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 testReadStandardVar() throws Exception { ncfileRead = NetcdfFile.open(filename); dsRead = NetcdfDataset.openDataset(filename); readDouble(); readByte2Short(); readByte(); readShortMissing(); readShort2FloatMissing(); readDoubleMissing(); ncfileRead.close(); dsRead.close(); }
public List<CoordinateSystemBean> getCoordinateSystemBeans(NetcdfDataset ds) { List<CoordinateSystemBean> vlist = new ArrayList<>(); for (CoordinateSystem elem : ds.getCoordinateSystems()) { vlist.add(new CoordinateSystemBean(elem)); } return vlist; }
public void showAtts() { if (ds == null) return; if (attTable == null) { // global attributes attTable = new BeanTable(AttributeBean.class, (PreferencesExt) prefs.node("AttributeBeans"), false); PopupMenu varPopup = new ucar.nc2.ui.widget.PopupMenu(attTable.getJTable(), "Options"); varPopup.addAction( "Show Attribute", new AbstractAction() { public void actionPerformed(ActionEvent e) { AttributeBean bean = (AttributeBean) attTable.getSelectedBean(); if (bean != null) { infoTA.setText(bean.att.toString()); infoTA.gotoTop(); infoWindow.show(); } } }); attWindow = new IndependentWindow("Global Attributes", BAMutil.getImage("netcdfUI"), attTable); attWindow.setBounds( (Rectangle) prefs.getBean("AttWindowBounds", new Rectangle(300, 100, 500, 800))); } List<AttributeBean> attlist = new ArrayList<>(); for (Attribute att : ds.getGlobalAttributes()) { attlist.add(new AttributeBean(att)); } attTable.setBeans(attlist); attWindow.show(); }
public void readByte2Short() throws Exception { Variable t2 = null; assert (null != (t2 = ncfileRead.findVariable("t2"))); assert (t2.getDataType() == DataType.BYTE); Attribute att = t2.findAttribute(CDM.SCALE_FACTOR); assert (null != att); assert (!att.isArray()); assert (1 == att.getLength()); assert (2 == att.getNumericValue().doubleValue()); assert (DataType.SHORT == att.getDataType()); assert (null != (t2 = dsRead.findVariable("t2"))); assert t2 instanceof VariableEnhanced; VariableDS vs = (VariableDS) t2; assert (vs.getDataType() == DataType.SHORT) : vs.getDataType(); assert (!vs.hasMissing()); Array A = vs.read(); assert (A.getElementType() == short.class) : A.getElementType(); Index ima = A.getIndex(); int[] shape = A.getShape(); int i, j; for (i = 0; i < shape[0]; i++) { for (j = 0; j < shape[1]; j++) { assert (A.getShort(ima.set(i, j)) == (2 * (i * 10 + j) + 77)); } } System.out.println("**************TestStandardVar readByte2Short"); }
/** * Wrap the given Variable, making it into a VariableDS. Delegate data reading to the original * variable. Take all metadata from original variable. Does not share cache, iosp. * * @param g logical container, if null use orgVar's group * @param orgVar the original Variable to wrap. The original Variable is not modified. Must not be * a Structure, use StructureDS instead. * @param enhance if true, use NetcdfDataset.defaultEnhanceMode to define what enhancements are * made. Note that this can change DataType and data values. You can also call enhance() * later. If orgVar is VariableDS, then enhance is inherited from there, and this parameter is * ignored. */ public VariableDS(Group g, Variable orgVar, boolean enhance) { super(orgVar); if (g != null) this.group = g; // otherwise super() sets group; this affects the long name and the dimensions. setDimensions(getDimensionsString()); // reset the dimensions if (orgVar instanceof Structure) throw new IllegalArgumentException( "VariableDS must not wrap a Structure; name=" + orgVar.getName()); // dont share cache, iosp : all IO is delegated this.ncfile = null; this.spiObject = null; createNewCache(); this.orgVar = orgVar; this.orgDataType = orgVar.getDataType(); if (orgVar instanceof VariableDS) { VariableDS ncVarDS = (VariableDS) orgVar; this.enhanceProxy = ncVarDS.enhanceProxy; this.scaleMissingProxy = ncVarDS.scaleMissingProxy; this.enhanceMode = ncVarDS.enhanceMode; } else { this.enhanceProxy = new EnhancementsImpl(this); if (enhance) { enhance(NetcdfDataset.getDefaultEnhanceMode()); } else { this.scaleMissingProxy = new EnhanceScaleMissingImpl(); } } }
public void setDataset(NetcdfDataset ds) { this.ds = ds; parseInfo = new Formatter(); List<VariableBean> beanList = new ArrayList<>(); List<AxisBean> axisList = new ArrayList<>(); setVariables(ds.getVariables(), axisList, beanList); varTable.setBeans(beanList); axisTable.setBeans(axisList); csTable.setBeans(getCoordinateSystemBeans(ds)); }
public void summaryInfo(Formatter f) { if (ds == null) return; f.format("%s%n", ds.getLocation()); int ngrids = 0; for (Object varo : varTable.getBeans()) { VariableBean varBean = (VariableBean) varo; if (varBean.getDataType().trim().equalsIgnoreCase("grid")) ngrids++; } int ncoordSys = csTable.getBeans().size(); int ncoords = axisTable.getBeans().size(); f.format(" ngrids=%d, ncoords=%d, ncoordSys=%d%n", ngrids, ncoords, ncoordSys); }
public void readShortMissing() throws Exception { Variable v = null; assert (null != (v = ncfileRead.findVariable("t4"))); assert (v.getDataType() == DataType.SHORT); // default use of missing_value assert (null != (v = dsRead.findVariable("t4"))); assert v instanceof VariableEnhanced; assert v instanceof VariableDS; VariableDS vs = (VariableDS) v; assert (vs.getDataType() == DataType.SHORT); Attribute att = vs.findAttribute(CDM.MISSING_VALUE); assert (null != att); assert (!att.isArray()); assert (1 == att.getLength()); System.out.println("missing_value = " + att.getNumericValue().shortValue()); assert (((short) -9999) == att.getNumericValue().shortValue()); assert (DataType.SHORT == att.getDataType()); assert (vs.hasMissing()); assert (vs.hasMissingValue()); assert (vs.isMissing((double) ((short) -9999))); assert (vs.isMissingValue((double) ((short) -9999))); Array A = vs.read(); Index ima = A.getIndex(); int[] shape = A.getShape(); int i, j; for (i = 0; i < shape[0]; i++) { for (j = 0; j < shape[1]; j++) { assert (A.getFloat(ima.set(i, j)) == (i * 10 + j)); } } // turn off missing data vs.setMissingDataIsMissing(false); assert (vs.getDataType() == DataType.SHORT); assert (!vs.hasMissing()); assert (vs.hasMissingValue()); assert (!vs.isMissing((double) ((short) -9999))); assert (vs.isMissingValue((double) ((short) -9999))); vs.setMissingDataIsMissing(true); assert (vs.hasMissing()); assert (vs.isMissing((double) ((short) -9999))); System.out.println("**************TestStandardVar Read readShortMissing"); }
public void readDouble() throws Exception { Variable t1 = null; assert (null != (t1 = ncfileRead.findVariable("t1"))); assert (t1.getDataType() == DataType.DOUBLE); Attribute att = t1.findAttribute(CDM.SCALE_FACTOR); assert (null != att); assert (!att.isArray()); assert (1 == att.getLength()); assert (2.0 == att.getNumericValue().doubleValue()); assert (DataType.DOUBLE == att.getDataType()); // read Array A = t1.read(); int i, j; Index ima = A.getIndex(); int[] shape = A.getShape(); for (i = 0; i < shape[0]; i++) { for (j = 0; j < shape[1]; j++) { assert (A.getDouble(ima.set(i, j)) == (double) (i * 10.0 + j)); } } assert (null != (t1 = dsRead.findVariable("t1"))); assert t1 instanceof VariableEnhanced; VariableEnhanced dsVar = (VariableEnhanced) t1; assert (dsVar.getDataType() == DataType.DOUBLE); A = dsVar.read(); ima = A.getIndex(); shape = A.getShape(); for (i = 0; i < shape[0]; i++) { for (j = 0; j < shape[1]; j++) { assert (A.getDouble(ima.set(i, j)) == (2.0 * (i * 10.0 + j) + 77.0)); } } assert (null == t1.findAttribute(CDM.SCALE_FACTOR)); assert (null == t1.findAttribute("add_offset")); System.out.println("**************TestStandardVar ReadDouble"); }
public void readDoubleMissing() throws Exception { VariableDS v = null; assert (null != (v = (VariableDS) dsRead.findVariable("m1"))); assert (v.getDataType() == DataType.DOUBLE); Array A = v.read(); Index ima = A.getIndex(); double val = A.getFloat(ima.set(1, 1)); assert Double.isNaN(val); assert v.isMissing(val); // reread with useNans off v.setUseNaNs(false); v.createNewCache(); A = v.read(); ima = A.getIndex(); val = A.getFloat(ima.set(1, 1)); assert TestAll.closeEnough(val, -999.99) : val; assert v.isMissing(val); }
public void readByte() throws Exception { Variable v = null; assert (null != (v = ncfileRead.findVariable("t3"))); assert (v.getDataType() == DataType.BYTE); assert (null != (v = dsRead.findVariable("t3"))); assert v instanceof VariableEnhanced; assert v instanceof VariableDS; VariableDS vs = (VariableDS) v; assert (vs.getDataType() == DataType.BYTE); Attribute att = vs.findAttribute("_FillValue"); assert (null != att); assert (!att.isArray()); assert (1 == att.getLength()); System.out.println("_FillValue = " + att.getNumericValue().byteValue()); assert (((byte) 255) == att.getNumericValue().byteValue()); assert (DataType.BYTE == att.getDataType()); assert (vs.hasMissing()); assert (vs.hasFillValue()); assert (vs.isMissing((double) ((byte) 255))); assert (vs.isFillValue((double) ((byte) 255))); Array A = vs.read(); assert (A.getElementType() == byte.class) : A.getElementType(); Index ima = A.getIndex(); int[] shape = A.getShape(); int i, j; for (i = 0; i < shape[0]; i++) { for (j = 0; j < shape[1]; j++) { assert (A.getFloat(ima.set(i, j)) == (i * 10 + j)); } } System.out.println("**************TestStandardVar ReadByte"); }
public void readShort2FloatMissing() throws Exception { Variable v = null; assert (null != (v = ncfileRead.findVariable("t5"))); assert (v.getDataType() == DataType.SHORT); // standard convert with missing data assert (null != (v = dsRead.findVariable("t5"))); assert v instanceof VariableEnhanced; assert v instanceof VariableDS; VariableDS vs = (VariableDS) v; assert (vs.getDataType() == DataType.FLOAT); assert (vs.hasMissing()); assert (vs.hasMissingValue()); double mv = 2 * (-9999) + 77; assert (vs.isMissing((double) mv)); assert (vs.isMissingValue((double) mv)); Array A = vs.read(); Index ima = A.getIndex(); int[] shape = A.getShape(); int i, j; assert (vs.isMissing(A.getFloat(ima.set(0, 0)))); for (i = 0; i < shape[0]; i++) { for (j = 1; j < shape[1]; j++) { float val = A.getFloat(ima.set(i, j)); float want = 2 * (i * 10 + j) + 77; if (val != want) System.out.println(i + " " + j + " " + val + " " + want); assert (val == want); } } // useNaNs vs.setUseNaNs(true); assert (vs.getDataType() == DataType.FLOAT); assert (vs.hasMissing()); assert (vs.hasMissingValue()); double mv2 = 2 * (-9999) + 77; assert (vs.isMissing((double) mv2)); assert (vs.isMissingValue((double) mv2)); Array A2 = vs.read(); Index ima2 = A2.getIndex(); int[] shape2 = A2.getShape(); double mval = A2.getFloat(ima2.set(0, 0)); assert vs.isMissing(mval); assert Double.isNaN(mval); for (i = 0; i < shape2[0]; i++) { for (j = 1; j < shape2[1]; j++) { float val = A2.getFloat(ima2.set(i, j)); float want = 2 * (i * 10 + j) + 77; if (val != want) System.out.println(i + " " + j + " " + val + " " + want); assert (val == want) : val + " != " + want; } } assert (null == vs.findAttribute(CDM.SCALE_FACTOR)); assert (null == vs.findAttribute("add_offset")); assert (null == vs.findAttribute(CDM.MISSING_VALUE)); System.out.println("**************TestStandardVar Read readShort2FloatMissing"); }
/** * Implement NcML Forecast Model Run Collection Aggregation with files that are complete runs (have * all forecast times in the same file) * * @author caron */ public class AggregationFmrc extends AggregationOuterDimension { protected static Set<NetcdfDataset.Enhance> fmrcEnhanceMode = NetcdfDataset.getDefaultEnhanceMode(); private Fmrc fmrc; private String runMatcher; // , forecastMatcher, offsetMatcher; // scanFmrc public AggregationFmrc(NetcdfDataset ncd, String dimName, String recheckS) { super(ncd, dimName, Type.forecastModelRunCollection, recheckS); } public void addDirectoryScanFmrc( String dirName, String suffix, String regexpPatternString, String subdirs, String olderThan, String runMatcher, String forecastMatcher, String offsetMatcher) throws IOException { // only one this.runMatcher = runMatcher; // this.forecastMatcher = forecastMatcher; // this.offsetMatcher = offsetMatcher; // this.enhance = NetcdfDataset.getDefaultEnhanceMode(); isDate = true; // DatasetScanner d = new DatasetScanner(null, dirName, suffix, regexpPatternString, subdirs, // olderThan); // datasetManager.addDirectoryScan(d); datasetManager.addDirectoryScan(dirName, suffix, regexpPatternString, subdirs, olderThan, null); if (runMatcher != null) { DateExtractor dateExtractor = new DateExtractorFromName(runMatcher, false); datasetManager.setDateExtractor(dateExtractor); } } @Override protected void makeDatasets(CancelTask cancelTask) throws IOException { super.makeDatasets(cancelTask); for (Dataset ds : datasets) ds.enhance = fmrcEnhanceMode; } @Override public void getDetailInfo(Formatter f) { super.getDetailInfo(f); if (runMatcher != null) f.format(" runMatcher=%s%n", runMatcher); /* if (forecastMatcher != null) f.format(" forecastMatcher=%s%n", forecastMatcher); if (offsetMatcher != null) f.format(" offsetMatcher=%s%n", offsetMatcher); */ } @Override protected void buildNetcdfDataset(CancelTask cancelTask) throws IOException { DateExtractor dateExtractor = null; if (runMatcher != null) dateExtractor = new DateExtractorFromName(runMatcher, false); // uses path if (dateExtractor == null && dateFormatMark != null) dateExtractor = new DateExtractorFromName(dateFormatMark, true); fmrc = new Fmrc(datasetManager, new FeatureCollectionConfig()); // fill in the ncDataset fmrc.getDataset2D(ncDataset); } // we assume the variables are complete, but the time dimensions and values have to be recomputed @Override protected void rebuildDataset() throws IOException { throw new UnsupportedOperationException(); // ncDataset.empty(); // fmrc.getDataset2D(false, true, ncDataset); } }