modifications to add Cohens kappa
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineGeoSpatialExtension@76856 82a268e6-3cf1-43bd-a215-b396298e98cf
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900e8ba880
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2f172d69d4
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@ -26,21 +26,21 @@ import org.jfree.data.general.DatasetUtilities;
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import org.jfree.data.xy.XYSeriesCollection;
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import org.opengis.metadata.Metadata;
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public class MapsComparator extends StandardLocalExternalAlgorithm{
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public class MapsComparator extends StandardLocalExternalAlgorithm {
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static String layer1 = "LayerTitle_1";
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static String layer2 = "LayerTitle_2";
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static String zString = "Z";
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static String t1 = "TimeIndex_1";
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static String t2 = "TimeIndex_2";
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static String valuesThr = "ValuesComparisonThreshold";
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protected SessionFactory dbConnection;
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@Override
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public void init() throws Exception {
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AnalysisLogger.getLogger().debug("Initialization");
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}
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@Override
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@ -58,174 +58,188 @@ public class MapsComparator extends StandardLocalExternalAlgorithm{
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String valuesthr$ = getInputParameter(valuesThr);
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String time1$ = getInputParameter(t1);
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String time2$ = getInputParameter(t2);
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int time1 = ((time1$!=null) && (time1$.trim().length()>0))? Integer.parseInt(time1$):0;
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int time2 = ((time2$!=null) && (time2$.trim().length()>0))? Integer.parseInt(time2$):0;
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if (time1<0)
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time1=0;
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if (time2<0)
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time2=0;
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int time1 = ((time1$ != null) && (time1$.trim().length() > 0)) ? Integer.parseInt(time1$) : 0;
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int time2 = ((time2$ != null) && (time2$.trim().length() > 0)) ? Integer.parseInt(time2$) : 0;
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if (time1 < 0)
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time1 = 0;
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if (time2 < 0)
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time2 = 0;
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double valuesthreshold = 0.1;
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if ((valuesthr$!=null)&&(valuesthr$.trim().length()>0))
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try{valuesthreshold =Double.parseDouble(valuesthr$);}catch(Exception ee){}
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if ((valuesthr$ != null) && (valuesthr$.trim().length() > 0))
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try {
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valuesthreshold = Double.parseDouble(valuesthr$);
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} catch (Exception ee) {
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}
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double z = 0;
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if ((z$!=null)&&(z$.trim().length()>0))
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try{z =Double.parseDouble(z$);}catch(Exception ee){}
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try{
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if ((z$ != null) && (z$.trim().length() > 0))
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try {
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z = Double.parseDouble(z$);
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} catch (Exception ee) {
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}
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try {
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String scope = config.getGcubeScope();
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AnalysisLogger.getLogger().debug("MapsComparator: Using Scope: "+scope+" Z: "+z+" Values Threshold: "+valuesthreshold+" Layer1: "+layerT1+" vs "+layerT2);
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AnalysisLogger.getLogger().debug("MapsComparator: Using Scope: " + scope + " Z: " + z + " Values Threshold: " + valuesthreshold + " Layer1: " + layerT1 + " vs " + layerT2);
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GeoIntersector intersector = new GeoIntersector(scope, config.getConfigPath());
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AnalysisLogger.getLogger().debug("MapsComparator: GeoIntersector initialized");
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double x1 = -180;
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double x2 = 180;
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double y1 = -90;
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double y2 = 90;
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status = 10;
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FeaturesManager fm = intersector.getFeaturer();
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AnalysisLogger.getLogger().debug("MapsComparator: Taking info for the layer: "+layerT1);
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Metadata meta1 = fm.checkForMetadatabyTitle(FeaturesManager.treatTitleForGN(layerT1), layerT1);
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double resolution1 = FeaturesManager.getResolution(meta1);
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AnalysisLogger.getLogger().debug("MapsComparator: Resolution: "+resolution1);
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FeaturesManager fm = intersector.getFeaturer();
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AnalysisLogger.getLogger().debug("MapsComparator: Taking info for the layer: " + layerT1);
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Metadata meta1 = fm.getGNInfobyUUIDorName(layerT1);
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if (meta1==null) throw new Exception("No Correspondence with Layer 1");
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double resolution1 = 0;
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try {
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resolution1 = FeaturesManager.getResolution(meta1);
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("MapsComparator: Undefined resolution");
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}
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AnalysisLogger.getLogger().debug("MapsComparator: Resolution: " + resolution1);
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status = 15;
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AnalysisLogger.getLogger().debug("MapsComparator: Taking info for the layer: "+layerT2);
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Metadata meta2 = fm.checkForMetadatabyTitle(FeaturesManager.treatTitleForGN(layerT2), layerT2);
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double resolution2 = FeaturesManager.getResolution(meta2);
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AnalysisLogger.getLogger().debug("MapsComparator: Resolution: "+resolution2);
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status = 20;
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//take the lowest resolution to perform the comparison
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double resolution = Math.max(resolution1, resolution2);
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if (resolution==0)
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resolution = 0.5d;
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AnalysisLogger.getLogger().debug("MapsComparator: Evaluation Resolution: "+resolution);
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AnalysisLogger.getLogger().debug("MapsComparator: Taking info for the layer: " + layerT2);
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AnalysisLogger.getLogger().debug("MapsComparator: Trying with UUID..." + layerT2);
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Metadata meta2 = fm.getGNInfobyUUIDorName(layerT2);
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if (meta2==null) throw new Exception("No Correspondence with Layer 2");
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double resolution2 = 0;
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try {
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resolution2 = FeaturesManager.getResolution(meta2);
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("MapsComparator: Undefined resolution");
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}
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AnalysisLogger.getLogger().debug("MapsComparator: Resolution: " + resolution2);
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status = 20;
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// take the lowest resolution to perform the comparison
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double resolution = Math.max(resolution1, resolution2);
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if (resolution == 0)
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resolution = 0.5d;
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AnalysisLogger.getLogger().debug("MapsComparator: Evaluation Resolution: " + resolution);
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AnalysisLogger.getLogger().debug("MapsComparator: ****Rasterizing map 1****");
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double[][] slice1 = intersector.takeTimeSlice(layerT1, time1, x1, x2, y1,y2,z,resolution,resolution);
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double[][] slice1 = intersector.takeTimeSlice(layerT1, time1, x1, x2, y1, y2, z, resolution, resolution);
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AnalysisLogger.getLogger().debug("MapsComparator: Dumping map 1");
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status = 30;
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RasterTable raster1 = new RasterTable(x1, x2, y1, y2, z, resolution, resolution, slice1, config);
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raster1.dumpGeoTable();
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String rastertable1 = raster1.getTablename();
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AnalysisLogger.getLogger().debug("MapsComparator: Map 1 was dumped in table: "+rastertable1);
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AnalysisLogger.getLogger().debug("MapsComparator: Map 1 was dumped in table: " + rastertable1);
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status = 40;
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AnalysisLogger.getLogger().debug("MapsComparator: ****Rasterizing map 2****");
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double[][] slice2 = intersector.takeTimeSlice(layerT2, time2, x1, x2, y1,y2,z,resolution,resolution);
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double[][] slice2 = intersector.takeTimeSlice(layerT2, time2, x1, x2, y1, y2, z, resolution, resolution);
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AnalysisLogger.getLogger().debug("MapsComparator: Dumping map 2");
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status = 50;
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RasterTable raster2 = new RasterTable(x1, x2, y1, y2, z, resolution, resolution, slice2, config);
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raster2.dumpGeoTable();
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String rastertable2 = raster2.getTablename();
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AnalysisLogger.getLogger().debug("MapsComparator: Map 2 was dumped in table: "+rastertable2);
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AnalysisLogger.getLogger().debug("MapsComparator: Map 2 was dumped in table: " + rastertable2);
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status = 60;
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/*
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String rastertable1 = "rstr909f60c1d3f1472e9de998e844990724";
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String rastertable2 = "rstre52e744c99224de3a1c5354263c6c8d8";
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String resolution = "0.5";
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*/
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* String rastertable1 = "rstr909f60c1d3f1472e9de998e844990724"; String rastertable2 = "rstre52e744c99224de3a1c5354263c6c8d8"; String resolution = "0.5";
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*/
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config.setNumberOfResources(1);
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config.setParam("FirstTable", rastertable1);
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config.setParam("SecondTable", rastertable2);
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config.setParam("FirstTableCsquareColumn", RasterTable.csquareColumn);
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config.setParam("SecondTableCsquareColumn",RasterTable.csquareColumn);
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config.setParam("SecondTableCsquareColumn", RasterTable.csquareColumn);
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config.setParam("FirstTableProbabilityColumn", RasterTable.probabilityColumn);
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config.setParam("SecondTableProbabilityColumn", RasterTable.probabilityColumn);
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config.setParam("ComparisonThreshold", ""+valuesthreshold);
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AnalysisLogger.getLogger().debug("MapsComparator: Analyzing discrepancy between maps: "+rastertable1+" and "+rastertable2);
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config.setParam("ComparisonThreshold", "" + valuesthreshold);
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AnalysisLogger.getLogger().debug("MapsComparator: Analyzing discrepancy between maps: " + rastertable1 + " and " + rastertable2);
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DiscrepancyAnalysis da = new DiscrepancyAnalysis();
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da.setConfiguration(config);
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da.init(false);
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outputParameters = da.analyze();
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outputParameters.put("Resolution", ""+resolution);
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outputParameters.put("Resolution", "" + resolution);
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status = 80;
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AnalysisLogger.getLogger().debug("MapsComparator: Output: "+outputParameters);
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//delete the tables
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AnalysisLogger.getLogger().debug("MapsComparator: Output: " + outputParameters);
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// delete the tables
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dbConnection = DatabaseUtils.initDBSession(config);
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AnalysisLogger.getLogger().debug("MapsComparator: Deleting table "+rastertable1);
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(rastertable1),dbConnection);
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AnalysisLogger.getLogger().debug("MapsComparator: Deleting table " + rastertable1);
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(rastertable1), dbConnection);
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status = 90;
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AnalysisLogger.getLogger().debug("MapsComparator: Deleting table "+rastertable2);
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(rastertable2),dbConnection);
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AnalysisLogger.getLogger().debug("MapsComparator: Elapsed: Whole operation completed in "+((double)(System.currentTimeMillis()-t0)/1000d)+"s");
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}catch(Exception e){
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AnalysisLogger.getLogger().debug("MapsComparator: Deleting table " + rastertable2);
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(rastertable2), dbConnection);
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AnalysisLogger.getLogger().debug("MapsComparator: 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("MapsComparator: ERROR!: "+e.getLocalizedMessage());
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}
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finally{
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AnalysisLogger.getLogger().debug("MapsComparator: ERROR!: " + e.getLocalizedMessage());
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} finally {
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DatabaseUtils.closeDBConnection(dbConnection);
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status = 100;
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}
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}
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@Override
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protected void setInputParameters() {
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addStringInput(layer1,"First Layer Title: The title of a layer indexed in the e-Infrastructure on GeoNetwork","Sarda australis");
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addStringInput(layer2,"Second Layer Title: The title of a second layer indexed in the e-Infrastructure on GeoNetwork","Sarda orientalis");
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addNumberInput(zString,"value of Z. Default is 0, that means comparison will be at surface level","0");
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addNumberInput(valuesThr,"A comparison threshold for the values in the map. Null equals to 0.1","0.1");
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addNumberInput(t1,"First Layer Time Index. The default is the first","0");
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addNumberInput(t2,"Second Layer Time Index. The default is the first","0");
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addStringInput(layer1, "First Layer Title or UUID: The title or the UUID (preferred) of a layer indexed in the e-Infrastructure on GeoNetwork - You can retrieve it from GeoExplorer", "Sarda australis");
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addStringInput(layer2, "Second Layer Title or UUID: The title or the UUID (preferred) of a second layer indexed in the e-Infrastructure on GeoNetwork - You can retrieve it from GeoExplorer", "Sarda orientalis");
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addNumberInput(zString, "value of Z. Default is 0, that means comparison will be at surface level", "0");
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addNumberInput(valuesThr, "A comparison threshold for the values in the map. Null equals to 0.1", "0.1");
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addNumberInput(t1, "First Layer Time Index. The default is the first", "0");
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addNumberInput(t2, "Second Layer Time Index. The default is the first", "0");
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addNumberInput("KThreshold", "Threshold for K-Statistic: over this threshold values will be considered 1 for agreement calculation. Default is 0.5","0.5");
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DatabaseType.addDefaultDBPars(inputs);
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}
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@Override
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public void shutdown() {
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AnalysisLogger.getLogger().debug("Shutdown");
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}
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@Override
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public StatisticalType getOutput() {
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//set the output map containing values
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PrimitiveType p = new PrimitiveType(Map.class.getName(), PrimitiveType.stringMap2StatisticalMap(outputParameters), PrimitiveTypes.MAP, "Discrepancy Analysis","");
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AnalysisLogger.getLogger().debug("MapsComparator: Producing Gaussian Distribution for the errors");
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//build image:
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// set the output map containing values
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PrimitiveType p = new PrimitiveType(Map.class.getName(), PrimitiveType.stringMap2StatisticalMap(outputParameters), PrimitiveTypes.MAP, "Discrepancy Analysis", "");
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AnalysisLogger.getLogger().debug("MapsComparator: Producing Gaussian Distribution for the errors");
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// build image:
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HashMap<String, Image> producedImages = new HashMap<String, Image>();
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//gaussian
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XYSeriesCollection xyseriescollection = new XYSeriesCollection();
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double mean = Double.parseDouble(outputParameters.get("MEAN"));
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double variance = Double.parseDouble(outputParameters.get("VARIANCE"));
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if (variance==0)
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variance=0.01;
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AnalysisLogger.getLogger().debug("MapsComparator: Adopting mean:"+ mean+" and variance:"+variance);
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NormalDistributionFunction2D normaldistributionfunction2d = new NormalDistributionFunction2D(mean,variance);
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org.jfree.data.xy.XYSeries xyseries = DatasetUtilities.sampleFunction2DToSeries(normaldistributionfunction2d, (mean-(2*variance)), (mean+(2*variance)), 121, "Distribution of the Error");
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xyseriescollection.addSeries(xyseries);
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//end gaussian
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JFreeChart chart = GaussianDistributionGraph.createStaticChart(xyseriescollection, mean, variance);
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Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
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producedImages.put("Gaussian Distribution of the Error", image);
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// gaussian
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XYSeriesCollection xyseriescollection = new XYSeriesCollection();
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double mean = Double.parseDouble(outputParameters.get("MEAN"));
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double variance = Double.parseDouble(outputParameters.get("VARIANCE"));
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if (variance == 0)
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variance = 0.01;
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AnalysisLogger.getLogger().debug("MapsComparator: Adopting mean:" + mean + " and variance:" + variance);
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NormalDistributionFunction2D normaldistributionfunction2d = new NormalDistributionFunction2D(mean, variance);
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org.jfree.data.xy.XYSeries xyseries = DatasetUtilities.sampleFunction2DToSeries(normaldistributionfunction2d, (mean - (2 * variance)), (mean + (2 * variance)), 121, "Distribution of the Error");
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xyseriescollection.addSeries(xyseries);
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// end gaussian
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JFreeChart chart = GaussianDistributionGraph.createStaticChart(xyseriescollection, mean, variance);
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Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
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producedImages.put("Gaussian Distribution of the Error", image);
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PrimitiveType images = new PrimitiveType(HashMap.class.getName(), producedImages, PrimitiveTypes.IMAGES, "ErrorRepresentation", "Graphical representation of the error spread");
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/*
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GaussianDistributionGraph graph = new GaussianDistributionGraph("Error Distribution");
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graph.mean=mean;graph.variance=variance;
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graph.render(xyseriescollection);
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*/
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//end build image
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* GaussianDistributionGraph graph = new GaussianDistributionGraph("Error Distribution"); graph.mean=mean;graph.variance=variance; graph.render(xyseriescollection);
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*/
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// end build image
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AnalysisLogger.getLogger().debug("MapsComparator: Gaussian Distribution Produced");
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//collect all the outputs
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// collect all the outputs
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LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
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map.put("Result", p);
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map.put("Images", images);
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//generate a primitive type for the collection
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// generate a primitive type for the collection
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PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map, PrimitiveTypes.MAP, "ResultsMap", "Results Map");
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return output;
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}
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