import java.io.*;
import java.awt.*;
import java.awt.image.*;
import java.awt.Color;
import java.awt.Point;
import java.io.OutputStream;
import java.io.IOException;
import ij.*;
import ij.io.*;
import ij.gui.*;
import ij.process.*;
import ij.plugin.PlugIn;
/**
* Class AnimatedGifEncoder2 - Encodes a GIF file consisting of one or
* more frames.
*
*
*
* Extensively Modified for ImagePlus
* Extended to handle 8 bit Images with more complex Color lookup tables with transparency index
*
* Ryan Raz March 2002
* raz@rraz.ca
* Version 1.01
** Extensively Modified for ImagePlus
* Extended to handle 8 bit Images with more complex Color lookup tables with transparency index
*
* Ryan Raz March 2002
* ryan@rraz.ca
* Version 1.01 Please report any bugs
*
* Operation Manual
*
*
* 1) Load stack with 8 bit or RGB images it is possible to use the animated gif reader but because the color
* table is lost it is best to also load a separate copy of the first image in the series this will allow
* extraction of the original image color look up table (see 1below)
* 2)Check the option list to bring up the option list.
* 3)Experiment with the option list. I usually use a global color table to save space, set to do not dispose if
* each consecutive image is overlayed on the previous image.
* 4)Color table can be imported from another image or extracted from 8bit stack images or loaded as the
* first 256 RGB triplets from a RGB images, the last mode takes either a imported image or current
* stack and creates the color table from scratch.
*
*
* To do list
*
* 1) Modify existing Animated Gif reader plug in to import in 8 bit mode (currently only works in
* RGB mode. Right now the best way to alter an animated gif is to save the first image separately
* and then read the single gif and use the plugin animated reader to read the animated gif to the
* stack. Let this plugin encode the stack using the single gif's color table.
* 2) Add support for background colors easy but I have no use for them
* 3) RGB to 8 bit converter is a linear search. Needs to be replaced with sorted list and fast search. But
* this update could cause problems with some types of gifs. Easy fix get a faster computer.
* 4) Try updating NN color converter seems to be heavily weighted towards quantity of pixels.
* example:
* if there is 90% of the image covered in shades of one color or grey the 10% of other colors tend
* to be poorly represented it over fits the shades and under fits the others. Works well if the
* distribution is balanced.
* 5) Add support for all sizes of Color Look Up tables.
* 6) Re-code to be cleaner. This is my second Java program and I started with some code with too
* many global variables and I added more switches so its a bit hard to follow.
*
* Credits for the base conversion codes
* No copyright asserted on the source code of this class. May be used
* for any purpose, however, refer to the Unisys LZW patent for restrictions
* on use of the associated LZWEncoder class. Please forward any corrections
* to kweiner@fmsware.com.
*
* @author Kevin Weiner, FM Software
* @version 1.0 December 2000
*
*
* Example:
* AnimatedGifEncoder2 e = new AnimatedGifEncoder2();
* e.start(outputFileName);
* e.addFrame(image1);
* e.addFrame(image2);
* " " "
* e.finish();
*
*
*
*/
class AnimatedGifEncoder2 {
protected int width; // image size
protected int height;
protected boolean transparent = false; // transparent color if given
protected int transIndex; // transparent index in color table
protected int repeat = -1; // no repeat
protected int delay = 50; // frame delay (hundredths)
protected boolean started = false; // ready to output frames
protected OutputStream out;
protected ImagePlus image; // current frame
protected byte[] pixels; // BGR byte array from frame
protected byte[] indexedPixels; // converted frame indexed to palette
protected int colorDepth; // number of bit planes
protected byte[] colorTab; // RGB palette
protected int lctSize = 7; // local color table size (bits-1)
protected int dispose = 0; // disposal code (-1 = use default)
protected boolean closeStream = false; // close stream when finished
protected boolean firstFrame = true;
protected boolean sizeSet = false; // if false, get size from first frame
protected int sample = 2; // default sample interval for quantizer distance should be small for small icons
protected byte[] gct = null; //Global color table
protected boolean gctused = false; // Set to true to use Global color table
protected boolean autotransparent = false; // Set True if transparency index coming from image 8 bit only
protected boolean GCTextracted = false; // Set if global color table extracted from rgb image
protected boolean GCTloadedExternal = false; // Set if global color table loaded directly from external image
protected int GCTred = 0; //Transparent Color
protected int GCTgrn = 0; // green
protected int GCTbl = 0; // blue
protected int GCTcindex = 0; //index into color table
protected boolean GCTsetTransparent = false; //If true then Color table transparency index is set
protected boolean GCToverideIndex = false; //If true Transparent index is set to index with closest colors
protected boolean GCToverideColor = false; //if true Color at Transparent index is set to GCTred, GCTgrn GCTbl
/**
* Adds next GIF frame. The frame is not written immediately, but is
* actually deferred until the next frame is received so that timing
* data can be inserted. Invoking finish() flushes all
* frames. If setSize was not invoked, the size of the
* first image is used for all subsequent frames.
*
* @param im containing frame to write.
* @return true if successful.
*/
public boolean addFrame(ImagePlus image) {
if ((image == null) || !started) return false;
boolean ok = true;
try {
if (firstFrame) {
if (!sizeSet) {
// use first frame's size
setSize(image.getWidth(), image.getHeight());
}
if(gctused)
writeLSDgct(); // logical screen descriptior
if (GCTloadedExternal){ //Using external image as color table
colorTab = gct;
TransparentIndex(colorTab); //check transparency color
writePalette(); // write global color table
if (repeat >= 0)
writeNetscapeExt(); // use NS app extension to indicate reps
}
if(!gctused) {
writeLSD();
if (repeat >= 0)
writeNetscapeExt(); // use NS app extension to indicate reps
}
firstFrame = false;
}
int type = image.getType();
// If indexed byte image then format does not need changing
int k;
if ((type == 0) ||( type == 3)){ //8 bit images
Process8bitCLT(image);
}
else if(type == 4) //4 for RGB
{
packrgb(image);
OverRideQuality(image.getWidth()*image.getHeight());
if (gctused && (gct == null)) { //quality should not depend on image size
analyzePixels(); // build global color table & map pixels
colorTab = gct;
TransparentIndex(colorTab); //check transparency color
writePalette(); // write global color table
if (repeat >= 0)
writeNetscapeExt(); // use NS app extension to indicate reps
}
else analyzePixels(); // build color table & map pixels
}
else throw new IllegalArgumentException("Image must be 8-bit or RGB");
TransparentIndex(colorTab); //check transparency color
writeGraphicCtrlExt(); // write graphic control extension
writeImageDesc(); // image descriptor
if(!gctused) writePalette(); // local color table
writePixels(); // encode and write pixel data
} catch (IOException e) { ok = false; }
return ok;
}
/*
Handles transparency color Index
Assumes colors and index are already checked for validity
*/
void TransparentIndex(byte[] colorTab){
if(autotransparent|| !GCTsetTransparent) return;
if(colorTab==null)throw new IllegalArgumentException("Color Table not loaded.");
int len = colorTab.length;
setTransparent(true); //Sets color tranparency flag
if(!(GCToverideColor||GCToverideIndex)){
transIndex = GCTcindex; //sets color index
return;
}
if(GCToverideIndex)GCTcindex= findClosest(colorTab, GCTred, GCTgrn, GCTbl);
//finds index in color Table
transIndex = GCTcindex;
int pindex = 3*GCTcindex;
if(pindex>(len-3))
throw new IllegalArgumentException("Index ("+transIndex+") too large for Color Lookup table.");
colorTab[pindex++] = (byte)GCTred; //Set Color Table[transparent index] with specified color
colorTab[pindex++] = (byte)GCTgrn;
colorTab[pindex] = (byte)GCTbl;
}
/*
* Get Options because options box has been checked
Some of the code being set
setTransparent(Color.black);
Dispose = 0;
setDelay(500); // time per frame in milliseconds
gctused = false; // Set to true to use Global color table
GCTextracted = false; // Set if global color table extracted from rgb image
GCTloadedExternal = false; // Set if global color table loaded directly from external image
GCTextracted = false; // Set if global color table extracted from rgb image
GCTred = 0; //Transparent Color
GCTgrn = 0; // green
GCTbl = 0; // blue
GCTcindex = 0; //index into color table
autotransparent = false; // Set True if transparency index coming from image 8 bit only
GCTsetTransparent = false; //If true then Color table transparency index is set
GCToverideIndex = false; //If true Transparent index is set to index with closest colors
GCToverideColor = false; //if true Color at Transparent index is set to GCTred, GCTgrn GCTbl
*/
public void setoptions(){
String[] GCTtype = {"Do not use","Load from Current Image", "Load from another Image RGB or 8 Bit",
"Use another RGB to create a new color table " };
String[] DisposalType = { "No Disposal","Do not Dispose", "Restore to Background", "Restore to previous" };
String[] TransparencyType ={"No Transparency", "Automatically Set if Available (8 bit only)", "Set to Index",
"Set to index with specified color", "Set to the index that is closest to specified color"};
int setdelay=delay*10;
int gctType=0;
int setTrans;
if(GCTloadedExternal) gctType = 2;
if(GCTextracted&&GCTloadedExternal) gctType =3;
if(gctused&&!(GCTextracted||GCTloadedExternal))gctType=1;
setTrans=1;
if(!(autotransparent||GCTsetTransparent||GCToverideIndex||GCToverideColor)) setTrans=0;
if(GCTsetTransparent&& !(GCToverideIndex||GCToverideColor)) setTrans = 2;
if(GCTsetTransparent&& GCToverideIndex && !GCToverideColor) setTrans = 4;
if(GCTsetTransparent&& !GCToverideIndex && GCToverideColor) setTrans = 3;
int red = GCTred;
int grn = GCTgrn;
int bl = GCTbl;
int cindex =GCTcindex;
int disposalType = dispose;
String title1 = "";
int[] wList = WindowManager.getIDList();
if (wList==null) {
IJ.error("No windows are open.");
return;
}
String[] titles = new String[wList.length];
for (int i=0; i= 0)setDelay(setdelay);
setRepeat( (int)gd.getNextNumber());
setTrans = gd.getNextChoiceIndex();
red = (int)gd.getNextNumber();
grn = (int)gd.getNextNumber();
bl = (int)gd.getNextNumber();
if((red< 0 )|| (red>255)) red = -1;
if((grn< 0 )|| (grn>255)) red = -1;
if((bl< 0 )|| (bl>255)) red = -1;
cindex = (int)gd.getNextNumber();
if((cindex< 0 )|| (cindex>255)) cindex = -1;
autotransparent=false; //no transparent index
GCTsetTransparent=false;
GCToverideIndex=false;
GCToverideColor=false;
setTransparent(false);
switch (setTrans) {
case 0: break;
case 1: autotransparent=true; //Set if available from image byte images only
break;
case 2: if(cindex>-1){
GCTsetTransparent=true; //set specified index as transparent color
GCTcindex=cindex;
}
else IJ.error("Incorrect color index must have value between 0 and 255");
break;
case 3: if((cindex>-1)&&(red>-1)){ //Set transparent index with specified color
GCTsetTransparent=true;
GCToverideColor=true;
GCTcindex=cindex;
GCTred=red;
GCTgrn=grn;
GCTbl=bl;
}
else
IJ.error("Incorrect colors or color index, they must have values between 0 and 255.");
break;
case 4: if(red>-1){
GCTsetTransparent=true; //Set transparent index to
GCToverideIndex=true; //index which is closest to the specified color
GCTred=red; // and replace the color at the index with
GCTgrn=grn;
GCTbl=bl;
}
else IJ.error("Incorrect colors, they must have values between 0 and 255.");
break;
default: break;
}
gctused = false; // Set to true to use Global color table
GCTextracted = false; // Set if global color table extracted from rgb image
GCTloadedExternal = false; // Set if global color table loaded directly from external image
if(gctType==1)gctused=true;
else if(gctType>=2){
ImagePlus img = WindowManager.getImage(wList[index1]);
if(img == null){
IJ.error("No window selected for generating color table");
return;
}
int type = img.getType();
if (!((type == 0) ||( type == 3)||(type ==4))){
IJ.error("Incorrect window type selected for generating color table (RGB or 8bit only).");
return;
}
if(gctType == 3){
if(type == 4) extractGCTrgb(img);
else {
IJ.error("RGB image only for this mode of generating color table.");
return;
}
}
if(gctType ==2){
if(type == 4)loadGCTrgb(img);
else loadGCT8bit(img);
}
}
}
/********************************************************
* Gets Color lookup Table from 8 bit image plus pointer to image
*/
void Process8bitCLT(ImagePlus image){
colorDepth = 8;
setTransparent(false);
ByteProcessor pg = new ByteProcessor(image.getImage());
ColorModel cm = pg.getColorModel();
if (cm instanceof IndexColorModel)
{
indexedPixels = (byte[])(pg.getPixels());
}
else throw new IllegalArgumentException("Image must be 8-bit");
IndexColorModel m = (IndexColorModel)cm;
if(autotransparent){
transIndex = m.getTransparentPixel();
if ((transIndex > -1) && (transIndex < 256)) setTransparent(true); //Sets color flag
else transIndex =0;
}
int mapSize = m.getMapSize();
int k;
if (gctused && (gct == null)) {
gct = new byte[mapSize*3]; //Global color table needs to be intialized
for (int i = 0; i < mapSize; i++) {
k=i*3;
gct[k] = (byte)m.getRed(i);
gct[k+2] = (byte)m.getBlue(i);
gct[k+1] = (byte)m.getGreen(i);
}
try{
if (! GCTloadedExternal) {
colorTab = gct;
writePalette(); // write global color table
if (repeat >= 0)
writeNetscapeExt(); // use NS app extension to indicate reps
}
} catch (IOException e) {
System.err.println("Caught IOException: " + e.getMessage());
}
}
if(gctused){
colorTab = gct;
}
else {
colorTab = new byte[mapSize*3];
for (int i = 0; i < mapSize; i++) {
k=i*3;
colorTab[k] = (byte)m.getRed(i);
colorTab[k+1] = (byte)m.getBlue(i);
colorTab[k+2] = (byte)m.getGreen(i);
}
}
m.finalize();
}
/**
* Flushes any pending data and closes output file.
* If writing to an OutputStream, the stream is not
* closed.
*/
public boolean finish() {
if (!started) return false;
boolean ok = true;
started = false;
try {
out.write(0x3b); // gif trailer
out.flush();
if (closeStream)
out.close();
} catch (IOException e) { ok = false; }
// reset for subsequent use
GCTextracted = false; // Set if global color table extracted from rgb image
GCTloadedExternal = false; // Set if global color table loaded directly from external image
transIndex = 0;
transparent = false;
gct = null; //Global color table
out = null;
image = null;
pixels = null;
indexedPixels = null;
colorTab = null;
closeStream = false;
firstFrame = true;
return ok;
}
/*
* Function to load Global Color Table from 8 bit ImagePlus
* This function has to be called before addFrame
*/
public void loadGCT8bit(ImagePlus image){
int type = image.getType();
if (!(((type == 0) ||( type == 3))&&(image!=null)))
throw new IllegalArgumentException("Color Table Image must be 8 bit");
gctused = true;
GCTloadedExternal = true;
gct = null;
Process8bitCLT(image);
}
/*
* Function to extract Global Color Table from RGB ImagePlus
* This function has to be called before addFrame
*/
public void extractGCTrgb(ImagePlus image){
if((image== null)||(4!=image.getType()))
throw new IllegalArgumentException("Color Table Image must be RGB");
packrgb(image);
gctused = true;
GCTextracted = true;
GCTloadedExternal =true;
gct = null;
OverRideQuality(image.getWidth()*image.getHeight());
analyzePixels(); // build color table
pixels = null;
}
void packrgb(ImagePlus image){
int len = image.getWidth()*image.getHeight();
ImageProcessor imp = image.getProcessor();
int[] pix = (int[]) imp.getPixels();
pixels = new byte[len*3];
//pack pixels
for(int i=0; i>16); //red
pixels[k+1] = (byte)((pix[i] & 0x00ff00)>>8); //green
pixels[k] = (byte)(pix[i] & 0x0000ff); //blue
}
}
/*
* Function to use the first up to 255 elements of a RGB ImagePlus to construct
* a global color table
* This function has to be called before addFrame
*/
public void loadGCTrgb(ImagePlus image){
if((image == null)||(4!=image.getType()))
throw new IllegalArgumentException("Color Table Image must be RGB");
int len = image.getWidth()*image.getHeight();
if(len>255)len=255;
ImageProcessor imp = image.getProcessor();
int[] pix = (int[]) imp.getPixels();
gct = new byte[len*3];
//pack pixels into color Table
for(int i=0; i>16); //red
gct[k+1] = (byte)((pix[i] & 0x00ff00)>>8); //green
gct[k+2] = (byte)(pix[i] & 0x0000ff); //blue
}
gctused = true;
GCTloadedExternal = true;
}
/*
* If gct = true then a global color table is use
*
*/
public void setGCT(boolean flag){
gctused = flag;
}
/**
* Sets the delay time between each frame, or changes it
* for subsequent frames (applies to last frame added).
*
* @param ms int delay time in milliseconds
*/
public void setDelay(int ms) {
delay = Math.round(ms / 10.0f);
}
/**
* Sets the GIF frame disposal code for the last added frame
* and any subsequent frames. Default is 0 if no transparent
* color has been set, otherwise 2.
* @param code int disposal code.
*/
public void setDispose(int code) {
if (code >= 0)
dispose = code;
}
/**
* Sets frame rate in frames per second. Equivalent to
* setDelay(1000/fps).
*
* @param fps float frame rate (frames per second)
*/
public void setFrameRate(float fps) {
if (fps != 0f) {
delay = Math.round(100f/fps);
}
}
/**
* Sets quality of color quantization (conversion of images
* to the maximum 256 colors allowed by the GIF specification).
* Lower values (minimum = 1) produce better colors, but slow
* processing significantly. 10 is the default, and produces
* good color mapping at reasonable speeds. Values greater
* than 20 do not yield significant improvements in speed.
*
* @param quality int greater than 0.
* @return
*/
public void setQuality(int quality) {
if (quality < 1) quality = 1;
sample = quality;
}
/**
* Set True for Global Color Table use
* This saves space in the output file but colors may not be so goodif the stack uses
* True color images
*/
public void GlobalColorTableused(boolean gtu){
gctused = gtu;
}
/**
* Sets the number of times the set of GIF frames
* should be played. Default is 1; 0 means play
* indefinitely. Must be invoked before the first
* image is added.
*
* @param iter int number of iterations.
* @return
*/
public void setRepeat(int iter) {
if (iter >= 0)
repeat = iter;
}
/**
* Sets the GIF frame size. The default size is the
* size of the first frame added if this method is
* not invoked.
*
* @param w int frame width.
* @param h int frame width.
*/
public void setSize(int w, int h) {
if (started && !firstFrame) return;
width = w;
height = h;
if (width < 1) width = 320;
if (height < 1) height = 240;
sizeSet = true;
}
/**
* Sets the transparent color for the last added frame
* and any subsequent frames.
* Since all colors are subject to modification
* in the quantization process, the color in the final
* palette for each frame closest to the given color
* becomes the transparent color for that frame.
* May be set to null to indicate no transparent color.
*
* @param c Color to be treated as transparent on display.
*/
public void setTransparent(boolean c) {
transparent = c;
}
/**
* Initiates GIF file creation on the given stream. The stream
* is not closed automatically.
*
* @param os OutputStream on which GIF images are written.
* @return false if initial write failed.
*/
public boolean start(OutputStream os) {
if (os == null) return false;
boolean ok = true;
closeStream = false;
out = os;
try {
writeString("GIF89a"); // header
} catch (IOException e) { ok = false; }
return started = ok;
}
/**
* Initiates writing of a GIF file with the specified name.
*
* @param file String containing output file name.
* @return false if open or initial write failed.
*/
public boolean start(String file) {
boolean ok = true;
try {
out = new BufferedOutputStream(new FileOutputStream(file));
ok = start(out);
closeStream = true;
} catch (IOException e) { ok = false; }
return started = ok;
}
/**
Sets Net sample size depending on image size
**/
public void OverRideQuality(int npixs){
if(npixs>100000) sample = 10;
else sample = npixs/10000;
if(sample < 1) sample = 1;
}
/**
* Analyzes image colors and creates color map.
*/
protected void analyzePixels() {
int len = pixels.length;
int nPix = len / 3;
indexedPixels = new byte[nPix];
if (gctused && (gct == null)) {
NeuQuant nq = new NeuQuant(pixels, len, sample); // initialize quantizer
colorTab = nq.process(); // create reduced palette
gct = new byte[colorTab.length];
// convert map from BGR to RGB
for (int i = 0; i < colorTab.length; i+=3) {
byte temp = colorTab[i];
colorTab[i] = colorTab[i+2];
colorTab[i+2] = temp;
gct[i] = colorTab[i];
gct[i+1] = colorTab[i+1];
gct[i+2] =colorTab[i+2];
}
if(GCTextracted){
indexedPixels= null;
return;
}
}
if (!gctused){
NeuQuant nq = new NeuQuant(pixels, len, sample); // initialize quantizer
colorTab = nq.process(); // create reduced palette
// convert map from BGR to RGB
for (int i = 0; i < colorTab.length; i+=3) {
byte temp = colorTab[i];
colorTab[i] = colorTab[i+2];
colorTab[i+2] = temp;
}
// map image pixels to new palette
int k = 0;
for (int i = 0; i < nPix; i++)
indexedPixels[i] =
(byte) nq.map(pixels[k++] & 0xff, pixels[k++] & 0xff, pixels[k++] & 0xff);
pixels = null;
colorDepth = 8;
lctSize = 7;
}
if(gctused){
// find closest match for all pixels This routine is not optimized real slow linear search.
colorTab = gct;
int k = 0;
int minpos;
for (int j = 0; j < nPix; j++){
int b = pixels[k++] & 0xff;
int g = pixels[k++] & 0xff;
int r = pixels[k++] & 0xff;
minpos = 0;
int dmin = 256*256*256;
int lenct = colorTab.length;
for (int i = 0; i < lenct; ) {
int dr = r - (colorTab[i++] & 0xff);
int dg = g - (colorTab[i++] & 0xff);
int db = b - (colorTab[i] & 0xff);
int d = dr*dr + dg*dg + db*db;
if (d < dmin) {
dmin = d;
minpos = i/3;
}
i++;
}//end inside for
indexedPixels[j]=(byte)minpos;
}//end for
pixels = null;
colorDepth = 8;
lctSize = 7;
} //end if
}
/**
* Returns index of palette color closest to c
*
*/
protected int findClosest(byte[] colorTab, int r, int g, int b) {
if (colorTab == null) return -1;
int minpos = 0;
int dmin = 256*256*256;
int len = colorTab.length;
for (int i = 0; i < len; ) {
int dr = r - (colorTab[i++] & 0xff);
int dg = g - (colorTab[i++] & 0xff);
int db = b - (colorTab[i] & 0xff);
int d = dr*dr + dg*dg + db*db;
if (d < dmin) {
dmin = d;
minpos = i/3;
}
i++;
}
return minpos;
}
/**
* Writes Graphic Control Extension
*/
protected void writeGraphicCtrlExt() throws IOException {
out.write(0x21); // extension introducer
out.write(0xf9); // GCE label
out.write(4); // data block size
int transp, disp;
if (!transparent) {
transp = 0;
disp = 0; // dispose = no action
} else {
transp = 1;
disp = 2; // force clear if using transparent color
}
if (dispose >= 0)
disp = dispose & 7; // user override
disp <<= 2;
// packed fields
out.write( 0 | // 1:3 reserved
disp | // 4:6 disposal
0 | // 7 user input - 0 = none
transp); // 8 transparency flag
writeShort(delay); // delay x 1/100 sec
out.write(transIndex); // transparent color index
out.write(0); // block terminator
}
/**
* Writes Image Descriptor
*/
protected void writeImageDesc() throws IOException {
out.write(0x2c); // image separator
writeShort(0); // image position x,y = 0,0
writeShort(0);
writeShort(width); // image size
writeShort(height);
// packed fields
if(gctused)
out.write(0x00); //global color table
else
out.write(0x80 | // 1 local color table 1=yes
0 | // 2 interlace - 0=no
0 | // 3 sorted - 0=no
0 | // 4-5 reserved
lctSize); // size of local color table
}
/**
* Writes Logical Screen Descriptor with global color table
*/
protected void writeLSDgct() throws IOException {
// logical screen size
writeShort(width);
writeShort(height);
// packed fields
out.write((0x80 | // 1 : global color table flag = 0 (nn
0x70 | // 2-4 : color resolution = 7
0x00 | // 5 : gct sort flag = 0
lctSize)); // 6-8 : gct size = 0
out.write(0); // background color index
out.write(0); // pixel aspect ratio - assume 1:1
}
/**
* Writes Logical Screen Descriptor without global color table
*/
protected void writeLSD() throws IOException {
// logical screen size
writeShort(width);
writeShort(height);
// packed fields
out.write((0x00 | // 1 : global color table flag = 0 (none)
0x70 | // 2-4 : color resolution = 7
0x00 | // 5 : gct sort flag = 0
0x00)); // 6-8 : gct size = 0
out.write(0); // background color index
out.write(0); // pixel aspect ratio - assume 1:1
}
/**
* Writes Netscape application extension to define
* repeat count.
*/
protected void writeNetscapeExt() throws IOException {
out.write(0x21); // extension introducer
out.write(0xff); // app extension label
out.write(11); // block size
writeString("NETSCAPE"+"2.0"); // app id + auth code
out.write(3); // sub-block size
out.write(1); // loop sub-block id
writeShort(repeat); // loop count (extra iterations, 0=repeat forever)
out.write(0); // block terminator
}
/**
* Writes color table
*/
protected void writePalette() throws IOException {
out.write(colorTab, 0, colorTab.length);
int n = (3 * 256) - colorTab.length;
for (int i = 0; i < n; i++)
out.write(0);
}
/**
* Encodes and writes pixel data
*/
protected void writePixels() throws IOException {
LZWEncoder encoder =
new LZWEncoder(width, height, indexedPixels, colorDepth);
encoder.encode(out);
}
/**
* Write 16-bit value to output stream, LSB first
*/
protected void writeShort(int value) throws IOException {
out.write(value & 0xff);
out.write((value >> 8) & 0xff);
}
/**
* Writes string to output stream
*/
protected void writeString(String s) throws IOException {
for (int i = 0; i < s.length(); i++)
out.write((byte) s.charAt(i));
}
}
/**
Writes a stack as an animated Gif
*/
public class Gif_Stack_Writer implements PlugIn {
static String type = "gif";
public void run(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.showMessage("Save As ", "No images are open.");
return;
}
String name = imp.getTitle();
int dotIndex = name.lastIndexOf(".");
if (dotIndex>=0)
name = name.substring(0, dotIndex);
GenericDialog gd = new GenericDialog("Animated Gif Writer", IJ.getInstance());
boolean options = false;
gd.addStringField("Name:", name, 12);
gd.addCheckbox("Check for options",false);
gd.showDialog();
if (gd.wasCanceled())
return;
name = gd.getNextString();
options =gd.getNextBoolean();
IJ.register(Gif_Stack_Writer.class);
SaveDialog sd = new SaveDialog("Save as "+type, name+"."+type, "."+type);
String file = sd.getFileName();
if (file == null) return;
String directory = sd.getDirectory();
ImageStack stack = imp.getStack();
ImagePlus tmp = new ImagePlus();
int nSlices = stack.getSize();
//String path = directory+name;
AnimatedGifEncoder2 fr = new AnimatedGifEncoder2();
if(options)fr.setoptions();
fr.start(directory+file);
for (int i=1; i<=nSlices; i++) {
IJ.showStatus("writing: "+i+"/"+nSlices);
IJ.showProgress((double)i/nSlices);
tmp.setProcessor(null, stack.getProcessor(i));
try {
fr.addFrame(tmp);
} catch(Exception e) {
IJ.showMessage("Save as "+type, ""+e);
}
System.gc();
}
fr.finish();
IJ.showStatus("");
IJ.showProgress(1.0);
}
}
//==============================================================================
// Adapted from Jef Poskanzer's Java port by way of J. M. G. Elliott.
// K Weiner 12/00
class LZWEncoder2 {
private static final int EOF = -1;
private int imgW, imgH;
private byte[] pixAry;
private int initCodeSize;
private int remaining;
private int curPixel;
// GIFCOMPR.C - GIF Image compression routines
//
// Lempel-Ziv compression based on 'compress'. GIF modifications by
// David Rowley (mgardi@watdcsu.waterloo.edu)
// General DEFINEs
static final int BITS = 12;
static final int HSIZE = 5003; // 80% occupancy
// GIF Image compression - modified 'compress'
//
// Based on: compress.c - File compression ala IEEE Computer, June 1984.
//
// By Authors: Spencer W. Thomas (decvax!harpo!utah-cs!utah-gr!thomas)
// Jim McKie (decvax!mcvax!jim)
// Steve Davies (decvax!vax135!petsd!peora!srd)
// Ken Turkowski (decvax!decwrl!turtlevax!ken)
// James A. Woods (decvax!ihnp4!ames!jaw)
// Joe Orost (decvax!vax135!petsd!joe)
int n_bits; // number of bits/code
int maxbits = BITS; // user settable max # bits/code
int maxcode; // maximum code, given n_bits
int maxmaxcode = 1 << BITS; // should NEVER generate this code
int[] htab = new int[HSIZE];
int[] codetab = new int[HSIZE];
int hsize = HSIZE; // for dynamic table sizing
int free_ent = 0; // first unused entry
// block compression parameters -- after all codes are used up,
// and compression rate changes, start over.
boolean clear_flg = false;
// Algorithm: use open addressing double hashing (no chaining) on the
// prefix code / next character combination. We do a variant of Knuth's
// algorithm D (vol. 3, sec. 6.4) along with G. Knott's relatively-prime
// secondary probe. Here, the modular division first probe is gives way
// to a faster exclusive-or manipulation. Also do block compression with
// an adaptive reset, whereby the code table is cleared when the compression
// ratio decreases, but after the table fills. The variable-length output
// codes are re-sized at this point, and a special CLEAR code is generated
// for the decompressor. Late addition: construct the table according to
// file size for noticeable speed improvement on small files. Please direct
// questions about this implementation to ames!jaw.
int g_init_bits;
int ClearCode;
int EOFCode;
// output
//
// Output the given code.
// Inputs:
// code: A n_bits-bit integer. If == -1, then EOF. This assumes
// that n_bits =< wordsize - 1.
// Outputs:
// Outputs code to the file.
// Assumptions:
// Chars are 8 bits long.
// Algorithm:
// Maintain a BITS character long buffer (so that 8 codes will
// fit in it exactly). Use the VAX insv instruction to insert each
// code in turn. When the buffer fills up empty it and start over.
int cur_accum = 0;
int cur_bits = 0;
int masks[] = { 0x0000, 0x0001, 0x0003, 0x0007, 0x000F,
0x001F, 0x003F, 0x007F, 0x00FF,
0x01FF, 0x03FF, 0x07FF, 0x0FFF,
0x1FFF, 0x3FFF, 0x7FFF, 0xFFFF };
// Number of characters so far in this 'packet'
int a_count;
// Define the storage for the packet accumulator
byte[] accum = new byte[256];
//----------------------------------------------------------------------------
LZWEncoder2(int width, int height, byte[] pixels, int color_depth)
{
imgW = width;
imgH = height;
pixAry = pixels;
initCodeSize = Math.max(2, color_depth);
}
// Add a character to the end of the current packet, and if it is 254
// characters, flush the packet to disk.
void char_out( byte c, OutputStream outs ) throws IOException
{
accum[a_count++] = c;
if ( a_count >= 254 )
flush_char( outs );
}
// Clear out the hash table
// table clear for block compress
void cl_block( OutputStream outs ) throws IOException
{
cl_hash( hsize );
free_ent = ClearCode + 2;
clear_flg = true;
output( ClearCode, outs );
}
// reset code table
void cl_hash( int hsize )
{
for ( int i = 0; i < hsize; ++i )
htab[i] = -1;
}
void compress( int init_bits, OutputStream outs ) throws IOException
{
int fcode;
int i /* = 0 */;
int c;
int ent;
int disp;
int hsize_reg;
int hshift;
// Set up the globals: g_init_bits - initial number of bits
g_init_bits = init_bits;
// Set up the necessary values
clear_flg = false;
n_bits = g_init_bits;
maxcode = MAXCODE( n_bits );
ClearCode = 1 << ( init_bits - 1 );
EOFCode = ClearCode + 1;
free_ent = ClearCode + 2;
a_count = 0; // clear packet
ent = nextPixel();
hshift = 0;
for ( fcode = hsize; fcode < 65536; fcode *= 2 )
++hshift;
hshift = 8 - hshift; // set hash code range bound
hsize_reg = hsize;
cl_hash( hsize_reg ); // clear hash table
output( ClearCode, outs );
outer_loop:
while ( (c = nextPixel()) != EOF )
{
fcode = ( c << maxbits ) + ent;
i = ( c << hshift ) ^ ent; // xor hashing
if ( htab[i] == fcode )
{
ent = codetab[i];
continue;
}
else if ( htab[i] >= 0 ) // non-empty slot
{
disp = hsize_reg - i; // secondary hash (after G. Knott)
if ( i == 0 )
disp = 1;
do
{
if ( (i -= disp) < 0 )
i += hsize_reg;
if ( htab[i] == fcode )
{
ent = codetab[i];
continue outer_loop;
}
}
while ( htab[i] >= 0 );
}
output( ent, outs );
ent = c;
if ( free_ent < maxmaxcode )
{
codetab[i] = free_ent++; // code -> hashtable
htab[i] = fcode;
}
else
cl_block( outs );
}
// Put out the final code.
output( ent, outs );
output( EOFCode, outs );
}
//----------------------------------------------------------------------------
void encode(OutputStream os) throws IOException
{
os.write(initCodeSize); // write "initial code size" byte
remaining = imgW * imgH; // reset navigation variables
curPixel = 0;
compress(initCodeSize + 1, os); // compress and write the pixel data
os.write(0); // write block terminator
}
// Flush the packet to disk, and reset the accumulator
void flush_char( OutputStream outs ) throws IOException
{
if ( a_count > 0 )
{
outs.write( a_count );
outs.write( accum, 0, a_count );
a_count = 0;
}
}
final int MAXCODE( int n_bits )
{
return ( 1 << n_bits ) - 1;
}
//----------------------------------------------------------------------------
// Return the next pixel from the image
//----------------------------------------------------------------------------
private int nextPixel()
{
if (remaining == 0)
return EOF;
--remaining;
byte pix = pixAry[curPixel++];
return pix & 0xff;
}
void output( int code, OutputStream outs ) throws IOException
{
cur_accum &= masks[cur_bits];
if ( cur_bits > 0 )
cur_accum |= ( code << cur_bits );
else
cur_accum = code;
cur_bits += n_bits;
while ( cur_bits >= 8 )
{
char_out( (byte) ( cur_accum & 0xff ), outs );
cur_accum >>= 8;
cur_bits -= 8;
}
// If the next entry is going to be too big for the code size,
// then increase it, if possible.
if ( free_ent > maxcode || clear_flg )
{
if ( clear_flg )
{
maxcode = MAXCODE(n_bits = g_init_bits);
clear_flg = false;
}
else
{
++n_bits;
if ( n_bits == maxbits )
maxcode = maxmaxcode;
else
maxcode = MAXCODE(n_bits);
}
}
if ( code == EOFCode )
{
// At EOF, write the rest of the buffer.
while ( cur_bits > 0 )
{
char_out( (byte) ( cur_accum & 0xff ), outs );
cur_accum >>= 8;
cur_bits -= 8;
}
flush_char( outs );
}
}
}
/* NeuQuant Neural-Net Quantization Algorithm
* ------------------------------------------
*
* Copyright (c) 1994 Anthony Dekker
*
* NEUQUANT Neural-Net quantization algorithm by Anthony Dekker, 1994.
* See "Kohonen neural networks for optimal colour quantization"
* in "Network: Computation in Neural Systems" Vol. 5 (1994) pp 351-367.
* for a discussion of the algorithm.
*
* Any party obtaining a copy of these files from the author, directly or
* indirectly, is granted, free of charge, a full and unrestricted irrevocable,
* world-wide, paid up, royalty-free, nonexclusive right and license to deal
* in this software and documentation files (the "Software"), including without
* limitation the rights to use, copy, modify, merge, publish, distribute, sublicense,
* and/or sell copies of the Software, and to permit persons who receive
* copies from any such party to do so, with the only requirement being
* that this copyright notice remain intact.
*/
// Ported to Java 12/00 K Weiner
class NeuQuant {
protected static final int netsize = 256; /* number of colours used */
/* four primes near 500 - assume no image has a length so large */
/* that it is divisible by all four primes */
protected static final int prime1 = 499;
protected static final int prime2 = 491;
protected static final int prime3 = 487;
protected static final int prime4 = 503;
protected static final int minpicturebytes = (3 * prime4);
/* minimum size for input image */
/* Program Skeleton
----------------
[select samplefac in range 1..30]
[read image from input file]
pic = (unsigned char*) malloc(3*width*height);
initnet(pic,3*width*height,samplefac);
learn();
unbiasnet();
[write output image header, using writecolourmap(f)]
inxbuild();
write output image using inxsearch(b,g,r) */
/* Network Definitions
------------------- */
protected static final int maxnetpos = (netsize - 1);
protected static final int netbiasshift = 4; /* bias for colour values */
protected static final int ncycles = 100; /* no. of learning cycles */
/* defs for freq and bias */
protected static final int intbiasshift = 16; /* bias for fractions */
protected static final int intbias = (((int) 1) << intbiasshift);
protected static final int gammashift = 10; /* gamma = 1024 */
protected static final int gamma = (((int) 1) << gammashift);
protected static final int betashift = 10;
protected static final int beta = (intbias >> betashift); /* beta = 1/1024 */
protected static final int betagamma = (intbias << (gammashift - betashift));
/* defs for decreasing radius factor */
protected static final int initrad = (netsize >> 3); /* for 256 cols, radius starts */
protected static final int radiusbiasshift = 6; /* at 32.0 biased by 6 bits */
protected static final int radiusbias = (((int) 1) << radiusbiasshift);
protected static final int initradius = (initrad * radiusbias); /* and decreases by a */
protected static final int radiusdec = 30; /* factor of 1/30 each cycle */
/* defs for decreasing alpha factor */
protected static final int alphabiasshift = 10; /* alpha starts at 1.0 */
protected static final int initalpha = (((int) 1) << alphabiasshift);
protected int alphadec; /* biased by 10 bits */
/* radbias and alpharadbias used for radpower calculation */
protected static final int radbiasshift = 8;
protected static final int radbias = (((int) 1) << radbiasshift);
protected static final int alpharadbshift = (alphabiasshift + radbiasshift);
protected static final int alpharadbias = (((int) 1) << alpharadbshift);
/* Types and Global Variables
-------------------------- */
protected byte[] thepicture; /* the input image itself */
protected int lengthcount; /* lengthcount = H*W*3 */
protected int samplefac; /* sampling factor 1..30 */
// typedef int pixel[4]; /* BGRc */
protected int[][] network; /* the network itself - [netsize][4] */
protected int[] netindex = new int[256]; /* for network lookup - really 256 */
protected int[] bias = new int[netsize]; /* bias and freq arrays for learning */
protected int[] freq = new int[netsize];
protected int[] radpower = new int[initrad]; /* radpower for precomputation */
/* Initialise network in range (0,0,0) to (255,255,255) and set parameters
----------------------------------------------------------------------- */
public NeuQuant(byte[] thepic, int len, int sample) {
int i;
int[] p;
thepicture = thepic;
lengthcount = len;
samplefac = sample;
network = new int[netsize][];
for (i = 0; i < netsize; i++) {
network[i] = new int[4];
p = network[i];
p[0] = p[1] = p[2] = (i << (netbiasshift + 8)) / netsize;
freq[i] = intbias / netsize; /* 1/netsize */
bias[i] = 0;
}
}
public byte[] colorMap() {
byte[] map = new byte[3*netsize];
int[] index = new int[netsize];
for (int i = 0; i < netsize; i++)
index[network[i][3]] = i;
int k = 0;
for (int i = 0; i < netsize; i++) {
int j = index[i];
map[k++] = (byte) (network[j][0]);
map[k++] = (byte) (network[j][1]);
map[k++] = (byte) (network[j][2]);
}
return map;
}
/* Insertion sort of network and building of netindex[0..255] (to do after unbias)
------------------------------------------------------------------------------- */
public void inxbuild() {
int i, j, smallpos, smallval;
int[] p;
int[] q;
int previouscol, startpos;
previouscol = 0;
startpos = 0;
for (i = 0; i < netsize; i++) {
p = network[i];
smallpos = i;
smallval = p[1]; /* index on g */
/* find smallest in i..netsize-1 */
for (j = i + 1; j < netsize; j++) {
q = network[j];
if (q[1] < smallval) { /* index on g */
smallpos = j;
smallval = q[1]; /* index on g */
}
}
q = network[smallpos];
/* swap p (i) and q (smallpos) entries */
if (i != smallpos) {
j = q[0]; q[0] = p[0]; p[0] = j;
j = q[1]; q[1] = p[1]; p[1] = j;
j = q[2]; q[2] = p[2]; p[2] = j;
j = q[3]; q[3] = p[3]; p[3] = j;
}
/* smallval entry is now in position i */
if (smallval != previouscol) {
netindex[previouscol] = (startpos + i) >> 1;
for (j = previouscol + 1; j < smallval; j++)
netindex[j] = i;
previouscol = smallval;
startpos = i;
}
}
netindex[previouscol] = (startpos + maxnetpos) >> 1;
for (j = previouscol + 1; j < 256; j++)
netindex[j] = maxnetpos; /* really 256 */
}
/* Main Learning Loop
------------------ */
public void learn() {
int i, j, b, g, r;
int radius, rad, alpha, step, delta, samplepixels;
byte[] p;
int pix, lim;
if (lengthcount < minpicturebytes)
samplefac = 1;
alphadec = 30 + ((samplefac - 1) / 3);
p = thepicture;
pix = 0;
lim = lengthcount;
samplepixels = lengthcount / (3 * samplefac);
delta = samplepixels / ncycles;
alpha = initalpha;
radius = initradius;
rad = radius >> radiusbiasshift;
if (rad <= 1)
rad = 0;
for (i = 0; i < rad; i++)
radpower[i] = alpha * (((rad * rad - i * i) * radbias) / (rad * rad));
//fprintf(stderr,"beginning 1D learning: initial radius=%d\n", rad);
if (lengthcount < minpicturebytes)
step = 3;
else if ((lengthcount % prime1) != 0)
step = 3 * prime1;
else {
if ((lengthcount % prime2) != 0)
step = 3 * prime2;
else {
if ((lengthcount % prime3) != 0)
step = 3 * prime3;
else
step = 3 * prime4;
}
}
i = 0;
while (i < samplepixels) {
b = (p[pix + 0] & 0xff) << netbiasshift;
g = (p[pix + 1] & 0xff) << netbiasshift;
r = (p[pix + 2] & 0xff) << netbiasshift;
j = contest(b, g, r);
altersingle(alpha, j, b, g, r);
if (rad != 0)
alterneigh(rad, j, b, g, r); /* alter neighbours */
pix += step;
if (pix >= lim)
pix -= lengthcount;
i++;
if (i % delta == 0) {
alpha -= alpha / alphadec;
radius -= radius / radiusdec;
rad = radius >> radiusbiasshift;
if (rad <= 1)
rad = 0;
for (j = 0; j < rad; j++)
radpower[j] = alpha * (((rad * rad - j * j) * radbias) / (rad * rad));
}
}
//fprintf(stderr,"finished 1D learning: final alpha=%f !\n",((float)alpha)/initalpha);
}
/* Search for BGR values 0..255 (after net is unbiased) and return colour index
---------------------------------------------------------------------------- */
public int map(int b, int g, int r) {
int i, j, dist, a, bestd;
int[] p;
int best;
bestd = 1000; /* biggest possible dist is 256*3 */
best = -1;
i = netindex[g]; /* index on g */
j = i - 1; /* start at netindex[g] and work outwards */
while ((i < netsize) || (j >= 0)) {
if (i < netsize) {
p = network[i];
dist = p[1] - g; /* inx key */
if (dist >= bestd)
i = netsize; /* stop iter */
else {
i++;
if (dist < 0)
dist = -dist;
a = p[0] - b;
if (a < 0)
a = -a;
dist += a;
if (dist < bestd) {
a = p[2] - r;
if (a < 0)
a = -a;
dist += a;
if (dist < bestd) {
bestd = dist;
best = p[3];
}
}
}
}
if (j >= 0) {
p = network[j];
dist = g - p[1]; /* inx key - reverse dif */
if (dist >= bestd)
j = -1; /* stop iter */
else {
j--;
if (dist < 0)
dist = -dist;
a = p[0] - b;
if (a < 0)
a = -a;
dist += a;
if (dist < bestd) {
a = p[2] - r;
if (a < 0)
a = -a;
dist += a;
if (dist < bestd) {
bestd = dist;
best = p[3];
}
}
}
}
}
return (best);
}
public byte[] process() {
learn();
unbiasnet();
inxbuild();
return colorMap();
}
/* Unbias network to give byte values 0..255 and record position i to prepare for sort
----------------------------------------------------------------------------------- */
public void unbiasnet() {
int i, j;
for (i = 0; i < netsize; i++) {
network[i][0] >>= netbiasshift;
network[i][1] >>= netbiasshift;
network[i][2] >>= netbiasshift;
network[i][3] = i; /* record colour no */
}
}
/* Move adjacent neurons by precomputed alpha*(1-((i-j)^2/[r]^2)) in radpower[|i-j|]
--------------------------------------------------------------------------------- */
protected void alterneigh(int rad, int i, int b, int g, int r) {
int j, k, lo, hi, a, m;
int[] p;
lo = i - rad;
if (lo < -1)
lo = -1;
hi = i + rad;
if (hi > netsize)
hi = netsize;
j = i + 1;
k = i - 1;
m = 1;
while ((j < hi) || (k > lo)) {
a = radpower[m++];
if (j < hi) {
p = network[j++];
try {
p[0] -= (a * (p[0] - b)) / alpharadbias;
p[1] -= (a * (p[1] - g)) / alpharadbias;
p[2] -= (a * (p[2] - r)) / alpharadbias;
} catch (Exception e) {} // prevents 1.3 miscompilation
}
if (k > lo) {
p = network[k--];
try {
p[0] -= (a * (p[0] - b)) / alpharadbias;
p[1] -= (a * (p[1] - g)) / alpharadbias;
p[2] -= (a * (p[2] - r)) / alpharadbias;
} catch (Exception e) {}
}
}
}
/* Move neuron i towards biased (b,g,r) by factor alpha
---------------------------------------------------- */
protected void altersingle(int alpha, int i, int b, int g, int r) {
/* alter hit neuron */
int[] n = network[i];
n[0] -= (alpha * (n[0] - b)) / initalpha;
n[1] -= (alpha * (n[1] - g)) / initalpha;
n[2] -= (alpha * (n[2] - r)) / initalpha;
}
/* Search for biased BGR values
---------------------------- */
protected int contest(int b, int g, int r) {
/* finds closest neuron (min dist) and updates freq */
/* finds best neuron (min dist-bias) and returns position */
/* for frequently chosen neurons, freq[i] is high and bias[i] is negative */
/* bias[i] = gamma*((1/netsize)-freq[i]) */
int i, dist, a, biasdist, betafreq;
int bestpos, bestbiaspos, bestd, bestbiasd;
int[] n;
bestd = ~(((int) 1) << 31);
bestbiasd = bestd;
bestpos = -1;
bestbiaspos = bestpos;
for (i = 0; i < netsize; i++) {
n = network[i];
dist = n[0] - b;
if (dist < 0)
dist = -dist;
a = n[1] - g;
if (a < 0)
a = -a;
dist += a;
a = n[2] - r;
if (a < 0)
a = -a;
dist += a;
if (dist < bestd) {
bestd = dist;
bestpos = i;
}
biasdist = dist - ((bias[i]) >> (intbiasshift - netbiasshift));
if (biasdist < bestbiasd) {
bestbiasd = biasdist;
bestbiaspos = i;
}
betafreq = (freq[i] >> betashift);
freq[i] -= betafreq;
bias[i] += (betafreq << gammashift);
}
freq[bestpos] += beta;
bias[bestpos] -= betagamma;
return (bestbiaspos);
}
}