// tokenizes a string for PBM and PGM headers and plain PBM and PGM data. If oneChar is true,
// then
// rather than parsing a whole string, a single character is read (not including whitespace or
// comments)
static String tokenizeString(InputStream stream, boolean oneChar) throws IOException {
final int EOF = -1;
StringBuilder b = new StringBuilder();
int c;
boolean inComment = false;
while (true) {
c = stream.read();
if (c == EOF)
throw new IOException(
"Stream ended prematurely, before table reading was completed."); // no more tokens
else if (inComment) {
if (c == '\r' || c == '\n') // escape the comment
inComment = false;
else {
} // do nothing
} else if (Character.isWhitespace((char) c)) {
} // do nothing
else if (c == '#') // start of a comment
{
inComment = true;
} else // start of a string
{
b.append((char) c);
break;
}
}
if (oneChar) return b.toString();
// at this point we have a valid string. We read until whitespace or a #
while (true) {
c = stream.read();
if (c == EOF) break;
else if (c == '#') // start of comment, read until a '\n'
{
while (true) {
c = stream.read(); // could hit EOF, which is fine
if (c == EOF) break;
else if (c == '\r' || c == '\n') break;
}
// break; // comments are not delimiters
} else if (Character.isWhitespace((char) c)) break;
else b.append((char) c);
}
return b.toString();
}
private String getStringFromStreamSource(StreamSource src, int length) throws Exception {
byte buf[] = null;
if (src == null) return null;
InputStream outStr = src.getInputStream();
if (outStr != null) {
int len = outStr.available();
if (outStr.markSupported()) outStr.reset();
buf = new byte[len];
outStr.read(buf, 0, len);
// System.out.println("From inputstream: "+new String(buf));
return new String(buf);
} else {
char buf1[] = new char[length];
Reader r = src.getReader();
if (r == null) return null;
r.reset();
r.read(buf1);
// System.out.println("From Reader: "+new String(buf));
return new String(buf1);
}
}
// Loads raw PGM files after the first-line header is stripped
static int[][] loadRawPGM(InputStream stream) throws IOException {
int width = tokenizeInt(stream);
int height = tokenizeInt(stream);
int maxVal = tokenizeInt(stream);
if (width < 0) throw new IOException("Invalid width: " + width);
if (height < 0) throw new IOException("Invalid height: " + height);
if (maxVal <= 0) throw new IOException("Invalid maximum value: " + maxVal);
// this single whitespace character will have likely already been consumed by reading maxVal
// stream.read(); // must be a whitespace
int[][] field = new int[width][height];
for (int i = 0; i < height; i++)
for (int j = 0; j < width; j++) {
if (maxVal < 256) // one byte
field[j][i] = stream.read();
else if (maxVal < 65536) // two bytes
field[j][i] =
(stream.read() << 8) & stream.read(); // two bytes, most significant byte first
else if (maxVal < 16777216) // three bytes -- this is nonstandard
field[j][i] =
(stream.read() << 16)
& (stream.read() << 8)
& stream.read(); // three bytes, most significant byte first
else // four bytes -- this is nonstandard
field[j][i] =
(stream.read() << 24)
& (stream.read() << 16)
& (stream.read() << 8)
& stream.read(); // three bytes, most significant byte first
}
return field;
}
/** 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;
}
// Loads raw PBM files after the first-line header is stripped
static int[][] loadRawPBM(InputStream stream) throws IOException {
int width = tokenizeInt(stream);
int height = tokenizeInt(stream);
if (width < 0) throw new IOException("Invalid width in PBM: " + width);
if (height < 0) throw new IOException("Invalid height in PBM: " + height);
// this single whitespace character will have likely already been consumed by reading height
// stream.read(); // must be a whitespace
int[][] field = new int[width][height];
for (int i = 0; i < height; i++) {
int data = 0;
int count = 0;
for (int j = 0; j < width; j++) {
if (count == 0) {
data = stream.read();
count = 8;
}
count--;
field[j][i] = (data >> count) & 0x1;
}
}
return field;
}
private static String readln(InputStream s) {
try {
int c;
StringBuffer sb = new StringBuffer();
while ((c = s.read()) > 0 && c != 255 && (c == '\n' || c == '\r'))
; // Skip carriage returns and line feeds
while (c > 0 && c != 255 && c != '\n' && c != '\r') {
sb.append((char) c);
c = s.read();
}
if ((c == -1 || c == 255) && sb.length() == 0) return null;
return new String(sb);
} catch (IOException e) {
return null;
}
}
/** 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 byte[] readStream(InputStream input) throws IOException {
ByteArrayOutputStream bytes = new ByteArrayOutputStream();
int read;
byte[] buffer = new byte[256];
while ((read = input.read(buffer, 0, 256)) != -1) {
bytes.write(buffer, 0, read);
}
return bytes.toByteArray();
}
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;
}
/**
* Reads GIF image from stream
*
* @param InputStream containing GIF file.
* @return read status code (0 = no errors)
*/
public int read(InputStream is) {
init();
if (is != null) {
if (!(is instanceof BufferedInputStream)) is = new BufferedInputStream(is);
in = (BufferedInputStream) is;
readHeader();
if (!err()) {
readContents();
if (frameCount < 0) {
status = STATUS_FORMAT_ERROR;
}
}
} else {
status = STATUS_OPEN_ERROR;
}
try {
is.close();
} catch (IOException e) {
}
return status;
}
public static void main(String[] args) {
// read filename and N 2 parameters
String fileName = args[0];
N = Integer.parseInt(args[1]);
// output two images, one original image at left, the other result image at right
BufferedImage imgOriginal =
new BufferedImage(IMAGE_WIDTH, IMAGE_HEIGHT, BufferedImage.TYPE_INT_RGB);
BufferedImage img = new BufferedImage(IMAGE_WIDTH, IMAGE_HEIGHT, BufferedImage.TYPE_INT_RGB);
try {
File file = new File(fileName);
InputStream is = new FileInputStream(file);
long len = file.length();
byte[] bytes = new byte[(int) len];
int offset = 0;
int numRead = 0;
while (offset < bytes.length
&& (numRead = is.read(bytes, offset, bytes.length - offset)) >= 0) {
offset += numRead;
}
int ind = 0;
for (int y = 0; y < IMAGE_HEIGHT; y++) {
for (int x = 0; x < IMAGE_WIDTH; x++) {
// for reading .raw image to show as a rgb image
byte r = bytes[ind];
byte g = bytes[ind];
byte b = bytes[ind];
// set pixel for display original image
int pixOriginal = 0xff000000 | ((r & 0xff) << 16) | ((g & 0xff) << 8) | (b & 0xff);
imgOriginal.setRGB(x, y, pixOriginal);
ind++;
}
}
is.close();
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
int[] vectorSpace = calculateVectorSpace(imgOriginal);
// quantization
for (int y = 0; y < IMAGE_HEIGHT; y++) {
for (int x = 0; x < IMAGE_WIDTH; x++) {
int clusterId = vectorSpace[IMAGE_WIDTH * y + x];
img.setRGB(x, y, clusters[clusterId].getPixel());
}
}
// Use a panel and label to display the image
JPanel panel = new JPanel();
panel.add(new JLabel(new ImageIcon(imgOriginal)));
panel.add(new JLabel(new ImageIcon(img)));
JFrame frame = new JFrame("Display images");
frame.getContentPane().add(panel);
frame.pack();
frame.setVisible(true);
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
}
public synchronized RenderedImage runDCRaw(dcrawMode mode, boolean secondaryPixels)
throws IOException, UnknownImageTypeException, BadImageFileException {
if (!m_decodable || (mode == dcrawMode.full && m_rawColors != 3))
throw new UnknownImageTypeException("Unsuported Camera");
RenderedImage result = null;
File of = null;
try {
if (mode == dcrawMode.preview) {
if (m_thumbWidth >= 1024 && m_thumbHeight >= 768) {
mode = dcrawMode.thumb;
}
}
long t1 = System.currentTimeMillis();
of = File.createTempFile("LZRAWTMP", ".ppm");
boolean four_colors = false;
final String makeModel = m_make + ' ' + m_model;
for (String s : four_color_cameras)
if (s.equalsIgnoreCase(makeModel)) {
four_colors = true;
break;
}
if (secondaryPixels) runDCRawInfo(true);
String cmd[];
switch (mode) {
case full:
if (four_colors)
cmd =
new String[] {
DCRAW_PATH,
"-F",
of.getAbsolutePath(),
"-v",
"-f",
"-H",
"1",
"-t",
"0",
"-o",
"0",
"-4",
m_fileName
};
else if (m_filters == -1 || (m_make != null && m_make.equalsIgnoreCase("SIGMA")))
cmd =
new String[] {
DCRAW_PATH,
"-F",
of.getAbsolutePath(),
"-v",
"-H",
"1",
"-t",
"0",
"-o",
"0",
"-4",
m_fileName
};
else if (secondaryPixels)
cmd =
new String[] {
DCRAW_PATH,
"-F",
of.getAbsolutePath(),
"-v",
"-j",
"-H",
"1",
"-t",
"0",
"-s",
"1",
"-d",
"-4",
m_fileName
};
else
cmd =
new String[] {
DCRAW_PATH,
"-F",
of.getAbsolutePath(),
"-v",
"-j",
"-H",
"1",
"-t",
"0",
"-d",
"-4",
m_fileName
};
break;
case preview:
cmd =
new String[] {
DCRAW_PATH,
"-F",
of.getAbsolutePath(),
"-v",
"-t",
"0",
"-o",
"1",
"-w",
"-h",
m_fileName
};
break;
case thumb:
cmd = new String[] {DCRAW_PATH, "-F", of.getAbsolutePath(), "-v", "-e", m_fileName};
break;
default:
throw new IllegalArgumentException("Unknown mode " + mode);
}
String ofName = null;
synchronized (DCRaw.class) {
Process p = null;
InputStream dcrawStdErr;
InputStream dcrawStdOut;
if (ForkDaemon.INSTANCE != null) {
ForkDaemon.INSTANCE.invoke(cmd);
dcrawStdErr = ForkDaemon.INSTANCE.getStdErr();
dcrawStdOut = ForkDaemon.INSTANCE.getStdOut();
} else {
p = Runtime.getRuntime().exec(cmd);
dcrawStdErr = new BufferedInputStream(p.getErrorStream());
dcrawStdOut = p.getInputStream();
}
String line, args;
// output expected on stderr
while ((line = readln(dcrawStdErr)) != null) {
// System.out.println(line);
if ((args = match(line, DCRAW_OUTPUT)) != null)
ofName = args.substring(0, args.indexOf(" ..."));
}
// Flush stdout just in case...
while ((line = readln(dcrawStdOut)) != null) ; // System.out.println(line);
if (p != null) {
dcrawStdErr.close();
try {
p.waitFor();
} catch (InterruptedException e) {
e.printStackTrace();
}
m_error = p.exitValue();
p.destroy();
} else m_error = 0;
}
System.out.println("dcraw value: " + m_error);
if (m_error > 0) {
of.delete();
throw new BadImageFileException(of);
}
if (!ofName.equals(of.getPath())) {
of.delete();
of = new File(ofName);
}
if (of.getName().endsWith(".jpg") || of.getName().endsWith(".tiff")) {
if (of.getName().endsWith(".jpg")) {
try {
LCJPEGReader jpegReader = new LCJPEGReader(of.getPath());
result = jpegReader.getImage();
} catch (Exception e) {
e.printStackTrace();
}
} else {
try {
LCTIFFReader tiffReader = new LCTIFFReader(of.getPath());
result = tiffReader.getImage(null);
} catch (Exception e) {
e.printStackTrace();
}
}
long t2 = System.currentTimeMillis();
int totalData =
result.getWidth()
* result.getHeight()
* result.getColorModel().getNumColorComponents()
* (result.getColorModel().getTransferType() == DataBuffer.TYPE_BYTE ? 1 : 2);
System.out.println("Read " + totalData + " bytes in " + (t2 - t1) + "ms");
} else {
ImageData imageData;
try {
imageData = readPPM(of);
} catch (Exception e) {
e.printStackTrace();
throw new BadImageFileException(of, e);
}
// do not change the initial image geometry
// m_width = Math.min(m_width, imageData.width);
// m_height = Math.min(m_height, imageData.height);
long t2 = System.currentTimeMillis();
int totalData =
imageData.width
* imageData.height
* imageData.bands
* (imageData.dataType == DataBuffer.TYPE_BYTE ? 1 : 2);
System.out.println("Read " + totalData + " bytes in " + (t2 - t1) + "ms");
final ColorModel cm;
if (mode == dcrawMode.full) {
if (imageData.bands == 1) {
cm =
new ComponentColorModel(
ColorSpace.getInstance(ColorSpace.CS_GRAY),
false,
false,
Transparency.OPAQUE,
DataBuffer.TYPE_USHORT);
} else {
cm = JAIContext.colorModel_linear16;
}
} else {
if (imageData.bands == 3)
cm =
new ComponentColorModel(
JAIContext.sRGBColorSpace,
false,
false,
Transparency.OPAQUE,
DataBuffer.TYPE_BYTE);
else if (imageData.bands == 4)
cm =
new ComponentColorModel(
JAIContext.CMYKColorSpace,
false,
false,
Transparency.OPAQUE,
imageData.dataType);
else throw new UnknownImageTypeException("Weird number of bands: " + imageData.bands);
}
final DataBuffer buf =
imageData.dataType == DataBuffer.TYPE_BYTE
? new DataBufferByte(
(byte[]) imageData.data, imageData.bands * imageData.width * imageData.height)
: new DataBufferUShort(
(short[]) imageData.data, imageData.bands * imageData.width * imageData.height);
final WritableRaster raster =
Raster.createInterleavedRaster(
buf,
imageData.width,
imageData.height,
imageData.bands * imageData.width,
imageData.bands,
imageData.bands == 3 ? new int[] {0, 1, 2} : new int[] {0},
null);
result = new BufferedImage(cm, raster, false, null);
}
} catch (IOException e) {
if (of != null) of.delete();
throw e;
} finally {
if (of != null) of.delete();
}
return result;
}
private void runDCRawInfo(boolean secondary) throws IOException {
String info[] = {DCRAW_PATH, "-v", "-i", "-t", "0", m_fileName};
String secondaryInfo[] = {DCRAW_PATH, "-v", "-i", "-s", "1", "-t", "0", m_fileName};
synchronized (DCRaw.class) {
Process p = null;
InputStream dcrawStdOut;
InputStream dcrawStdErr;
if (ForkDaemon.INSTANCE != null) {
ForkDaemon.INSTANCE.invoke(secondary ? secondaryInfo : info);
dcrawStdOut = ForkDaemon.INSTANCE.getStdOut();
dcrawStdErr = ForkDaemon.INSTANCE.getStdErr();
} else {
p = Runtime.getRuntime().exec(secondary ? secondaryInfo : info);
dcrawStdOut = p.getInputStream();
dcrawStdErr = new BufferedInputStream(p.getErrorStream());
}
// output expected on stdout
String line, args;
while ((line = readln(dcrawStdOut)) != null) {
// System.out.println(line);
String search;
if (secondary) {
if (line.startsWith(search = CAMERA_MULTIPLIERS)) {
String multipliers[] = line.substring(search.length()).split("\\s");
m_secondary_cam_mul[0] = Float.parseFloat(multipliers[0]);
m_secondary_cam_mul[1] = Float.parseFloat(multipliers[1]);
m_secondary_cam_mul[2] = Float.parseFloat(multipliers[2]);
m_secondary_cam_mul[3] = Float.parseFloat(multipliers[3]);
}
} else {
// if (line.startsWith(search = FILENAME)) {
// String filename = line.substring(search.length());
// } else
if (line.startsWith(search = TIMESTAMP)) {
String timestamp = line.substring(search.length());
try {
m_captureDateTime = new SimpleDateFormat().parse(timestamp).getTime();
} catch (ParseException e) {
m_captureDateTime = 0;
}
} else if (line.startsWith(search = CAMERA)) {
String camera = line.substring(search.length());
m_make = camera.substring(0, camera.indexOf(' '));
m_model = camera.substring(m_make.length() + 1);
} else if (line.startsWith(search = ISO)) {
String iso = line.substring(search.length());
m_iso = Integer.decode(iso);
} else if (line.startsWith(search = SHUTTER)) {
String shutterSpeed = line.substring(search.length() + 2);
float exposureTime = 0;
try {
exposureTime = Float.valueOf(shutterSpeed.substring(0, shutterSpeed.indexOf(" sec")));
if (exposureTime != 0) m_shutterSpeed = 1 / exposureTime;
} catch (NumberFormatException e) {
}
} else if (line.startsWith(search = APERTURE)) {
String aperture = line.substring(search.length() + 2);
try {
m_aperture = Float.valueOf(aperture);
} catch (NumberFormatException e) {
}
} else if (line.startsWith(search = FOCAL_LENGTH)) {
String focalLenght = line.substring(search.length());
try {
m_focalLength = Float.valueOf(focalLenght.substring(0, focalLenght.indexOf(" mm")));
} catch (NumberFormatException e) {
}
// } else if (line.startsWith(search = NUM_RAW_IMAGES)) {
// String numRawImages = line.substring(search.length());
// } else if (line.startsWith(search = EMBEDDED_ICC_PROFILE)) {
// String embeddedICCProfile = line.substring(search.length());
} else if (line.startsWith(CANNOT_DECODE)) {
m_decodable = false;
} else if ((args = match(line, THUMB_SIZE)) != null) {
String sizes[] = args.split(" x ");
m_thumbWidth = Integer.decode(sizes[0]);
m_thumbHeight = Integer.decode(sizes[1]);
} else if ((args = match(line, FULL_SIZE)) != null) {
String sizes[] = args.split(" x ");
m_fullWidth = Integer.decode(sizes[0]);
m_fullHeight = Integer.decode(sizes[1]);
} else if ((args = match(line, IMAGE_SIZE)) != null) {
String sizes[] = args.split(" x ");
m_rawWidth = Integer.decode(sizes[0]);
m_rawHeight = Integer.decode(sizes[1]);
} else if ((args = match(line, OUTPUT_SIZE)) != null) {
String sizes[] = args.split(" x ");
m_width = Integer.decode(sizes[0]);
m_height = Integer.decode(sizes[1]);
} else if (line.startsWith(search = RAW_COLORS)) {
String rawColors = line.substring(search.length());
m_rawColors = Integer.decode(rawColors);
} else if (line.startsWith(search = FILTER_PATTERN)) {
String pattern = line.substring(search.length());
if (pattern.length() >= 8 && !pattern.substring(0, 4).equals(pattern.substring(4, 8)))
m_filters = -1;
else if (pattern.startsWith("BGGR")) m_filters = 0x16161616;
else if (pattern.startsWith("GRBG")) m_filters = 0x61616161;
else if (pattern.startsWith("GBRG")) m_filters = 0x49494949;
else if (pattern.startsWith("RGGB")) m_filters = 0x94949494;
else m_filters = -1;
} else if (line.startsWith(search = DAYLIGHT_MULTIPLIERS)) {
String multipliers[] = line.substring(search.length()).split("\\s");
m_pre_mul[0] = Float.parseFloat(multipliers[0]);
m_pre_mul[1] = Float.parseFloat(multipliers[1]);
m_pre_mul[2] = Float.parseFloat(multipliers[2]);
m_pre_mul[3] = m_pre_mul[1];
} else if (line.startsWith(search = CAMERA_MULTIPLIERS)) {
String multipliers[] = line.substring(search.length()).split("\\s");
m_cam_mul[0] = Float.parseFloat(multipliers[0]);
m_cam_mul[1] = Float.parseFloat(multipliers[1]);
m_cam_mul[2] = Float.parseFloat(multipliers[2]);
m_cam_mul[3] = Float.parseFloat(multipliers[3]);
} else if (line.startsWith(CAMERA_RGB_PROFILE)) {
String rgb_cam[] = line.substring(CAMERA_RGB_PROFILE.length()).split("\\s");
m_rgb_cam = new float[9];
for (int i = 0; i < 9; i++) {
m_rgb_cam[i] = Float.parseFloat(rgb_cam[i]);
}
} else if (line.startsWith(CAMERA_XYZ_PROFILE)) {
String xyz_cam[] = line.substring(CAMERA_XYZ_PROFILE.length()).split("\\s");
m_xyz_cam = new float[9];
for (int i = 0; i < 9; i++) {
m_xyz_cam[i] = Float.parseFloat(xyz_cam[i]);
}
}
}
}
// Flush stderr just in case...
while ((line = readln(dcrawStdErr)) != null) ; // System.out.println(line);
if (p != null) {
dcrawStdOut.close();
try {
p.waitFor();
} catch (InterruptedException e) {
e.printStackTrace();
}
m_error = p.exitValue();
p.destroy();
} else m_error = 0;
}
}