// takes the reader lock
BufferedImage getAssociatedImage(String name) throws IOException {
Lock rl = lock.readLock();
rl.lock();
try {
checkDisposed();
long dim[] = new long[2];
OpenSlideJNI.openslide_get_associated_image_dimensions(osr, name, dim);
checkError();
if (dim[0] == -1) {
// non-terminal error
throw new IOException("Failure reading associated image");
}
BufferedImage img =
new BufferedImage((int) dim[0], (int) dim[1], BufferedImage.TYPE_INT_ARGB_PRE);
int data[] = ((DataBufferInt) img.getRaster().getDataBuffer()).getData();
OpenSlideJNI.openslide_read_associated_image(osr, name, data);
checkError();
return img;
} finally {
rl.unlock();
}
}
// call with the reader lock held, or from the constructor
private void checkError() throws IOException {
String msg = OpenSlideJNI.openslide_get_error(osr);
if (msg != null) {
throw new IOException(msg);
}
}
// takes the writer lock
public void dispose() {
Lock wl = lock.writeLock();
wl.lock();
try {
if (osr != 0) {
OpenSlideJNI.openslide_close(osr);
osr = 0;
}
} finally {
wl.unlock();
}
}
// takes the reader lock
public void paintRegionARGB(int dest[], long x, long y, int level, int w, int h)
throws IOException {
if ((long) w * (long) h > dest.length) {
throw new ArrayIndexOutOfBoundsException(
"Size of data (" + dest.length + ") is less than w * h");
}
if (w < 0 || h < 0) {
throw new IllegalArgumentException("w and h must be nonnegative");
}
Lock rl = lock.readLock();
rl.lock();
try {
checkDisposed();
OpenSlideJNI.openslide_read_region(osr, dest, x, y, level, w, h);
checkError();
} finally {
rl.unlock();
}
}
public final class OpenSlide implements Closeable {
private static final FileFilter FILE_FILTER =
new FileFilter() {
@Override
public boolean accept(File f) {
return f.isDirectory() || OpenSlide.detectVendor(f) != null;
}
@Override
public String getDescription() {
return "Virtual slide";
}
};
private static final String LIBRARY_VERSION = OpenSlideJNI.openslide_get_version();
public static final String PROPERTY_NAME_COMMENT = "openslide.comment";
public static final String PROPERTY_NAME_VENDOR = "openslide.vendor";
public static final String PROPERTY_NAME_QUICKHASH1 = "openslide.quickhash-1";
public static final String PROPERTY_NAME_BACKGROUND_COLOR = "openslide.background-color";
public static final String PROPERTY_NAME_OBJECTIVE_POWER = "openslide.objective-power";
public static final String PROPERTY_NAME_MPP_X = "openslide.mpp-x";
public static final String PROPERTY_NAME_MPP_Y = "openslide.mpp-y";
public static final String PROPERTY_NAME_BOUNDS_X = "openslide.bounds-x";
public static final String PROPERTY_NAME_BOUNDS_Y = "openslide.bounds-y";
public static final String PROPERTY_NAME_BOUNDS_WIDTH = "openslide.bounds-width";
public static final String PROPERTY_NAME_BOUNDS_HEIGHT = "openslide.bounds-height";
private long osr;
private final ReadWriteLock lock = new ReentrantReadWriteLock();
private final long levelWidths[];
private final long levelHeights[];
private final double levelDownsamples[];
private final int levelCount;
private final Map<String, String> properties;
private final Map<String, AssociatedImage> associatedImages;
private final File canonicalFile;
private final int hashCodeVal;
// vartika on 5 august
private String filePath;
public static String detectVendor(File file) {
return OpenSlideJNI.openslide_detect_vendor(file.getPath());
}
// vartika doubt on 4 august
// this also does not seem right..what if two people open the same file
// maybe add requester name??
static HashMap<String, OpenSlide> instanceArray = new HashMap<String, OpenSlide>();
public static OpenSlide createOpenSlideInstance(String filePath) throws IOException {
if (!instanceArray.containsKey(filePath)) {
File file = new File(filePath);
OpenSlide os = new OpenSlide(file);
instanceArray.put(filePath, os);
}
return instanceArray.get(filePath);
}
public OpenSlide(File file) throws IOException {
if (!file.exists()) {
throw new FileNotFoundException(file.toString());
}
// vartika on 5 august
filePath = file.getPath();
osr = OpenSlideJNI.openslide_open(file.getPath());
if (osr == 0) {
throw new IOException(file + ": Not a file that OpenSlide can recognize");
}
// dispose on error, we are in the constructor
try {
checkError();
} catch (IOException e) {
dispose();
throw e;
}
// store level count
levelCount = OpenSlideJNI.openslide_get_level_count(osr);
// store dimensions
levelWidths = new long[levelCount];
levelHeights = new long[levelCount];
levelDownsamples = new double[levelCount];
for (int i = 0; i < levelCount; i++) {
long dim[] = new long[2];
OpenSlideJNI.openslide_get_level_dimensions(osr, i, dim);
levelWidths[i] = dim[0];
levelHeights[i] = dim[1];
levelDownsamples[i] = OpenSlideJNI.openslide_get_level_downsample(osr, i);
}
// properties
HashMap<String, String> props = new HashMap<String, String>();
for (String s : OpenSlideJNI.openslide_get_property_names(osr)) {
props.put(s, OpenSlideJNI.openslide_get_property_value(osr, s));
}
properties = Collections.unmodifiableMap(props);
// associated images
HashMap<String, AssociatedImage> associated = new HashMap<String, AssociatedImage>();
for (String s : OpenSlideJNI.openslide_get_associated_image_names(osr)) {
associated.put(s, new AssociatedImage(s, this));
}
associatedImages = Collections.unmodifiableMap(associated);
// store info for hash and equals
canonicalFile = file.getCanonicalFile();
String quickhash1 = getProperties().get(PROPERTY_NAME_QUICKHASH1);
if (quickhash1 != null) {
hashCodeVal = (int) Long.parseLong(quickhash1.substring(0, 8), 16);
} else {
hashCodeVal = canonicalFile.hashCode();
}
// dispose on error, we are in the constructor
try {
checkError();
} catch (IOException e) {
dispose();
throw e;
}
}
// call with the reader lock held, or from the constructor
private void checkError() throws IOException {
String msg = OpenSlideJNI.openslide_get_error(osr);
if (msg != null) {
throw new IOException(msg);
}
}
// takes the writer lock
public void dispose() {
Lock wl = lock.writeLock();
wl.lock();
try {
if (osr != 0) {
OpenSlideJNI.openslide_close(osr);
osr = 0;
}
} finally {
wl.unlock();
}
}
public int getLevelCount() {
return levelCount;
}
// call with the reader lock held
private void checkDisposed() {
if (osr == 0) {
throw new OpenSlideDisposedException();
}
}
public long getLevel0Width() {
return levelWidths[0];
}
public long getLevel0Height() {
return levelHeights[0];
}
public long getLevelWidth(int level) {
return levelWidths[level];
}
public long getLevelHeight(int level) {
return levelHeights[level];
}
// vartika says - to change this tomorrow
public void paintRegionOfLevel(
Graphics2D g, int dx, int dy, int sx, int sy, int w, int h, int level) throws IOException {
// vartika says on 3 august
// paintRegion(g, dx, dy, sx, sy, w, h, levelDownsamples[level]);
ReturnObject returnObject = paintRegion(sx, sy, w, h, levelDownsamples[level]);
// vartika doubt on 3 august - shouldn't this be at client?? -who calls it?
g.drawImage(returnObject.getImg(), dx, dy, w, h, null);
if (debug) {
System.out.println(returnObject.getImg());
if (debugThingy == 0) {
g.setColor(new Color(1.0f, 0.0f, 0.0f, 0.4f));
debugThingy = 1;
} else {
g.setColor(new Color(0.0f, 1.0f, 0.0f, 0.4f));
debugThingy = 0;
}
g.fillRect(dx, dy, returnObject.getW(), returnObject.getH());
}
}
// takes the reader lock
public void paintRegionARGB(int dest[], long x, long y, int level, int w, int h)
throws IOException {
if ((long) w * (long) h > dest.length) {
throw new ArrayIndexOutOfBoundsException(
"Size of data (" + dest.length + ") is less than w * h");
}
if (w < 0 || h < 0) {
throw new IllegalArgumentException("w and h must be nonnegative");
}
Lock rl = lock.readLock();
rl.lock();
try {
checkDisposed();
OpenSlideJNI.openslide_read_region(osr, dest, x, y, level, w, h);
checkError();
} finally {
rl.unlock();
}
}
// vartika says on 3 august
public ReturnObject createReturnObject(byte[] byteArray, BufferedImage img, int w, int h) {
return new ReturnObject(byteArray, img, w, h);
}
// vartika says on 3 august
// public void paintRegion(Graphics2D g, int dx, int dy, long sx, long sy,
public ReturnObject paintRegion(long sx, long sy, int w, int h, double downsample)
throws IOException {
if (downsample < 1.0) {
throw new IllegalArgumentException("downsample (" + downsample + ") must be >= 1.0");
}
// get the level
int level = getBestLevelForDownsample(downsample);
// figure out its downsample
double levelDS = levelDownsamples[level];
// compute the difference
double relativeDS = downsample / levelDS;
// scale source coordinates into level coordinates
long baseX = (long) (downsample * sx);
long baseY = (long) (downsample * sy);
long levelX = (long) (relativeDS * sx);
long levelY = (long) (relativeDS * sy);
// scale width and height by relative downsample
int levelW = (int) Math.round(relativeDS * w);
int levelH = (int) Math.round(relativeDS * h);
// clip to edge of image
levelW = (int) Math.min(levelW, getLevelWidth(level) - levelX);
levelH = (int) Math.min(levelH, getLevelHeight(level) - levelY);
w = (int) Math.round(levelW / relativeDS);
h = (int) Math.round(levelH / relativeDS);
if (debug) {
System.out.println(
"levelW " + levelW + ", levelH " + levelH + ", baseX " + baseX + ", baseY " + baseY);
}
if (levelW <= 0 || levelH <= 0) {
// nothing to draw
return null;
}
BufferedImage img = new BufferedImage(levelW, levelH, BufferedImage.TYPE_INT_ARGB_PRE);
int data[] = ((DataBufferInt) img.getRaster().getDataBuffer()).getData();
paintRegionARGB(data, baseX, baseY, level, img.getWidth(), img.getHeight());
// vartika says on 5 august
System.out.println("data in paintRegion: " + data);
System.out.println("img in paintRegion: " + img);
// from here return the buffered image to client for drawing
// below code should be at client
// vartika says on 2 august
// g.scale(1.0 / relativeDS, 1.0 / relativeDS);
// vartika on 6 august
// trying to convert int data[] to byte [] or String...
ByteBuffer byteBuffer = ByteBuffer.allocate(data.length * 4);
IntBuffer intBuffer = byteBuffer.asIntBuffer();
intBuffer.put(data);
byte[] byteArray = byteBuffer.array();
// vartika on 10 august
// saving buffered image to disk as png
// try {
// vartika on 13 august to for demo
// File outputFile = new File("/home/vartika/humintec/image_files/BufferedImageToPng.png");
// ImageIO.write(img, "png", outputFile);
// } catch(IOException e) {
// e.printStackTrace();
// }
// instead of using int[]data to create bytearray, use the buffered image to create byte []
ByteArrayOutputStream baos = new ByteArrayOutputStream();
ImageIO.write(img, "png", baos);
baos.flush();
byte[] byteArrayFromBufferedImage = baos.toByteArray();
baos.close();
ReturnObject tmpobj = createReturnObject(byteArrayFromBufferedImage, img, w, h);
return tmpobj;
// vartika to uncomment later - 10 august
// vartika says on 3 august
/*ReturnObject obj = createReturnObject(byteArray, img, w, h);
return obj;*/
/* g.drawImage(img, dx, dy, w, h, null);
if (debug) {
System.out.println(img);
if (debugThingy == 0) {
g.setColor(new Color(1.0f, 0.0f, 0.0f, 0.4f));
debugThingy = 1;
} else {
g.setColor(new Color(0.0f, 1.0f, 0.0f, 0.4f));
debugThingy = 0;
}
g.fillRect(dx, dy, w, h);
}*/
}
final boolean debug = false;
private int debugThingy = 0;
public BufferedImage createThumbnailImage(
int x, int y, long w, long h, int maxSize, int bufferedImageType) throws IOException {
double ds;
if (w > h) {
ds = (double) w / maxSize;
} else {
ds = (double) h / maxSize;
}
if (ds < 1.0) {
ds = 1.0;
}
int sw = (int) (w / ds);
int sh = (int) (h / ds);
int sx = (int) (x / ds);
int sy = (int) (y / ds);
BufferedImage result = new BufferedImage(sw, sh, bufferedImageType);
Graphics2D g = result.createGraphics();
// vartika says on 3 august
// vartika doubt on 3 august - where is this draw being called from? need to move it to client
ReturnObject returnObject = paintRegion(sx, sy, sw, sh, ds);
g.drawImage(returnObject.getImg(), 0, 0, returnObject.getW(), returnObject.getH(), null);
if (debug) {
System.out.println(returnObject.getImg());
if (debugThingy == 0) {
g.setColor(new Color(1.0f, 0.0f, 0.0f, 0.4f));
debugThingy = 1;
} else {
g.setColor(new Color(0.0f, 1.0f, 0.0f, 0.4f));
debugThingy = 0;
}
g.fillRect(0, 0, returnObject.getW(), returnObject.getH());
}
g.dispose();
return result;
}
public BufferedImage createThumbnailImage(int x, int y, long w, long h, int maxSize)
throws IOException {
return createThumbnailImage(x, y, w, h, maxSize, BufferedImage.TYPE_INT_RGB);
}
public BufferedImage createThumbnailImage(int maxSize) throws IOException {
return createThumbnailImage(0, 0, getLevel0Width(), getLevel0Height(), maxSize);
}
public double getLevelDownsample(int level) {
return levelDownsamples[level];
}
public int getBestLevelForDownsample(double downsample) {
// too small, return first
if (downsample < levelDownsamples[0]) {
return 0;
}
// find where we are in the middle
for (int i = 1; i < levelCount; i++) {
if (downsample < levelDownsamples[i]) {
return i - 1;
}
}
// too big, return last
return levelCount - 1;
}
public Map<String, String> getProperties() {
return properties;
}
public Map<String, AssociatedImage> getAssociatedImages() {
return associatedImages;
}
// takes the reader lock
BufferedImage getAssociatedImage(String name) throws IOException {
Lock rl = lock.readLock();
rl.lock();
try {
checkDisposed();
long dim[] = new long[2];
OpenSlideJNI.openslide_get_associated_image_dimensions(osr, name, dim);
checkError();
if (dim[0] == -1) {
// non-terminal error
throw new IOException("Failure reading associated image");
}
BufferedImage img =
new BufferedImage((int) dim[0], (int) dim[1], BufferedImage.TYPE_INT_ARGB_PRE);
int data[] = ((DataBufferInt) img.getRaster().getDataBuffer()).getData();
OpenSlideJNI.openslide_read_associated_image(osr, name, data);
checkError();
return img;
} finally {
rl.unlock();
}
}
public static String getLibraryVersion() {
return LIBRARY_VERSION;
}
public static FileFilter getFileFilter() {
return FILE_FILTER;
}
@Override
public int hashCode() {
return hashCodeVal;
}
@Override
public boolean equals(Object obj) {
if (obj == this) {
return true;
}
if (obj instanceof OpenSlide) {
OpenSlide os2 = (OpenSlide) obj;
String quickhash1 = getProperties().get(PROPERTY_NAME_QUICKHASH1);
String os2_quickhash1 = os2.getProperties().get(PROPERTY_NAME_QUICKHASH1);
if (quickhash1 != null && os2_quickhash1 != null) {
return quickhash1.equals(os2_quickhash1);
} else if (quickhash1 == null && os2_quickhash1 == null) {
return canonicalFile.equals(os2.canonicalFile);
} else {
return false;
}
}
return false;
}
@Override
public void close() {
dispose();
}
}
public OpenSlide(File file) throws IOException {
if (!file.exists()) {
throw new FileNotFoundException(file.toString());
}
// vartika on 5 august
filePath = file.getPath();
osr = OpenSlideJNI.openslide_open(file.getPath());
if (osr == 0) {
throw new IOException(file + ": Not a file that OpenSlide can recognize");
}
// dispose on error, we are in the constructor
try {
checkError();
} catch (IOException e) {
dispose();
throw e;
}
// store level count
levelCount = OpenSlideJNI.openslide_get_level_count(osr);
// store dimensions
levelWidths = new long[levelCount];
levelHeights = new long[levelCount];
levelDownsamples = new double[levelCount];
for (int i = 0; i < levelCount; i++) {
long dim[] = new long[2];
OpenSlideJNI.openslide_get_level_dimensions(osr, i, dim);
levelWidths[i] = dim[0];
levelHeights[i] = dim[1];
levelDownsamples[i] = OpenSlideJNI.openslide_get_level_downsample(osr, i);
}
// properties
HashMap<String, String> props = new HashMap<String, String>();
for (String s : OpenSlideJNI.openslide_get_property_names(osr)) {
props.put(s, OpenSlideJNI.openslide_get_property_value(osr, s));
}
properties = Collections.unmodifiableMap(props);
// associated images
HashMap<String, AssociatedImage> associated = new HashMap<String, AssociatedImage>();
for (String s : OpenSlideJNI.openslide_get_associated_image_names(osr)) {
associated.put(s, new AssociatedImage(s, this));
}
associatedImages = Collections.unmodifiableMap(associated);
// store info for hash and equals
canonicalFile = file.getCanonicalFile();
String quickhash1 = getProperties().get(PROPERTY_NAME_QUICKHASH1);
if (quickhash1 != null) {
hashCodeVal = (int) Long.parseLong(quickhash1.substring(0, 8), 16);
} else {
hashCodeVal = canonicalFile.hashCode();
}
// dispose on error, we are in the constructor
try {
checkError();
} catch (IOException e) {
dispose();
throw e;
}
}
public static String detectVendor(File file) {
return OpenSlideJNI.openslide_detect_vendor(file.getPath());
}
