Ejemplo n.º 1
0
 byte[] uncompress(byte[] input) {
   if (fi.compression == FileInfo.PACK_BITS)
     return packBitsUncompress(input, fi.rowsPerStrip * fi.width * fi.getBytesPerPixel());
   else if (fi.compression == FileInfo.LZW || fi.compression == FileInfo.LZW_WITH_DIFFERENCING)
     return lzwUncompress(input);
   else if (fi.compression == FileInfo.ZIP) return zipUncompress(input);
   else return input;
 }
Ejemplo n.º 2
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;
 }
Ejemplo n.º 3
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;
 }
Ejemplo n.º 4
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;
 }
Ejemplo n.º 5
0
 Object readRGB48(InputStream in) throws IOException {
   if (fi.compression > FileInfo.COMPRESSION_NONE) return readCompressedRGB48(in);
   int channels = fi.samplesPerPixel;
   short[][] stack = new short[channels][nPixels];
   DataInputStream dis = new DataInputStream(in);
   int pixel = 0;
   int min = 65535, max = 0;
   if (fi.stripLengths == null) {
     fi.stripLengths = new int[fi.stripOffsets.length];
     fi.stripLengths[0] = width * height * bytesPerPixel;
   }
   for (int i = 0; i < fi.stripOffsets.length; i++) {
     if (i > 0) {
       long skip =
           (fi.stripOffsets[i] & 0xffffffffL)
               - (fi.stripOffsets[i - 1] & 0xffffffffL)
               - fi.stripLengths[i - 1];
       if (skip > 0L) dis.skip(skip);
     }
     int len = fi.stripLengths[i];
     int bytesToGo = (nPixels - pixel) * channels * 2;
     if (len > bytesToGo) len = bytesToGo;
     byte[] buffer = new byte[len];
     dis.readFully(buffer);
     int value;
     int channel = 0;
     boolean intel = fi.intelByteOrder;
     for (int base = 0; base < len; base += 2) {
       if (intel) value = ((buffer[base + 1] & 0xff) << 8) | (buffer[base] & 0xff);
       else value = ((buffer[base] & 0xff) << 8) | (buffer[base + 1] & 0xff);
       if (value < min) min = value;
       if (value > max) max = value;
       stack[channel][pixel] = (short) (value);
       channel++;
       if (channel == channels) {
         channel = 0;
         pixel++;
       }
     }
     showProgress(i + 1, fi.stripOffsets.length);
   }
   this.min = min;
   this.max = max;
   return stack;
 }
Ejemplo n.º 6
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" : ""));
 }
Ejemplo n.º 7
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;
 }
Ejemplo n.º 8
0
 public Hashtable processData(
     ServletInputStream is, String boundary, String saveInDir, int clength)
     throws IllegalArgumentException, IOException {
   if (is == null) throw new IllegalArgumentException("InputStream");
   if (boundary == null || boundary.trim().length() < 1)
     throw new IllegalArgumentException("\"" + boundary + "\" is an illegal boundary indicator");
   boundary = "--" + boundary;
   StringTokenizer stLine = null, stFields = null;
   FileInfo fileInfo = null;
   Hashtable dataTable = new Hashtable(5);
   String line = null, field = null, paramName = null;
   boolean saveFiles = (saveInDir != null && saveInDir.trim().length() > 0);
   boolean isFile = false;
   if (saveFiles) { // Create the required directory (including parent dirs)
     File f = new File(saveInDir);
     f.mkdirs();
   }
   line = getLine(is);
   if (line == null || !line.startsWith(boundary))
     throw new IOException("Boundary not found; boundary = " + boundary + ", line = " + line);
   while (line != null) {
     if (line == null || !line.startsWith(boundary)) return dataTable;
     line = getLine(is);
     if (line == null) return dataTable;
     stLine = new StringTokenizer(line, ";\r\n");
     if (stLine.countTokens() < 2) throw new IllegalArgumentException("Bad data in second line");
     line = stLine.nextToken().toLowerCase();
     if (line.indexOf("form-data") < 0)
       throw new IllegalArgumentException("Bad data in second line");
     stFields = new StringTokenizer(stLine.nextToken(), "=\"");
     if (stFields.countTokens() < 2)
       throw new IllegalArgumentException("Bad data in second line");
     fileInfo = new FileInfo();
     stFields.nextToken();
     paramName = stFields.nextToken();
     isFile = false;
     if (stLine.hasMoreTokens()) {
       field = stLine.nextToken();
       stFields = new StringTokenizer(field, "=\"");
       if (stFields.countTokens() > 1) {
         if (stFields.nextToken().trim().equalsIgnoreCase("filename")) {
           fileInfo.name = paramName;
           String value = stFields.nextToken();
           if (value != null && value.trim().length() > 0) {
             fileInfo.clientFileName = value;
             isFile = true;
           } else {
             line = getLine(is); // Skip "Content-Type:" line
             line = getLine(is); // Skip blank line
             line = getLine(is); // Skip blank line
             line = getLine(is); // Position to boundary line
             continue;
           }
         }
       } else if (field.toLowerCase().indexOf("filename") >= 0) {
         line = getLine(is); // Skip "Content-Type:" line
         line = getLine(is); // Skip blank line
         line = getLine(is); // Skip blank line
         line = getLine(is); // Position to boundary line
         continue;
       }
     }
     boolean skipBlankLine = true;
     if (isFile) {
       line = getLine(is);
       if (line == null) return dataTable;
       if (line.trim().length() < 1) skipBlankLine = false;
       else {
         stLine = new StringTokenizer(line, ": ");
         if (stLine.countTokens() < 2)
           throw new IllegalArgumentException("Bad data in third line");
         stLine.nextToken(); // Content-Type
         fileInfo.fileContentType = stLine.nextToken();
       }
     }
     if (skipBlankLine) {
       line = getLine(is);
       if (line == null) return dataTable;
     }
     if (!isFile) {
       line = getLine(is);
       if (line == null) return dataTable;
       dataTable.put(paramName, line);
       // If parameter is dir, change saveInDir to dir
       if (paramName.equals("dir")) saveInDir = line;
       line = getLine(is);
       continue;
     }
     try {
       UplInfo uplInfo = new UplInfo(clength);
       UploadMonitor.set(fileInfo.clientFileName, uplInfo);
       OutputStream os = null;
       String path = null;
       if (saveFiles)
         os = new FileOutputStream(path = getFileName(saveInDir, fileInfo.clientFileName));
       else os = new ByteArrayOutputStream(ONE_MB);
       boolean readingContent = true;
       byte previousLine[] = new byte[2 * ONE_MB];
       byte temp[] = null;
       byte currentLine[] = new byte[2 * ONE_MB];
       int read, read3;
       if ((read = is.readLine(previousLine, 0, previousLine.length)) == -1) {
         line = null;
         break;
       }
       while (readingContent) {
         if ((read3 = is.readLine(currentLine, 0, currentLine.length)) == -1) {
           line = null;
           uplInfo.aborted = true;
           break;
         }
         if (compareBoundary(boundary, currentLine)) {
           os.write(previousLine, 0, read - 2);
           line = new String(currentLine, 0, read3);
           break;
         } else {
           os.write(previousLine, 0, read);
           uplInfo.currSize += read;
           temp = currentLine;
           currentLine = previousLine;
           previousLine = temp;
           read = read3;
         } // end else
       } // end while
       os.flush();
       os.close();
       if (!saveFiles) {
         ByteArrayOutputStream baos = (ByteArrayOutputStream) os;
         fileInfo.setFileContents(baos.toByteArray());
       } else fileInfo.file = new File(path);
       dataTable.put(paramName, fileInfo);
       uplInfo.currSize = uplInfo.totalSize;
     } // end try
     catch (IOException e) {
       throw e;
     }
   }
   return dataTable;
 }
Ejemplo n.º 9
0
 /**
  * Reads the image from the InputStream and returns the pixel array (byte, short, int or float).
  * Returns null if there was an IO exception. Does not close the InputStream.
  */
 public Object readPixels(InputStream in) {
   Object pixels;
   startTime = System.currentTimeMillis();
   try {
     switch (fi.fileType) {
       case FileInfo.GRAY8:
       case FileInfo.COLOR8:
         bytesPerPixel = 1;
         skip(in);
         pixels = (Object) read8bitImage(in);
         break;
       case FileInfo.GRAY16_SIGNED:
       case FileInfo.GRAY16_UNSIGNED:
         bytesPerPixel = 2;
         skip(in);
         pixels = (Object) read16bitImage(in);
         break;
       case FileInfo.GRAY32_INT:
       case FileInfo.GRAY32_UNSIGNED:
       case FileInfo.GRAY32_FLOAT:
         bytesPerPixel = 4;
         skip(in);
         pixels = (Object) read32bitImage(in);
         break;
       case FileInfo.GRAY64_FLOAT:
         bytesPerPixel = 8;
         skip(in);
         pixels = (Object) read64bitImage(in);
         break;
       case FileInfo.RGB:
       case FileInfo.BGR:
       case FileInfo.ARGB:
       case FileInfo.ABGR:
       case FileInfo.BARG:
       case FileInfo.CMYK:
         bytesPerPixel = fi.getBytesPerPixel();
         skip(in);
         pixels = (Object) readChunkyRGB(in);
         break;
       case FileInfo.RGB_PLANAR:
         bytesPerPixel = 3;
         skip(in);
         pixels = (Object) readPlanarRGB(in);
         break;
       case FileInfo.BITMAP:
         bytesPerPixel = 1;
         skip(in);
         pixels = (Object) read1bitImage(in);
         break;
       case FileInfo.RGB48:
         bytesPerPixel = 6;
         skip(in);
         pixels = (Object) readRGB48(in);
         break;
       case FileInfo.RGB48_PLANAR:
         bytesPerPixel = 2;
         skip(in);
         pixels = (Object) readRGB48Planar(in);
         break;
       case FileInfo.GRAY12_UNSIGNED:
         skip(in);
         short[] data = read12bitImage(in);
         pixels = (Object) data;
         break;
       case FileInfo.GRAY24_UNSIGNED:
         skip(in);
         pixels = (Object) read24bitImage(in);
         break;
       default:
         pixels = null;
     }
     showProgress(1, 1);
     return pixels;
   } catch (IOException e) {
     IJ.log("" + e);
     return null;
   }
 }
Ejemplo n.º 10
0
 /**
  * Constructs a new ImageReader using a FileInfo object to describe the file to be read.
  *
  * @see ij.io.FileInfo
  */
 public ImageReader(FileInfo fi) {
   this.fi = fi;
   width = fi.width;
   height = fi.height;
   skipCount = fi.getOffset();
 }