Master generic netcdf

.gitignore

@@ -9,4 +9,6 @@ opendaTestReports/
 **/build-test
 **/MANIFEST.MF
 **/tests/*.log
+**/*_temp_build/
+**/castor_temp_src/
 OpenDATimings_*.txt

core/java/src/org/openda/exchange/GenericNetcdfArrayExchangeItem.java

@@ -0,0 +1,64 @@
+package org.openda.exchange;
+
+import org.openda.exchange.dataobjects.GenericNetcdfDataObject;
+import org.openda.interfaces.IExchangeItem;
+
+public class GenericNetcdfArrayExchangeItem extends ExchangeItem implements IExchangeItem {
+
+	private final GenericNetcdfDataObject genericNetcdfDataObject;
+
+	public GenericNetcdfArrayExchangeItem(String exchangeItemId, GenericNetcdfDataObject genericNetcdfDataObject){
+		super(exchangeItemId);
+		this.genericNetcdfDataObject = genericNetcdfDataObject;
+	}
+
+	@Override
+	public ValueType getValuesType() {
+		throw new RuntimeException("org.openda.exchange.GenericNetcdfArrayExchangeItem.getValuesType not implemented yet");
+	}
+
+	@Override
+	public Class getValueType() {
+		throw new RuntimeException("org.openda.exchange.GenericNetcdfArrayExchangeItem.getValueType not implemented yet");
+	}
+
+	@Override
+	public Object getValues() {
+		throw new RuntimeException("org.openda.exchange.GenericNetcdfArrayExchangeItem.getValues not implemented yet");
+	}
+
+	@Override
+	public double[] getValuesAsDoubles() {
+		return this.genericNetcdfDataObject.getArrayExchangeItemValues(this.getId());
+	}
+
+	@Override
+	public void axpyOnValues(double alpha, double[] axpyValues) {
+		double[] values = getValuesAsDoubles();
+		for (int i = 0; i < values.length; i++) {
+			if (Double.isNaN(values[i])) {
+				System.out.println("OrgVal Nan at " + i);
+			}
+			values[i] += alpha * axpyValues[i];
+			if (Double.isNaN(values[i])) {
+				System.out.println("ModVal Nan at " + i);
+			}
+		}
+		setValuesAsDoubles(values);
+	}
+
+	@Override
+	public void multiplyValues(double[] multiplicationFactors) {
+		throw new RuntimeException("org.openda.exchange.GenericNetcdfArrayExchangeItem.multiplyValues not implemented yet");
+	}
+
+	@Override
+	public void setValues(Object values) {
+		throw new RuntimeException("org.openda.exchange.GenericNetcdfArrayExchangeItem.setValues not implemented yet");
+	}
+
+	@Override
+	public void setValuesAsDoubles(double[] values) {
+		this.genericNetcdfDataObject.setArrayExchangeItemValues(this.getId(), values);
+	}
+}

core/java/src/org/openda/exchange/dataobjects/GenericNetcdfArrayConfig.java

@@ -0,0 +1,33 @@
+package org.openda.exchange.dataobjects;
+
+import org.openda.utils.DimensionIndex;
+
+import java.util.HashMap;
+
+public class GenericNetcdfArrayConfig {
+	private final String exchangeitemId;
+	private final String netcdf_variable_name;
+	private final HashMap<String, DimensionIndex> netcdf_dimension_var;
+
+	public GenericNetcdfArrayConfig(String id, String variable_name, HashMap<String, DimensionIndex> dimensions) {
+		exchangeitemId = id;
+		netcdf_variable_name = variable_name;
+		netcdf_dimension_var = dimensions;
+	}
+
+	public String getExchangeitemId(){
+		return exchangeitemId;
+	}
+
+	public String getNetcdfVariableName(){
+		return netcdf_variable_name;
+	}
+
+	public String[] getNetcdfDimensionVariables(){
+		return netcdf_dimension_var.keySet().toArray(new String[0]);
+	}
+
+	public DimensionIndex getDimensionIndex(String dimension_variable_id){
+		return netcdf_dimension_var.get(dimension_variable_id);
+	}
+}

core/java/src/org/openda/exchange/dataobjects/GenericNetcdfConfig.java

@@ -0,0 +1,13 @@
+package org.openda.exchange.dataobjects;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+
+public class GenericNetcdfConfig {
+
+//	ArrayList<GenericNetcdfTSConfig> tsConfigs = new ArrayList<>();
+//	ArrayList<GenericNetcdfArrayConfig> arrayConfigs = new ArrayList<>();
+
+	HashMap<String, GenericNetcdfTSConfig> tsConfigs = new HashMap<>();
+	HashMap<String, GenericNetcdfArrayConfig> arrayConfigs = new HashMap<>();
+}

core/java/src/org/openda/exchange/dataobjects/GenericNetcdfConfigReader.java

@@ -0,0 +1,64 @@
+package org.openda.exchange.dataobjects;
+
+import org.openda.core.io.castorgenerated.*;
+import org.openda.utils.DimensionIndex;
+import org.openda.utils.io.CastorUtils;
+
+import java.io.File;
+import java.util.HashMap;
+
+public class GenericNetcdfConfigReader {
+
+	private GenericNetcdfConfig genericNetcdfConfig;
+
+	public GenericNetcdfConfigReader(File genericNetcdfConfigFile) {
+		TNC_dataObjectConfig tncDataObjectConfig = (TNC_dataObjectConfig) CastorUtils.parse(genericNetcdfConfigFile, TNC_dataObjectConfig.class);
+		genericNetcdfConfig = parseGenericNetcdfConfig(genericNetcdfConfigFile, tncDataObjectConfig);
+	}
+
+	public GenericNetcdfConfig getGenericNetcdfConfig() {
+		return genericNetcdfConfig;
+	}
+
+	public static GenericNetcdfConfig parseGenericNetcdfConfig(File genericNetcdfConfigFile, TNC_dataObjectConfig tncDataObjectConfig) {
+
+		GenericNetcdfConfig netcdfConfig = new GenericNetcdfConfig();
+
+		org.openda.core.io.castorgenerated.TNC_arrayExchangeItem[] arrayExchangeItemsXML = tncDataObjectConfig.getArrayExchangeItem();
+		for (org.openda.core.io.castorgenerated.TNC_arrayExchangeItem arrayExchangeItemXML: arrayExchangeItemsXML) {
+			String id = arrayExchangeItemXML.getId().getContent();
+			String variable_name = arrayExchangeItemXML.getValues().getSelection().getVariable()[0].getName(); // only 1 variable is possible for array exchange item
+			int nDimension = arrayExchangeItemXML.getValues().getSelection().getVariable()[0].getDimensionCount();
+			HashMap<String, DimensionIndex> dimensions = new HashMap<>();
+			if (nDimension>0){
+				dimensions = new HashMap<>();
+				for (int i=0; i<nDimension; i++){
+					String dimension_name = arrayExchangeItemXML.getValues().getSelection().getVariable()[0].getDimension(i).getName();
+					String dimension_index_string = arrayExchangeItemXML.getValues().getSelection().getVariable()[0].getDimension(i).getIndex();
+					DimensionIndex dimension_index = new DimensionIndex(dimension_index_string,0); //TODO: check if it is okay to assume that dimensionBase is always 0
+					dimensions.put(dimension_name,dimension_index);
+				}
+			}
+			GenericNetcdfArrayConfig arrayConfig = new GenericNetcdfArrayConfig(id,variable_name,dimensions);
+			netcdfConfig.arrayConfigs.put(id,arrayConfig);
+		}
+
+		TNC_timeSeriesExchangeItem[] timeseriesExchangeItemsXML = tncDataObjectConfig.getTimeSeriesExchangeItem();
+		for (TNC_timeSeriesExchangeItem timeseriesExchangeItemXML: timeseriesExchangeItemsXML) {
+			TNC_id tnc_id = timeseriesExchangeItemXML.getId();
+			String template = tnc_id.getTemplate();
+			String id = null;
+			if (template == null) {
+				id = timeseriesExchangeItemXML.getId().getContent();
+			}
+			GenericNetcdfTSConfig tsConfig = new GenericNetcdfTSConfig(id,template,timeseriesExchangeItemXML);
+			if (id==null){
+				netcdfConfig.tsConfigs.put(template,tsConfig);
+			} else {
+				netcdfConfig.tsConfigs.put(id, tsConfig);
+			}
+		}
+
+		return netcdfConfig;
+	}
+}