Merge pull request #2 in IM/ch.psi.imagej.hdf5 from virtualstack to master

# By ebner
# Via ebner
* commit 'e5331e0c2d5d33dffee6906b5db5bda33f144e5a':
  Updated version CTRLHA-109
  Fixed memory leak that was introduced with the VirtualStack workaround - its still a workaround so CTRLHA-109
  tried to implement close of file CTRLHA-109
  implemented a HDF5 Virtual Stack CTRLHA-109

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ch.psi</groupId>
 	<artifactId>imagej.hdf5</artifactId>
-	<version>0.8.0</version>
+	<version>0.9.0</version>
 
 	<dependencies>
 		<dependency>

src/main/java/ch/psi/imagej/hdf5/DatasetSelection.java

@@ -12,6 +12,7 @@ public class DatasetSelection {
 	private Integer slice;
 	// Intervall to read images
 	private Integer modulo;
+	private boolean virtualStack;
 	
 	public List<Dataset> getDatasets() {
 		return datasets;
@@ -37,4 +38,10 @@ public class DatasetSelection {
 	public Integer getModulo() {
 		return modulo;
 	}
+	public void setVirtualStack(boolean virtualStack) {
+		this.virtualStack = virtualStack;
+	}
+	public boolean isVirtualStack(){
+		return this.virtualStack;
+	}
 }

src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java

@@ -51,6 +51,7 @@ public class HDF5Reader implements PlugIn {
 		
 		// Read HDF5 file
 		H5File file = null;
+		boolean close = true;
 		try {
 			file = new H5File(filename, H5File.READ);
 			file.setMaxMembers(Integer.MAX_VALUE);
@@ -58,6 +59,8 @@ public class HDF5Reader implements PlugIn {
 
 			List<Dataset> datasets = HDF5Utilities.getDatasets(file);
 			DatasetSelection selectedDatasets = selectDatasets(datasets);
+			// TODO to be removed - Workaround virtual stack - keep HDF5 file open at the end 
+			close=!selectedDatasets.isVirtualStack();
 
 			
 			// TODO Remove
@@ -208,68 +211,74 @@ public class HDF5Reader implements PlugIn {
 
 					ImageStack stack;
 					
-					if(selectedDatasets.getSlice()!=null){
-						
-						// Select what to readout
-						long[] selected = var.getSelectedDims();
-						selected[0] = 1;
-						selected[1] = dimensions[1];
-						selected[2] = dimensions[2];
-						
-						long[] start = var.getStartDims();
-						start[0] = selectedDatasets.getSlice();
-
-						Object wholeDataset = var.read();
-						
-						stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
-						int size = (int) (dimensions[1] * dimensions[2]);
-						
-//						int startIdx = selectedDatasets.getSlice() * size;
-						addSlice(stack, wholeDataset, 0, size);
+					if(selectedDatasets.isVirtualStack()){
+						logger.info("Use virtual stack");
+						stack = new VirtualStackHDF5(file, var);
 					}
-					else if(selectedDatasets.getModulo()!=null){
-						logger.info("Read every "+selectedDatasets.getModulo()+" image");
-						// Select what to readout
-						
-						stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
-						
-						for(int indexToRead=0;indexToRead<dimensions[0]; indexToRead=indexToRead+selectedDatasets.getModulo()){
+					else{
+						if(selectedDatasets.getSlice()!=null){
 							
+							// Select what to readout
 							long[] selected = var.getSelectedDims();
 							selected[0] = 1;
 							selected[1] = dimensions[1];
 							selected[2] = dimensions[2];
 							
 							long[] start = var.getStartDims();
-							start[0] = indexToRead;
+							start[0] = selectedDatasets.getSlice();
 	
 							Object wholeDataset = var.read();
 							
+							stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
 							int size = (int) (dimensions[1] * dimensions[2]);
-//							int startIdx = selectedDatasets.getSlice() * size;
+							
+	//						int startIdx = selectedDatasets.getSlice() * size;
 							addSlice(stack, wholeDataset, 0, size);
 						}
-					}
-					else{
-						// Select what to readout
-						long[] selected = var.getSelectedDims();
-						selected[0] = dimensions[0];
-						selected[1] = dimensions[1];
-						selected[2] = dimensions[2];
+						else if(selectedDatasets.getModulo()!=null){
+							logger.info("Read every "+selectedDatasets.getModulo()+" image");
+							// Select what to readout
+							
+							stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
+							
+							for(int indexToRead=0;indexToRead<dimensions[0]; indexToRead=indexToRead+selectedDatasets.getModulo()){
+								
+								long[] selected = var.getSelectedDims();
+								selected[0] = 1;
+								selected[1] = dimensions[1];
+								selected[2] = dimensions[2];
+		
+								long[] start = var.getStartDims();
+								start[0] = indexToRead;
+								
+								Object wholeDataset = var.read();
+		
+								int size = (int) (dimensions[1] * dimensions[2]);
+	//							int startIdx = selectedDatasets.getSlice() * size;
+								addSlice(stack, wholeDataset, 0, size);
+							}
+						}
+						else{
+							// Select what to readout
+							long[] selected = var.getSelectedDims();
+							selected[0] = dimensions[0];
+							selected[1] = dimensions[1];
+							selected[2] = dimensions[2];
 	
 							
-						Object wholeDataset = var.read();
+							Object wholeDataset = var.read();
 	
-						stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
-						int size = (int) (dimensions[1] * dimensions[2]);
+							stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
+							int size = (int) (dimensions[1] * dimensions[2]);
 							
-						for (int lev = 0; lev < dimensions[0]; ++lev) {
-							int startIdx = lev * size;
-							addSlice(stack, wholeDataset, startIdx, size);
+							for (int lev = 0; lev < dimensions[0]; ++lev) {
+								int startIdx = lev * size;
+								addSlice(stack, wholeDataset, startIdx, size);
+							}
 						}
 					}
 
-					ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack);
+					ImagePlus imp = new ImagePlusHDF5(filename + " " + datasetName, stack);
 					imp.resetDisplayRange();
 					imp.show();
 					
@@ -297,8 +306,11 @@ public class HDF5Reader implements PlugIn {
 			IJ.outOfMemory("Out of memory while loading file: " + filename);
 		} finally {
 			try {
-				if (file != null) {
-					file.close();
+				// TODO workaround - to be removed
+				if(close){
+					if (file != null) {
+						file.close();
+					}
 				}
 			} catch (HDF5Exception e) {
 				logger.log(Level.WARNING, "Error while closing: " + filename, e);
@@ -335,6 +347,7 @@ public class HDF5Reader implements PlugIn {
 				selectedDatasets.setGroup(panel.groupValues());
 				selectedDatasets.setSlice(panel.getSlice());
 				selectedDatasets.setModulo(panel.getModulo());
+				selectedDatasets.setVirtualStack(panel.useVirtualStack());
 			}
 		
 		return selectedDatasets;

src/main/java/ch/psi/imagej/hdf5/ImagePlusHDF5.java

@@ -0,0 +1,64 @@
+package ch.psi.imagej.hdf5;
+
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.util.logging.Logger;
+
+import ij.ImagePlus;
+import ij.ImageStack;
+
+public class ImagePlusHDF5 extends ImagePlus {
+	
+	
+	private static final Logger logger = Logger.getLogger(ImagePlusHDF5.class.getName());
+	
+	public ImagePlusHDF5(String title, ImageStack stack) {
+		super(title, stack);
+	}
+	
+	@Override
+	public void show() {
+		super.show();
+		getWindow().addWindowListener(new WindowListener() {
+			
+			@Override
+			public void windowOpened(WindowEvent e) {
+				logger.info("");
+			}
+			
+			@Override
+			public void windowIconified(WindowEvent e) {
+				logger.info("");
+			}
+			
+			@Override
+			public void windowDeiconified(WindowEvent e) {
+				logger.info("");
+			}
+			
+			@Override
+			public void windowDeactivated(WindowEvent e) {
+				logger.info("");
+			}
+			
+			@Override
+			public void windowClosing(WindowEvent e) {
+				logger.info("Closing");
+			}
+			
+			@Override
+			public void windowClosed(WindowEvent e) {
+				logger.info("Closed");
+				ImageStack stack = getStack();
+				if(stack instanceof VirtualStackHDF5){
+					((VirtualStackHDF5) stack).close();
+				}
+			}
+			
+			@Override
+			public void windowActivated(WindowEvent e) {
+				logger.info("");
+			}
+		});
+	}
+}

src/main/java/ch/psi/imagej/hdf5/SelectionPanel.java

@@ -24,7 +24,7 @@ public class SelectionPanel extends JPanel {
 
 	private final JList<Dataset> list;
 	private JCheckBox checkbox;
-	private JCheckBox chckbxNewCheckBox;
+	private JCheckBox checkBoxVirtualStack;
 	private JLabel lblSlice;
 	private JPanel panel;
 	private JTextField textField;
@@ -63,8 +63,9 @@ public class SelectionPanel extends JPanel {
 		checkbox = new JCheckBox("Group Datasets (2D datasets only)");
 		add(checkbox);
 		
-		chckbxNewCheckBox = new JCheckBox("Virtual Stack");
-		add(chckbxNewCheckBox);
+		checkBoxVirtualStack = new JCheckBox("Virtual Stack");
+		checkBoxVirtualStack.setSelected(true);
+		add(checkBoxVirtualStack);
 		
 		panel = new JPanel();
 		FlowLayout flowLayout = (FlowLayout) panel.getLayout();
@@ -102,4 +103,8 @@ public class SelectionPanel extends JPanel {
 		}
 		return null;
 	}
+	
+	public boolean useVirtualStack(){
+		return checkBoxVirtualStack.isSelected();
+	}
 }

src/main/java/ch/psi/imagej/hdf5/VirtualStackHDF5.java

@@ -0,0 +1,174 @@
+package ch.psi.imagej.hdf5;
+
+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;
+import ij.process.FloatProcessor;
+import ij.process.ImageProcessor;
+import ij.process.ShortProcessor;
+
+public class VirtualStackHDF5 extends ImageStack {
+	
+	
+	private static final Logger logger = Logger.getLogger(VirtualStackHDF5.class.getName());
+	
+	private int bitDepth = 0;
+	private Dataset dataset;
+	private H5File file;
+	
+	public VirtualStackHDF5(H5File file, Dataset dataset){
+		super((int) dataset.getDims()[2], (int) dataset.getDims()[1]);
+		this.dataset = dataset;
+		this.file = file;
+	}
+	
+	/** Does noting. */
+	public void addSlice(String sliceLabel, Object pixels) {
+	}
+
+	/** Does nothing.. */
+	public void addSlice(String sliceLabel, ImageProcessor ip) {
+	}
+
+	/** Does noting. */
+	public void addSlice(String sliceLabel, ImageProcessor ip, int n) {
+	}
+
+	/** Does noting. */
+	public void deleteSlice(int n) {
+	}
+
+	/** Does noting. */
+	public void deleteLastSlice() {
+	}
+
+	public Object getPixels(int slice) {
+		try {
+			long[] dimensions = dataset.getDims();
+
+			// Select what to readout
+			long[] selected = dataset.getSelectedDims();
+			selected[0] = 1;
+			selected[1] = dimensions[1];
+			selected[2] = dimensions[2];
+
+			long[] start = dataset.getStartDims();
+			start[0] = slice-1; // Indexing at image J starts at 1
+
+			Object wholeDataset = dataset.read();
+
+			if (wholeDataset instanceof byte[]) {
+				return (byte[]) wholeDataset;
+			} else if (wholeDataset instanceof short[]) {
+				return (short[]) wholeDataset;
+			} else if (wholeDataset instanceof int[]) {
+				return HDF5Utilities.convertToFloat((int[]) wholeDataset);
+			} else if (wholeDataset instanceof long[]) {
+				return HDF5Utilities.convertToFloat((long[]) wholeDataset);
+			} else if (wholeDataset instanceof float[]) {
+				return (float[]) wholeDataset;
+			} else if (wholeDataset instanceof double[]) {
+				return HDF5Utilities.convertToFloat((double[]) wholeDataset);
+			} else {
+				logger.warning("Datatype not supported");
+			}
+		} catch (OutOfMemoryError | Exception e) {
+			logger.log(Level.WARNING, "Unable to open slice", e);
+		}
+		
+		return null;
+	}
+
+	/**
+	 * Assigns a pixel array to the specified slice, were 1<=n<=nslices.
+	 */
+	public void setPixels(Object pixels, int n) {
+	}
+
+	/**
+	 * Returns an ImageProcessor for the specified slice, were 1<=n<=nslices.
+	 * Returns null if the stack is empty.
+	 */
+	public ImageProcessor getProcessor(int slice) {
+		
+		long[] dimensions = dataset.getDims();
+		final Object pixels = getPixels(slice);
+		
+		// Todo support more ImageProcessor types
+		ImageProcessor ip;		
+		
+		if (pixels instanceof byte[]){
+			ip = new ByteProcessor((int) dimensions[2], (int) dimensions[1]);
+		}
+		else if (pixels instanceof short[]){
+			ip = new ShortProcessor((int) dimensions[2], (int) dimensions[1]);
+		}
+		else if (pixels instanceof int[]){
+			ip = new ColorProcessor((int) dimensions[2], (int) dimensions[1]);
+		}
+		else if (pixels instanceof float[]){
+			ip = new FloatProcessor((int) dimensions[2], (int) dimensions[1]);
+		}
+		else {
+			throw new IllegalArgumentException("Unknown stack type");
+		}
+		
+		ip.setPixels(pixels);
+		return ip;
+	}
+
+	/** Returns the number of slices in this stack. */
+	public int getSize() {
+		return (int) this.dataset.getDims()[0];
+	}
+
+	/** Returns the label of the Nth image. */
+	public String getSliceLabel(int slice) {
+		return "Slice: "+slice;
+	}
+
+	/** Returns null. */
+	public Object[] getImageArray() {
+		return null;
+	}
+
+	/** Does nothing. */
+	public void setSliceLabel(String label, int n) {
+	}
+
+	/** Always return true. */
+	public boolean isVirtual() {
+		return true;
+	}
+
+	/** Does nothing. */
+	public void trim() {
+	}
+
+	/**
+	 * Returns the bit depth (8, 16, 24 or 32), or 0 if the bit depth is not
+	 * known.
+	 */
+	public int getBitDepth() {
+		return bitDepth;
+	}
+	
+	/**
+	 * Close HDF5 file
+	 */
+	public void close() {		
+		logger.info("Closing HDF5 file");
+		try{
+			file.close();
+		}
+		catch(Exception e){
+			logger.log(Level.WARNING, "Unable to close HDF5 file", e);
+		}
+		
+	}
+}