fill spectralwindow table from header
  void fillSpectralWindowTable();

  // fill Field table from FITS SU table
  void fillFieldTable(BinaryTable& bt, Int nField);

  // fill Field table from header (single source fits)
  void fillFieldTable(Int nField);

  // fill the Pointing table (from Field table, all antennas are assumed
  // to point in the field direction) and possibly the Source table.
  void fillExtraTables();

  // fix up the EPOCH MEASURE_REFERENCE keywords using the value found
  // in the (last) AN table
  void fixEpochReferences();

  // Returns the Direction Measure reference for UVW and other appropriate columns
  // in msc_p (which must exist but have empty columns before you can set it!).
  MDirection::Types getDirectionFrame(Double epoch);
  
  // Check the frame if there is an SU table
  void setFreqFrameVar(BinaryTable& binTab);
  // update a the Spectral window post filling if necessary
  void updateSpectralWindowTable();

  void readRandomGroupUVFits(Int obsType);
  void readPrimaryTableUVFits(Int obsType);

private:
  //# The default constructor is private and undefined
  MSFitsInput();
  //# The copy constructor is private and undefined
  MSFitsInput(const MSFitsInput& other);
  //# The assignment operator is private and undefined
  MSFitsInput& operator=(const MSFitsInput& other);

  FitsInput* _infile;
  String _msFile;
  MSPrimaryGroupHolder _priGroup;
  MSPrimaryTableHolder _priTable;
  MeasurementSet _ms;
  MSColumns* _msc;
  Int _nIF;
  Vector<Int> _nPixel, _corrType;
  Block<Int> _corrIndex;
  Matrix<Int> _corrProduct;
  Vector<String> _coordType;
  Vector<Double> _refVal, _refPix, _delta;
  String _array, _object, _timsys;
  Double _epoch;
  MDirection::Types _epochRef; // This is a direction measure reference code
                                // determined by epoch_p, hence the name and type.
  // unique antennas found in the visibility data
  // NOTE These are 1-based
  std::set<Int> _uniqueAnts;
  // number of rows in the created MS ANTENNA table
  Int _nAntRow;
  Int _nArray;
  Vector<Double> _receptorAngle;
  MFrequency::Types _freqsys;
  Double _restfreq; // used for images
  Bool _addSourceTable;
  LogIO _log;
  Record _header;
  Double _refFreq;
  Bool _useAltrval;
  Vector<Double> _chanFreq;
  Bool _newNameStyle;
  Vector<Double> _obsTime;

  Matrix<Double> _restFreq; // used for UVFITS
  Matrix<Double> _sysVel;
  Bool _msCreated, _rotateAnts;

  std::pair<Int, Int> _extractAntennas(Float baseline);

};


} //# NAMESPACE CASACORE - END

#endif