Examples with TiffEncoder ij.io.TiffEncoder used on opensource projects

Example 1 with TiffEncoder

use of ij.io.TiffEncoder in project TrakEM2 by trakem2.

the class Patch method writeAlphaMask.

private final synchronized boolean writeAlphaMask(final ByteProcessor bp, final long amID) {
    RandomAccessFile ra = null;
    try {
        final File f = new File(createAlphaMaskFilePath(amID));
        Utils.ensure(f);
        ra = new RandomAccessFile(f, "rw");
        final ByteArrayOutputStream ba = new ByteArrayOutputStream(bp.getWidth() * bp.getHeight());
        final ZipOutputStream zos = new ZipOutputStream(ba);
        // ImageJ looks for ".tif" extension in the ZipEntry
        final ImagePlus imp = new ImagePlus("mask.tif", bp);
        zos.putNextEntry(new ZipEntry(imp.getTitle()));
        final TiffEncoder te = new TiffEncoder(imp.getFileInfo());
        te.write(zos);
        zos.flush();
        zos.closeEntry();
        zos.close();
        ra.write((byte[]) ImageSaver.Bbuf.get(ba), 0, ba.size());
        return true;
    } catch (final Throwable e) {
        IJError.print(e);
    } finally {
        try {
            if (null != ra)
                ra.close();
        } catch (final Throwable t) {
            IJError.print(t);
        }
    }
    return false;
}

Example 2 with TiffEncoder

use of ij.io.TiffEncoder in project TrakEM2 by trakem2.

the class Loader method createZippedStream.

/**
 *Returns the ImagePlus as a zipped InputStream of bytes; the InputStream has to be closed by whoever is calling this method.
 */
protected InputStream createZippedStream(final ImagePlus imp) throws Exception {
    final FileInfo fi = imp.getFileInfo();
    final Object info = imp.getProperty("Info");
    if (info != null && (info instanceof String)) {
        fi.info = (String) info;
    }
    if (null == fi.description) {
        fi.description = new ij.io.FileSaver(imp).getDescriptionString();
    }
    // see whether this is a stack or not
    /*	//never the case in my program
		if (fi.nImages > 1) {
			IJ.log("saving a stack!");
			//virtual stacks would be supported? I don't think so because the FileSaver.saveAsTiffStack(String path) doesn't.
			if (fi.pixels == null && imp.getStack().isVirtual()) {
				//don't save it!
				IJ.showMessage("Virtual stacks not supported.");
				return false;
			}
			//setup stack things as in FileSaver.saveAsTiffStack(String path)
			fi.sliceLabels = imp.getStack().getSliceLabels();
		}
		*/
    final TiffEncoder te = new TiffEncoder(fi);
    ByteArrayInputStream i_stream = null;
    ByteArrayOutputStream o_bytes = new ByteArrayOutputStream();
    DataOutputStream o_stream = null;
    try {
        /* // works, but not significantly faster and breaks older databases (can't read zipped images properly)
			byte[] bytes = null;
			// compress in RAM
			o_stream = new DataOutputStream(new BufferedOutputStream(o_bytes));
			te.write(o_stream);
			o_stream.flush();
			o_stream.close();
			Deflater defl = new Deflater();
			byte[] unzipped_bytes = o_bytes.toByteArray();
			defl.setInput(unzipped_bytes);
			defl.finish();
			bytes = new byte[unzipped_bytes.length]; // this length *should* be enough
			int length = defl.deflate(bytes);
			if (length < unzipped_bytes.length) {
				byte[] bytes2 = new byte[length];
				System.arraycopy(bytes, 0, bytes2, 0, length);
				bytes = bytes2;
			}
			*/
        // old, creates temp file
        // clearing
        o_bytes = new ByteArrayOutputStream();
        final ZipOutputStream zos = new ZipOutputStream(o_bytes);
        o_stream = new DataOutputStream(new BufferedOutputStream(zos));
        zos.putNextEntry(new ZipEntry(imp.getTitle()));
        te.write(o_stream);
        // this was missing and was 1) truncating the Path images and 2) preventing the snapshots (which are very small) to be saved at all!!
        o_stream.flush();
        // this should ensure the flush above anyway. This can work because closing a ByteArrayOutputStream has no effect.
        o_stream.close();
        final byte[] bytes = o_bytes.toByteArray();
        // Utils.showStatus("Zipping " + bytes.length + " bytes...", false);
        // Utils.debug("Zipped ImagePlus byte array size = " + bytes.length);
        i_stream = new ByteArrayInputStream(bytes);
    } catch (final Exception e) {
        Utils.log("Loader: ImagePlus NOT zipped! Problems at writing the ImagePlus using the TiffEncoder.write(dos) :\n " + e);
        // attempt to cleanup:
        try {
            if (null != o_stream)
                o_stream.close();
            if (null != i_stream)
                i_stream.close();
        } catch (final IOException ioe) {
            Utils.log("Loader: Attempt to clean up streams failed.");
            IJError.print(ioe);
        }
        return null;
    }
    return i_stream;
}

Example 3 with TiffEncoder

use of ij.io.TiffEncoder in project TrakEM2 by trakem2.

the class ImageSaver method saveAsZip.

/**
 * Returns true on success.
 * <p>
 *  Core functionality adapted from {@code ij.io.FileSaver} class by Wayne Rasband.
 *  </p>
 */
public static final boolean saveAsZip(final ImagePlus imp, String path) {
    // safety checks
    if (null == imp) {
        Utils.log("Null imp, can't saveAsZip");
        return false;
    }
    if (!checkPath(path))
        return false;
    // ok, onward:
    FileInfo fi = imp.getFileInfo();
    if (!path.endsWith(".zip"))
        path = path + ".zip";
    String name = imp.getTitle();
    if (name.endsWith(".zip"))
        name = name.substring(0, name.length() - 4);
    if (!name.endsWith(".tif"))
        name = name + ".tif";
    fi.description = ImageSaver.getDescriptionString(imp, fi);
    Object info = imp.getProperty("Info");
    if (info != null && (info instanceof String))
        fi.info = (String) info;
    fi.sliceLabels = imp.getStack().getSliceLabels();
    try {
        ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(path));
        DataOutputStream out = new DataOutputStream(new BufferedOutputStream(zos));
        zos.putNextEntry(new ZipEntry(name));
        TiffEncoder te = new TiffEncoder(fi);
        te.write(out);
        out.close();
    } catch (IOException e) {
        IJError.print(e);
        return false;
    }
    return true;
}

Example 4 with TiffEncoder

use of ij.io.TiffEncoder in project GDSC-SMLM by aherbert.

the class TiffSeriesViewer method saveAsTiff.

private static void saveAsTiff(ImagePlus imp, String path) throws IOException {
    final FileInfo fi = imp.getFileInfo();
    fi.nImages = imp.getStackSize();
    try (OutputStream out = new BufferedOutputStream(new FileOutputStream(path))) {
        new TiffEncoder(fi).write(out);
    }
}

Example 5 with TiffEncoder

use of ij.io.TiffEncoder in project GDSC-SMLM by aherbert.

the class SeriesImageSourceTest method saveAsTiff.

private static void saveAsTiff(ImagePlus imp, String path, boolean intelByteOrder) throws IOException {
    // IJ.saveAsTiff(imp, path);
    final FileInfo fi = imp.getFileInfo();
    fi.nImages = imp.getStackSize();
    ij.Prefs.intelByteOrder = intelByteOrder;
    try (DataOutputStream out = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(path)))) {
        final TiffEncoder file = new TiffEncoder(fi);
        file.write(out);
    }
}