downstripped code ...

src/main/java/ch/psi/imagej/hdf5/HDF5Utilities.java

@@ -1,11 +1,19 @@
 package ch.psi.imagej.hdf5;
 
+import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.logging.Logger;
 
+import javax.swing.tree.DefaultMutableTreeNode;
+
 import ncsa.hdf.object.Attribute;
+import ncsa.hdf.object.Dataset;
+import ncsa.hdf.object.FileFormat;
+import ncsa.hdf.object.Group;
 import ncsa.hdf.object.HObject;
+import ncsa.hdf.object.h5.H5File;
 
 public class HDF5Utilities {
 	
@@ -36,4 +44,182 @@ public class HDF5Utilities {
 		
 		return attributes;
 	}
+	
+	
+	/**
+	 * TODO: to be replaced by a simple regex expression
+	 * 
+	 * Retrieve relative group descriptor for given descriptor
+	 * 
+	 * Example:
+	 * The group descriptor of /test/one/two/three is test/one/two
+	 * 
+	 * @param descriptor 	Full qualified descriptor
+	 * @return	Group descriptor
+	 */
+	public static String getGroupDescriptor(String descriptor) {
+		String groupName = descriptor;
+
+		// Trim leading and trailing slashes
+		while (groupName.charAt(0) == '/') {
+			groupName = groupName.substring(1);
+		}
+		while (groupName.charAt(groupName.length() - 1) == '/') {
+			groupName = groupName.substring(0, groupName.length() - 2);
+		}
+		
+		int posOfLastSlash = groupName.lastIndexOf('/');
+		if (posOfLastSlash == -1)
+			return null;
+		else
+			return groupName.substring(0, posOfLastSlash);
+	}
+	
+	/**
+	 * TODO: to be replaced by a simple regex expression
+	 * 
+	 * Get relative dataset descriptor
+	 * 
+	 * Example:
+	 * 
+	 * /a/b/c/d/ returns d
+	 *  
+	 * @param descriptor
+	 * @return relative dataset descriptor
+	 */
+	public static String getDataSetDescriptor(String descriptor) {
+		String dataSetName = descriptor;
+		
+		// Trim leading and trailing slashes
+		while (dataSetName.charAt(0) == '/') {
+			dataSetName = dataSetName.substring(1);
+		}
+		while (dataSetName.charAt(dataSetName.length() - 1) == '/') {
+			dataSetName = dataSetName.substring(0, dataSetName.length() - 2);
+		}
+		int posOfLastSlash = dataSetName.lastIndexOf('/');
+		if (posOfLastSlash == -1)
+			return dataSetName;
+		else
+			return dataSetName.substring(posOfLastSlash + 1);
+	}
+	
+	/**
+	 * Creates group recursively relative to the given base group
+	 * 
+	 * @param groupRelativName relative group to be created
+	 * @param group	Base group - if null create group relative to /
+	 * @param file	File handle
+	 * @return
+	 */
+	public static Group createGroup(String groupRelativName, Group group, FileFormat file) {
+		if (groupRelativName == null || file == null)
+			return null;
+
+		if (group == null){
+			group = (Group) ((DefaultMutableTreeNode) file.getRootNode()).getUserObject();
+		}
+
+		// Trim leading and trailing slashes
+		while (groupRelativName.charAt(0) == '/') {
+			groupRelativName = groupRelativName.substring(1);
+		}
+		while (groupRelativName.charAt(groupRelativName.length() - 1) == '/') {
+			groupRelativName = groupRelativName.substring(0, groupRelativName.length() - 2);
+		}
+
+		int posOfSlash = groupRelativName.indexOf('/');
+
+		if (posOfSlash == -1) {
+			try {
+				Group newGroup;
+				String newGroupName;
+				if (group.isRoot()){
+					newGroupName = "/" + groupRelativName;
+				}
+				else{
+					newGroupName = group.getFullName() + "/" + groupRelativName;
+				}
+				newGroup = (Group) file.get(newGroupName);
+				if (newGroup == null){
+					newGroup = file.createGroup(newGroupName, group);
+				}
+				return newGroup;
+			} catch (Exception e) {
+				return null;
+			}
+		} else {
+			String subgroupRelativName = groupRelativName.substring(posOfSlash);
+			String currentGroup = groupRelativName.substring(0, posOfSlash);
+			logger.info("Create: " + currentGroup);
+			logger.info("Call back for: " + subgroupRelativName);
+			try {
+				Group newGroup;
+				String newGroupName;
+				if (group.isRoot()){
+					newGroupName = "/" + currentGroup;
+				}
+				else {
+					newGroupName = group.getFullName() + "/" + currentGroup;
+				}
+
+				logger.info("try opening: " + newGroupName);
+				newGroup = (Group) file.get(newGroupName);
+
+				if (newGroup == null) {
+					newGroup = file.createGroup(newGroupName, group);
+				}
+
+				return createGroup(subgroupRelativName, newGroup, file);
+			} catch (Exception e) {
+				return null;
+			}
+
+		}
+		// never come here
+	}
+	
+	
+	/**
+	 * Get all datasets of a file
+	 * @param file
+	 * @return
+	 */
+	public static  List<Dataset> getDatasets(H5File file) {
+		Group rootNode = (Group) ((javax.swing.tree.DefaultMutableTreeNode) file.getRootNode()).getUserObject();
+		List<Dataset> datasets = getDatasets(rootNode);
+		return datasets;
+	}
+	
+	/**
+	 * Get all datasets of a group
+	 * @param group	Group to search for datasets
+	 * @return	List of datasets If group is null datasets will be empty
+	 */
+	public static  List<Dataset> getDatasets(Group group){
+		List<Dataset> datasets = new ArrayList<>();
+		return getDatasets(group, datasets);
+	}
+	
+	/**
+	 * Recursively get list of all datasets in file
+	 * @param group		Group to search for datasets
+	 * @param datasets	List of datasets
+	 * @return	List of datasets. If group is null datasets will be empty
+	 */
+	public static  List<Dataset> getDatasets(Group group, List<Dataset> datasets) {
+		if (group == null){
+			return datasets;
+		}
+
+		for (HObject o: group.getMemberList()) {
+			if (o instanceof Dataset) {
+				((Dataset) o).init();
+				datasets.add((Dataset) o);
+			} else if (o instanceof Group) {
+				datasets = (getDatasets((Group) o, datasets));
+			}
+		}
+		return datasets;
+	}
 }

src/main/java/ch/psi/imagej/hdf5/HDF5Writer.java

@@ -28,8 +28,6 @@ import ij.gui.*;
 
 import java.util.logging.Logger;
 
-import javax.swing.tree.DefaultMutableTreeNode;
-
 import ncsa.hdf.object.*; // the common object package
 import ncsa.hdf.object.h5.*; // the HDF5 implementation
 import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
@@ -144,12 +142,14 @@ public class HDF5Writer implements PlugInFilter {
 						IJ.showProgress(f, nFrames);
 						for (int c = 0; c < nChannels; c++) {
 							String fullName = makeDataSetName(formatTokens, f, c);
-							String dataSetName = getDataSetDescriptor(fullName);
+
-							logger.info("dataset name: " + dataSetName);
+							String dataSetName = HDF5Utilities.getDataSetDescriptor(fullName);
-							String groupName = getGroupDescriptor(fullName);
+							String groupName = HDF5Utilities.getGroupDescriptor(fullName);
-							logger.info("group name: " + groupName);
+							logger.info("group name: " + groupName + " dataset name: " + dataSetName);
+							
 							// ensure group exists
-							Group group = createGroupRecursive(groupName, null, outFile);
+							Group group = HDF5Utilities.createGroup(groupName, null, outFile);
+							
 							// create data set
 							Dataset dataset = null;
 							// select hyperslabs
@@ -258,13 +258,12 @@ public class HDF5Writer implements PlugInFilter {
 
 				logger.info("writing data to variable: " + varName);
 
-				String dataSetName = getDataSetDescriptor(varName);
+				String dataSetName = HDF5Utilities.getDataSetDescriptor(varName);
-				logger.info("dataset name: " + dataSetName);
+				String groupName = HDF5Utilities.getGroupDescriptor(varName);
-				String groupName = getGroupDescriptor(varName);
+				logger.info("group name: " + groupName + " dataset name: " + dataSetName);
-				logger.info("group name: " + groupName);
 
 				// ensure group exists
-				Group group = createGroupRecursive(groupName, null, outFile);
+				Group group = HDF5Utilities.createGroup(groupName, null, outFile);
 
 				
 
@@ -390,102 +389,6 @@ public class HDF5Writer implements PlugInFilter {
 
 	}
 
-	private static Group createGroupRecursive(String groupRelativName, Group group, FileFormat file) {
-		if (groupRelativName == null || file == null)
-			return null;
-
-		if (group == null)
-			group = (Group) ((DefaultMutableTreeNode) file.getRootNode()).getUserObject();
-
-		while (groupRelativName.charAt(0) == '/') {
-			// trim leading slash
-			groupRelativName = groupRelativName.substring(1);
-		}
-		while (groupRelativName.charAt(groupRelativName.length() - 1) == '/') {
-			// trim last slash
-			groupRelativName = groupRelativName.substring(0, groupRelativName.length() - 2);
-		}
-
-		int posOfSlash = groupRelativName.indexOf('/');
-
-		if (posOfSlash == -1) {
-			try {
-				Group newGroup;
-				String newGroupName;
-				if (group.isRoot())
-					newGroupName = "/" + groupRelativName;
-				else
-					newGroupName = group.getFullName() + "/" + groupRelativName;
-				newGroup = (Group) file.get(newGroupName);
-				if (newGroup == null)
-					newGroup = file.createGroup(newGroupName, group);
-				return newGroup;
-			} catch (Exception e) {
-				return null;
-			}
-		} else {
-			String subgroupRelativName = groupRelativName.substring(posOfSlash);
-			String currentGroup = groupRelativName.substring(0, posOfSlash);
-			logger.info("Create: " + currentGroup);
-			logger.info("Call back for: " + subgroupRelativName);
-			try {
-				Group newGroup;
-				String newGroupName;
-				if (group.isRoot())
-					newGroupName = "/" + currentGroup;
-				else
-					newGroupName = group.getFullName() + "/" + currentGroup;
-
-				logger.info("try opening: " + newGroupName);
-				newGroup = (Group) file.get(newGroupName);
-
-				if (newGroup == null)
-					newGroup = file.createGroup(newGroupName, group);
-
-				return createGroupRecursive(subgroupRelativName, newGroup, file);
-			} catch (Exception e) {
-				return null;
-			}
-
-		}
-		// never come here
-	}
-
-	private static String getGroupDescriptor(String absName) {
-		String groupName = absName;
-
-		while (groupName.charAt(0) == '/') {
-			// trim leading slash
-			groupName = groupName.substring(1);
-		}
-		while (groupName.charAt(groupName.length() - 1) == '/') {
-			// trim last slash
-			groupName = groupName.substring(0, groupName.length() - 2);
-		}
-		int posOfLastSlash = groupName.lastIndexOf('/');
-		if (posOfLastSlash == -1)
-			return null;
-		else
-			return groupName.substring(0, posOfLastSlash);
-	}
-
-	private static String getDataSetDescriptor(String absName) {
-		String dataSetName = absName;
-		while (dataSetName.charAt(0) == '/') {
-			// trim leading slash
-			dataSetName = dataSetName.substring(1);
-		}
-		while (dataSetName.charAt(dataSetName.length() - 1) == '/') {
-			// trim last slash
-			dataSetName = dataSetName.substring(0, dataSetName.length() - 2);
-		}
-		int posOfLastSlash = dataSetName.lastIndexOf('/');
-		if (posOfLastSlash == -1)
-			return dataSetName;
-		else
-			return dataSetName.substring(posOfLastSlash + 1);
-	}
-
 	long[] findOptimalChunksize(int Rank, long[] dataDims) {
 		long[] best_chunksize = new long[Rank];
 		int maxChunkVol = 262144;