imagej/ch.psi.imagej.hdf5
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Exchanges lots of code with standard constructs

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ebner 2014-08-28 11:56:50 +02:00
parent e1910dcd7f
commit 7ff965bc08
4 changed files with 159 additions and 177 deletions
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6
.project
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@ -15,9 +15,15 @@
<arguments> <arguments>
</arguments> </arguments>
</buildCommand> </buildCommand>
<buildCommand>
<name>ch.acanda.eclipse.pmd.builder.PMDBuilder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec> </buildSpec>
<natures> <natures>
<nature>org.eclipse.jdt.core.javanature</nature> <nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature> <nature>org.eclipse.m2e.core.maven2Nature</nature>
<nature>ch.acanda.eclipse.pmd.builder.PMDNature</nature>
</natures> </natures>
</projectDescription> </projectDescription>

2
Readme.md
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@ -75,6 +75,8 @@ cd <FIJI_HOME>
<fiji> --java-home /usr/lib/jvm/jre-1.7.0-openjdk.x86_64 -Djava.library.path=lib/linux64 <fiji> --java-home /usr/lib/jvm/jre-1.7.0-openjdk.x86_64 -Djava.library.path=lib/linux64
``` ```
Starting with Java 8 just the LD_LIBRARY_PATH variable need to be set. For MacOSX it is export `DYLD_LIBRARY_PATH=lib/mac64/:$DYLD_LIBRARY_PATH`.
# Development # Development
To create an all in one zip file for installation in a ImageJ installation use: To create an all in one zip file for installation in a ImageJ installation use:
`mvn clean compile assembly:assembly` `mvn clean compile assembly:assembly`

310
src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java
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@ -31,7 +31,10 @@ import ij.process.ImageProcessor;
import java.io.File; import java.io.File;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List; import java.util.List;
import java.util.Map;
import java.util.logging.Level; import java.util.logging.Level;
import java.util.logging.Logger; import java.util.logging.Logger;
import java.awt.*; import java.awt.*;
@ -42,19 +45,19 @@ import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
public class HDF5Reader implements PlugIn { public class HDF5Reader implements PlugIn {
private static final Logger logger = Logger.getLogger(HDF5Reader.class.getName());
public static void main(String[] args){ public static void main(String[] args){
HDF5Reader r = new HDF5Reader(); HDF5Reader r = new HDF5Reader();
r.run(""); r.run("");
} }
private static final Logger logger = Logger.getLogger(HDF5Reader.class.getName());
public void run(String arg) { public void run(String arg) {
// make sure default values for config are written // make sure default values for config are written
// HDF5_Config.setDefaultsIfNoValueExists(); // HDF5_Config.setDefaultsIfNoValueExists();
// run plugin // Run plugin
String directory = ""; String directory = "";
String name = ""; String name = "";
boolean tryAgain; boolean tryAgain;
@ -71,7 +74,7 @@ public class HDF5Reader implements PlugIn {
name = od.getFileName(); name = od.getFileName();
if (name == null) if (name == null)
return; return;
if (name == "") if (name.equals(""))
return; return;
File testFile = new File(directory + name); File testFile = new File(directory + name);
@ -93,11 +96,7 @@ public class HDF5Reader implements PlugIn {
inFile = new H5File(directory + name, H5File.READ); inFile = new H5File(directory + name, H5File.READ);
inFile.open(); inFile.open();
// Parse the file
/*-------------------------------------------------------------------
* parse the file
*-------------------------------------------------------------------*/
Group rootNode = (Group) ((javax.swing.tree.DefaultMutableTreeNode) inFile.getRootNode()).getUserObject(); Group rootNode = (Group) ((javax.swing.tree.DefaultMutableTreeNode) inFile.getRootNode()).getUserObject();
List<Dataset> varList = getDataSetList(rootNode, new ArrayList<Dataset>()); List<Dataset> varList = getDataSetList(rootNode, new ArrayList<Dataset>());
@ -191,7 +190,7 @@ public class HDF5Reader implements PlugIn {
logger.info(""); logger.info("");
IJ.showStatus("Reading Variable: " + var.getName() + " (" + extent[0] + " slices)"); IJ.showStatus("Reading Variable: " + var.getName() + " (" + extent[0] + " slices)");
Attribute elemsize_att = getAttribute(var, "element_size_um"); Attribute elemsize_att = getAttributes(var).get("element_size_um");
double[] elem_sizes = new double[3]; double[] elem_sizes = new double[3];
if (elemsize_att == null) { if (elemsize_att == null) {
elem_sizes[0] = 1.0; elem_sizes[0] = 1.0;
@ -219,6 +218,7 @@ public class HDF5Reader implements PlugIn {
} }
logger.info(" Element-Size in um (level,row,col): " + elem_sizes[0] + ", " + elem_sizes[1] + ", " + elem_sizes[2]); logger.info(" Element-Size in um (level,row,col): " + elem_sizes[0] + ", " + elem_sizes[1] + ", " + elem_sizes[2]);
// nice gadget to update the progress bar // nice gadget to update the progress bar
long progressDivisor = extent[0] / 50; // we assume 50 process steps long progressDivisor = extent[0] / 50; // we assume 50 process steps
if (progressDivisor < 1) if (progressDivisor < 1)
@ -296,6 +296,7 @@ public class HDF5Reader implements PlugIn {
long stackSize = extent[2] * extent[3]; long stackSize = extent[2] * extent[3];
long singleVolumeSize = extent[1] * stackSize; long singleVolumeSize = extent[1] * stackSize;
int size = (int) stackSize;
for (int volIDX = 0; volIDX < extent[0]; ++volIDX) { for (int volIDX = 0; volIDX < extent[0]; ++volIDX) {
if ((volIDX % progressDivisor) == 0) if ((volIDX % progressDivisor) == 0)
@ -306,14 +307,15 @@ public class HDF5Reader implements PlugIn {
// select hyperslab for lev // select hyperslab for lev
// start[1] = lev; // start[1] = lev;
// Object slice = var.read(); // Object slice = var.read();
long startIdx = (volIDX * singleVolumeSize * 3) + (lev * stackSize * 3); int startIdx = (int)((volIDX * singleVolumeSize * 3) + (lev * stackSize * 3));
long numElements = stackSize * 3; // long numElements = stackSize * 3;
int endIdx = (int)(startIdx+stackSize*3-1);
if (wholeDataset instanceof byte[]) { if (wholeDataset instanceof byte[]) {
byte[] tmp = (byte[]) extractSubarray(wholeDataset, startIdx, numElements); byte[] tmp = Arrays.copyOfRange((byte[]) wholeDataset, startIdx, endIdx);
byte[] rChannel = new byte[(int) stackSize]; byte[] rChannel = new byte[size];
byte[] gChannel = new byte[(int) stackSize]; byte[] gChannel = new byte[size];
byte[] bChannel = new byte[(int) stackSize]; byte[] bChannel = new byte[size];
for (int row = 0; row < extent[2]; ++row) { for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) { for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3); int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
@ -327,10 +329,10 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, gChannel); stack.addSlice(null, gChannel);
stack.addSlice(null, bChannel); stack.addSlice(null, bChannel);
} else if (wholeDataset instanceof short[]) { } else if (wholeDataset instanceof short[]) {
short[] tmp = (short[]) extractSubarray(wholeDataset, startIdx, numElements); short[] tmp = Arrays.copyOfRange((short[]) wholeDataset, startIdx, endIdx);
short[] rChannel = new short[(int) stackSize]; short[] rChannel = new short[size];
short[] gChannel = new short[(int) stackSize]; short[] gChannel = new short[size];
short[] bChannel = new short[(int) stackSize]; short[] bChannel = new short[size];
for (int row = 0; row < extent[2]; ++row) { for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) { for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3); int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
@ -345,10 +347,10 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, bChannel); stack.addSlice(null, bChannel);
} else if (wholeDataset instanceof int[]) { } else if (wholeDataset instanceof int[]) {
if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) { if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
float[] tmp = convertInt32ToFloat((int[]) extractSubarray(wholeDataset, startIdx, numElements)); float[] tmp = convertInt32ToFloat(Arrays.copyOfRange((int[]) wholeDataset, startIdx, endIdx));
float[] rChannel = new float[(int) stackSize]; float[] rChannel = new float[size];
float[] gChannel = new float[(int) stackSize]; float[] gChannel = new float[size];
float[] bChannel = new float[(int) stackSize]; float[] bChannel = new float[size];
for (int row = 0; row < extent[2]; ++row) { for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) { for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3); int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
@ -363,10 +365,10 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, bChannel); stack.addSlice(null, bChannel);
} }
if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) { if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) {
short[] tmp = convertInt32ToShort((int[]) extractSubarray(wholeDataset, startIdx, numElements)); short[] tmp = convertInt32ToShort(Arrays.copyOfRange((int[]) wholeDataset, startIdx, endIdx));
short[] rChannel = new short[(int) stackSize]; short[] rChannel = new short[size];
short[] gChannel = new short[(int) stackSize]; short[] gChannel = new short[size];
short[] bChannel = new short[(int) stackSize]; short[] bChannel = new short[size];
for (int row = 0; row < extent[2]; ++row) { for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) { for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3); int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
@ -382,10 +384,10 @@ public class HDF5Reader implements PlugIn {
} }
} else if (wholeDataset instanceof long[]) { } else if (wholeDataset instanceof long[]) {
if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) { if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
float[] tmp = convertInt64ToFloat((long[]) extractSubarray(wholeDataset, startIdx, numElements)); float[] tmp = convertInt64ToFloat(Arrays.copyOfRange((long[]) wholeDataset, startIdx, endIdx));
float[] rChannel = new float[(int) stackSize]; float[] rChannel = new float[size];
float[] gChannel = new float[(int) stackSize]; float[] gChannel = new float[size];
float[] bChannel = new float[(int) stackSize]; float[] bChannel = new float[size];
for (int row = 0; row < extent[2]; ++row) { for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) { for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3); int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
@ -400,10 +402,10 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, bChannel); stack.addSlice(null, bChannel);
} }
if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) { if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) {
short[] tmp = convertInt64ToShort((long[]) extractSubarray(wholeDataset, startIdx, numElements)); short[] tmp = convertInt64ToShort(Arrays.copyOfRange((long[]) wholeDataset, startIdx, endIdx));
short[] rChannel = new short[(int) stackSize]; short[] rChannel = new short[size];
short[] gChannel = new short[(int) stackSize]; short[] gChannel = new short[size];
short[] bChannel = new short[(int) stackSize]; short[] bChannel = new short[size];
for (int row = 0; row < extent[2]; ++row) { for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) { for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3); int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
@ -418,10 +420,10 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, bChannel); stack.addSlice(null, bChannel);
} }
} else if (wholeDataset instanceof float[]) { } else if (wholeDataset instanceof float[]) {
float[] tmp = (float[]) extractSubarray(wholeDataset, startIdx, numElements); float[] tmp = Arrays.copyOfRange((float[]) wholeDataset, startIdx, endIdx);
float[] rChannel = new float[(int) stackSize]; float[] rChannel = new float[size];
float[] gChannel = new float[(int) stackSize]; float[] gChannel = new float[size];
float[] bChannel = new float[(int) stackSize]; float[] bChannel = new float[size];
for (int row = 0; row < extent[2]; ++row) { for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) { for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3); int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
@ -435,10 +437,10 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, gChannel); stack.addSlice(null, gChannel);
stack.addSlice(null, bChannel); stack.addSlice(null, bChannel);
} else if (wholeDataset instanceof double[]) { } else if (wholeDataset instanceof double[]) {
float[] tmp = convertDoubleToFloat((double[]) extractSubarray(wholeDataset, startIdx, numElements)); float[] tmp = convertDoubleToFloat(Arrays.copyOfRange((double[]) wholeDataset, startIdx, endIdx));
float[] rChannel = new float[(int) stackSize]; float[] rChannel = new float[size];
float[] gChannel = new float[(int) stackSize]; float[] gChannel = new float[size];
float[] bChannel = new float[(int) stackSize]; float[] bChannel = new float[size];
for (int row = 0; row < extent[2]; ++row) { for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) { for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3); int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
@ -452,8 +454,7 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, gChannel); stack.addSlice(null, gChannel);
stack.addSlice(null, bChannel); stack.addSlice(null, bChannel);
} else { } else {
// try to put pixels on stack logger.warning("Datatype not supported");
stack.addSlice(null, extractSubarray(wholeDataset, startIdx, numElements));
} }
} }
} }
@ -537,13 +538,14 @@ public class HDF5Reader implements PlugIn {
// start[0] = lev; // start[0] = lev;
// Object slice = var.read(); // Object slice = var.read();
long startIdx = lev * stackSize; int startIdx = (int)(lev * stackSize);
long numElements = stackSize; // long numElements = stackSize;
Object slice = extractSubarray(wholeDataset, startIdx, numElements); int endIdx = (int)(startIdx+stackSize-1);
// Object slice = extractSubarray(wholeDataset, startIdx, numElements);
int size = (int) (extent[2] * extent[1]); int size = (int) (extent[2] * extent[1]);
if (slice instanceof byte[]) { if (wholeDataset instanceof byte[]) {
byte[] tmp = (byte[]) slice; byte[] tmp = Arrays.copyOfRange((byte[]) wholeDataset, startIdx, endIdx);
byte[] rChannel = new byte[size]; byte[] rChannel = new byte[size];
byte[] gChannel = new byte[size]; byte[] gChannel = new byte[size];
byte[] bChannel = new byte[size]; byte[] bChannel = new byte[size];
@ -559,8 +561,8 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, rChannel); stack.addSlice(null, rChannel);
stack.addSlice(null, gChannel); stack.addSlice(null, gChannel);
stack.addSlice(null, bChannel); stack.addSlice(null, bChannel);
} else if (slice instanceof short[]) { } else if (wholeDataset instanceof short[]) {
short[] tmp = (short[]) slice; short[] tmp = Arrays.copyOfRange((short[]) wholeDataset, startIdx, endIdx);
short[] rChannel = new short[size]; short[] rChannel = new short[size];
short[] gChannel = new short[size]; short[] gChannel = new short[size];
short[] bChannel = new short[size]; short[] bChannel = new short[size];
@ -576,8 +578,8 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, rChannel); stack.addSlice(null, rChannel);
stack.addSlice(null, gChannel); stack.addSlice(null, gChannel);
stack.addSlice(null, bChannel); stack.addSlice(null, bChannel);
} else if (slice instanceof int[]) { } else if (wholeDataset instanceof int[]) {
int[] tmp = (int[]) slice; int[] tmp = Arrays.copyOfRange((int[]) wholeDataset, startIdx, endIdx);
int[] rChannel = new int[size]; int[] rChannel = new int[size];
int[] gChannel = new int[size]; int[] gChannel = new int[size];
int[] bChannel = new int[size]; int[] bChannel = new int[size];
@ -593,8 +595,8 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, rChannel); stack.addSlice(null, rChannel);
stack.addSlice(null, gChannel); stack.addSlice(null, gChannel);
stack.addSlice(null, bChannel); stack.addSlice(null, bChannel);
} else if (slice instanceof long[]) { } else if (wholeDataset instanceof long[]) {
long[] tmp = (long[]) slice; long[] tmp = Arrays.copyOfRange((long[]) wholeDataset, startIdx, endIdx);
long[] rChannel = new long[size]; long[] rChannel = new long[size];
long[] gChannel = new long[size]; long[] gChannel = new long[size];
long[] bChannel = new long[size]; long[] bChannel = new long[size];
@ -610,8 +612,8 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, rChannel); stack.addSlice(null, rChannel);
stack.addSlice(null, gChannel); stack.addSlice(null, gChannel);
stack.addSlice(null, bChannel); stack.addSlice(null, bChannel);
} else if (slice instanceof float[]) { } else if (wholeDataset instanceof float[]) {
float[] tmp = (float[]) slice; float[] tmp = Arrays.copyOfRange((float[]) wholeDataset, startIdx, endIdx);
float[] rChannel = new float[size]; float[] rChannel = new float[size];
float[] gChannel = new float[size]; float[] gChannel = new float[size];
float[] bChannel = new float[size]; float[] bChannel = new float[size];
@ -627,8 +629,8 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, rChannel); stack.addSlice(null, rChannel);
stack.addSlice(null, gChannel); stack.addSlice(null, gChannel);
stack.addSlice(null, bChannel); stack.addSlice(null, bChannel);
} else if (slice instanceof double[]) { } else if (wholeDataset instanceof double[]) {
double[] tmp = (double[]) slice; double[] tmp = Arrays.copyOfRange((double[]) wholeDataset, startIdx, endIdx);
double[] rChannel = new double[size]; double[] rChannel = new double[size];
double[] gChannel = new double[size]; double[] gChannel = new double[size];
double[] bChannel = new double[size]; double[] bChannel = new double[size];
@ -716,17 +718,18 @@ public class HDF5Reader implements PlugIn {
// select hyperslab for lev // select hyperslab for lev
// start[1] = lev; // start[1] = lev;
// Object slice = var.read(); // Object slice = var.read();
long startIdx = (volIDX * singleVolumeSize) + (lev * stackSize); int startIdx = (int)((volIDX * singleVolumeSize) + (lev * stackSize));
long numElements = stackSize; int endIdx = (int)(startIdx+stackSize-1);
// long numElements = stackSize;
if (wholeDataset instanceof byte[]) { if (wholeDataset instanceof byte[]) {
byte[] tmp = (byte[]) extractSubarray(wholeDataset, startIdx, numElements); byte[] tmp = Arrays.copyOfRange((byte[]) wholeDataset, startIdx, endIdx);
stack.addSlice(null, tmp); stack.addSlice(null, tmp);
} else if (wholeDataset instanceof short[]) { } else if (wholeDataset instanceof short[]) {
short[] tmp = (short[]) extractSubarray(wholeDataset, startIdx, numElements); short[] tmp = Arrays.copyOfRange((short[]) wholeDataset, startIdx, endIdx);
stack.addSlice(null, tmp); stack.addSlice(null, tmp);
} else if (wholeDataset instanceof int[]) { } else if (wholeDataset instanceof int[]) {
int[] tmp = (int[]) extractSubarray(wholeDataset, startIdx, numElements); int[] tmp = Arrays.copyOfRange((int[]) wholeDataset, startIdx, endIdx);
if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) { if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
stack.addSlice(null, convertInt32ToFloat(tmp)); stack.addSlice(null, convertInt32ToFloat(tmp));
} }
@ -734,7 +737,7 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, convertInt32ToShort(tmp)); stack.addSlice(null, convertInt32ToShort(tmp));
} }
} else if (wholeDataset instanceof long[]) { } else if (wholeDataset instanceof long[]) {
long[] tmp = (long[]) extractSubarray(wholeDataset, startIdx, numElements); long[] tmp = Arrays.copyOfRange((long[]) wholeDataset, startIdx, endIdx);
if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) { if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
stack.addSlice(null, convertInt64ToFloat(tmp)); stack.addSlice(null, convertInt64ToFloat(tmp));
} }
@ -742,14 +745,13 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, convertInt64ToShort(tmp)); stack.addSlice(null, convertInt64ToShort(tmp));
} }
} else if (wholeDataset instanceof float[]) { } else if (wholeDataset instanceof float[]) {
float[] tmp = (float[]) extractSubarray(wholeDataset, startIdx, numElements); float[] tmp = Arrays.copyOfRange((float[]) wholeDataset, startIdx, endIdx);
stack.addSlice(null, tmp); stack.addSlice(null, tmp);
} else if (wholeDataset instanceof double[]) { } else if (wholeDataset instanceof double[]) {
float[] tmp = convertDoubleToFloat((double[]) extractSubarray(wholeDataset, startIdx, numElements)); float[] tmp = convertDoubleToFloat(Arrays.copyOfRange((double[]) wholeDataset, startIdx, endIdx));
stack.addSlice(null, tmp); stack.addSlice(null, tmp);
} else { } else {
// try to put pixels on stack logger.warning("Datatype not supported");
stack.addSlice(null, extractSubarray(wholeDataset, startIdx, numElements));
} }
} }
} }
@ -760,12 +762,12 @@ public class HDF5Reader implements PlugIn {
int nChannels = 1; int nChannels = 1;
int nSlices = (int) extent[1]; int nSlices = (int) extent[1];
int nFrames = (int) extent[0]; int nFrames = (int) extent[0];
Integer nFramesI = new Integer(nFrames); Integer nFramesI = nFrames;
Integer nSlicesI = new Integer(nSlices); Integer nSlicesI = nSlices;
logger.info("nFrames: " + nFramesI.toString()); logger.info("nFrames: " + nFramesI.toString());
logger.info("nSlices: " + nSlicesI.toString()); logger.info("nSlices: " + nSlicesI.toString());
Integer myStackSize = new Integer(stack.getSize()); Integer myStackSize = stack.getSize();
logger.info("stackSize: " + myStackSize.toString()); logger.info("stackSize: " + myStackSize.toString());
imp.setDimensions(nChannels, nSlices, nFrames); imp.setDimensions(nChannels, nSlices, nFrames);
@ -977,16 +979,17 @@ public class HDF5Reader implements PlugIn {
// start[0] = lev; // start[0] = lev;
// Object slice = var.read(); // Object slice = var.read();
long startIdx = lev * stackSize; int startIdx = (int)(lev * stackSize);
long numElements = stackSize; int endIdx = (int)(startIdx+stackSize-1);
// long numElements = stackSize;
if (wholeDataset instanceof byte[]) { if (wholeDataset instanceof byte[]) {
byte[] tmp = (byte[]) extractSubarray(wholeDataset, startIdx, numElements); byte[] tmp = Arrays.copyOfRange((byte[]) wholeDataset, startIdx, endIdx);
stack.addSlice(null, tmp); stack.addSlice(null, tmp);
} else if (wholeDataset instanceof short[]) { } else if (wholeDataset instanceof short[]) {
short[] tmp = (short[]) extractSubarray(wholeDataset, startIdx, numElements); short[] tmp = Arrays.copyOfRange((short[]) wholeDataset, startIdx, endIdx);
stack.addSlice(null, tmp); stack.addSlice(null, tmp);
} else if (wholeDataset instanceof int[]) { } else if (wholeDataset instanceof int[]) {
int[] tmp = (int[]) extractSubarray(wholeDataset, startIdx, numElements); int[] tmp = Arrays.copyOfRange((int[]) wholeDataset, startIdx, endIdx);
if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) { if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
stack.addSlice(null, convertInt32ToFloat(tmp)); stack.addSlice(null, convertInt32ToFloat(tmp));
} }
@ -994,7 +997,8 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, convertInt32ToShort(tmp)); stack.addSlice(null, convertInt32ToShort(tmp));
} }
} else if (wholeDataset instanceof long[]) { } else if (wholeDataset instanceof long[]) {
long[] tmp = (long[]) extractSubarray(wholeDataset, startIdx, numElements);
long[] tmp = Arrays.copyOfRange((long[]) wholeDataset, startIdx, endIdx);
if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) { if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
stack.addSlice(null, convertInt64ToFloat(tmp)); stack.addSlice(null, convertInt64ToFloat(tmp));
} }
@ -1002,14 +1006,13 @@ public class HDF5Reader implements PlugIn {
stack.addSlice(null, convertInt64ToShort(tmp)); stack.addSlice(null, convertInt64ToShort(tmp));
} }
} else if (wholeDataset instanceof float[]) { } else if (wholeDataset instanceof float[]) {
float[] tmp = (float[]) extractSubarray(wholeDataset, startIdx, numElements); float[] tmp = Arrays.copyOfRange((float[]) wholeDataset, startIdx, endIdx);
stack.addSlice(null, tmp); stack.addSlice(null, tmp);
} else if (wholeDataset instanceof double[]) { } else if (wholeDataset instanceof double[]) {
float[] tmp = convertDoubleToFloat((double[]) extractSubarray(wholeDataset, startIdx, numElements)); float[] tmp = convertDoubleToFloat(Arrays.copyOfRange((double[]) wholeDataset, startIdx, endIdx));
stack.addSlice(null, tmp); stack.addSlice(null, tmp);
} else { } else {
// try to put pixels on stack logger.warning("Not supported array type");
stack.addSlice(null, extractSubarray(wholeDataset, startIdx, numElements));
} }
} }
IJ.showProgress(1.f); IJ.showProgress(1.f);
@ -1131,6 +1134,7 @@ public class HDF5Reader implements PlugIn {
} catch (OutOfMemoryError o) { } catch (OutOfMemoryError o) {
IJ.outOfMemory("Load HDF5"); IJ.outOfMemory("Load HDF5");
} }
// make sure the file is closed after working with it // make sure the file is closed after working with it
// FIXME: should happen in catch-part, too! // FIXME: should happen in catch-part, too!
try { try {
@ -1145,54 +1149,56 @@ public class HDF5Reader implements PlugIn {
IJ.showProgress(1.0); IJ.showProgress(1.0);
} }
/**
private static List<Dataset> getDataSetList(Group g, List<Dataset> datasets) throws Exception { * Recursively get list of all datasets in file
if (g == null){ * @param group Group to search for datasets
* @param datasets List of datasets
* @return List of datasets or null if group is null
*/
private List<Dataset> getDataSetList(Group group, List<Dataset> datasets) {
if (group == null){
return datasets; return datasets;
} }
List<HObject> members = g.getMemberList(); for (HObject o: group.getMemberList()) {
for (HObject obj: members) { if (o instanceof Dataset) {
if (obj instanceof Dataset) { ((Dataset) o).init();
((Dataset) obj).init(); datasets.add((Dataset) o);
datasets.add((Dataset) obj); } else if (o instanceof Group) {
} else if (obj instanceof Group) { datasets = (getDataSetList((Group) o, datasets));
datasets = (getDataSetList((Group) obj, datasets));
} }
} }
return datasets; return datasets;
} }
private static List<Attribute> getAttrList(HObject ds) throws Exception { /**
if (ds == null){ * Get attributes from object
* @param object Object to retrieve the attributes from
* @return Map of attributes or null if an error occurred while retrieving the attributes or the passed object is null
*/
private Map<String,Attribute> getAttributes(HObject object) {
if (object == null){
return null; return null;
} }
List<Attribute> attributes = new ArrayList<Attribute>(); Map<String, Attribute> attributes = new HashMap<>();
List<?> members = ds.getMetadata(); try{
int n = members.size(); for(Object m: object.getMetadata()){
Metadata obj = null; if(m instanceof Attribute){
for (int i = 0; i < n; i++) { attributes.put(((Attribute) m).getName(), (Attribute) m);
obj = (Metadata) members.get(i); }
if (obj instanceof Attribute) {
attributes.add((Attribute) obj);
} }
} }
catch(Exception e){
logger.warning("Unable to retrieve metadata from object");
return null;
}
return attributes; return attributes;
} }
private static Attribute getAttribute(Dataset ds, String attrName) throws Exception {
for(Attribute a: getAttrList((HObject) ds)){
if (a.getName().equals(attrName)) {
return a;
}
}
return null;
}
private float[] convertDoubleToFloat(double[] dataIn) { private float[] convertDoubleToFloat(double[] dataIn) {
float[] dataOut = new float[dataIn.length]; float[] dataOut = new float[dataIn.length];
for (int index = 0; index < dataIn.length; index++) { for (int index = 0; index < dataIn.length; index++) {
@ -1201,36 +1207,37 @@ public class HDF5Reader implements PlugIn {
return dataOut; return dataOut;
} }
private float[] convertInt32ToFloat(int[] dataIn) {
float[] dataOut = new float[dataIn.length]; private float[] convertInt32ToFloat(int[] array) {
for (int index = 0; index < dataIn.length; index++) { float[] narray = new float[array.length];
dataOut[index] = dataIn[index]; for (int index = 0; index < array.length; index++) {
narray[index] = array[index];
} }
return dataOut; return narray;
} }
private short[] convertInt32ToShort(int[] dataIn) { private short[] convertInt32ToShort(int[] array) {
short[] dataOut = new short[dataIn.length]; short[] narray = new short[array.length];
for (int index = 0; index < dataIn.length; index++) { for (int index = 0; index < array.length; index++) {
dataOut[index] = (short) dataIn[index]; narray[index] = (short) array[index];
} }
return dataOut; return narray;
} }
private float[] convertInt64ToFloat(long[] dataIn) { private float[] convertInt64ToFloat(long[] array) {
float[] dataOut = new float[dataIn.length]; float[] narray = new float[array.length];
for (int index = 0; index < dataIn.length; index++) { for (int index = 0; index < array.length; index++) {
dataOut[index] = dataIn[index]; narray[index] = array[index];
} }
return dataOut; return narray;
} }
private short[] convertInt64ToShort(long[] dataIn) { private short[] convertInt64ToShort(long[] array) {
short[] dataOut = new short[dataIn.length]; short[] narray = new short[array.length];
for (int index = 0; index < dataIn.length; index++) { for (int index = 0; index < array.length; index++) {
dataOut[index] = (short) dataIn[index]; narray[index] = (short) array[index];
} }
return dataOut; return narray;
} }
private Object convertToUnsigned(Object dataIn, int unsignedConvSelec) { private Object convertToUnsigned(Object dataIn, int unsignedConvSelec) {
@ -1258,43 +1265,6 @@ public class HDF5Reader implements PlugIn {
return dataOut; return dataOut;
} }
private Object extractSubarray(Object data, long startIdx, long numElements) {
Object subarray = null;
if (data instanceof byte[]) {
subarray = new byte[(int) numElements];
for (long idx = startIdx; idx < startIdx + numElements; idx++) {
((byte[]) subarray)[(int) (idx - startIdx)] = ((byte[]) data)[(int) (idx)];
}
} else if (data instanceof short[]) {
subarray = new short[(int) numElements];
for (long idx = startIdx; idx < startIdx + numElements; idx++) {
((short[]) subarray)[(int) (idx - startIdx)] = ((short[]) data)[(int) (idx)];
}
} else if (data instanceof int[]) {
subarray = new int[(int) numElements];
for (long idx = startIdx; idx < startIdx + numElements; idx++) {
((int[]) subarray)[(int) (idx - startIdx)] = ((int[]) data)[(int) (idx)];
}
} else if (data instanceof long[]) {
subarray = new long[(int) numElements];
for (long idx = startIdx; idx < startIdx + numElements; idx++) {
((long[]) subarray)[(int) (idx - startIdx)] = ((long[]) data)[(int) (idx)];
}
} else if (data instanceof float[]) {
subarray = new float[(int) numElements];
for (long idx = startIdx; idx < startIdx + numElements; idx++) {
((float[]) subarray)[(int) (idx - startIdx)] = ((float[]) data)[(int) (idx)];
}
} else if (data instanceof double[]) {
subarray = new double[(int) numElements];
for (long idx = startIdx; idx < startIdx + numElements; idx++) {
((double[]) subarray)[(int) (idx - startIdx)] = ((double[]) data)[(int) (idx)];
}
}
return subarray;
}
/** Adds AWT scroll bars to the given container. */ /** Adds AWT scroll bars to the given container. */
public static void addScrollBars(Container pane) { public static void addScrollBars(Container pane) {
GridBagLayout layout = (GridBagLayout) pane.getLayout(); GridBagLayout layout = (GridBagLayout) pane.getLayout();

16
src/main/java/ch/psi/imagej/hdf5/TimeFrame.java
View File

@ -32,14 +32,18 @@ public class TimeFrame implements Comparable<TimeFrame> {
} }
public String toString() { public String toString() {
String s = "FrameIdx: " + Integer.toString(frameIndex) + "; "; StringBuffer b = new StringBuffer();
s = s + "nChannels: " + Integer.toString(channels.size()) + "; "; b.append("FrameIdx: ");
s = s + "channels: "; b.append(frameIndex);
for (int i = 0; i < channels.size(); i++){ b.append("; nChannels: ");
s = s + Integer.toString(channels.get(i)) + ";"; b.append(channels.size());
b.append("; Channels: ");
for(Integer c: channels){
b.append(c);
b.append(";");
} }
return s; return b.toString();
} }
public int getNChannels() { public int getNChannels() {