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*
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// $Id: SingleTrajectoryObsDataset.java 63 2006-07-12 21:50:51Z edavis $
package ucar.nc2.dt.trajectory;
import ucar.ma2.*;
import ucar.nc2.*;
import ucar.nc2.dataset.VariableDS;
import ucar.nc2.dataset.NetcdfDataset;
import ucar.nc2.StructurePseudo;
import ucar.nc2.VariableSimpleIF;
import ucar.nc2.dt.VariableSimpleSubclass;
import ucar.nc2.dt.*;
import ucar.nc2.units.DateUnit;
import ucar.nc2.units.SimpleUnit;
import ucar.unidata.geoloc.LatLonRect;
import java.io.IOException;
import java.util.*;
/**
* Superclass for for implementations of TrajectoryObsDataset using a
* NetcdfFile underneath that contains a single trajectory. The file
* must have a single coordinate variable for time. The time dimension
* may be UNLIMITED (if time is not UNLIMITED, there must be no UNLIMITED
* dimension). The file must also have a latitude variable, a longitude
* variable, and an elevation variable each on the time dimension only.
* The data variables also must be on the time dimension but they can
* also have other dimensions.
* For instance:
* <pre>
* time( time) - convertable to -> double
* lat( time) - convertable to -> double
* lon( time) - convertable to -> double
* elev( time) - convertable to -> double
* var1( time[, dim#]*)
* ...
* varN( time[, dim#]*)
* </pre>
*
* @deprecated use ucar.nc2.ft.*
* @author edavis
* @since 5 May 2005 10:12 -0600
*/
public class SingleTrajectoryObsDataset
extends TypedDatasetImpl
implements TrajectoryObsDataset
{
protected String trajectoryId; // the Id String for the trajectory.
protected int trajectoryNumPoint; // the num of points in the trajectory.
protected HashMap trajectoryVarsMap; // a Map of all the TypedDataVariables in the trajectory keyed by their names.
protected Dimension timeDim;
protected Variable timeVar;
protected Structure recordVar;
protected Variable latVar;
protected Variable lonVar;
protected Variable elevVar;
protected String timeVarUnitsString;
protected double elevVarUnitsConversionFactor;
protected TrajectoryObsDatatype trajectory;
public SingleTrajectoryObsDataset() {}
public SingleTrajectoryObsDataset( NetcdfDataset ncfile)
{
super( ncfile);
}
/** Setup needed for all SingleTrajectoryObsDatatypes. Can only be called once.
*
* Units of time varible must be udunits time units.
* Units of latitude variable must be convertible to "degrees_north" by udunits.
* Units of longitude variable must be convertible to "degrees_east" by udunits.
* Units of altitude variable must be convertible to "meters" by udunits.
*
* @throws IllegalArgumentException if units of time, latitude, longitude, or altitude variables are not as required.
* @throws IllegalStateException if this method has already been called.
*/
public void setTrajectoryInfo( Config trajConfig )
throws IOException
{
if ( timeDim != null )
throw new IllegalStateException( "The setTrajectoryInfo() method can only be called once.");
this.trajectoryId = trajConfig.getTrajectoryId();
this.timeDim = trajConfig.getTimeDim();
this.timeVar = trajConfig.getTimeVar();
this.latVar = trajConfig.getLatVar();
this.lonVar = trajConfig.getLonVar();
this.elevVar = trajConfig.getElevVar();
trajectoryNumPoint = this.timeDim.getLength();
timeVarUnitsString = this.timeVar.findAttribute( "units" ).getStringValue();
// Check that time, lat, lon, elev units are acceptable.
if ( DateUnit.getStandardDate( timeVarUnitsString ) == null )
{
throw new IllegalArgumentException( "Units of time variable <" + timeVarUnitsString + "> not a date unit." );
}
String latVarUnitsString = this.latVar.findAttribute( "units").getStringValue();
if ( ! SimpleUnit.isCompatible( latVarUnitsString, "degrees_north" ) )
{
throw new IllegalArgumentException( "Units of lat var <" + latVarUnitsString + "> not compatible with \"degrees_north\"." );
}
String lonVarUnitsString = this.lonVar.findAttribute( "units" ).getStringValue();
if ( !SimpleUnit.isCompatible( lonVarUnitsString, "degrees_east" ) )
{
throw new IllegalArgumentException( "Units of lon var <" + lonVarUnitsString + "> not compatible with \"degrees_east\"." );
}
String elevVarUnitsString = this.elevVar.findAttribute( "units" ).getStringValue();
if ( !SimpleUnit.isCompatible( elevVarUnitsString, "meters" ) )
{
throw new IllegalArgumentException( "Units of elev var <" + elevVarUnitsString + "> not compatible with \"meters\"." );
}
try
{
elevVarUnitsConversionFactor = getMetersConversionFactor( elevVarUnitsString);
}
catch ( Exception e )
{
throw new IllegalArgumentException( "Exception on getMetersConversionFactor() for the units of elev var <" + elevVarUnitsString + ">." );
}
if ( this.ncfile.hasUnlimitedDimension() && this.ncfile.getUnlimitedDimension().equals( timeDim ) )
{
Object result = this.ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
if ((result != null) && (Boolean) result )
this.recordVar = (Structure) this.ncfile.getRootGroup().findVariable( "record");
else
this.recordVar = new StructurePseudo( this.ncfile, null, "record", timeDim );
} else {
this.recordVar = new StructurePseudo( this.ncfile, null, "record", timeDim);
}
// @todo HACK, HACK, HACK - remove once addRecordStructure() deals with ncd attribute changes.
Variable elevVarInRecVar = this.recordVar.findVariable( this.elevVar.getFullNameEscaped());
if ( ! elevVarUnitsString.equals( elevVarInRecVar.findAttribute( "units").getStringValue()))
{
elevVarInRecVar.addAttribute( new Attribute( "units", elevVarUnitsString));
}
trajectoryVarsMap = new HashMap();
//for ( Iterator it = this.recordVar.getVariables().iterator(); it.hasNext(); )
for ( Iterator it = this.ncfile.getRootGroup().getVariables().iterator(); it.hasNext(); )
{
Variable curVar = (Variable) it.next();
if ( curVar.getRank() > 0 &&
!curVar.equals( this.timeVar) &&
! curVar.equals( this.latVar) &&
! curVar.equals( this.lonVar) &&
! curVar.equals( this.elevVar) &&
( this.recordVar == null ? true : ! curVar.equals( this.recordVar)))
{
MyTypedDataVariable typedVar = new MyTypedDataVariable( new VariableDS( null, curVar, true ) );
dataVariables.add( typedVar);
trajectoryVarsMap.put( typedVar.getShortName(), typedVar);
}
}
trajectory = new SingleTrajectory( this.trajectoryId, trajectoryNumPoint,
this.timeVar, timeVarUnitsString,
this.latVar, this.lonVar, this.elevVar,
dataVariables, trajectoryVarsMap);
startDate = trajectory.getTime( 0);
endDate = trajectory.getTime( trajectoryNumPoint - 1);
( (SingleTrajectory) trajectory).setStartDate( startDate );
( (SingleTrajectory) trajectory).setEndDate( endDate );
}
protected static double getMetersConversionFactor( String unitsString ) throws Exception
{
SimpleUnit unit = SimpleUnit.factoryWithExceptions( unitsString );
return unit.convertTo( 1.0, SimpleUnit.meterUnit );
}
protected void setStartDate() {}
protected void setEndDate() {}
protected void setBoundingBox() {}
public List getTrajectoryIds()
{
List l = new ArrayList();
l.add( trajectoryId);
return( l);
}
public List getTrajectories() // throws IOException;
{
List l = new ArrayList();
l.add( trajectory);
return( l);
}
public TrajectoryObsDatatype getTrajectory( String trajectoryId ) // throws IOException;
{
if ( ! trajectoryId.equals( this.trajectoryId)) return( null);
return( trajectory);
}
public String getDetailInfo()
{
StringBuffer sbuff = new StringBuffer();
sbuff.append( "TrajectoryObsDataset\n" );
sbuff.append( " adapter = " + getClass().getName() + "\n" );
sbuff.append( " trajectories:" + "\n" );
for ( Iterator it = this.getTrajectoryIds().iterator(); it.hasNext(); )
{
sbuff.append( " " + (String) it.next() + "\n" );
}
sbuff.append( super.getDetailInfo() );
return sbuff.toString();
}
public boolean syncExtend()
{
if ( ! this.ncfile.hasUnlimitedDimension()) return false;
try
{
if ( ! this.ncfile.syncExtend() ) return false;
}
catch ( IOException e )
{
return false;
}
// Update number of points in this TrajectoryObsDataset and in the child TrajectoryObsDatatype.
int newNumPoints = this.timeDim.getLength();
if ( this.trajectoryNumPoint >= newNumPoints )
return false;
this.trajectoryNumPoint = newNumPoints;
( (SingleTrajectory) this.trajectory).setNumPoints( this.trajectoryNumPoint);
// Update end date in this TrajectoryObsDataset and in the child TrajectoryObsDatatype.
try
{
endDate = trajectory.getTime( trajectoryNumPoint - 1 );
}
catch ( IOException e )
{
return false;
}
( (SingleTrajectory) trajectory ).setEndDate( endDate );
return true;
}
public static class Config
{
protected String trajectoryId; // the Id String for the trajectory.
protected Dimension timeDim;
protected Variable timeVar;
protected Variable latVar;
protected Variable lonVar;
protected Variable elevVar;
public Config() {}
public Config( String trajectoryId, Dimension timeDim, Variable timeVar,
Variable latVar, Variable lonVar, Variable elevVar )
{
this.trajectoryId = trajectoryId;
this.timeDim = timeDim;
this.timeVar = timeVar;
this.latVar = latVar;
this.lonVar = lonVar;
this.elevVar = elevVar;
}
public void setTrajectoryId( String trajectoryId )
{
this.trajectoryId = trajectoryId;
}
public void setTimeDim( Dimension timeDim )
{
this.timeDim = timeDim;
}
public void setTimeVar( Variable timeVar )
{
this.timeVar = timeVar;
}
public void setLatVar( Variable latVar )
{
this.latVar = latVar;
}
public void setLonVar( Variable lonVar )
{
this.lonVar = lonVar;
}
public void setElevVar( Variable elevVar )
{
this.elevVar = elevVar;
}
public String getTrajectoryId()
{
return trajectoryId;
}
public Dimension getTimeDim()
{
return timeDim;
}
public Variable getTimeVar()
{
return timeVar;
}
public Variable getLatVar()
{
return latVar;
}
public Variable getLonVar()
{
return lonVar;
}
public Variable getElevVar()
{
return elevVar;
}
}
private class SingleTrajectory implements TrajectoryObsDatatype
{
private String id;
private String description;
private int numPoints;
private Date startDate;
private Date endDate;
private String timeVarUnitsString;
private Variable timeVar;
private Variable latVar;
private Variable lonVar;
private Variable elevVar;
private List variables;
private HashMap variablesMap;
//private Structure struct;
private SingleTrajectory( String id, int numPoints,
Variable timeVar, String timeVarUnitsString,
Variable latVar, Variable lonVar, Variable elevVar,
List variables, HashMap variablesMap )
{
this.description = null;
this.id = id;
this.numPoints = numPoints;
this.timeVarUnitsString = timeVarUnitsString;
this.timeVar = timeVar;
this.variables = variables;
this.variablesMap = variablesMap;
this.latVar = latVar;
this.lonVar = lonVar;
this.elevVar = elevVar;
//this.struct = new Structure( ncfile, ncfile.getRootGroup(), null, "struct for building StructureDatas");
}
protected void setNumPoints( int numPoints )
{
this.numPoints = numPoints;
}
protected void setStartDate( Date startDate )
{
if ( this.startDate != null ) throw new IllegalStateException( "Can only call setStartDate() once." );
this.startDate = startDate;
}
protected void setEndDate( Date endDate )
{
//if ( this.endDate != null ) throw new IllegalStateException( "Can only call setEndDate() once.");
this.endDate = endDate;
}
public String getId()
{
return( id);
}
public String getDescription()
{
return( description);
}
public int getNumberPoints()
{
return( numPoints);
}
public List getDataVariables()
{
return ( variables );
}
public VariableSimpleIF getDataVariable( String name )
{
return ( (VariableSimpleIF) variablesMap.get( name ) );
}
public PointObsDatatype getPointObsData( int point ) throws IOException
{
return( new MyPointObsDatatype( point));
}
public Date getStartDate()
{
return( startDate);
}
public Date getEndDate()
{
return( endDate);
}
public LatLonRect getBoundingBox()
{
return null;
}
public Date getTime( int point ) throws IOException
{
return ( DateUnit.getStandardDate( getTimeValue( point ) + " " + timeVarUnitsString ) );
}
public ucar.unidata.geoloc.EarthLocation getLocation( int point ) throws IOException
{
return ( new MyEarthLocation( point ) );
}
public String getTimeUnitsIdentifier()
{
return( timeVarUnitsString);
}
public double getTimeValue( int point ) throws IOException
{
Array array = null;
try
{
array = getTime( this.getPointRange( point ) );
}
catch ( InvalidRangeException e )
{
IllegalArgumentException iae = new IllegalArgumentException( "Point <" + point + "> not in valid range <0, " + ( this.getNumberPoints() - 1 ) + ">: " + e.getMessage() );
iae.initCause( e );
throw iae;
}
if ( array instanceof ArrayDouble)
{
return( array.getDouble( array.getIndex()));
}
else if ( array instanceof ArrayFloat)
{
return( array.getFloat( array.getIndex()));
}
else if ( array instanceof ArrayInt )
{
return ( array.getInt( array.getIndex() ) );
}
else
{
throw new IOException( "Time variable not float, double, or integer <" + array.getElementType().toString() + ">.");
}
}
// @todo Make sure units are degrees_north
public double getLatitude( int point ) throws IOException // required, units degrees_north
{
Array array = null;
try
{
array = getLatitude( this.getPointRange( point));
}
catch ( InvalidRangeException e )
{
IllegalArgumentException iae = new IllegalArgumentException( "Point <" + point + "> not in valid range <0, " + (this.getNumberPoints()-1) + ">: " + e.getMessage());
iae.initCause( e);
throw iae;
}
if ( array instanceof ArrayDouble)
{
return( array.getDouble( array.getIndex()));
}
else if ( array instanceof ArrayFloat)
{
return( array.getFloat( array.getIndex()));
}
else
{
throw new IOException( "Latitude variable not float or double <" + array.getElementType().toString() + ">.");
}
}
// @todo Make sure units are degrees_east
public double getLongitude( int point ) throws IOException // required, units degrees_east
{
Array array = null;
try
{
array = getLongitude( this.getPointRange( point));
}
catch ( InvalidRangeException e )
{
IllegalArgumentException iae = new IllegalArgumentException( "Point <" + point + "> not in valid range <0, " + (this.getNumberPoints()-1) + ">: " + e.getMessage());
iae.initCause( e);
throw iae;
}
if ( array instanceof ArrayDouble)
{
return( array.getDouble( array.getIndex()));
}
else if ( array instanceof ArrayFloat)
{
return( array.getFloat( array.getIndex()));
}
else
{
throw new IOException( "Longitude variable not float or double <" + array.getElementType().toString() + ">.");
}
}
// @todo Make sure units are meters
public double getElevation( int point ) throws IOException // optional; units meters; missing = NaN.
{
Array array = null;
try
{
array = getElevation( this.getPointRange( point));
}
catch ( InvalidRangeException e )
{
IllegalArgumentException iae = new IllegalArgumentException( "Point <" + point + "> not in valid range <0, " + (this.getNumberPoints()-1) + ">: " + e.getMessage());
iae.initCause( e);
throw iae;
}
if ( array instanceof ArrayDouble)
{
return array.getDouble( array.getIndex());
}
else if ( array instanceof ArrayFloat)
{
return array.getFloat( array.getIndex());
}
else
{
throw new IOException( "Elevation variable not float or double <" + array.getElementType().toString() + ">.");
}
}
public StructureData getData( int point ) throws IOException, InvalidRangeException
{
return SingleTrajectoryObsDataset.this.recordVar.readStructure( point );
}
public Array getData( int point, String parameterName ) throws IOException
{
try
{
return( getData( this.getPointRange( point), parameterName));
}
catch ( InvalidRangeException e )
{
IllegalArgumentException iae = new IllegalArgumentException( "Point <" + point + "> not in valid range <0, " + (this.getNumberPoints()-1) + ">: " + e.getMessage());
iae.initCause( e);
throw iae;
}
}
public Range getFullRange()
{
Range range = null;
try
{
range = new Range(0, this.getNumberPoints()-1);
}
catch ( InvalidRangeException e )
{
IllegalStateException ise = new IllegalStateException( "Full trajectory range invalid <0, " + (this.getNumberPoints()-1) + ">: " + e.getMessage());
ise.initCause( e);
throw( ise);
}
return range;
}
public Range getPointRange( int point ) throws InvalidRangeException
{
if ( point >= this.getNumberPoints()) throw new InvalidRangeException( "Point <" + point + "> not in acceptible range <0, " + (this.getNumberPoints()-1) + ">.");
return( new Range(point, point));
}
public Range getRange( int start, int end, int stride ) throws InvalidRangeException
{
if ( end >= this.getNumberPoints()) throw new InvalidRangeException( "End point <" + end + "> not in acceptible range <0, " + (this.getNumberPoints()-1) + ">.");
return( new Range( start, end, stride));
}
public Array getTime( Range range ) throws IOException, InvalidRangeException
{
List section = new ArrayList(1);
section.add( range);
return( timeVar.read( section));
}
// @todo Make sure units are degrees_north
public Array getLatitude( Range range ) throws IOException, InvalidRangeException
{
List section = new ArrayList(1);
section.add( range);
return( latVar.read( section));
}
// @todo Make sure units are degrees_east
public Array getLongitude( Range range ) throws IOException, InvalidRangeException
{
List section = new ArrayList(1);
section.add( range);
return( lonVar.read( section));
}
// @todo Make sure units are meters
public Array getElevation( Range range ) throws IOException, InvalidRangeException
{
List section = new ArrayList(1);
section.add( range);
Array a = elevVar.read( section);
if ( elevVarUnitsConversionFactor == 1.0) return( a);
for ( IndexIterator it = a.getIndexIterator(); it.hasNext(); )
{
if ( elevVar.getDataType() == DataType.DOUBLE )
{
double val = it.getDoubleNext();
it.setDoubleCurrent( val * elevVarUnitsConversionFactor );
}
else if ( elevVar.getDataType() == DataType.FLOAT )
{
float val = it.getFloatNext();
it.setFloatCurrent( (float) ( val * elevVarUnitsConversionFactor ) );
}
else if ( elevVar.getDataType() == DataType.INT )
{
int val = it.getIntNext();
it.setIntCurrent( (int) ( val * elevVarUnitsConversionFactor ) );
}
else if ( elevVar.getDataType() == DataType.LONG )
{
long val = it.getLongNext();
it.setLongCurrent( (long) ( val * elevVarUnitsConversionFactor ) );
}
else
{
throw new IllegalStateException( "Elevation variable type <" + elevVar.getDataType().toString() + "> not double, float, int, or long." );
}
}
return( a);
}
public Array getData( Range range, String parameterName ) throws IOException, InvalidRangeException
{
Variable variable = ncfile.getRootGroup().findVariable( parameterName );
int varRank = variable.getRank();
int [] varShape = variable.getShape();
List section = new ArrayList( varRank);
section.add( range);
for ( int i = 1; i < varRank; i++)
{
section.add( new Range( 0, varShape[i]-1 ) );
}
Array array = variable.read( section);
if ( array.getShape()[0] == 1 )
{
return ( array.reduce( 0 ) );
}
else
{
return ( array );
}
//return( array.getShape()[0] == 1 ? array.reduce( 0 ) : array);
}
public DataIterator getDataIterator( int bufferSize ) throws IOException
{
return new PointDatatypeIterator( recordVar, bufferSize );
}
private class PointDatatypeIterator extends DatatypeIterator
{
protected Object makeDatatypeWithData( int recnum, StructureData sdata )
{
return new MyPointObsDatatype( recnum, sdata );
}
PointDatatypeIterator( Structure struct, int bufferSize )
{
super( struct, bufferSize );
}
}
// PointObsDatatype implementation used by SingleTrajectory.
private class MyPointObsDatatype implements PointObsDatatype
{
private int point;
private StructureData sdata;
private double time;
private ucar.unidata.geoloc.EarthLocation earthLoc;
private MyPointObsDatatype( int point) throws IOException
{
this.point = point;
this.time = SingleTrajectory.this.getTimeValue( point);
this.earthLoc = SingleTrajectory.this.getLocation( point);
}
private MyPointObsDatatype( int point, StructureData sdata )
{
this.point = point;
this.sdata = sdata;
this.time = sdata.convertScalarDouble( SingleTrajectory.this.timeVar.getShortName());
this.earthLoc = new MyEarthLocation( sdata);
}
public double getNominalTime()
{
return ( this.time );
}
public double getObservationTime()
{
return ( this.time );
}
public Date getNominalTimeAsDate() {
String dateStr = getNominalTime() + " " + timeVarUnitsString;
return DateUnit.getStandardDate( dateStr );
}
public Date getObservationTimeAsDate() {
String dateStr = getObservationTime() + " " + timeVarUnitsString;
return DateUnit.getStandardDate( dateStr );
}
public ucar.unidata.geoloc.EarthLocation getLocation()
{
return( this.earthLoc);
}
public StructureData getData() throws IOException
{
if ( sdata != null ) return sdata;
try {
return( SingleTrajectory.this.getData( point));
} catch (InvalidRangeException e) {
throw new IllegalStateException( e.getMessage());
}
}
}
// EarthLocation implementation used by SingleTrajectory.
private class MyEarthLocation extends ucar.unidata.geoloc.EarthLocationImpl
{
private double latitude;
private double longitude;
private double elevation;
private MyEarthLocation( int point) throws IOException
{
this.latitude = SingleTrajectory.this.getLatitude( point);
this.longitude = SingleTrajectory.this.getLongitude( point);
this.elevation = SingleTrajectory.this.getElevation( point);
}
private MyEarthLocation( StructureData sdata )
{
this.latitude = sdata.convertScalarDouble( SingleTrajectory.this.latVar.getShortName() );
this.longitude = sdata.convertScalarDouble( SingleTrajectory.this.lonVar.getShortName() );
this.elevation = sdata.convertScalarDouble( SingleTrajectory.this.elevVar.getShortName() );
if ( elevVarUnitsConversionFactor != 1.0 ) this.elevation *= elevVarUnitsConversionFactor;
}
public double getLatitude()
{
return( this.latitude);
}
public double getLongitude()
{
return( this.longitude);
}
public double getAltitude()
{
return( this.elevation);
}
}
}
private class MyTypedDataVariable extends VariableSimpleSubclass
{
private int rank;
private int[] shape;
private MyTypedDataVariable( VariableDS v )
{
super( v );
// Calculate the rank and shape of the variable, removing trajectory dimesion.
rank = super.getRank() - 1;
int[] varShape = super.getShape();
shape = new int[ varShape.length - 1];
int trajDimIndex = v.findDimensionIndex( SingleTrajectoryObsDataset.this.timeDim.getName());
for ( int i = 0, j = 0; i < varShape.length; i++)
{
if ( i == trajDimIndex) continue;
shape[ j++] = varShape[ i];
}
}
public int getRank()
{
return( rank);
}
public int[] getShape()
{
return( shape);
}
}
}