diff --git a/pom.xml b/pom.xml index 250dcb2..d5279e7 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 ch.psi imagej.hdf5 - 0.5.0 + 0.6.0 diff --git a/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java b/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java index 9197863..f06a155 100644 --- a/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java +++ b/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java @@ -11,7 +11,6 @@ import ij.plugin.PlugIn; import java.io.File; import java.lang.reflect.Array; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; import java.util.logging.Level; import java.util.logging.Logger; @@ -25,52 +24,40 @@ public class HDF5Reader implements PlugIn { private static final Logger logger = Logger.getLogger(HDF5Reader.class.getName()); + /** + * Main function for testing + * @param args + */ public static void main(String[] args){ HDF5Reader r = new HDF5Reader(); r.run(""); } + /** + * Main function plugin + */ public void run(String arg) { - String directory = ""; - String name = ""; - boolean tryAgain; - String openMSG = "Open HDF5..."; - do { - tryAgain = false; - OpenDialog od; - if (directory.equals("")) - od = new OpenDialog(openMSG, arg); - else - od = new OpenDialog(openMSG, directory, arg); + OpenDialog od = new OpenDialog("Open HDF5 ...", arg); - directory = od.getDirectory(); - name = od.getFileName(); - if (name == null) - return; - if (name.equals("")) - return; + + File tfile = new File(od.getDirectory() + od.getFileName()); + if (!tfile.exists() || !tfile.canRead()) { + IJ.showMessage("Cannot open file: "+tfile.getAbsolutePath()); + return; + } + String filename = tfile.getAbsolutePath(); - File testFile = new File(directory + name); - if (!testFile.exists() || !testFile.canRead()) - return; - - if (testFile.isDirectory()) { - directory = directory + name; - tryAgain = true; - } - } while (tryAgain); - - IJ.showStatus("Loading HDF5 File: " + directory + name); + IJ.showStatus("Loading HDF5 File: " + filename); IJ.showProgress(0.0); // Read HDF5 file - H5File inFile = null; + H5File file = null; try { - inFile = new H5File(directory + name, H5File.READ); - inFile.open(); + file = new H5File(filename, H5File.READ); + file.open(); - List datasets = HDF5Utilities.getDatasets(inFile); + List datasets = HDF5Utilities.getDatasets(file); List selectedDatasets = selectDatasets(datasets); for (Dataset var : selectedDatasets) { @@ -78,14 +65,11 @@ public class HDF5Reader implements PlugIn { // Read dataset attributes and properties String datasetName = var.getName(); Datatype datatype = var.getDatatype(); - Datatype datatypeIfUnsupported = null; int numberOfDimensions = var.getRank(); long[] dimensions= var.getDims(); logger.info("Reading dataset: " + datasetName + " Dimensions: " + numberOfDimensions + " Type: " + datatype.getDatatypeDescription()); - // Check if datatype is supported - datatypeIfUnsupported = checkIfDatatypeSupported(datatype); // Read dataset if (numberOfDimensions == 5 && dimensions[4] == 3) { @@ -101,7 +85,6 @@ public class HDF5Reader implements PlugIn { selected[4] = dimensions[4]; Object wholeDataset = var.read(); - wholeDataset = checkUnsigned(datatype, wholeDataset); ImageStack stack = new ImageStack((int) dimensions[3], (int) dimensions[2]); int stackSize = (int) (dimensions[2] * dimensions[3] * 3); @@ -113,7 +96,7 @@ public class HDF5Reader implements PlugIn { } } - ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack); + ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack); imp.setDimensions(3, (int) dimensions[1], (int) dimensions[0]); imp = new CompositeImage(imp, CompositeImage.COMPOSITE); imp.setOpenAsHyperStack(true); @@ -132,7 +115,6 @@ public class HDF5Reader implements PlugIn { selected[3] = dimensions[3]; Object wholeDataset = var.read(); - wholeDataset = checkUnsigned(datatype, wholeDataset); ImageStack stack = new ImageStack((int) dimensions[2], (int) dimensions[1]); int stackSize = (int) (dimensions[1] * dimensions[2] * 3); @@ -141,7 +123,7 @@ public class HDF5Reader implements PlugIn { addSliceRGB( stack, wholeDataset, (int) dimensions[1], (int) dimensions[2], startIdx); } - ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack); + ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack); imp.setDimensions(3, (int) dimensions[0], 1); imp = new CompositeImage(imp, CompositeImage.COMPOSITE); imp.setOpenAsHyperStack(true); @@ -160,20 +142,18 @@ public class HDF5Reader implements PlugIn { selected[3] = dimensions[3]; Object wholeDataset = var.read(); - wholeDataset = checkUnsigned(datatype, wholeDataset); ImageStack stack = new ImageStack((int) dimensions[3], (int) dimensions[2]); - long stackSize = dimensions[2] * dimensions[3]; - long singleVolumeSize = dimensions[1] * stackSize; + int size = (int) (dimensions[2] * dimensions[3]); + long singleVolumeSize = dimensions[1] * size; for (int volIDX = 0; volIDX < dimensions[0]; ++volIDX) { for (int lev = 0; lev < dimensions[1]; ++lev) { - int startIdx = (int) ((volIDX * singleVolumeSize) + (lev * stackSize)); - int endIdx = (int) (startIdx + stackSize); - addSlice(datatypeIfUnsupported, stack, wholeDataset, startIdx, endIdx); + int startIdx = (int) ((volIDX * singleVolumeSize) + (lev * size)); + addSlice(stack, wholeDataset, startIdx, size); } } - ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack); + ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack); imp.setDimensions(1, (int) dimensions[1], (int) dimensions[0]); imp.setOpenAsHyperStack(true); imp.resetDisplayRange(); @@ -190,12 +170,11 @@ public class HDF5Reader implements PlugIn { selected[2] = dimensions[2]; Object wholeDataset = var.read(); - wholeDataset = checkUnsigned(datatype, wholeDataset); ImageStack stack = new ImageStack((int) dimensions[1], (int) dimensions[0]); addSliceRGB(stack, wholeDataset, (int) dimensions[0], (int) dimensions[1]); - ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack); + ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack); imp.setDimensions(3, 1, 1); imp = new CompositeImage(imp, CompositeImage.COMPOSITE); imp.setOpenAsHyperStack(true); @@ -212,17 +191,15 @@ public class HDF5Reader implements PlugIn { selected[2] = dimensions[2]; Object wholeDataset = var.read(); - wholeDataset = checkUnsigned(datatype, wholeDataset); ImageStack stack = new ImageStack((int) dimensions[2], (int) dimensions[1]); - int stackSize = (int) (dimensions[1] * dimensions[2]); + int size = (int) (dimensions[1] * dimensions[2]); for (int lev = 0; lev < dimensions[0]; ++lev) { - int startIdx = lev * stackSize; - int endIdx = startIdx + stackSize; - addSlice(datatypeIfUnsupported, stack, wholeDataset, startIdx, endIdx); + int startIdx = lev * size; + addSlice(stack, wholeDataset, startIdx, size); } - ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack); + ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack); imp.resetDisplayRange(); imp.show(); @@ -230,101 +207,38 @@ public class HDF5Reader implements PlugIn { logger.info("2D Image"); Object wholeDataset = var.read(); - wholeDataset = checkUnsigned(datatype, wholeDataset); ImageStack stack = new ImageStack((int) dimensions[1], (int) dimensions[0]); - addSlice(datatypeIfUnsupported, stack, wholeDataset); + addSlice(stack, wholeDataset); - ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack); + ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack); imp.resetDisplayRange(); imp.show(); } else { - System.err.println(" Error: Variable Dimensions " + numberOfDimensions + " not supported (yet)."); IJ.showStatus("Variable Dimension " + numberOfDimensions + " not supported"); } } } catch (Exception e) { - logger.log(Level.WARNING, "Error while opening '" + directory + name + "'", e); - IJ.showStatus("Error while opening file '" + directory + name + "'"); - } catch (OutOfMemoryError o) { - IJ.outOfMemory("Out of memory while loading file '" + directory + name + "'"); + logger.log(Level.WARNING, "Error while opening: " + filename, e); + IJ.showStatus("Error while opening file: " + filename); + } catch (OutOfMemoryError e) { + IJ.outOfMemory("Out of memory while loading file: " + filename); } finally { try { - if (inFile != null) { - inFile.close(); + if (file != null) { + file.close(); } - } catch (HDF5Exception err) { - logger.log(Level.WARNING, "Error while closing '" + directory + name + "'", err); - IJ.showStatus("Error while closing '" + directory + name + "'"); + } catch (HDF5Exception e) { + logger.log(Level.WARNING, "Error while closing: " + filename, e); + IJ.showStatus("Error while closing: " + filename); } } IJ.showProgress(1.0); } - - /** - * @param datatype - * @param wholeDataset - * @return - */ - private Object checkUnsigned(Datatype datatype, Object wholeDataset) { - // check for unsigned datatype - if (!datatype.isUnsigned() && (datatype.getDatatypeClass() == Datatype.CLASS_INTEGER) && (datatype.getDatatypeSize() == 2)) { - GenericDialog dialog = new GenericDialog("Unsigned to signed conversion"); - dialog.addMessage("Detected unsigned datatype, which is not supported."); - String[] convOptions = {"cut off values", "convert to float"}; - dialog.addChoice("Please select an conversion option:", convOptions, convOptions[0]); - dialog.showDialog(); - if (!dialog.wasCanceled()){ - int unsignedConvSelec = dialog.getNextChoiceIndex(); - if (wholeDataset instanceof short[]) { - if (unsignedConvSelec == 0) { - wholeDataset = HDF5Utilities.cutoffNegative((short[]) wholeDataset); - } else if (unsignedConvSelec == 1) { - wholeDataset = HDF5Utilities.convertToFloat((short[]) wholeDataset); - } - } - } - } - return wholeDataset; - } - - - /** - * Returns a datatype if native datatype is not supported. Returns null if datatype is supported. - * @param datatype - * @return - */ - private Datatype checkIfDatatypeSupported(Datatype datatype) { - Datatype datatypeIfUnsupported = null; - if (datatype.getDatatypeClass() == Datatype.CLASS_INTEGER && (datatype.getDatatypeSize() == 4 || datatype.getDatatypeSize() == 8)) { - logger.info("Datatype not supported by ImageJ"); - GenericDialog typeSelDiag = new GenericDialog("Datatype Selection"); - typeSelDiag.addMessage("The datatype `" + datatype.getDatatypeDescription() + "` is not supported by ImageJ.\n\n"); - typeSelDiag.addMessage("Please select datatype to convert to.\n"); - String[] choices = new String[2]; - choices[0] = "float"; - choices[1] = "short"; - typeSelDiag.addChoice(" Possible types are", choices, "float"); - typeSelDiag.showDialog(); - - if (!typeSelDiag.wasCanceled()) { - int selection = typeSelDiag.getNextChoiceIndex(); - if (selection == 0) { - datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1); - } - if (selection == 1) { - datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_INTEGER, 2, Datatype.NATIVE, -1); - } - } - } - return datatypeIfUnsupported; - } - - /** * Selection of the datasets to visualize * @@ -397,88 +311,42 @@ public class HDF5Reader implements PlugIn { } } - return selectedDatasets; } /** * Add slice to image stack - * @param datatypeIfUnsupported - * @param stack - * @param wholeDataset - * @param startIdx - * @param endIdx + * @param stack Stack to add slice + * @param dataset Dataset to create slice from + * @param startIdx Index of dataset to start to create slice + * @param size Size of dataset to add */ - private void addSlice(Datatype datatypeIfUnsupported, ImageStack stack, Object wholeDataset, int startIdx, int endIdx) { - if (wholeDataset instanceof byte[]) { - byte[] tmp = Arrays.copyOfRange((byte[]) wholeDataset, startIdx, endIdx); - stack.addSlice(null, tmp); - } else if (wholeDataset instanceof short[]) { - short[] tmp = Arrays.copyOfRange((short[]) wholeDataset, startIdx, endIdx); - stack.addSlice(null, tmp); - } else if (wholeDataset instanceof int[]) { - int[] tmp = Arrays.copyOfRange((int[]) wholeDataset, startIdx, endIdx); - if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) { - stack.addSlice(null, HDF5Utilities.convertToFloat(tmp)); - } - if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) { - stack.addSlice(null, HDF5Utilities.convertToShort(tmp)); - } - } else if (wholeDataset instanceof long[]) { - long[] tmp = Arrays.copyOfRange((long[]) wholeDataset, startIdx, endIdx); - if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) { - stack.addSlice(null, HDF5Utilities.convertToFloat(tmp)); - } - if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) { - stack.addSlice(null, HDF5Utilities.convertToShort(tmp)); - } - } else if (wholeDataset instanceof float[]) { - float[] tmp = Arrays.copyOfRange((float[]) wholeDataset, startIdx, endIdx); - stack.addSlice(null, tmp); - } else if (wholeDataset instanceof double[]) { - float[] tmp = HDF5Utilities.convertToFloat(Arrays.copyOfRange((double[]) wholeDataset, startIdx, endIdx)); - stack.addSlice(null, tmp); - } else { - logger.warning("Datatype not supported"); - } + private void addSlice(ImageStack stack, Object dataset, int startIdx, int size) { + Object copy = Array.newInstance(dataset.getClass().getComponentType(), size); + System.arraycopy(dataset, startIdx, copy, 0, size); + addSlice(stack, copy); } + /** * Add slice to image stack - * @param datatypeIfUnsupported - * @param stack - * @param wholeDataset + * @param stack Stack to add slice + * @param dataset Dataset to create slice from */ - private void addSlice(Datatype datatypeIfUnsupported, ImageStack stack, Object wholeDataset){ - if (wholeDataset instanceof byte[]) { - byte[] tmp = (byte[]) wholeDataset; - stack.addSlice(null, tmp); - } else if (wholeDataset instanceof short[]) { - short[] tmp = (short[]) wholeDataset; - stack.addSlice(null, tmp); - } else if (wholeDataset instanceof int[]) { - int[] tmp = (int[]) wholeDataset; - if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) { - stack.addSlice(null, HDF5Utilities.convertToFloat(tmp)); - } - if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) { - stack.addSlice(null, HDF5Utilities.convertToShort(tmp)); - } - } else if (wholeDataset instanceof long[]) { - long[] tmp = (long[]) wholeDataset; - if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) { - stack.addSlice(null, HDF5Utilities.convertToFloat(tmp)); - } - if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) { - stack.addSlice(null, HDF5Utilities.convertToShort(tmp)); - } - } else if (wholeDataset instanceof float[]) { - float[] tmp = (float[]) wholeDataset; - stack.addSlice(null, tmp); - } else if (wholeDataset instanceof double[]) { - float[] tmp = HDF5Utilities.convertToFloat((double[]) wholeDataset); - stack.addSlice(null, tmp); + private void addSlice(ImageStack stack, Object dataset){ + if (dataset instanceof byte[]) { + stack.addSlice(null, (byte[]) dataset); + } else if (dataset instanceof short[]) { + stack.addSlice(null, (short[]) dataset); + } else if (dataset instanceof int[]) { + stack.addSlice(null, HDF5Utilities.convertToFloat((int[]) dataset)); + } else if (dataset instanceof long[]) { + stack.addSlice(null, HDF5Utilities.convertToFloat((long[]) dataset)); + } else if (dataset instanceof float[]) { + stack.addSlice(null, (float[]) dataset); + } else if (dataset instanceof double[]) { + stack.addSlice(null, HDF5Utilities.convertToFloat((double[]) dataset)); } else { logger.warning("Datatype not supported"); } @@ -486,33 +354,28 @@ public class HDF5Reader implements PlugIn { /** - * Add RGB slice to stack - * @param stack - * @param wholeDataset - * @param nRows - * @param nColumns - * @param startIdx - * @param endIdx + * Add RGB slice to image stack + * @param stack Stack to add slice + * @param dataset Dataset to create slice from + * @param nRows Number of rows of the dataset + * @param nColumns Number of columns of the dataset */ - private void addSliceRGB(ImageStack stack, Object wholeDataset, int nRows, int nColumns, int startIdx) { - if(wholeDataset.getClass().isArray()){ - int size = nRows*nColumns; - Object copy = Array.newInstance(wholeDataset.getClass().getComponentType(), size); - System.arraycopy(wholeDataset, startIdx, copy, 0, size); - addSliceRGB(stack, copy, nRows, nColumns); - } + private void addSliceRGB(ImageStack stack, Object dataset, int nRows, int nColumns) { + addSliceRGB(stack, dataset, nRows, nColumns, 0); } + /** - * Add RGB slice to stack - * @param stack - * @param wholeDataset - * @param nRows - * @param nColumns + * Add RGB slice to image stack + * @param stack Stack to add slice + * @param dataset Dataset to create slice from + * @param nRows Number of rows of the dataset + * @param nColumns Number of columns of the dataset + * @param startIdx Index of dataset to start to create slice */ - private void addSliceRGB(ImageStack stack, Object wholeDataset, int nRows, int nColumns) { + private void addSliceRGB(ImageStack stack, Object dataset, int nRows, int nColumns, int startIdx) { int size = nRows*nColumns; - Class type = wholeDataset.getClass().getComponentType(); + Class type = dataset.getClass().getComponentType(); Object r = Array.newInstance(type, size); Object g = Array.newInstance(type, size); @@ -520,11 +383,11 @@ public class HDF5Reader implements PlugIn { for (int row = 0; row < nRows; ++row) { for (int col = 0; col < nColumns; ++col) { - int offsetRGB = (row * nColumns * 3) + (col * 3); + int offsetRGB = startIdx + (row * nColumns * 3) + (col * 3); int offset = (row * nColumns) + col; - Array.set(r, offset,Array.get(wholeDataset,offsetRGB + 0)); - Array.set(g, offset,Array.get(wholeDataset,offsetRGB + 1)); - Array.set(b, offset,Array.get(wholeDataset,offsetRGB + 2)); + Array.set(r, offset,Array.get(dataset,offsetRGB + 0)); + Array.set(g, offset,Array.get(dataset,offsetRGB + 1)); + Array.set(b, offset,Array.get(dataset,offsetRGB + 2)); } } stack.addSlice(null, r); @@ -534,7 +397,8 @@ public class HDF5Reader implements PlugIn { /** - * Add AWT scroll bars to the given container. + * 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(); diff --git a/src/main/java/ch/psi/imagej/hdf5/HDF5Utilities.java b/src/main/java/ch/psi/imagej/hdf5/HDF5Utilities.java index 9d5acbd..fd7708c 100644 --- a/src/main/java/ch/psi/imagej/hdf5/HDF5Utilities.java +++ b/src/main/java/ch/psi/imagej/hdf5/HDF5Utilities.java @@ -4,7 +4,10 @@ import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; +import java.util.Objects; import java.util.logging.Logger; +import java.util.regex.Matcher; +import java.util.regex.Pattern; import javax.swing.tree.DefaultMutableTreeNode; @@ -25,9 +28,7 @@ public class HDF5Utilities { * @return Map of attributes or null if an error occurred while retrieving the attributes or the passed object is null */ public static Map getAttributes(HObject object) { - if (object == null){ - return null; - } + Objects.requireNonNull(object); Map attributes = new HashMap<>(); try{ @@ -47,61 +48,33 @@ public class HDF5Utilities { /** - * 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 + * Example: /test/one/two/three returns 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); + Pattern p = Pattern.compile("^/?(.*)/"); + Matcher m = p.matcher(descriptor); + m.find(); + return m.group(1); } /** - * TODO: to be replaced by a simple regex expression + * Get dataset name * - * Get relative dataset descriptor - * - * Example: - * - * /a/b/c/d/ returns d + * Example: /a/b/c/d/ returns d * * @param descriptor - * @return relative dataset descriptor + * @return Dataset name */ - 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); + public static String getDatasetName(String descriptor) { + Pattern p = Pattern.compile("/+([^/]*)/?$"); + Matcher m = p.matcher(descriptor); + m.find(); + return m.group(1); } /** @@ -123,70 +96,31 @@ public class HDF5Utilities { * @return */ public static Group createGroup( FileFormat file, Group group, String groupName) { - if (groupName == null || file == null) - return null; + Objects.requireNonNull(file); + Objects.requireNonNull(groupName); if (group == null){ group = (Group) ((DefaultMutableTreeNode) file.getRootNode()).getUserObject(); } - // 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 posOfSlash = groupName.indexOf('/'); - - if (posOfSlash == -1) { - try { - Group newGroup; - String newGroupName; - if (group.isRoot()){ - newGroupName = "/" + groupName; - } - else{ - newGroupName = group.getFullName() + "/" + groupName; - } - newGroup = (Group) file.get(newGroupName); - if (newGroup == null){ - newGroup = file.createGroup(newGroupName, group); - } - return newGroup; - } catch (Exception e) { - return null; + Group ngroup = group; + + try{ + String[] groups = groupName.split("/"); + for(String g: groups){ + Group cgroup = (Group) file.get(ngroup.getFullName()+"/"+g); // check if already exist + if (cgroup == null){ + ngroup = file.createGroup(g, ngroup); } - } else { - String subgroupRelativName = groupName.substring(posOfSlash); - String currentGroup = groupName.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(file, newGroup, subgroupRelativName ); - } catch (Exception e) { - return null; + else{ + ngroup = cgroup; } - } - // never come here + return ngroup; + } + catch(Exception e){ + throw new RuntimeException("Unable to create group "); + } } @@ -233,33 +167,6 @@ public class HDF5Utilities { return datasets; } - /** - * Cut of negative values from array. This function will modify the passed array! - * @param array Array with values to cut off - * @return array holding cut off values - */ - public static short[] cutoffNegative(short[] array) { - for (int i = 0; i < array.length; i++) { - if (array[i] < 0) { - array[i] = 0; - } - } - return array; - } - - /** - * Convert short to float array - * @param array short array to convert - * @return Converted float array - */ - public static float[] convertToFloat(short[] array) { - float[] narray = new float[array.length]; - for (int i = 0; i < array.length; i++) { - narray[i] = (float) array[i]; - } - return narray; - } - /** * Convert double to float array * @param array double array to convert @@ -267,8 +174,8 @@ public class HDF5Utilities { */ public static float[] convertToFloat(double[] array) { float[] narray = new float[array.length]; - for (int index = 0; index < array.length; index++) { - narray[index] = (float) array[index]; + for (int i = 0; i < array.length; i++) { + narray[i] = (float) array[i]; } return narray; } @@ -281,26 +188,13 @@ public class HDF5Utilities { */ public static float[] convertToFloat(int[] array) { float[] narray = new float[array.length]; - for (int index = 0; index < array.length; index++) { - narray[index] = array[index]; + for (int i = 0; i < array.length; i++) { + narray[i] = array[i]; } return narray; } - /** - * Convert int to short array - * @param array int array to convert - * @return Converted short array - */ - public static short[] convertToShort(int[] array) { - short[] narray = new short[array.length]; - for (int index = 0; index < array.length; index++) { - narray[index] = (short) array[index]; - } - return narray; - } - /** * Convert long (or int64) to float * @param array long array to convert @@ -308,22 +202,10 @@ public class HDF5Utilities { */ public static float[] convertToFloat(long[] array) { float[] narray = new float[array.length]; - for (int index = 0; index < array.length; index++) { - narray[index] = array[index]; + for (int i = 0; i < array.length; i++) { + narray[i] = array[i]; } return narray; } - /** - * Convert long (or int64) to short - * @param array long array to convert - * @return Converted short array - */ - public static short[] convertToShort(long[] array) { - short[] narray = new short[array.length]; - for (int index = 0; index < array.length; index++) { - narray[index] = (short) array[index]; - } - return narray; - } } diff --git a/src/main/java/ch/psi/imagej/hdf5/HDF5Writer.java b/src/main/java/ch/psi/imagej/hdf5/HDF5Writer.java index c0210ed..eb8508c 100644 --- a/src/main/java/ch/psi/imagej/hdf5/HDF5Writer.java +++ b/src/main/java/ch/psi/imagej/hdf5/HDF5Writer.java @@ -115,7 +115,7 @@ public class HDF5Writer implements PlugInFilter { fullName = fullName.replaceAll("$F", f + ""); fullName = fullName.replaceAll("$C", c + ""); - String dataSetName = HDF5Utilities.getDataSetDescriptor(fullName); + String dataSetName = HDF5Utilities.getDatasetName(fullName); String groupName = HDF5Utilities.getGroupDescriptor(fullName); // Ensure group exists @@ -194,7 +194,7 @@ public class HDF5Writer implements PlugInFilter { } file.open(); - String datasetName = HDF5Utilities.getDataSetDescriptor(varName); + String datasetName = HDF5Utilities.getDatasetName(varName); String groupName = HDF5Utilities.getGroupDescriptor(varName); // Ensure group exists diff --git a/src/test/java/ch/psi/imagej/hdf5/HDF5UtilitiesTest.java b/src/test/java/ch/psi/imagej/hdf5/HDF5UtilitiesTest.java new file mode 100644 index 0000000..a9e066a --- /dev/null +++ b/src/test/java/ch/psi/imagej/hdf5/HDF5UtilitiesTest.java @@ -0,0 +1,25 @@ +package ch.psi.imagej.hdf5; + +import static org.junit.Assert.*; + +import org.junit.Test; + +public class HDF5UtilitiesTest { + + @Test + public void testGetGroupDescriptor() { + String descriptor = "/test/one/two/three"; + String gdescriptor = HDF5Utilities.getGroupDescriptor(descriptor); + System.out.println(gdescriptor); + assertEquals(gdescriptor, "test/one/two"); + } + + @Test + public void testGetDatasetDescriptor() { + String descriptor = "/test/one/two/three"; + String gdescriptor = HDF5Utilities.getDatasetName(descriptor); + System.out.println(gdescriptor); + assertEquals(gdescriptor, "three"); + } + +}