Package ucar.ma2

Examples of ucar.ma2.Index4D

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      GridDatatype grid = gds.findGridDatatype(gridName);
      GridCoordSystem gcsOrg = grid.getCoordinateSystem();
      CoordinateAxis1DTime timeAxis = gcsOrg.getTimeAxis1D();

      // make subset if needed
      Range timeRange = null;
      if ((dateRange != null) && (timeAxis != null)) {
        int startIndex = timeAxis.findTimeIndexFromDate(dateRange.getStart().getDate());
        int endIndex = timeAxis.findTimeIndexFromDate(dateRange.getEnd().getDate());
        if (startIndex < 0)
          throw new InvalidRangeException("start time=" + dateRange.getStart().getDate() + " must be >= " + timeAxis.getTimeDate(0));
        if (endIndex < 0)
          throw new InvalidRangeException("end time=" + dateRange.getEnd().getDate() + " must be >= " + timeAxis.getTimeDate(0));
        timeRange = new Range(startIndex, endIndex);
      }

      if ((null != timeRange) || (zRange != null) || (llbb != null) || (horizStride > 1)) {
        grid = grid.makeSubset(timeRange, zRange, llbb, 1, horizStride, horizStride);
      }
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  public boolean hasNext() { // have to actually fetch the thing here
    if (totalNelemsDone >= totalNelems) return false;

    if ((index == null) || !index.hasNext()) { // get new data node
      try {
        Section dataSection;
        DataChunk dataChunk;

        while (true) { // look for intersecting sections

          if (!chunkIterator.hasNext()) {
            next = null;
            return false;
          }

          // get next dataChunk
          try {
            dataChunk = chunkIterator.next();
          } catch (IOException e) {
            e.printStackTrace();
            next = null;
            return false;
          }

          // make the dataSection for this chunk
          dataSection = new Section(dataChunk.offset, chunkSize);
          if (dataSection.intersects(want)) // does it intersect ?
            break;
        }

        if (debug)
          System.out.println(" found intersecting section: " + dataSection + " for filePos " + dataChunk.filePos);
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  public boolean hasNext() { // have to actually fetch the thing
    if (totalNelemsDone >= totalNelems) return false;

    if ((index == null) || !index.hasNext()) { // get new data node
      try {
        Section dataSection;
        DataChunk dataChunk;

        while (true) { // look for intersecting sections
          if (!chunkIterator.hasNext()) {
            next = null;
            return false;
          }

          // get next dataChunk
          try {
            dataChunk = chunkIterator.next();
          } catch (IOException e) {
            e.printStackTrace();
            next = null;
            return false;
          }

          // make the dataSection for this chunk
          dataSection = new Section(dataChunk.getOffset(), chunkSize);
          if (debugIntersection)
            System.out.println(" test intersecting: " + dataSection + " want: " + want);
          if (dataSection.intersects(want)) // does it intersect ?
            break;
        }

        if (debug)
          System.out.println(" found intersecting dataSection: " + dataSection+" intersect= "+dataSection.intersect(want));

        index = new IndexChunkerTiled(dataSection, want); // new indexer into this chunk
        next = new Chunk( dataChunk.getByteBuffer()); // this does the uncompression

      } catch (InvalidRangeException e) {
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    this.done = 0;

    // LOOK - need test for "all" common case

    // The actual wanted data we can get from this section
    Section intersect = dataSection.intersect(wantSection);
    this.total = intersect.computeSize();
    if (total <= 0) {
      System.out.println("hey");
    }
    assert total > 0;
    int varRank = intersect.getRank();

    // create the List<Dim>
    // Section shifted = intersect.shiftOrigin(dataSection); // want reletive to dataSection
    int wantStride = 1;
    int dataStride = 1;
    for (int ii = varRank - 1; ii >= 0; ii--) {
      Range dr = dataSection.getRange(ii);
      Range wr = wantSection.getRange(ii);
      Range ir = intersect.getRange(ii);
      dimList.add(new Dim(dr, wr, ir, dataStride, wantStride)); // note reversed : fastest first
      dataStride *= dr.length();
      wantStride *= wr.length();
    }

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      NetcdfFile ncfile = TestH5.open(filename);
      //System.out.println("\n"+ncfile);

      for (Variable v : ncfile.getVariables()) {
        if (v.getSize() > max_size) {
          Section s = makeSubset(v);
          System.out.println("  Try to read variable " + v.getNameAndDimensions() + " size= " + v.getSize() + " section= " + s);
          v.read(s);
        } else {
          System.out.println("  Try to read variable " + v.getNameAndDimensions() + " size= " + v.getSize());
          v.read();
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  static int max_size = 1000 * 1000 * 10;
  static Section makeSubset(Variable v) throws InvalidRangeException {
    int[] shape = v.getShape();
    shape[0] = 1;
    Section s = new Section(shape);
    long size = s.computeSize();
    shape[0] = (int) Math.max(1, max_size / size);
    return new Section(shape);
  }
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    if (null == axis) throw new IllegalArgumentException("There is no GeoZ coordinate");
    return readValue( axis, fromVar, index);
  }

  public double readValue(Variable targetVar, Variable fromVar, int[] index) throws InvalidRangeException, IOException {
    Section axisElement = mapIndex( targetVar, fromVar, index);
    Array result = targetVar.read(axisElement);
    return result.nextDouble();
  }
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  }

  public Section mapIndex(Variable targetVar, Variable fromVar, int[] fromIndex) throws InvalidRangeException {
    List<Dimension> toDims = targetVar.getDimensions();
    List<Dimension> fromDims = fromVar.getDimensions();
    Section result = new Section();

    // each dimension in the target must be present in the source
    for (int i=0; i<toDims.size(); i++) {
      Dimension dim = toDims.get(i);
      int varIndex = fromDims.indexOf(toDims.get(i));
      if (varIndex < 0) throw new IllegalArgumentException("Dimension "+dim+" does not exist");
      result.appendRange(fromIndex[varIndex], fromIndex[varIndex]);
    }
    return result;
  }
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    Variable v2 = ncfile.findVariable("Opaque");
    assert v2 != null;

    Array data = v2.read();
    assert data.getElementType() == ByteBuffer.class : data.getElementType();
    System.out.println( "data size= "+new Section(data.getShape()));
    NCdump.printArray(data, "Opaque data", System.out, null);


    Array odata = v2.read(new Section("1:20"));
    assert odata.getElementType() == ByteBuffer.class;
    assert odata.getSize() == 20;
    ncfile.close();
  }
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    // try subset
    data = v.read("0:9:2, :");
    NCdumpW.printArray(data, "read(0:9:2,:)",  new PrintWriter( System.out), null);

    data = v.read(new Section().appendRange(0,9,2).appendRange(null));
    NCdumpW.printArray(data, "read(Section)",  new PrintWriter( System.out), null);

    // fail
    //int[] origin = new int[] {0, 0};
    //int[] size = new int[] {3, -1};
    //data = v.read(origin, size);

    // from bruno
    int initialIndex = 5;
    int finalIndex = 5;
    data = v.read(initialIndex + ":" + finalIndex + ",:");
    //NCdumpW.printArray(data, "read()",  new PrintWriter(System.out), null);

    System.out.println("Size: " + data.getSize());
    System.out.println("Data: " + data);
    System.out.println("Class: " + data.getClass().getName());
    // loop over outer dimension

    int x = 0;
    while (data.hasNext()) {
      Array as = (Array) data.next(); // inner variable length array of short
      System.out.println("Shape: " + new Section(as.getShape()));
      System.out.println(as);
    }


    ncfile.close();
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  • org.geotools.imageio.netcdf.NetCDFImageReader
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