232 lines
9.0 KiB
Java
232 lines
9.0 KiB
Java
package org.gcube.dataanalysis.geo.matrixmodel;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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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.utils.Tuple;
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import org.gcube.dataanalysis.geo.connectors.asc.ASC;
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import org.gcube.dataanalysis.geo.connectors.asc.AscDataExplorer;
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import org.gcube.dataanalysis.geo.connectors.geotiff.GeoTiff;
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import org.gcube.dataanalysis.geo.connectors.netcdf.NetCDF;
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import org.gcube.dataanalysis.geo.connectors.table.Table;
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import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation;
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import org.gcube.dataanalysis.geo.connectors.wcs.WCS;
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import org.gcube.dataanalysis.geo.connectors.wfs.WFS;
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import org.gcube.dataanalysis.geo.infrastructure.GeoNetworkInspector;
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import org.gcube.dataanalysis.geo.interfaces.GISDataConnector;
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import org.gcube.dataanalysis.geo.meta.GenericLayerMetadata;
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import org.gcube.dataanalysis.geo.utils.VectorOperations;
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import org.opengis.metadata.Metadata;
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import org.opengis.metadata.identification.Identification;
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public class MatrixExtractor {
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private GeoNetworkInspector gnInspector;
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private AlgorithmConfiguration configuration;
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public static int maxSignalLength = 100000;
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public static int maxzLength = 100000;
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boolean log = true;
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protected double currentResolution = 0.5;
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public List<Double> currentTimeValues;
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public List<Tuple<Double>> currentTuples;
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public MatrixExtractor(AlgorithmConfiguration configuration) {
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AnalysisLogger.getLogger().debug("Matrix Extractor: setting GeoNetwork search scope to " + configuration.getGcubeScope());
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gnInspector = new GeoNetworkInspector();
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gnInspector.setScope(configuration.getGcubeScope());
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this.configuration = configuration;
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}
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public GeoNetworkInspector getFeaturer() {
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return gnInspector;
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}
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public boolean isTable() {
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if (configuration.getParam(TableMatrixRepresentation.tableNameParameter) != null)
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return true;
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else
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return false;
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}
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protected List<Double> getRawValuesInTimeInstantAndBoundingBox(String layerTitle, int time, List<Tuple<Double>> coordinates3d, double xL, double xR, double yL, double yR, double resolution) throws Exception {
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return getRawValuesInTimeInstantAndBoundingBox(layerTitle, time, coordinates3d, xL, xR, yL, yR, resolution, false);
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}
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public GISDataConnector currentconnector;
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public String layerName;
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public String layerURL;
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public GISDataConnector getConnector(String layerTitle, double resolution) throws Exception {
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// get the layer
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Metadata meta = null;
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GISDataConnector connector = null;
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if (currentconnector != null)
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connector = currentconnector;
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else {
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if (isTable()) {
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AnalysisLogger.getLogger().debug("Extracting grid from table " + configuration.getParam(TableMatrixRepresentation.tableNameParameter));
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connector = new Table(configuration, resolution);
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currentconnector = connector;
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} else {
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try {
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meta = gnInspector.getGNInfobyUUIDorName(layerTitle);
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} catch (Exception e) {
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}
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// if the layer is not on GeoNetwork
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if (meta == null) {
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AnalysisLogger.getLogger().debug("Forcing setting of the meta");
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String[] urls = { layerTitle };
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String[] protocols = { "HTTP" };
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meta = new GenericLayerMetadata().createBasicMeta(urls, protocols);
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}
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layerName = gnInspector.getLayerName(meta);
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if (layerName == null)
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layerName = layerTitle;
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layerURL = "";
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if (gnInspector.isNetCDFFile(meta)) {
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Identification id = meta.getIdentificationInfo().iterator().next();
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String title = id.getCitation().getTitle().toString();
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AnalysisLogger.getLogger().debug("found a netCDF file with title " + title + " and layer name " + layerName);
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layerURL = gnInspector.getOpenDapLink(meta);
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connector = new NetCDF(layerURL, layerName);
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} else if (gnInspector.isAscFile(meta)) {
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AnalysisLogger.getLogger().debug("managing ASC File");
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layerURL = gnInspector.getHttpLink(meta);
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connector = new ASC();
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} else if (gnInspector.isWFS(meta)) {
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AnalysisLogger.getLogger().debug("found a Geo Layer with reference " + layerURL + " and layer name " + layerName);
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// layerURL = gnInspector.getGeoserverLink(meta);
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layerURL = gnInspector.getWFSLink(meta);
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connector = new WFS();
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} else if (gnInspector.isWCS(meta)) {
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AnalysisLogger.getLogger().debug("found a WCS Layer with reference " + layerURL + " and layer name " + layerName);
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layerURL = gnInspector.getWCSLink(meta);
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connector = new WCS(configuration, layerURL);
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} else if (gnInspector.isGeoTiff(meta)) {
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layerURL = gnInspector.getGeoTiffLink(meta);
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AnalysisLogger.getLogger().debug("found a GeoTiff with reference " + layerURL + " and layer name " + layerName);
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connector = new GeoTiff(configuration);
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} else {
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// treat as geotiff
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layerURL = layerTitle;
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AnalysisLogger.getLogger().debug("guessing a GeoTiff with reference " + layerURL + " and layer name " + layerName);
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connector = new GeoTiff(configuration);
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}
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}
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}
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currentconnector = connector;
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return currentconnector;
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}
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// 4D Extraction
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/**
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* Extract raw values in a time instant according to a set of grid points and a bounding box
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*/
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public GISDataConnector connector;
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public List<Double> getRawValuesInTimeInstantAndBoundingBox(String layerTitle, int time, List<Tuple<Double>> coordinates3d, double xL, double xR, double yL, double yR, double resolution, boolean saveLayer) throws Exception {
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connector = getConnector(layerTitle, resolution);
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// execute connector
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if (connector != null)
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return connector.getFeaturesInTimeInstantAndArea(layerURL, layerName, time, coordinates3d, xL, xR, yL, yR);
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else
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throw new Exception("ERROR: Connector not found for layer " + layerTitle + " - Cannot Rasterize!");
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}
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public GISDataConnector getCurrentConnector() {
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return connector;
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}
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public double zmin;
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public double zmax;
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public double correctZ(double zValue, String layerURL, double resolution) throws Exception {
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GISDataConnector connector = getConnector(layerURL, resolution);
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zmin = connector.getMinZ(layerURL, layerName);
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zmax = connector.getMaxZ(layerURL, layerName);
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if (zValue < zmin)
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zValue = zmin;
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else if (zValue > zmax)
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zValue = zmax;
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return zValue;
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}
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/**
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* Extract a grid of XY points with fixed time and z
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*
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* @param layerTitle
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* @param timeInstant
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* @param x1
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* @param x2
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* @param y1
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* @param y2
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* @param z
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* @param xResolution
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* @param yResolution
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* @param cachelayer
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* @return
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* @throws Exception
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*/
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public double[][] extractXYGridWithFixedTZ(String layerTitle, int timeInstant, double x1, double x2, double y1, double y2, double z, double xResolution, double yResolution, boolean cachelayer) throws Exception {
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currentResolution = (double) (xResolution + yResolution) / 2d;
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boolean faolayer = false;
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if (layerTitle == null)
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layerTitle = "";
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if (layerTitle.toLowerCase().contains("MatrixExtractor->FAO aquatic species distribution map")) {
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AnalysisLogger.getLogger().debug("MatrixExtractor->FAO DISTRIBUTION LAYER ... TO APPY PATCH!");
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faolayer = true;
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}
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if ((x2 < x1) || (y2 < y1)) {
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AnalysisLogger.getLogger().debug("MatrixExtractor->ERROR: BAD BOUNDING BOX!!!");
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return new double[0][0];
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}
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// adjust the BB in the case of one single point
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if (x2 == x1) {
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x2 = x2 + (xResolution / 2d);
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x1 = x1 - (xResolution / 2d);
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}
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if (y2 == y1) {
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y2 = y2 + (yResolution / 2d);
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y1 = y1 - (yResolution / 2d);
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}
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if (log)
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AnalysisLogger.getLogger().debug("Bounding box: (" + x1 + "," + x2 + ";" + y1 + "," + y2 + ")");
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List<Tuple<Double>> tuples = VectorOperations.generateCoordinateTripletsInBoundingBox(x1, x2, y1, y2, z, xResolution, yResolution);
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if (log) {
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AnalysisLogger.getLogger().debug("MatrixExtractor->Building the points grid according to YRes:" + yResolution + " and XRes:" + xResolution);
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AnalysisLogger.getLogger().debug("MatrixExtractor->Assigning "+tuples.size()+" values to the grid");
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}
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// long t0=System.currentTimeMillis();
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currentTimeValues = getRawValuesInTimeInstantAndBoundingBox(layerTitle, timeInstant, tuples, x1, x2, y1, y2, currentResolution, cachelayer);
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currentTuples = tuples;
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// AnalysisLogger.getLogger().debug("Elapsed:"+(System.currentTimeMillis()-t0));
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double[][] slice = VectorOperations.vectorToMatix(currentTimeValues, x1, x2, y1, y2, xResolution, yResolution);
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if (log) {
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AnalysisLogger.getLogger().debug("Taken " + currentTimeValues.size() + " values");
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AnalysisLogger.getLogger().debug("MatrixExtractor->Reassigned:" + (slice.length * slice[0].length));
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}
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// applyNearestNeighbor();
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if (log)
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AnalysisLogger.getLogger().debug("Features map: rows " + slice.length + ", cols " + slice[0].length);
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return slice;
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}
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}
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