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This commit is contained in:
ebner 2014-09-24 14:03:36 +02:00
parent 3fe26723ef
commit 74aae47436
3 changed files with 745 additions and 726 deletions
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1156
src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java
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186
src/main/java/ch/psi/imagej/hdf5/HDF5Utilities.java
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@ -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;
}
}

119
src/main/java/ch/psi/imagej/hdf5/HDF5Writer.java
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@ -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 groupName = getGroupDescriptor(fullName);
logger.info("group name: " + groupName);
String dataSetName = HDF5Utilities.getDataSetDescriptor(fullName);
String groupName = HDF5Utilities.getGroupDescriptor(fullName);
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);
logger.info("dataset name: " + dataSetName);
String groupName = getGroupDescriptor(varName);
logger.info("group name: " + groupName);
String dataSetName = HDF5Utilities.getDataSetDescriptor(varName);
String groupName = HDF5Utilities.getGroupDescriptor(varName);
logger.info("group name: " + groupName + " dataset name: " + dataSetName);
// 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;