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;
}
/** 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;
}
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;
}
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;
}
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;
}
/**
* 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;
}
}
/**
* 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();
}