Algorithms for FAO Ocean Area codes
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineGeoSpatialExtension@111820 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
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@ -26,8 +26,8 @@ public class CSquaresCreator extends StandardLocalExternalAlgorithm {
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static String yDim = "Latitude_Column";
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static String inputTableParameter = "InputTable";
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static String outputTableParameter = "OutputTableName";
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static String resolutionParameter = "CSquare_Resolution";
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static String csquarecolumnName = "csquare_code";
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String resolutionParameter = "CSquare_Resolution";
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String codecolumnName = "csquare_code";
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String outTable = "";
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String outTableLabel = "";
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double resolution = 0.1;
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@ -79,7 +79,7 @@ public class CSquaresCreator extends StandardLocalExternalAlgorithm {
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String x = IOHelper.getInputParameter(config, xDim);
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String y = IOHelper.getInputParameter(config, yDim);
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String table = IOHelper.getInputParameter(config, inputTableParameter);
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outTable = ("csq_" + UUID.randomUUID()).replace("-", "");
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outTable = ("code_" + UUID.randomUUID()).replace("-", "");
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resolution = Double.parseDouble(IOHelper.getInputParameter(config, resolutionParameter));
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outTableLabel = IOHelper.getInputParameter(config, outputTableParameter);
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@ -88,23 +88,58 @@ public class CSquaresCreator extends StandardLocalExternalAlgorithm {
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status = 10;
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if (x == null || x.trim().length() == 0 || y == null || y.trim().length() == 0)
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throw new Exception("Error please provide information for the input layers");
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try{
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addCodeColumToTable(table);
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AnalysisLogger.getLogger().debug("CSquareCreator: finished");
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} catch (Throwable e) {
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throw new Exception(e.getMessage());
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} finally {
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status = 100;
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}
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}
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AnalysisLogger.getLogger().debug("CSquareCreator: initializing connection");
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public String selectInformationForTransformation (AlgorithmConfiguration config, String table, int limit, int offset){
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String x = IOHelper.getInputParameter(config, xDim);
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String y = IOHelper.getInputParameter(config, yDim);
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String select = "select *," + x + "," + y + " from " + table + " order by " + x + " limit " + limit + " offset " + offset;
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return select;
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}
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public String rowToCode (Object[] rowArray){
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// take x and y
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String xValue = "" + rowArray[rowArray.length - 2];
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String yValue = "" + rowArray[rowArray.length - 1];
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// generate csquarecodes
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String csquare = "";
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try {
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double xV = Double.parseDouble(xValue);
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double yV = Double.parseDouble(yValue);
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csquare = CSquareCodesConverter.convertAtResolution(yV, xV, resolution);
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} catch (Exception e) {
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}
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return csquare;
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}
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public void addCodeColumToTable(String table) throws Exception{
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AnalysisLogger.getLogger().debug("CodeCreator: initializing connection");
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long t0 = System.currentTimeMillis();
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try {
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connection = DatabaseUtils.initDBSession(config);
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AnalysisLogger.getLogger().debug("CSquareCreator: database: " + config.getDatabaseURL());
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AnalysisLogger.getLogger().debug("CodeCreator: database: " + config.getDatabaseURL());
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// create a new output table
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AnalysisLogger.getLogger().debug("CSquareCreator: dropping table " + outTable + " if exists");
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AnalysisLogger.getLogger().debug("CodeCreator: dropping table " + outTable + " if exists");
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try {
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(outTable), connection);
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("CSquareCreator: table " + outTable + " does not exist yet");
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AnalysisLogger.getLogger().debug("CodeCreator: table " + outTable + " does not exist yet");
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}
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AnalysisLogger.getLogger().debug("CSquareCreator: creating the new table " + outTable);
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AnalysisLogger.getLogger().debug("CodeCreator: creating the new table " + outTable);
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.createBlankTableFromAnotherStatement(table, outTable), connection);
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AnalysisLogger.getLogger().debug("CSquareCreator: adding new column to " + outTable);
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.addColumnStatement(outTable, csquarecolumnName, "character varying"), connection);
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AnalysisLogger.getLogger().debug("CSquareCreator: getting columns from " + outTable);
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AnalysisLogger.getLogger().debug("CodeCreator: adding new column to " + outTable);
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.addColumnStatement(outTable, codecolumnName, "character varying"), connection);
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AnalysisLogger.getLogger().debug("CodeCreator: getting columns from " + outTable);
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// get columns names
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List<Object> names = DatabaseFactory.executeSQLQuery(DatabaseUtils.getColumnsNamesStatement(outTable), connection);
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StringBuffer colnames = new StringBuffer();
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@ -114,42 +149,33 @@ public class CSquaresCreator extends StandardLocalExternalAlgorithm {
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if (i < nnames - 1)
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colnames.append(",");
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}
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AnalysisLogger.getLogger().debug("CSquareCreator: columns are: " + colnames.toString());
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AnalysisLogger.getLogger().debug("CSquareCreator: taking chunks ... ");
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AnalysisLogger.getLogger().debug("CodeCreator: columns are: " + colnames.toString());
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AnalysisLogger.getLogger().debug("CodeCreator: taking chunks ... ");
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// take chunks of the table
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int initIdx = 0;
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int limit = 5000;
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long maxRows = DatabaseUtils.estimateNumberofRows(table, connection);
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AnalysisLogger.getLogger().debug("CSquareCreator: estimated number of rows " + maxRows);
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AnalysisLogger.getLogger().debug("CodeCreator: estimated number of rows " + maxRows);
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status = 20;
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while (true) {
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String select = "select *," + x + "," + y + " from " + table + " order by " + x + " limit " + limit + " offset " + initIdx;
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AnalysisLogger.getLogger().debug("CSquareCreator: from " + initIdx + " to " + (initIdx + limit));
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String select = selectInformationForTransformation(config, table, limit, initIdx);
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AnalysisLogger.getLogger().debug("CodeCreator: from " + initIdx + " to " + (initIdx + limit));
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List<Object> rows = DatabaseFactory.executeSQLQuery(select, connection);
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if (rows == null || rows.size() == 0) {
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AnalysisLogger.getLogger().debug("CSquareCreator: no more rows");
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AnalysisLogger.getLogger().debug("CodeCreator: no more rows");
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break;
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}
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AnalysisLogger.getLogger().debug("CSquareCreator: transforming");
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AnalysisLogger.getLogger().debug("CodeCreator: transforming");
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// take x and y
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List<String[]> stringrows = new ArrayList<String[]>();
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for (Object row : rows) {
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Object[] rowArray = (Object[]) row;
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// take x and y
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String xValue = "" + rowArray[rowArray.length - 2];
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String yValue = "" + rowArray[rowArray.length - 1];
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// generate csquarecodes
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String csquare = "";
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try {
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double xV = Double.parseDouble(xValue);
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double yV = Double.parseDouble(yValue);
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csquare = CSquareCodesConverter.convertAtResolution(yV, xV, resolution);
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} catch (Exception e) {
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}
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rowArray[rowArray.length - 2] = csquare;
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String[] stringArray = new String[rowArray.length - 1];
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String code = rowToCode(rowArray);
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rowArray[nnames-1] = code;
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String[] stringArray = new String[nnames];
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// convert all the objects into Strings
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for (int k = 0; k < stringArray.length; k++) {
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stringArray[k] = "" + rowArray[k];
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@ -180,10 +206,9 @@ public class CSquaresCreator extends StandardLocalExternalAlgorithm {
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} finally {
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shutdown();
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AnalysisLogger.getLogger().debug("CSquareCreator finished in " + (System.currentTimeMillis() - t0) + " ms");
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status = 100;
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}
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}
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@Override
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public void shutdown() {
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AnalysisLogger.getLogger().debug("CSquareCreator shutdown");
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@ -0,0 +1,71 @@
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package org.gcube.dataanalysis.geo.algorithms;
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import java.util.ArrayList;
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import java.util.List;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType;
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import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
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import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
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import org.gcube.dataanalysis.ecoengine.utils.IOHelper;
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import org.gcube.dataanalysis.geo.utils.FAOOceanAreaConverter;
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public class FAOOceanAreaCreator extends CSquaresCreator {
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public FAOOceanAreaCreator(){
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resolutionParameter = "Resolution";
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codecolumnName = "fao_ocean_area";
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}
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@Override
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protected void setInputParameters() {
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List<TableTemplates> templates = new ArrayList<TableTemplates>();
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templates.add(TableTemplates.GENERIC);
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InputTable tinput = new InputTable(templates, inputTableParameter, "The table to which the algorithm adds the csquare column");
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inputs.add(tinput);
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ColumnType xDimension = new ColumnType(inputTableParameter, xDim, "The column containing Longitude information", "x", false);
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ColumnType yDimension = new ColumnType(inputTableParameter, yDim, "The column containing Latitude information", "y", false);
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inputs.add(xDimension);
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inputs.add(yDimension);
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IOHelper.addDoubleInput(inputs, resolutionParameter, "The resolution of the FAO Ocean Area codes", "5");
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IOHelper.addStringInput(inputs, outputTableParameter, "The name of the output table", "faooceanarea_");
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DatabaseType.addDefaultDBPars(inputs);
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}
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@Override
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public String getDescription() {
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return "An algorithm that adds a column containing the FAO Ocean Area codes associated to longitude and latitude columns.";
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}
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public String selectInformationForTransformation (AlgorithmConfiguration config, String table, int limit, int offset){
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String x = IOHelper.getInputParameter(config, xDim);
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String y = IOHelper.getInputParameter(config, yDim);
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String select = "select *," + x + "," + y + " from " + table + " order by " + x + " limit " + limit + " offset " + offset;
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return select;
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}
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public String rowToCode (Object[] rowArray){
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// take x and y
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String xValue = "" + rowArray[rowArray.length - 2];
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String yValue = "" + rowArray[rowArray.length - 1];
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// generate csquarecodes
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String code = "";
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try {
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double xV = Double.parseDouble(xValue);
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double yV = Double.parseDouble(yValue);
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FAOOceanAreaConverter converter = new FAOOceanAreaConverter();
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code = converter.FAOOceanArea(-1, xV, yV, (int)resolution);
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} catch (Exception e) {
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}
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return code;
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}
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}
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@ -0,0 +1,81 @@
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package org.gcube.dataanalysis.geo.algorithms;
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import java.util.ArrayList;
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import java.util.List;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType;
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import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
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import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
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import org.gcube.dataanalysis.ecoengine.utils.IOHelper;
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import org.gcube.dataanalysis.geo.utils.FAOOceanAreaConverter;
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public class FAOOceanAreaCreatorQuadrant extends FAOOceanAreaCreator {
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static String quadrantDim = "Quadrant_column";
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public FAOOceanAreaCreatorQuadrant(){
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super();
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}
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@Override
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protected void setInputParameters() {
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List<TableTemplates> templates = new ArrayList<TableTemplates>();
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templates.add(TableTemplates.GENERIC);
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InputTable tinput = new InputTable(templates, inputTableParameter, "The table to which the algorithm adds the csquare column");
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inputs.add(tinput);
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ColumnType xDimension = new ColumnType(inputTableParameter, xDim, "The column containing Longitude information", "x", false);
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ColumnType yDimension = new ColumnType(inputTableParameter, yDim, "The column containing Latitude information", "y", false);
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ColumnType quadrantDimension = new ColumnType(inputTableParameter, quadrantDim, "The column containing Quadrant information", "quadrant", false);
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inputs.add(xDimension);
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inputs.add(yDimension);
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inputs.add(quadrantDimension);
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IOHelper.addDoubleInput(inputs, resolutionParameter, "The resolution of the FAO Ocean Area codes", "5");
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IOHelper.addStringInput(inputs, outputTableParameter, "The name of the output table", "faooceanarea_");
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DatabaseType.addDefaultDBPars(inputs);
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}
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@Override
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public String getDescription() {
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return "An algorithm that adds a column containing the FAO Ocean Area codes associated to longitude, latitude and quadrant columns.";
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}
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@Override
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public String selectInformationForTransformation (AlgorithmConfiguration config, String table, int limit, int offset){
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String x = IOHelper.getInputParameter(config, xDim);
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String y = IOHelper.getInputParameter(config, yDim);
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String quadrant = IOHelper.getInputParameter(config, quadrantDim);
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String select = "select *," + x + "," + y +","+quadrant+ " from " + table + " order by " + x + " limit " + limit + " offset " + offset;
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return select;
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}
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@Override
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public String rowToCode (Object[] rowArray){
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// take x and y
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String xValue = "" + rowArray[rowArray.length - 3];
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String yValue = "" + rowArray[rowArray.length - 2];
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String quadrantValue = "" + rowArray[rowArray.length - 1];
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// generate csquarecodes
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String code = "";
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try {
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double xV = Double.parseDouble(xValue);
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double yV = Double.parseDouble(yValue);
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int quadrantV = (int)(Double.parseDouble(quadrantValue));
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FAOOceanAreaConverter converter = new FAOOceanAreaConverter();
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code = converter.FAOOceanArea(quadrantV, xV, yV, (int)resolution);
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} catch (Exception e) {
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}
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return code;
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}
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}
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@ -0,0 +1,41 @@
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package org.gcube.dataanalysis.geo.test;
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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.geo.algorithms.FAOOceanAreaCreator;
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public class TestFAOAreaCodesCreator {
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public static void main(String[] args) throws Exception{
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AnalysisLogger.setLogger("./cfg/" + AlgorithmConfiguration.defaultLoggerFile);
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AlgorithmConfiguration config = new AlgorithmConfiguration();
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config.setConfigPath("./cfg/");
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config.setPersistencePath("./");
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config.setParam("DatabaseUserName", "utente");
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config.setParam("DatabasePassword", "d4science");
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config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
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config.setParam("DatabaseDriver", "org.postgresql.Driver");
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// config.setParam("Longitude_Column", "centerlong");
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// config.setParam("Latitude_Column", "centerlat");
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config.setParam("Longitude_Column", "long");
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config.setParam("Latitude_Column", "lat");
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// config.setParam("InputTable", "interp_2024_linear_01355325354899");
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// config.setParam("InputTable", "interp_2036_linear_11384851795640");
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config.setParam("InputTable", "generic_id6ef3e4fa_6a06_4df1_9445_553f2e918102");
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config.setParam("OutputTableName", "csqout");
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config.setParam("Resolution", "5");
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config.setGcubeScope("/gcube/devsec/devVRE");
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FAOOceanAreaCreator cscreator = new FAOOceanAreaCreator();
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cscreator.setConfiguration(config);
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cscreator.compute();
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System.out.println("DONE! "+cscreator.getOutput());
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}
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}
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@ -0,0 +1,41 @@
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package org.gcube.dataanalysis.geo.test;
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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.geo.algorithms.FAOOceanAreaCreator;
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import org.gcube.dataanalysis.geo.algorithms.FAOOceanAreaCreatorQuadrant;
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public class TestFAOAreaCodesQuadrantCreator {
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public static void main(String[] args) throws Exception{
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AnalysisLogger.setLogger("./cfg/" + AlgorithmConfiguration.defaultLoggerFile);
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AlgorithmConfiguration config = new AlgorithmConfiguration();
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config.setConfigPath("./cfg/");
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config.setPersistencePath("./");
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config.setParam("DatabaseUserName", "utente");
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config.setParam("DatabasePassword", "d4science");
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config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
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config.setParam("DatabaseDriver", "org.postgresql.Driver");
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config.setParam("Quadrant_column", "quadrant");
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config.setParam("Longitude_Column", "long");
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config.setParam("Latitude_Column", "lat");
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config.setParam("InputTable", "generic_id6ef3e4fa_6a06_4df1_9445_553f2e918102");
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// config.setParam("InputTable", "interp_2036_linear_11384851795640");
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// config.setParam("InputTable", "generic_id35e6ded3_4adc_48ba_a575_35a02b67514a");
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config.setParam("OutputTableName", "csqout");
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config.setParam("Resolution", "5");
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config.setGcubeScope("/gcube/devsec/devVRE");
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FAOOceanAreaCreatorQuadrant cscreator = new FAOOceanAreaCreatorQuadrant();
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cscreator.setConfiguration(config);
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cscreator.compute();
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System.out.println("DONE! "+cscreator.getOutput());
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}
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}
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@ -0,0 +1,97 @@
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package org.gcube.dataanalysis.geo.utils;
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public class FAOOceanAreaConverter {
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public static void main(String[] args) {
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FAOOceanAreaConverter converter = new FAOOceanAreaConverter();
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int quadrant = -1;
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//double longitude = 12.5;
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//double latitude = 12.5;
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//double longitude = 129;
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//double latitude = -29;
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double longitude = -1;
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double latitude = -56.1;
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int resolution = 5;
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String conv = converter.FAOOceanArea(quadrant, longitude, latitude, resolution);
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System.out.println(conv);
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||||
}
|
||||
|
||||
public String padLongitude(int longitude){
|
||||
String longi = ""+longitude;
|
||||
if (longi.length()==1)
|
||||
longi = "00"+longi;
|
||||
else if (longi.length()==2)
|
||||
longi = "0"+longi;
|
||||
return longi;
|
||||
}
|
||||
|
||||
public String padLatitude(int latitude){
|
||||
String lati = ""+latitude;
|
||||
if (lati.length()==1)
|
||||
lati = "0"+lati;
|
||||
return lati;
|
||||
}
|
||||
|
||||
public int getQuadrant(double longitude,double latitude){
|
||||
if (longitude>=0 && latitude>=0)
|
||||
return 1;
|
||||
else if (longitude>=0 && latitude<0)
|
||||
return 2;
|
||||
else if (longitude<0 && latitude<0)
|
||||
return 3;
|
||||
else
|
||||
return 4;
|
||||
}
|
||||
|
||||
public int[] getBounding(int resolution, double dimension){
|
||||
|
||||
int lowDim = (int)(resolution*Math.floor(dimension/resolution));
|
||||
int upDim = (int) (resolution*Math.ceil(dimension/resolution));
|
||||
int[] bounding = {lowDim,upDim};
|
||||
return bounding;
|
||||
}
|
||||
|
||||
public double getDistanceFromCenter(double x, double y){
|
||||
return Math.sqrt(x*x+y*y);
|
||||
}
|
||||
|
||||
public String FAOOceanArea(int quadrant, double longitude,double latitude, int resolution){
|
||||
|
||||
if (quadrant<=0||quadrant>4){
|
||||
quadrant = getQuadrant(longitude, latitude);
|
||||
}
|
||||
if (longitude>180 || longitude<-180)
|
||||
return null;
|
||||
if (latitude>90 || latitude<-90)
|
||||
return null;
|
||||
if (resolution<=0 || resolution>90)
|
||||
return null;
|
||||
|
||||
double alongitude = Math.abs(longitude);
|
||||
double alatitude = Math.abs(latitude);
|
||||
int [] bblons = getBounding(resolution, alongitude);
|
||||
int [] bblats = getBounding(resolution, alatitude);
|
||||
int bestlon = -1;
|
||||
int bestlat = -1;
|
||||
double bestdist = Double.MAX_VALUE;
|
||||
for (int bblon:bblons){
|
||||
for (int bblat:bblats){
|
||||
double dist = getDistanceFromCenter(bblon, bblat);
|
||||
if (dist<bestdist){
|
||||
bestdist=dist;
|
||||
bestlon = bblon;
|
||||
bestlat = bblat;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
String FaoOceanArea = quadrant+padLatitude(bestlat)+padLongitude(bestlon);
|
||||
if (FaoOceanArea.length()!=6)
|
||||
return null;
|
||||
|
||||
return FaoOceanArea;
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue