//
// TiffJAIReader.java
//
/*
OME Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package loci.formats.in;
import java.awt.image.BufferedImage;
import java.awt.image.RenderedImage;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import loci.common.FileHandle;
import loci.common.IRandomAccess;
import loci.common.Location;
import loci.common.ReflectException;
import loci.common.ReflectedUniverse;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.MissingLibraryException;
import loci.formats.gui.AWTImageTools;
import loci.formats.meta.MetadataStore;
/**
* TiffJAIReader is a file format reader for TIFF images. It uses the
* Java Advanced Imaging library (javax.media.jai) to read the data.
*
* Much of this code was adapted from
* <a href="http://java.sun.com/products/java-media/jai/forDevelopers/samples/MultiPageRead.java">this example</a>.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/src/loci/formats/in/TiffJAIReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/TiffJAIReader.java;hb=HEAD">Gitweb</a></dd></dl>
*
* @author Curtis Rueden ctrueden at wisc.edu
*/
public class TiffJAIReader extends BIFormatReader {
// -- Constants --
private static final String NO_JAI_MSG =
"Java Advanced Imaging (JAI) is required to read some TIFF files. " +
"Please install JAI from https://jai.dev.java.net/";
// -- Fields --
/** Reflection tool for JAI calls. */
protected ReflectedUniverse r;
// -- Constructor --
/** Constructs a new TIFF reader that uses Java Image I/O. */
public TiffJAIReader() {
super("Tagged Image File Format", TiffReader.TIFF_SUFFIXES);
domains = new String[] {FormatTools.GRAPHICS_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#openPlane(int, int, int, int, int int) */
public Object openPlane(int no, int x, int y, int w, int h)
throws FormatException, IOException
{
FormatTools.checkPlaneParameters(this, no, -1, x, y, w, h);
BufferedImage img = openBufferedImage(no);
return AWTImageTools.getSubimage(img, isLittleEndian(), x, y, w, h);
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
LOGGER.info("Checking for JAI");
try {
r = new ReflectedUniverse();
r.exec("import javax.media.jai.NullOpImage");
r.exec("import javax.media.jai.OpImage");
r.exec("import com.sun.media.jai.codec.FileSeekableStream");
r.exec("import com.sun.media.jai.codec.ImageDecoder");
r.exec("import com.sun.media.jai.codec.ImageCodec");
}
catch (ReflectException exc) {
throw new MissingLibraryException(NO_JAI_MSG, exc);
}
super.initFile(id);
LOGGER.info("Reading movie dimensions");
// map Location to File or RandomAccessFile, if possible
IRandomAccess ira = Location.getMappedFile(id);
if (ira != null) {
if (ira instanceof FileHandle) {
FileHandle fh = (FileHandle) ira;
r.setVar("file", fh.getRandomAccessFile());
}
else {
throw new FormatException(
"Unsupported handle type" + ira.getClass().getName());
}
}
else {
String mapId = Location.getMappedId(id);
File file = new File(mapId);
if (file.exists()) {
r.setVar("file", file);
}
else throw new FileNotFoundException(id);
}
r.setVar("tiff", "tiff");
r.setVar("param", null);
// create TIFF decoder
int numPages;
try {
r.exec("s = new FileSeekableStream(file)");
r.exec("dec = ImageCodec.createImageDecoder(tiff, s, param)");
numPages = ((Integer) r.exec("dec.getNumPages()")).intValue();
}
catch (ReflectException exc) {
throw new FormatException(exc);
}
if (numPages < 0) {
throw new FormatException("Invalid page count: " + numPages);
}
// decode first image plane
BufferedImage img = openBufferedImage(0);
if (img == null) throw new FormatException("Invalid image stream");
LOGGER.info("Populating metadata");
core[0].imageCount = numPages;
core[0].sizeX = img.getWidth();
core[0].sizeY = img.getHeight();
core[0].sizeZ = 1;
core[0].sizeC = img.getSampleModel().getNumBands();
core[0].sizeT = numPages;
core[0].rgb = core[0].sizeC > 1;
core[0].dimensionOrder = "XYCZT";
core[0].pixelType = AWTImageTools.getPixelType(img);
core[0].interleaved = true;
core[0].littleEndian = false;
core[0].metadataComplete = true;
core[0].indexed = false;
core[0].falseColor = false;
// populate the metadata store
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
MetadataTools.setDefaultCreationDate(store, id, 0);
}
/** Obtains a BufferedImage from the given data source using JAI. */
protected BufferedImage openBufferedImage(int no) throws FormatException {
r.setVar("no", no);
RenderedImage img;
try {
r.exec("img = dec.decodeAsRenderedImage(no)");
img = (RenderedImage)
r.exec("new NullOpImage(img, null, OpImage.OP_IO_BOUND, null)");
}
catch (ReflectException exc) {
throw new FormatException(exc);
}
return AWTImageTools.convertRenderedImage(img);
}
}