mirror of
https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5.git
synced 2025-04-20 05:00:03 +02:00
downstripped code ...
This commit is contained in:
parent
3fe26723ef
commit
74aae47436
@ -94,131 +94,28 @@ public class HDF5Reader implements PlugIn {
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inFile = new H5File(directory + name, H5File.READ);
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inFile.open();
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// Parse the file
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Group rootNode = (Group) ((javax.swing.tree.DefaultMutableTreeNode) inFile.getRootNode()).getUserObject();
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List<Dataset> varList = getDatasets(rootNode, new ArrayList<Dataset>());
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List<Dataset> datasets = HDF5Utilities.getDatasets(inFile);
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List<Dataset> selectedDatasets = selectDatasets(datasets);
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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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if (varList.size() < 1) {
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IJ.error("The file did not contain variables. (broken?)");
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inFile.close();
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return;
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} else if (varList.size() > 1000) {
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logger.info("#######");
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for(Dataset d: varList){
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logger.info(d.getFullName());
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}
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logger.info("#######");
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/*-----------------------------------------------------------------
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* FIXME: quick an dirty hack for files with more than 1000
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* datasets
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*-----------------------------------------------------------------*/
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gd = new GenericDialog("Variable Name Selection");
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gd.addMessage("Too many variables in your file! " + "(More than 1000)\n\n" + "Please enter the full name of your desired dataset.");
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gd.addStringField("dataset name", "");
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gd.showDialog();
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if (gd.wasCanceled()) {
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return;
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}
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String dsName = gd.getNextString();
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varList = new ArrayList<Dataset>();
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try {
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HObject ds = inFile.get(dsName);
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if (ds != null && ds instanceof Dataset) {
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varList.add((Dataset) ds);
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gd.addCheckbox("single variable", true);
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} else {
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IJ.error("The file does not contain a variable with name " + "`" + dsName + "`!");
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inFile.close();
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return;
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}
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} catch (Exception e) {
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IJ.error("The file does not contain a variable with name " + "`" + dsName + "`!");
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inFile.close();
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return;
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}
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} else {
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String[] varSelections = new String[varList.size()];
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boolean[] defaultValues = new boolean[varList.size()];
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for (int i = 0; i < varList.size(); i++) {
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Dataset var = varList.get(i);
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int rank = var.getRank();
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String title = rank + "D: " + var.getFullName() + " " + var.getDatatype().getDatatypeDescription() + "( ";
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long[] extent = var.getDims();
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for (int d = 0; d < rank; ++d) {
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if (d != 0)
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title += "x";
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title += extent[d];
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}
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title += ")";
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varSelections[i] = title;
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defaultValues[i] = false;
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}
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logger.info("addcheckboxgroup with " + varList.size() + " rows");
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gd.addCheckboxGroup(varList.size(), 1, varSelections, defaultValues);
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addScrollBars(gd);
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gd.showDialog();
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if (gd.wasCanceled()) {
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return;
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}
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}
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// varList should have size=0 if only grouping is wanted
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// use old style
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for (int i = 0; i < varList.size(); ++i) {
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if (gd.getNextBoolean()) {
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Dataset var = varList.get(i);
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for (Dataset var : selectedDatasets) {
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// Read dataset attributes and properties
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String datasetName = var.getName();
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int rank = var.getRank();
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Datatype datatype = var.getDatatype();
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Datatype datatypeIfUnsupported = null;
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long[] extent = var.getDims();
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long[] extent = var.getDims(); // Extent in px (level,row,col)
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logger.info("Reading Variable: " + var.getName());
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logger.info(" Rank = " + rank + ", Data-type = " + datatype.getDatatypeDescription());
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System.out.print(" Extent in px (level,row,col):");
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for (int d = 0; d < rank; ++d)
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System.out.print(" " + extent[d]);
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logger.info("");
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IJ.showStatus("Reading Variable: " + var.getName() + " (" + extent[0] + " slices)");
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logger.info("Reading dataset: " + datasetName + " Rank: " + rank + " Type: " + datatype.getDatatypeDescription());
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Attribute elemsize_att = HDF5Utilities.getAttributes(var).get("element_size_um");
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double[] elem_sizes = new double[3];
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if (elemsize_att == null) {
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elem_sizes[0] = 1.0;
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elem_sizes[1] = 1.0;
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elem_sizes[2] = 1.0;
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} else {
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logger.info("Reading element_size_um");
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Object tmp = elemsize_att.getValue();
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if (tmp instanceof float[]) {
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elem_sizes[0] = ((float[]) tmp)[0];
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elem_sizes[1] = ((float[]) tmp)[1];
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elem_sizes[2] = ((float[]) tmp)[2];
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} else if (tmp instanceof double[]) {
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elem_sizes[0] = ((double[]) tmp)[0];
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elem_sizes[1] = ((double[]) tmp)[1];
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elem_sizes[2] = ((double[]) tmp)[2];
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} else {
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String title = "Error Reading Element Size";
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String msg = "The element_size_um attribute has " + "wrong format!\n" + "Setting to default size of (1,1,1)...";
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new ij.gui.MessageDialog(null, title, msg);
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elem_sizes[0] = 1.0;
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elem_sizes[1] = 1.0;
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elem_sizes[2] = 1.0;
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}
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}
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logger.info(" Element-Size in um (level,row,col): " + elem_sizes[0] + ", " + elem_sizes[1] + ", " + elem_sizes[2]);
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double pixelWith = 1.0;
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double pixelHeight = 1.0;
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double pixelDepth = 1.0;
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IJ.showStatus("Reading Variable: " + datasetName + " (" + extent[0] + " slices)");
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// nice gadget to update the progress bar
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long progressDivisor = extent[0] / 50; // we assume 50 process steps
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long progressDivisor = extent[0] / 50; // we assume 50 process
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// steps
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if (progressDivisor < 1)
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progressDivisor = 1;
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@ -305,16 +202,16 @@ public class HDF5Reader implements PlugIn {
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// select hyperslab for lev
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// start[1] = lev;
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// Object slice = var.read();
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int startIdx = (int)((volIDX * singleVolumeSize * 3) + (lev * stackSize * 3));
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// long numElements = stackSize * 3;
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int endIdx = (int)(startIdx+stackSize*3-1);
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int startIdx = (int) ((volIDX * singleVolumeSize * 3) + (lev * stackSize * 3));
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// long numElements = stackSize * 3;
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int endIdx = (int) (startIdx + stackSize * 3 - 1);
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copyPixels3(datatypeIfUnsupported, extent, stack, wholeDataset, size, startIdx, endIdx);
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}
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}
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IJ.showProgress(1.f);
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ImagePlus imp = new ImagePlus(directory + name + " " + var.getName(), stack);
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ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
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// new for hyperstack
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int nChannels = 3;
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int nSlices = (int) extent[1];
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@ -327,18 +224,9 @@ public class HDF5Reader implements PlugIn {
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imp.setDimensions(nChannels, nSlices, nFrames);
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imp = new CompositeImage(imp, CompositeImage.COMPOSITE);
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imp.setOpenAsHyperStack(true);
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// imp = imp.createHyperStack(directory + name + " "
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// + var.getName(),
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// nChannels,
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// nSlices,
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// nFrames,32);
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// imp.setStack(stack,nChannels,nSlices,nFrames);
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imp.getCalibration().pixelDepth = elem_sizes[0];
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imp.getCalibration().pixelHeight = elem_sizes[1];
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imp.getCalibration().pixelWidth = elem_sizes[2];
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// getMinMax();
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// imp.setDisplayRange(0,229);
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imp.getCalibration().pixelDepth = pixelDepth;
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imp.getCalibration().pixelHeight = pixelHeight;
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imp.getCalibration().pixelWidth = pixelWith;
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imp.resetDisplayRange();
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imp.show();
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} else if (rank == 4) {
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@ -392,15 +280,16 @@ public class HDF5Reader implements PlugIn {
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// start[0] = lev;
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// Object slice = var.read();
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int startIdx = (int)(lev * stackSize);
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// long numElements = stackSize;
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int endIdx = (int)(startIdx+stackSize-1);
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// Object slice = extractSubarray(wholeDataset, startIdx, numElements);
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int startIdx = (int) (lev * stackSize);
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// long numElements = stackSize;
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int endIdx = (int) (startIdx + stackSize - 1);
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// Object slice = extractSubarray(wholeDataset,
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// startIdx, numElements);
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int size = (int) (extent[2] * extent[1]);
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copyPixel1(extent, stack, wholeDataset, startIdx, endIdx, size);
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copyPixels1(extent, stack, wholeDataset, startIdx, endIdx, size);
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}
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ImagePlus imp = new ImagePlus(directory + name + " " + var.getName(), stack);
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ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
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// new for hyperstack
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int nChannels = 3;
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int nSlices = (int) extent[0];
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@ -408,12 +297,9 @@ public class HDF5Reader implements PlugIn {
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imp.setDimensions(nChannels, nSlices, nFrames);
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imp = new CompositeImage(imp, CompositeImage.COMPOSITE);
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imp.setOpenAsHyperStack(true);
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imp.getCalibration().pixelDepth = elem_sizes[0];
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imp.getCalibration().pixelHeight = elem_sizes[1];
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imp.getCalibration().pixelWidth = elem_sizes[2];
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// getMinMax();
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imp.getCalibration().pixelDepth = pixelDepth;
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imp.getCalibration().pixelHeight = pixelHeight;
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imp.getCalibration().pixelWidth = pixelWith;
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imp.resetDisplayRange();
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imp.show();
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imp.updateStatusbarValue();
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@ -470,16 +356,16 @@ public class HDF5Reader implements PlugIn {
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// select hyperslab for lev
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// start[1] = lev;
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// Object slice = var.read();
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int startIdx = (int)((volIDX * singleVolumeSize) + (lev * stackSize));
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int endIdx = (int)(startIdx+stackSize-1);
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// long numElements = stackSize;
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int startIdx = (int) ((volIDX * singleVolumeSize) + (lev * stackSize));
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int endIdx = (int) (startIdx + stackSize - 1);
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// long numElements = stackSize;
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convertDatatypesAndSlice(datatypeIfUnsupported, stack, wholeDataset, startIdx, endIdx);
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}
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}
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IJ.showProgress(1.f);
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ImagePlus imp = new ImagePlus(directory + name + " " + var.getName(), stack);
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ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
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// new for hyperstack
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int nChannels = 1;
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int nSlices = (int) extent[1];
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@ -494,12 +380,9 @@ public class HDF5Reader implements PlugIn {
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imp.setDimensions(nChannels, nSlices, nFrames);
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imp.setOpenAsHyperStack(true);
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imp.getCalibration().pixelDepth = elem_sizes[0];
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imp.getCalibration().pixelHeight = elem_sizes[1];
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imp.getCalibration().pixelWidth = elem_sizes[2];
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// getMinMax();
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// imp.setDisplayRange(0,229);
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imp.getCalibration().pixelDepth = pixelDepth;
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imp.getCalibration().pixelHeight = pixelHeight;
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imp.getCalibration().pixelWidth = pixelWith;
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imp.resetDisplayRange();
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imp.show();
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}
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@ -538,10 +421,10 @@ public class HDF5Reader implements PlugIn {
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int size = (int) (extent[1] * extent[0]);
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// ugly but working: copy pixel by pixel
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copyPixels(extent, stack, slice, size);
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copyPixels2(extent, stack, slice, size);
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IJ.showProgress(1.f);
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ImagePlus imp = new ImagePlus(directory + name + " " + var.getName(), stack);
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ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
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// new for hyperstack
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int nChannels = 3;
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int nSlices = 1;
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@ -549,11 +432,9 @@ public class HDF5Reader implements PlugIn {
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imp.setDimensions(nChannels, nSlices, nFrames);
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imp = new CompositeImage(imp, CompositeImage.COMPOSITE);
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imp.setOpenAsHyperStack(true);
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imp.getCalibration().pixelDepth = elem_sizes[0];
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imp.getCalibration().pixelHeight = elem_sizes[1];
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imp.getCalibration().pixelWidth = elem_sizes[2];
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// getMinMax();
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imp.getCalibration().pixelDepth = pixelDepth;
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imp.getCalibration().pixelHeight = pixelHeight;
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imp.getCalibration().pixelWidth = pixelWith;
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imp.resetDisplayRange();
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imp.show();
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imp.updateStatusbarValue();
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@ -600,17 +481,16 @@ public class HDF5Reader implements PlugIn {
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// start[0] = lev;
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// Object slice = var.read();
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int startIdx = (int)(lev * stackSize);
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int endIdx = (int)(startIdx+stackSize-1);
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// long numElements = stackSize;
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int startIdx = (int) (lev * stackSize);
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int endIdx = (int) (startIdx + stackSize - 1);
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// long numElements = stackSize;
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convertDatatypesAndSlice(datatypeIfUnsupported, stack, wholeDataset, startIdx, endIdx);
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}
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IJ.showProgress(1.f);
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ImagePlus imp = new ImagePlus(directory + name + " " + var.getName(), stack);
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imp.getCalibration().pixelDepth = elem_sizes[0];
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imp.getCalibration().pixelHeight = elem_sizes[1];
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imp.getCalibration().pixelWidth = elem_sizes[2];
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// getMinMax();
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ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
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imp.getCalibration().pixelDepth = pixelDepth;
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imp.getCalibration().pixelHeight = pixelHeight;
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imp.getCalibration().pixelWidth = pixelWith;
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imp.resetDisplayRange();
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imp.show();
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imp.updateStatusbarValue();
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@ -697,7 +577,7 @@ public class HDF5Reader implements PlugIn {
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stack.addSlice(null, slice);
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}
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IJ.showProgress(1.f);
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ImagePlus imp = new ImagePlus(directory + name + " " + var.getName(), stack);
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ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
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imp.getProcessor().resetMinAndMax();
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imp.show();
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@ -716,7 +596,6 @@ public class HDF5Reader implements PlugIn {
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IJ.showStatus("Variable Dimension " + rank + " not supported");
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}
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}
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}
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} catch (Exception e) {
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logger.log(Level.WARNING, "Error while opening '" + directory + name + "'", e);
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@ -724,22 +603,99 @@ public class HDF5Reader implements PlugIn {
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} catch (OutOfMemoryError o) {
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IJ.outOfMemory("Load HDF5");
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}
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// make sure the file is closed after working with it
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// FIXME: should happen in catch-part, too!
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finally{
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try {
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if (inFile != null)
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if (inFile != null){
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inFile.close();
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}
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} catch (HDF5Exception err) {
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System.err.println("Error while closing '" + directory + name + "'");
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System.err.println(err);
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IJ.showStatus("Error closing file.");
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}
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}
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IJ.showProgress(1.0);
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}
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/**
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* Selection of the datasets to visualize
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*
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* @param datasets
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* @return List of datasets to visualize. If nothing selected the list will be empty
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* @throws HDF5Exception
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*/
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private List<Dataset> selectDatasets(List<Dataset> datasets) throws HDF5Exception {
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List<Dataset> selectedDatasets = new ArrayList<>();
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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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if (datasets.size() < 1) {
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IJ.error("The file does not contain datasets");
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} else if (datasets.size() > 1000) {
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logger.info("#######");
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for(Dataset d: datasets){
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logger.info(d.getFullName());
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}
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logger.info("#######");
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gd = new GenericDialog("Variable Name Selection");
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gd.addMessage("There are lots of datasets in your file (check the log output which datasets are available)! Please enter the full path of the dataset to be displayed");
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gd.addStringField("Dataset", "");
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gd.showDialog();
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if (!gd.wasCanceled()) {
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String dsName = gd.getNextString();
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for(Dataset d: datasets){
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if(d.getFullName().equals(dsName)){
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selectedDatasets.add(d);
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}
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}
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if(selectedDatasets.isEmpty()){
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IJ.error("The file does not contain a variable with name " + "`" + dsName + "`!");
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}
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}
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} else {
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String[] varSelections = new String[datasets.size()];
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boolean[] defaultValues = new boolean[datasets.size()];
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for (int i = 0; i < datasets.size(); i++) {
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Dataset var = datasets.get(i);
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int rank = var.getRank();
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String title = rank + "D: " + var.getFullName() + " " + var.getDatatype().getDatatypeDescription() + "( ";
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long[] extent = var.getDims();
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for (int d = 0; d < rank; ++d) {
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if (d != 0){
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title += "x";
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}
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title += extent[d];
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}
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title += ")";
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varSelections[i] = title;
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defaultValues[i] = false;
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}
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logger.info("Add checkbox group with " + datasets.size() + " rows");
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gd.addCheckboxGroup(datasets.size(), 1, varSelections, defaultValues);
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addScrollBars(gd);
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gd.showDialog();
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if (!gd.wasCanceled()) {
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// Get selected datasets
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for (int i = 0; i < datasets.size(); ++i) {
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if (gd.getNextBoolean()) {
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selectedDatasets.add(datasets.get(i));
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}
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}
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}
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||||
}
|
||||
|
||||
|
||||
return selectedDatasets;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @param datatypeIfUnsupported
|
||||
* @param stack
|
||||
@ -945,7 +901,7 @@ public class HDF5Reader implements PlugIn {
|
||||
* @param slice
|
||||
* @param size
|
||||
*/
|
||||
private void copyPixels(long[] extent, ImageStack stack, Object slice, int size) {
|
||||
private void copyPixels2(long[] extent, ImageStack stack, Object slice, int size) {
|
||||
if (slice instanceof byte[]) {
|
||||
byte[] tmp = (byte[]) slice;
|
||||
byte[] rChannel = new byte[size];
|
||||
@ -1060,7 +1016,7 @@ public class HDF5Reader implements PlugIn {
|
||||
* @param endIdx
|
||||
* @param size
|
||||
*/
|
||||
private void copyPixel1(long[] extent, ImageStack stack, Object wholeDataset, int startIdx, int endIdx, int size) {
|
||||
private void copyPixels1(long[] extent, ImageStack stack, Object wholeDataset, int startIdx, int endIdx, int size) {
|
||||
if (wholeDataset instanceof byte[]) {
|
||||
byte[] tmp = Arrays.copyOfRange((byte[]) wholeDataset, startIdx, endIdx);
|
||||
byte[] rChannel = new byte[size];
|
||||
@ -1166,32 +1122,6 @@ public class HDF5Reader implements PlugIn {
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Recursively get list of all datasets in file
|
||||
* @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> 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;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
private float[] convertDoubleToFloat(double[] dataIn) {
|
||||
float[] dataOut = new float[dataIn.length];
|
||||
for (int index = 0; index < dataIn.length; index++) {
|
||||
|
||||
@ -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;
|
||||
}
|
||||
}
|
||||
|
||||
@ -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;
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user