mirror of
https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5.git
synced 2025-06-06 18:40:42 +02:00
Add quick and dirty hack
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 ...
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parent
eca2294000
commit
3c9fd2b97e
@ -10,10 +10,7 @@ import ij.plugin.PlugIn;
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import java.io.File;
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import java.lang.reflect.Array;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.*;
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import java.util.logging.Level;
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import java.util.logging.Logger;
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@ -31,8 +28,12 @@ public class HDF5Reader implements PlugIn {
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*/
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public static void main(String[] args){
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HDF5Reader r = new HDF5Reader();
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r.run("path=/Users/ebner/Desktop/ open=A8_d_400N030_.h5");
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// IJ.run("HDF5...", "/Users/ebner/Desktop/A8_d_400N030_.h5");
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// r.run("");
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r.open("",false, "/Users/ebner/Desktop/A8_d_400N030_.h5", "/exchange/data", true);
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}
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public void run(String arg) {
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open(arg, true, null, null, true);
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}
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/**
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@ -45,26 +46,33 @@ public class HDF5Reader implements PlugIn {
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* dataset=/your/path/to/dataset
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*
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*/
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public void run(String arg) {
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public ImageStack open(String arg, boolean interactive, String filename, String nameOfDataset, boolean virtualstack) {
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Map arguments = HDF5Reader.parseArguments(arg);
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// Map arguments = HDF5Reader.parseArguments(arg);
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OpenDialog od = new OpenDialog("Open HDF5 ...", arg);
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File tfile = null;
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if(interactive) {
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OpenDialog od = new OpenDialog("Open HDF5 ...", arg);
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tfile = new File(od.getDirectory() + od.getFileName());
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if (!tfile.exists() || !tfile.canRead()) {
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IJ.showMessage("Cannot open file: "+tfile.getAbsolutePath());
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return null;
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}
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// Overwrite filename with selected filename
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filename = tfile.getAbsolutePath();
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File tfile = new File(od.getDirectory() + od.getFileName());
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if (!tfile.exists() || !tfile.canRead()) {
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IJ.showMessage("Cannot open file: "+tfile.getAbsolutePath());
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return;
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IJ.showStatus("Loading HDF5 File: " + filename);
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IJ.showProgress(0.0);
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}
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String filename = tfile.getAbsolutePath();
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IJ.showStatus("Loading HDF5 File: " + filename);
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IJ.showProgress(0.0);
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// Read HDF5 file
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H5File file = null;
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boolean close = true;
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List<ImageStack> stacks = new ArrayList<>();
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ImageStack stack = null;
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try {
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file = new H5File(filename, H5File.READ);
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file.setMaxMembers(Integer.MAX_VALUE);
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@ -73,25 +81,30 @@ public class HDF5Reader implements PlugIn {
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List<Dataset> datasets = HDF5Utilities.getDatasets(file);
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DatasetSelection selectedDatasets = null;
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if(arguments.containsKey("dataset")){
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logger.info("Using automatic selection");
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selectedDatasets = selectDatasets(datasets, arguments);
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}
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else{
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if(interactive){
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logger.info("Using manual selection");
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// Manual selection of the dataset and other parameters via a dialog
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selectedDatasets = selectDatasets(datasets);
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}
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else{
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logger.info("Using automatic selection");
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selectedDatasets = new DatasetSelection();
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for(Dataset dataset: datasets){
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if(dataset.getFullName().equals(nameOfDataset)){
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selectedDatasets.getDatasets().add(dataset);
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break; // we only support one selection for the time being
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}
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}
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selectedDatasets.setVirtualStack(virtualstack);
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}
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// TODO to be removed - Workaround virtual stack - keep HDF5 file open at the end
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close=!selectedDatasets.isVirtualStack();
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// TODO Remove
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// Hack as a proof of principle
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if(selectedDatasets.isGroup()){
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ImageStack stack = null;
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for (Dataset var : selectedDatasets.getDatasets()) {
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if(stack == null){
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@ -106,9 +119,10 @@ public class HDF5Reader implements PlugIn {
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ImagePlus imp = new ImagePlus(filename, stack);
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imp.resetDisplayRange();
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imp.show();
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return;
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}
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stacks.add(stack);
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return stack; // TODO should return stacks instead of stack
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}
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for (Dataset var : selectedDatasets.getDatasets()) {
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@ -136,7 +150,8 @@ public class HDF5Reader implements PlugIn {
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Object wholeDataset = var.read();
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ImageStack stack = new ImageStack((int) dimensions[3], (int) dimensions[2]);
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stack = new ImageStack((int) dimensions[3], (int) dimensions[2]);
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stacks.add(stack);
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int stackSize = (int) (dimensions[2] * dimensions[3] * 3);
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int singleVolumeSize = (int) (dimensions[1] * stackSize);
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for (int volIDX = 0; volIDX < dimensions[0]; ++volIDX) {
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@ -166,7 +181,8 @@ public class HDF5Reader implements PlugIn {
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Object wholeDataset = var.read();
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ImageStack stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
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stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
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stacks.add(stack);
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int stackSize = (int) (dimensions[1] * dimensions[2] * 3);
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for (int lev = 0; lev < dimensions[0]; ++lev) {
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int startIdx = lev * stackSize;
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@ -193,7 +209,8 @@ public class HDF5Reader implements PlugIn {
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Object wholeDataset = var.read();
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ImageStack stack = new ImageStack((int) dimensions[3], (int) dimensions[2]);
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stack = new ImageStack((int) dimensions[3], (int) dimensions[2]);
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stacks.add(stack);
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int size = (int) (dimensions[2] * dimensions[3]);
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long singleVolumeSize = dimensions[1] * size;
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for (int volIDX = 0; volIDX < dimensions[0]; ++volIDX) {
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@ -221,7 +238,8 @@ public class HDF5Reader implements PlugIn {
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Object wholeDataset = var.read();
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ImageStack stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
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stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
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stacks.add(stack);
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addSliceRGB(stack, wholeDataset, (int) dimensions[0], (int) dimensions[1]);
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ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack);
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@ -234,8 +252,6 @@ public class HDF5Reader implements PlugIn {
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} else if (numberOfDimensions == 3) {
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logger.info("3D Image");
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ImageStack stack;
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if(selectedDatasets.isVirtualStack()){
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logger.info("Use virtual stack");
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stack = new VirtualStackHDF5(file, var);
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@ -303,6 +319,7 @@ public class HDF5Reader implements PlugIn {
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}
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}
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stacks.add(stack);
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ImagePlus imp = new ImagePlusHDF5(filename + " " + datasetName, stack);
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imp.resetDisplayRange();
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imp.show();
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@ -312,7 +329,8 @@ public class HDF5Reader implements PlugIn {
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Object wholeDataset = var.read();
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ImageStack stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
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stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
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stacks.add(stack);
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addSlice(stack, wholeDataset);
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ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack);
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@ -344,6 +362,8 @@ public class HDF5Reader implements PlugIn {
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}
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IJ.showProgress(1.0);
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return stack; // TODO should return stacks instead of stack
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}
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/**
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@ -378,42 +398,6 @@ public class HDF5Reader implements PlugIn {
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return selectedDatasets;
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}
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private DatasetSelection selectDatasets(List<Dataset> datasets, Map<String,String> arguments) throws HDF5Exception {
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GenericDialog gd = new GenericDialog("Variable Name Selection");
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gd.addMessage("Please select variables to be loaded.\n");
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SelectionPanel panel = new SelectionPanel(datasets);
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gd = new GenericDialog("Variable Name Selection");
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gd.add(panel);
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gd.addMessage("");
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gd.pack();
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gd.showDialog();
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DatasetSelection selectedDatasets = new DatasetSelection();
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for(Dataset dataset: datasets){
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if(dataset.getFullName().equals(arguments.get("dataset"))){
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selectedDatasets.getDatasets().add(dataset);
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break; // we only support one selection for the time being
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}
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}
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// selectedDatasets.setGroup(panel.groupValues());
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// selectedDatasets.setSlice(panel.getSlice());
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// selectedDatasets.setModulo(panel.getModulo());
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if(arguments.containsKey("virtualstack") && arguments.get("virtualstack").equalsIgnoreCase("false")){
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selectedDatasets.setVirtualStack(false);
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}
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else{
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selectedDatasets.setVirtualStack(true);
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}
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return selectedDatasets;
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}
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/**
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* Add slice to image stack
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* @param stack Stack to add slice
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