From 9ab9b8b355588b58d0557781664da80f26680cf0 Mon Sep 17 00:00:00 2001
From: ebner <simon.ebner@psi.ch>
Date: Tue, 14 Apr 2015 13:55:19 +0200
Subject: [PATCH] tried to implement close of file CTRLHA-109

---
 .../java/ch/psi/imagej/hdf5/HDF5Reader.java   |  2 +-
 .../ch/psi/imagej/hdf5/SelectionPanel.java    |  1 +
 .../ch/psi/imagej/hdf5/VirtualStackHDF5.java  | 19 ++++++++++++++++++-
 3 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java b/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java
index 63262a7..a6b1191 100644
--- a/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java
+++ b/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java
@@ -213,7 +213,7 @@ public class HDF5Reader implements PlugIn {
 					
 					if(selectedDatasets.isVirtualStack()){
 						logger.info("Use virtual stack");
-						stack = new VirtualStackHDF5(var);
+						stack = new VirtualStackHDF5(file, var);
 					}
 					else{
 						if(selectedDatasets.getSlice()!=null){
diff --git a/src/main/java/ch/psi/imagej/hdf5/SelectionPanel.java b/src/main/java/ch/psi/imagej/hdf5/SelectionPanel.java
index 5ed4652..6def54e 100644
--- a/src/main/java/ch/psi/imagej/hdf5/SelectionPanel.java
+++ b/src/main/java/ch/psi/imagej/hdf5/SelectionPanel.java
@@ -64,6 +64,7 @@ public class SelectionPanel extends JPanel {
 		add(checkbox);
 		
 		checkBoxVirtualStack = new JCheckBox("Virtual Stack");
+		checkBoxVirtualStack.setSelected(true);
 		add(checkBoxVirtualStack);
 		
 		panel = new JPanel();
diff --git a/src/main/java/ch/psi/imagej/hdf5/VirtualStackHDF5.java b/src/main/java/ch/psi/imagej/hdf5/VirtualStackHDF5.java
index 3716f1d..0cfc5d1 100644
--- a/src/main/java/ch/psi/imagej/hdf5/VirtualStackHDF5.java
+++ b/src/main/java/ch/psi/imagej/hdf5/VirtualStackHDF5.java
@@ -4,6 +4,7 @@ import java.util.logging.Level;
 import java.util.logging.Logger;
 
 import ncsa.hdf.object.Dataset;
+import ncsa.hdf.object.h5.H5File;
 import ij.ImageStack;
 import ij.process.ByteProcessor;
 import ij.process.ColorProcessor;
@@ -18,10 +19,12 @@ public class VirtualStackHDF5 extends ImageStack {
 	
 	private int bitDepth = 0;
 	private Dataset dataset;
+	private H5File file;
 	
-	public VirtualStackHDF5(Dataset dataset){
+	public VirtualStackHDF5(H5File file, Dataset dataset){
 		super((int) dataset.getDims()[2], (int) dataset.getDims()[1]);
 		this.dataset = dataset;
+		this.file = file;
 	}
 	
 	/** Does noting. */
@@ -154,4 +157,18 @@ public class VirtualStackHDF5 extends ImageStack {
 	public int getBitDepth() {
 		return bitDepth;
 	}
+	
+	@Override
+	protected void finalize() throws Throwable {
+		super.finalize();
+		
+		logger.info("Closing HDF5 file");
+		try{
+			file.close();
+		}
+		catch(Exception e){
+			logger.log(Level.WARNING, "Unable to close HDF5 file", e);
+		}
+		
+	}
 }