// $Id:Index2NC.java 63 2006-07-12 21:50:51Z edavis $
/*
 * Copyright 1997-2006 Unidata Program Center/University Corporation for
 * Atmospheric Research, P.O. Box 3000, Boulder, CO 80307,
 * support@unidata.ucar.edu.
 *
 * This library is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation; either version 2.1 of the License, or (at
 * your option) any later version.
 *
 * This library 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 Lesser
 * General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; if not, strlenwrite to the Free Software Foundation,
 * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 */
package ucar.nc2.iosp.bufr;

import ucar.bufr.*;
import ucar.nc2.*;
import ucar.nc2.dataset.conv._Coordinate;
import ucar.nc2.util.CancelTask;
import ucar.ma2.DataType;

import java.io.PrintStream;
import java.util.*;

/**
 * Netcdf header reading and writing for version 3 file format.
 */

public class Index2NC {

  private ucar.nc2.NetcdfFile ncfile;
  private PrintStream out = System.out;
  private Structure recordStructure = null, levelStructure = null;
  private boolean setTime = true, setLat = true, setLon = true, setHgt = true;
  private HashMap dimensions = new HashMap();
  private ArrayList parameters;


  void open( Index index, ucar.nc2.NetcdfFile ncf, CancelTask cancelTask ) {

    ncfile = ncf;
    HashMap atts = index.getGlobalAttributes();
    // find out what type of dataset, so proper ncfile structure can be created
    boolean pointDS = false, stationDS = false, trajectoryDS = false, satelliteDS = false;
    String category = (String)atts.get( "category");
    if( category.startsWith( "4 Single")) {
      trajectoryDS = true;
    } else if( category.startsWith( "2 Vertical")) {
      stationDS = true;
    } else if( category.startsWith( "3 Vertical")) {
      satelliteDS = true;
    } else {
      pointDS = true;
    }
    // parameters in this DS
    parameters = index.getParameters();

    recordStructure = new Structure(ncfile, ncfile.getRootGroup(), null, "record");

   // global Dimensions / Attributes
  /**
   * Dimensions have:
   * name name must be unique within group. Can be null only if not shared.
   * length length, or UNLIMITED.length or UNKNOWN.length
   * isShared whether its shared or local to Variable.
   * isUnlimited whether the length can grow.
   * isVariableLength whether the length is unknown until the data is read.
   */
    Dimension stnsDim = null, levelsDim = null, trajsDim = null;
    if( stationDS ) {
       stnsDim = new Dimension("stns", index.getLocations().size(), true, false, false);
       ncfile.addDimension( null, stnsDim );
       //levelsDim = new Dimension("levels", Dimension.UNKNOWN.getLength(), true, false, true);
       //ncfile.addDimension( null, levelsDim );
    } else if( trajectoryDS ) {
       trajsDim = new Dimension("trajectories", index.getLocations().size(), true, false, false);
       ncfile.addDimension( null, trajsDim );
    } else if( satelliteDS ) {
       levelsDim = new Dimension("levels", 41, true, false, false);
       ncfile.addDimension( null, levelsDim );
    }

    Dimension obsDim = new Dimension("obs", index.getNumberObs(), true, true, false);
    ncfile.addDimension( null, obsDim );
    recordStructure.setDimensions(obsDim.getName());

    // create/add variable dimensions
    for( int i = 0; i < parameters.size(); i++ ) {
        ucar.bufr.Index.parameter p = 
           (ucar.bufr.Index.parameter) parameters.get( i );
        //System.out.println( "p.dim ="+ p.dim );
        if( p.dimension != 1 ) { // 1 = obsDim
            String dim = "dim"+ Integer.toString( p.dimension );
            if( ! dimensions.containsKey( dim ) ) {
                if( p.dimension > 10 ) {
                   dimensions.put( dim, levelsDim );
                } else {
                   Dimension d =
                      new Dimension( dim, p.dimension, true, false, false);
                   ncfile.addDimension( null, d );
                   dimensions.put( dim, d );
                }
            }
        }
    }

    ncfile.addAttribute( null, new Attribute( "Conventions", "Unidata Observation Dataset v1.0" ) );
    ncfile.addAttribute( null, new Attribute( "observationDimension", "obs" ) );
    if( stationDS ) {
       ncfile.addAttribute( null, new Attribute( "stationsDimension", "stns" ) );
       ncfile.addAttribute( null, new Attribute( "parent_index_coordinate", "record.parent_index" ) );
    } else if( trajectoryDS ) {
       ncfile.addAttribute( null, new Attribute( "trajectoryDimension", "trajectories" ) );
    }
    //ncfile.addAttribute( null, new Attribute( "time_nominal_coordinate", "record.time_nominal" ));
    ncfile.addAttribute( null, new Attribute( "time_coverage_start", (String)index.getObsTimes().get( 0 ) ));
    ncfile.addAttribute( null, new Attribute( "time_coverage_end", (String)index.getObsTimes().get( index.getObsTimes().size() -1 ) ));
    ncfile.addAttribute( null, new Attribute( "geospatial_lat_max", "90" ) );
    ncfile.addAttribute( null, new Attribute( "geospatial_lat_min", "-90" ) );
    ncfile.addAttribute( null, new Attribute( "geospatial_lon_max", "360" ) );
    ncfile.addAttribute( null, new Attribute( "geospatial_lon_min", "0" ) );
    if( pointDS || satelliteDS ) {
      ncfile.addAttribute( null, new Attribute( "cdm_data_type", thredds.catalog.DataType.POINT.toString() ) );
    } else if( stationDS ) {
      ncfile.addAttribute( null, new Attribute( "cdm_data_type", thredds.catalog.DataType.STATION.toString() ) );
    } else if( trajectoryDS ) {
      ncfile.addAttribute( null, new Attribute( "cdm_data_type", thredds.catalog.DataType.TRAJECTORY.toString() ) );
    }
    // create variables
    if( stationDS ) {
       createStnNC( stnsDim, levelsDim );
    } else if( trajectoryDS ) {
       createTrajNC( trajsDim );
    } else if( satelliteDS ) {
       createSatVertNC( levelsDim );
    } else {
       // Dimension for variables
       ArrayList dl = new ArrayList();
       //System.out.println("parameters.size() =" + parameters.size() );
       for( int i = 0; i < parameters.size(); i++ ) {
          ucar.bufr.Index.parameter p = 
             (ucar.bufr.Index.parameter) parameters.get( i );
          if( p.dimension != 1 ) {
              String dim = "dim"+ Integer.toString( p.dimension );
              Dimension d = (Dimension) dimensions.get( dim );
              dl.add( d );
              addVariable( recordStructure, dl, p );
              dl.remove( 0 );
          } else {
             addVariable( recordStructure, dl, p );
          }
       }
    }
    ncfile.addVariable(null, recordStructure);
/*
    if( levelStructure != null ) {
       levelStructure.setDimensions( levelsDim.getName());
       ncfile.addVariable(null, levelStructure);
    }
*/
    // finish
    ncfile.finish();

  }

  void createStnNC( Dimension stnsDim, Dimension levelsDim )
  {
    // Dimensions
    ArrayList dl = new ArrayList();
    ArrayList ds = new ArrayList();
    ds.add( stnsDim );
    // create variables
    Variable v;
    v = new Variable(ncfile, ncfile.getRootGroup(), null, "number_stations" );
    v.addAttribute( new Attribute("long_name", "number of stations"));
    v.setDimensions( dl );
    v.setDataType( DataType.INT  );
    ncfile.addVariable(null, v);
    v = new Variable(ncfile, ncfile.getRootGroup(), null, "station_id" );
    v.addAttribute( new Attribute("long_name", "Station Identification"));
    v.setDimensions( ds );
    v.setDataType( DataType.STRING  );
    ncfile.addVariable(null, v);
    v = new Variable(ncfile, ncfile.getRootGroup(), null, "firstChild" );
    v.addAttribute( new Attribute("long_name", "firstChild for this station"));
    v.setDimensions( ds );
    v.setDataType( DataType.INT  );
    ncfile.addVariable(null, v);
    v = new Variable(ncfile, ncfile.getRootGroup(), null, "numChildren" );
    v.addAttribute( new Attribute("long_name", "number of obs for this station"));
    v.setDimensions( ds );
    v.setDataType( DataType.INT  );
    ncfile.addVariable(null, v);
    v = new Variable(ncfile, ncfile.getRootGroup(), null, "latitude" );
    v.addAttribute( new Attribute("long_name", "latitude for this station"));
    v.addAttribute( new Attribute( _Coordinate.AxisType, "Lat" ) );
    setLat = false;
    v.setDimensions( ds );
    v.setDataType( DataType.FLOAT  );
    ncfile.addVariable(null, v);
    v = new Variable(ncfile, ncfile.getRootGroup(), null, "longitude" );
    v.addAttribute( new Attribute("long_name", "longitude for this station"));
    v.addAttribute( new Attribute( _Coordinate.AxisType, "Lon" ) );
    setLon = false;
    v.setDimensions( ds );
    v.setDataType( DataType.FLOAT  );
    ncfile.addVariable(null, v);
    v = new Variable(ncfile, ncfile.getRootGroup(), null, "altitude" );
    v.addAttribute( new Attribute("long_name", "altitude for this station"));
    v.addAttribute( new Attribute( _Coordinate.AxisType, "Height" ) );
    setHgt = false;
    v.setDimensions( ds );
    v.setDataType( DataType.INT  );
    ncfile.addVariable(null, v);

    v = new Variable(ncfile, ncfile.getRootGroup(), recordStructure, "parent_index");
    v.addAttribute( new Attribute("long_name", "index of this station for the record"));
    v.setDimensions( dl );
    v.setDataType( DataType.INT  );
    recordStructure.addMemberVariable( v );

    //levelStructure = new Structure(ncfile, ncfile.getRootGroup(), recordStructure, "level");
    //levelStructure.setDimensions( levelsDim.getName());

    //System.out.println("parameters.size() =" + parameters.size() );
    boolean levelIncrement = false;
    Dimension d;
    for( int i = 0; i < parameters.size(); i++ ) {
        ucar.bufr.Index.parameter p = 
           (ucar.bufr.Index.parameter) parameters.get( i );
        if( p.key.equals( "0-7-5" ) ) {
           levelIncrement = true;
           d = new Dimension( "dim43", 43, true, false, false);
           ncfile.addDimension( null, d );
           dimensions.put( "dim43", d );
           d = new Dimension( "dim86", 86, true, false, false);
           ncfile.addDimension( null, d );
           dimensions.put( "dim86", d );
        }
        // skip station type variables, already entered above
        if( p.key.equals( "0-5-1" ) || p.key.equals( "0-5-2" ) ||
           p.key.equals( "0-6-1" ) || p.key.equals( "0-6-2" ) ||
           p.key.equals( "0-7-1" ) || p.key.equals( "0-7-2" ) || 
           p.key.equals( "0-1-18" ) ) {
              continue;
        }
        if( p.key.equals( "0-2-134" ) || p.key.equals( "0-2-135" ) ||
            p.key.equals( "0-7-5" ) ) {
            d = (Dimension) dimensions.get( "dim3" );
            dl.add( d );
            addVariable( recordStructure, dl, p );
            dl.remove( 0 );
        } else if( levelIncrement && p.dimension != 1) {
            if( p.key.equals( "0-8-22" ) ){
               d = (Dimension) dimensions.get( "dim86" );
            } else {
               d = (Dimension) dimensions.get( "dim43" );
            }
            dl.add( d );
            //addVariable( levelStructure, dl, p );
            addVariable( recordStructure, dl, p );
            dl.remove( 0 );
        } else if( p.dimension != 1 ) {
             if( levelStructure == null ) {
                 levelsDim = new Dimension("levels", Dimension.UNKNOWN.getLength(), true, false, true);
                 ncfile.addDimension( null, levelsDim );
                 levelStructure = new Structure(ncfile, ncfile.getRootGroup(), recordStructure, "level");
                 levelStructure.setDimensions( levelsDim.getName());
             }
            //String dim = "dim"+ Integer.toString( p.dimension );
            //Dimension d = (Dimension) dimensions.get( dim );
            //dl.add( d );
            addVariable( levelStructure, dl, p );
            //addVariable( recordStructure, dl, p );
            //dl.remove( 0 );
            //break;
        } else {
           addVariable( recordStructure, dl, p );
        }
    }
    if( levelStructure != null )
        recordStructure.addMemberVariable( levelStructure );
  }

  void createTrajNC( Dimension trajsDim )
  {
    // Dimensions
    ArrayList dl = new ArrayList();
    ArrayList dt = new ArrayList();
    dt.add( trajsDim );
    // create variables
    Variable v;
    v = new Variable(ncfile, ncfile.getRootGroup(), null, "number_trajectories" );
    v.addAttribute( new Attribute("long_name", "number of trajectories"));
    v.setDimensions( dl );
    v.setDataType( DataType.INT  );
    ncfile.addVariable(null, v);
    v = new Variable(ncfile, ncfile.getRootGroup(), null, "trajectory_id" );
    v.addAttribute( new Attribute("long_name", "Trajectory Identification"));
    v.setDimensions( dt );
    v.setDataType( DataType.STRING  );
    ncfile.addVariable(null, v);
    v = new Variable(ncfile, ncfile.getRootGroup(), null, "firstChild" );
    v.addAttribute( new Attribute("long_name", "firstChild for this trajectory"));
    v.setDimensions( dt );
    v.setDataType( DataType.INT  );
    ncfile.addVariable(null, v);
    v = new Variable(ncfile, ncfile.getRootGroup(), null, "numChildren" );
    v.addAttribute( new Attribute("long_name", "number of obs in this trajectory"));
    v.setDimensions( dt );
    v.setDataType( DataType.INT  );
    ncfile.addVariable(null, v);

    v = new Variable(ncfile, ncfile.getRootGroup(), recordStructure, "parent_index");
    v.addAttribute( new Attribute("long_name", "index of this trajectory for the record"));
    v.setDimensions( dl );
    v.setDataType( DataType.INT  );
    recordStructure.addMemberVariable( v );

    //System.out.println("parameters.size() =" + parameters.size() );
    for( int i = 0; i < parameters.size(); i++ ) {
        ucar.bufr.Index.parameter p = 
           (ucar.bufr.Index.parameter) parameters.get( i );
        if( p.dimension != 1 ) {
            String dim = "dim"+ Integer.toString( p.dimension );
            Dimension d = (Dimension) dimensions.get( dim );
            dl.add( d );
            addVariable( recordStructure, dl, p );
            dl.remove( 0 );
        } else {
           addVariable( recordStructure, dl, p );
        }
    }
  }

  void createSatVertNC( Dimension levelsDim )
  {
    // Dimensions
    Dimension dim35 = new Dimension("dim35", 35, true, false, false);
    ncfile.addDimension( null, dim35 );
    dimensions.put( "dim35", dim35 );
    Dimension dim40 = new Dimension("dim40", 40, true, false, false);
    ncfile.addDimension( null, dim40 );
    dimensions.put( "dim40", dim40 );
    ArrayList dl = new ArrayList();
    //ArrayList dt = new ArrayList();
    //dt.add( levelsDim );
    // create variables
    Variable v;

    //System.out.println("parameters.size() =" + parameters.size() );
    Dimension d;
    for( int i = 0; i < parameters.size(); i++ ) {
        ucar.bufr.Index.parameter p = 
           (ucar.bufr.Index.parameter) parameters.get( i );
        if( p.dimension != 1 ) {
            if( p.key.equals( "0-5-42" ) || p.key.equals( "0-12-63" )) {
               d = (Dimension) dimensions.get( "dim35" );
            } else if( p.key.equals( "0-13-2" )) {
               d = (Dimension) dimensions.get( "dim40" );
            } else {
                String dim = "dim"+ Integer.toString( p.dimension );
                d = (Dimension) dimensions.get( dim );
            }
            dl.add( d );
            addVariable( recordStructure, dl, p );
            dl.remove( 0 );
        } else {
           addVariable( recordStructure, dl, p );
        }
    }
  }

  void addVariable( Structure struct, ArrayList dims, ucar.bufr.Index.parameter parm )
  {

    Variable v;
    if( parm.key.equals( "0-4-250" ) ) {
      v = new Variable(ncfile, ncfile.getRootGroup(), recordStructure, "time_observation");
      if( setTime )
         v.addAttribute( new Attribute( _Coordinate.AxisType, "Time" ) );
      setTime = false;
    } else if( parm.key.equals( "0-5-1" ) || parm.key.equals( "0-5-2" ) ||
      parm.key.equals( "0-27-1" ) || parm.key.equals( "0-27-2" ) ) {
      v = new Variable(ncfile, ncfile.getRootGroup(), recordStructure, parm.name);
      if( setLat )
        v.addAttribute( new Attribute( _Coordinate.AxisType, "Lat" ) );
      setLat = false;

    } else if( parm.key.equals( "0-6-1" ) || parm.key.equals( "0-6-2" ) ||
      parm.key.equals( "0-28-1" ) || parm.key.equals( "0-28-2" ) ) {
      v = new Variable(ncfile, ncfile.getRootGroup(), recordStructure, parm.name);
      if( setLon )
        v.addAttribute( new Attribute( _Coordinate.AxisType, "Lon" ) );
      setLon = false;

    } else if( parm.key.equals( "0-7-1" ) || parm.key.equals( "0-7-2" ) || parm.key.equals( "0-7-6" ) ) {
    //} else if( parm.key.equals( "0-7-2" ) || parm.key.equals( "0-7-5" ) || parm.key.equals( "0-7-6" ) ) {
      //parm.key.equals( "0-10-1" ) || parm.key.equals( "0-10-2" ) || parm.key.equals( "0-10-7" )) {
      v = new Variable(ncfile, ncfile.getRootGroup(), recordStructure, parm.name);
      if( setHgt )
        v.addAttribute( new Attribute( _Coordinate.AxisType, "Height" ) );
      setHgt = false;

    } else {
      v = new Variable(ncfile, ncfile.getRootGroup(), recordStructure, parm.name);
    }
    v.addAttribute( new Attribute( "Bufr_key", parm.key ) );

    if( parm.name.equals( "time_observation" ) ) {
       //v.setDataType( DataType.LONG );
       //v.setDataType( DataType.DOUBLE );
       v.setDataType( DataType.INT );
    } else if( parm.isNumeric ) {
      v.setDataType( DataType.FLOAT );
      v.addAttribute( new Attribute( "MissingValue", "-9999" ) );
    } else {
      v.setDataType( DataType.STRING );
    }
    v.setDimensions( dims );
    //v.addAttribute( new Attribute("long_name", parm.getDescription()));
    if( ! parm.units.equals( "" ) )
       v.addAttribute( new Attribute("units", parm.units));

    struct.addMemberVariable( v );
  }



}
/* Change History:
   $Log: Index2NC.java,v $
   Revision 1.5  2006/06/15 22:31:54  rkambic
   compressed data works

   Revision 1.4  2006/05/31 15:14:25  rkambic
   cleanup

   Revision 1.3  2006/05/24 17:47:45  caron
   bug in ArraySequence

   Revision 1.2  2006/05/24 15:42:16  rkambic
   inprogrss

   Revision 1.1  2006/05/03 17:09:37  rkambic
   converts Bufr data to netCDF object

   Revision 1.3  2006/03/31 20:55:26  rkambic
   time observation and nominal time fixes

   Revision 1.2  2006/03/30 20:04:30  rkambic
   updata

   Revision 1.1  2006/03/13 21:18:05  rkambic
   bufr isop

 */