Beispiel #1
0
 /** 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;
 }
Beispiel #2
0
 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;
 }
Beispiel #3
0
 /** 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;
 }
Beispiel #4
0
 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" : ""));
 }
Beispiel #5
0
 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;
 }