imagej/ch.psi.imagej.hdf5
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Finished refactoring

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This commit is contained in:
ebner 2014-10-01 08:59:59 +02:00
parent 133796730a
commit 9619aac78c
5 changed files with 157 additions and 386 deletions
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2
pom.xml
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@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ch.psi</groupId>
<artifactId>imagej.hdf5</artifactId>
<version>0.5.0</version>
<version>0.6.0</version>
<dependencies>
<dependency>

314
src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java
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@ -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<Dataset> datasets = HDF5Utilities.getDatasets(inFile);
List<Dataset> datasets = HDF5Utilities.getDatasets(file);
List<Dataset> 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();

198
src/main/java/ch/psi/imagej/hdf5/HDF5Utilities.java
View File

@ -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<String,Attribute> getAttributes(HObject object) {
if (object == null){
return null;
}
Objects.requireNonNull(object);
Map<String, Attribute> 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;
}
}

4
src/main/java/ch/psi/imagej/hdf5/HDF5Writer.java
View File

@ -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

25
src/test/java/ch/psi/imagej/hdf5/HDF5UtilitiesTest.java Normal file
View File

@ -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");
}
}