194 lines
7.1 KiB
Java
194 lines
7.1 KiB
Java
package org.gcube.dataanalysis.geo.algorithms;
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import java.awt.Image;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.LinkedHashMap;
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import java.util.List;
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import java.util.Map;
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import org.gcube.common.scope.api.ScopeProvider;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
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import org.gcube.dataanalysis.ecoengine.datatypes.OutputTable;
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import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
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import org.gcube.dataanalysis.ecoengine.signals.SignalProcessing;
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import org.gcube.dataanalysis.ecoengine.utils.IOHelper;
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import org.gcube.dataanalysis.ecoengine.utils.Tuple;
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import org.gcube.dataanalysis.geo.connectors.wfs.WFS;
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import org.gcube.dataanalysis.geo.matrixmodel.RasterTable;
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import org.gcube.dataanalysis.geo.matrixmodel.ZExtractor;
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public class ZExtraction extends XYExtraction{
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@Override
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public String getDescription() {
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return "An algorithm to extract the Z values from a geospatial features repository (e.g. NETCDF, ASC, GeoTiff files etc. ). " +
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"The algorithm analyses the repository and automatically extracts the Z values according to the resolution wanted by the user. " +
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"It produces one chart of the Z values and one table containing the values.";
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}
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public static String x = "X";
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public static String y = "Y";
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public static String resolution = "Resolution";
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public double xValue;
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public double yValue;
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public double resolutionValue;
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public double signal[];
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@Override
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public List<StatisticalType> getInputParameters() {
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List<StatisticalType> previnputs = super.getInputParameters();
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inputs = new ArrayList<StatisticalType>();
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//layername
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inputs.add(previnputs.get(0));
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inputs.add(previnputs.get(5));
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inputs.add(previnputs.get(6));
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IOHelper.addDoubleInput(inputs, x, "X coordinate", "0");
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IOHelper.addDoubleInput(inputs, y, "Y coordinate", "0");
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inputs.add(previnputs.get(8));
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IOHelper.addDoubleInput(inputs, resolution, "Step for Z values", "100");
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DatabaseType.addDefaultDBPars(inputs);
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return inputs;
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}
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protected void getParameters() {
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layerNameValue = IOHelper.getInputParameter(config, layerName);
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AnalysisLogger.getLogger().debug("Extraction: Layer " + layerNameValue);
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time = Integer.parseInt(IOHelper.getInputParameter(config, t));
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xValue = Double.parseDouble(IOHelper.getInputParameter(config, x));
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yValue = Double.parseDouble(IOHelper.getInputParameter(config, y));
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resolutionValue=Double.parseDouble(IOHelper.getInputParameter(config, resolution));
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AnalysisLogger.getLogger().debug("Extraction: T " + time);
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AnalysisLogger.getLogger().debug("Extraction: X " + xValue);
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AnalysisLogger.getLogger().debug("Extraction: Y " + yValue);
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AnalysisLogger.getLogger().debug("Extraction: Res " + resolutionValue);
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tableNameValue = IOHelper.getInputParameter(config, tableName);
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tableLabelValue = IOHelper.getInputParameter(config, tableLabel);
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AnalysisLogger.getLogger().debug("Extraction: tableName " + tableNameValue);
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AnalysisLogger.getLogger().debug("Extraction: tableLabel " + tableLabelValue);
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String scope = config.getGcubeScope();
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AnalysisLogger.getLogger().debug("Extraction: Externally set scope " + scope);
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if (scope == null) {
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scope = ScopeProvider.instance.get();
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config.setGcubeScope(scope);
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}
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}
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Image signalimage;
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Image spectrogramImage;
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@Override
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public void compute() throws Exception {
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try {
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status = 30;
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AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
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getParameters();
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AnalysisLogger.getLogger().debug("Extracting Time Series from layer");
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ZExtractor extractor = new ZExtractor(config);
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extractor.correctZ(0, layerNameValue,resolutionValue);
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long t0 = System.currentTimeMillis();
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signal = extractor.extractZ(layerNameValue, xValue,yValue, time, resolutionValue);
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AnalysisLogger.getLogger().debug("ELAPSED TIME: "+(System.currentTimeMillis()-t0));
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AnalysisLogger.getLogger().debug("Signal: "+signal.length);
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status = 30;
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if (signal.length==1)
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AnalysisLogger.getLogger().debug("Extractor: Signal is only one point!");
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status = 70;
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AnalysisLogger.getLogger().debug("Extractor: Matrix Extracted");
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AnalysisLogger.getLogger().debug("Extractor: ****Rasterizing grid into table****");
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double matrix[][] = new double[1][];
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matrix[0] = signal;
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HashMap<Double,Map<String, String>> polygonsFeatures = null;
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if (extractor.currentconnector instanceof WFS)
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polygonsFeatures = ((WFS) extractor.currentconnector).getPolygonsFeatures();
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RasterTable raster = new RasterTable(xValue, xValue, yValue, yValue, zValue, time,resolutionValue, resolutionValue, matrix, polygonsFeatures,config);
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int signalRate = 1;
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double zline[] = new double[signal.length];
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int j=0;
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for (double z=extractor.zmin;z<=extractor.zmax;z=z+resolutionValue){
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zline[j]=z;
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j++;
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}
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List<Tuple<Double>> coordinates=new ArrayList<Tuple<Double>>();
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for (int i=0;i<zline.length;i++)
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coordinates.add(new Tuple<Double>(xValue,yValue,zline[i],(double)time));
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raster.setTablename(tableNameValue);
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raster.setCoordinates(coordinates);
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raster.deleteTable();
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raster.dumpGeoTable();
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signalimage = SignalProcessing.renderSignalWithGenericTime(signal, zline, "Z");
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AnalysisLogger.getLogger().debug("Extractor: Map was dumped in table: " + tableNameValue);
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status = 80;
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AnalysisLogger.getLogger().debug("Extractor: Elapsed: Whole operation completed in " + ((double) (System.currentTimeMillis() - t0) / 1000d) + "s");
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} catch (Exception e) {
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e.printStackTrace();
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AnalysisLogger.getLogger().debug("Extractor: ERROR!: " + e.getLocalizedMessage());
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throw e;
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} finally {
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status = 100;
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}
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}
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@Override
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public StatisticalType getOutput() {
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LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
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List<TableTemplates> templateHspec = new ArrayList<TableTemplates>();
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templateHspec.add(TableTemplates.TIMESERIES);
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OutputTable p = new OutputTable(templateHspec, tableLabelValue, tableNameValue, "Output table");
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map.put("OutputTable", p);
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if (signalimage!=null){
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HashMap<String, Image> producedImages = new HashMap<String, Image>();
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producedImages.put("Z Modulations Visualization", signalimage);
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PrimitiveType images = new PrimitiveType("Images", producedImages, PrimitiveTypes.IMAGES, "Modulations of Z", "The modulations of Z");
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map.put("Images", images);
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}
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// generate a primitive type for the collection
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PrimitiveType outputm = new PrimitiveType(HashMap.class.getName(), map, PrimitiveTypes.MAP, "ResultsMap", "Results Map");
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return outputm;
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}
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}
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