/** Returns an InputStream for the image described by this FileInfo. */
public InputStream createInputStream(FileInfo fi) throws IOException, MalformedURLException {
InputStream is = null;
boolean gzip =
fi.fileName != null && (fi.fileName.endsWith(".gz") || fi.fileName.endsWith(".GZ"));
if (fi.inputStream != null) is = fi.inputStream;
else if (fi.url != null && !fi.url.equals("")) is = new URL(fi.url + fi.fileName).openStream();
else {
if (fi.directory.length() > 0 && !fi.directory.endsWith(Prefs.separator))
fi.directory += Prefs.separator;
File f = new File(fi.directory + fi.fileName);
if (gzip) fi.compression = FileInfo.COMPRESSION_UNKNOWN;
if (f == null || f.isDirectory() || !validateFileInfo(f, fi)) is = null;
else is = new FileInputStream(f);
}
if (is != null) {
if (fi.compression >= FileInfo.LZW) is = new RandomAccessStream(is);
else if (gzip) is = new GZIPInputStream(is, 50000);
}
return is;
}
static boolean validateFileInfo(File f, FileInfo fi) {
long offset = fi.getOffset();
long length = 0;
if (fi.width <= 0 || fi.height < 0) {
error("Width or height <= 0.", fi, offset, length);
return false;
}
if (offset >= 0 && offset < 1000L) return true;
if (offset < 0L) {
error("Offset is negative.", fi, offset, length);
return false;
}
if (fi.fileType == FileInfo.BITMAP || fi.compression != FileInfo.COMPRESSION_NONE) return true;
length = f.length();
long size = fi.width * fi.height * fi.getBytesPerPixel();
size = fi.nImages > 1 ? size : size / 4;
if (fi.height == 1) size = 0; // allows plugins to read info of unknown length at end of file
if (offset + size > length) {
error("Offset + image size > file length.", fi, offset, length);
return false;
}
return true;
}
/** 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;
}
static void error(String msg, FileInfo fi, long offset, long length) {
IJ.error(
"FileOpener",
"FileInfo parameter error. \n"
+ msg
+ "\n \n"
+ " Width: "
+ fi.width
+ "\n"
+ " Height: "
+ fi.height
+ "\n"
+ " Offset: "
+ offset
+ "\n"
+ " Bytes/pixel: "
+ fi.getBytesPerPixel()
+ "\n"
+ (length > 0 ? " File length: " + length + "\n" : ""));
}
public Properties decodeDescriptionString(FileInfo fi) {
if (fi.description == null || fi.description.length() < 7) return null;
if (IJ.debugMode) IJ.log("Image Description: " + new String(fi.description).replace('\n', ' '));
if (!fi.description.startsWith("ImageJ")) return null;
Properties props = new Properties();
InputStream is = new ByteArrayInputStream(fi.description.getBytes());
try {
props.load(is);
is.close();
} catch (IOException e) {
return null;
}
fi.unit = props.getProperty("unit", "");
Double n = getNumber(props, "cf");
if (n != null) fi.calibrationFunction = n.intValue();
double c[] = new double[5];
int count = 0;
for (int i = 0; i < 5; i++) {
n = getNumber(props, "c" + i);
if (n == null) break;
c[i] = n.doubleValue();
count++;
}
if (count >= 2) {
fi.coefficients = new double[count];
for (int i = 0; i < count; i++) fi.coefficients[i] = c[i];
}
fi.valueUnit = props.getProperty("vunit");
n = getNumber(props, "images");
if (n != null && n.doubleValue() > 1.0) fi.nImages = (int) n.doubleValue();
if (fi.nImages > 1) {
double spacing = getDouble(props, "spacing");
if (spacing != 0.0) {
if (spacing < 0) spacing = -spacing;
fi.pixelDepth = spacing;
}
}
return props;
}
