@Override
public RecordReader<IntWritable, Text> createRecordReader(InputSplit is, TaskAttemptContext tac)
throws IOException, InterruptedException {
ImageReader ir = new ImageReader();
ir.initialize(is, tac);
return ir;
}
/** Reads the pixel data from an image described by a FileInfo object. */
Object readPixels(FileInfo fi) {
Object pixels = null;
try {
InputStream is = createInputStream(fi);
if (is == null) return null;
ImageReader reader = new ImageReader(fi);
pixels = reader.readPixels(is);
minValue = reader.min;
maxValue = reader.max;
is.close();
} catch (Exception e) {
if (!Macro.MACRO_CANCELED.equals(e.getMessage())) IJ.handleException(e);
}
return pixels;
}
/** Opens a stack of images. */
ImagePlus openStack(ColorModel cm, boolean show) {
ImageStack stack = new ImageStack(fi.width, fi.height, cm);
long skip = fi.getOffset();
Object pixels;
try {
ImageReader reader = new ImageReader(fi);
InputStream is = createInputStream(fi);
if (is == null) return null;
IJ.resetEscape();
for (int i = 1; i <= fi.nImages; i++) {
if (!silentMode) IJ.showStatus("Reading: " + i + "/" + fi.nImages);
if (IJ.escapePressed()) {
IJ.beep();
IJ.showProgress(1.0);
silentMode = false;
return null;
}
pixels = reader.readPixels(is, skip);
if (pixels == null) break;
stack.addSlice(null, pixels);
skip = fi.gapBetweenImages;
if (!silentMode) IJ.showProgress(i, fi.nImages);
}
is.close();
} catch (Exception e) {
IJ.log("" + e);
} catch (OutOfMemoryError e) {
IJ.outOfMemory(fi.fileName);
stack.trim();
}
if (!silentMode) IJ.showProgress(1.0);
if (stack.getSize() == 0) return null;
if (fi.sliceLabels != null && fi.sliceLabels.length <= stack.getSize()) {
for (int i = 0; i < fi.sliceLabels.length; i++) stack.setSliceLabel(fi.sliceLabels[i], i + 1);
}
ImagePlus imp = new ImagePlus(fi.fileName, stack);
if (fi.info != null) imp.setProperty("Info", fi.info);
if (show) imp.show();
imp.setFileInfo(fi);
setCalibration(imp);
ImageProcessor ip = imp.getProcessor();
if (ip.getMin() == ip.getMax()) // find stack min and max if first slice is blank
setStackDisplayRange(imp);
if (!silentMode) IJ.showProgress(1.0);
silentMode = false;
return imp;
}
/**
* Gets a list of <code>IIOImage</code> objects for an image file.
*
* @param imageFile input image file. It can be any of the supported formats, including TIFF,
* JPEG, GIF, PNG, BMP, JPEG, and PDF if GPL Ghostscript is installed
* @return a list of <code>IIOImage</code> objects
* @throws Exception
*/
public static List<IIOImage> getIIOImageList(File imageFile) throws IOException {
File workingTiffFile = null;
ImageReader reader = null;
ImageInputStream iis = null;
try {
// convert PDF to TIFF
if (imageFile.getName().toLowerCase().endsWith(".pdf")) {
workingTiffFile = PdfUtilities.convertPdf2Tiff(imageFile);
imageFile = workingTiffFile;
}
List<IIOImage> iioImageList = new ArrayList<IIOImage>();
String imageFileName = imageFile.getName();
String imageFormat = imageFileName.substring(imageFileName.lastIndexOf('.') + 1);
if (imageFormat.matches("(pbm|pgm|ppm)")) {
imageFormat = "pnm";
} else if (imageFormat.equals("jp2")) {
imageFormat = "jpeg2000";
}
Iterator<ImageReader> readers = ImageIO.getImageReadersByFormatName(imageFormat);
reader = readers.next();
if (reader == null) {
throw new RuntimeException(
"Need to install JAI Image I/O package.\nhttps://jai-imageio.dev.java.net");
}
iis = ImageIO.createImageInputStream(imageFile);
reader.setInput(iis);
int imageTotal = reader.getNumImages(true);
for (int i = 0; i < imageTotal; i++) {
// IIOImage oimage = new IIOImage(reader.read(i), null,
// reader.getImageMetadata(i));
IIOImage oimage = reader.readAll(i, reader.getDefaultReadParam());
iioImageList.add(oimage);
}
return iioImageList;
} finally {
try {
if (iis != null) {
iis.close();
}
if (reader != null) {
reader.dispose();
}
} catch (Exception e) {
// ignore
}
if (workingTiffFile != null && workingTiffFile.exists()) {
workingTiffFile.delete();
}
}
}
private static MalletTexture.Meta createMeta(final String _path, final InputStream _stream) {
try (final ImageInputStream in = ImageIO.createImageInputStream(_stream)) {
final Iterator<ImageReader> readers = ImageIO.getImageReaders(in);
if (readers.hasNext()) {
final ImageReader reader = readers.next();
try {
reader.setInput(in);
// Add additional Meta information to MalletTexture as
// and when it becomes needed. It shouldn't hold too much (RGB, RGBA, Mono, endinese,
// 32, 24-bit, etc)
// data as a game-developer shouldn't need detailed information.
return new MalletTexture.Meta(_path, reader.getHeight(0), reader.getWidth(0));
} finally {
reader.dispose();
}
}
} catch (IOException ex) {
ex.printStackTrace();
}
return null;
}
/**
* Creates a list of TIFF image files from an image file. It basically converts images of other
* formats to TIFF format, or a multi-page TIFF image to multiple TIFF image files.
*
* @param imageFile input image file
* @param index an index of the page; -1 means all pages, as in a multi-page TIFF image
* @return a list of TIFF image files
* @throws Exception
*/
public static List<File> createTiffFiles(File imageFile, int index) throws IOException {
List<File> tiffFiles = new ArrayList<File>();
String imageFileName = imageFile.getName();
String imageFormat = imageFileName.substring(imageFileName.lastIndexOf('.') + 1);
Iterator<ImageReader> readers = ImageIO.getImageReadersByFormatName(imageFormat);
ImageReader reader = readers.next();
if (reader == null) {
throw new RuntimeException(
"Need to install JAI Image I/O package.\nhttps://jai-imageio.dev.java.net");
}
ImageInputStream iis = ImageIO.createImageInputStream(imageFile);
reader.setInput(iis);
// Read the stream metadata
// IIOMetadata streamMetadata = reader.getStreamMetadata();
// Set up the writeParam
TIFFImageWriteParam tiffWriteParam = new TIFFImageWriteParam(Locale.US);
tiffWriteParam.setCompressionMode(ImageWriteParam.MODE_DISABLED);
// Get tif writer and set output to file
Iterator<ImageWriter> writers = ImageIO.getImageWritersByFormatName(TIFF_FORMAT);
ImageWriter writer = writers.next();
// Read the stream metadata
IIOMetadata streamMetadata = writer.getDefaultStreamMetadata(tiffWriteParam);
int imageTotal = reader.getNumImages(true);
for (int i = 0; i < imageTotal; i++) {
// all if index == -1; otherwise, only index-th
if (index == -1 || i == index) {
// BufferedImage bi = reader.read(i);
// IIOImage oimage = new IIOImage(bi, null, reader.getImageMetadata(i));
IIOImage oimage = reader.readAll(i, reader.getDefaultReadParam());
File tiffFile = File.createTempFile(OUTPUT_FILE_NAME, TIFF_EXT);
ImageOutputStream ios = ImageIO.createImageOutputStream(tiffFile);
writer.setOutput(ios);
writer.write(streamMetadata, oimage, tiffWriteParam);
ios.close();
tiffFiles.add(tiffFile);
}
}
writer.dispose();
reader.dispose();
return tiffFiles;
}
public static void main(String[] args)
throws DependencyException, FormatException, IOException, ServiceException {
if (args.length < 1) {
System.out.println("Please specify a (small) image file.");
System.exit(1);
}
String path = args[0];
// read in entire file
System.out.println("Reading file into memory from disk...");
File inputFile = new File(path);
int fileSize = (int) inputFile.length();
DataInputStream in = new DataInputStream(new FileInputStream(inputFile));
byte[] inBytes = new byte[fileSize];
in.readFully(inBytes);
System.out.println(fileSize + " bytes read.");
// determine input file suffix
String fileName = inputFile.getName();
int dot = fileName.lastIndexOf(".");
String suffix = dot < 0 ? "" : fileName.substring(dot);
// map input id string to input byte array
String inId = "inBytes" + suffix;
Location.mapFile(inId, new ByteArrayHandle(inBytes));
// read data from byte array using ImageReader
System.out.println();
System.out.println("Reading image data from memory...");
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
IMetadata omeMeta = service.createOMEXMLMetadata();
ImageReader reader = new ImageReader();
reader.setMetadataStore(omeMeta);
reader.setId(inId);
int seriesCount = reader.getSeriesCount();
int imageCount = reader.getImageCount();
int sizeX = reader.getSizeX();
int sizeY = reader.getSizeY();
int sizeZ = reader.getSizeZ();
int sizeC = reader.getSizeC();
int sizeT = reader.getSizeT();
// output some details
System.out.println("Series count: " + seriesCount);
System.out.println("First series:");
System.out.println("\tImage count = " + imageCount);
System.out.println("\tSizeX = " + sizeX);
System.out.println("\tSizeY = " + sizeY);
System.out.println("\tSizeZ = " + sizeZ);
System.out.println("\tSizeC = " + sizeC);
System.out.println("\tSizeT = " + sizeT);
// map output id string to output byte array
String outId = fileName + ".ome.tif";
ByteArrayHandle outputFile = new ByteArrayHandle();
Location.mapFile(outId, outputFile);
// write data to byte array using ImageWriter
System.out.println();
System.out.print("Writing planes to destination in memory: ");
ImageWriter writer = new ImageWriter();
writer.setMetadataRetrieve(omeMeta);
writer.setId(outId);
byte[] plane = null;
for (int i = 0; i < imageCount; i++) {
if (plane == null) {
// allow reader to allocate a new byte array
plane = reader.openBytes(i);
} else {
// reuse previously allocated byte array
reader.openBytes(i, plane);
}
writer.saveBytes(i, plane);
System.out.print(".");
}
reader.close();
writer.close();
System.out.println();
byte[] outBytes = outputFile.getBytes();
outputFile.close();
// flush output byte array to disk
System.out.println();
System.out.println("Flushing image data to disk...");
File outFile = new File(fileName + ".ome.tif");
DataOutputStream out = new DataOutputStream(new FileOutputStream(outFile));
out.write(outBytes);
out.close();
}
public void setInput(Object input, boolean seekForwardOnly, boolean ignoreMetadata) {
super.setInput(input, seekForwardOnly, ignoreMetadata);
iis = (ImageInputStream) input; // Always works
if (iis != null) iis.setByteOrder(ByteOrder.LITTLE_ENDIAN);
gotHeader = false;
}