mirror of
https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5.git
synced 2025-04-23 06:20:05 +02:00
more cleanup in reader function
This commit is contained in:
parent
87a195dd4d
commit
1ad581d126
@ -27,7 +27,6 @@ import ij.ImageStack;
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import ij.gui.GenericDialog;
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import ij.io.OpenDialog;
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import ij.plugin.PlugIn;
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import ij.process.ImageProcessor;
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import java.io.File;
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import java.util.ArrayList;
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@ -86,539 +85,306 @@ public class HDF5Reader implements PlugIn {
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} while (tryAgain);
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IJ.showStatus("Loading HDF5 File: " + directory + name);
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IJ.showProgress(0.0);
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// Read HDF5 file
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H5File inFile = null;
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try {
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inFile = new H5File(directory + name, H5File.READ);
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inFile.open();
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List<Dataset> datasets = HDF5Utilities.getDatasets(inFile);
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List<Dataset> selectedDatasets = selectDatasets(datasets);
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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(); // Extent in px (level,row,col)
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int numberOfDimensions = var.getRank();
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long[] dimensions= var.getDims();
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logger.info("Reading dataset: " + datasetName + " Rank: " + rank + " Type: " + datatype.getDatatypeDescription());
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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
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// steps
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if (progressDivisor < 1)
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progressDivisor = 1;
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logger.info("Reading dataset: " + datasetName + " Dimensions: " + numberOfDimensions + " Type: " + datatype.getDatatypeDescription());
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// check if we have an unsupported datatype
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if (datatype.getDatatypeClass() == Datatype.CLASS_INTEGER && (datatype.getDatatypeSize() == 4 || datatype.getDatatypeSize() == 8)) {
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logger.info("Datatype not supported by ImageJ");
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GenericDialog typeSelDiag = new GenericDialog("Datatype Selection");
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typeSelDiag.addMessage("The datatype `" + datatype.getDatatypeDescription() + "` is not supported by ImageJ.\n\n");
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typeSelDiag.addMessage("Please select your wanted datatype.\n");
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String[] choices = new String[2];
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choices[0] = "float";
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choices[1] = "short";
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typeSelDiag.addChoice(" Possible types are", choices, "float");
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typeSelDiag.showDialog();
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// Check if datatype is supported
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datatypeIfUnsupported = checkIfDatatypeSupported(datatype);
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if (typeSelDiag.wasCanceled()) {
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return;
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}
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int selection = typeSelDiag.getNextChoiceIndex();
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if (selection == 0) {
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logger.info("float selected");
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datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
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}
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if (selection == 1) {
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logger.info("short selected");
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int typeSizeInByte = 2;
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datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_INTEGER, typeSizeInByte, Datatype.NATIVE, -1);
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}
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}
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// Read dataset
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if (numberOfDimensions == 5 && dimensions[4] == 3) {
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logger.info("4D RGB Image (HyperVolume)");
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// read dataset
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if (rank == 5 && extent[4] == 3) {
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logger.info(" Detected HyperVolume (type RGB).");
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// Select what to readout - read the whole dataset, since
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// reading chunked datasets slice-wise is too slow
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long[] selected = var.getSelectedDims();
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selected[0] = dimensions[0];
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selected[1] = dimensions[1];
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selected[2] = dimensions[2];
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selected[3] = dimensions[3];
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selected[4] = dimensions[4];
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// create a new image stack and fill in the data
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ImageStack stack = new ImageStack((int) extent[3], (int) extent[2]);
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// read the whole dataset, since reading chunked
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// datasets
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// slice-wise is too slow
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long[] dims = var.getDims(); // the dimension sizes
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// of the dataset
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long[] selected = var.getSelectedDims(); // the
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// selected
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// size of
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// the
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// dataet
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selected[0] = dims[0];
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selected[1] = dims[1];
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selected[2] = dims[2];
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selected[3] = dims[3];
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selected[4] = dims[4];// 3
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// the selection
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Object wholeDataset = var.read();
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// check for unsigned datatype
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int unsignedConvSelec = 0;
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Datatype dType = var.getDatatype();
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boolean isSigned16Bit = !dType.isUnsigned() && (dType.getDatatypeClass() == Datatype.CLASS_INTEGER) && (dType.getDatatypeSize() == 2);
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wholeDataset = checkUnsigned(datatype, wholeDataset);
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if (isSigned16Bit) {
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GenericDialog convDiag = new GenericDialog("Unsigend to signed conversion");
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convDiag.addMessage("Detected unsigned datatype, which " + "is not supported.");
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String[] convOptions = new String[2];
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convOptions[0] = "cut off values";
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convOptions[1] = "convert to float";
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convDiag.addChoice("Please select an conversion option:", convOptions, convOptions[0]);
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convDiag.showDialog();
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if (convDiag.wasCanceled())
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return;
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unsignedConvSelec = convDiag.getNextChoiceIndex();
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wholeDataset = convertToUnsigned(wholeDataset, unsignedConvSelec);
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}
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long stackSize = extent[2] * extent[3];
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long singleVolumeSize = extent[1] * stackSize;
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int size = (int) stackSize;
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for (int volIDX = 0; volIDX < extent[0]; ++volIDX) {
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if ((volIDX % progressDivisor) == 0)
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IJ.showProgress((float) volIDX / (float) extent[0]);
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// start[0] = volIDX;
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for (int lev = 0; lev < extent[1]; ++lev) {
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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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ImageStack stack = new ImageStack((int) dimensions[3], (int) dimensions[2]);
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long stackSize = dimensions[2] * dimensions[3];
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long singleVolumeSize = dimensions[1] * stackSize;
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for (int volIDX = 0; volIDX < dimensions[0]; ++volIDX) {
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for (int lev = 0; lev < dimensions[1]; ++lev) {
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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, (int)extent[2], (int)extent[3], stack, wholeDataset, size, startIdx, endIdx);
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copyPixels3(datatypeIfUnsupported, (int) dimensions[2], (int) dimensions[3], stack, wholeDataset, (int) stackSize, 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 + " " + 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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int nFrames = (int) extent[0];
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logger.info("nFrames: " + Integer.toString(nFrames));
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logger.info("nSlices: " + Integer.toString(nSlices));
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logger.info("stackSize: " + Integer.toString(stack.getSize()));
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imp.setDimensions(nChannels, nSlices, nFrames);
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imp.setDimensions(3, (int) dimensions[1], (int) dimensions[0]);
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imp = new CompositeImage(imp, CompositeImage.COMPOSITE);
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imp.setOpenAsHyperStack(true);
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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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if (extent[3] == 3) {
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logger.info(" Detected color Image (type RGB).");
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} else if (numberOfDimensions == 4 && dimensions[3] == 3) {
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logger.info("3D RGB Image");
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// create a new image stack and fill in the data
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ImageStack stack = new ImageStack((int) extent[2], (int) extent[1]);
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// Select what to readout - read the whole dataset, since
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// reading chunked datasets slice-wise is too slow
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long[] selected = var.getSelectedDims();
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selected[0] = dimensions[0];
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selected[1] = dimensions[1];
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selected[2] = dimensions[2];
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selected[3] = dimensions[3];
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long[] dims = var.getDims(); // the dimension sizes
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// of the dataset
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long[] selected = var.getSelectedDims(); // the
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// selected
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// size of
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// the
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// dataet
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selected[0] = dims[0];
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selected[1] = dims[1];
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selected[2] = dims[2];
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selected[3] = dims[3];
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// long[] start = var.getStartDims(); // the off set
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// of
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// // the selection
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Object wholeDataset = var.read();
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// check for unsigned datatype
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int unsignedConvSelec = 0;
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Datatype dType = var.getDatatype();
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boolean isSigned16Bit = !dType.isUnsigned() && (dType.getDatatypeClass() == Datatype.CLASS_INTEGER) && (dType.getDatatypeSize() == 2);
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if (isSigned16Bit) {
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GenericDialog convDiag = new GenericDialog("Unsigend to signed conversion");
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convDiag.addMessage("Detected unsigned datatype, which " + "is not supported.");
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String[] convOptions = new String[2];
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convOptions[0] = "cut off values";
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convOptions[1] = "convert to float";
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convDiag.addChoice("Please select an conversion option:", convOptions, convOptions[0]);
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convDiag.showDialog();
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if (convDiag.wasCanceled())
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return;
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unsignedConvSelec = convDiag.getNextChoiceIndex();
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wholeDataset = convertToUnsigned(wholeDataset, unsignedConvSelec);
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}
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long stackSize = extent[1] * extent[2] * 3;
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for (int lev = 0; lev < extent[0]; ++lev) {
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if ((lev % progressDivisor) == 0)
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IJ.showProgress((float) lev / (float) extent[0]);
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// // select hyperslab for lev
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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,
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// startIdx, numElements);
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int size = (int) (extent[2] * extent[1]);
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copyPixels1((int)extent[1], (int)extent[2], stack, wholeDataset, startIdx, endIdx, size);
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}
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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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int nFrames = 1;
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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 = 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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} else // we have a HyperVolume
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{
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logger.info(" Detected HyperVolume (type GREYSCALE).");
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// create a new image stack and fill in the data
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ImageStack stack = new ImageStack((int) extent[3], (int) extent[2]);
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// read the whole dataset, since reading chunked
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// datasets
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// slice-wise is too slow
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long[] dims = var.getDims(); // the dimension sizes
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// of the dataset
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long[] selected = var.getSelectedDims(); // the
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// selected
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// size of
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// the
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// dataet
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selected[0] = dims[0];
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selected[1] = dims[1];
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selected[2] = dims[2];
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selected[3] = dims[3];
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// the selection
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Object wholeDataset = var.read();
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// check for unsigned datatype
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int unsignedConvSelec = 0;
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Datatype dType = var.getDatatype();
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boolean isSigned16Bit = !dType.isUnsigned() && (dType.getDatatypeClass() == Datatype.CLASS_INTEGER) && (dType.getDatatypeSize() == 2);
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if (isSigned16Bit) {
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GenericDialog convDiag = new GenericDialog("Unsigend to signed conversion");
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convDiag.addMessage("Detected unsigned datatype, which " + "is not supported.");
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String[] convOptions = new String[2];
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convOptions[0] = "cut off values";
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convOptions[1] = "convert to float";
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convDiag.addChoice("Please select an conversion option:", convOptions, convOptions[0]);
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convDiag.showDialog();
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if (convDiag.wasCanceled())
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return;
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unsignedConvSelec = convDiag.getNextChoiceIndex();
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wholeDataset = convertToUnsigned(wholeDataset, unsignedConvSelec);
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}
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long stackSize = extent[2] * extent[3];
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long singleVolumeSize = extent[1] * stackSize;
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for (int volIDX = 0; volIDX < extent[0]; ++volIDX) {
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if ((volIDX % progressDivisor) == 0)
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IJ.showProgress((float) volIDX / (float) extent[0]);
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// start[0] = volIDX;
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for (int lev = 0; lev < extent[1]; ++lev) {
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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);
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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 + " " + 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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int nFrames = (int) extent[0];
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Integer nFramesI = nFrames;
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Integer nSlicesI = nSlices;
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logger.info("nFrames: " + nFramesI.toString());
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logger.info("nSlices: " + nSlicesI.toString());
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Integer myStackSize = stack.getSize();
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logger.info("stackSize: " + myStackSize.toString());
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imp.setDimensions(nChannels, nSlices, nFrames);
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imp.setOpenAsHyperStack(true);
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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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} else if (rank == 3 && extent[2] == 3) {
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logger.info("This is an rgb image");
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// create a new image stack and fill in the data
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ImageStack stack = new ImageStack((int) extent[1], (int) extent[0]);
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long[] selected = var.getSelectedDims(); // the
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// selected
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// size of
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// the
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// dataet
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selected[0] = extent[0];
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selected[1] = extent[1];
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selected[2] = extent[2];
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Object slice = var.read();
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// check for unsigned datatype
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int unsignedConvSelec = 0;
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Datatype dType = var.getDatatype();
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boolean isSigned16Bit = !dType.isUnsigned() && (dType.getDatatypeClass() == Datatype.CLASS_INTEGER) && (dType.getDatatypeSize() == 2);
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if (isSigned16Bit) {
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GenericDialog convDiag = new GenericDialog("Unsigend to signed conversion");
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convDiag.addMessage("Detected unsigned datatype, which " + "is not supported.");
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String[] convOptions = new String[2];
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convOptions[0] = "cut off values";
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convOptions[1] = "convert to float";
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convDiag.addChoice("Please select an conversion option:", convOptions, convOptions[0]);
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convDiag.showDialog();
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if (convDiag.wasCanceled())
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return;
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unsignedConvSelec = convDiag.getNextChoiceIndex();
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slice = convertToUnsigned(slice, unsignedConvSelec);
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}
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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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copyPixels2((int)extent[0], (int)extent[1], stack, slice, size);
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IJ.showProgress(1.f);
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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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int nFrames = 1;
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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 = 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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} else if (rank == 3) {
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logger.info("Rank is 3");
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// create a new image stack and fill in the data
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ImageStack stack = new ImageStack((int) extent[2], (int) extent[1]);
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long[] selected = var.getSelectedDims(); // the
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// selected
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// size of
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// the
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// dataet
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selected[0] = extent[0];
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selected[1] = extent[1];
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selected[2] = extent[2];
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Object wholeDataset = var.read();
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// check for unsigned datatype
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int unsignedConvSelec = 0;
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Datatype dType = var.getDatatype();
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boolean isSigned16Bit = !dType.isUnsigned() && (dType.getDatatypeClass() == Datatype.CLASS_INTEGER) && (dType.getDatatypeSize() == 2);
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wholeDataset = checkUnsigned(datatype, wholeDataset);
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if (isSigned16Bit) {
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GenericDialog convDiag = new GenericDialog("Unsigend to signed conversion");
|
||||
convDiag.addMessage("Detected unsigned datatype, which " + "is not supported.");
|
||||
String[] convOptions = new String[2];
|
||||
convOptions[0] = "cut off values";
|
||||
convOptions[1] = "convert to float";
|
||||
convDiag.addChoice("Please select an conversion option:", convOptions, convOptions[0]);
|
||||
convDiag.showDialog();
|
||||
if (convDiag.wasCanceled())
|
||||
return;
|
||||
unsignedConvSelec = convDiag.getNextChoiceIndex();
|
||||
wholeDataset = convertToUnsigned(wholeDataset, unsignedConvSelec);
|
||||
ImageStack stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
|
||||
long stackSize = dimensions[1] * dimensions[2] * 3;
|
||||
for (int lev = 0; lev < dimensions[0]; ++lev) {
|
||||
int startIdx = (int) (lev * stackSize);
|
||||
int endIdx = (int) (startIdx + stackSize - 1);
|
||||
int size = (int) (dimensions[2] * dimensions[1]);
|
||||
copyPixels1((int) dimensions[1], (int) dimensions[2], stack, wholeDataset, size, startIdx, endIdx);
|
||||
}
|
||||
|
||||
long stackSize = extent[1] * extent[2];
|
||||
ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
|
||||
imp.setDimensions(3, (int) dimensions[0], 1);
|
||||
imp = new CompositeImage(imp, CompositeImage.COMPOSITE);
|
||||
imp.setOpenAsHyperStack(true);
|
||||
imp.resetDisplayRange();
|
||||
imp.show();
|
||||
|
||||
} else if (numberOfDimensions == 4) {
|
||||
logger.info("4D Image (HyperVolume)");
|
||||
|
||||
for (int lev = 0; lev < extent[0]; ++lev) {
|
||||
if ((lev % progressDivisor) == 0)
|
||||
IJ.showProgress((float) lev / (float) extent[0]);
|
||||
// select hyperslab for lev
|
||||
// start[0] = lev;
|
||||
// Object slice = var.read();
|
||||
// Select what to readout - read the whole dataset, since
|
||||
// reading chunked datasets slice-wise is too slow
|
||||
long[] selected = var.getSelectedDims();
|
||||
selected[0] = dimensions[0];
|
||||
selected[1] = dimensions[1];
|
||||
selected[2] = dimensions[2];
|
||||
selected[3] = dimensions[3];
|
||||
|
||||
Object wholeDataset = var.read();
|
||||
wholeDataset = checkUnsigned(datatype, wholeDataset);
|
||||
|
||||
ImageStack stack = new ImageStack((int) dimensions[3], (int) dimensions[2]);
|
||||
long stackSize = dimensions[2] * dimensions[3];
|
||||
long singleVolumeSize = dimensions[1] * stackSize;
|
||||
for (int volIDX = 0; volIDX < dimensions[0]; ++volIDX) {
|
||||
for (int lev = 0; lev < dimensions[1]; ++lev) {
|
||||
int startIdx = (int) ((volIDX * singleVolumeSize) + (lev * stackSize));
|
||||
int endIdx = (int) (startIdx + stackSize);
|
||||
convertDatatypesAndSlice(datatypeIfUnsupported, stack, wholeDataset, startIdx, endIdx);
|
||||
}
|
||||
}
|
||||
|
||||
ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
|
||||
imp.setDimensions(1, (int) dimensions[1], (int) dimensions[0]);
|
||||
imp.setOpenAsHyperStack(true);
|
||||
imp.resetDisplayRange();
|
||||
imp.show();
|
||||
|
||||
} else if (numberOfDimensions == 3 && dimensions[2] == 3) {
|
||||
logger.info("2D RGB Image");
|
||||
|
||||
// Select what to readout - read the whole dataset, since
|
||||
// reading chunked datasets slice-wise is too slow
|
||||
long[] selected = var.getSelectedDims();
|
||||
selected[0] = dimensions[0];
|
||||
selected[1] = dimensions[1];
|
||||
selected[2] = dimensions[2];
|
||||
|
||||
Object wholeDataset = var.read();
|
||||
wholeDataset = checkUnsigned(datatype, wholeDataset);
|
||||
|
||||
ImageStack stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
|
||||
copyPixels2((int) dimensions[0], (int) dimensions[1], stack, wholeDataset, (int) (dimensions[1] * dimensions[0]));
|
||||
|
||||
ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
|
||||
imp.setDimensions(3, 1, 1);
|
||||
imp = new CompositeImage(imp, CompositeImage.COMPOSITE);
|
||||
imp.setOpenAsHyperStack(true);
|
||||
imp.resetDisplayRange();
|
||||
imp.show();
|
||||
|
||||
} else if (numberOfDimensions == 3) {
|
||||
logger.info("3D Image");
|
||||
|
||||
// Select what to readout
|
||||
long[] selected = var.getSelectedDims();
|
||||
selected[0] = dimensions[0];
|
||||
selected[1] = dimensions[1];
|
||||
selected[2] = dimensions[2];
|
||||
|
||||
Object wholeDataset = var.read();
|
||||
wholeDataset = checkUnsigned(datatype, wholeDataset);
|
||||
|
||||
ImageStack stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
|
||||
long stackSize = dimensions[1] * dimensions[2];
|
||||
for (int lev = 0; lev < dimensions[0]; ++lev) {
|
||||
int startIdx = (int) (lev * stackSize);
|
||||
int endIdx = (int) (startIdx + stackSize);
|
||||
// long numElements = stackSize;
|
||||
convertDatatypesAndSlice(datatypeIfUnsupported, stack, wholeDataset, startIdx, endIdx);
|
||||
}
|
||||
IJ.showProgress(1.f);
|
||||
|
||||
ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
|
||||
imp.getCalibration().pixelDepth = pixelDepth;
|
||||
imp.getCalibration().pixelHeight = pixelHeight;
|
||||
imp.getCalibration().pixelWidth = pixelWith;
|
||||
imp.resetDisplayRange();
|
||||
imp.show();
|
||||
imp.updateStatusbarValue();
|
||||
} else if (rank == 2) {
|
||||
|
||||
} else if (numberOfDimensions == 2) {
|
||||
logger.info("2D Image");
|
||||
|
||||
Object wholeDataset = var.read();
|
||||
wholeDataset = checkUnsigned(datatype, wholeDataset);
|
||||
|
||||
// check if we have an unsupported datatype
|
||||
if (datatype.getDatatypeClass() == Datatype.CLASS_INTEGER && (datatype.getDatatypeSize() == 4 || datatype.getDatatypeSize() == 8)) {
|
||||
logger.info("Datatype not supported by ImageJ");
|
||||
GenericDialog typeSelDiag = new GenericDialog("Datatype Selection");
|
||||
typeSelDiag.addMessage("The datatype `" + datatype.getDatatypeDescription() + "` is not supported by ImageJ.\n\n");
|
||||
typeSelDiag.addMessage("Please select your wanted datatype.\n");
|
||||
String[] choices = new String[2];
|
||||
choices[0] = "float";
|
||||
choices[1] = "short";
|
||||
typeSelDiag.addChoice(" Possible types are", choices, "float");
|
||||
typeSelDiag.showDialog();
|
||||
|
||||
if (typeSelDiag.wasCanceled()) {
|
||||
return;
|
||||
}
|
||||
int selection = typeSelDiag.getNextChoiceIndex();
|
||||
if (selection == 0) {
|
||||
logger.info("float selected");
|
||||
datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
|
||||
}
|
||||
if (selection == 1) {
|
||||
logger.info("short selected");
|
||||
int typeSizeInByte = 2;
|
||||
datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_INTEGER, typeSizeInByte, Datatype.NATIVE, -1);
|
||||
}
|
||||
}
|
||||
IJ.showProgress(0.f);
|
||||
ImageStack stack = new ImageStack((int) extent[1], (int) extent[0]);
|
||||
Object slice = var.read();
|
||||
// check for unsigned datatype
|
||||
int unsignedConvSelec = 0;
|
||||
Datatype dType = var.getDatatype();
|
||||
boolean isSigned16Bit = !dType.isUnsigned() && (dType.getDatatypeClass() == Datatype.CLASS_INTEGER) && (dType.getDatatypeSize() == 2);
|
||||
if (isSigned16Bit) {
|
||||
GenericDialog convDiag = new GenericDialog("Unsigend to signed conversion");
|
||||
convDiag.addMessage("Detected unsigned datatype, which " + "is not supported.");
|
||||
String[] convOptions = new String[2];
|
||||
convOptions[0] = "cut off values";
|
||||
convOptions[1] = "convert to float";
|
||||
convDiag.addChoice("Please select an conversion option:", convOptions, convOptions[0]);
|
||||
convDiag.showDialog();
|
||||
if (convDiag.wasCanceled())
|
||||
return;
|
||||
unsignedConvSelec = convDiag.getNextChoiceIndex();
|
||||
slice = convertToUnsigned(slice, unsignedConvSelec);
|
||||
}
|
||||
|
||||
if (slice instanceof byte[]) {
|
||||
byte[] tmp = (byte[]) slice;
|
||||
ImageStack stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
|
||||
if (wholeDataset instanceof byte[]) {
|
||||
byte[] tmp = (byte[]) wholeDataset;
|
||||
stack.addSlice(null, tmp);
|
||||
} else if (slice instanceof short[]) {
|
||||
short[] tmp = (short[]) slice;
|
||||
} else if (wholeDataset instanceof short[]) {
|
||||
short[] tmp = (short[]) wholeDataset;
|
||||
stack.addSlice(null, tmp);
|
||||
} else if (slice instanceof int[]) {
|
||||
int[] tmp = (int[]) slice;
|
||||
} else if (wholeDataset instanceof int[]) {
|
||||
int[] tmp = (int[]) wholeDataset;
|
||||
if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
|
||||
stack.addSlice(null, convertInt32ToFloat(tmp));
|
||||
}
|
||||
if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) {
|
||||
stack.addSlice(null, convertInt32ToShort(tmp));
|
||||
}
|
||||
} else if (slice instanceof long[]) {
|
||||
long[] tmp = (long[]) slice;
|
||||
} else if (wholeDataset instanceof long[]) {
|
||||
long[] tmp = (long[]) wholeDataset;
|
||||
if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
|
||||
stack.addSlice(null, convertInt64ToFloat(tmp));
|
||||
}
|
||||
if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) {
|
||||
stack.addSlice(null, convertInt64ToShort(tmp));
|
||||
}
|
||||
} else if (slice instanceof float[]) {
|
||||
float[] tmp = (float[]) slice;
|
||||
} else if (wholeDataset instanceof float[]) {
|
||||
float[] tmp = (float[]) wholeDataset;
|
||||
stack.addSlice(null, tmp);
|
||||
} else if (slice instanceof double[]) {
|
||||
float[] tmp = convertDoubleToFloat((double[]) slice);
|
||||
|
||||
} else if (wholeDataset instanceof double[]) {
|
||||
float[] tmp = convertDoubleToFloat((double[]) wholeDataset);
|
||||
stack.addSlice(null, tmp);
|
||||
} else {
|
||||
// try to put pixels on stack
|
||||
stack.addSlice(null, slice);
|
||||
stack.addSlice(null, wholeDataset);
|
||||
}
|
||||
IJ.showProgress(1.f);
|
||||
|
||||
ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
|
||||
imp.getProcessor().resetMinAndMax();
|
||||
imp.resetDisplayRange();
|
||||
imp.show();
|
||||
|
||||
ImageProcessor ips = imp.getProcessor();
|
||||
|
||||
double imgMax = ips.getMax();
|
||||
double imgMin = ips.getMin();
|
||||
|
||||
logger.info(" Min = " + imgMin + ", Max = " + imgMax);
|
||||
ips.setMinAndMax(imgMin, imgMax);
|
||||
imp.updateAndDraw();
|
||||
imp.show();
|
||||
imp.updateStatusbarValue();
|
||||
|
||||
} else {
|
||||
System.err.println(" Error: Variable Dimensions " + rank + " not supported (yet).");
|
||||
IJ.showStatus("Variable Dimension " + rank + " not supported");
|
||||
System.err.println(" Error: Variable Dimensions " + numberOfDimensions + " not supported (yet).");
|
||||
IJ.showStatus("Variable Dimension " + numberOfDimensions + " not supported");
|
||||
}
|
||||
}
|
||||
|
||||
} catch (Exception e) {
|
||||
logger.log(Level.WARNING, "Error while opening '" + directory + name + "'", e);
|
||||
IJ.showStatus("Error opening file.");
|
||||
IJ.showStatus("Error while opening file '" + directory + name + "'");
|
||||
} catch (OutOfMemoryError o) {
|
||||
IJ.outOfMemory("Load HDF5");
|
||||
}
|
||||
finally{
|
||||
IJ.outOfMemory("Out of memory while loading file '" + directory + name + "'");
|
||||
} finally {
|
||||
try {
|
||||
if (inFile != null){
|
||||
if (inFile != null) {
|
||||
inFile.close();
|
||||
}
|
||||
} catch (HDF5Exception err) {
|
||||
System.err.println("Error while closing '" + directory + name + "'");
|
||||
System.err.println(err);
|
||||
IJ.showStatus("Error closing file.");
|
||||
logger.log(Level.WARNING, "Error while closing '" + directory + name + "'", err);
|
||||
IJ.showStatus("Error while closing '" + directory + name + "'");
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
IJ.showProgress(1.0);
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @param datatype
|
||||
* @param wholeDataset
|
||||
* @return
|
||||
*/
|
||||
private Object checkUnsigned(Datatype datatype, Object wholeDataset) {
|
||||
// check for unsigned datatype
|
||||
int unsignedConvSelec = 0;
|
||||
boolean isSigned16Bit = !datatype.isUnsigned() && (datatype.getDatatypeClass() == Datatype.CLASS_INTEGER) && (datatype.getDatatypeSize() == 2);
|
||||
if (isSigned16Bit) {
|
||||
GenericDialog convDiag = new GenericDialog("Unsigend to signed conversion");
|
||||
convDiag.addMessage("Detected unsigned datatype, which " + "is not supported.");
|
||||
String[] convOptions = new String[2];
|
||||
convOptions[0] = "cut off values";
|
||||
convOptions[1] = "convert to float";
|
||||
convDiag.addChoice("Please select an conversion option:", convOptions, convOptions[0]);
|
||||
convDiag.showDialog();
|
||||
if (convDiag.wasCanceled())
|
||||
return wholeDataset;
|
||||
unsignedConvSelec = convDiag.getNextChoiceIndex();
|
||||
wholeDataset = convertToUnsigned(wholeDataset, unsignedConvSelec);
|
||||
}
|
||||
return wholeDataset;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Returns a datatype if native datatype is not supported. Returns null if datatype is supported.
|
||||
* @param datatype
|
||||
* @return
|
||||
*/
|
||||
private Datatype checkIfDatatypeSupported(Datatype datatype) {
|
||||
Datatype datatypeIfUnsupported = null;
|
||||
// check if we have an unsupported datatype
|
||||
if (datatype.getDatatypeClass() == Datatype.CLASS_INTEGER && (datatype.getDatatypeSize() == 4 || datatype.getDatatypeSize() == 8)) {
|
||||
logger.info("Datatype not supported by ImageJ");
|
||||
GenericDialog typeSelDiag = new GenericDialog("Datatype Selection");
|
||||
typeSelDiag.addMessage("The datatype `" + datatype.getDatatypeDescription() + "` is not supported by ImageJ.\n\n");
|
||||
typeSelDiag.addMessage("Please select your wanted datatype.\n");
|
||||
String[] choices = new String[2];
|
||||
choices[0] = "float";
|
||||
choices[1] = "short";
|
||||
typeSelDiag.addChoice(" Possible types are", choices, "float");
|
||||
typeSelDiag.showDialog();
|
||||
|
||||
if (typeSelDiag.wasCanceled()) {
|
||||
return null;
|
||||
}
|
||||
int selection = typeSelDiag.getNextChoiceIndex();
|
||||
if (selection == 0) {
|
||||
logger.info("float selected");
|
||||
datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
|
||||
}
|
||||
if (selection == 1) {
|
||||
logger.info("short selected");
|
||||
int typeSizeInByte = 2;
|
||||
datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_INTEGER, typeSizeInByte, Datatype.NATIVE, -1);
|
||||
}
|
||||
}
|
||||
return datatypeIfUnsupported;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Selection of the datasets to visualize
|
||||
*
|
||||
@ -901,12 +667,12 @@ public class HDF5Reader implements PlugIn {
|
||||
* @param nRows (extent[0])
|
||||
* @param nColumns (extent[1])
|
||||
* @param stack
|
||||
* @param slice
|
||||
* @param wholeDataset
|
||||
* @param size
|
||||
*/
|
||||
private void copyPixels2(int nRows, int nColumns, ImageStack stack, Object slice, int size) {
|
||||
if (slice instanceof byte[]) {
|
||||
byte[] tmp = (byte[]) slice;
|
||||
private void copyPixels2(int nRows, int nColumns, ImageStack stack, Object wholeDataset, int size) {
|
||||
if (wholeDataset instanceof byte[]) {
|
||||
byte[] tmp = (byte[]) wholeDataset;
|
||||
byte[] rChannel = new byte[size];
|
||||
byte[] gChannel = new byte[size];
|
||||
byte[] bChannel = new byte[size];
|
||||
@ -922,8 +688,8 @@ public class HDF5Reader implements PlugIn {
|
||||
stack.addSlice(null, rChannel);
|
||||
stack.addSlice(null, gChannel);
|
||||
stack.addSlice(null, bChannel);
|
||||
} else if (slice instanceof short[]) {
|
||||
short[] tmp = (short[]) slice;
|
||||
} else if (wholeDataset instanceof short[]) {
|
||||
short[] tmp = (short[]) wholeDataset;
|
||||
short[] rChannel = new short[size];
|
||||
short[] gChannel = new short[size];
|
||||
short[] bChannel = new short[size];
|
||||
@ -939,8 +705,8 @@ public class HDF5Reader implements PlugIn {
|
||||
stack.addSlice(null, rChannel);
|
||||
stack.addSlice(null, gChannel);
|
||||
stack.addSlice(null, bChannel);
|
||||
} else if (slice instanceof int[]) {
|
||||
int[] tmp = (int[]) slice;
|
||||
} else if (wholeDataset instanceof int[]) {
|
||||
int[] tmp = (int[]) wholeDataset;
|
||||
int[] rChannel = new int[size];
|
||||
int[] gChannel = new int[size];
|
||||
int[] bChannel = new int[size];
|
||||
@ -956,8 +722,8 @@ public class HDF5Reader implements PlugIn {
|
||||
stack.addSlice(null, rChannel);
|
||||
stack.addSlice(null, gChannel);
|
||||
stack.addSlice(null, bChannel);
|
||||
} else if (slice instanceof long[]) {
|
||||
long[] tmp = (long[]) slice;
|
||||
} else if (wholeDataset instanceof long[]) {
|
||||
long[] tmp = (long[]) wholeDataset;
|
||||
long[] rChannel = new long[size];
|
||||
long[] gChannel = new long[size];
|
||||
long[] bChannel = new long[size];
|
||||
@ -973,8 +739,8 @@ public class HDF5Reader implements PlugIn {
|
||||
stack.addSlice(null, rChannel);
|
||||
stack.addSlice(null, gChannel);
|
||||
stack.addSlice(null, bChannel);
|
||||
} else if (slice instanceof float[]) {
|
||||
float[] tmp = (float[]) slice;
|
||||
} else if (wholeDataset instanceof float[]) {
|
||||
float[] tmp = (float[]) wholeDataset;
|
||||
float[] rChannel = new float[size];
|
||||
float[] gChannel = new float[size];
|
||||
float[] bChannel = new float[size];
|
||||
@ -990,8 +756,8 @@ public class HDF5Reader implements PlugIn {
|
||||
stack.addSlice(null, rChannel);
|
||||
stack.addSlice(null, gChannel);
|
||||
stack.addSlice(null, bChannel);
|
||||
} else if (slice instanceof double[]) {
|
||||
double[] tmp = (double[]) slice;
|
||||
} else if (wholeDataset instanceof double[]) {
|
||||
double[] tmp = (double[]) wholeDataset;
|
||||
double[] rChannel = new double[size];
|
||||
double[] gChannel = new double[size];
|
||||
double[] bChannel = new double[size];
|
||||
@ -1020,7 +786,7 @@ public class HDF5Reader implements PlugIn {
|
||||
* @param endIdx
|
||||
* @param size
|
||||
*/
|
||||
private void copyPixels1(int nRows, int nColumns, ImageStack stack, Object wholeDataset, int startIdx, int endIdx, int size) {
|
||||
private void copyPixels1(int nRows, int nColumns, ImageStack stack, Object wholeDataset, int size, int startIdx, int endIdx) {
|
||||
if (wholeDataset instanceof byte[]) {
|
||||
byte[] tmp = Arrays.copyOfRange((byte[]) wholeDataset, startIdx, endIdx);
|
||||
byte[] rChannel = new byte[size];
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user