NetCDF Java Library - dump to JSON (Draft)
This is only a draft, please do not rely on it!
JsonNetCDF.java:
package jsonnetcdf;
import com.google.gson.*;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
import ucar.ma2.Array;
import ucar.ma2.InvalidRangeException;
import ucar.ma2.Range;
import ucar.nc2.Dimension;
import ucar.nc2.NetcdfFile;
import ucar.nc2.Variable;
import ucar.nc2.dataset.NetcdfDataset;
public class JsonNetCDF {
private String queryJSON = "";
public JsonNetCDF() {
}
public JsonNetCDF(String queryJSON) {
this.queryJSON = queryJSON;
}
public void replaceJson(String queryJSON) {
this.queryJSON = queryJSON;
}
public String toJson() {
Gson gson = new Gson();
try {
Query query = gson.fromJson(queryJSON, Query.class);
NetcdfDataset gid = NetcdfDataset.openDataset(query.file);
NetcdfFile gidFile = gid.getReferencedFile();
if (query.searchType.equals("getList")) {
return gson.toJson(getList(query, gid, gidFile));
} else if (query.searchType.equals("getData")) {
return gson.toJson(getData(query, gid, gidFile));
}
} catch (IOException ex) {
Logger.getLogger(JsonNetCDF.class.getName()).log(Level.SEVERE, null, ex);
}
return "Error!";
}
private HashMap getList(Query query, NetcdfDataset gid, NetcdfFile gidFile) {
List<Variable> variables = null;
HashMap response = new HashMap();
ArrayList variablesArray = new ArrayList();
response.put("list", variablesArray);
response.put("type", "list");
if ((query.table != null) && (!query.table.equals(""))) {
variables = Arrays.asList(gidFile.findVariable(query.table));
} else {
variables = gidFile.getVariables();
}
for (int i = 0; i < variables.size(); i++) {
Variable variable = variables.get(i);
HashMap variableHash = new HashMap();
variableHash.put("description", variable.getDescription());
variableHash.put("attributes", variable.getAttributes().toString());
variableHash.put("dataType", variable.getDataType().toString());
variableHash.put("dimensions", variable.getDimensions().toString());
variableHash.put("dimensionsString", variable.getDimensionsString());
variableHash.put("elementSize", variable.getElementSize());
variableHash.put("name", variable.getName());
variableHash.put("nameEscaped", variable.getNameEscaped());
variableHash.put("rank", variable.getRank());
variableHash.put("shapeAsSection", variable.getShapeAsSection().toString());
variableHash.put("shortName", variable.getShortName());
variableHash.put("size", variable.getSize());
variableHash.put("unitString", variable.getUnitsString());
variableHash.put("isCoordinateVariable", variable.isCoordinateVariable());
variableHash.put("isMetadata", variable.isMetadata());
variableHash.put("isScalar", variable.isScalar());
ArrayList dimensionArray = new ArrayList();
for (int j = 0; j < variable.getDimensions().size(); j++) {
HashMap dimensionHash = new HashMap();
Dimension dimension = variable.getDimension(j);
dimensionHash.put("length", dimension.getLength());
dimensionHash.put("name", dimension.getName());
if ((gidFile.findVariable(dimension.getName()) != null)) {
if (gidFile.findVariable(dimension.getName()).findAttribute("_CoordinateAxisType") != null) {
dimensionHash.put("dimensionType", gidFile.findVariable(dimension.getName()).findAttribute("_CoordinateAxisType").getStringValue());
}
dimensionHash.put("unitString", gidFile.findVariable(dimension.getName()).getUnitsString());
} else {
dimensionHash.put("unitString", "");
}
dimensionArray.add(dimensionHash);
}
variableHash.put("dimensionArray", dimensionArray);
variablesArray.add(variableHash);
}
return response;
}
private HashMap getData(Query query, NetcdfDataset gid, NetcdfFile gidFile) {
HashMap response = new HashMap();
response.put("type", "data");
if ((query.table == null) || (query.table.equals(""))) {
response.put("status", "Error!");
return response;
}
Array dataArray;
int dimensionTotal = 1;
ArrayList dimensionsSequence = new ArrayList();
HashMap dimensionsList = new HashMap();
try {
List<Dimension> dimensions = gid.findVariable(query.table).getDimensions();
ArrayList ranges = new ArrayList();
for (int i = 0; i < dimensions.size(); i++) {
String dimensionType = gidFile.findVariable(dimensions.get(i).getName()).findAttribute("_CoordinateAxisType").getStringValue();
Array dimensionValues = gidFile.findVariable(dimensions.get(i).getName()).read();
ArrayList<Float> values = new ArrayList();
for (int j = 0; j < dimensionValues.getSize(); j++) {
values.add(dimensionValues.getFloat(j));
}
int min = 0;
int max = values.size() - 1;
//check constraint
if (query.constraint != null) {
for (int j = 0; j < query.constraint.length; j++) {
if ((query.constraint[j].min != (float) -999999999) && (query.constraint[j].max != (float) -999999999) && (query.constraint[j].max < query.constraint[j].min)) {
response.put("status", "Error!");
return response;
}
if (query.constraint[j].name.equals(dimensionType)) {
boolean hasSetMin = false;
boolean hasSetMax = false;
if (values.get(values.size() - 1) > values.get(0)) {
for (int k = 0; k < values.size(); k++) {
if ((query.constraint[j].min != (float) -999999999) && (values.get(k) < query.constraint[j].min)) {
min = k + 1;
}
if ((!hasSetMax) && (query.constraint[j].max != (float) -999999999) && (values.get(k) > query.constraint[j].max)) {
max = k - 1;
hasSetMax = true;
}
}
} else {
for (int k = (values.size() - 1); k >= 0; k--) {
if ((!hasSetMin) && (query.constraint[j].min != (float) -999999999) && (values.get(k) < query.constraint[j].min)) {
min = k - 1;
hasSetMin = true;
}
if ((query.constraint[j].max != (float) -999999999) && (values.get(k) > query.constraint[j].max)) {
max = k + 1;
}
}
}
break;
}
}
}
ArrayList<Float> newValues = new ArrayList();
for (int j = min; j < (max + 1); j++) {
newValues.add(values.get(j));
}
dimensionsSequence.add(dimensionType);
dimensionsList.put(dimensionType, newValues);
try {
ranges.add(new Range(min, max));
} catch (InvalidRangeException ex) {
Logger.getLogger(JsonNetCDF.class.getName()).log(Level.SEVERE, null, ex);
}
}
System.out.println(dimensionsSequence);
System.out.println(dimensionsList);
for (int i = 0; i < dimensionsSequence.size(); i++) {
ArrayList<Float> values = (ArrayList<Float>) dimensionsList.get(dimensionsSequence.get(i));
dimensionTotal *= values.size();
}
try {
dataArray = gid.findVariable(query.table).read(ranges);
} catch (InvalidRangeException ex) {
Logger.getLogger(JsonNetCDF.class.getName()).log(Level.SEVERE, null, ex);
response.put("status", "Error!");
return response;
}
} catch (IOException ex) {
Logger.getLogger(JsonNetCDF.class.getName()).log(Level.SEVERE, null, ex);
response.put("status", "Error!");
return response;
}
ArrayList dataList = new ArrayList();
response.put("data", dataList);
float[] data = (float[]) dataArray.copyTo1DJavaArray();
for (int i = 0; i < data.length; i++) {
HashMap dataMap = new HashMap();
int previousDimensionTotal = dimensionTotal;
for (int j = 0; j < dimensionsSequence.size(); j++) {
previousDimensionTotal /= ((ArrayList<Float>)dimensionsList.get(dimensionsSequence.get(j))).size();
int arrayNumber = (i / previousDimensionTotal) % ((ArrayList<Float>)dimensionsList.get(dimensionsSequence.get(j))).size();
Float dimensionValue = ((ArrayList<Float>)dimensionsList.get(dimensionsSequence.get(j))).get(arrayNumber);
dataMap.put(dimensionsSequence.get(j), dimensionValue);
}
dataMap.put("value", data[i]);
dataList.add(dataMap);
}
return response;
}
}
class Query {
public String searchType;
public String file;
public String table;
public Constraint[] constraint;
}
class Constraint {
public String name;
public float min = (float) -999999999;
public float max = (float) -999999999;
}
Test program: Main.java:
package jsonnetcdf;
public class Main {
public static void main(String[] args) {
JsonNetCDF a = new JsonNetCDF("{file: 'gfs.t06z.mastergrb2f48', " +
"searchType: 'getList', table: 'lat'}");
System.out.println(a.toJson());
a = new JsonNetCDF("{file: 'gfs.t06z.mastergrb2f48', " +
"searchType: 'getData'," +
"table: 'Temperature'," +
"constraint: [{name: 'Lat', max: 22.5}, {name: 'Lon', min: 114.5, max: 114.5}]}");
System.out.println(a.toJson());
}
}
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