Fixed problem with that not all entries were shown ...

...

Readme.md

@@ -21,7 +21,7 @@ File > SaveAs > HDF5
 # Installation
 To be able to install this plugin ImageJ need to be run with a Java 7 or greater JVM.
 
-* Download latest HDF5 ImageJ plugin from [here](http://slsyoke4.psi.ch:8081/artifactory/releases/HDF5_Viewer-0.6.0.zip).
+* Download latest HDF5 ImageJ plugin from [releases](https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5/releases).
 
 * Go into the ImageJ installation folder and extract the downloaded zip.
 

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ch.psi</groupId>
 	<artifactId>imagej.hdf5</artifactId>
-	<version>0.6.0</version>
+	<version>0.8.0</version>
 
 	<dependencies>
 		<dependency>

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

@@ -16,6 +16,15 @@ import java.util.logging.Level;
 import java.util.logging.Logger;
 import java.awt.*;
 
+import javax.swing.BoxLayout;
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.ScrollPaneConstants;
+
 import ncsa.hdf.object.*;
 import ncsa.hdf.object.h5.*;
 import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
@@ -55,12 +64,36 @@ public class HDF5Reader implements PlugIn {
 		H5File file = null;
 		try {
 			file = new H5File(filename, H5File.READ);
+			file.setMaxMembers(Integer.MAX_VALUE);
 			file.open();
 
 			List<Dataset> datasets = HDF5Utilities.getDatasets(file);
-			List<Dataset> selectedDatasets = selectDatasets(datasets);
+			SelectedDatasets selectedDatasets = selectDatasets(datasets);
 
-			for (Dataset var : selectedDatasets) {
+			
+			// TODO Remove
+			// Hack as a proof of principle
+			if(selectedDatasets.isGroup()){
+				ImageStack stack = null;
+				
+				for (Dataset var : selectedDatasets.getDatasets()) {
+					if(stack == null){
+						long[] dimensions= var.getDims();
+						stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
+					}
+					
+					Object wholeDataset = var.read();
+					addSlice(stack, wholeDataset);
+				}
+				
+				ImagePlus imp = new ImagePlus(filename, stack);
+				imp.resetDisplayRange();
+				imp.show();
+				return;
+			}
+			
+			
+			for (Dataset var : selectedDatasets.getDatasets()) {
 
 				// Read dataset attributes and properties
 				String datasetName = var.getName();
@@ -246,70 +279,51 @@ public class HDF5Reader implements PlugIn {
 	 * @return	List of datasets to visualize. If nothing selected the list will be empty
 	 * @throws HDF5Exception
 	 */
-	private List<Dataset> selectDatasets(List<Dataset> datasets) throws HDF5Exception {
+	private SelectedDatasets selectDatasets(List<Dataset> datasets) throws HDF5Exception {
 		
-		List<Dataset> selectedDatasets = new ArrayList<>();
 		GenericDialog gd = new GenericDialog("Variable Name Selection");
 		gd.addMessage("Please select variables to be loaded.\n");
 		
-		if (datasets.size() < 1) {
+			// Filter datasets that are not potential images / that cannot be displayed
-			IJ.error("The file does not contain datasets");
+			List<Dataset> fdatasets = new ArrayList<Dataset>();
-		} else if (datasets.size() > 1000) {
-			
-			logger.info("#######");
 			for(Dataset d: datasets){
-				logger.info(d.getFullName());
+				if(d.getRank()>=2 && d.getRank()<=5){
+					fdatasets.add(d);
+				}
 			}
-			logger.info("#######");
+			
+			JList<Dataset> list = new JList<>(fdatasets.toArray(new Dataset[fdatasets.size()]));
+			list.setCellRenderer(new DefaultListCellRenderer() {
+				private static final long serialVersionUID = 1L;
+				public Component getListCellRendererComponent(JList<?> list, Object value, int index, boolean isSelected, boolean cellHasFocus)	{
+					JLabel label = (JLabel) super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
+					final Dataset d = ((Dataset) value);
+					label.setText(d.getFullName()+" ("+d.getRank()+"D)");
+					return label;
+
+				}
+			});
+		    
+		    JScrollPane scroll = new JScrollPane(list);
+		    scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
+		    
+			JPanel panel = new JPanel();
+			panel.setLayout(new BoxLayout(panel,BoxLayout.Y_AXIS));
+			panel.add(scroll);
+			JCheckBox checkbox = new JCheckBox("Group Datasets (2D datasets only)");
+			panel.add(checkbox);
 			
 			gd = new GenericDialog("Variable Name Selection");
-			gd.addMessage("There are lots of datasets in your file (check the log output which datasets are available)! Please enter the full path of the dataset to be displayed");
+			gd.add(panel);
-			gd.addStringField("Dataset", "");
+			gd.addMessage("");
+			gd.pack();
 			gd.showDialog();
 
+			SelectedDatasets selectedDatasets = new SelectedDatasets();
 			if (!gd.wasCanceled()) {
-				String dsName = gd.getNextString();
+				selectedDatasets.setDatasets(list.getSelectedValuesList());
-				for(Dataset d: datasets){
+				selectedDatasets.setGroup(checkbox.isSelected());
-					if(d.getFullName().equals(dsName)){
-						selectedDatasets.add(d);
-					}
-				}
-				if(selectedDatasets.isEmpty()){
-					IJ.error("The file does not contain a variable with name " + "`" + dsName + "`!");
-				}
 			}
-		} else {
-			String[] varSelections = new String[datasets.size()];
-			boolean[] defaultValues = new boolean[datasets.size()];
-			for (int i = 0; i < datasets.size(); i++) {
-				Dataset var = datasets.get(i);
-				int rank = var.getRank();
-				String title = rank + "D: " + var.getFullName() + "              " + var.getDatatype().getDatatypeDescription() + "( ";
-				long[] extent = var.getDims();
-				for (int d = 0; d < rank; ++d) {
-					if (d != 0){
-						title += "x";
-					}
-					title += extent[d];
-				}
-				title += ")";
-				varSelections[i] = title;
-				defaultValues[i] = false;
-			}
-			logger.info("Add checkbox group with " + datasets.size() + " rows");
-			gd.addCheckboxGroup(datasets.size(), 1, varSelections, defaultValues);
-			addScrollBars(gd);
-			gd.showDialog();
-
-			if (!gd.wasCanceled()) {
-				// Get selected datasets
-				for (int i = 0; i < datasets.size(); ++i) {
-					if (gd.getNextBoolean()) {
-						selectedDatasets.add(datasets.get(i));
-					}
-				}
-			}
-		}
 		
 		return selectedDatasets;
 	}
@@ -394,74 +408,4 @@ public class HDF5Reader implements PlugIn {
 		stack.addSlice(null, g);
 		stack.addSlice(null, b);
 	}
-
-	
-	/**
-	 * Add AWT scroll bars to the given container
-	 * @param pane Pane to add scrollbar to
-	 */
-	public static void addScrollBars(Container pane) {
-		GridBagLayout layout = (GridBagLayout) pane.getLayout();
-
-		// extract components
-		int count = pane.getComponentCount();
-		Component[] c = new Component[count];
-		GridBagConstraints[] gbc = new GridBagConstraints[count];
-		for (int i = 0; i < count; i++) {
-			c[i] = pane.getComponent(i);
-			gbc[i] = layout.getConstraints(c[i]);
-		}
-
-		// clear components
-		pane.removeAll();
-		layout.invalidateLayout(pane);
-
-		// create new container panel
-		Panel newPane = new Panel();
-		GridBagLayout newLayout = new GridBagLayout();
-		newPane.setLayout(newLayout);
-		for (int i = 0; i < count; i++) {
-			newLayout.setConstraints(c[i], gbc[i]);
-			newPane.add(c[i]);
-		}
-
-		Frame f = new Frame();
-		f.setLayout(new BorderLayout());
-		f.add(newPane, BorderLayout.WEST);
-		f.pack();
-		final Dimension size = newPane.getSize();
-		f.remove(newPane);
-		f.dispose();
-
-		// compute best size for scrollable viewport
-		size.width += 15;
-		size.height += 15;
-		Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
-		int maxWidth = 3 * screen.width / 4;
-		int maxHeight = 3 * screen.height / 4;
-		if (size.width > maxWidth){
-			size.width = maxWidth;
-		}
-		if (size.height > maxHeight){
-			size.height = maxHeight;
-		}
-
-		// create scroll pane
-		ScrollPane scroll = new ScrollPane() {
-			private static final long serialVersionUID = 1L;
-			public Dimension getPreferredSize() {
-				return size;
-			}
-		};
-		scroll.add(newPane);
-
-		// add scroll pane to original container
-		GridBagConstraints constraints = new GridBagConstraints();
-		constraints.anchor = GridBagConstraints.WEST;
-		constraints.fill = GridBagConstraints.BOTH;
-		constraints.weightx = 1.0;
-		constraints.weighty = 1.0;
-		layout.setConstraints(scroll, constraints);
-		pane.add(scroll);
-	}
 }

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

@@ -0,0 +1,26 @@
+package ch.psi.imagej.hdf5;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import ncsa.hdf.object.Dataset;
+
+public class SelectedDatasets {
+
+	private List<Dataset> datasets = new ArrayList<Dataset>();
+	private boolean group = false;
+	
+	public List<Dataset> getDatasets() {
+		return datasets;
+	}
+	public void setDatasets(List<Dataset> datasets) {
+		this.datasets = datasets;
+	}
+	public boolean isGroup() {
+		return group;
+	}
+	public void setGroup(boolean group) {
+		this.group = group;
+	}
+	
+}