ucar.nc2.dt.fmrc.FmrcDefinition Maven / Gradle / Ivy
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/*
* Copyright 1998-2009 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
* and understandings on the user. The user is granted the right, without
* any fee or cost, to use, copy, modify, alter, enhance and distribute
* this software, and any derivative works thereof, and its supporting
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* and/or Unidata, however, may not be used in any advertising or publicity
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package ucar.nc2.dt.fmrc;
import org.jdom.output.XMLOutputter;
import org.jdom.output.Format;
import org.jdom.Document;
import org.jdom.Element;
import org.jdom.JDOMException;
import org.jdom.input.SAXBuilder;
import java.io.*;
import java.util.*;
import ucar.nc2.dataset.CoordinateAxis1D;
import ucar.unidata.util.StringUtil;
/**
* Defines the expected inventory of a Forecast Model Run Collection.
*
*
* Data Structures
*
* List VertTimeCoord
* double[] values
*
* List TimeCoord
* double[] offsetHour
*
* List RunSeq
* List Run - runHour dependent TimeCoord
* double hour
* TimeCoord
*
* List Grid
* String name
* VertTimeCoord - time dependent vertical coordinate
* VertCoord
* TimeCoord (optional)
*
*
* Abstractly, the data is a table:
* Run Grid TimeCoord VertCoord
* Run Grid TimeCoord VertCoord
* Run Grid TimeCoord VertCoord
* ...
*
* We will use the notation ({} means list)
* {Run, Grid, TimeCoord, VertCoord}
*
* The simplest case would be if all runs have the same grids, which all use the same time coord, and each grid always
* uses the same vert coord :
* (1) {runTime} X {Grid, VertCoord} X TimeCoord (X means product)
*
* The usual case is that there are multiple TimeCoords, but a grid always uses the same one:
* (2) {runTime} X {Grid, VertCoord, TimeCoord}
*
* Since all runTimes are the same, the definition only need be:
* (2d) {Grid, VertCoord, TimeCoord}
*
* Another case is that different run hours use different TimeCoords. We will call this a RunSeq, and we associate with each
* RunSeq the list of grids that use it:
* Run = runHour, TimeCoord
* RunSeq = {runHour, TimeCoord} X {Grid, VertCoord}
*
* Different grids use different RunSeqs, so we have a list of RunSeq:
* (3d) {{runHour, TimeCoord} X {Grid, VertCoord}}
*
* We can recast (2d), when all runHours are the same, as:
* (2d') {TimeCoord X {Grid, VertCoord}}
* which means that we are grouping grids by unique TimeCoord. (1d) would be the case where there is only one in the list.
*
* Another case is when the VertCoord depends on the TimeCoord, but all run hours are the same:
* (4d) {TimeCoord X {Grid, VertCoord(TimeCoord)}}
*
* Which lead us to generalize a VertCoord to a time-dependent one, called VertTimeCoord.
*
* The most general case is then
* {{runHour, TimeCoord} X {Grid, VertTimeCoord}}
*
*
*
* @author caron
*/
public class FmrcDefinition implements ucar.nc2.dt.fmr.FmrcCoordSys {
static private org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(FmrcDefinition.class);
///////////////////////////////////////////////////////////////////
private List vertTimeCoords;
private List timeCoords;
private List ensCoords;
private List runSequences;
private String name;
private String suffixFilter;
public FmrcDefinition() {
cal.setTimeZone(TimeZone.getTimeZone("UTC"));
}
public String getSuffixFilter() {
return suffixFilter;
}
public List getRunSequences() {
return runSequences;
}
public boolean hasVariable(String searchName) {
return findGridByName(searchName) != null;
}
public ucar.nc2.dt.fmr.FmrcCoordSys.VertCoord findVertCoordForVariable(String searchName) {
Grid grid = findGridByName(searchName);
return (grid.vtc == null) ? null : grid.vtc.vc;
}
public ucar.nc2.dt.fmr.FmrcCoordSys.TimeCoord findTimeCoordForVariable(String searchName, java.util.Date runTime) {
for (RunSeq runSeq : runSequences) {
Grid grid = runSeq.findGrid(searchName);
if (null != grid) {
ForecastModelRunInventory.TimeCoord from = runSeq.findTimeCoordByRuntime(runTime);
// we need to wrap it, giving it the name of the RunSeq
return new ForecastModelRunInventory.TimeCoord(runSeq.num, from);
}
}
return null;
}
private ForecastModelRunInventory.TimeCoord findTimeCoord(String id) {
for (ForecastModelRunInventory.TimeCoord tc : timeCoords) {
if (tc.getId().equals(id))
return tc;
}
return null;
}
///////////////////////////////////////////////////////////////////////////////////////////////
// encapsolates a Grid and its vertical coordinate, which may be time-dependent
public static class Grid implements Comparable {
private String name; // , searchName;
private VertTimeCoord vtc = null;
private ForecastModelRunInventory.EnsCoord ec = null;
Grid(String name) {
this.name = name;
}
public EnsCoord getEnsTimeCoord() {
return ec;
}
//public String getName() { return name; }
//public void setName(String name) { this.name = name; }
public VertTimeCoord getVertTimeCoord() {
return vtc;
}
public int countVertCoords(double offsetHour) {
return (vtc == null) ? 1 : vtc.countVertCoords(offsetHour);
}
/**
* Get inventory as an array of vert coords, at a particular time coord = hourOffset
*
* @param hourOffset : may or may not be in the list of time coords
* @return array of vert coords. NaN = missing; -0.0 = surface.
*/
public double[] getVertCoords(double hourOffset) {
if (vtc == null) {
double[] result = new double[1]; // if 2D return -0.0
result[0] = -0.0;
return result;
}
return vtc.getVertCoords(hourOffset);
}
public int compareTo(Object o) {
Grid other = (Grid) o;
return name.compareTo(other.name);
}
}
class Run {
double runHour; // hour since 00:00
ForecastModelRunInventory.TimeCoord tc;
Run(ForecastModelRunInventory.TimeCoord tc, double runHour) {
this.tc = tc;
this.runHour = runHour;
}
}
// A sequence of Runs.
// each RunSeq is a unique time coordinate
private int runseq_num = 0;
public class RunSeq {
private boolean isAll = false; // true if they all use the same OffsetHours
private ForecastModelRunInventory.TimeCoord allUseOffset; // they all use this one
private List runs = new ArrayList(); // list of Run
private List vars = new ArrayList(); // list of Grid
private int num = 0;
RunSeq(String id) {
this.isAll = true;
this.allUseOffset = findTimeCoord(id);
num = runseq_num++;
}
RunSeq(List runs) {
this.runs = runs;
num = runseq_num++;
// complete a 24 hour cycle
int matchIndex = 0;
Run last = runs.get(runs.size() - 1);
double runHour = last.runHour;
while (runHour < 24.0) {
Run match = runs.get(matchIndex);
Run next = runs.get(matchIndex + 1);
double incr = next.runHour - match.runHour;
if (incr <= 0)
break;
runHour += incr;
runs.add(new Run(next.tc, runHour));
matchIndex++;
}
}
public String getName() {
return (num == 0) ? "time" : "time" + num;
}
/**
* Find the TimeCoord the should be used for this runTime
*
* @param runTime run date
* @return TimeCoord, or null if no match.
*/
public ForecastModelRunInventory.TimeCoord findTimeCoordByRuntime(Date runTime) {
if (isAll)
return allUseOffset;
double hour = getHour(runTime);
Run run = findRun(hour);
if (run == null) return null;
return run.tc;
}
/**
* @param hour run hour
* @return the Run that matches the run hour
*/
Run findRun(double hour) {
for (Run run : runs) {
if (run.runHour == hour) return run;
}
return null;
}
public Grid findGrid(String name) {
if (name == null) return null;
for (Grid grid : vars) {
if (name.equals(grid.name))
return grid;
}
return null;
}
} // RunSeq
public RunSeq findSeqForVariable(String name) {
for (RunSeq runSeq : runSequences) {
if (runSeq.findGrid(name) != null)
return runSeq;
}
return null;
}
Grid findGridByName(String name) {
for (RunSeq runSeq : runSequences) {
Grid grid = runSeq.findGrid(name);
if (null != grid)
return grid;
}
return null;
}
VertTimeCoord findVertCoord(String id) {
if (id == null)
return null;
for (VertTimeCoord vc : vertTimeCoords) {
if (vc.getId().equals(id))
return vc;
}
return null;
}
VertTimeCoord findVertCoordByName(String name) {
for (VertTimeCoord vc : vertTimeCoords) {
if (vc.getName().equals(name))
return vc;
}
return null;
}
boolean replaceVertCoord(ForecastModelRunInventory.VertCoord vc) {
for (VertTimeCoord vtc : vertTimeCoords) {
if (vtc.getName().equals(vc.getName())) {
vtc.vc.values1 = vc.values1;
vtc.vc.values2 = vc.values2;
vtc.vc.setId(vc.getId());
vtc.vc.setUnits(vc.getUnits());
return true;
}
}
// make a new one
vertTimeCoords.add(new VertTimeCoord(vc));
return false;
}
///////////////////////////////////////////////////////////////////////////////////////////////
/* vertical coordinates that depend on the offset hour */
class VertTimeCoord implements Comparable {
ForecastModelRunInventory.VertCoord vc;
ForecastModelRunInventory.TimeCoord tc; // optional
int ntimes, nverts;
double[][] vcForTimeIndex; // vcForTimeIndex[ntimes]
List restrictList;
VertTimeCoord(ForecastModelRunInventory.VertCoord vc) {
this.vc = vc;
ntimes = (tc == null) ? 1 : tc.getOffsetHours().length;
nverts = vc.getValues1().length;
}
VertTimeCoord(ForecastModelRunInventory.VertCoord vc, RunSeq runSeq) {
if (runSeq.isAll) {
this.tc = runSeq.allUseOffset;
} else {
// make union timeCoord
Set valueSet = new HashSet();
for (Run run : runSeq.runs) {
addValues(valueSet, run.tc.getOffsetHours());
}
List valueList = Arrays.asList((Double[]) valueSet.toArray(new Double[valueSet.size()]));
Collections.sort(valueList);
double[] values = new double[valueList.size()];
for (int i = 0; i < valueList.size(); i++) {
values[i] = valueList.get(i);
}
this.tc = new ForecastModelRunInventory.TimeCoord();
this.tc.setOffsetHours(values);
this.tc.setId("union");
}
this.vc = vc;
ntimes = (tc == null) ? 1 : tc.getOffsetHours().length;
nverts = vc.getValues1().length;
}
private void addValues(Set valueSet, double[] values) {
for (double value : values) valueSet.add(value);
}
String getId() {
return vc.getId();
}
String getName() {
return vc.getName();
}
//double[] getValues() { return vc.getValues(); }
void addRestriction(String vertCoordsString, String timeCoords) {
StringTokenizer stoker = new StringTokenizer(vertCoordsString, " ,");
int n = stoker.countTokens();
double[] vertCoords = new double[n];
int count = 0;
while (stoker.hasMoreTokens()) {
vertCoords[count++] = Double.parseDouble(stoker.nextToken());
}
if (vcForTimeIndex == null) {
restrictList = new ArrayList();
vcForTimeIndex = new double[ntimes][];
for (int i = 0; i < vcForTimeIndex.length; i++) {
vcForTimeIndex[i] = vc.getValues1(); // LOOK WRONG
}
}
// save these in case we have to write them back out
restrictList.add(vertCoordsString);
restrictList.add(timeCoords);
stoker = new StringTokenizer(timeCoords, " ,");
while (stoker.hasMoreTokens()) {
double hour = Double.parseDouble(stoker.nextToken());
int index = tc.findIndex(hour);
if (index < 0)
log.error("hour Offset" + hour + " not found in TimeCoord " + tc.getId());
vcForTimeIndex[index] = vertCoords;
}
}
double[] getVertCoords(double offsetHour) {
if ((tc == null) || (null == vcForTimeIndex))
return vc.getValues1(); // LOOK WRONG
int index = tc.findIndex(offsetHour);
if (index < 0)
return new double[0];
return vcForTimeIndex[index];
}
int countVertCoords(double offsetHour) {
if ((tc == null) || (null == vcForTimeIndex))
return vc.getValues1().length;
int index = tc.findIndex(offsetHour);
if (index < 0)
return 0;
return vcForTimeIndex[index].length;
}
public int compareTo(Object o) {
VertTimeCoord other = (VertTimeCoord) o;
return getName().compareTo(other.getName());
}
}
private ForecastModelRunInventory.EnsCoord findEnsCoord(String id) {
if (id == null)
return null;
for (ForecastModelRunInventory.EnsCoord ec : ensCoords) {
if (ec.getId().equals(id))
return ec;
}
return null;
}
//////////////////////////////////////////////////////////////////////////////////
public String writeDefinitionXML() {
XMLOutputter fmt = new XMLOutputter(Format.getPrettyFormat());
return fmt.outputString(makeDefinitionXML());
}
public void writeDefinitionXML(OutputStream os) throws IOException {
XMLOutputter fmt = new XMLOutputter(Format.getPrettyFormat());
fmt.output(makeDefinitionXML(), os);
}
/**
* Create an XML document for the entire collection
*
* @return an XML document for the entire collection
*/
public Document makeDefinitionXML() {
Element rootElem = new Element("fmrcDefinition");
Document doc = new Document(rootElem);
if (name != null)
rootElem.setAttribute("dataset", name);
if (null != suffixFilter)
rootElem.setAttribute("suffixFilter", suffixFilter);
// list all the ensemble coordinaates
Collections.sort(ensCoords);
for (ForecastModelRunInventory.EnsCoord ec : ensCoords) {
Element ecElem = new Element("ensCoord");
rootElem.addContent(ecElem);
ecElem.setAttribute("id", ec.getId());
ecElem.setAttribute("name", ec.getName());
ecElem.setAttribute("product_definition", Integer.toString(ec.getPDN()));
StringBuilder sbuff = new StringBuilder();
int[] ensTypes = ec.getEnsTypes(); //new int[ ec.getNEnsembles() ];
for (int j = 0; j < ensTypes.length; j++) {
if (j > 0) sbuff.append(" ");
sbuff.append(Integer.toString(ensTypes[j]));
}
ecElem.addContent(sbuff.toString());
}
// list all the vertical coordinaates
Collections.sort(vertTimeCoords);
for (VertTimeCoord vtc : vertTimeCoords) {
ForecastModelRunInventory.VertCoord vc = vtc.vc;
Element vcElem = new Element("vertCoord");
rootElem.addContent(vcElem);
vcElem.setAttribute("id", vc.getId());
vcElem.setAttribute("name", vc.getName());
if (null != vc.getUnits())
vcElem.setAttribute("units", vc.getUnits());
StringBuilder sbuff = new StringBuilder();
double[] values1 = vc.getValues1();
double[] values2 = vc.getValues2();
for (int j = 0; j < values1.length; j++) {
if (j > 0) sbuff.append(" ");
sbuff.append(Double.toString(values1[j]));
if (values2 != null) {
sbuff.append(",");
sbuff.append(Double.toString(values2[j]));
}
}
vcElem.addContent(sbuff.toString());
}
// list all the offset hours
Collections.sort(timeCoords);
for (ForecastModelRunInventory.TimeCoord tc : timeCoords) {
Element offsetElem = new Element("offsetHours");
rootElem.addContent(offsetElem);
offsetElem.setAttribute("id", tc.getId());
StringBuilder sbuff = new StringBuilder();
double[] offset = tc.getOffsetHours();
for (int j = 0; j < offset.length; j++) {
if (j > 0) sbuff.append(" ");
sbuff.append(Double.toString(offset[j]));
}
offsetElem.addContent(sbuff.toString());
}
// list all the time sequences, containing variables
for (RunSeq runSeq : runSequences) {
Element seqElem = new Element("runSequence");
rootElem.addContent(seqElem);
if (runSeq.isAll) {
seqElem.setAttribute("allUseSeq", runSeq.allUseOffset.getId());
} else { // otherwise show each run
for (Run run : runSeq.runs) {
Element runElem = new Element("run");
seqElem.addContent(runElem);
runElem.setAttribute("runHour", Double.toString(run.runHour));
runElem.setAttribute("offsetHourSeq", run.tc.getId());
}
}
for (Grid grid : runSeq.vars) {
Element varElem = new Element("variable");
seqElem.addContent(varElem);
varElem.setAttribute("name", grid.name);
if (grid.ec != null)
varElem.setAttribute("ensCoord", grid.ec.getId());
if (grid.vtc != null) {
varElem.setAttribute("vertCoord", grid.vtc.getId());
// look for time-dependent vert coordinates - always specific to one variable
if (grid.vtc.restrictList != null) {
Iterator iter = grid.vtc.restrictList.iterator();
while (iter.hasNext()) {
Element vtElem = new Element("vertCoord");
varElem.addContent(vtElem);
vtElem.setAttribute("restrict", (String) iter.next());
vtElem.setText((String) iter.next());
}
}
}
}
}
return doc;
}
public boolean readDefinitionXML(String xmlLocation) throws IOException {
File xml = new File(xmlLocation);
if (!xml.exists()) return false;
InputStream is = new BufferedInputStream(new FileInputStream(xmlLocation));
org.jdom.Document doc;
try {
SAXBuilder builder = new SAXBuilder();
doc = builder.build(is);
} catch (JDOMException e) {
throw new IOException(e.getMessage());
}
Element rootElem = doc.getRootElement();
name = rootElem.getAttributeValue("name");
suffixFilter = rootElem.getAttributeValue("suffixFilter");
ensCoords = new ArrayList();
java.util.List eList = rootElem.getChildren("ensCoord");
for (Element ecElem : eList) {
ForecastModelRunInventory.EnsCoord ec = new ForecastModelRunInventory.EnsCoord();
ec.setId(ecElem.getAttributeValue("id"));
ec.setName(ecElem.getAttributeValue("name"));
ec.setPDN(Integer.parseInt(ecElem.getAttributeValue("product_definition")));
// parse the values
String values = ecElem.getText();
StringTokenizer stoke = new StringTokenizer(values);
int n = stoke.countTokens();
ec.setNEnsembles(n);
int[] ensType = new int[n];
int count = 0;
while (stoke.hasMoreTokens()) {
String toke = stoke.nextToken();
int pos = toke.indexOf(',');
if (pos < 0)
ensType[count] = Integer.parseInt(toke);
count++;
}
ec.setEnsTypes(ensType);
ensCoords.add(ec);
}
vertTimeCoords = new ArrayList();
java.util.List vList = rootElem.getChildren("vertCoord");
for (Element vcElem : vList) {
ForecastModelRunInventory.VertCoord vc = new ForecastModelRunInventory.VertCoord();
vc.setId(vcElem.getAttributeValue("id"));
vc.setName(vcElem.getAttributeValue("name"));
vc.setUnits(vcElem.getAttributeValue("units"));
/* parse the values
String values = vcElem.getText();
StringTokenizer stoke = new StringTokenizer(values);
int n = stoke.countTokens();
double[] vals = new double[n];
int count = 0;
while (stoke.hasMoreTokens()) {
vals[count++] = Double.parseDouble( stoke.nextToken());
}
vc.setValues( vals); */
// parse the values
String values = vcElem.getText();
StringTokenizer stoke = new StringTokenizer(values);
int n = stoke.countTokens();
double[] values1 = new double[n];
double[] values2 = null;
int count = 0;
while (stoke.hasMoreTokens()) {
String toke = stoke.nextToken();
int pos = toke.indexOf(',');
if (pos < 0)
values1[count] = Double.parseDouble(toke);
else {
if (values2 == null)
values2 = new double[n];
String val1 = toke.substring(0, pos);
String val2 = toke.substring(pos + 1);
values1[count] = Double.parseDouble(val1);
values2[count] = Double.parseDouble(val2);
}
count++;
}
vc.setValues1(values1);
if (values2 != null)
vc.setValues2(values2);
// wrap it as a VertTimeCoord
VertTimeCoord vtc = new VertTimeCoord(vc);
vertTimeCoords.add(vtc);
}
timeCoords = new ArrayList();
java.util.List tList = rootElem.getChildren("offsetHours");
for (Element timeElem : tList) {
ForecastModelRunInventory.TimeCoord tc = new ForecastModelRunInventory.TimeCoord();
timeCoords.add(tc);
tc.setId(timeElem.getAttributeValue("id"));
// parse the values
String values = timeElem.getText();
StringTokenizer stoke = new StringTokenizer(values);
int n = stoke.countTokens();
double[] offset = new double[n];
int count = 0;
while (stoke.hasMoreTokens()) {
offset[count++] = Double.parseDouble(stoke.nextToken());
}
tc.setOffsetHours(offset);
}
runSequences = new ArrayList();
java.util.List runseqList = rootElem.getChildren("runSequence");
for (Element runseqElem : runseqList) {
RunSeq rseq;
String allUseId = runseqElem.getAttributeValue("allUseSeq");
if (allUseId != null) {
rseq = new RunSeq(allUseId);
} else {
List runs = new ArrayList();
List runList = runseqElem.getChildren("run");
for (Element runElem : runList) {
String id = runElem.getAttributeValue("offsetHourSeq");
ForecastModelRunInventory.TimeCoord tc = findTimeCoord(id);
String hour = runElem.getAttributeValue("runHour");
Run run = new Run(tc, Double.parseDouble(hour));
runs.add(run);
}
rseq = new RunSeq(runs);
}
runSequences.add(rseq);
List varList = runseqElem.getChildren("variable");
for (Element varElem : varList) {
String name = varElem.getAttributeValue("name");
Grid grid = new Grid(name);
rseq.vars.add(grid);
grid.ec = findEnsCoord(varElem.getAttributeValue("ensCoord"));
//grid.ec = ForecastModelRunInventory.findEnsCoord(ensCoords, varElem.getAttributeValue("ensCoord"));
grid.vtc = findVertCoord(varElem.getAttributeValue("vertCoord"));
// look for time dependent vert coordinates - always specific to one variable
List rList = varElem.getChildren("vertTimeCoord");
// gotta be inside a useAllSeq runSeq
if (rList.size() > 0) {
grid.vtc = new VertTimeCoord(grid.vtc.vc, rseq);
for (Element vtElem : rList) {
String vertCoords = vtElem.getAttributeValue("restrict");
String timeCoords = vtElem.getText();
grid.vtc.addRestriction(vertCoords, timeCoords);
}
}
}
Collections.sort(rseq.vars);
}
return true;
}
//////////////////////////////////////////////////////////////////////
public void makeFromCollectionInventory(FmrcInventory fmrc) {
this.name = fmrc.getName();
this.timeCoords = fmrc.getTimeCoords();
this.ensCoords = fmrc.getEnsCoords();
this.vertTimeCoords = new ArrayList();
for (int i = 0; i < fmrc.getVertCoords().size(); i++) {
ForecastModelRunInventory.VertCoord vc = fmrc.getVertCoords().get(i);
vertTimeCoords.add(new VertTimeCoord(vc));
}
this.runSequences = new ArrayList();
// Convert the run sequences, containing variables
List seqs = fmrc.getRunSequences();
for (FmrcInventory.RunSeq invSeq : seqs) {
// check to see if all runs use the same tc
boolean isAll = true;
ForecastModelRunInventory.TimeCoord oneTc = null;
for (int j = 0; j < invSeq.runs.size(); j++) {
FmrcInventory.Run run = invSeq.runs.get(j);
if (j == 0)
oneTc = run.tc;
else {
if (oneTc != run.tc)
isAll = false;
}
}
RunSeq runSeq;
if (isAll) {
runSeq = new RunSeq(oneTc.getId());
} else {
List runs = new ArrayList();
for (FmrcInventory.Run invRun : invSeq.runs) {
Run run = new Run(invRun.tc, getHour(invRun.runTime));
runs.add(run);
}
runSeq = new RunSeq(runs);
}
runSequences.add(runSeq);
// convert UberGrids to Grid
List vars = invSeq.getVariables();
for (FmrcInventory.UberGrid uv : vars) {
Grid grid = new Grid(uv.getName());
runSeq.vars.add(grid);
if (uv.vertCoordUnion != null)
grid.vtc = new VertTimeCoord(uv.vertCoordUnion);
if (uv.ensCoordUnion != null)
grid.ec = uv.ensCoordUnion;
}
}
// sort vert coords
Collections.sort(this.vertTimeCoords);
}
/**
* Add just the vertical coord info to the definition
*
* @param fmrc the collection inventory
*/
public void addVertCoordsFromCollectionInventory(FmrcInventory fmrc) {
this.vertTimeCoords = new ArrayList();
for (int i = 0; i < fmrc.getVertCoords().size(); i++) {
ForecastModelRunInventory.VertCoord vc = fmrc.getVertCoords().get(i);
vertTimeCoords.add(new VertTimeCoord(vc));
}
// Convert the run sequences, containing variables
List seqs = fmrc.getRunSequences();
for (FmrcInventory.RunSeq invSeq : seqs) {
// convert UberGrids to Grid
List vars = invSeq.getVariables();
for (FmrcInventory.UberGrid uv : vars) {
if (uv.vertCoordUnion != null) {
String sname = uv.getName();
Grid grid = findGridByName(sname);
grid.vtc = new VertTimeCoord(uv.vertCoordUnion);
}
}
}
}
// utilities - move to fmrc ?
private Calendar cal = new GregorianCalendar(); // for date computations
private double getHour(Date d) {
cal.setTime(d);
int hour = cal.get(Calendar.HOUR_OF_DAY);
double min = (double) cal.get(Calendar.MINUTE);
return hour + min / 60;
}
////////////////////////////////////////////////////////////////////////////////////////////////////
// ad-hoc manipulations of the definitions
// replace ids
static void convertIds(String datasetName, String defName) throws IOException {
System.out.println(datasetName);
ForecastModelRunInventory fmrInv = ForecastModelRunInventory.open(null, datasetName, ForecastModelRunInventory.OPEN_FORCE_NEW, true);
FmrcDefinition fmrDef = new FmrcDefinition();
fmrDef.readDefinitionXML(defName);
boolean changed = false;
// make hashmap
Map hash = new HashMap();
for (RunSeq runSeq : fmrDef.runSequences) {
for (Grid gridDef : runSeq.vars) {
String munged = StringUtil.replace(gridDef.name, '_', "");
hash.put(munged, gridDef);
}
}
// make sure each grid in fmrInv is also in fmrDef
List fmrInvTimeCoords = fmrInv.getTimeCoords();
for (ForecastModelRunInventory.TimeCoord tc : fmrInvTimeCoords) {
List fmrInvGrids = tc.getGrids();
for (ForecastModelRunInventory.Grid invGrid : fmrInvGrids) {
Grid defGrid = fmrDef.findGridByName(invGrid.name);
if (null == defGrid) {
String munged = StringUtil.replace(invGrid.name, "-", "");
munged = StringUtil.replace(munged, "_", "");
Grid gridDefnew = hash.get(munged);
if (gridDefnew != null) {
System.out.println(" replace " + gridDefnew.name + " with " + invGrid.name);
gridDefnew.name = invGrid.name;
changed = false; // true;
} else {
System.out.println("*** cant find replacement for grid= " + invGrid.name + " in the definition");
}
}
}
}
if (changed) {
int pos = defName.lastIndexOf("/");
String newDef = defName.substring(0, pos) + "/new/" + defName.substring(pos);
FileOutputStream fout = new FileOutputStream(newDef);
fmrDef.writeDefinitionXML(fout);
}
}
static boolean showState = false;
static void convert(String datasetName, String defName) throws IOException {
System.out.println(datasetName);
ForecastModelRunInventory fmrInv = ForecastModelRunInventory.open(null, datasetName, ForecastModelRunInventory.OPEN_FORCE_NEW, true);
FmrcDefinition fmrDef = new FmrcDefinition();
fmrDef.readDefinitionXML(defName);
// replace vert coords
List vcList = fmrInv.getVertCoords();
for (ForecastModelRunInventory.VertCoord vc : vcList) {
CoordinateAxis1D axis = vc.axis;
if (axis == null)
System.out.println("*** No Axis " + vc.getName());
else {
// boolean isLayer = null != axis.findAttribute(_Coordinate.ZisLayer);
//if (isLayer) {
if (showState) System.out.print(" " + vc.getName() + " contig= " + axis.isContiguous());
// see if theres any TimeCoord that use this
//findGridsForVertCoord( fmrDef, vc);
boolean ok = fmrDef.replaceVertCoord(vc);
if (showState) System.out.println(" = " + ok);
//}
}
}
Collections.sort(fmrDef.vertTimeCoords);
// reset vert id on grids
for (RunSeq runSeq : fmrDef.runSequences) {
for (Grid gridDef : runSeq.vars) {
ForecastModelRunInventory.Grid gridInv = fmrInv.findGrid(gridDef.name);
if (gridInv == null) {
System.out.println("*** cant find def grid= " + gridDef.name + " in the inventory ");
continue;
}
if (gridInv.vc != null) {
VertTimeCoord new_vtc = fmrDef.findVertCoordByName(gridInv.vc.getName());
if (new_vtc == null) {
System.out.println("*** cant find VertCoord= " + gridInv.vc.getName());
continue;
}
gridDef.vtc = new_vtc;
if (showState) System.out.println(" ok= " + gridDef.name);
}
}
}
int pos = defName.lastIndexOf("/");
String newDef = defName.substring(0, pos) + "/new/" + defName.substring(pos);
FileOutputStream fout = new FileOutputStream(newDef);
fmrDef.writeDefinitionXML(fout);
// make sure each grid in fmrInv is also in fmrDef
List fmrInvTimeCoords = fmrInv.getTimeCoords();
for (ForecastModelRunInventory.TimeCoord tc : fmrInvTimeCoords) {
List fmrInvGrids = tc.getGrids();
for (ForecastModelRunInventory.Grid invGrid : fmrInvGrids) {
Grid defGrid = fmrDef.findGridByName(invGrid.name);
if (null == defGrid)
System.out.println("*** cant find inv grid= " + invGrid.name + " in the definition");
else {
ForecastModelRunInventory.VertCoord inv_vc = invGrid.vc;
if ((inv_vc == null) && (defGrid.vtc == null)) continue; // ok
if ((inv_vc != null) && (defGrid.vtc == null)) {
System.out.println("*** mismatch " + invGrid.name + " VertCoord: inv= " + inv_vc.getSize() + ", no def ");
continue;
}
if ((inv_vc == null) && (defGrid.vtc != null)) {
ForecastModelRunInventory.VertCoord def_vc = defGrid.vtc.vc;
System.out.println("*** mismatch " + invGrid.name + " VertCoord: def= " + def_vc.getSize() + ", no inv ");
continue;
}
ForecastModelRunInventory.VertCoord def_vc = defGrid.vtc.vc;
if (inv_vc.getSize() != def_vc.getSize()) {
System.out.println("*** mismatch " + invGrid.name + " VertCoord size: inv= " + inv_vc.getSize() + ", def = " + def_vc.getSize());
}
}
}
}
}
static void showVertCoords(String datasetName, String defName) throws IOException {
System.out.println("--------------------------------------");
System.out.println(defName);
FmrcDefinition fmrDef = new FmrcDefinition();
fmrDef.readDefinitionXML(defName);
/* List vtList = fmrDef.vertTimeCoords;
for (int i = 0; i < vtList.size(); i++) {
VertTimeCoord vtc = (VertTimeCoord) vtList.get(i);
System.out.println(" "+vtc.getName());
} */
System.out.println(datasetName);
ForecastModelRunInventory fmrInv = ForecastModelRunInventory.open(null, datasetName, ForecastModelRunInventory.OPEN_FORCE_NEW, true);
List vcList = fmrInv.getVertCoords();
for (ForecastModelRunInventory.VertCoord vc : vcList) {
CoordinateAxis1D axis = vc.axis;
if (axis == null)
System.out.println(" No Axis " + vc.getName());
else {
if (axis.isInterval()) {
System.out.println(" Layer " + vc.getName() + " contig= " + axis.isContiguous());
// see if theres any TimeCoord that use this
findGridsForVertCoord(fmrDef, vc);
}
}
boolean got = fmrDef.findVertCoordByName(vc.getName()) != null;
if (!got)
System.out.println(" ***NOT " + vc.getName());
}
}
static void findGridsForVertCoord(FmrcDefinition fmrDef, ForecastModelRunInventory.VertCoord vc) {
for (RunSeq runSeq : fmrDef.runSequences) {
for (Grid grid : runSeq.vars) {
if ((grid.vtc != null) && (grid.vtc.vc == vc)) {
List restrictList = grid.vtc.restrictList;
if (restrictList != null && restrictList.size() > 0)
System.out.println(" TimeVertCoord refers to this vertical coordinate");
}
}
}
}
public static String[] fmrcDatasets = {
"NCEP/GFS/Alaska_191km",
"NCEP/GFS/CONUS_80km",
"NCEP/GFS/CONUS_95km",
"NCEP/GFS/CONUS_191km",
"NCEP/GFS/Global_0p5deg",
"NCEP/GFS/Global_onedeg",
"NCEP/GFS/Global_2p5deg",
"NCEP/GFS/Hawaii_160km",
"NCEP/GFS/N_Hemisphere_381km",
"NCEP/GFS/Puerto_Rico_191km",
"NCEP/NAM/Alaska_11km",
"NCEP/NAM/Alaska_22km",
"NCEP/NAM/Alaska_45km/noaaport",
"NCEP/NAM/Alaska_45km/conduit",
"NCEP/NAM/Alaska_95km",
"NCEP/NAM/CONUS_12km/conduit",
"NCEP/NAM/CONUS_20km/surface",
"NCEP/NAM/CONUS_20km/selectsurface",
"NCEP/NAM/CONUS_20km/noaaport",
"NCEP/NAM/CONUS_40km/conduit",
"NCEP/NAM/CONUS_80km",
"NCEP/NAM/Polar_90km",
"NCEP/RUC2/CONUS_20km/surface",
"NCEP/RUC2/CONUS_20km/pressure",
"NCEP/RUC2/CONUS_20km/hybrid",
"NCEP/RUC2/CONUS_40km",
"NCEP/RUC/CONUS_80km",
"NCEP/DGEX/CONUS_12km",
"NCEP/DGEX/Alaska_12km",
/*
"NCEP/GEFS/Global_1p0deg_Ensemble/derived",
"NCEP/GEFS/Global_1p0deg_Ensemble/member",
*/
"NCEP/SREF/CONUS_40km/ensprod",
"NCEP/SREF/CONUS_40km/ensprod_biasc",
/* "NCEP/SREF/CONUS_40km/pgrb_biasc", */
"NCEP/SREF/Alaska_45km/ensprod",
"NCEP/SREF/PacificNE_0p4/ensprod",
"NCEP/NDFD/CONUS_5km",
"NCEP/WW3/Alaskan_4minute",
"NCEP/WW3/Alaskan_10minute",
"NCEP/WW3/Atlantic_4minute",
"NCEP/WW3/Atlantic_10minute",
"NCEP/WW3/EasternPacific_10minute",
"NCEP/WW3/Global_30minute",
"NCEP/WW3/WestCoast_4minute",
"NCEP/WW3/WestCoast_10minute",
};
public static String[] fmrcDatasets_41 = {
"NCEP/GFS/Alaska_191km",
"NCEP/GFS/CONUS_80km",
"NCEP/GFS/CONUS_95km",
"NCEP/GFS/CONUS_191km",
"NCEP/GFS/Global_0p5deg",
"NCEP/GFS/Global_onedeg",
"NCEP/GFS/Global_2p5deg",
"NCEP/GFS/Hawaii_160km",
"NCEP/GFS/N_Hemisphere_381km",
"NCEP/GFS/Puerto_Rico_191km",
"NCEP/NAM/Alaska_11km",
"NCEP/NAM/Alaska_22km",
"NCEP/NAM/Alaska_45km/noaaport",
"NCEP/NAM/Alaska_45km/conduit",
"NCEP/NAM/Alaska_95km",
"NCEP/NAM/CONUS_12km/conduit",
"NCEP/NAM/CONUS_20km/surface",
"NCEP/NAM/CONUS_20km/selectsurface",
"NCEP/NAM/CONUS_20km/noaaport",
"NCEP/NAM/CONUS_40km/conduit",
"NCEP/NAM/CONUS_80km",
"NCEP/NAM/Polar_90km",
"NCEP/RUC2/CONUS_20km/surface",
"NCEP/RUC2/CONUS_20km/pressure",
"NCEP/RUC2/CONUS_20km/hybrid",
"NCEP/RUC2/CONUS_40km",
"NCEP/RUC/CONUS_80km",
"NCEP/DGEX/CONUS_12km",
"NCEP/DGEX/Alaska_12km",
/*
"NCEP/GEFS/Global_1p0deg_Ensemble/derived",
"NCEP/GEFS/Global_1p0deg_Ensemble/member",
"NCEP/SREF/CONUS_40km/ensprod",
"NCEP/SREF/CONUS_40km/ensprod_biasc",
// "NCEP/SREF/CONUS_40km/pgrb_biasc",
"NCEP/SREF/Alaska_45km/ensprod",
"NCEP/SREF/PacificNE_0p4/ensprod",
*/
"NCEP/NDFD/CONUS_5km",
};
private static String fmrcDefinitionDir = "C:/dev/tds/thredds/tds/src/main/webapp/WEB-INF/altContent/idd/thredds/modelInventory/";
private static String[] fmrcDefinitionFiles;
public static String[] getDefinitionFiles() {
if (fmrcDefinitionFiles == null) {
fmrcDefinitionFiles = new String[fmrcDatasets.length];
int count = 0;
for (String ds : fmrcDatasets) {
fmrcDefinitionFiles[count++] = fmrcDefinitionDir + StringUtil.replace(ds, '/', "-") + ".fmrcDefinition.xml";
}
}
return fmrcDefinitionFiles;
}
///////////////////////////////////////////////////////////////////////////////////////////////////////////////
private static String[] exampleFiles = {
/* "R:/testdata2/motherlode/grid/GFS_Alaska_191km_20060802_1200.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-GFS-Alaska_191km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/GFS_CONUS_80km_20060802_0600.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-GFS-CONUS_80km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/GFS_CONUS_191km_20060802_0000.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-GFS-CONUS_191km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/GFS_CONUS_95km_20060802_0000.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-GFS-CONUS_95km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/GFS_Global_2p5deg_20060801_1200.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-GFS-Global_2p5deg.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/GFS_Global_onedeg_20060802_0600.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-GFS-Global_onedeg.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/GFS_Hawaii_160km_20060730_0000.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-GFS-Hawaii_160km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/GFS_N_Hemisphere_381km_20060801_0000.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-GFS-N_Hemisphere_381km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/GFS_Puerto_Rico_191km_20060731_0000.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-GFS-Puerto_Rico_191km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NAM_Alaska_22km_20060731_1200.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NAM-Alaska_22km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NAM_Alaska_45km_conduit_20060801_0000.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NAM-Alaska_45km-conduit.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NAM_Alaska_45km_noaaport_20060730_0000.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NAM-Alaska_45km-noaaport.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NAM_Alaska_95km_20060801_0000.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NAM-Alaska_95km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NAM_CONUS_20km_noaaport_20060731_0600.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NAM-CONUS_20km-noaaport.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NAM_CONUS_20km_selectsurface_20060801_0600.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NAM-CONUS_20km-selectsurface.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NAM_CONUS_20km_surface_20060801_0000.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NAM-CONUS_20km-surface.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NAM_CONUS_40km_conduit_20060801_0600.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NAM-CONUS_40km-conduit.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NAM_CONUS_40km_noaaport_20060731_1800.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NAM-CONUS_40km-noaaport.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NAM_CONUS_80km_20060728_1200.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NAM-CONUS_80km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NAM_Polar_90km_20060730_0000.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NAM-Polar_90km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/RUC2_CONUS_20km_hybrid_20060802_2100.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-RUC2-CONUS_20km-hybrid.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/RUC2_CONUS_20km_pressure_20060802_2000.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-RUC2-CONUS_20km-pressure.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/RUC2_CONUS_20km_surface_20060802_1700.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-RUC2-CONUS_20km-surface.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/RUC_CONUS_40km_20060802_2000.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-RUC-CONUS_40km.fmrcDefinition.xml", //
"R:/testdata2/motherlode/grid/RUC_CONUS_80km_20060802_2000.grib1", "R:/testdata2/motherlode/grid/modelDefs/NCEP-RUC-CONUS_80km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/DGEX_Alaska_12km_20060731_0000.grib2", "R:/testdata2/motherlode/grid/modelDefs/NCEP-DGEX-Alaska_12km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/DGEX_CONUS_12km_20060730_1800.grib2", "R:/testdata2/motherlode/grid/modelDefs/NCEP-DGEX-CONUS_12km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/GFS_Global_0p5deg_20060726_0600.grib2", "R:/testdata2/motherlode/grid/modelDefs/NCEP-GFS-Global_0p5deg.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NAM_Alaska_11km_20060802_1200.grib2", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NAM-Alaska_11km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NAM_CONUS_12km_20060801_1200.grib2", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NAM-CONUS_12km.fmrcDefinition.xml",
"R:/testdata2/motherlode/grid/NDFD_CONUS_5km_20060731_1200.grib2", "R:/testdata2/motherlode/grid/modelDefs/NCEP-NDFD-CONUS_5km.fmrcDefinition.xml", // */
"R:/testdata/motherlode/grid/RUC2_CONUS_20km_surface_20060825_1400.grib2", "R:/testdata/motherlode/grid/modelDefs/NCEP-RUC2-CONUS_20km-surface.fmrcDefinition.xml",
};
public static void main(String args[]) throws IOException {
for (int i = 0; i < exampleFiles.length; i += 2)
convertIds(exampleFiles[i], exampleFiles[i + 1]);
//for (int i = 0; i < defs.length; i+=2)
// showVertCoords(defs[i], defs[i+1]);
}
}
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