Removed marytts-d4science #20135
This commit is contained in:
Giancarlo Panichi
parent
d82ca437d8
commit
49ff55c145
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@ -1,5 +1,5 @@
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# Changelog
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## [1.5.2] 2021-01-18
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## [1.5.2-SNAPSHOT] 2021-01-18
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- update gis-interface lower bound range
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- replaced repositories defined into the pom with the new nexus url (nexus.d4science.org). update version to 1.5.2-SNAPSHOT
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2
pom.xml
2
pom.xml
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@ -9,7 +9,7 @@
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</parent>
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<groupId>org.gcube.dataanalysis</groupId>
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<artifactId>ecological-engine-geospatial-extensions</artifactId>
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<version>1.5.2</version>
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<version>1.5.2-SNAPSHOT</version>
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<name>ecological-engine-geospatial-extensions</name>
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<description>ecological-engine-geospatial-extension</description>
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@ -1,227 +0,0 @@
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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.PeriodicityDetector;
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import org.gcube.dataanalysis.ecoengine.signals.SignalConverter;
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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.TimeSeriesExtractor;
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public class TimeExtraction extends XYExtraction{
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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 static String samplingFrequency = "SamplingFreq";
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public static String minFrequency = "MinFrequency";
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public static String maxFrequency = "MaxFrequency";
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public static String expectedFrequencyError = "FrequencyError";
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public static String FFTSamplesParam = "FFTSamples";
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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 int samplingFrequencyValue;
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public double minFrequencyValue;
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public double maxFrequencyValue;
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public double expectedFrequencyErrorValue;
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public int FFTSamples;
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public PeriodicityDetector pd;
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public double signal[];
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public double timeline[];
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@Override
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public String getDescription() {
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return "An algorithm to extract a time series of values associated to a geospatial features repository (e.g. NETCDF, ASC, GeoTiff files etc. ). The algorithm analyses the time series and automatically searches for hidden periodicities. It produces one chart of the time series, one table containing the time series values and possibly the spectrogram.";
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}
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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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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(7));
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IOHelper.addDoubleInput(inputs, resolution, "Extraction point resolution", "0.5");
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IOHelper.addIntegerInput(inputs, samplingFrequency, "Sampling frequency in Hz. Leave it to -1 if unknown or under 1", "-1");
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// IOHelper.addDoubleInput(inputs, minFrequency, "Minimum expected frequency in Hz. Can be decimal", "-1");
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// IOHelper.addDoubleInput(inputs, maxFrequency, "Maximum expected frequency in Hz. Can be decimal", "-1");
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//IOHelper.addDoubleInput(inputs, expectedFrequencyError, "Expected precision on periodicity detection in Hz or 1/samples. Can be decimal and depends on the signal length. Default is 0.1", "0.1");
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// IOHelper.addIntegerInput(inputs, FFTSamplesParam, "Number of samples to use in the Fourier Analysis. All samples will be used at maximum.", "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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zValue = Double.parseDouble(IOHelper.getInputParameter(config, z));
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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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samplingFrequencyValue=Integer.parseInt(IOHelper.getInputParameter(config, samplingFrequency));
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// minFrequencyValue=Double.parseDouble(IOHelper.getInputParameter(config, minFrequency));
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// maxFrequencyValue=Double.parseDouble(IOHelper.getInputParameter(config, maxFrequency));
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expectedFrequencyErrorValue=-1;
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AnalysisLogger.getLogger().debug("Extraction: Z " + zValue);
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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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AnalysisLogger.getLogger().debug("Extraction: SamplingF " + samplingFrequency);
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AnalysisLogger.getLogger().debug("Extraction: minF " + minFrequencyValue);
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AnalysisLogger.getLogger().debug("Extraction: maxF " + maxFrequencyValue);
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AnalysisLogger.getLogger().debug("Extraction: expectedError " + expectedFrequencyErrorValue);
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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 = 10;
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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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TimeSeriesExtractor intersector = new TimeSeriesExtractor(config);
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long t0 = System.currentTimeMillis();
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//take best z
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zValue = intersector.correctZ(zValue, layerNameValue, resolutionValue);
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AnalysisLogger.getLogger().debug("TimeExtraction->Best Z for this reference layer: " + zValue);
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outputParameters.put("Matching Z value in the layer", ""+zValue);
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outputParameters.put("Min Z value in the Layer", ""+intersector.zmin);
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outputParameters.put("Max Z value in the Layer", ""+intersector.zmax);
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AnalysisLogger.getLogger().debug("Z allowed to be: "+zValue);
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signal = intersector.extractT(layerNameValue, xValue,yValue, zValue, 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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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 (intersector.currentconnector instanceof WFS)
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polygonsFeatures = ((WFS) intersector.currentconnector).getPolygonsFeatures();
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RasterTable raster = new RasterTable(xValue, xValue, yValue, yValue, zValue, resolutionValue, resolutionValue, matrix, polygonsFeatures, config);
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int signalRate = 1;
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if (samplingFrequencyValue>0)
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signalRate=samplingFrequencyValue;
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timeline = SignalConverter.signalTimeLine(signal.length, signalRate);
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List<Tuple<Double>> coordinates=new ArrayList<Tuple<Double>>();
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for (int i=0;i<timeline.length;i++)
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coordinates.add(new Tuple<Double>(xValue,yValue,zValue,timeline[i]));
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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, timeline, "Signal");
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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 (signal!=null && signal.length>0){
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HashMap<String, Image> producedImages = new HashMap<String, Image>();
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if (signalimage!=null)
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producedImages.put("Time Series Visualization", signalimage);
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if (spectrogramImage!=null)
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producedImages.put("Spectrogram", spectrogramImage);
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/*
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try {
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ImageIO.write(ImageTools.toBufferedImage(signalimage), "png", new File("signal.png"));
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ImageIO.write(ImageTools.toBufferedImage(spectrogramImage), "png", new File("spectrogram.png"));
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} catch (IOException e) {
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e.printStackTrace();
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}
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*/
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PrimitiveType images = new PrimitiveType("Images", producedImages, PrimitiveTypes.IMAGES, "Signal Processing", "Visualization of the signal and spectrogram");
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for (String key:outputParameters.keySet()){
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String value = outputParameters.get(key);
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PrimitiveType val = new PrimitiveType(String.class.getName(), "" + value, PrimitiveTypes.STRING, key, key);
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map.put(key, val);
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}
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map.put("Images", images);
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}
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else
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map.put("Note", new PrimitiveType(String.class.getName(), "The signal contains only one point. The charts will not be displayed.", PrimitiveTypes.STRING,"Note","Note about the signal"));
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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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@ -1,193 +0,0 @@
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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");
|
||||
map.put("OutputTable", p);
|
||||
if (signalimage!=null){
|
||||
HashMap<String, Image> producedImages = new HashMap<String, Image>();
|
||||
producedImages.put("Z Modulations Visualization", signalimage);
|
||||
PrimitiveType images = new PrimitiveType("Images", producedImages, PrimitiveTypes.IMAGES, "Modulations of Z", "The modulations of Z");
|
||||
map.put("Images", images);
|
||||
}
|
||||
|
||||
// generate a primitive type for the collection
|
||||
PrimitiveType outputm = new PrimitiveType(HashMap.class.getName(), map, PrimitiveTypes.MAP, "ResultsMap", "Results Map");
|
||||
|
||||
return outputm;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue