/**
* Obtains an object which represents a given sub-image of a plane within the file.
*
* @param id The path to the file.
* @param planeNumber The plane or section within the file to obtain.
* @param buf Pre-allocated buffer which has a <i>length</i> that can fit the byte count of the
* sub-image.
* @param x X coordinate of the upper-left corner of the sub-image
* @param y Y coordinate of the upper-left corner of the sub-image
* @param w width of the sub-image
* @param h height of the sub-image
* @return an object which represents the sub-image of the plane.
* @throws FormatException If there is an error parsing the file.
* @throws IOException If there is an error reading from the file or acquiring permissions to read
* the file.
*/
public PixelData openPlane2D(String id, int planeNumber, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException {
// FIXME: HACK! The ChannelSeparator isn't exactly what one would call
// "complete" so we have to work around the fact that it still copies
// all of the plane data (all three channels) from the file if the file
// is RGB.
ByteBuffer plane;
if (iReader.isRGB() || isLeicaReader()) {
// System.err.println("RGB, not using cached buffer.");
byte[] bytePlane = openBytes(planeNumber, x, y, w, h);
plane = ByteBuffer.wrap(bytePlane);
} else {
// System.err.println("Not RGB, using cached buffer.");
plane = ByteBuffer.wrap(openBytes(planeNumber, buf, x, y, w, h));
}
plane.order(isLittleEndian() ? ByteOrder.LITTLE_ENDIAN : ByteOrder.BIG_ENDIAN);
return new PixelData(FormatTools.getPixelTypeString(getPixelType()), plane);
}
/** Thumbnail loading routine. */
public void run() {
while (loaderAlive) {
try {
Thread.sleep(100);
} catch (InterruptedException exc) {
LOGGER.info("", exc);
}
try { // catch-all for unanticipated exceptions
final String id = loadId;
if (id == lastId) continue;
if (id != null && lastId != null) {
String[] files = reader.getUsedFiles();
boolean found = false;
for (int i = 0; i < files.length; i++) {
if (id.equals(files[i])) {
found = true;
lastId = id;
break;
}
}
if (found) continue;
}
lastId = id;
icon = null;
iconText = id == null ? "" : "Reading...";
formatText = resText = zctText = typeText = "";
iconTip = id;
formatTip = resTip = zctTip = typeTip = "";
if (id == null) {
SwingUtilities.invokeLater(refresher);
continue;
}
try {
reader.setId(id);
} catch (FormatException exc) {
LOGGER.debug("Failed to initialize {}", id, exc);
boolean badFormat = exc.getMessage().startsWith("Unknown file format");
iconText = "Unsupported " + (badFormat ? "format" : "file");
formatText = resText = "";
SwingUtilities.invokeLater(refresher);
lastId = null;
continue;
} catch (IOException exc) {
LOGGER.debug("Failed to initialize {}", id, exc);
iconText = "Unsupported file";
formatText = resText = "";
SwingUtilities.invokeLater(refresher);
lastId = null;
continue;
}
if (id != loadId) {
SwingUtilities.invokeLater(refresher);
continue;
}
icon = id == null ? null : new ImageIcon(makeImage("Loading..."));
iconText = "";
String format = reader.getFormat();
formatText = format;
formatTip = format;
resText = reader.getSizeX() + " x " + reader.getSizeY();
zctText = reader.getSizeZ() + "Z x " + reader.getSizeT() + "T x " + reader.getSizeC() + "C";
typeText =
reader.getRGBChannelCount()
+ " x "
+ FormatTools.getPixelTypeString(reader.getPixelType());
SwingUtilities.invokeLater(refresher);
// open middle image thumbnail
int z = reader.getSizeZ() / 2;
int t = reader.getSizeT() / 2;
int ndx = reader.getIndex(z, 0, t);
BufferedImage thumb = null;
try {
thumb = reader.openThumbImage(ndx);
} catch (FormatException exc) {
LOGGER.debug("Failed to read thumbnail #{} from {}", new Object[] {ndx, id}, exc);
} catch (IOException exc) {
LOGGER.debug("Failed to read thumbnail #{} from {}", new Object[] {ndx, id}, exc);
}
icon = new ImageIcon(thumb == null ? makeImage("Failed") : thumb);
iconText = "";
SwingUtilities.invokeLater(refresher);
} catch (Exception exc) {
LOGGER.info("", exc);
icon = null;
iconText = "Thumbnail failure";
formatText = resText = zctText = typeText = "";
iconTip = loadId;
formatTip = resTip = zctTip = typeTip = "";
SwingUtilities.invokeLater(refresher);
}
}
}
