Exemple #1
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();
  }
Exemple #2
0
  @Test
  public void testFloatingPointCompare() throws Exception {
    String spec =
        TestDir.cdmUnitTestDir + "ft/fmrc/fp_precision/sediment_thickness_#yyMMddHHmm#.*\\.nc$";
    System.out.printf("%n====================FMRC dataset %s%n", spec);
    Formatter errlog = new Formatter();
    Fmrc fmrc = Fmrc.open(spec, errlog);
    assert (fmrc != null) : errlog;

    try (ucar.nc2.dt.GridDataset gridDs = fmrc.getDatasetBest()) {
      GridDatatype v = gridDs.findGridByShortName("thickness_of_sediment");
      assert v != null;
      GridCoordSystem gcs = v.getCoordinateSystem();
      CoordinateAxis1DTime time = gcs.getTimeAxis1D();

      Assert.assertEquals("hours since 2015-03-08 12:51:00.000 UTC", time.getUnitsString());
      Assert.assertEquals(74, time.getSize());
      Array data = time.read();
      System.out.printf("%s%n", NCdumpW.toString(data));

      for (CalendarDate cd : time.getCalendarDates()) {
        assert cd.getFieldValue(CalendarPeriod.Field.Minute) == 0 : System.out.printf("%s%n", cd);
      }
    }
  }
  private void showDeclaration(BeanTableSorted from, boolean isNcml) {
    Variable v = getCurrentVariable(from);
    if (v == null) return;
    infoTA.clear();
    if (isNcml) {
      Formatter out = new Formatter();
      try {
        NCdumpW.writeNcMLVariable(v, out);
      } catch (IOException e) {
        e.printStackTrace();
      }
      infoTA.appendLine(out.toString());

    } else {
      infoTA.appendLine(v.toString());
    }

    if (Debug.isSet("Xdeveloper")) {
      infoTA.appendLine("\n");
      infoTA.appendLine("FULL NAME = " + v.getFullName());
      infoTA.appendLine("\n");
      infoTA.appendLine(v.toStringDebug());
    }
    infoTA.gotoTop();
    infoWindow.setTitle("Variable Info");
    infoWindow.show();
  }
  /*
   Structure {
    int a_name;
    byte b_name(3);
    byte c_name(3);
    short d_name(3);
    int e_name(3);
    long f_name(3);
    int g_name(3);
    short h_name(3);
    int i_name(3);
    long j_name(3);
    float k_name(3);
    double l_name(3);
  } CompoundNative(15);
      type = Layout(8);  type= 1 (contiguous) storageSize = (15,144) dataSize=0 dataAddress=2048
  */
  @Test
  public void testReadH5StructureArrayMembers() throws java.io.IOException {
    try (NetcdfFile ncfile = TestH5.openH5("complex/compound_native.h5")) {

      Variable dset = ncfile.findVariable("CompoundNative");
      assert (null != dset);
      assert (dset.getDataType() == DataType.STRUCTURE);
      assert (dset.getRank() == 1);
      assert (dset.getSize() == 15);

      Dimension d = dset.getDimension(0);
      assert (d.getLength() == 15);

      Structure s = (Structure) dset;

      // read all with the iterator
      StructureDataIterator iter = s.getStructureIterator();
      while (iter.hasNext()) {
        StructureData sd = iter.next();

        for (StructureMembers.Member m : sd.getMembers()) {
          Array data = sd.getArray(m);
          NCdumpW.printArray(data, m.getName(), out, null);
        }
      }
    }
    System.out.println("*** testReadH5StructureArrayMembers ok");
  }
 public String getValue() {
   Array value = att.getValues();
   try {
     return NCdumpW.printArray(value, null, null);
   } catch (IOException e) {
     return e.getMessage();
   }
 }
Exemple #6
0
  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));
  }
  private void showValueDiffs(CoordinateAxis axis) {
    if (!axis.isNumeric()) return;
    try {
      if (axis instanceof CoordinateAxis1D) {
        CoordinateAxis1D axis1D = (CoordinateAxis1D) axis;
        double[] mids = axis1D.getCoordValues();
        double[] diffs = new double[mids.length];
        for (int i = 0; i < mids.length - 1; i++) diffs[i] = mids[i + 1] - mids[i];
        printArrays("midpoint differences", mids, diffs);

      } else if (axis instanceof CoordinateAxis2D) {
        CoordinateAxis2D axis2D = (CoordinateAxis2D) axis;
        ArrayDouble.D2 mids = axis2D.getCoordValuesArray();
        int[] shape = mids.getShape();
        ArrayDouble.D2 diffx =
            (ArrayDouble.D2) Array.factory(DataType.DOUBLE, new int[] {shape[0], shape[1] - 1});
        for (int j = 0; j < shape[0]; j++) {
          for (int i = 0; i < shape[1] - 1; i++) {
            double diff = mids.get(j, i + 1) - mids.get(j, i);
            diffx.set(j, i, diff);
          }
        }
        infoTA.appendLine(NCdumpW.toString(diffx, "diff in x", null));

        ArrayDouble.D2 diffy =
            (ArrayDouble.D2) Array.factory(DataType.DOUBLE, new int[] {shape[0] - 1, shape[1]});
        for (int j = 0; j < shape[0] - 1; j++) {
          for (int i = 0; i < shape[1]; i++) {
            double diff = mids.get(j + 1, i) - mids.get(j, i);
            diffy.set(j, i, diff);
          }
        }
        infoTA.appendLine("\n\n\n");
        infoTA.appendLine(NCdumpW.toString(diffy, "diff in y", null));
      }

    } catch (Exception e1) {
      e1.printStackTrace();
      infoTA.appendLine(e1.getMessage());
    }
  }
 String ncdumpmetadata(NetcdfDataset ncfile) throws Exception {
   StringWriter sw = new StringWriter();
   // Print the meta-databuffer using these args to NcdumpW
   try {
     if (!ucar.nc2.NCdumpW.print(ncfile, "-unsigned", sw, null))
       throw new Exception("NcdumpW failed");
   } catch (IOException ioe) {
     throw new Exception("NcdumpW failed", ioe);
   }
   sw.close();
   return sw.toString();
 }
  private void showValues(CoordinateAxis axis) {

    try {

      if (axis instanceof CoordinateAxis1D && axis.isNumeric()) {
        CoordinateAxis1D axis1D = (CoordinateAxis1D) axis;
        printArray("midpoints=", axis1D.getCoordValues());

        if (!axis1D.isInterval()) {
          printArray("edges=", axis1D.getCoordEdges());

        } else {
          printArray("bound1=", axis1D.getBound1());
          printArray("bound2=", axis1D.getBound2());

          Formatter f = new Formatter();
          double[] mid = axis1D.getCoordValues();
          double[] b1 = axis1D.getBound1();
          double[] b2 = axis1D.getBound2();
          for (int i = 0; i < b1.length; i++) {
            f.format("%f (%f,%f) = %f%n", mid[i], b1[i], b2[i], b2[i] - b1[i]);
          }
          infoTA.appendLine(f.toString());
        }

      } else if (axis instanceof CoordinateAxis2D && axis.isNumeric()) {
        infoTA.appendLine(NCdumpW.printVariableData(axis, null));
        showValues2D((CoordinateAxis2D) axis);

      } else {
        infoTA.appendLine(NCdumpW.printVariableData(axis, null));
      }

    } catch (IOException e1) {
      e1.printStackTrace();
      infoTA.appendLine(e1.getMessage());
    }
  }
 String ncdumpdata(NetcdfDataset ncfile) throws Exception {
   StringWriter sw = new StringWriter();
   // Dump the databuffer
   sw = new StringWriter();
   try {
     if (!ucar.nc2.NCdumpW.print(ncfile, "-vall -unsigned", sw, null))
       throw new Exception("NCdumpW failed");
   } catch (IOException ioe) {
     ioe.printStackTrace();
     throw new Exception("NCdumpW failed", ioe);
   }
   sw.close();
   return sw.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();
    }
  }
  @Test
  public void testH5StructureDS() throws java.io.IOException {
    int a_name = 0;
    String[] b_name =
        new String[] {
          "A fight is a contract that takes two people to honor.",
          "A combative stance means that you've accepted the contract.",
          "In which case, you deserve what you get.",
          "  --  Professor Cheng Man-ch'ing"
        };
    String c_name = "Hello!";

    // H5header.setDebugFlags(new ucar.nc2.util.DebugFlagsImpl("H5header/header"));
    try (NetcdfDataset ncfile =
        NetcdfDataset.openDataset(TestH5.testDir + "complex/compound_complex.h5")) {

      Variable dset = ncfile.findVariable("CompoundComplex");
      assert (null != dset);
      assert (dset.getDataType() == DataType.STRUCTURE);
      assert (dset.getRank() == 1);
      assert (dset.getSize() == 6);

      Dimension d = dset.getDimension(0);
      assert (d.getLength() == 6);

      Structure s = (Structure) dset;

      // read all with the iterator
      StructureDataIterator iter = s.getStructureIterator();
      while (iter.hasNext()) {
        StructureData sd = iter.next();
        assert sd.getScalarInt("a_name") == a_name;
        a_name++;
        assert sd.getScalarString("c_name").equals(c_name);
        String[] results = sd.getJavaArrayString(sd.findMember("b_name"));
        assert results.length == b_name.length;
        int count = 0;
        for (String r : results) assert r.equals(b_name[count++]);

        for (StructureMembers.Member m : sd.getMembers()) {
          Array data = sd.getArray(m);
          NCdumpW.printArray(data, m.getName(), out, null);
        }
      }
    }
    System.out.println("*** testH5StructureDS ok");
  }
  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());
    }
  }
 public String getValue() {
   Array value = att.getValues();
   return NCdumpW.toString(value, null, null);
 }