/** 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;
}
public void run(String arg) {
String ijDir = System.getProperty("ij.dir");
if (!ijDir.endsWith("/")) ijDir += "/";
if (arg == null || "".equals(arg)) {
OpenDialog dialog = new OpenDialog("Which Fiji component", ijDir + "plugins", "");
if (dialog.getDirectory() == null) return;
arg = dialog.getDirectory() + dialog.getFileName();
}
if (arg.startsWith(ijDir)) arg = arg.substring(ijDir.length());
final JFrame frame = new JFrame("Building " + arg + "...");
Container panel = frame.getContentPane();
panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
JTextArea textArea = new JTextArea("Calling Fiji Build\n", 25, 80);
textArea.setFont(new Font("Courier", Font.PLAIN, 12));
textArea.setEditable(false);
panel.add(new JScrollPane(textArea));
final JButton okay = new JButton("okay");
okay.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
frame.dispose();
}
});
okay.setEnabled(false);
okay.setAlignmentX(Component.CENTER_ALIGNMENT);
panel.add(okay);
frame.pack();
frame.setLocationRelativeTo(null);
okay.requestFocus();
frame.setVisible(true);
try {
Fake fake = new Fake();
fake.out = fake.err = new PrintStream(new JTextAreaOutputStream(textArea));
Parser parser = fake.parse(new FileInputStream(ijDir + "/Fakefile"), new File(ijDir));
final Rule all = parser.parseRules(Arrays.asList(arg.split("\\s+")));
all.make();
fake.out.println("Finished.");
frame.setTitle("Built " + arg);
okay.setEnabled(true);
} catch (Exception e) {
IJ.handleException(e);
}
}
/**
* Open a file. If it's a directory, ask to open all images as a sequence in a stack or
* individually.
*/
public void openFile(File f) {
if (IJ.debugMode) IJ.log("DragAndDrop.openFile: " + f);
try {
if (null == f) return;
String path = f.getCanonicalPath();
if (f.exists()) {
if (f.isDirectory()) openDirectory(f, path);
else {
if (openAsVirtualStack && (path.endsWith(".tif") || path.endsWith(".TIF")))
(new FileInfoVirtualStack()).run(path);
else (new Opener()).openAndAddToRecent(path);
OpenDialog.setLastDirectory(f.getParent() + File.separator);
OpenDialog.setLastName(f.getName());
}
} else {
IJ.log("File not found: " + path);
}
} catch (Throwable e) {
if (!Macro.MACRO_CANCELED.equals(e.getMessage())) IJ.handleException(e);
}
}
@Override
protected void log(final Throwable t) {
IJ.handleException(t);
}
/** Attemps to open a tiff file as a stack. Returns an ImagePlus object if successful. */
public ImagePlus openTiffStack(FileInfo[] info) {
if (info.length > 1 && !allSameSizeAndType(info)) return null;
FileInfo fi = info[0];
if (fi.nImages > 1) return new FileOpener(fi).open(false); // open contiguous images as stack
else {
ColorModel cm = createColorModel(fi);
ImageStack stack = new ImageStack(fi.width, fi.height, cm);
Object pixels = null;
long skip = fi.getOffset();
int imageSize = fi.width * fi.height * fi.getBytesPerPixel();
if (info[0].fileType == FileInfo.GRAY12_UNSIGNED) {
imageSize = (int) (fi.width * fi.height * 1.5);
if ((imageSize & 1) == 1) imageSize++; // add 1 if odd
}
if (info[0].fileType == FileInfo.BITMAP) {
int scan = (int) Math.ceil(fi.width / 8.0);
imageSize = scan * fi.height;
}
long loc = 0L;
int nChannels = 1;
try {
InputStream is = createInputStream(fi);
ImageReader reader = new ImageReader(fi);
IJ.resetEscape();
for (int i = 0; i < info.length; i++) {
nChannels = 1;
Object[] channels = null;
if (!silentMode) IJ.showStatus("Reading: " + (i + 1) + "/" + info.length);
if (IJ.escapePressed()) {
IJ.beep();
IJ.showProgress(1.0);
return null;
}
fi.stripOffsets = info[i].stripOffsets;
fi.stripLengths = info[i].stripLengths;
int bpp = info[i].getBytesPerPixel();
if (info[i].samplesPerPixel > 1 && !(bpp == 3 || bpp == 4 || bpp == 6)) {
nChannels = fi.samplesPerPixel;
channels = new Object[nChannels];
for (int c = 0; c < nChannels; c++) {
pixels = reader.readPixels(is, c == 0 ? skip : 0L);
channels[c] = pixels;
}
} else pixels = reader.readPixels(is, skip);
if (pixels == null && channels == null) break;
loc += imageSize * nChannels + skip;
if (i < (info.length - 1)) {
skip = info[i + 1].getOffset() - loc;
if (info[i + 1].compression >= FileInfo.LZW) skip = 0;
if (skip < 0L) {
IJ.error("Opener", "Unexpected image offset");
break;
}
}
if (fi.fileType == FileInfo.RGB48) {
Object[] pixels2 = (Object[]) pixels;
stack.addSlice(null, pixels2[0]);
stack.addSlice(null, pixels2[1]);
stack.addSlice(null, pixels2[2]);
isRGB48 = true;
} else if (nChannels > 1) {
for (int c = 0; c < nChannels; c++) {
if (channels[c] != null) stack.addSlice(null, channels[c]);
}
} else stack.addSlice(null, pixels);
IJ.showProgress(i, info.length);
}
is.close();
} catch (Exception e) {
IJ.handleException(e);
} catch (OutOfMemoryError e) {
IJ.outOfMemory(fi.fileName);
stack.deleteLastSlice();
stack.deleteLastSlice();
}
IJ.showProgress(1.0);
if (stack.getSize() == 0) return null;
if (fi.fileType == FileInfo.GRAY16_UNSIGNED
|| fi.fileType == FileInfo.GRAY12_UNSIGNED
|| fi.fileType == FileInfo.GRAY32_FLOAT
|| fi.fileType == FileInfo.RGB48) {
ImageProcessor ip = stack.getProcessor(1);
ip.resetMinAndMax();
stack.update(ip);
}
// if (fi.whiteIsZero)
// new StackProcessor(stack, stack.getProcessor(1)).invert();
ImagePlus imp = new ImagePlus(fi.fileName, stack);
new FileOpener(fi).setCalibration(imp);
imp.setFileInfo(fi);
if (fi.info != null) imp.setProperty("Info", fi.info);
if (fi.description != null && fi.description.contains("order=zct"))
new HyperStackConverter().shuffle(imp, HyperStackConverter.ZCT);
int stackSize = stack.getSize();
if (nChannels > 1 && (stackSize % nChannels) == 0) {
imp.setDimensions(nChannels, stackSize / nChannels, 1);
imp = new CompositeImage(imp, IJ.COMPOSITE);
imp.setOpenAsHyperStack(true);
} else if (imp.getNChannels() > 1) imp = makeComposite(imp, fi);
IJ.showProgress(1.0);
return imp;
}
}