/**
* Create a new GridVertCoord for a layer
*
* @param record layer record
* @param levelName name of this level
* @param lookup lookup table
* @param level1 level 1
* @param level2 level 2
*/
GridVertCoord(
GridRecord record,
String levelName,
GridTableLookup lookup,
double[] level1,
double[] level2) {
this.typicalRecord = record;
this.levelName = levelName;
this.lookup = lookup;
// dontUseVertical = !lookup.isVerticalCoordinate(record);
positive = lookup.isPositiveUp(record) ? "up" : "down";
units = lookup.getLevelUnit(record);
usesBounds = lookup.isLayer(this.typicalRecord);
levels = new ArrayList<LevelCoord>(level1.length);
for (int i = 0; i < level1.length; i++) {
levels.add(new LevelCoord(level1[i], (level2 == null) ? 0.0 : level2[i]));
}
Collections.sort(levels);
if (positive.equals("down")) {
Collections.reverse(levels);
}
dontUseVertical = (levels.size() == 1);
}
// @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);
}
private void createProfiles(int nprofiles) throws IOException {
this.nprofiles = nprofiles;
// add the dimensions
Dimension profileDim = ncfile.addDimension(profileDimName, nprofiles);
profileDims.add(profileDim);
Variable v = ncfile.addVariable(numObsName, DataType.INT, profileDimName);
ncfile.addVariableAttribute(
v, new Attribute("long_name", "number of children in linked list for this profile"));
v = ncfile.addVariable(numProfilesTotalName, DataType.INT, "");
ncfile.addVariableAttribute(v, new Attribute("long_name", "number of valid profiles"));
v = ncfile.addVariable(firstObsName, DataType.INT, profileDimName);
ncfile.addVariableAttribute(
v,
new Attribute("long_name", "record number of first obs in linked list for this profile"));
// time variable
Variable timeVar = ncfile.addStringVariable(timeName, profileDims, 20);
ncfile.addVariableAttribute(
timeVar, new Attribute("long_name", "ISO-8601 Date - time of observation"));
v = ncfile.addVariable(parentStationIndex, DataType.INT, profileDimName);
ncfile.addVariableAttribute(v, new Attribute("long_name", "index of parent station"));
v = ncfile.addVariable(nextProfileName, DataType.INT, profileDimName);
ncfile.addVariableAttribute(
v, new Attribute("long_name", "index of next profile in linked list for this station"));
}
public List<VariableBean> getStructureVariables(Structure s) {
List<VariableBean> vlist = new ArrayList<VariableBean>();
for (Variable v : s.getVariables()) {
vlist.add(new VariableBean(v));
}
return vlist;
}
public List<VariableBean> getVariableBeans(NetcdfFile ds) {
List<VariableBean> vlist = new ArrayList<VariableBean>();
for (Variable v : ds.getVariables()) {
vlist.add(new VariableBean(v));
}
return vlist;
}
public void showAtts() {
if (ds == null) return;
if (attTable == null) {
// global attributes
attTable =
new BeanTableSorted(
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<AttributeBean>();
for (Attribute att : ds.getGlobalAttributes()) {
attlist.add(new AttributeBean(att));
}
attTable.setBeans(attlist);
attWindow.show();
}
public Array getData(Range range, String parameterName)
throws IOException, InvalidRangeException {
Variable variable = ncfile.getRootGroup().findVariable(parameterName);
int varRank = variable.getRank();
int[] varShape = variable.getShape();
List section = new ArrayList(varRank);
section.add(range);
for (int i = 1; i < varRank; i++) {
section.add(new Range(0, varShape[i] - 1));
}
Array array = variable.read(section);
if (array.getShape()[0] == 1) {
return (array.reduce(0));
} else {
return (array);
}
// return( array.getShape()[0] == 1 ? array.reduce( 0 ) : array);
}
private void setSelected(Variable v) {
eventsOK = false;
List<Variable> vchain = new ArrayList<Variable>();
vchain.add(v);
Variable vp = v;
while (vp.isMemberOfStructure()) {
vp = vp.getParentStructure();
vchain.add(0, vp); // reverse
}
for (int i = 0; i < vchain.size(); i++) {
vp = vchain.get(i);
NestedTable ntable = setNestedTable(i, vp.getParentStructure());
ntable.setSelected(vp);
}
eventsOK = true;
}
/**
* Constructor.
*
* @param ncfile the netccdf file
* @param typedDataVariables list of data variables; all record variables will be added to this
* list, except . You can remove extra
* @param obsTimeVName observation time variable name (required)
* @param nomTimeVName nominal time variable name (may be null)
* @throws IllegalArgumentException if ncfile has no unlimited dimension and recDimName is null.
*/
public RecordDatasetHelper(
NetcdfDataset ncfile,
String obsTimeVName,
String nomTimeVName,
List<VariableSimpleIF> typedDataVariables,
String recDimName,
Formatter errBuffer) {
this.ncfile = ncfile;
this.obsTimeVName = obsTimeVName;
this.nomTimeVName = nomTimeVName;
this.errs = errBuffer;
// check if we already have a structure vs if we have to add it.
if (this.ncfile.hasUnlimitedDimension()) {
this.ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
this.recordVar = (StructureDS) this.ncfile.getRootGroup().findVariable("record");
this.obsDim = ncfile.getUnlimitedDimension();
} else {
if (recDimName == null)
throw new IllegalArgumentException(
"File <"
+ this.ncfile.getLocation()
+ "> has no unlimited dimension, specify psuedo record dimension with observationDimension global attribute.");
this.obsDim = this.ncfile.getRootGroup().findDimension(recDimName);
this.recordVar = new StructurePseudoDS(this.ncfile, null, "record", null, obsDim);
}
// create member variables
List<Variable> recordMembers = ncfile.getVariables();
for (Variable v : recordMembers) {
if (v == recordVar) continue;
if (v.isScalar()) continue;
if (v.getDimension(0) == this.obsDim) typedDataVariables.add(v);
}
// need the time units
Variable timeVar = ncfile.findVariable(obsTimeVName);
String timeUnitString =
ncfile.findAttValueIgnoreCase(timeVar, CDM.UNITS, "seconds since 1970-01-01");
try {
timeUnit = new DateUnit(timeUnitString);
} catch (Exception e) {
if (null != errs) errs.format("Error on string = %s == %s%n", timeUnitString, e.getMessage());
try {
timeUnit = new DateUnit("seconds since 1970-01-01");
} catch (Exception e1) {
// cant happen
}
}
}
private NestedTable setNestedTable(int level, Structure s) {
NestedTable ntable;
if (nestedTableList.size() < level + 1) {
ntable = new NestedTable(level);
nestedTableList.add(ntable);
} else {
ntable = nestedTableList.get(level);
}
if (s != null) // variables inside of records
ntable.table.setBeans(getStructureVariables(s));
ntable.show();
return ntable;
}
/**
* Constructor.
*
* @param dataset belongs to this dataset
* @param dsvar wraps this Variable
* @param gcs has this grid coordinate system
*/
public GeoGrid(GridDataset dataset, VariableDS dsvar, GridCoordSys gcs) {
this.dataset = dataset;
this.vs = dsvar;
this.gcs = gcs;
CoordinateAxis xaxis = gcs.getXHorizAxis();
if (xaxis instanceof CoordinateAxis1D) {
xDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(0));
yDimOrgIndex = findDimension(gcs.getYHorizAxis().getDimension(0));
} else { // 2D case
yDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(0));
xDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(1));
}
if (gcs.getVerticalAxis() != null)
zDimOrgIndex = findDimension(gcs.getVerticalAxis().getDimension(0));
if (gcs.getTimeAxis() != null) {
if (gcs.getTimeAxis1D() != null)
tDimOrgIndex = findDimension(gcs.getTimeAxis1D().getDimension(0));
else tDimOrgIndex = findDimension(gcs.getTimeAxis().getDimension(1));
}
if (gcs.getEnsembleAxis() != null)
eDimOrgIndex = findDimension(gcs.getEnsembleAxis().getDimension(0));
if (gcs.getRunTimeAxis() != null)
rtDimOrgIndex = findDimension(gcs.getRunTimeAxis().getDimension(0));
// construct canonical dimension list
int count = 0;
this.mydims = new ArrayList<Dimension>();
if ((rtDimOrgIndex >= 0) && (rtDimOrgIndex != tDimOrgIndex)) {
mydims.add(dsvar.getDimension(rtDimOrgIndex));
rtDimNewIndex = count++;
}
if (eDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(eDimOrgIndex));
eDimNewIndex = count++;
}
if (tDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(tDimOrgIndex));
tDimNewIndex = count++;
}
if (zDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(zDimOrgIndex));
zDimNewIndex = count++;
}
if (yDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(yDimOrgIndex));
yDimNewIndex = count++;
}
if (xDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(xDimOrgIndex));
xDimNewIndex = count;
}
}
private void writeHeader(ProfileFeature profile, PointFeature obs) throws IOException {
Formatter coordNames = new Formatter().format("%s %s %s", profileTimeName, latName, lonName);
List<VariableSimpleIF> coords = new ArrayList<>();
if (useAlt) {
coords.add(
VariableSimpleImpl.makeScalar(
altitudeCoordinateName, "obs altitude", altUnits, DataType.DOUBLE)
.add(new Attribute(CF.STANDARD_NAME, "altitude"))
.add(
new Attribute(
CF.POSITIVE,
CF1Convention.getZisPositive(altitudeCoordinateName, altUnits))));
coordNames.format(" %s", altitudeCoordinateName);
}
super.writeHeader(
coords, profile.getFeatureData(), obs.getFeatureData(), coordNames.toString());
}
/**
* Match levels
*
* @param records records to match
* @return true if they have the same levels
*/
boolean matchLevels(List<GridRecord> records) {
// first create a new list
List<LevelCoord> levelList = new ArrayList<LevelCoord>(records.size());
for (GridRecord record : records) {
LevelCoord lc = new LevelCoord(record.getLevel1(), record.getLevel2());
if (!levelList.contains(lc)) {
levelList.add(lc);
}
}
Collections.sort(levelList);
if (positive.equals("down")) {
Collections.reverse(levelList);
}
// gotta equal existing list
return levelList.equals(levels);
}
protected void makeFeatureVariables(StructureData featureData, boolean isExtended)
throws IOException {
// LOOK why not unlimited here ?
Dimension profileDim = writer.addDimension(null, profileDimName, nfeatures);
// Dimension profileDim = isExtendedModel ? writer.addUnlimitedDimension(profileDimName) :
// writer.addDimension(null, profileDimName, nprofiles);
// add the profile Variables using the profile dimension
List<VariableSimpleIF> profileVars = new ArrayList<>();
profileVars.add(
VariableSimpleImpl.makeScalar(latName, "profile latitude", CDM.LAT_UNITS, DataType.DOUBLE));
profileVars.add(
VariableSimpleImpl.makeScalar(
lonName, "profile longitude", CDM.LON_UNITS, DataType.DOUBLE));
profileVars.add(
VariableSimpleImpl.makeString(profileIdName, "profile identifier", null, id_strlen)
.add(new Attribute(CF.CF_ROLE, CF.PROFILE_ID))); // profileId:cf_role = "profile_id";
profileVars.add(
VariableSimpleImpl.makeScalar(
numberOfObsName, "number of obs for this profile", null, DataType.INT)
.add(
new Attribute(
CF.SAMPLE_DIMENSION, recordDimName))); // rowSize:sample_dimension = "obs"
profileVars.add(
VariableSimpleImpl.makeScalar(
profileTimeName,
"nominal time of profile",
timeUnit.getUnitsString(),
DataType.DOUBLE));
for (StructureMembers.Member m : featureData.getMembers()) {
VariableSimpleIF dv = getDataVar(m.getName());
if (dv != null) profileVars.add(dv);
}
if (isExtended) {
profileStruct =
(Structure)
writer.addVariable(null, profileStructName, DataType.STRUCTURE, profileDimName);
addCoordinatesExtended(profileStruct, profileVars);
} else {
addCoordinatesClassic(profileDim, profileVars, featureVarMap);
}
}
/**
* Add levels
*
* @param records GridRecords, one for each level
*/
void addLevels(List<GridRecord> records) {
for (int i = 0; i < records.size(); i++) {
GridRecord record = records.get(i);
if (coordIndex(record) < 0) {
levels.add(new LevelCoord(record.getLevel1(), record.getLevel2()));
if (dontUseVertical && (levels.size() > 1)) {
if (GridServiceProvider.debugVert) {
logger.warn(
"GribCoordSys: unused level coordinate has > 1 levels = "
+ levelName
+ " "
+ record.getLevelType1()
+ " "
+ levels.size());
}
}
}
}
Collections.sort(levels);
if (positive.equals("down")) {
Collections.reverse(levels);
}
}
public static void main(String args[]) throws Exception {
long start = System.currentTimeMillis();
Map<String, ucar.unidata.geoloc.Station> staHash =
new HashMap<String, ucar.unidata.geoloc.Station>();
String location = "R:/testdata/sounding/netcdf/Upperair_20070401_0000.nc";
NetcdfDataset ncfile = NetcdfDataset.openDataset(location);
ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
// look through record varibles, for those that have "manLevel" dimension
// make a StructureData object for those
StructureMembers sm = new StructureMembers("manLevel");
Dimension manDim = ncfile.findDimension("manLevel");
Structure record = (Structure) ncfile.findVariable("record");
List<Variable> allList = record.getVariables();
List<VariableSimpleIF> varList = new ArrayList<VariableSimpleIF>();
for (Variable v : allList) {
if ((v.getRank() == 1) && v.getDimension(0).equals(manDim)) {
// public VariableDS(NetcdfDataset ds, Group group, Structure parentStructure, String
// shortName, DataType dataType,
// String dims, String units, String desc) {
varList.add(
new VariableDS(
ncfile,
null,
null,
v.getShortName(),
v.getDataType(),
"",
v.getUnitsString(),
v.getDescription()));
// (String name, String desc, String units, DataType dtype, int []shape)
sm.addMember(
v.getShortName(),
v.getDescription(),
v.getUnitsString(),
v.getDataType(),
new int[0]); // scalar
}
}
ArrayStructureMA manAS = new ArrayStructureMA(sm, new int[] {manDim.getLength()});
// need the date units
Variable time = ncfile.findVariable("synTime");
String timeUnits = ncfile.findAttValueIgnoreCase(time, "units", null);
timeUnits = StringUtil.remove(timeUnits, '('); // crappy fsl'ism
timeUnits = StringUtil.remove(timeUnits, ')');
DateUnit timeUnit = new DateUnit(timeUnits);
// extract stations
int nrecs = 0;
StructureDataIterator iter = record.getStructureIterator();
while (iter.hasNext()) {
StructureData sdata = iter.next();
String name = sdata.getScalarString("staName");
ucar.unidata.geoloc.Station s = staHash.get(name);
if (s == null) {
float lat = sdata.convertScalarFloat("staLat");
float lon = sdata.convertScalarFloat("staLon");
float elev = sdata.convertScalarFloat("staElev");
s = new StationImpl(name, "", lat, lon, elev);
staHash.put(name, s);
}
nrecs++;
}
List<ucar.unidata.geoloc.Station> stnList =
Arrays.asList(staHash.values().toArray(new ucar.unidata.geoloc.Station[staHash.size()]));
Collections.sort(stnList);
// create the writer
WriterProfileObsDataset writer =
new WriterProfileObsDataset(location + ".out", "rewrite " + location);
writer.writeHeader(stnList, varList, nrecs, "prMan");
// extract records
iter = record.getStructureIterator();
while (iter.hasNext()) {
StructureData sdata = iter.next();
String name = sdata.getScalarString("staName");
double timeValue = sdata.convertScalarDouble("synTime");
Date date = timeUnit.makeDate(timeValue);
// transfer to the ArrayStructure
List<String> names = sm.getMemberNames();
for (String mname : names) {
manAS.setMemberArray(mname, sdata.getArray(mname));
}
// each level is weritten as a seperate structure
int numMand = sdata.getScalarInt("numMand");
if (numMand >= manDim.getLength()) continue;
for (int i = 0; i < numMand; i++) {
StructureData useData = manAS.getStructureData(i);
writer.writeRecord(name, date, useData);
}
}
writer.finish();
long took = System.currentTimeMillis() - start;
System.out.println("That took = " + took);
}
private void createStations(List<ucar.unidata.geoloc.Station> stnList) throws IOException {
int nstns = stnList.size();
// see if there's altitude, wmoId for any stations
for (int i = 0; i < nstns; i++) {
ucar.unidata.geoloc.Station stn = stnList.get(i);
// if (!Double.isNaN(stn.getAltitude()))
// useAlt = true;
if ((stn.getWmoId() != null) && (stn.getWmoId().trim().length() > 0)) useWmoId = true;
}
/* if (useAlt)
ncfile.addGlobalAttribute("altitude_coordinate", altName); */
// find string lengths
for (int i = 0; i < nstns; i++) {
ucar.unidata.geoloc.Station station = stnList.get(i);
name_strlen = Math.max(name_strlen, station.getName().length());
desc_strlen = Math.max(desc_strlen, station.getDescription().length());
if (useWmoId) wmo_strlen = Math.max(wmo_strlen, station.getName().length());
}
LatLonRect llbb = getBoundingBox(stnList);
ncfile.addGlobalAttribute(
"geospatial_lat_min", Double.toString(llbb.getLowerLeftPoint().getLatitude()));
ncfile.addGlobalAttribute(
"geospatial_lat_max", Double.toString(llbb.getUpperRightPoint().getLatitude()));
ncfile.addGlobalAttribute(
"geospatial_lon_min", Double.toString(llbb.getLowerLeftPoint().getLongitude()));
ncfile.addGlobalAttribute(
"geospatial_lon_max", Double.toString(llbb.getUpperRightPoint().getLongitude()));
// add the dimensions
Dimension recordDim = ncfile.addUnlimitedDimension(recordDimName);
recordDims.add(recordDim);
Dimension stationDim = ncfile.addDimension(stationDimName, nstns);
stationDims.add(stationDim);
// add the station Variables using the station dimension
Variable v = ncfile.addVariable(latName, DataType.DOUBLE, stationDimName);
ncfile.addVariableAttribute(v, new Attribute("units", "degrees_north"));
ncfile.addVariableAttribute(v, new Attribute("long_name", "station latitude"));
v = ncfile.addVariable(lonName, DataType.DOUBLE, stationDimName);
ncfile.addVariableAttribute(v, new Attribute("units", "degrees_east"));
ncfile.addVariableAttribute(v, new Attribute("long_name", "station longitude"));
if (useAlt) {
v = ncfile.addVariable(altName, DataType.DOUBLE, stationDimName);
ncfile.addVariableAttribute(v, new Attribute("units", "meters"));
ncfile.addVariableAttribute(v, new Attribute("long_name", "station altitude"));
}
v = ncfile.addStringVariable(idName, stationDims, name_strlen);
ncfile.addVariableAttribute(v, new Attribute("long_name", "station identifier"));
v = ncfile.addStringVariable(descName, stationDims, desc_strlen);
ncfile.addVariableAttribute(v, new Attribute("long_name", "station description"));
if (useWmoId) {
v = ncfile.addStringVariable(wmoName, stationDims, wmo_strlen);
ncfile.addVariableAttribute(v, new Attribute("long_name", "station WMO id"));
}
v = ncfile.addVariable(numProfilesName, DataType.INT, stationDimName);
ncfile.addVariableAttribute(
v, new Attribute("long_name", "number of profiles in linked list for this station"));
v = ncfile.addVariable(firstProfileName, DataType.INT, stationDimName);
ncfile.addVariableAttribute(
v, new Attribute("long_name", "index of first profile in linked list for this station"));
}
// @todo Make sure units are degrees_east
public Array getLongitude(Range range) throws IOException, InvalidRangeException {
List section = new ArrayList(1);
section.add(range);
return (lonVar.read(section));
}
public List getTrajectories() // throws IOException;
{
List l = new ArrayList();
l.add(trajectory);
return (l);
}
public List getTrajectoryIds() {
List l = new ArrayList();
l.add(trajectoryId);
return (l);
}
