imagej/ch.psi.imagej.hdf5
1
0
Fork 0
mirror of https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5.git synced 2025-06-07 02:50:42 +02:00
Code Issues Packages Projects Releases Wiki Activity

Add quick and dirty hack

Browse Source 
Quick and dirty hack to allow imagej (python) scripts to open hdf5 files via a routine and do operation with them.
This is far from perfect and needs major cleanup! It is implemented like this due to lack of time ...
This commit is contained in:
ebner 2017-08-28 17:13:10 +02:00
parent eca2294000
commit 3c9fd2b97e
1 changed files with 56 additions and 72 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

114
src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java
View File

@ -10,10 +10,7 @@ import ij.plugin.PlugIn;
import java.io.File; import java.io.File;
import java.lang.reflect.Array; import java.lang.reflect.Array;
import java.util.Arrays; import java.util.*;
import java.util.HashMap;
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;
@ -31,8 +28,12 @@ public class HDF5Reader implements PlugIn {
*/ */
public static void main(String[] args){ public static void main(String[] args){
HDF5Reader r = new HDF5Reader(); HDF5Reader r = new HDF5Reader();
r.run("path=/Users/ebner/Desktop/ open=A8_d_400N030_.h5"); // r.run("");
// IJ.run("HDF5...", "/Users/ebner/Desktop/A8_d_400N030_.h5"); r.open("",false, "/Users/ebner/Desktop/A8_d_400N030_.h5", "/exchange/data", true);
}
public void run(String arg) {
open(arg, true, null, null, true);
} }
/** /**
@ -45,26 +46,33 @@ public class HDF5Reader implements PlugIn {
* dataset=/your/path/to/dataset * dataset=/your/path/to/dataset
* *
*/ */
public void run(String arg) { public ImageStack open(String arg, boolean interactive, String filename, String nameOfDataset, boolean virtualstack) {
Map arguments = HDF5Reader.parseArguments(arg); // Map arguments = HDF5Reader.parseArguments(arg);
File tfile = null;
if(interactive) {
OpenDialog od = new OpenDialog("Open HDF5 ...", arg); OpenDialog od = new OpenDialog("Open HDF5 ...", arg);
tfile = new File(od.getDirectory() + od.getFileName());
File tfile = new File(od.getDirectory() + od.getFileName());
if (!tfile.exists() || !tfile.canRead()) { if (!tfile.exists() || !tfile.canRead()) {
IJ.showMessage("Cannot open file: "+tfile.getAbsolutePath()); IJ.showMessage("Cannot open file: "+tfile.getAbsolutePath());
return; return null;
} }
String filename = tfile.getAbsolutePath();
// Overwrite filename with selected filename
filename = tfile.getAbsolutePath();
IJ.showStatus("Loading HDF5 File: " + filename); IJ.showStatus("Loading HDF5 File: " + filename);
IJ.showProgress(0.0); IJ.showProgress(0.0);
}
// Read HDF5 file // Read HDF5 file
H5File file = null; H5File file = null;
boolean close = true; boolean close = true;
List<ImageStack> stacks = new ArrayList<>();
ImageStack stack = null;
try { try {
file = new H5File(filename, H5File.READ); file = new H5File(filename, H5File.READ);
file.setMaxMembers(Integer.MAX_VALUE); file.setMaxMembers(Integer.MAX_VALUE);
@ -73,25 +81,30 @@ public class HDF5Reader implements PlugIn {
List<Dataset> datasets = HDF5Utilities.getDatasets(file); List<Dataset> datasets = HDF5Utilities.getDatasets(file);
DatasetSelection selectedDatasets = null; DatasetSelection selectedDatasets = null;
if(arguments.containsKey("dataset")){ if(interactive){
logger.info("Using automatic selection");
selectedDatasets = selectDatasets(datasets, arguments);
}
else{
logger.info("Using manual selection"); logger.info("Using manual selection");
// Manual selection of the dataset and other parameters via a dialog // Manual selection of the dataset and other parameters via a dialog
selectedDatasets = selectDatasets(datasets); selectedDatasets = selectDatasets(datasets);
} }
else{
logger.info("Using automatic selection");
selectedDatasets = new DatasetSelection();
for(Dataset dataset: datasets){
if(dataset.getFullName().equals(nameOfDataset)){
selectedDatasets.getDatasets().add(dataset);
break; // we only support one selection for the time being
}
}
selectedDatasets.setVirtualStack(virtualstack);
}
// TODO to be removed - Workaround virtual stack - keep HDF5 file open at the end // TODO to be removed - Workaround virtual stack - keep HDF5 file open at the end
close=!selectedDatasets.isVirtualStack(); close=!selectedDatasets.isVirtualStack();
// TODO Remove // TODO Remove
// Hack as a proof of principle // Hack as a proof of principle
if(selectedDatasets.isGroup()){ if(selectedDatasets.isGroup()){
ImageStack stack = null;
for (Dataset var : selectedDatasets.getDatasets()) { for (Dataset var : selectedDatasets.getDatasets()) {
if(stack == null){ if(stack == null){
@ -106,9 +119,10 @@ public class HDF5Reader implements PlugIn {
ImagePlus imp = new ImagePlus(filename, stack); ImagePlus imp = new ImagePlus(filename, stack);
imp.resetDisplayRange(); imp.resetDisplayRange();
imp.show(); imp.show();
return;
}
stacks.add(stack);
return stack; // TODO should return stacks instead of stack
}
for (Dataset var : selectedDatasets.getDatasets()) { for (Dataset var : selectedDatasets.getDatasets()) {
@ -136,7 +150,8 @@ public class HDF5Reader implements PlugIn {
Object wholeDataset = var.read(); Object wholeDataset = var.read();
ImageStack stack = new ImageStack((int) dimensions[3], (int) dimensions[2]); stack = new ImageStack((int) dimensions[3], (int) dimensions[2]);
stacks.add(stack);
int stackSize = (int) (dimensions[2] * dimensions[3] * 3); int stackSize = (int) (dimensions[2] * dimensions[3] * 3);
int singleVolumeSize = (int) (dimensions[1] * stackSize); int singleVolumeSize = (int) (dimensions[1] * stackSize);
for (int volIDX = 0; volIDX < dimensions[0]; ++volIDX) { for (int volIDX = 0; volIDX < dimensions[0]; ++volIDX) {
@ -166,7 +181,8 @@ public class HDF5Reader implements PlugIn {
Object wholeDataset = var.read(); Object wholeDataset = var.read();
ImageStack stack = new ImageStack((int) dimensions[2], (int) dimensions[1]); stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
stacks.add(stack);
int stackSize = (int) (dimensions[1] * dimensions[2] * 3); int stackSize = (int) (dimensions[1] * dimensions[2] * 3);
for (int lev = 0; lev < dimensions[0]; ++lev) { for (int lev = 0; lev < dimensions[0]; ++lev) {
int startIdx = lev * stackSize; int startIdx = lev * stackSize;
@ -193,7 +209,8 @@ public class HDF5Reader implements PlugIn {
Object wholeDataset = var.read(); Object wholeDataset = var.read();
ImageStack stack = new ImageStack((int) dimensions[3], (int) dimensions[2]); stack = new ImageStack((int) dimensions[3], (int) dimensions[2]);
stacks.add(stack);
int size = (int) (dimensions[2] * dimensions[3]); int size = (int) (dimensions[2] * dimensions[3]);
long singleVolumeSize = dimensions[1] * size; long singleVolumeSize = dimensions[1] * size;
for (int volIDX = 0; volIDX < dimensions[0]; ++volIDX) { for (int volIDX = 0; volIDX < dimensions[0]; ++volIDX) {
@ -221,7 +238,8 @@ public class HDF5Reader implements PlugIn {
Object wholeDataset = var.read(); Object wholeDataset = var.read();
ImageStack stack = new ImageStack((int) dimensions[1], (int) dimensions[0]); stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
stacks.add(stack);
addSliceRGB(stack, wholeDataset, (int) dimensions[0], (int) dimensions[1]); addSliceRGB(stack, wholeDataset, (int) dimensions[0], (int) dimensions[1]);
ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack); ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack);
@ -234,8 +252,6 @@ public class HDF5Reader implements PlugIn {
} else if (numberOfDimensions == 3) { } else if (numberOfDimensions == 3) {
logger.info("3D Image"); logger.info("3D Image");
ImageStack stack;
if(selectedDatasets.isVirtualStack()){ if(selectedDatasets.isVirtualStack()){
logger.info("Use virtual stack"); logger.info("Use virtual stack");
stack = new VirtualStackHDF5(file, var); stack = new VirtualStackHDF5(file, var);
@ -303,6 +319,7 @@ public class HDF5Reader implements PlugIn {
} }
} }
stacks.add(stack);
ImagePlus imp = new ImagePlusHDF5(filename + " " + datasetName, stack); ImagePlus imp = new ImagePlusHDF5(filename + " " + datasetName, stack);
imp.resetDisplayRange(); imp.resetDisplayRange();
imp.show(); imp.show();
@ -312,7 +329,8 @@ public class HDF5Reader implements PlugIn {
Object wholeDataset = var.read(); Object wholeDataset = var.read();
ImageStack stack = new ImageStack((int) dimensions[1], (int) dimensions[0]); stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
stacks.add(stack);
addSlice(stack, wholeDataset); addSlice(stack, wholeDataset);
ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack); ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack);
@ -344,6 +362,8 @@ public class HDF5Reader implements PlugIn {
} }
IJ.showProgress(1.0); IJ.showProgress(1.0);
return stack; // TODO should return stacks instead of stack
} }
/** /**
@ -378,42 +398,6 @@ public class HDF5Reader implements PlugIn {
return selectedDatasets; return selectedDatasets;
} }
private DatasetSelection selectDatasets(List<Dataset> datasets, Map<String,String> arguments) throws HDF5Exception {
GenericDialog gd = new GenericDialog("Variable Name Selection");
gd.addMessage("Please select variables to be loaded.\n");
SelectionPanel panel = new SelectionPanel(datasets);
gd = new GenericDialog("Variable Name Selection");
gd.add(panel);
gd.addMessage("");
gd.pack();
gd.showDialog();
DatasetSelection selectedDatasets = new DatasetSelection();
for(Dataset dataset: datasets){
if(dataset.getFullName().equals(arguments.get("dataset"))){
selectedDatasets.getDatasets().add(dataset);
break; // we only support one selection for the time being
}
}
// selectedDatasets.setGroup(panel.groupValues());
// selectedDatasets.setSlice(panel.getSlice());
// selectedDatasets.setModulo(panel.getModulo());
if(arguments.containsKey("virtualstack") && arguments.get("virtualstack").equalsIgnoreCase("false")){
selectedDatasets.setVirtualStack(false);
}
else{
selectedDatasets.setVirtualStack(true);
}
return selectedDatasets;
}
/** /**
* Add slice to image stack * Add slice to image stack
* @param stack Stack to add slice * @param stack Stack to add slice