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The NetCDF-Java Library is a Java interface to NetCDF files,
as well as to many other types of scientific data formats.
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/*
* Copyright 1998-2014 University Corporation for Atmospheric Research/Unidata
*
* Portions of this software were developed by the Unidata Program at the
* University Corporation for Atmospheric Research.
*
* Access and use of this software shall impose the following obligations
* and understandings on the user. The user is granted the right, without
* any fee or cost, to use, copy, modify, alter, enhance and distribute
* this software, and any derivative works thereof, and its supporting
* documentation for any purpose whatsoever, provided that this entire
* notice appears in all copies of the software, derivative works and
* supporting documentation. Further, UCAR requests that the user credit
* UCAR/Unidata in any publications that result from the use of this
* software or in any product that includes this software. The names UCAR
* and/or Unidata, however, may not be used in any advertising or publicity
* to endorse or promote any products or commercial entity unless specific
* written permission is obtained from UCAR/Unidata. The user also
* understands that UCAR/Unidata is not obligated to provide the user with
* any support, consulting, training or assistance of any kind with regard
* to the use, operation and performance of this software nor to provide
* the user with any updates, revisions, new versions or "bug fixes."
*
* THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
* IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
* INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
* FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
* NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
* WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
*/
package ucar.nc2.dataset;
import ucar.ma2.*;
import ucar.nc2.*;
import ucar.nc2.constants.AxisType;
import ucar.nc2.constants.CDM;
import ucar.nc2.constants.CF;
import ucar.nc2.dataset.conv.CF1Convention;
import ucar.nc2.dataset.conv.COARDSConvention;
import ucar.nc2.time.Calendar;
import java.io.IOException;
import java.util.Formatter;
/**
* A Coordinate Axis is a Variable that specifies one of the coordinates of a CoordinateSystem.
* Mathematically it is a scalar function F from index space to S:
*
* F:D -> S
* where D is a product set of dimensions (aka index space), and S is the set of reals (R) or Strings.
*
*
* If its element type is char, it is considered a string-valued Coordinate Axis and rank is reduced by one,
* since the outermost dimension is considered the string length: v(i, j, .., strlen).
* If its element type is String, it is a string-valued Coordinate Axis.
* Otherwise it is numeric-valued, and isNumeric() is true.
*
* The one-dimensional case F(i) -> R is the common case which affords important optimizations.
* In that case, use the subtype CoordinateAxis1D. The factory methods will return
* either a CoordinateAxis1D if the variable is one-dimensional, a CoordinateAxis2D if its 2D, or a
* CoordinateAxis for the general case.
*
* A CoordinateAxis is optionally marked as georeferencing with an AxisType. It should have
* a units string and optionally a description string.
*
* A Structure cannot be a CoordinateAxis, although members of Structures can.
*
* @author john caron
*/
public class CoordinateAxis extends VariableDS {
static private org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(CoordinateAxis.class);
static private final int axisSizeToCache = 100 * 1000; // bytes
protected NetcdfDataset ncd; // container dataset
protected AxisType axisType = null;
protected String positive = null;
protected String boundaryRef = null;
protected boolean isContiguous = true;
/**
* Create a coordinate axis from an existing Variable.
*
* @param ncd the containing dataset
* @param vds an existing Variable in dataset.
* @return CoordinateAxis or one of its subclasses (CoordinateAxis1D, CoordinateAxis2D, or CoordinateAxis1DTime).
*/
static public CoordinateAxis factory(NetcdfDataset ncd, VariableDS vds) {
if ((vds.getRank() == 1) || (vds.getRank() == 2 && vds.getDataType() == DataType.CHAR)) {
return new CoordinateAxis1D(ncd, vds);
} else if (vds.getRank() == 2)
return new CoordinateAxis2D(ncd, vds);
else
return new CoordinateAxis(ncd, vds);
}
/**
* Create a coordinate axis from an existing Variable.
* General case.
*
* @param ncd the containing dataset
* @param vds an existing Variable
*/
protected CoordinateAxis(NetcdfDataset ncd, VariableDS vds) {
super(vds, false);
this.ncd = ncd;
if (vds instanceof CoordinateAxis) {
CoordinateAxis axis = (CoordinateAxis) vds;
this.axisType = axis.axisType;
this.boundaryRef = axis.boundaryRef;
this.isContiguous = axis.isContiguous;
this.positive = axis.positive;
}
setSizeToCache(axisSizeToCache);
}
/**
* Constructor when theres no underlying variable. You better set the values too!
*
* @param ds the containing dataset.
* @param group the containing group; if null, use rootGroup
* @param shortName axis name.
* @param dataType data type
* @param dims list of dimension names
* @param units units of coordinates, preferably udunit compatible.
* @param desc long name.
*/
public CoordinateAxis(NetcdfDataset ds, Group group, String shortName, DataType dataType, String dims, String units, String desc) {
super(ds, group, null, shortName, dataType, dims, units, desc);
this.ncd = ds;
setSizeToCache(axisSizeToCache);
}
/**
* Make a copy, with an independent cache.
*
* @return copy of this CoordinateAxis
*/
public CoordinateAxis copyNoCache() {
CoordinateAxis axis = new CoordinateAxis(ncd, getParentGroup(), getShortName(), getDataType(), getDimensionsString(),
getUnitsString(), getDescription());
// other state
axis.axisType = this.axisType;
axis.boundaryRef = this.boundaryRef;
axis.isContiguous = this.isContiguous;
axis.positive = this.positive;
axis.cache = new Variable.Cache(); // decouple cache
return axis;
}
// for section and slice
@Override
protected Variable copy() {
return new CoordinateAxis(this.ncd, this);
}
/**
* Get type of axis
*
* @return type of axis, or null if none.
*/
public AxisType getAxisType() {
return axisType;
}
/**
* Set type of axis, or null if none. Default is none.
*
* @param axisType set to this value
*/
public void setAxisType(AxisType axisType) {
this.axisType = axisType;
}
@Override
public String getUnitsString() {
String units = super.getUnitsString();
return units == null ? "" : units;
}
/**
* Does the axis have numeric values.
*
* @return true if the CoordAxis is numeric, false if its string valued ("nominal").
*/
public boolean isNumeric() {
return (getDataType() != DataType.CHAR) &&
(getDataType() != DataType.STRING) &&
(getDataType() != DataType.STRUCTURE);
}
/**
* If the edges are contiguous or disjoint
* Caution: many datasets do not explicitly specify this info, this is often a guess; default is true.
*
* @return true if the edges are contiguous or false if disjoint. Assumed true unless set otherwise.
*/
public boolean isContiguous() {
return isContiguous;
}
/**
* An interval coordinate consists of two numbers, bound1 and bound2.
* The coordinate value must lie between them, but otherwise is somewhat arbitrary.
* If not interval, then it has one number, the coordinate value.
* @return true if its an interval coordinate.
*/
public boolean isInterval() {
return false; // interval detection is done in subclasses
}
// causes TDS ERROR thredds.server.opendap.NcDDS: NcDDS: Variable time1_run missing coordinate variable in hash; dataset=fmrc/NCEP/GFS/Global_onedeg/NCEP-GFS-Global_onedeg_best.ncd
//@Override
//public boolean isCoordinateVariable() {
// return true;
//}
/*
* Set if the edges are contiguous or disjoint.
*
* @param isContiguous true if the adjacent edges touch
*
protected void setContiguous(boolean isContiguous) {
this.isContiguous = isContiguous;
} */
/**
* Get the direction of increasing values, used only for vertical Axes.
*
* @return POSITIVE_UP, POSITIVE_DOWN, or null if unknown.
*/
public String getPositive() {
return positive;
}
/**
* Set the direction of increasing values, used only for vertical Axes.
*
* @param positive POSITIVE_UP, POSITIVE_DOWN, or null if you dont know..
*/
public void setPositive(String positive) {
this.positive = positive;
}
/**
* The name of this coordinate axis' boundary variable
*
* @return the name of this coordinate axis' boundary variable, or null if none.
*/
public String getBoundaryRef() {
return boundaryRef;
}
/**
* Set a reference to a boundary variable.
*
* @param boundaryRef the name of a boundary coordinate variable in the same dataset.
*/
public void setBoundaryRef(String boundaryRef) {
this.boundaryRef = boundaryRef;
}
////////////////////////////////
private MAMath.MinMax minmax = null;
private void init() {
try {
Array data = read();
minmax = MAMath.getMinMax(data);
} catch (IOException ioe) {
log.error("Error reading coordinate values ", ioe);
throw new IllegalStateException(ioe);
}
}
/**
* The smallest coordinate value. Only call if isNumeric.
*
* @return the minimum coordinate value
*/
public double getMinValue() {
if (minmax == null) init();
return minmax.min;
}
/**
* The largest coordinate value. Only call if isNumeric.
*
* @return the maximum coordinate value
*/
public double getMaxValue() {
if (minmax == null) init();
return minmax.max;
}
//////////////////////
/**
* Get a string representation
*
* @param buf place info here
*/
public void getInfo(Formatter buf) {
buf.format("%-30s", getNameAndDimensions());
buf.format("%-20s", getUnitsString());
if (axisType != null) {
buf.format("%-10s", axisType.toString());
}
buf.format("%s", getDescription());
/* if (isNumeric) {
boolean debugCoords = ucar.util.prefs.ui.Debug.isSet("Dataset/showCoordValues");
int ndigits = debugCoords ? 9 : 4;
for (int i=0; i< getNumElements(); i++) {
buf.append(Format.d(getCoordValue(i), ndigits));
buf.append(" ");
}
if (debugCoords) {
buf.append("\n ");
for (int i=0; i<=getNumElements(); i++) {
buf.append(Format.d(getCoordEdge(i), ndigits));
buf.append(" ");
}
}
} else {
for (int i=0; i< getNumElements(); i++) {
buf.append(getCoordName(i));
buf.append(" ");
}
} */
//buf.append("\n");
}
/**
* Standard sort on Coordinate Axes
*/
static public class AxisComparator implements java.util.Comparator {
public int compare(CoordinateAxis c1, CoordinateAxis c2) {
AxisType t1 = c1.getAxisType();
AxisType t2 = c2.getAxisType();
if ((t1 == null) && (t2 == null))
return c1.getShortName().compareTo(c2.getShortName());
if (t1 == null)
return -1;
if (t2 == null)
return 1;
return t1.axisOrder() - t2.axisOrder();
}
public boolean equals(Object obj) {
return (this == obj);
}
}
/**
* Instances which have same content are equal.
*/
public boolean equals(Object oo) {
if (this == oo) return true;
if (!(oo instanceof CoordinateAxis)) return false;
if (!super.equals(oo)) return false;
CoordinateAxis o = (CoordinateAxis) oo;
if (getAxisType() != null)
if (!getAxisType().equals(o.getAxisType())) return false;
if (getPositive() != null)
if (!getPositive().equals(o.getPositive())) return false;
return true;
}
/**
* Override Object.hashCode() to implement equals.
*/
public int hashCode() {
if (hashCode == 0) {
int result = super.hashCode();
if (getAxisType() != null)
result = 37 * result + getAxisType().hashCode();
if (getPositive() != null)
result = 37 * result + getPositive().hashCode();
hashCode = result;
}
return hashCode;
}
private int hashCode = 0;
/////////////////////////////////////
// needed by time coordinates
protected ucar.nc2.time.Calendar getCalendarFromAttribute() {
Attribute cal = findAttribute(CF.CALENDAR);
String s = (cal == null) ? null : cal.getStringValue();
if (s == null) { // default for CF and COARDS
Attribute convention = (ncd == null) ? null : ncd.getRootGroup().findAttribute(CDM.CONVENTIONS);
if (convention != null) {
String hasName = convention.getStringValue();
int version = CF1Convention.getVersion(hasName);
if (version >= 0) {
return Calendar.gregorian;
//if (version < 7 ) return Calendar.gregorian;
//if (version >= 7 ) return Calendar.proleptic_gregorian; //
}
if (COARDSConvention.isMine(hasName)) return Calendar.gregorian;
}
}
return ucar.nc2.time.Calendar.get(s);
}
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