Re: 20020607: Java netCDF read error

Normally you should show what the error message is.

I assume you have a class cast exception on

Iterator gi = nc.getGlobalAttributeIterator();
while( gi.hasNext() ) {
  Variable v = (Variable) gi.next();

The docs say:
getGlobalAttributeIterator
public java.util.Iterator getGlobalAttributeIterator()
  Returns the set of attributes associated with this file, also know as the
"global" attributes. CHANGE TO GENERIC


    Returns:
    Iterator objects are type Attribute
So the iterator returns objects of type Attribute, not Variable


>
> ------- Forwarded Message
>
> >From: address@hidden
> >Organization: NOAA/NODC
> >Keywords: 200206071844.g57IiHJ14153 netCDF Java
>
>                                            June 7, 2002
> To Whom It May Concern:
>
>    The following 4 Java modules successfully read
> data from a "netCDF" file.
>
>    In attempting to read global data, however, I was
> not successful.  The failure is shown in the commented out
> portion of "dumpCDF.java" found near the beginning
> of the while loop.
>
>    Could you please send me code which will work.  Or,
> please contact me somehow.
>
>
>
>                           Robert Van Wie
>
>                       at "address@hidden"
>                       also at "address@hidden"
>
>
>
> import ucar.ma2.*;
> import ucar.nc2.*;
> import java.io.IOException;
> import java.util.*;
> import java.util.Iterator;
>
> public class dumpCDF extends aux {
>
>   public static void main( String args[] ) {
>
>      if (args.length > 0 ) new dumpCDF( args[0], args[1] );
>        else new dumpCDF( "example.nc", "outCDF" );
>   }
>
>   public dumpCDF( String inFile, String outFile ) {  // constructor
>     int    numDep = 0;
>     byte   ix = 0;
>      short ig = 0;
>     String global = "";
>     String defName = "";
>     String DP = "Depth";
>
>    try { NetcdfFile nc = new NetcdfFile( inFile );   // readonly
>
> /*    Iterator gi = nc.getGlobalAttributeIterator();      does not work !
>       while( gi.hasNext() ) {
>         Variable v = (Variable) gi.next();
>         Array varMa = v.read();
>         global = v.getName();
>         System.out.print( v.getName() + " =" );
>         global = findAttValueIgnoreCase( null, "title", defName );
>         System.out.println( ig + "  global " + global );
>         ig++;
>       }     // end while  */
>
>       Iterator it = nc.getVariableIterator();
>       while( it.hasNext() ) {
>         Variable v = (Variable) it.next();
>         Array varMa = v.read();
>         var = v.getName();
>         varCode = getParmCode();        // numeric identifier of variable
>         if ( varCode > -1 ) {
>           array = ArrayToString( varMa );
>           if ( varCode == 0 ) {                       // depth/press
>             numDep = store( array, varCode );         // store variable in
"depVal"
>             alignDepth( numDep );
>             if ( var.indexOf( "press" ) > -1 ) DP = "Press";
>             ix++;
>           } else store( array, varCode );             // store variable in
"depVal"
>           if ( varCode == 2 ) {                       // salinity
>             alignSal( numDep );                       // align salinity
column
>             for ( int l=0; l < numDep; l++ )
>               Writer(
GAP9+depVal[0][l]+GAP8+depVal[1][l]+GAP7+depVal[2][l], outFile );
>           }
>         } else {                                     // non-profile
variable
>            if (var.startsWith( "woce_date") ) WOCEdate=ArrayToString(
varMa );
>            if ( var.startsWith( "woce_time" ) ) {    // process woce_time
>              woce_time = ArrayToString( varMa );
>              if ( woce_time.length() < 6 ) WOCEtime = "0" + woce_time;
>                else WOCEtime = woce_time;
>              myTime = parse( WOCEtime );            // change format of
time
>              myDate = parse( WOCEdate );            // change format of
date
>              Writer( "\n    Date & Time: " + myDate + "  " + myTime ,
outFile );
>            }
>            if ( var.startsWith( "longitude" ) ) {
>              ix++;
>              longitude = ArrayToString( varMa );
>              Writer( "\n    Position: Latitude  " + latitude + ";
Longitude  " + longitude, outFile );
>            }
>            else if ( var.startsWith( "latitude" ) ) latitude =
ArrayToString( varMa );
>         }
>         if ( ix > 1 ) {
>           Writer( "\n           " + DP + "    Temperature   Salinity",
outFile );
>           ix = 0;
>         }
>       }     // end while
>     } catch (java.io.IOException e) { e.printStackTrace(); }
>   }         // end dumpCDF constructor
>
>   public String ArrayToString( Array ma ) {
>      StringBuffer buf =
>        new StringBuffer( toArray( ma, new IndentLevel() ));
>      return buf.toString();
>   }          // end ArrayToString
>
>   private String toArray( Array ma, IndentLevel ilev ) {
>     final int rank = ma.getRank();
>
>     Index ima = ma.getIndex();
>     if ( rank == 0 ) return ma.getObject(ima).toString();
>
>     StringBuffer buf = new StringBuffer();
>     ilev.incr();
>     final int [] dims = ma.getShape();
>     final int    last = dims[0];
>     for ( int ii=0; ii < last; ii++ ) {
>        Array slice = ma.slice( 0, ii );
>        buf.append( toArray( slice, ilev ) );
>        if ( varCode == 0 )
>          if ( ii != last-1 ) buf.append( " " );
>     }
>     ilev.decr();
>     if ( rank > 1 ) buf.append( "\n" + ilev.getIndent() );
>     return buf.toString();
>   }                // end toArray
>
> }                                            // end class dumpCDF
> import ucar.ma2.*;
> import ucar.nc2.*;
> import java.io.*;
> import java.io.IOException;
> import java.util.*;
>
> public class OrigAux {
>
>   final static String GAP7 = "       ", GAP8 = "        ", GAP9 = "
";
>   final static String BLANKS = "      ";
>   byte    varCode = -2;            // numeric identifier of data column
>    int    maxTempL = 0;            // string length of highest temperature
>   String  WOCEdate, WOCEtime, woce_time, depVal[][] = new String[3][9000];
>   String  var, array, myDate, myTime, latitude, longitude, park;
>   IndentLevel il;                  // id of "IndentLevel" class
>
>   protected void alignDepth( int numDp ) {
>                                             // align depth column
>     int lenDiff, ln, len;
>
>     len = depVal[0][numDp-1].length();       // string length of max depth
>     for ( int n=0; n < numDp-1; n++ ) {
>        park = depVal[0][n];
>        ln = park.length();
>        lenDiff = len - ln;
>        if ( lenDiff > 0 ) depVal[0][n] = BLANKS.substring( 0, lenDiff ) +
park;
>     }
>     maxTempL = 0;
>   }                   // end alignDepth
>
>   protected void alignSal( int numDp ) {
>                                             // align salinity column
>       int lenDiff, ln;
>    String sal = "";
>
>      for( int n=0; n < numDp; n++ ) {
>        park = depVal[1][n];
>        ln = park.length();
>        lenDiff = maxTempL - ln;
>        if ( lenDiff > 0 ) {
>          sal = depVal[2][n];
>          depVal[2][n] = BLANKS.substring( 0, lenDiff ) + sal;
>        }
>      }        // for loop
>   }           // end alignSal
>
>   protected void Writer( String text, String outfle ) {    // write single
string
>     try {
>       Writer w = new BufferedWriter( new FileWriter( outfle, true ));
>       w.write( text + "\n" );
>       w.close();
>     }                                 // try
>     catch (IOException e ) { System.err.println(outfle+" Output file
error..."); }
>     catch ( Exception e ) { System.err.println("Input error..Exception in
method Writer"); }
>   }                           // end Writer
>
> }      // end class OrigAux.java
> import ucar.ma2.*;
> import ucar.nc2.*;
> import java.io.IOException;
> import java.util.*;
>
> public class aux extends OrigAux {
>
>   protected int store( String array, byte i ) {
>      int l = 0;                                      // store in "depVal"
array
>      int ln = 0;
>
>      StringTokenizer st = new StringTokenizer(array);
>      while ( st.hasMoreTokens() ) {
>        depVal[i][l] = st.nextToken().trim();
>        if ( i == 1 ) {
>          ln =  depVal[1][l].length();               // length of
temperature string
>          if ( ln > maxTempL ) maxTempL = ln;        // max temp length
>        }
>        l++;                                         // depth level counter
>      }
>      return l;
>   }         // end store
>
>   protected byte getParmCode( ) {                     // depth/press:    0
>      byte parmCode = -1;                              // temperature:    1
>                                                       // salinity   :    2
>      if (var.startsWith("press") ) parmCode = 0;
>        else if (var.startsWith("dep") ) parmCode = 0;
>          else if (var.startsWith("temp") ) parmCode = 1;
>            else if (var.startsWith("sal") ) parmCode = 2;
>      return parmCode;
>   }
>
>   protected String parse( String primative ) {
>                                        // reformat date & time fields
>      String part[] = new String[3];
>      String sep = "/";               // date field seperator
>        byte n = 0, end = 4;          // length of year field
>
>     if ( primative.length() == 6 ) {    // length of time field
>        sep = ":";                       // time field seperator
>        end = 2;                         // length of hour field
>     }
>        String whole = "";               // will hold reformatted string
>        for ( byte i=0; i < 3; i++ ) {
>           part[i] = primative.substring( n, end );  // individual field
>           n = end;
>           end += 2;
>           whole += part[i];
>           if ( i < 2 ) whole += sep;
>        }
>        return whole;                   // return reformatted string
>   }                       // end method parse
>
> }      // end class aux.java
> import ucar.ma2.*;
> import ucar.nc2.*;
> import java.io.IOException;
> import java.util.*;
>
> public class IndentLevel {
>
>     private int indentation, level = 0;
>     private StringBuffer indent, blanks;
>
>     IndentLevel() { this(4); }     // end constructor
>
>     IndentLevel( int indentation) {
>       if (indentation > 0) this.indentation = indentation;
>       indent = new StringBuffer();
>       blanks = new StringBuffer();
>       for( int i=0; i < indentation; i++ )
>          blanks.append(" ");
>     }                                   // end constructor
>
>     public void incr() {
>         level += indentation;
>         indent.append( blanks );
>     }
>
>     public void decr() {
>         level -= indentation;
>         indent.setLength( level );
>     }
>
>     public String getIndent() {
>         return indent.toString();
>     }
>   }           // end class IndentLevel
>
>
> ------- End of Forwarded Message
>