/*
* Copyright 1998-2014 University Corporation for Atmospheric Research/Unidata
*
* Portions of this software were developed by the Unidata Program at the
* University Corporation for Atmospheric Research.
*
* Access and use of this software shall impose the following obligations
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* any fee or cost, to use, copy, modify, alter, enhance and distribute
* this software, and any derivative works thereof, and its supporting
* documentation for any purpose whatsoever, provided that this entire
* notice appears in all copies of the software, derivative works and
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* and/or Unidata, however, may not be used in any advertising or publicity
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*
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* DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
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*/
package ucar.nc2.ft.point.standard;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;
import ucar.nc2.Dimension;
import ucar.nc2.NetcdfFile;
import ucar.nc2.Structure;
import ucar.nc2.Variable;
import ucar.nc2.constants.AxisType;
import ucar.nc2.constants.CDM;
import ucar.nc2.constants.FeatureType;
import ucar.nc2.dataset.CoordinateAxis;
import ucar.nc2.dataset.NetcdfDataset;
import ucar.nc2.ft.FeatureDatasetFactoryManager;
import ucar.nc2.ft.point.standard.plug.*;
import java.io.IOException;
import java.lang.reflect.Method;
import java.util.*;
/**
* Analyzes the coordinate systems of a dataset to try to identify the Feature Type and the
* structure of the data.
* Used by PointDatasetStandardFactory.
*
* @author caron
* @since Mar 20, 2008
*/
public class TableAnalyzer {
static private org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(TableAnalyzer.class);
static private final List<Configurator> conventionList = new ArrayList<>();
static private boolean userMode = false;
static private final boolean debug = false;
// search in the order added
static {
registerAnalyzer("CDM", CdmDirect.class, null);
registerAnalyzer(CDM.CF_EXTENDED, CFpointObsExt.class, null);
registerAnalyzer("CF-1.", CFpointObs.class, new ConventionNameOk() {
public boolean isMatch(String convName, String wantName) {
return convName.startsWith(wantName); // && !convName.equals("CF-1.0"); // throw 1.0 to default analyser
}
});
registerAnalyzer("GEMPAK/CDM", GempakCdm.class, null);
registerAnalyzer("Unidata Observation Dataset v1.0", UnidataPointObs.class, null);
registerAnalyzer("Cosmic", Cosmic.class, null);
registerAnalyzer("Jason", Jason.class, null);
registerAnalyzer("FslWindProfiler", FslWindProfiler.class, null);
registerAnalyzer("MADIS-ACARS", MadisAcars.class, null); // must be before Madis
registerAnalyzer("MADIS surface observations, v1.0", Madis.class, null); // must be before FslRaob
registerAnalyzer("FSL Raobs", FslRaob.class, null); // must be before FslRaob
registerAnalyzer("IRIDL", Iridl.class, null);
registerAnalyzer("Ndbc", NdbcCoards.class, null);
registerAnalyzer("Suomi-Station-CDM", Suomi.class, null);
registerAnalyzer("BuoyShip-NetCDF", BuoyShipSynop.class, null);
registerAnalyzer("NCAR-RAF/nimbus", RafNimbus.class, null);
registerAnalyzer("NLDN-CDM", Nldn.class, null);
registerAnalyzer("SimpleTrajectory", SimpleTrajectory.class, null);
// further calls to registerConvention are by the user
userMode = true;
}
static public void registerAnalyzer(String conventionName, Class c, ConventionNameOk match) {
if (!(TableConfigurer.class.isAssignableFrom(c)))
throw new IllegalArgumentException("Class " + c.getName() + " must implement TableConfigurer");
// fail fast - check newInstance works
TableConfigurer tc;
try {
tc = (TableConfigurer) c.newInstance();
} catch (InstantiationException e) {
throw new IllegalArgumentException("TableConfigurer Class " + c.getName() + " cannot instantiate, probably need default Constructor");
} catch (IllegalAccessException e) {
throw new IllegalArgumentException("TableConfigurer Class " + c.getName() + " is not accessible");
}
Configurator anal = new Configurator(conventionName, c, tc, match);
if (userMode) // user stuff gets put at top
conventionList.add(0, anal);
else
conventionList.add(anal);
}
static private interface ConventionNameOk {
boolean isMatch(String convName, String wantName);
}
static private class Configurator {
String convName;
Class confClass;
TableConfigurer confInstance;
ConventionNameOk match;
Configurator(String convName, Class confClass, TableConfigurer confInstance, ConventionNameOk match) {
this.convName = convName;
this.confClass = confClass;
this.confInstance = confInstance;
this.match = match;
}
}
static private Configurator matchConfigurator(String convName) {
for (Configurator anal : conventionList) {
if ((anal.match == null) && anal.convName.equalsIgnoreCase(convName)) return anal;
if ((anal.match != null) && anal.match.isMatch(convName, anal.convName)) return anal;
}
return null;
}
/**
* Find a TableConfigurer for this dataset, if there is one.
*
* @param wantFeatureType want this FeatureType
* @param ds for this dataset
* @return TableConfigurer or null if not found
* @throws IOException on read error
*/
static public TableConfigurer getTableConfigurer(FeatureType wantFeatureType, NetcdfDataset ds) throws IOException {
String convUsed = null;
// look for the Conventions attribute
String convName = ds.findAttValueIgnoreCase(null, CDM.CONVENTIONS, null);
if (convName == null)
convName = ds.findAttValueIgnoreCase(null, "Convention", null);
// now look for TableConfigurer using that Convention
Configurator anal = null;
if (convName != null) {
convName = convName.trim();
// look for Convention parsing class
anal = matchConfigurator(convName);
if (anal != null) {
convUsed = convName;
if (debug) System.out.println(" TableConfigurer found using convName "+convName);
}
// now look for comma or semicolon or / delimited list
if (anal == null) {
List<String> names = new ArrayList<>();
if ((convName.indexOf(',') > 0) || (convName.indexOf(';') > 0)) {
StringTokenizer stoke = new StringTokenizer(convName, ",;");
while (stoke.hasMoreTokens()) {
String name = stoke.nextToken();
names.add(name.trim());
}
} else if ((convName.indexOf('/') > 0)) {
StringTokenizer stoke = new StringTokenizer(convName, "/");
while (stoke.hasMoreTokens()) {
String name = stoke.nextToken();
names.add(name.trim());
}
}
if (names.size() > 0) {
// search the registered conventions, in order
for (Configurator conv : conventionList) {
for (String name : names) {
if (name.equalsIgnoreCase(conv.convName)) {
anal = conv;
convUsed = name;
if (debug) System.out.println(" TableConfigurer found using convName "+convName);
}
}
if (anal != null) break;
}
}
}
}
// look for ones that dont use Convention attribute, in order added.
// call method isMine() using reflection.
if (anal == null) {
for (Configurator conv : conventionList) {
Class c = conv.confClass;
Method isMineMethod;
try {
isMineMethod = c.getMethod("isMine", new Class[]{FeatureType.class, NetcdfDataset.class});
} catch (NoSuchMethodException ex) {
continue;
}
try {
Boolean result = (Boolean) isMineMethod.invoke(conv.confInstance, wantFeatureType, ds);
if (debug) System.out.println(" TableConfigurer.isMine "+c.getName()+ " result = " + result);
if (result) {
anal = conv;
convUsed = conv.convName;
break;
}
} catch (Exception ex) {
System.out.println("ERROR: Class " + c.getName() + " Exception invoking isMine method%n" + ex);
}
}
}
// Instantiate a new TableConfigurer object
TableConfigurer tc = null;
if (anal != null) {
try {
tc = (TableConfigurer) anal.confClass.newInstance();
tc.setConvName( convName);
tc.setConvUsed( convUsed);
} catch (InstantiationException | IllegalAccessException e) {
log.error("TableConfigurer create failed", e);
}
}
return tc;
}
/**
* Create a TableAnalyser for this dataset with the given TableConfigurer
*
* @param tc TableConfigurer, may be null.
* @param wantFeatureType want this FeatureType
* @param ds for this dataset
* @return TableAnalyser
* @throws IOException on read error
*/
static public TableAnalyzer factory(TableConfigurer tc, FeatureType wantFeatureType, NetcdfDataset ds) throws IOException {
// Create a TableAnalyzer with this TableConfigurer (may be null)
TableAnalyzer analyzer = new TableAnalyzer(ds, tc);
if (tc != null) {
if (tc.getConvName() == null)
analyzer.userAdvice.format(" No 'Conventions' global attribute.%n");
else
analyzer.userAdvice.format(" Conventions global attribute = %s %n", tc.getConvName());
// add the convention name used
if (tc.getConvUsed() != null) {
analyzer.setConventionUsed(tc.getConvUsed());
if (!tc.getConvUsed().equals(tc.getConvName()))
analyzer.userAdvice.format(" TableConfigurer used = "+tc.getConvUsed()+".%n");
}
} else {
analyzer.userAdvice.format(" No TableConfigurer found, using default analysis.%n");
}
// construct the nested table object
analyzer.analyze(wantFeatureType);
return analyzer;
}
////////////////////////////////////////////////////////////////////////////////////////////////
private TableConfigurer tc;
private NetcdfDataset ds;
private Map<String, TableConfig> tableFind = new HashMap<>();
private Set<TableConfig> tableSet = new HashSet<>();
private List<NestedTable> leaves = new ArrayList<>();
private FeatureType ft;
private TableConfig configResult;
private TableAnalyzer(NetcdfDataset ds, TableConfigurer tc) {
this.tc = tc;
this.ds = ds;
if (tc == null)
userAdvice.format("Using default TableConfigurer.%n");
}
public List<NestedTable> getFlatTables() {
return leaves;
}
public boolean featureTypeOk(FeatureType ftype, Formatter errlog) {
for (NestedTable nt : leaves) {
if (!nt.hasCoords()) {
errlog.format("Table %s featureType %s: lat/lon/time coord not found%n", nt.getName(), nt.getFeatureType());
try {
writeConfigXML(errlog);
} catch (IOException e) {
log.error("featuretypeOk", e);
}
}
if (!FeatureDatasetFactoryManager.featureTypeOk(ftype, nt.getFeatureType()))
errlog.format("Table %s featureType %s doesnt match desired type %s%n", nt.getName(), nt.getFeatureType(), ftype);
if (nt.hasCoords() && FeatureDatasetFactoryManager.featureTypeOk(ftype, nt.getFeatureType()))
return true;
}
return false;
}
public String getName() {
if (tc != null) return tc.getClass().getName();
return "Default";
}
// for debugging messages
public FeatureType getFirstFeatureType() {
for (NestedTable nt : leaves) {
if (nt.hasCoords())
return nt.getFeatureType();
}
return null;
}
public NetcdfDataset getNetcdfDataset() {
return ds;
}
private Formatter userAdvice = new Formatter();
private Formatter errlog = new Formatter();
public String getUserAdvice() {
return userAdvice.toString();
}
public String getErrlog() {
return errlog.toString();
}
private String conventionName;
private void setConventionUsed(String convName) {
this.conventionName = convName;
}
TableConfig getTableConfig() {
return this.configResult;
}
TableConfigurer getTableConfigurer() {
return tc;
}
/////////////////////////////////////////////////////////
/**
* Make a NestedTable object for the dataset.
* @param wantFeatureType want this FeatureType
* @throws IOException on read error
*/
private void analyze(FeatureType wantFeatureType) throws IOException {
// for netcdf-3 files, convert record dimension to structure
// LOOK may be problems when served via opendap
boolean structAdded = (Boolean) ds.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
if (tc == null) {
makeTablesDefault(structAdded);
makeNestedTables();
} else {
configResult = tc.getConfig(wantFeatureType, ds, errlog);
if (configResult != null)
addTableRecurse( configResult); // kinda stupid
else { // use default
makeTablesDefault(structAdded);
makeNestedTables();
}
}
// find the leaves
for (TableConfig config : tableSet) {
if (config.children == null) { // its a leaf
NestedTable flatTable = new NestedTable(ds, config, errlog);
leaves.add(flatTable);
}
}
if (PointDatasetStandardFactory.showTables)
getDetailInfo( new Formatter( System.out));
}
private void addTable(TableConfig t) {
tableFind.put(t.name, t);
if (t.dimName != null)
tableFind.put(t.dimName, t);
tableSet.add(t);
}
private void addTableRecurse(TableConfig t) {
addTable(t);
if (t.children != null) {
for (TableConfig child : t.children)
addTableRecurse(child);
}
}
///////////////////////////////////////////////////////////
// default analasis aka guessing
// no TableConfig was passed in - gotta wing it
private void makeTablesDefault(boolean structAdded) throws IOException {
// make Structures into a table
List<Variable> vars = new ArrayList<>(ds.getVariables());
Iterator<Variable> iter = vars.iterator();
while (iter.hasNext()) {
Variable v = iter.next();
if (v instanceof Structure) { // handles Sequences too
TableConfig st = new TableConfig(Table.Type.Structure, v.getFullName());
CoordSysEvaluator.findCoords(st, ds, null);
st.structName = v.getFullName();
st.nestedTableName = v.getShortName();
addTable(st);
checkIfTrajectory(st);
iter.remove();
findNestedStructures((Structure) v, st); // look for nested structures
} else if (structAdded && v.isUnlimited()) {
iter.remove();
}
}
if (tableSet.size() > 0) return;
// look at dimensions that lat, lon, time coordinates use
Set<Dimension> dimSet = new HashSet<>(10);
for (CoordinateAxis axis : ds.getCoordinateAxes()) {
if ((axis.getAxisType() == AxisType.Lat) || (axis.getAxisType() == AxisType.Lon)|| (axis.getAxisType() == AxisType.Time))
for (Dimension dim : axis.getDimensions())
dimSet.add(dim);
}
// lat, lon, time all use same dimension - use it
if (dimSet.size() == 1) {
final Dimension obsDim = (Dimension) dimSet.toArray()[0];
TableConfig st = new TableConfig(Table.Type.Structure, obsDim.getShortName());
st.structureType = obsDim.isUnlimited() ? TableConfig.StructureType.Structure : TableConfig.StructureType.PsuedoStructure;
st.structName = obsDim.isUnlimited() ? "record" : obsDim.getShortName();
st.dimName = obsDim.getShortName();
CoordSysEvaluator.findCoords(st, ds, new CoordSysEvaluator.Predicate() {
public boolean match(CoordinateAxis axis) {
return obsDim.equals(axis.getDimension(0));
}
});
CoordinateAxis time = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
if ((time != null) && (time.getRank() == 0)) {
st.addJoin(new JoinArray(time, JoinArray.Type.scalar, 0));
st.time = time.getShortName();
}
addTable( st);
checkIfTrajectory(st);
}
if (tableSet.size() > 0) return;
// try the time dimension
CoordinateAxis time = null;
for (CoordinateAxis axis : ds.getCoordinateAxes()) {
if ((axis.getAxisType() == AxisType.Time) && axis.isCoordinateVariable()) {
time = axis;
break;
}
}
if (time != null) {
Dimension obsDim = time.getDimension(0);
TableConfig st = new TableConfig(Table.Type.Structure, obsDim.getShortName());
st.structureType = TableConfig.StructureType.PsuedoStructure;
st.dimName = obsDim.getShortName();
CoordSysEvaluator.findCoords(st, ds, null);
addTable( st);
}
}
private void checkIfTrajectory(TableConfig st) {
// deal with possible trajectory - only do this if dataset has metadata
FeatureType ft = FeatureDatasetFactoryManager.findFeatureType(ds);
if (ft == FeatureType.TRAJECTORY) {
st.featureType = FeatureType.TRAJECTORY;
TableConfig pc = new TableConfig(Table.Type.Top, "single");
st.parent = pc;
pc.addChild(st);
} else
st.featureType = FeatureType.POINT;
}
private void findNestedStructures(Structure s, TableConfig parent) {
for (Variable v : s.getVariables()) {
if (v instanceof Structure) { // handles Sequences too
TableConfig nestedTable = new TableConfig(Table.Type.NestedStructure, v.getFullName());
nestedTable.structName = v.getFullName();
nestedTable.nestedTableName = v.getShortName();
addTable(nestedTable);
parent.addChild(nestedTable);
// LOOK why not add the join(parent,child) here ?
//nestedTable.join = new TableConfig.JoinConfig(Join.Type.NestedStructure);
//joins.add(nestedTable.join);
findNestedStructures((Structure) v, nestedTable); // look for nested structures
}
}
}
private void makeNestedTables() {
// We search among all the possible Tables in a dataset for joins, and coordinate
// variables. Based on those, we form "interesting" sets and make them into NestedTables.
/* link the tables together with joins
for (TableConfig.JoinConfig join : joins) {
NestedTable.Table parent = join.parent;
NestedTable.Table child = join.child;
if (child.parent != null) throw new IllegalStateException("Multiple parents");
child.parent = parent;
child.join = join;
if (parent.children == null) parent.children = new ArrayList<Join>();
parent.children.add(join);
} */
}
/////////////////////////////////////////////////////
/* track station info
private StationInfo stationInfo = new StationInfo();
private StationInfo getStationInfo() {
return stationInfo;
}
public class StationInfo {
public String stationId, stationDesc, stationNpts;
public int nstations;
public String latName, lonName, elevName;
} */
////////////////////////////////////////////////////////////////////////////////////////////////
/* public void showCoordSys(java.util.Formatter sf) {
sf.format("%nCoordinate Systems%n");
for (CoordinateSystem cs : ds.getCoordinateSystems()) {
sf.format(" %s%n", cs);
}
}
public void showCoordAxes(java.util.Formatter sf) {
sf.format("%nAxes%n");
for (CoordinateAxis axis : ds.getCoordinateAxes()) {
sf.format(" %s %s%n", axis.getAxisType(), axis.getNameAndDimensions());
}
} */
/* public void showTables(java.util.Formatter sf) {
sf.format("%nTables%n");
for (NestedTable.Table t : tableSet)
sf.format(" %s%n", t);
sf.format("%nJoins%n");
for (Join j : joins)
sf.format(" %s%n", j);
} */
public void showNestedTables(java.util.Formatter sf) {
for (NestedTable nt : leaves) {
nt.show(sf);
}
}
public String getImplementationName() {
return (tc != null) ? tc.getClass().getSimpleName() : "defaultAnalyser";
}
public void getDetailInfo(java.util.Formatter sf) {
sf.format("-----------------------------------------------------%nTableAnalyzer on Dataset %s%n", ds.getLocation());
sf.format(" TableAnalyser = %s%n", getName());
showNestedTables(sf);
String errlogS = errlog.toString();
if (errlogS.length() > 0)
sf.format("%n Errlog=%n%s",errlogS);
String userAdviceS = userAdvice.toString();
if (userAdviceS.length() > 0)
sf.format("%n userAdvice=%n%s%n",userAdviceS);
try {
writeConfigXML(sf);
} catch (IOException e) {
e.printStackTrace();
}
}
private void writeConfigXML(java.util.Formatter sf) throws IOException {
if (configResult != null) {
PointConfigXML tcx = new PointConfigXML();
tcx.writeConfigXML(configResult, getName(), sf);
return;
}
XMLOutputter fmt = new XMLOutputter( Format.getPrettyFormat());
sf.format("%s", fmt.outputString ( makeDocument()));
}
/** Create an XML document from this info
* @return netcdfDatasetInfo XML document
*/
private Document makeDocument() {
Element rootElem = new Element("featureDataset");
Document doc = new Document(rootElem);
rootElem.setAttribute("location", ds.getLocation());
rootElem.addContent( new Element("analyser").setAttribute("class", getName()));
if (ft != null)
rootElem.setAttribute("featureType", ft.toString());
for (NestedTable nt : leaves) {
writeTable( rootElem, nt.getLeaf());
}
return doc;
}
private Element writeTable( Element parent, Table table) {
if (table.parent != null) {
parent = writeTable( parent, table.parent);
}
Element tableElem = new Element("table");
parent.addContent( tableElem);
if (table.getName() != null)
tableElem.setAttribute("name", table.getName());
if (table.getFeatureType() != null)
tableElem.setAttribute("featureType", table.getFeatureType().toString());
tableElem.setAttribute("class", table.getClass().toString());
addCoordinates(tableElem, table);
for (String colName : table.cols.keySet()) {
if (!table.nondataVars.contains(colName))
tableElem.addContent( new Element("variable").addContent(colName));
}
if (table.extraJoins != null) {
for (Join j : table.extraJoins) {
if (j instanceof JoinArray)
tableElem.addContent( writeJoinArray( (JoinArray)j));
else if (j instanceof JoinMuiltdimStructure)
tableElem.addContent( writeJoinMuiltdimStructure( (JoinMuiltdimStructure) j));
else if (j instanceof JoinParentIndex)
tableElem.addContent( writeJoinParentIndex( (JoinParentIndex) j));
}
}
return tableElem;
}
private void addCoordinates( Element tableElem, Table table) {
addCoord(tableElem, table.lat, "lat");
addCoord(tableElem, table.lon, "lon");
addCoord(tableElem, table.elev, "elev");
addCoord(tableElem, table.time, "time");
addCoord(tableElem, table.timeNominal, "timeNominal");
addCoord(tableElem, table.stnId, "stnId");
addCoord(tableElem, table.stnDesc, "stnDesc");
addCoord(tableElem, table.stnNpts, "stnNpts");
addCoord(tableElem, table.stnWmoId, "stnWmoId");
addCoord(tableElem, table.stnAlt, "stnAlt");
addCoord(tableElem, table.limit, "limit");
}
private void addCoord(Element tableElem, String name, String kind) {
if (name != null) {
Element elem = new Element("coordinate").setAttribute("kind", kind);
elem.addContent(name);
tableElem.addContent(elem);
}
}
private Element writeJoinArray(JoinArray join) {
Element joinElem = new Element("join");
joinElem.setAttribute("class", join.getClass().toString());
if (join.type != null)
joinElem.setAttribute("type", join.type.toString());
if (join.v != null)
joinElem.addContent( new Element("variable").setAttribute("name", join.v.getFullName()));
joinElem.addContent( new Element("param").setAttribute("value", Integer.toString(join.param)));
return joinElem;
}
private Element writeJoinMuiltdimStructure(JoinMuiltdimStructure join) {
Element joinElem = new Element("join");
joinElem.setAttribute("class", join.getClass().toString());
if (join.parentStructure != null)
joinElem.addContent( new Element("parentStructure").setAttribute("name", join.parentStructure.getFullName()));
joinElem.addContent( new Element("dimLength").setAttribute("value", Integer.toString(join.dimLength)));
return joinElem;
}
private Element writeJoinParentIndex(JoinParentIndex join) {
Element joinElem = new Element("join");
joinElem.setAttribute("class", join.getClass().toString());
if (join.parentStructure != null)
joinElem.addContent( new Element("parentStructure").setAttribute("name", join.parentStructure.getFullName()));
if (join.parentIndex != null)
joinElem.addContent( new Element("parentIndex").setAttribute("name", join.parentIndex));
return joinElem;
}
////////////////////////////////////////////////////////////////////////////////
static void doit(String filename) throws IOException {
System.out.println(filename);
NetcdfDataset ncd = ucar.nc2.dataset.NetcdfDataset.openDataset(filename);
TableAnalyzer csa = TableAnalyzer.factory(null, null, ncd);
csa.getDetailInfo(new Formatter(System.out));
System.out.println("%n-----------------");
}
static public void main(String args[]) throws IOException {
/* doit("C:/data/dt2/station/Surface_METAR_20080205_0000.nc");
doit("C:/data/bufr/edition3/idd/profiler/PROFILER_3.bufr");
doit("C:/data/bufr/edition3/idd/profiler/PROFILER_2.bufr");
doit("C:/data/profile/PROFILER_wind_01hr_20080410_2300.nc"); */
//doit("C:/data/test/20070301.nc");
//doit("C:/data/dt2/profile/PROFILER_3.bufr");
//doit("C:/data/dt2/station/ndbc.nc");
//doit("C:/data/dt2/station/madis2.sao");
// doit("C:/data/metars/Surface_METAR_20070326_0000.nc"); // ok
//doit("C:/data/dt2/station/Sean_multidim_20070301.nc"); // ok
//doit("Q:/cdmUnitTest/formats/gempak/surface/20090521_sao.gem");
doit("D:/datasets/metars/Surface_METAR_20070513_0000.nc");
//doit("C:/data/profile/PROFILER_wind_01hr_20080410_2300.nc");
//doit("C:/data/cadis/tempting");
}
}