Added support for slice / tested

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

@@ -5,10 +5,11 @@ import java.util.List;
 
 import ncsa.hdf.object.Dataset;
 
-public class SelectedDatasets {
+public class DatasetSelection {
 
 	private List<Dataset> datasets = new ArrayList<Dataset>();
 	private boolean group = false;
+	private Integer slice;
 	
 	public List<Dataset> getDatasets() {
 		return datasets;
@@ -22,5 +23,10 @@ public class SelectedDatasets {
 	public void setGroup(boolean group) {
 		this.group = group;
 	}
-	
+	public void setSlice(Integer slice) {
+		this.slice = slice;
+	}
+	public Integer getSlice() {
+		return slice;
+	}
 }

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

@@ -68,7 +68,7 @@ public class HDF5Reader implements PlugIn {
 			file.open();
 
 			List<Dataset> datasets = HDF5Utilities.getDatasets(file);
-			SelectedDatasets selectedDatasets = selectDatasets(datasets);
+			DatasetSelection selectedDatasets = selectDatasets(datasets);
 
 			
 			// TODO Remove
@@ -217,20 +217,45 @@ public class HDF5Reader implements PlugIn {
 				} else if (numberOfDimensions == 3) {
 					logger.info("3D Image");
 
+					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);
+					}
+					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();
 
-					ImageStack stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
+						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);
 						}
+					}
 
 					ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack);
 					imp.resetDisplayRange();
@@ -279,7 +304,7 @@ public class HDF5Reader implements PlugIn {
 	 * @return	List of datasets to visualize. If nothing selected the list will be empty
 	 * @throws HDF5Exception
 	 */
-	private SelectedDatasets selectDatasets(List<Dataset> datasets) throws HDF5Exception {
+	private DatasetSelection selectDatasets(List<Dataset> datasets) throws HDF5Exception {
 		
 		GenericDialog gd = new GenericDialog("Variable Name Selection");
 		gd.addMessage("Please select variables to be loaded.\n");
@@ -292,10 +317,11 @@ public class HDF5Reader implements PlugIn {
 			gd.pack();
 			gd.showDialog();
 
-			SelectedDatasets selectedDatasets = new SelectedDatasets();
+			DatasetSelection selectedDatasets = new DatasetSelection();
 			if (!gd.wasCanceled()) {
 				selectedDatasets.setDatasets(panel.getSelectedValues());
 				selectedDatasets.setGroup(panel.groupValues());
+				selectedDatasets.setSlice(panel.getSlice());
 			}
 		
 		return selectedDatasets;

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

@@ -16,7 +16,6 @@ import javax.swing.ScrollPaneConstants;
 
 import ncsa.hdf.object.Dataset;
 import javax.swing.JTextField;
-import javax.swing.JSpinner;
 import java.awt.FlowLayout;
 
 public class SelectionPanel extends JPanel {
@@ -72,7 +71,7 @@ public class SelectionPanel extends JPanel {
 		flowLayout.setAlignment(FlowLayout.LEFT);
 		add(panel);
 		
-		lblSlice = new JLabel("Slice:");
+		lblSlice = new JLabel("Slice (3D only):");
 		panel.add(lblSlice);
 		
 		textField = new JTextField();
@@ -87,4 +86,12 @@ public class SelectionPanel extends JPanel {
 	public boolean groupValues(){
 		return checkbox.isSelected();
 	}
+	
+	public Integer getSlice(){
+		String text = textField.getText();
+		if(text.matches("[0-9]+")){
+			return new Integer(text);
+		}
+		return null;
+	}
 }