Package com.google.refine.pcaxis

Examples of com.google.refine.pcaxis.PCAxisTableDataReader$Dimension

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      assertTrue( "Couldn't open file <" + testDataFileOut + ">: " + e.getMessage(),
                  false );
      return;
    }

    Dimension timeDim = ncf.getRootGroup().findDimension( "time");
    int timeDimSize = timeDim.getLength();
    Variable timeVar = ncf.getRootGroup().findVariable( "time");
    Variable latVar = ncf.getRootGroup().findVariable( "latitude");
    Variable lonVar = ncf.getRootGroup().findVariable( "longitude");
    Variable altVar = ncf.getRootGroup().findVariable( "altitude");

    Attribute timeUnits = timeVar.findAttribute( "units");
    String newUnits = "test unit string";
    System.out.println( "Switching time units from \"" + timeUnits.toString() + " \" to \"" + newUnits + "\"" );
    timeVar.addAttribute( new Attribute( "units", newUnits) );

    Array latArray;
    try
    {
      latArray = latVar.read();
    }
    catch ( IOException e )
    {
      assertTrue( "Couldn't read latitude data: " + e.getMessage(),
                  false );
      return;
    }

    try { Thread.sleep( 5000);
    }
    catch ( InterruptedException e ) {
    }

    boolean extended;
    try
    {
      extended = ncf.syncExtend();
    }
    catch ( IOException e )
    {
      assertTrue( "Couldn't syncExtend() file <" + testDataFileOut + ">: " + e.getMessage(),
                  false );
      return;
    }

    if ( ! extended )
    {
      System.out.println( "Did not extend file <" + testDataFileOut + ">." );
    }

    Dimension timeDim2 = ncf.getRootGroup().findDimension( "time");
    if ( timeDim == timeDim2 )
      System.out.println( "Time dimension the same." );
    else
      System.out.println( "Time dimension not the same." );

    System.out.println( "Initial time dim size = " + timeDimSize );
    System.out.println( "New time dim size = " + timeDim2.getLength() );
    System.out.println( "New time dim size (1) = " + timeDim.getLength() );

    System.out.println( "Time var units string: " + timeVar.findAttribute( "units").toString() );

    if ( latVar == ncf.getRootGroup().findVariable( "latitude"))
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      return false;
    return true;
  }

  public TableConfig getConfig(FeatureType wantFeatureType, NetcdfDataset ds, Formatter errlog) {
    Dimension stationDim = CoordSysEvaluator.findDimensionByType(ds, AxisType.Lat);
    if (stationDim == null) {
      errlog.format("Must have a latitude coordinate");
      return null;
    }

    Variable stationVar = ds.findVariable(stationDim.getName());
    if (stationVar == null) {
      errlog.format("Must have a station coordinate variable");
      return null;
    }

    Dimension obsDim = CoordSysEvaluator.findDimensionByType(ds, AxisType.Time);
    if (obsDim == null) {
      errlog.format("Must have a Time coordinate");
      return null;
    }

    // station table
    TableConfig stationTable = new TableConfig(Table.Type.Structure, "station");
    stationTable.structName = "station";
    stationTable.structureType = TableConfig.StructureType.PsuedoStructure;
    stationTable.featureType = FeatureType.STATION;
    stationTable.dimName = stationDim.getName();

    stationTable.stnId = stationVar.getShortName();

    stationTable.lat = CoordSysEvaluator.findCoordNameByType(ds, AxisType.Lat);
    stationTable.lon = CoordSysEvaluator.findCoordNameByType(ds, AxisType.Lon);
    stationTable.stnAlt = CoordSysEvaluator.findCoordNameByType(ds, AxisType.Height);

    // obs table
    TableConfig obsTable;
    obsTable = new TableConfig(Table.Type.MultidimInner, "obs");
    obsTable.time = CoordSysEvaluator.findCoordNameByType(ds, AxisType.Time);
    obsTable.outerName = stationDim.getName();
    obsTable.dimName = obsDim.getName();

    stationTable.addChild(obsTable);
    return stationTable;
  }
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  </stationCollection>
   */

  public TableConfig getConfig(FeatureType wantFeatureType, NetcdfDataset ds, Formatter errlog) {

    Dimension obsDim = Evaluator.getDimension(ds, "recNum", errlog);
    if (obsDim == null) {
      errlog.format("MADIS: must have an Observation dimension: named recNum");
      return null;
    }
    VNames vn = getVariableNames(ds, errlog);

    String levVarName = null;
    String levDimName = null;
    boolean hasStruct = Evaluator.hasRecordStructure(ds);
    FeatureType ft = Evaluator.getFeatureType(ds, ":thredds_data_type", errlog);
    if (null == ft) {
      if ((ds.findDimension("manLevel") != null) && (ds.findVariable("prMan") != null)) {
        ft = FeatureType.STATION_PROFILE;
        levVarName = "prMan";
        levDimName = "manLevel";
      } else if ((ds.findDimension("level") != null) && (ds.findVariable("levels") != null)) {
        ft = FeatureType.STATION_PROFILE;
        levVarName = "levels";
        levDimName = "level";
      }
    }
    if (null == ft) ft = FeatureType.POINT;

    // points
    if ((wantFeatureType == FeatureType.POINT) || (ft == FeatureType.POINT)) {
      TableConfig ptTable = new TableConfig(Table.Type.Structure, hasStruct ? "record" : obsDim.getName() );
      ptTable.structName = "record";
      ptTable.featureType = FeatureType.POINT;
      ptTable.structureType = hasStruct ? TableConfig.StructureType.Structure : TableConfig.StructureType.PsuedoStructure;     

      ptTable.dimName = obsDim.getName();
      ptTable.time = vn.obsTime;
      ptTable.timeNominal = vn.nominalTime;
      ptTable.lat = vn.lat;
      ptTable.lon = vn.lon;
      ptTable.elev = vn.elev;
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    Variable time = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
    if (time.getRank() != 1) {
      errlog.format("CFpointObs type=point: coord time must have rank 1, coord var= %s %n", time.getNameAndDimensions());
      return null;
    }
    Dimension obsDim = time.getDimension(0);

    TableConfig obsTable = makeSingle(ds, obsDim, errlog);
    obsTable.featureType = FeatureType.POINT;
    return obsTable;
  }
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    if (info == null) return null;

    // obs dimension
    VariableDS time = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
    Variable parentId = identifyParent(ds, CF.FeatureType.timeSeries);
    Dimension obsDim = info.childDim;

    // make station table
    TableConfig stnTable = makeStationTable(ds, FeatureType.STATION, info, errlog);
    if (stnTable == null) return null;
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    VariableDS time = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
    if (time == null) {
      errlog.format("Must have a Time coordinate%n");
      return null;
    }
    Dimension obsDim = null;
    if (time.getRank() > 0)
      obsDim = time.getDimension(time.getRank() - 1); // may be time(time) or time(stn, obs)
    else if (time.getParentStructure() != null) {
      Structure parent = time.getParentStructure(); // if time axis is a structure member, try pulling dimension out of parent structure
      obsDim = parent.getDimension(parent.getRank() - 1);
    }
    if (obsDim == null) {
      errlog.format("Must have a non-scalar Time coordinate%n");
      return null;
    }

    // station dimension
    Variable lat = CoordSysEvaluator.findCoordByType(ds, AxisType.Lat);
    if (lat == null) {
      errlog.format("Must have a Latitude coordinate%n");
      return null;
    }
    if (lat.getRank() == 0)
      return new EncodingInfo(Encoding.single, (Dimension) null, obsDim);
    Dimension stnDim = lat.getDimension(0);

    if (obsDim == stnDim)
      return new EncodingInfo(Encoding.flat, (Dimension) null, obsDim);

    // the raggeds
    Variable ragged_rowSize = Evaluator.getVariableWithAttributeValue(ds, CF.RAGGED_ROWSIZE, obsDim.getName());
    if (ragged_rowSize != null) {
      return new EncodingInfo(Encoding.raggedContiguous, stnDim, obsDim);
    }
    Variable ragged_parentIndex = Evaluator.getVariableWithAttributeValue(ds, CF.RAGGED_PARENTINDEX, stnDim.getName());
    if (ragged_parentIndex != null) {
      return new EncodingInfo(Encoding.raggedIndex, stnDim, obsDim);
    }

    if (lat.getRank() == 1)
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    VariableDS time = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
    if (time == null) {
      errlog.format("Must have a Time coordinate%n");
      return null;
    }
    Dimension obsDim = null;
    if (time.getRank() > 0)
      obsDim = time.getDimension(time.getRank() - 1); // may be time(time) or time(traj, obs)
    else if (time.getParentStructure() != null) {
      Structure parent = time.getParentStructure(); // if time axis is a structure member, try pulling dimension out of parent structure
      obsDim = parent.getDimension(parent.getRank() - 1);
    }
    if (obsDim == null) {
      errlog.format("Must have a non-scalar Time coordinate%n");
      return null;
    }

    // parent dimension
    Dimension parentDim = null;
    if (time.getRank() > 1) {
      parentDim = time.getDimension(0);
      return new EncodingInfo(Encoding.multidim, parentDim, obsDim);
    }
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    VariableDS z = CoordSysEvaluator.findCoordByType(ds, AxisType.Height);
    if (z == null) {
      errlog.format("Must have a Height coordinate%n");
      return null;
    }
    Dimension obsDim = null;
    if (z.getRank() > 0)
      obsDim = z.getDimension(z.getRank() - 1); // may be z(z) or alt(profile, z)
    else if (z.getParentStructure() != null) {
      Structure parent = z.getParentStructure(); // if time axis is a structure member, try pulling dimension out of parent structure
      obsDim = parent.getDimension(parent.getRank() - 1);
    }
    if (obsDim == null) {
      errlog.format("Must have a non-scalar Height coordinate%n");
      return null;
    }

    // parent dimension
    Dimension parentDim = null;
    if (z.getRank() > 1) {
      parentDim = z.getDimension(0);
      return new EncodingInfo(Encoding.multidim, parentDim, obsDim);
    }
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    VariableDS z = CoordSysEvaluator.findCoordByType(ds, AxisType.Height);
    if (z == null) {
      errlog.format("Must have a Height coordinate%n");
      return null;
    }
    Dimension obsDim = null;
    if (z.getRank() > 0)
      obsDim = z.getDimension(z.getRank() - 1); // may be z(z) or alt(profile, z)
    else if (z.getParentStructure() != null) {
      Structure parent = z.getParentStructure(); // if time axis is a structure member, try pulling dimension out of parent structure
      obsDim = parent.getDimension(parent.getRank() - 1);
    }
    if (obsDim == null) {
      errlog.format("Must have a non-scalar Height coordinate%n");
      return null;
    }

    // parent dimension
    Dimension trajDim = null;
    Dimension profileDim = null;
    if (z.getRank() > 2) {
      trajDim = z.getDimension(0);
      profileDim = z.getDimension(1);
      return new EncodingInfo(Encoding.multidim, trajDim, profileDim, obsDim);
    }
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    if (z.getRank() == 0) {
      errlog.format("timeSeriesProfile cannot have a scalar z coordinate%n");
      return null;
    }

    Dimension obsDim = z.getDimension(z.getRank() - 1); // may be z(z) or alt(profile, z)

    // parent dimension
    Dimension stnDim = null;
    Dimension profileDim = null;
    if (z.getRank() > 2) {
      stnDim = z.getDimension(0);
      profileDim = z.getDimension(1);
      return new EncodingInfo(Encoding.multidim, stnDim, profileDim, obsDim);
    }
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