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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.
The newest version!
/*
* 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;
import ucar.ma2.*;
import ucar.nc2.constants.CDM;
import ucar.nc2.dataset.NetcdfDataset;
import ucar.nc2.util.CancelTask;
import ucar.nc2.util.URLnaming;
import ucar.nc2.util.Indent;
import ucar.unidata.util.StringUtil2;
import java.io.*;
import java.math.BigInteger;
import java.util.StringTokenizer;
import java.util.List;
import java.util.Formatter;
import java.nio.ByteBuffer;
/**
* Print contents of an existing netCDF file, using a Writer.
*
* A difference with ncdump is that the nesting of multidimensional array data is represented by nested brackets,
* so the output is not legal CDL that can be used as input for ncgen. Also, the default is header only (-h)
*
* @author caron
* @since Nov 4, 2007
*/
public class NCdumpW {
private static String usage = "usage: NCdumpW [-unsigned] [-cdl | -ncml] [-c | -vall] [-v varName1;varName2;..] [-v varName(0:1,:,12)]\n";
/**
* Tell NCdumpW if you want values printed.
*/
static public enum WantValues {
none, coordsOnly, all
}
// Being lazy, I just make this flag global
static boolean useUnsigned = false;
static final public BigInteger BIG_UMASK64 = new BigInteger("FFFFFFFFFFFFFFFF", 16);
static Object
fixUnsigned(Object o, boolean isunsigned) {
if (!useUnsigned || !isunsigned || !(o instanceof Number))
return o;
if (o instanceof Byte) {
int i = ((Byte) o).intValue();
i &= 0xFF;
return i;
}
if (o instanceof Short) {
int i = ((Short) o).intValue();
i &= 0xFFFF;
return i;
}
if (o instanceof Integer) {
long l = ((Integer) o).longValue();
l &= 0xFFFFFFFFL;
return l;
}
if (o instanceof Long) {
long l = (Long) o;
BigInteger bi = BigInteger.valueOf(l);
bi = bi.and(BIG_UMASK64);
return bi;
}
return o; // probably some form of float
}
/**
* Print netcdf "header only" in CDL.
*
* @param fileName open this file
* @param out print to this Writer
* @return true if successful
* @throws java.io.IOException on write error
*/
public static boolean printHeader(String fileName, Writer out) throws java.io.IOException {
return print(fileName, out, false, false, false, false, null, null);
}
/**
* print NcML representation of this netcdf file, showing coordinate variable data.
*
* @param fileName open this file
* @param out print to this Writer
* @return true if successful
* @throws java.io.IOException on write error
*/
public static boolean printNcML(String fileName, Writer out) throws java.io.IOException {
return print(fileName, out, false, true, true, false, null, null);
}
/**
* NCdump that parses a command string, using default options.
* Usage:
* NCdump filename [-ncml] [-c | -vall] [-v varName;...]
*
* @param command command string
* @param out send output here
* @return true if successful
* @throws java.io.IOException on write error
*/
public static boolean print(String command, Writer out) throws java.io.IOException {
return print(command, out, null);
}
/**
* ncdump that parses a command string.
* Usage:
* NCdump filename [-ncml] [-c | -vall] [-v varName;...]
*
* @param command command string
* @param out send output here
* @param ct allow task to be cancelled; may be null.
* @return true if successful
* @throws java.io.IOException on write error
*/
public static boolean print(String command, Writer out, ucar.nc2.util.CancelTask ct) throws java.io.IOException {
// pull out the filename from the command
String filename;
StringTokenizer stoke = new StringTokenizer(command);
if (stoke.hasMoreTokens())
filename = stoke.nextToken();
else {
out.write(usage);
return false;
}
NetcdfFile nc = null;
try {
nc = NetcdfDataset.openFile(filename, ct);
// the rest of the command
int pos = command.indexOf(filename);
command = command.substring(pos + filename.length());
return print(nc, command, out, ct);
} catch (java.io.FileNotFoundException e) {
out.write("file not found= ");
out.write(filename);
return false;
} finally {
if (nc != null) nc.close();
out.flush();
}
}
/**
* ncdump, parsing command string, file already open.
*
* @param nc apply command to this file
* @param command : command string
* @param out send output here
* @param ct allow task to be cancelled; may be null.
* @return true if successful
* @throws java.io.IOException on write error
*/
public static boolean print(NetcdfFile nc, String command, Writer out, ucar.nc2.util.CancelTask ct) throws java.io.IOException {
WantValues showValues = WantValues.none;
boolean ncml = false;
boolean strict = false;
String varNames = null;
useUnsigned = false;
if (command != null) {
StringTokenizer stoke = new StringTokenizer(command);
while (stoke.hasMoreTokens()) {
String toke = stoke.nextToken();
if (toke.equalsIgnoreCase("-help")) {
out.write(usage);
out.write('\n');
return true;
}
if (toke.equalsIgnoreCase("-vall"))
showValues = WantValues.all;
if (toke.equalsIgnoreCase("-c") && (showValues == WantValues.none))
showValues = WantValues.coordsOnly;
if (toke.equalsIgnoreCase("-ncml"))
ncml = true;
if (toke.equalsIgnoreCase("-unsigned"))
useUnsigned = true;
if (toke.equalsIgnoreCase("-cdl") || toke.equalsIgnoreCase("-strict"))
strict = true;
if (toke.equalsIgnoreCase("-v") && stoke.hasMoreTokens())
varNames = stoke.nextToken();
}
}
return print(nc, out, showValues, ncml, strict, varNames, ct);
}
/**
* ncdump-like print of netcdf file.
*
* @param filename NetcdfFile to open
* @param out print to this stream
* @param showAll dump all variable data
* @param showCoords only print header and coordinate variables
* @param ncml print NcML representation (other arguments are ignored)
* @param strict print strict CDL representation
* @param varNames semicolon delimited list of variables whose data should be printed
* @param ct allow task to be cancelled; may be null.
* @return true if successful
* @throws java.io.IOException on write error
*/
public static boolean print(String filename, Writer out, boolean showAll, boolean showCoords,
boolean ncml, boolean strict, String varNames, ucar.nc2.util.CancelTask ct) throws java.io.IOException {
NetcdfFile nc = null;
try {
//nc = NetcdfFileCache.acquire(fileName, ct);
nc = NetcdfDataset.openFile(filename, ct);
return print(nc, out, showAll, showCoords, ncml, strict, varNames, ct);
} catch (java.io.FileNotFoundException e) {
out.write("file not found= ");
out.write(filename);
out.flush();
return false;
} finally {
if (nc != null) nc.close();
}
}
/**
* ncdump-like print of netcdf file.
*
* @param nc already opened NetcdfFile
* @param out print to this stream
* @param showAll dump all variable data
* @param showCoords only print header and coordinate variables
* @param ncml print NcML representation (other arguments are ignored)
* @param strict print strict CDL representation
* @param varNames semicolon delimited list of variables whose data should be printed. May have
* Fortran90 like selector: eg varName(1:2,*,2)
* @param ct allow task to be cancelled; may be null.
* @return true if successful
* @throws java.io.IOException on write error
*/
public static boolean print(NetcdfFile nc, Writer out, boolean showAll, boolean showCoords,
boolean ncml, boolean strict, String varNames, ucar.nc2.util.CancelTask ct) throws java.io.IOException {
WantValues showValues = WantValues.none;
if (showAll)
showValues = WantValues.all;
else if (showCoords)
showValues = WantValues.coordsOnly;
return print(nc, out, showValues, ncml, strict, varNames, ct);
}
///////////////////////////////////////////////////////////////////////////////////////////////////////
// heres where the work is done
/**
* ncdump-like print of netcdf file.
*
* @param nc already opened NetcdfFile
* @param out print to this stream
* @param showValues do you want the variable values printed?
* @param ncml print NcML representation (other arguments are ignored)
* @param strict print strict CDL representation
* @param varNames semicolon delimited list of variables whose data should be printed. May have
* Fortran90 like selector: eg varName(1:2,*,2)
* @param ct allow task to be cancelled; may be null.
* @return true if successful
* @throws java.io.IOException on write error
*/
public static boolean print(NetcdfFile nc, Writer out, WantValues showValues,
boolean ncml, boolean strict, String varNames, ucar.nc2.util.CancelTask ct) throws java.io.IOException {
boolean headerOnly = (showValues == WantValues.none) && (varNames == null);
try {
if (ncml)
writeNcML(nc, out, showValues, null); // output schema in NcML
else if (headerOnly)
nc.writeCDL(new PrintWriter(out), strict); // output schema in CDL form (like ncdump)
else {
PrintWriter ps = new PrintWriter(out);
nc.toStringStart(ps, strict);
ps.print(" data:\n");
if (showValues == WantValues.all) { // dump all data
for (Variable v : nc.getVariables()) {
printArray(v.read(), v.getFullName(), ps, ct);
if (ct != null && ct.isCancel()) return false;
}
} else if (showValues == WantValues.coordsOnly) { // dump coordVars
for (Variable v : nc.getVariables()) {
if (v.isCoordinateVariable())
printArray(v.read(), v.getFullName(), ps, ct);
if (ct != null && ct.isCancel()) return false;
}
}
if ((showValues != WantValues.all) && (varNames != null)) { // dump the list of variables
StringTokenizer stoke = new StringTokenizer(varNames, ";");
while (stoke.hasMoreTokens()) {
String varSubset = stoke.nextToken(); // variable name and optionally a subset
if (varSubset.indexOf('(') >= 0) { // has a selector
Array data = nc.readSection(varSubset);
printArray(data, varSubset, ps, ct);
} else { // do entire variable
Variable v = nc.findVariable(varSubset);
if (v == null) {
ps.print(" cant find variable: " + varSubset + "\n " + usage);
continue;
}
// dont print coord vars if they are already printed
if ((showValues != WantValues.coordsOnly) || v.isCoordinateVariable())
printArray(v.read(), v.getFullName(), ps, ct);
}
if (ct != null && ct.isCancel()) return false;
}
}
nc.toStringEnd(ps);
}
} catch (Exception e) {
e.printStackTrace();
out.write(e.getMessage());
out.flush();
return false;
}
out.flush();
return true;
}
/**
* Print all the data of the given Variable.
*
* @param v variable to print
* @param ct allow task to be cancelled; may be null.
* @return String result
* @throws java.io.IOException on write error
*/
static public String printVariableData(VariableIF v, ucar.nc2.util.CancelTask ct) throws IOException {
Array data = v.read();
/* try {
data = v.isMemberOfStructure() ? v.readAllStructures(null, true) : v.read();
}
catch (InvalidRangeException ex) {
return ex.getMessage();
} */
StringWriter writer = new StringWriter(10000);
printArray(data, v.getFullName(), new PrintWriter(writer), ct);
return writer.toString();
}
/**
* Print a section of the data of the given Variable.
*
* @param v variable to print
* @param sectionSpec string specification
* @param ct allow task to be cancelled; may be null.
* @return String result formatted data ouptut
* @throws IOException on write error
* @throws InvalidRangeException is specified section doesnt match variable shape
*/
static public String printVariableDataSection(Variable v, String sectionSpec, ucar.nc2.util.CancelTask ct) throws IOException, InvalidRangeException {
Array data = v.read(sectionSpec);
StringWriter writer = new StringWriter(20000);
printArray(data, v.getFullName(), new PrintWriter(writer), ct);
return writer.toString();
}
/**
* Print the data array.
*
* @param array data to print.
* @param name title the output.
* @param out send output here.
* @param ct allow task to be cancelled; may be null.
* @throws java.io.IOException on read error
*/
static public void printArray(Array array, String name, PrintWriter out, CancelTask ct) throws IOException {
printArray(array, name, null, out, new Indent(2), ct, true);
out.flush();
}
/**
*
* @deprecated use toString()
*/
static public String printArray(Array array, String name, CancelTask ct) {
return toString(array, name, ct);
}
static public String toString(Array array, String name, CancelTask ct) {
CharArrayWriter carray = new CharArrayWriter(100000);
PrintWriter pw = new PrintWriter(carray);
printArray(array, name, null, pw, new Indent(2), ct, true);
return carray.toString();
}
static private void printArray(Array array, String name, String units, PrintWriter out, Indent ilev, CancelTask ct, boolean printSeq) { // throws IOException {
if (ct != null && ct.isCancel()) return;
if (name != null) out.print(ilev + name + " =");
ilev.incr();
if (array == null) {
out.println("null array for " + name);
ilev.decr();
// throw new IllegalArgumentException("null array for " + name);
return;
}
if ((array instanceof ArrayChar) && (array.getRank() > 0)) {
printStringArray(out, (ArrayChar) array, ilev, ct);
} else if (array.getElementType() == String.class) {
printStringArray(out, array, ilev, ct);
} else if (array instanceof ArraySequence) {
if (printSeq) printSequence(out, (ArraySequence) array, ilev, ct);
} else if (array instanceof ArrayStructure) {
if (array.getSize() == 1)
printStructureData(out, (StructureData) array.getObject(array.getIndex()), ilev, ct);
else
printStructureDataArray(out, (ArrayStructure) array, ilev, ct);
} else if (array.getElementType() == ByteBuffer.class) { // opaque type
array.resetLocalIterator();
while (array.hasNext()) {
printByteBuffer(out, (ByteBuffer) array.next(), ilev);
out.println(array.hasNext() ? "," : ";");// peek ahead
if (ct != null && ct.isCancel()) return;
}
} else if (array instanceof ArrayObject) {
printVariableArray(out, (ArrayObject) array, ilev, ct);
} else {
printArray(array, out, ilev, ct);
}
if (units != null)
out.print(" " + units);
out.print("\n");
ilev.decr();
out.flush();
}
static private void printArray(Array ma, PrintWriter out, Indent indent, CancelTask ct) {
if (ct != null && ct.isCancel()) return;
int rank = ma.getRank();
Index ima = ma.getIndex();
// scalar
if (rank == 0) {
Object o = ma.getObject(ima);
o = fixUnsigned(o, ma.isUnsigned());
out.print(o.toString());
return;
}
int[] dims = ma.getShape();
int last = dims[0];
out.print("\n" + indent + "{");
if ((rank == 1) && (ma.getElementType() != StructureData.class)) {
for (int ii = 0; ii < last; ii++) {
Object o = ma.getObject(ima.set(ii));
o = fixUnsigned(o, ma.isUnsigned());
out.print(o.toString());
if (ii != last - 1) out.print(", ");
if (ct != null && ct.isCancel()) return;
}
out.print("}");
return;
}
indent.incr();
for (int ii = 0; ii < last; ii++) {
Array slice = ma.slice(0, ii);
printArray(slice, out, indent, ct);
if (ii != last - 1) out.print(",");
if (ct != null && ct.isCancel()) return;
}
indent.decr();
out.print("\n" + indent + "}");
}
static void printStringArray(PrintWriter out, ArrayChar ma, Indent indent, ucar.nc2.util.CancelTask ct) {
if (ct != null && ct.isCancel()) return;
int rank = ma.getRank();
if (rank == 1) {
out.print(" \"" + ma.getString() + "\"");
return;
}
if (rank == 2) {
boolean first = true;
ArrayChar.StringIterator iter = ma.getStringIterator();
while (iter.hasNext()) {
if (!first) out.print(", ");
out.print("\"" + iter.next() + "\"");
first = false;
if (ct != null && ct.isCancel()) return;
}
return;
}
int[] dims = ma.getShape();
int last = dims[0];
out.print("\n" + indent + "{");
indent.incr();
for (int ii = 0; ii < last; ii++) {
ArrayChar slice = (ArrayChar) ma.slice(0, ii);
printStringArray(out, slice, indent, ct);
if (ii != last - 1) out.print(",");
if (ct != null && ct.isCancel()) return;
}
indent.decr();
out.print("\n" + indent + "}");
}
private static void printByteBuffer(PrintWriter out, ByteBuffer bb, Indent indent) {
out.print(indent + "0x");
int last = bb.limit() - 1;
if(last < 0)
out.printf("00");
else
for (int i = 0; i <= last; i++) {
out.printf("%02x", bb.get(i));
}
}
static void printStringArray(PrintWriter out, Array ma, Indent indent, ucar.nc2.util.CancelTask ct) {
if (ct != null && ct.isCancel()) return;
int rank = ma.getRank();
Index ima = ma.getIndex();
if (rank == 0) {
out.print(" \"" + ma.getObject(ima) + "\"");
return;
}
if (rank == 1) {
boolean first = true;
for (int i = 0; i < ma.getSize(); i++) {
if (!first) out.print(", ");
out.print(" \"" + ma.getObject(ima.set(i)) + "\"");
first = false;
}
return;
}
int[] dims = ma.getShape();
int last = dims[0];
out.print("\n" + indent + "{");
indent.incr();
for (int ii = 0; ii < last; ii++) {
ArrayObject slice = (ArrayObject) ma.slice(0, ii);
printStringArray(out, slice, indent, ct);
if (ii != last - 1) out.print(",");
//out.print("\n");
}
indent.decr();
out.print("\n" + indent + "}");
}
static private void printStructureDataArray(PrintWriter out, ArrayStructure array, Indent indent, ucar.nc2.util.CancelTask ct) { // throws IOException {
StructureDataIterator sdataIter = array.getStructureDataIterator();
int count = 0;
try {
while (sdataIter.hasNext()) {
StructureData sdata = sdataIter.next();
out.println("\n" + indent + "{");
printStructureData(out, sdata, indent, ct);
//ilev.setIndentLevel(saveIndent);
out.print(indent + "} " + sdata.getName() + "(" + count + ")");
if (ct != null && ct.isCancel()) return;
count++;
}
} catch (IOException e) {
e.printStackTrace(); // shouldnt happen ?
} finally {
sdataIter.finish();
}
}
static private void printVariableArray(PrintWriter out, ArrayObject array, Indent indent, CancelTask ct) { // throws IOException {
out.println("\n" + indent + "{");
indent.incr();
IndexIterator iter = array.getIndexIterator();
while (iter.hasNext()) {
Array data = (Array) iter.next();
printArray(data, out, indent, ct);
}
indent.decr();
out.print(indent + "}");
}
static private void printSequence(PrintWriter out, ArraySequence seq, Indent indent, CancelTask ct) { // throws IOException {
StructureDataIterator iter = seq.getStructureDataIterator();
try {
while (iter.hasNext()) {
StructureData sdata = iter.next();
out.println("\n" + indent + "{");
printStructureData(out, sdata, indent, ct);
out.print(indent + "} " + sdata.getName());
if (ct != null && ct.isCancel()) return;
}
} catch (IOException e) {
e.printStackTrace(); // shouldnt happen ??
} finally {
iter.finish();
}
}
/**
* Print contents of a StructureData.
*
* @param out send output here.
* @param sdata StructureData to print.
* @throws java.io.IOException on read error
*/
static public void printStructureData(PrintWriter out, StructureData sdata) throws IOException {
printStructureData(out, sdata, new Indent(2), null);
out.flush();
}
static private void printStructureData(PrintWriter out, StructureData sdata, Indent indent, CancelTask ct) { // throws IOException {
indent.incr();
for (StructureMembers.Member m : sdata.getMembers()) {
Array sdataArray = sdata.getArray(m);
printArray(sdataArray, m.getName(), m.getUnitsString(), out, indent, ct, true);
if (ct != null && ct.isCancel()) return;
}
indent.decr();
}
static public String toString(StructureData sdata) throws IOException {
CharArrayWriter carray = new CharArrayWriter(1000);
PrintWriter pw = new PrintWriter(carray);
for (StructureMembers.Member m : sdata.getMembers()) {
Array memData = sdata.getArray(m);
if (memData instanceof ArrayChar)
pw.print(((ArrayChar) memData).getString());
else
printArray(memData, pw);
pw.print(',');
}
return carray.toString();
}
/**
* Print array as undifferentiated sequence of values.
*
* @param ma any Array except ArrayStructure
* @param out print to here
*/
static public void printArray(Array ma, PrintWriter out) {
ma.resetLocalIterator();
while (ma.hasNext()) {
out.print(ma.next());
out.print(' ');
}
}
static public void printArray(Array ma) {
PrintWriter out = new PrintWriter( new OutputStreamWriter(System.out, CDM.utf8Charset));
printArray(ma, out);
out.flush();
}
static public String toString(Array ma) throws IOException {
return toString(ma, "", null);
}
//////////////////////////////////////////////////////////////////////////////////////
// standard NCML writing.
/**
* Write the NcML representation for a file.
* Note that ucar.nc2.dataset.NcMLWriter has a JDOM implementation, for complete NcML.
* This method implements only the "core" NcML for plain ole netcdf files.
*
* @param ncfile write NcML for this file
* @param os write to this Writer. Must be using UTF-8 encoding (where applicable)
* @param showCoords show coordinate variable values.
* @param url use this for the url attribute; if null use getLocation(). // ??
* @throws IOException on write error
*/
static public void writeNcML(NetcdfFile ncfile, java.io.Writer os, boolean showCoords, String url) throws IOException {
writeNcML(ncfile, os, showCoords ? WantValues.coordsOnly : WantValues.none, url);
}
static public void writeNcML(NetcdfFile ncfile, java.io.Writer os, WantValues showValues, String url) throws IOException {
writeNcML(ncfile, new Formatter(os), showValues, url);
}
static public void writeNcML(NetcdfFile ncfile, Formatter out, WantValues showValues, String url) throws IOException {
out.format("%n");
out.format("%n%n", StringUtil2.quoteXmlAttribute(url));
else
out.format(" location='%s' >%n%n", StringUtil2.quoteXmlAttribute(URLnaming.canonicalizeWrite(ncfile.getLocation())));
if (ncfile.getId() != null)
out.format(" id='%s'%n", StringUtil2.quoteXmlAttribute(ncfile.getId()));
if (ncfile.getTitle() != null)
out.format(" title='%s'%n", StringUtil2.quoteXmlAttribute(ncfile.getTitle()));
writeNcMLGroup(ncfile, ncfile.getRootGroup(), out, new Indent(2), showValues);
out.format(" %n");
out.flush();
}
static public void writeNcMLVariable(Variable v, Formatter out) throws IOException {
if (v instanceof Structure) {
writeNcMLStructure((Structure) v, out, new Indent(2), WantValues.none);
} else {
writeNcMLVariable(v, out, new Indent(2), WantValues.none);
}
}
static private void writeNcMLGroup(NetcdfFile ncfile, Group g, Formatter out, Indent indent, WantValues showValues) throws IOException {
if (g != ncfile.getRootGroup())
out.format("%s%n", indent, StringUtil2.quoteXmlAttribute(g.getShortName()));
indent.incr();
List dimList = g.getDimensions();
for (Dimension dim : dimList) {
out.format("%s attList = g.getAttributes();
for (Attribute att : attList) {
writeNcMLAtt(att, out, indent);
}
if (attList.size() > 0)
out.format("%n");
for (Variable v : g.getVariables()) {
if (v instanceof Structure) {
writeNcMLStructure((Structure) v, out, indent, showValues);
} else {
writeNcMLVariable(v, out, indent, showValues);
}
}
// nested groups
List groupList = g.getGroups();
for (int i = 0; i < groupList.size(); i++) {
if (i > 0) out.format("%n");
Group nested = (Group) groupList.get(i);
writeNcMLGroup(ncfile, nested, out, indent, showValues);
}
indent.decr();
if (g != ncfile.getRootGroup()) {
out.format("%s %n", indent);
}
}
static private void writeNcMLStructure(Structure s, Formatter out, Indent indent, WantValues showValues) throws IOException {
out.format("%s 0) {
writeNcMLDimension(v, out);
}
indent.incr();
boolean closed = false;
// any attributes ?
java.util.List atts = v.getAttributes();
if (atts.size() > 0) {
out.format(" >%n");
closed = true;
for (Attribute att : atts) {
writeNcMLAtt(att, out, indent);
}
}
// print data ?
if ((showValues == WantValues.all) ||
((showValues == WantValues.coordsOnly) && v.isCoordinateVariable())) {
if (!closed) {
out.format(" >%n");
closed = true;
}
writeNcMLValues(v, out, indent);
}
indent.decr();
// close variable element
if (!closed)
out.format(" />%n");
else {
out.format("%s%n", indent);
}
}
// LOOK anon dimensions
static private void writeNcMLDimension(Variable v, Formatter out) {
out.format(" shape='");
java.util.List dims = v.getDimensions();
for (int j = 0; j < dims.size(); j++) {
Dimension dim = dims.get(j);
if (j != 0)
out.format(" ");
if (dim.isShared())
out.format("%s", StringUtil2.quoteXmlAttribute(dim.getShortName()));
else
out.format("%d", dim.getLength());
}
out.format("'");
}
@SuppressWarnings({"ObjectToString"})
static private void writeNcMLAtt(Attribute att, Formatter out, Indent indent) {
out.format("%s", out, 0, indent);
IndexIterator ii = data.getIndexIterator();
while (ii.hasNext())
width = formatValues(ii.next() + " ", out, width, indent);
formatValues(" \n", out, width, indent);
}
static private int formatValues(String s, Formatter out, int width, Indent indent) {
int len = s.length();
int totalWidth = 80;
if (len + width > totalWidth) {
out.format("%n%s", indent);
width = indent.toString().length();
}
out.format("%s", s);
width += len;
return width;
}
private static char[] org = {'\b', '\f', '\n', '\r', '\t', '\\', '\'', '\"'};
private static String[] replace = {"\\b", "\\f", "\\n", "\\r", "\\t", "\\\\", "\\\'", "\\\""};
/**
* Replace special characters '\t', '\n', '\f', '\r'.
*
* @param s string to quote
* @return equivilent string replacing special chars
*/
static public String encodeString(String s) {
return StringUtil2.replace(s, org, replace);
}
////////////////////////////////////////////////////////////////////////////////////////////
/**
* Main program.
* ucar.nc2.NCdump filename [-cdl | -ncml] [-c | -vall] [-v varName1;varName2;..] [-v varName(0:1,:,12)]
*
where:
* - filename : path of any CDM readable file
*
- cdl or ncml: output format is CDL or NcML
*
- -vall : dump all variable data
*
- -c : dump coordinate variable data
*
- -v varName1;varName2; : dump specified variable(s)
*
- -v varName(0:1,:,12) : dump specified variable section
*
* Default is to dump the header info only.
*
* @param args arguments
*/
public static void main(String[] args) {
if (args.length == 0) {
System.out.println(usage);
return;
}
StringBuilder sbuff = new StringBuilder();
for (String arg : args) {
sbuff.append(arg);
sbuff.append(" ");
}
try {
Writer writer = new BufferedWriter(new OutputStreamWriter(System.out, CDM.utf8Charset));
NCdumpW.print(sbuff.toString(), writer, null);
} catch (java.io.IOException ioe) {
ioe.printStackTrace();
}
}
}
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