コード例 #1
0
ファイル: FireInputer.java プロジェクト: hgenet/dostem
  void initTransientFire(boolean useseverity, String dir) {
    String filename = dir + "fire.nc";

    NetcdfFile ncfile = null;
    File spfile = new File(filename);
    if (spfile.exists()) {
      try {
        ncfile = NetcdfFile.open(filename);
        Variable fyearV = ncfile.findVariable("FIRE");
        trfireyearA = fyearV.read();

        Variable fseasonV = ncfile.findVariable("SEASON");
        trfireseasonA = fseasonV.read();

        if (useseverity) {
          Variable fsevV = ncfile.findVariable("SEVERITY");
          trseverityA = fsevV.read();
        }

      } catch (IOException ioe) {
        System.out.println(ioe.getMessage());
      } finally {
        if (ncfile != null) {
          try {
            ncfile.close();
          } catch (IOException ioee) {
            System.out.println(ioee.getMessage());
          }
        }
      }
    } else { // file not exist
      System.out.println("Input file: " + filename + " NOT existed");
      System.exit(-1);
    }
  };
コード例 #2
0
ファイル: VariableReader.java プロジェクト: bcdev/beam
 Array readFully() throws IOException {
   if (origin == null) {
     return binVariable.read();
   } else {
     try {
       return binVariable.read(origin, shape).reduce();
     } catch (InvalidRangeException e) {
       throw new IOException(e.getMessage());
     }
   }
 }
コード例 #3
0
ファイル: CompareNetcdf2.java プロジェクト: jnbek/thredds
  private void compareVariableData(
      Variable var1, Variable var2, boolean showCompare, boolean justOne) throws IOException {
    Array data1 = var1.read();
    Array data2 = var2.read();

    if (showCompare)
      f.format(
          " compareArrays %s unlimited=%s size=%d%n",
          var1.getNameAndDimensions(), var1.isUnlimited(), data1.getSize());
    compareData(var1.getFullName(), data1, data2, justOne);
    if (showCompare) f.format("   ok%n");
  }
コード例 #4
0
ファイル: VariableReader.java プロジェクト: bcdev/beam
 Array read(int firstIndex, int length) throws IOException {
   try {
     if (origin == null) {
       return binVariable.read(new int[] {firstIndex}, new int[] {length});
     } else {
       int[] originFull = origin.clone();
       int[] shapeFull = shape.clone();
       originFull[binDimIndex] = firstIndex;
       shapeFull[binDimIndex] = length;
       return binVariable.read(originFull, shapeFull).reduce();
     }
   } catch (InvalidRangeException e) {
     throw new IOException(e.getMessage());
   }
 }
コード例 #5
0
ファイル: NcSDFloat64.java プロジェクト: jon4than/visad
  /** Read the value (parameters are ignored). */
  public boolean read(String datasetName, Object specialO) throws IOException {
    ArrayDouble.D0 a = (ArrayDouble.D0) ncVar.read();
    setValue(a.get());

    setRead(true);
    return (false);
  }
コード例 #6
0
ファイル: SeadasFileReader.java プロジェクト: bcdev/seadas
  public void addInputParamMetadata(Product product) throws ProductIOException {

    Variable inputParams = ncFile.findVariable("Input_Parameters");
    if (inputParams != null) {
      final MetadataElement inputParamsMeta = new MetadataElement("Input_Parameters");
      Array array;
      try {
        array = inputParams.read();
      } catch (IOException e) {
        throw new ProductIOException(e.getMessage());
      }

      String[] lines = array.toString().split("\n");
      for (String line : lines) {
        String[] parts = line.split("=");
        if (parts.length == 2) {
          final String name = parts[0].trim();
          final String value = parts[1].trim();
          final ProductData data = ProductData.createInstance(ProductData.TYPE_ASCII, value);
          final MetadataAttribute attribute = new MetadataAttribute(name, data, true);
          inputParamsMeta.addAttribute(attribute);
        }
      }

      final MetadataElement metadataRoot = product.getMetadataRoot();
      metadataRoot.addElement(inputParamsMeta);
    }
  }
コード例 #7
0
 // @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);
 }
コード例 #8
0
ファイル: Write2ncRect.java プロジェクト: nbald/thredds
  private void copySome(NetcdfFileWriteable ncfile, Variable oldVar, int nelems)
      throws IOException {
    String newName = N3iosp.makeValidNetcdfObjectName(oldVar.getShortName());

    int[] shape = oldVar.getShape();
    int[] origin = new int[oldVar.getRank()];
    int size = shape[0];

    for (int i = 0; i < size; i += nelems) {
      origin[0] = i;
      int left = size - i;
      shape[0] = Math.min(nelems, left);

      Array data;
      try {
        data = oldVar.read(origin, shape);
        if (oldVar.getDataType() == DataType.STRING) {
          data = convertToChar(ncfile.findVariable(newName), data);
        }
        if (data.getSize() > 0) { // zero when record dimension = 0
          ncfile.write(newName, origin, data);
          if (debug) System.out.println("write " + data.getSize() + " bytes");
        }

      } catch (InvalidRangeException e) {
        e.printStackTrace();
        throw new IOException(e.getMessage());
      }
    }
  }
コード例 #9
0
  public void testAggCoordVar(NetcdfFile ncfile) {

    Variable time = ncfile.findVariable("time");
    assert null != time;
    assert time.getShortName().equals("time");
    assert time.getRank() == 1 : time.getRank();
    assert time.getShape()[0] == 3;
    assert time.getDataType() == DataType.INT;

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

    try {
      Array data = time.read();

      assert (data instanceof ArrayInt.D1) : data.getClass().getName();
      ArrayInt.D1 dataI = (ArrayInt.D1) data;
      assert dataI.get(0) == 0;
      assert dataI.get(1) == 10;
      assert dataI.get(2) == 99;

    } catch (IOException io) {
      io.printStackTrace();
      assert false;
    }
  }
コード例 #10
0
  public void testAggCoordVar2(NetcdfFile ncfile) {

    Variable time = ncfile.findVariable("time");
    assert null != time;
    assert time.getShortName().equals("time");
    assert time.getRank() == 1 : time.getRank();
    assert time.getShape()[0] == 3;
    assert time.getDataType() == DataType.INT;

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

    try {
      Array data = time.read();

      assert (data instanceof ArrayInt);
      IndexIterator dataI = data.getIndexIterator();
      assert dataI.getIntNext() == 0 : dataI.getIntCurrent();
      assert dataI.getIntNext() == 1 : dataI.getIntCurrent();
      assert dataI.getIntNext() == 2 : dataI.getIntCurrent();

    } catch (IOException io) {
      io.printStackTrace();
      assert false;
    }
  }
コード例 #11
0
  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;
    }
  }
コード例 #12
0
ファイル: HdfEos.java プロジェクト: julienchastang/thredds
  private static String getStructMetadata(Group eosGroup) throws IOException {
    StringBuilder sbuff = null;
    String structMetadata = null;

    int n = 0;
    while (true) {
      Variable structMetadataVar = eosGroup.findVariable("StructMetadata." + n);
      if (structMetadataVar == null) break;
      if ((structMetadata != null) && (sbuff == null)) { // more than 1 StructMetadata
        sbuff = new StringBuilder(64000);
        sbuff.append(structMetadata);
      }

      // read and parse the ODL
      Array A = structMetadataVar.read();
      if (A instanceof ArrayChar.D1) {
        ArrayChar ca = (ArrayChar) A;
        structMetadata = ca.getString(); // common case only StructMetadata.0, avoid extra copy
      } else if (A instanceof ArrayObject.D0) {
        ArrayObject ao = (ArrayObject) A;
        structMetadata = (String) ao.getObject(0);
      } else {
        log.error("Unsupported array type {} for StructMetadata", A.getElementType());
      }

      if (sbuff != null) sbuff.append(structMetadata);
      n++;
    }
    return (sbuff != null) ? sbuff.toString() : structMetadata;
  }
コード例 #13
0
ファイル: SeadasFileReader.java プロジェクト: bcdev/seadas
  private void handleMetadataGroup(Group group, MetadataElement metadataElement)
      throws ProductIOException {
    List<Variable> variables = group.getVariables();
    for (Variable variable : variables) {
      final String name = variable.getShortName();
      final int dataType = getProductDataType(variable);
      Array array;
      try {
        array = variable.read();
      } catch (IOException e) {
        throw new ProductIOException(e.getMessage());
      }
      final ProductData data = ProductData.createInstance(dataType, array.getStorage());
      final MetadataAttribute attribute = new MetadataAttribute("data", data, true);

      final MetadataElement sdsElement = new MetadataElement(name);
      sdsElement.addAttribute(attribute);
      metadataElement.addElement(sdsElement);

      final List<Attribute> list = variable.getAttributes();
      for (Attribute hdfAttribute : list) {
        final String attribName = hdfAttribute.getShortName();
        if ("units".equals(attribName)) {
          attribute.setUnit(hdfAttribute.getStringValue());
        } else if ("long_name".equals(attribName)) {
          attribute.setDescription(hdfAttribute.getStringValue());
        } else {
          addAttributeToElement(sdsElement, hdfAttribute);
        }
      }
    }
  }
コード例 #14
0
ファイル: TestDorade.java プロジェクト: msdsoftware/thredds
 private float testReadScalar(Variable v) throws IOException {
   if (show) System.out.printf(" read %s%n", v.getNameAndDimensions());
   assert (null != v);
   Array a = v.read();
   assert (null != a);
   IndexIterator ii = a.getIndexIterator();
   return ii.getFloatNext();
 }
コード例 #15
0
  @Ignore("files not available")
  @Test
  public void testCacheTiming() throws IOException, InvalidRangeException {
    String filename = "file:testCacheTiming.xml";
    System.out.printf("%s%n", filename);

    String cacheDirName = TestDir.temporaryLocalDataDir + "testAggExistingCache/";
    System.out.printf("cacheDir=%s%n", cacheDirName);
    File cacheDir = new File(cacheDirName);
    FileUtils.deleteDirectory(cacheDir); // from commons-io
    assert !cacheDir.exists();

    DiskCache2 cache = new DiskCache2(cacheDirName, false, 0, 0);
    cache.setAlwaysUseCache(true);
    Assert.assertEquals(cache.getRootDirectory(), cacheDirName);
    assert new File(cache.getRootDirectory()).exists();

    Aggregation.setPersistenceCache(cache);
    AggregationExisting.countCacheUse = 0;

    long start = System.currentTimeMillis();

    try (NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(ncml2), filename, null)) {
      System.out.printf("%nTestNcmlAggExisting.open %s%n", filename);
      Variable time = ncfile.findVariable("time");
      System.out.printf(" Variable %s%n", time.getNameAndDimensions());
      time.read();
    }
    System.out.printf(" countCacheUse = %d%n", AggregationExisting.countCacheUse);

    long took = System.currentTimeMillis() - start;
    System.out.printf(" first took %d msecs%n", took);

    AggregationExisting.countCacheUse = 0;
    start = System.currentTimeMillis();

    try (NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(ncml2), filename, null)) {
      System.out.printf("%nTestNcmlAggExisting.open %s%n", filename);
      Variable time = ncfile.findVariable("time");
      System.out.printf(" Variable %s%n", time.getNameAndDimensions());
      time.read();
    }
    System.out.printf(" countCacheUse = %d%n", AggregationExisting.countCacheUse);
    took = System.currentTimeMillis() - start;
    System.out.printf(" second took %d msecs%n", took);
  }
コード例 #16
0
  /* (non-Javadoc)
   * @see loci.formats.NetCDFService#getArray(java.lang.String, int[], int[])
   */
  public Object getArray(String path, int[] origin, int[] shape) throws ServiceException {
    String groupName = getDirectory(path);
    String variableName = getName(path);
    Group group = getGroup(groupName);

    Variable variable = group.findVariable(variableName);
    try {
      if (origin != null && shape != null) {
        return variable.read(origin, shape).reduce().copyToNDJavaArray();
      }
      return variable.read().copyToNDJavaArray();
    } catch (InvalidRangeException e) {
      throw new ServiceException(e);
    } catch (IOException e) {
      throw new ServiceException(e);
    }
  }
コード例 #17
0
 void CheckInt16(Variable v) throws IOException {
   // int16
   // assert(null != (v = dodsfile.findVariable("types.integers.i16")));
   // assert v.getName().equals("types.integers.i16");
   assert v.getRank() == 0;
   assert v.getSize() == 1;
   assert v.getDataType() == DataType.SHORT;
   CheckInt16Value(v.read());
 }
コード例 #18
0
ファイル: TestDorade.java プロジェクト: msdsoftware/thredds
  private void testReadData(Variable v) throws IOException {
    if (show) System.out.printf(" read %s%n", v.getNameAndDimensions());
    assert (null != v);

    assert (null != v.getDimension(0));
    Array a = v.read();
    assert (null != a);
    assert (v.getSize() == a.getSize());
  }
コード例 #19
0
  void CheckS(Variable v) throws IOException {

    // string
    // assert(null != (v = dodsfile.findVariable("types.strings.s")));
    // assert v.getName().equals("types.strings.s");
    assert v.getRank() == 0;
    assert v.getDataType() == DataType.STRING : v.getDataType();
    CheckSValue(v.read());
  }
コード例 #20
0
ファイル: SeadasFileReader.java プロジェクト: bcdev/seadas
  public synchronized void readBandData(
      Band destBand,
      int sourceOffsetX,
      int sourceOffsetY,
      int sourceWidth,
      int sourceHeight,
      int sourceStepX,
      int sourceStepY,
      ProductData destBuffer,
      ProgressMonitor pm)
      throws IOException, InvalidRangeException {

    if (mustFlipY) {
      sourceOffsetY = destBand.getSceneRasterHeight() - (sourceOffsetY + sourceHeight);
    }
    if (mustFlipX) {
      sourceOffsetX = destBand.getSceneRasterWidth() - (sourceOffsetX + sourceWidth);
    }
    sourceOffsetY += leadLineSkip;
    start[0] = sourceOffsetY;
    start[1] = sourceOffsetX;
    stride[0] = sourceStepY;
    stride[1] = sourceStepX;
    count[0] = sourceHeight;
    count[1] = sourceWidth;
    Object buffer = destBuffer.getElems();
    Variable variable = variableMap.get(destBand);

    pm.beginTask("Reading band '" + variable.getShortName() + "'...", sourceHeight);
    try {
      Section section = new Section(start, count, stride);

      Array array;
      int[] newshape = {sourceHeight, sourceWidth};

      array = variable.read(section);
      if (array.getRank() == 3) {
        array = array.reshapeNoCopy(newshape);
      }
      Object storage;

      if (mustFlipX && !mustFlipY) {
        storage = array.flip(1).copyTo1DJavaArray();
      } else if (!mustFlipX && mustFlipY) {
        storage = array.flip(0).copyTo1DJavaArray();
      } else if (mustFlipX && mustFlipY) {
        storage = array.flip(0).flip(1).copyTo1DJavaArray();
      } else {
        storage = array.copyTo1DJavaArray();
      }

      arraycopy(storage, 0, buffer, 0, destBuffer.getNumElems());
    } finally {
      pm.done();
    }
  }
コード例 #21
0
  void CheckLong32(Variable v) throws IOException {

    // uint32
    // assert(null != (v = dodsfile.findVariable("types.integers.ui32")));
    // assert v.getName().equals("types.integers.ui32");
    assert v.getRank() == 0;
    assert v.getSize() == 1;
    assert v.getDataType() == DataType.LONG : v.getDataType();
    CheckLongValue(v.read());
  }
コード例 #22
0
  void CheckF(Variable v) throws IOException {

    // float
    // assert(null != (v = dodsfile.findVariable("types.floats.f32")));
    // assert v.getName().equals("types.floats.f32");
    assert v.getRank() == 0;
    assert v.getSize() == 1;
    assert v.getDataType() == DataType.FLOAT : v.getDataType();
    CheckFValue(v.read());
  }
コード例 #23
0
 /**
  * Read data from a top level Variable of FLOAT data type and return a memory resident Array.
  *
  * @param index LayoutRegular object
  * @param v2 Variable has FLOAT data type.
  * @return Array of data which will be read from Variable through this call.
  */
 public Array readFloatData(LayoutRegular index, Variable v2) throws IOException {
   float[] var = (float[]) (v2.read().get1DJavaArray(v2.getDataType().getPrimitiveClassType()));
   float[] data = new float[(int) index.getTotalNelems()];
   while (index.hasNext()) {
     Layout.Chunk chunk = index.next();
     System.arraycopy(
         var, (int) chunk.getSrcPos() / 4, data, (int) chunk.getDestElem(), chunk.getNelems());
   }
   return Array.factory(data);
 }
コード例 #24
0
  void CheckD(Variable v) throws IOException {

    // double
    // assert(null != (v = dodsfile.findVariable("types.floats.f64")));
    // assert v.getName().equals("types.floats.f64");
    assert v.getRank() == 0;
    assert v.getSize() == 1;
    assert v.getDataType() == DataType.DOUBLE : v.getDataType();
    CheckDValue(v.read());
  }
コード例 #25
0
ファイル: TestNcMLStrides.java プロジェクト: kenkyu/thredds
  public void testStride(String stride) throws IOException, InvalidRangeException {
    Variable time = ncfile.findVariable("time");
    ArrayInt all = (ArrayInt) time.read();

    ArrayInt correct = (ArrayInt) all.section(new Section(stride).getRanges());
    System.out.printf("correct(%s) %s", stride, NCdumpW.toString(correct));
    ArrayInt data = (ArrayInt) time.read(stride);
    System.out.printf("data(%s) %s%n", stride, NCdumpW.toString(data));
    Index ci = correct.getIndex();
    Index di = data.getIndex();
    for (int i = 0; i < data.getSize(); i++)
      assert (data.getInt(di.set(i)) == correct.getInt(ci.set(i)))
          : stride
              + " index "
              + i
              + " = "
              + data.getInt(di.set(i))
              + " != "
              + correct.getInt(ci.set(i));
  }
コード例 #26
0
ファイル: TestNcMLStrides.java プロジェクト: kenkyu/thredds
  public void testStride() throws IOException, InvalidRangeException {
    System.out.println("ncfile opened = " + location + "\n" + ncfile);
    Variable time = ncfile.findVariable("time");

    ArrayInt all = (ArrayInt) time.read();
    for (int i = 0; i < all.getSize(); i++) assert (all.getInt(i) == i + 1);

    testStride("0:13:3");

    for (int i = 1; i < 12; i++) testStride("0:13:" + i);
  }
コード例 #27
0
  // do not call directly
  @Override
  public Array reallyRead(Variable client, Section section, CancelTask cancelTask)
      throws IOException, InvalidRangeException {
    // see if its really a full read
    if ((null == section) || section.computeSize() == getSize())
      return reallyRead(client, cancelTask);

    if (orgVar == null) return getMissingDataArray(section.getShape());

    return orgVar.read(section);
  }
コード例 #28
0
ファイル: SeadasFileReader.java プロジェクト: bcdev/seadas
  public ProductData readData(Variable variable) throws ProductIOException {
    final int dataType = getProductDataType(variable);
    Array array;
    try {
      array = variable.read();

    } catch (IOException e) {
      throw new ProductIOException(e.getMessage());
    }
    return ProductData.createInstance(dataType, array.getStorage());
  }
コード例 #29
0
  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++;
    }
  }
コード例 #30
0
ファイル: L3BinFileReader.java プロジェクト: bcdev/beam
  private RowInfo[] createRowInfos() throws IOException {
    final ISINGrid grid = this.grid;
    final RowInfo[] binLines = new RowInfo[sceneHeight];
    final Variable idxVariable =
        ncFile.getRootGroup().findGroup("Level-3_Binned_Data").findVariable("BinList");
    final Structure idxStructure = (Structure) idxVariable;
    final Variable idx = idxStructure.findVariable("bin_num");
    final int[] idxValues;
    synchronized (ncFile) {
      idxValues = (int[]) idx.read().getStorage();
    }
    if (bins == null) {
      bins = idxValues; // (int[]) idxVariable.read().copyTo1DJavaArray();
    }
    final Point gridPoint = new Point();
    int lastBinIndex = -1;
    int lastRowIndex = -1;
    int lineOffset = 0;
    int lineLength = 0;
    for (int i = 0; i < idxValues.length; i++) {

      final int binIndex = idxValues[i];
      if (binIndex < lastBinIndex) {
        throw new IOException(
            "Unrecognized level-3 format. Bins numbers expected to appear in ascending order.");
      }
      lastBinIndex = binIndex;

      grid.getGridPoint(binIndex, gridPoint);
      final int rowIndex = gridPoint.y;

      if (rowIndex != lastRowIndex) {
        if (lineLength > 0) {
          binLines[lastRowIndex] = new RowInfo(lineOffset, lineLength);
        }
        lineOffset = i;
        lineLength = 0;
      }

      lineLength++;
      lastRowIndex = rowIndex;
    }

    if (lineLength > 0) {
      binLines[lastRowIndex] = new RowInfo(lineOffset, lineLength);
    }

    return binLines;
  }