From 70931d99609be0a95cc0cae807df9d042fb99cd3 Mon Sep 17 00:00:00 2001
From: Gianpaolo Coro <gianpaolo.coro@isti.cnr.it>
Date: Fri, 3 May 2013 09:28:20 +0000
Subject: [PATCH] git-svn-id:
 https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineGeoSpatialExtension@74469
 82a268e6-3cf1-43bd-a215-b396298e98cf

---
 .../geo/retrieval/GeoIntersector.java         | 55 ++++++++++++-------
 1 file changed, 35 insertions(+), 20 deletions(-)

diff --git a/src/main/java/org/gcube/dataanalysis/geo/retrieval/GeoIntersector.java b/src/main/java/org/gcube/dataanalysis/geo/retrieval/GeoIntersector.java
index cc6bcea..243b829 100644
--- a/src/main/java/org/gcube/dataanalysis/geo/retrieval/GeoIntersector.java
+++ b/src/main/java/org/gcube/dataanalysis/geo/retrieval/GeoIntersector.java
@@ -58,8 +58,8 @@ public class GeoIntersector {
 		return features;
 	}
 
-	public List<LinkedHashMap<String, Double>> getFeaturesInTime(String layerTitle, List<Tuple<Double>> triplets) throws Exception {
-		List<LinkedHashMap<String, Double>> featuresSets = new ArrayList<LinkedHashMap<String, Double>>();
+	public List<Double> getFeaturesInTimeInstant(String layerTitle, int time, List<Tuple<Double>> triplets, double xL,double xR, double yL, double yR) throws Exception {
+		List<Double> features = new ArrayList<Double>();
 		// get the layer
 		Metadata meta = featurer.checkForMetadatabyTitle(FeaturesManager.treatTitleForGN(layerTitle), layerTitle);
 		// if the layer is good
@@ -72,6 +72,8 @@ public class GeoIntersector {
 				Identification id = meta.getIdentificationInfo().iterator().next();
 				String title = id.getCitation().getTitle().toString();
 				AnalysisLogger.getLogger().debug("found a netCDF file with title " + title + " and layer name " + layer);
+				features  = getFeaturesFromNetCDF(featurer.getOpenDapLink(meta), layer, time, triplets, xL,xR, yL, yR);
+				/*
 				for (Tuple<Double> triplet : triplets) {
 					double x = triplet.getElements().get(0);
 					double y = triplet.getElements().get(1);
@@ -84,9 +86,11 @@ public class GeoIntersector {
 					AnalysisLogger.getLogger().debug("Got: (" + features + ")");
 					featuresSets.add(features);
 				}
-
+				 */
 			} else {
+				//TODO: adjust WFS take
 				AnalysisLogger.getLogger().debug("found a Geo Layer with title " + layerTitle + " and layer name " + layer);
+				/*
 				for (Tuple<Double> triplet : triplets) {
 					double x = triplet.getElements().get(0);
 					double y = triplet.getElements().get(1);
@@ -95,12 +99,19 @@ public class GeoIntersector {
 					features = getFeaturesFromWFS(featurer.getWFSLink(meta), layer, x, y);
 					featuresSets.add(features);
 				}
+				*/
 			}
 		}
-
-		return featuresSets;
+		return features;
 	}
 
+	private List<Double> getFeaturesFromNetCDF(String opendapURL, String layer, int time, List<Tuple<Double>> triplets, double xL,double xR, double yL, double yR) {
+		if (opendapURL == null)
+			return null;
+
+		return ThreddsDataExplorer.retrieveDataFromNetCDF(opendapURL, layer, time, triplets, xL,xR, yL, yR);
+	}
+	
 	private LinkedHashMap<String, Double> getFeaturesFromNetCDF(String opendapURL, String layer, double x, double y, double z) {
 		if (opendapURL == null)
 			return null;
@@ -140,52 +151,56 @@ public class GeoIntersector {
 			}
 		}
 
-		AnalysisLogger.getLogger().debug("Taking " + ysteps + " values...");
-		List<LinkedHashMap<String, Double>> time = getFeaturesInTime(layerTitle, tuples);
+		AnalysisLogger.getLogger().debug("Taking " + ysteps + " values per "+xsteps+"="+(ysteps*xsteps)+ "...");
+		List<Double> time = getFeaturesInTimeInstant(layerTitle, 0, tuples, x1, x2, y1,y2);
 		AnalysisLogger.getLogger().debug("Taken " + time.size() + " values");
 
 		// build back the values matrix
 		int k = 0;
 		int g = 0;
-		int ntriplets = ysteps * xsteps;
+		int ntriplets = time.size();
 		//cycle on all the triplets to recontruct the matrix
 		for (int t = 0; t < ntriplets; t++) {
 			//take the corresponding (time,value) pair
-			LinkedHashMap<String, Double> tvalues = time.get(t);
+			Double value = time.get(t);
 			//if there is value, then set it, otherwise set NaN
 			//the layer is undefined in that point and a value must be generated
-			double value = Double.NaN;
-			for (Double val : tvalues.values()) {
-				value = val;
-				break;
-			}
 			//assign a value to the matrix
 			slice[k][g] = value;
 			//increase the x step according to the matrix
-			g++;
 			if (g == xsteps) {
 				g = 0;
 				k++;
 			}
+			else
+				g++;
 		}
 		AnalysisLogger.getLogger().debug("Applying nearest Neighbor to all the rows");
 		//apply nearest neighbor to each row
 		AlgorithmConfiguration config = new AlgorithmConfiguration();
 		config.setConfigPath(configDir);
+		boolean rapidinit = false;
 		for (int i=0;i<slice.length;i++){
-			AnalysisLogger.getLogger().debug("Checking for unfilled values");
+//			AnalysisLogger.getLogger().debug("Checking for unfilled values");
 			boolean tofill = false;
 			for (int j=0;j<slice[i].length;j++) {
-				if (slice[i][j]==Double.NaN)
+				if (new Double(slice[i][j]).equals(Double.NaN))
 					tofill = true;
 			}
 			if (tofill){
+				if (!rapidinit){
+					config.initRapidMiner();
+					rapidinit=true;
+				}
 				AnalysisLogger.getLogger().debug("Filling signal");
-				slice[i] = SignalProcessing.fillSignal(slice[i]);
+				double[] ssliced = SignalProcessing.fillSignal(slice[i]);
+				slice[i] = ssliced;
 			}
-			else
-				AnalysisLogger.getLogger().debug("Signal yet complete");
+//			else
+//				AnalysisLogger.getLogger().debug("Signal yet complete");
 		}
+		
+		AnalysisLogger.getLogger().debug("Features map: "+slice.length+","+slice[0].length);
 		return slice;
 	}
 }