private void showValues2D(CoordinateAxis2D axis2D) {

    Formatter f = new Formatter();

    if (axis2D.isInterval()) {
      ArrayDouble.D2 coords = axis2D.getCoordValuesArray();
      ArrayDouble.D3 bounds = axis2D.getCoordBoundsArray();
      if (bounds == null) {
        infoTA.appendLine("No bounds for interval " + axis2D.getFullName());
        return;
      }

      IndexIterator coordIter = coords.getIndexIterator();
      IndexIterator boundsIter = bounds.getIndexIterator();
      while (coordIter.hasNext()) {
        double coordValue = coordIter.getDoubleNext();
        if (!boundsIter.hasNext()) break;
        double bounds1 = boundsIter.getDoubleNext();
        if (!boundsIter.hasNext()) break;
        double bounds2 = boundsIter.getDoubleNext();
        f.format("%f (%f,%f) = %f%n", coordValue, bounds1, bounds2, bounds2 - bounds1);
      }

    } else {
      ArrayDouble.D2 coords = axis2D.getCoordValuesArray();
      IndexIterator coordIter = coords.getIndexIterator();
      while (coordIter.hasNext()) {
        double coordValue = coordIter.getDoubleNext();
        f.format("%f%n", coordValue);
      }
    }

    infoTA.appendLine(f.toString());
  }
  private void writeCoordinateVariable(VariableEntry variable, NetcdfFileWriteable ncFile)
      throws IOException, InvalidRangeException {

    int[] dimensions = {variable.getSize()};
    Array array;

    // so far, everything is a float or an int
    // way too much code duplication but I'm done fightin java for now
    if (variable.getType() == DataType.INT) {
      array = new ArrayInt(dimensions);
      int tempInt = 0;
      IndexIterator iter = array.getIndexIterator();

      while (iter.hasNext()) {
        iter.getIntNext();
        iter.setIntCurrent(tempInt);
        tempInt++;
      }

      ncFile.write(variable.getVariableName(), array);
    } else if (variable.getType() == DataType.FLOAT) {
      array = new ArrayFloat(dimensions);
      float tempFloat = 0;
      IndexIterator iter = array.getIndexIterator();

      while (iter.hasNext()) {
        iter.getFloatNext();
        iter.setFloatCurrent(tempFloat);
        tempFloat++;
      }

      ncFile.write(variable.getVariableName(), array);
    } else if (variable.getType() == DataType.LONG) {
      array = new ArrayLong(dimensions);
      long tempLong = 0;
      IndexIterator iter = array.getIndexIterator();

      while (iter.hasNext()) {
        iter.getLongNext();
        iter.setLongCurrent(tempLong);
        tempLong++;
      }

      ncFile.write(variable.getVariableName(), array);
    }

    // ncFile.write(variable.getVariableName(),array);

  }
 // @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);
 }
Beispiel #4
0
  public void testEnhanceDefer() throws IOException {
    NetcdfDataset ncd =
        NetcdfDataset.openDataset(
            filename, EnumSet.of(NetcdfDataset.Enhance.ScaleMissing), -1, null, null);
    VariableDS enhancedVar = (VariableDS) ncd.findVariable("t1");

    NetcdfDataset ncdefer =
        NetcdfDataset.openDataset(
            filename, EnumSet.of(NetcdfDataset.Enhance.ScaleMissingDefer), -1, null, null);
    VariableDS deferVar = (VariableDS) ncdefer.findVariable("t1");

    Array data = enhancedVar.read();
    Array dataDefer = deferVar.read();

    System.out.printf("Enhanced=");
    NCdumpW.printArray(data);
    System.out.printf("%nDeferred=");
    NCdumpW.printArray(dataDefer);
    System.out.printf("%nProcessed=");

    CompareNetcdf2 nc = new CompareNetcdf2(new Formatter(System.out), false, false, true);
    assert !nc.compareData(enhancedVar.getShortName(), data, dataDefer, false);

    IndexIterator ii = dataDefer.getIndexIterator();
    while (ii.hasNext()) {
      double val = deferVar.convertScaleOffsetMissing(ii.getDoubleNext());
      ii.setDoubleCurrent(val);
    }
    NCdumpW.printArray(dataDefer);

    assert nc.compareData(enhancedVar.getShortName(), data, dataDefer, false);

    ncd.close();
    ncdefer.close();
  }
  public void testAggCoordVar(NetcdfFile ncfile) {
    Variable time = ncfile.findVariable("time");
    assert null != time;

    assert time.getShortName().equals("time");
    assert time.getRank() == 1;
    assert time.getSize() == 3;
    assert time.getShape()[0] == 3;
    assert time.getDataType() == DataType.DOUBLE;

    assert time.getDimension(0) == ncfile.findDimension("time");

    try {
      Array data = time.read();
      assert data.getRank() == 1;
      assert data.getSize() == 3;
      assert data.getShape()[0] == 3;
      assert data.getElementType() == double.class;

      int count = 0;
      IndexIterator dataI = data.getIndexIterator();
      while (dataI.hasNext()) {
        assert Misc.closeEnough(dataI.getDoubleNext(), result[count]);
        count++;
      }

    } catch (IOException io) {
      io.printStackTrace();
      assert false;
    }
  }
 /**
  * Read data from a top level Variable and send data to a WritableByteChannel.
  *
  * @param v2 Variable
  * @param section wanted section of data of Variable. The section list is a list of ucar.ma2.Range
  *     which define the requested data subset.
  * @param channel WritableByteChannel object - channel that can write bytes.
  * @return the number of bytes written, possibly zero.
  */
 public long readToByteChannel11(
     ucar.nc2.Variable v2, Section section, WritableByteChannel channel)
     throws java.io.IOException, ucar.ma2.InvalidRangeException {
   Array data = readData(v2, section);
   float[] ftdata = new float[(int) data.getSize()];
   byte[] bytedata = new byte[(int) data.getSize() * 4];
   IndexIterator iter = data.getIndexIterator();
   int i = 0;
   ByteBuffer buffer = ByteBuffer.allocateDirect(bytedata.length);
   while (iter.hasNext()) {
     ftdata[i] = iter.getFloatNext();
     bytedata[i] = new Float(ftdata[i]).byteValue();
     buffer.put(bytedata[i]);
     i++;
   }
   buffer = ByteBuffer.wrap(bytedata);
   // write the bytes to the channel
   int count = channel.write(buffer);
   System.out.println("COUNT=" + count);
   // check if all bytes where written
   if (buffer.hasRemaining()) {
     // if not all bytes were written, move the unwritten bytes to the beginning and
     // set position just after the last unwritten byte
     buffer.compact();
   } else {
     buffer.clear();
   }
   return (long) count;
 }
 private void convertScaleOffsetUnsignedInt(IndexIterator iterIn, IndexIterator iterOut) {
   boolean checkMissing = useNaNs && hasMissing();
   while (iterIn.hasNext()) {
     int valb = iterIn.getIntNext();
     double val = scale * DataType.unsignedIntToLong(valb) + offset;
     iterOut.setDoubleNext(checkMissing && isMissing_(val) ? Double.NaN : val);
   }
 }
  /**
   * Translate missing data to NaNs. Data must be DOUBLE or FLOAT
   *
   * @param in convert this array
   * @return same array, with missing values replaced by NaNs
   */
  private Array convertMissing(Array in) {
    if (debugRead) System.out.println("convertMissing ");

    IndexIterator iterIn = in.getIndexIterator();
    if (in.getElementType() == double.class) {
      while (iterIn.hasNext()) {
        double val = iterIn.getDoubleNext();
        if (isMissing_(val)) iterIn.setDoubleCurrent(Double.NaN);
      }
    } else if (in.getElementType() == float.class) {
      while (iterIn.hasNext()) {
        float val = iterIn.getFloatNext();
        if (isMissing_(val)) iterIn.setFloatCurrent(Float.NaN);
      }
    }
    return in;
  }
  private void showValuesAsDates(CoordinateAxis axis) {
    String units = axis.getUnitsString();
    String cal = getCalendarAttribute(axis);
    CalendarDateUnit cdu = CalendarDateUnit.of(cal, units);

    try {
      infoTA.appendLine(units);
      infoTA.appendLine(NCdumpW.printVariableData(axis, null));

      if (axis.getDataType().isNumeric()) {
        if (axis instanceof CoordinateAxis2D) {
          showDates2D((CoordinateAxis2D) axis, cdu);

        } else if (axis instanceof CoordinateAxis1D) { // 1D
          showDates1D((CoordinateAxis1D) axis, cdu);

        } else { // > 2D
          Array data = axis.read();
          IndexIterator ii = data.getIndexIterator();
          while (ii.hasNext()) {
            double val = ii.getDoubleNext();
            infoTA.appendLine(makeCalendarDateStringOrMissing(cdu, val));
          }
        }

      } else { // must be iso dates
        Array data = axis.read();
        Formatter f = new Formatter();
        if (data instanceof ArrayChar) {
          ArrayChar dataS = (ArrayChar) data;
          ArrayChar.StringIterator iter = dataS.getStringIterator();
          while (iter.hasNext()) f.format(" %s%n", iter.next());
          infoTA.appendLine(f.toString());

        } else if (data instanceof ArrayObject) {
          IndexIterator iter = data.getIndexIterator();
          while (iter.hasNext()) f.format(" %s%n", iter.next());
          infoTA.appendLine(f.toString());
        }
      }
    } catch (Exception ex) {
      ex.printStackTrace();
      infoTA.appendLine(ex.getMessage());
    }
  }
  // get a list of station obs for this station
  public List getData(Station s, CancelTask cancel) throws IOException {
    ArrayStructure stationData = readData("ID " + s.getName(), cancel);

    ArrayList stationObs = new ArrayList();
    IndexIterator ii = stationData.getIndexIterator();
    while (ii.hasNext()) {
      stationObs.add(new StationObs((Station) s, (StructureData) ii.getObjectNext()));
    }
    return stationObs;
  }
  public void testAggCoordVarSubsetDefeatLocalCache(NetcdfFile ncfile)
      throws InvalidRangeException, IOException {
    Variable time = ncfile.findVariable("time");
    assert null != time;

    assert time.getShortName().equals("time");
    assert time.getRank() == 1;
    assert time.getSize() == 3;
    assert time.getShape()[0] == 3;
    assert time.getDataType() == DataType.DOUBLE;

    assert time.getDimension(0) == ncfile.findDimension("time");

    time.setCachedData(null, false);
    Array data = time.read("1:2");
    assert data.getRank() == 1;
    assert data.getSize() == 2;
    assert data.getShape()[0] == 2;
    assert data.getElementType() == double.class;

    int count = 0;
    IndexIterator dataI = data.getIndexIterator();
    while (dataI.hasNext()) {
      assert Misc.closeEnough(dataI.getDoubleNext(), result[count + 1]);
      count++;
    }

    time.setCachedData(null, false);
    data = time.read("0:2:2");
    assert data.getRank() == 1;
    assert data.getSize() == 2;
    assert data.getShape()[0] == 2;
    assert data.getElementType() == double.class;

    count = 0;
    dataI = data.getIndexIterator();
    while (dataI.hasNext()) {
      assert Misc.closeEnough(dataI.getDoubleNext(), result[count * 2]);
      count++;
    }
  }
Beispiel #12
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 private Array convertToChar(Variable newVar, Array oldData) {
   ArrayChar newData = (ArrayChar) Array.factory(DataType.CHAR, newVar.getShape());
   Index ima = newData.getIndex();
   IndexIterator ii = oldData.getIndexIterator();
   while (ii.hasNext()) {
     String s = (String) ii.getObjectNext();
     int[] c = ii.getCurrentCounter();
     for (int i = 0; i < c.length; i++) ima.setDim(i, c[i]);
     newData.setString(ima, s);
   }
   return newData;
 }
Beispiel #13
0
  // for jon blower
  private Array getEnhancedArray(VariableDS vds) throws IOException {
    Array data = vds.read();
    EnumSet<NetcdfDataset.Enhance> mode = vds.getEnhanceMode();
    if (mode.contains(NetcdfDataset.Enhance.ScaleMissing)) return data;
    if (!mode.contains(NetcdfDataset.Enhance.ScaleMissingDefer))
      throw new IllegalStateException("Must include " + NetcdfDataset.Enhance.ScaleMissingDefer);

    IndexIterator ii = data.getIndexIterator();
    while (ii.hasNext()) {
      double val = vds.convertScaleOffsetMissing(ii.getDoubleNext());
      ii.setDoubleCurrent(val);
    }
    return data;
  }
Beispiel #14
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  /**
   * Get the minimum and the maximum data value of the previously read Array, skipping missing
   * values as defined by isMissingData(double val).
   *
   * @param a Array to get min/max values
   * @return both min and max value.
   */
  public MAMath.MinMax getMinMaxSkipMissingData(Array a) {
    if (!hasMissingData()) return MAMath.getMinMax(a);

    IndexIterator iter = a.getIndexIterator();
    double max = -Double.MAX_VALUE;
    double min = Double.MAX_VALUE;
    while (iter.hasNext()) {
      double val = iter.getDoubleNext();
      if (isMissingData(val)) continue;
      if (val > max) max = val;
      if (val < min) min = val;
    }
    return new MAMath.MinMax(min, max);
  }
  private void showDates2D(CoordinateAxis2D axis2D, CalendarDateUnit cdu) {
    Formatter f = new Formatter();

    if (axis2D.isInterval()) {
      ArrayDouble.D2 coords = axis2D.getCoordValuesArray();
      ArrayDouble.D3 bounds = axis2D.getCoordBoundsArray();
      if (bounds == null) {
        infoTA.appendLine("No bounds for interval " + axis2D.getFullName());
        return;
      }

      IndexIterator coordIter = coords.getIndexIterator();
      IndexIterator boundsIter = bounds.getIndexIterator();
      while (coordIter.hasNext()) {
        double coordValue = coordIter.getDoubleNext();
        if (!boundsIter.hasNext()) break;
        double bounds1 = boundsIter.getDoubleNext();
        if (!boundsIter.hasNext()) break;
        double bounds2 = boundsIter.getDoubleNext();
        f.format(
            "%s (%s,%s)%n",
            makeCalendarDateStringOrMissing(cdu, coordValue),
            makeCalendarDateStringOrMissing(cdu, bounds1),
            makeCalendarDateStringOrMissing(cdu, bounds2));
      }

    } else {
      ArrayDouble.D2 coords = axis2D.getCoordValuesArray();
      IndexIterator coordIter = coords.getIndexIterator();
      while (coordIter.hasNext()) {
        double coordValue = coordIter.getDoubleNext();
        f.format("%s%n", makeCalendarDateStringOrMissing(cdu, coordValue));
      }
    }

    infoTA.appendLine(f.toString());
  }
  // test offset only gets applied once
  public void testWrapOnce() throws IOException {
    String filename = TestAll.cdmUnitTestDir + "ncml/coords/testCoordScaling.ncml";
    System.out.printf("%s%n", filename);
    NetcdfDataset ncd = ucar.nc2.dataset.NetcdfDataset.openDataset(filename);
    Variable v = ncd.findCoordinateAxis("Longitude");
    assert v != null;
    assert v instanceof CoordinateAxis1D;

    // if offset is applied twice, the result is not in +-180 range
    Array data = v.read();
    NCdumpW.printArray(data);
    IndexIterator ii = data.getIndexIterator();
    while (ii.hasNext()) {
      assert Math.abs(ii.getDoubleNext()) < 180 : ii.getDoubleCurrent();
    }
  }
  /**
   * Convert Data with scale and offset. Also translate missing data to NaNs if useNaNs = true.
   *
   * @param in data to convert
   * @return converted data.
   */
  private Array convertScaleOffset(Array in) {
    if (!hasScaleOffset) return in;
    if (debugRead) System.out.println("convertScaleOffset ");

    Array out = Array.factory(convertedDataType.getPrimitiveClassType(), in.getShape());
    IndexIterator iterIn = in.getIndexIterator();
    IndexIterator iterOut = out.getIndexIterator();

    if (isUnsigned && in.getElementType() == byte.class)
      convertScaleOffsetUnsignedByte(iterIn, iterOut);
    else if (isUnsigned && in.getElementType() == short.class)
      convertScaleOffsetUnsignedShort(iterIn, iterOut);
    else if (isUnsigned && in.getElementType() == int.class)
      convertScaleOffsetUnsignedInt(iterIn, iterOut);
    else {
      boolean checkMissing = useNaNs && hasMissing();
      while (iterIn.hasNext()) {
        double val = scale * iterIn.getDoubleNext() + offset;
        iterOut.setDoubleNext(checkMissing && isMissing_(val) ? Double.NaN : val);
      }
    }

    return out;
  }
Beispiel #18
0
  private boolean compareData(String name, Array data1, Array data2, double tol, boolean justOne) {
    boolean ok = true;
    if (data1.getSize() != data2.getSize()) {
      f.format(" DIFF %s: size %d !== %d%n", name, data1.getSize(), data2.getSize());
      ok = false;
    }

    if (data1.getElementType() != data2.getElementType()) {
      f.format(
          " DIFF %s: element type %s !== %s%n",
          name, data1.getElementType(), data2.getElementType());
      ok = false;
    }

    if (!ok) return false;

    DataType dt = DataType.getType(data1.getElementType());

    IndexIterator iter1 = data1.getIndexIterator();
    IndexIterator iter2 = data2.getIndexIterator();

    if (dt == DataType.DOUBLE) {
      while (iter1.hasNext() && iter2.hasNext()) {
        double v1 = iter1.getDoubleNext();
        double v2 = iter2.getDoubleNext();
        if (!Double.isNaN(v1) || !Double.isNaN(v2))
          if (!closeEnough(v1, v2, tol)) {
            f.format(
                " DIFF %s: %f != %f count=%s diff = %f pdiff = %f %n",
                name, v1, v2, iter1, diff(v1, v2), pdiff(v1, v2));
            ok = false;
            if (justOne) break;
          }
      }
    } else if (dt == DataType.FLOAT) {
      while (iter1.hasNext() && iter2.hasNext()) {
        float v1 = iter1.getFloatNext();
        float v2 = iter2.getFloatNext();
        if (!Float.isNaN(v1) || !Float.isNaN(v2))
          if (!closeEnough(v1, v2, (float) tol)) {
            f.format(
                " DIFF %s: %f != %f count=%s diff = %f pdiff = %f %n",
                name, v1, v2, iter1, diff(v1, v2), pdiff(v1, v2));
            ok = false;
            if (justOne) break;
          }
      }
    } else if (dt == DataType.INT) {
      while (iter1.hasNext() && iter2.hasNext()) {
        int v1 = iter1.getIntNext();
        int v2 = iter2.getIntNext();
        if (v1 != v2) {
          f.format(
              " DIFF %s: %d != %d count=%s diff = %f pdiff = %f %n",
              name, v1, v2, iter1, diff(v1, v2), pdiff(v1, v2));
          ok = false;
          if (justOne) break;
        }
      }
    } else if (dt == DataType.SHORT) {
      while (iter1.hasNext() && iter2.hasNext()) {
        short v1 = iter1.getShortNext();
        short v2 = iter2.getShortNext();
        if (v1 != v2) {
          f.format(
              " DIFF %s: %d != %d count=%s diff = %f pdiff = %f %n",
              name, v1, v2, iter1, diff(v1, v2), pdiff(v1, v2));
          ok = false;
          if (justOne) break;
        }
      }
    } else if (dt == DataType.BYTE) {
      while (iter1.hasNext() && iter2.hasNext()) {
        byte v1 = iter1.getByteNext();
        byte v2 = iter2.getByteNext();
        if (v1 != v2) {
          f.format(
              " DIFF %s: %d != %d count=%s diff = %f pdiff = %f %n",
              name, v1, v2, iter1, diff(v1, v2), pdiff(v1, v2));
          ok = false;
          if (justOne) break;
        }
      }
    } else if (dt == DataType.STRUCTURE) {
      while (iter1.hasNext() && iter2.hasNext()) {
        compareStructureData(
            (StructureData) iter1.next(), (StructureData) iter2.next(), tol, justOne);
      }
    }

    return ok;
  }
  private void makeCoordinateDataWithMissing(
      int datatype,
      Variable time,
      Variable elev,
      Variable azi,
      Variable nradialsVar,
      Variable ngatesVar,
      List groups) {

    Array timeData = Array.factory(time.getDataType().getPrimitiveClassType(), time.getShape());
    Index timeIndex = timeData.getIndex();

    Array elevData = Array.factory(elev.getDataType().getPrimitiveClassType(), elev.getShape());
    Index elevIndex = elevData.getIndex();

    Array aziData = Array.factory(azi.getDataType().getPrimitiveClassType(), azi.getShape());
    Index aziIndex = aziData.getIndex();

    Array nradialsData =
        Array.factory(nradialsVar.getDataType().getPrimitiveClassType(), nradialsVar.getShape());
    IndexIterator nradialsIter = nradialsData.getIndexIterator();

    Array ngatesData =
        Array.factory(ngatesVar.getDataType().getPrimitiveClassType(), ngatesVar.getShape());
    IndexIterator ngatesIter = ngatesData.getIndexIterator();

    // first fill with missing data
    IndexIterator ii = timeData.getIndexIterator();
    while (ii.hasNext()) ii.setIntNext(MISSING_INT);

    ii = elevData.getIndexIterator();
    while (ii.hasNext()) ii.setFloatNext(MISSING_FLOAT);

    ii = aziData.getIndexIterator();
    while (ii.hasNext()) ii.setFloatNext(MISSING_FLOAT);

    // now set the  coordinate variables from the Cinrad2Record radial
    int last_msecs = Integer.MIN_VALUE;
    int nscans = groups.size();
    try {
      for (int scan = 0; scan < nscans; scan++) {
        List scanGroup = (List) groups.get(scan);
        int nradials = scanGroup.size();

        Cinrad2Record first = null;
        for (int j = 0; j < nradials; j++) {
          Cinrad2Record r = (Cinrad2Record) scanGroup.get(j);
          if (first == null) first = r;

          int radial = r.radial_num - 1;
          timeData.setInt(timeIndex.set(scan, radial), r.data_msecs);
          elevData.setFloat(elevIndex.set(scan, radial), r.getElevation());
          aziData.setFloat(aziIndex.set(scan, radial), r.getAzimuth());

          if (r.data_msecs < last_msecs)
            logger.warn("makeCoordinateData time out of order " + r.data_msecs);
          last_msecs = r.data_msecs;
        }

        nradialsIter.setIntNext(nradials);
        ngatesIter.setIntNext(first.getGateCount(datatype));
      }
    } catch (java.lang.ArrayIndexOutOfBoundsException ae) {
      logger.debug("Cinrad2IOSP.uncompress ", ae);
    }
    time.setCachedData(timeData, false);
    elev.setCachedData(elevData, false);
    azi.setCachedData(aziData, false);
    nradialsVar.setCachedData(nradialsData, false);
    ngatesVar.setCachedData(ngatesData, false);
  }
  private int populateFile2(
      NetcdfFileWriteable ncFile,
      String varName,
      DataType dataType,
      int[] dimensions,
      int valueCounter,
      Random generator)
      throws IOException, InvalidRangeException {

    long singleWriteSize = maxMemory / dataType.getSize();
    int highestNonWriteDim = determineHighestNonWriteDimension(dimensions, singleWriteSize);
    int[] singleStep = createWriteStep(dimensions, singleWriteSize, highestNonWriteDim);
    int numStepWrites = determineNumberOfStepWrites(singleStep, singleWriteSize);

    System.out.println(
        "SingleWriteSize: "
            + singleWriteSize
            + " datatype size: "
            + dataType.getSize()
            + " singleStep: "
            + arrayToString(singleStep)
            + " numberStepsPerWrite: "
            + numStepWrites);

    int[] allOnes = new int[dimensions.length];
    int[] allZeros = new int[dimensions.length];

    for (int i = 0; i < allOnes.length; i++) {
      allOnes[i] = 1;
      allZeros[i] = 0;
    }

    Index origin = new Index(dimensions, allOnes);

    long totalSize = origin.getSize();
    long writtenSoFar = 0;

    boolean done = false;

    while (!done) {
      for (int i = 0; i < numStepWrites; i++) {
        // this is a crack at an optimization

        if ((highestNonWriteDim >= 0)
            && ((origin.getCurrentCounter()[highestNonWriteDim] + numStepWrites)
                <= dimensions[highestNonWriteDim])) {
          singleStep[highestNonWriteDim] = numStepWrites;
          System.out.println("JUST OPTIMIZED. New write step: " + arrayToString(singleStep));
          // keep 'i' right
          i += numStepWrites - 1;
        } else {
          singleStep[highestNonWriteDim] = 1;
        }

        Array array = new ArrayInt(singleStep);
        IndexIterator iter = array.getIndexIterator();

        while (iter.hasNext()) {
          iter.getIntNext();
          // uncomment the following line for a random distribution
          // iter.setIntCurrent((int)  (Math.abs(generator.nextGaussian()) * 40) );
          // uncomment this line for an incrementing value
          iter.setIntCurrent(valueCounter);
          valueCounter++;

          // book keeping
          writtenSoFar++;
          // origin.incr();
        }

        System.out.println(
            "Writing to file: "
                + ncFile.getLocation()
                + ". var_name: "
                + varName
                + " origin: "
                + arrayToString(origin.getCurrentCounter())
                + " writeSize: "
                + array.getSize()
                + " write shape: "
                + arrayToString(singleStep));

        // write to the actual file
        ncFile.write(varName, origin.getCurrentCounter(), array);

        // update origin accordingly

        for (int j = 0; j < Index.computeSize(singleStep); j++) {
          // writtenSoFar++;
          origin.incr();
        }

        System.out.println(
            "\tcurrentIndex: "
                + arrayToString(origin.getCurrentCounter())
                + " currentElement: "
                + origin.currentElement()
                + " totalsize: "
                + (totalSize)
                + " writtenSoFar: "
                + writtenSoFar);

        if (writtenSoFar >= totalSize) {
          done = true;
          break;
        }
      }
    }

    return valueCounter;
  }