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https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5.git
synced 2025-06-04 09:40:39 +02:00
cleanup ...
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@ -75,78 +75,62 @@ public class HDF5Writer implements PlugInFilter {
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ImagePlus imp = WindowManager.getCurrentImage();
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int nFrames = imp.getNFrames();
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int nChannels = imp.getNChannels();
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int nSlices = imp.getNSlices();
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int stackSize = imp.getStackSize();
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int nRows = imp.getHeight();
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int nCols = imp.getWidth();
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int imgColorDepth = imp.getBitDepth();
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int imgColorType = imp.getType();
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Datatype type = null;
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if (imgColorType == ImagePlus.GRAY8) {
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logger.info(" bit depth: " + imgColorDepth + ", type: GRAY8");
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type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
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} else if (imgColorType == ImagePlus.GRAY16) {
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logger.info(" bit depth: " + imgColorDepth + ", type: GRAY16");
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type = new H5Datatype(Datatype.CLASS_INTEGER, 2, Datatype.NATIVE, Datatype.SIGN_NONE);
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} else if (imgColorType == ImagePlus.GRAY32) {
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logger.info(" bit depth: " + imgColorDepth + ", type: GRAY32");
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type = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
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} else if (imgColorType == ImagePlus.COLOR_RGB) {
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logger.info(" bit depth: " + imgColorDepth + ", type: COLOR_RGB");
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type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
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}
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GenericDialog gd = null;
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gd = new GenericDialog("Variable Name Selection");
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// check for hyperstack
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if (imp.getOpenAsHyperStack() || imp.isHyperStack()) {
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logger.info("This is a hyperstack");
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boolean splitChannels = true;
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gd.addCheckbox("Split frames and channels", splitChannels);
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gd.addStringField(imp.getTitle(), "/t$T/channel$C");
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String title = imp.getTitle();
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int nDims = imp.getNDimensions();
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int nFrames = imp.getNFrames();
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int nChannels = imp.getNChannels();
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int nLevs = imp.getNSlices();
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int nRows = imp.getHeight();
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int nCols = imp.getWidth();
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boolean isComposite = imp.isComposite();
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logger.info("isComposite: " + Boolean.toString(isComposite));
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logger.info("Saving image \"" + title + "\"");
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logger.info("nDims: " + Integer.toString(nDims));
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logger.info("nFrames: " + Integer.toString(nFrames));
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logger.info("nChannels: " + Integer.toString(nChannels));
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logger.info("nSlices: " + Integer.toString(nLevs));
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logger.info("nRows: " + Integer.toString(nRows));
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logger.info("nCols: " + Integer.toString(nCols));
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gd.showDialog();
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if (gd.wasCanceled()) {
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IJ.error("Plugin canceled!");
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return;
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}
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splitChannels = gd.getNextBoolean();
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String formatString = gd.getNextString();
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logger.info("formatString: " + formatString);
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logger.info("Bitdepth: " + imp.getBitDepth());
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logger.info("Saving HDF5 File: " + filename);
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int imgColorDepth = imp.getBitDepth();
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int imgColorType = imp.getType();
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Datatype type = null;
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if (imgColorType == ImagePlus.GRAY8) {
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logger.info(" bit depth: " + imgColorDepth + ", type: GRAY8");
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type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
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} else if (imgColorType == ImagePlus.GRAY16) {
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logger.info(" bit depth: " + imgColorDepth + ", type: GRAY16");
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int typeSizeInByte = 2;
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type = new H5Datatype(Datatype.CLASS_INTEGER, typeSizeInByte, Datatype.NATIVE, Datatype.SIGN_NONE);
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} else if (imgColorType == ImagePlus.GRAY32) {
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logger.info(" bit depth: " + imgColorDepth + ", type: GRAY32");
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// int typeSizeInByte = 4;
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type = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
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}
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// open the outfile
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H5File outFile = null;
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// Open the file
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try {
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outFile = (H5File) fileFormat.createFile(filename, FileFormat.FILE_CREATE_OPEN);
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H5File outFile = (H5File) fileFormat.createFile(filename, FileFormat.FILE_CREATE_OPEN);
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if (!outFile.canWrite()) {
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IJ.error("File `" + filename + "`is readonly!");
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return;
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}
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// open the file
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outFile.open();
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if (splitChannels) {
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// Split frames and channels
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// parse format string
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String[] formatTokens = HDF5GroupedVarnames.parseFormatString(formatString, "[0-9]+"); // dummy
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// regexp
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long[] channelDims = null;
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if (nLevs > 1) {
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if (nSlices > 1) {
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channelDims = new long[3];
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channelDims[0] = nLevs;
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channelDims[0] = nSlices;
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channelDims[1] = nRows;
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channelDims[2] = nCols;
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} else {
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@ -195,7 +179,7 @@ public class HDF5Writer implements PlugInFilter {
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logger.info("selected.length: " + Integer.toString(selected.length));
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logger.info("channelDims.length: " + Integer.toString(channelDims.length));
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if (nLevs == 1) {
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if (nSlices == 1) {
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System.arraycopy(channelDims, 0, selected, 0, selected.length);
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int stackIndex = imp.getStackIndex(c + 1, 1, f + 1);
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logger.info("Stackindex: " + Integer.toString(stackIndex));
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@ -211,12 +195,8 @@ public class HDF5Writer implements PlugInFilter {
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} else {
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selected[0] = 1;
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System.arraycopy(channelDims, 1, selected, 1, selected.length - 1);
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long[] start = dataset.getStartDims(); // the
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// off
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// set
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// of
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// the selection
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for (int lvl = 0; lvl < nLevs; ++lvl) {
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long[] start = dataset.getStartDims();
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for (int lvl = 0; lvl < nSlices; ++lvl) {
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// select hyperslab
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start[0] = lvl;
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int stackIndex = imp.getStackIndex(c + 1, lvl + 1, f + 1);
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@ -232,9 +212,6 @@ public class HDF5Writer implements PlugInFilter {
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}
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}
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}
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} else {
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// write one big array
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}
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outFile.close();
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} catch (HDF5Exception err) {
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IJ.error(err.getMessage());
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@ -245,22 +222,6 @@ public class HDF5Writer implements PlugInFilter {
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}
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} else {
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logger.info("This is NO hyperstack");
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// String title = imp.getTitle();
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// int nDims = imp.getNDimensions();
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// int nFrames = imp.getNFrames();
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// int nChannels = imp.getNChannels();
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// int nLevs = imp.getNSlices();
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// int nRows = imp.getHeight();
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// int nCols = imp.getWidth();
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// boolean isComposite = imp.isComposite() ;
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// logger.info("isComposite: "+Boolean.toString(isComposite));
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// logger.info("Saving image \""+title+"\"");
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// logger.info("nDims: "+Integer.toString(nDims));
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// logger.info("nFrames: "+Integer.toString(nFrames));
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// logger.info("nChannels: "+Integer.toString(nChannels));
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// logger.info("nSlices: "+Integer.toString(nLevs));
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// logger.info("nRows: "+Integer.toString(nRows));
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// logger.info("nCols: "+Integer.toString(nCols));
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gd.addStringField(imp.getTitle(), "");
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gd.showDialog();
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@ -274,7 +235,8 @@ public class HDF5Writer implements PlugInFilter {
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IJ.error("No data set name given. Plugin canceled!");
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return;
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}
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// write data set
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try {
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H5File outFile = null;
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try {
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@ -288,12 +250,11 @@ public class HDF5Writer implements PlugInFilter {
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return;
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}
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outFile.open();
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// first create all dimensions and variables
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// Image color depth and color type
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int imgColorDepth;
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int imgColorType;
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logger.info("writing data to variable: " + varName);
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@ -305,16 +266,12 @@ public class HDF5Writer implements PlugInFilter {
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// ensure group exists
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Group group = createGroupRecursive(groupName, null, outFile);
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int nLevels = imp.getStackSize();
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int nRows = imp.getHeight();
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int nCols = imp.getWidth();
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// get image type (bit depth)
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imgColorDepth = imp.getBitDepth();
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imgColorType = imp.getType();
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long[] dims;
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if (imgColorType == ImagePlus.COLOR_RGB || imgColorType == ImagePlus.COLOR_256) {
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if (nLevels == 1) {
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if (stackSize == 1) {
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// color image
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dims = new long[3];
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dims[0] = nRows;
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@ -325,13 +282,13 @@ public class HDF5Writer implements PlugInFilter {
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// have 3.
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logger.info("adding 4 dimensions");
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dims = new long[4];
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dims[0] = nLevels;
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dims[0] = stackSize;
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dims[1] = nRows;
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dims[2] = nCols;
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dims[3] = 3;
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}
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} else {
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if (nLevels == 1) {
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if (stackSize == 1) {
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// color image
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dims = new long[2];
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dims[0] = nRows;
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@ -339,54 +296,12 @@ public class HDF5Writer implements PlugInFilter {
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} else {
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logger.info("adding 3 dimensions");
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dims = new long[3];
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dims[0] = nLevels;
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dims[0] = stackSize;
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dims[1] = nRows;
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dims[2] = nCols;
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}
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}
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// The following is a list of a few example of H5Datatype.
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//
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// 1. to create unsigned native integer
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// H5Datatype type = new H5Dataype(CLASS_INTEGER, NATIVE,
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// NATIVE, SIGN_NONE);
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// 2. to create 16-bit signed integer with big endian
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// H5Datatype type = new H5Dataype(CLASS_INTEGER, 2,
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// ORDER_BE, NATIVE);
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// 3. to create native float
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// H5Datatype type = new H5Dataype(CLASS_FLOAT, NATIVE,
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// NATIVE, -1);
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// 4. to create 64-bit double
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// H5Datatype type = new H5Dataype(CLASS_FLOAT, 8, NATIVE,
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// -1);
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// H5Datatype type = new
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// H5Datatype(H5Datatype.CLASS_INTEGER,
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// H5Datatype.NATIVE, H5Datatype.NATIVE,
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// H5Datatype.SIGN_NONE);
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Datatype type = null;
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// supported data types
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// FIXME: set the right signed and precision stuff
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if (imgColorType == ImagePlus.GRAY8) {
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logger.info(" bit depth: " + imgColorDepth + ", type: GRAY8");
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type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
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} else if (imgColorType == ImagePlus.GRAY16) {
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logger.info(" bit depth: " + imgColorDepth + ", type: GRAY16");
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int typeSizeInByte = 2;
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type = new H5Datatype(Datatype.CLASS_INTEGER, typeSizeInByte, Datatype.NATIVE, Datatype.SIGN_NONE);
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} else if (imgColorType == ImagePlus.GRAY32) {
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logger.info(" bit depth: " + imgColorDepth + ", type: GRAY32");
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// int typeSizeInByte = 4;
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type = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
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} else if (imgColorType == ImagePlus.COLOR_RGB) {
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logger.info(" bit depth: " + imgColorDepth + ", type: COLOR_RGB");
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type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
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} else if (imgColorType == ImagePlus.COLOR_256) {
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// FIXME: not supported yet
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logger.info(" bit depth: " + imgColorDepth + ", type: COLOR_256");
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logger.info(" ERROR: untested, this might fail.");
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type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
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}
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// select hyperslabs
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long[] maxdims = dims;
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// long[] chunks = findOptimalChunksize( nDims,
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@ -403,7 +318,6 @@ public class HDF5Writer implements PlugInFilter {
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dataset = null;
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}
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if (dataset == null) {
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dataset = outFile.createScalarDS(dataSetName, group, type, dims, maxdims, chunks, gzip, null);
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}
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dataset.init();
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@ -413,12 +327,12 @@ public class HDF5Writer implements PlugInFilter {
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// the
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// dataet
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ImageStack stack = imp.getStack();
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if (nLevels == 1) {
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if (stackSize == 1) {
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System.arraycopy(dims, 0, selected, 0, selected.length);
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// get raw data
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Object slice = stack.getPixels(nLevels);
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Object slice = stack.getPixels(stackSize);
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if (imgColorType == ImagePlus.COLOR_RGB)
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slice = computeRgbSlice(stack.getPixels(nLevels));
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slice = computeRgbSlice(stack.getPixels(stackSize));
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// write data
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dataset.write(slice);
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@ -427,8 +341,8 @@ public class HDF5Writer implements PlugInFilter {
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System.arraycopy(dims, 1, selected, 1, selected.length - 1);
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long[] start = dataset.getStartDims(); // the off set of
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// the selection
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for (int lvl = 0; lvl < nLevels; ++lvl) {
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IJ.showProgress(lvl, nLevels);
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for (int lvl = 0; lvl < stackSize; ++lvl) {
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IJ.showProgress(lvl, stackSize);
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// select hyperslab
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start[0] = lvl;
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