WIP: N5Exporter - first look

vcell-core/src/main/java/cbit/vcell/simdata/n5/N5Exporter.java

@@ -0,0 +1,48 @@
+package cbit.vcell.simdata.n5;
+
+import cbit.vcell.export.server.ExportConstants;
+import cbit.vcell.resource.PropertyLoader;
+import cbit.vcell.simdata.*;
+import cbit.vcell.solver.VCSimulationDataIdentifier;
+import cbit.vcell.solver.VCSimulationIdentifier;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.vcell.util.document.KeyValue;
+import org.vcell.util.document.User;
+
+import java.io.File;
+import java.util.Arrays;
+
+public class N5Exporter implements ExportConstants {
+    private final static Logger lg = LogManager.getLogger(N5Exporter.class);
+
+    public N5Exporter() {
+
+    }
+
+    public static void main(String[] args) throws Exception {
+        String primaryDirStr = "~/.vcell/simdata/temp";
+        PropertyLoader.loadProperties();
+        //System.setProperty(PropertyLoader.installationRoot,"/Users/schaff/workspace/vcell");
+        User user = new User("schaff", new KeyValue("17"));
+        KeyValue simKey = new KeyValue("1128909032");
+        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, user);
+        VCSimulationDataIdentifier vcdID = new VCSimulationDataIdentifier(vcSimID, 0);
+
+        Cachetable cachetable = new Cachetable(10 * Cachetable.minute, 1000000L);
+        File primaryDir = new File(primaryDirStr);
+        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cachetable, primaryDir, null);
+        double[] allTimes = dataSetControllerImpl.getDataSetTimes(vcdID);
+
+        // get dataset identifier for vcSimID
+        VCData vcData = dataSetControllerImpl.getVCData(vcdID);
+        OutputContext outputContext = new OutputContext(null);
+        DataIdentifier[] dataIdentifiers = vcData.getVarAndFunctionDataIdentifiers(outputContext);
+        DataIdentifier DexDataIdentifier = Arrays.stream(dataIdentifiers).filter(di -> di.getName().equals("Dex")).findFirst().get();
+        SimDataBlock simDataBlock = vcData.getSimDataBlock(outputContext, DexDataIdentifier.getName(), allTimes[0]);
+        double[] Dex_dataBlockValues = simDataBlock.getData(); // X,Y,Z raster for time 0 for variable cAMP
+        System.out.println("Dex_dataBlockValues.length = " + Dex_dataBlockValues.length);
+        System.out.println("Dex_dataBlockValues[0] = " + Dex_dataBlockValues[0]);
+
+    }
+}