Revision: 20094
http://sourceforge.net/p/jmol/code/20094
Author: hansonr
Date: 2014-11-09 22:12:09 +0000 (Sun, 09 Nov 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.8_2014.11.09"
new feature: CAPTURE "filename0000.png"
-- captures set of PNG files
-- 0000 is not required
new feature: CAPTURE "filename0000.gif"
-- captures set of GIF files
-- 0000 IS required in order to distinguish this from animated GIF
bug fix: GIF writer not properly handling large numbers of colors
-- use of CIE L*a*b gives GIMP-like color quantification
bug fix: WRITE command should remove "t" or "j" in WRITE xxx.PNGJ, WRITE
xxx.PNGT, WRITE xxx.GIFT
-- specifically when no PNGJ, GIFT, or PNGT designation is made.
bug fix: PDB reader limited to 20 connections per atom
code: code clean-up in GData, Graphics3D, and Export3D
code: PDB reader CONECT efficiency
Modified Paths:
--------------
trunk/Jmol/src/javajs/img/GifEncoder.java
trunk/Jmol/src/javajs/util/OC.java
trunk/Jmol/src/org/jmol/awtjs2d/JSFile.java
trunk/Jmol/src/org/jmol/io/JmolUtil.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/OutputManager.java
trunk/Jmol/src/org/jmol/viewer/OutputManagerAwt.java
Modified: trunk/Jmol/src/javajs/img/GifEncoder.java
===================================================================
--- trunk/Jmol/src/javajs/img/GifEncoder.java 2014-11-08 17:41:04 UTC (rev
20093)
+++ trunk/Jmol/src/javajs/img/GifEncoder.java 2014-11-09 22:12:09 UTC (rev
20094)
@@ -22,10 +22,11 @@
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
-// useful page: http://www.htmlhexcolor.com/0ac906
+// Final encoding code from
http://acme.com/resources/classes/Acme/JPM/Encoders/GifEncoder.java
//
// GifEncoder - write out an image as a GIF
//
+//
// Transparency handling and variable bit size courtesy of Jack Palevich.
//
// Copyright (C)1996,1998 by Jef Poskanzer <j...@mail.acme.com>. All rights
reserved.
@@ -65,27 +66,30 @@
import javajs.util.CU;
import javajs.util.Lst;
+import javajs.util.M3;
import javajs.util.P3;
-import java.util.Arrays;
import java.util.Hashtable;
import java.util.Map;
import java.io.IOException;
/**
*
- * GifEncoder extensively modified for Jmol by Bob Hanson
+ * GifEncoder extensively adapted for Jmol by Bob Hanson
*
- * -- using median-cut with rgb
+ * Color quantization roughly follows the GIMP method
+ * "dither Floyd-Steinberg standard" but with some twists.
+ * (For example, we exclude the background color.)
*
- * -- adds adaptive color reduction to generate 256 colors using the median-cut
- * algorithm. Some problems still with systems having > 2000 colors.
+ * Note that although GIMP code annotation refers to "median-cut",
+ * it is really uses MEAN-cut. That is what I use here as well.
*
- * -- TODO use median-cut with HSL
+ * -- commented code allows visualization of the color space using Jmol. Very
+ * enlightening!
*
* -- much simplified interface with ImageEncoder
*
- * -- uses simple Hashtable with Integer()
+ * -- uses simple Hashtable with Integer() to catalog colors
*
* -- allows progressive production of animated GIF via Jmol CAPTURE command
*
@@ -94,32 +98,32 @@
*
* -- allows JavaScript port
*
- * -- Bob Hanson, 24 Sep 2013
+ * -- Bob Hanson, first try: 24 Sep 2013; final coding: 9 Nov 2014
*
+ *
* @author Bob Hanson hans...@stolaf.edu
*/
public class GifEncoder extends ImageEncoder {
- private int bitsPerPixel = 1;
- private P3[] errors;
- private P3[] pixelsLab;
+ private Map<String, Object> params;
+ private P3[] palette;
+ private int backgroundColor;
+
private boolean interlaced;
private boolean addHeader = true;
private boolean addImage = true;
private boolean addTrailer = true;
- private int delayTime100ths = -1;
- private boolean looping;
- private Map<String, Object> params;
- private int byteCount;
private boolean isTransparent;
private boolean floydSteinberg = true;
- int backgroundColor;
- Map<Integer, ColorCell> colorMap;
- Map<Integer, ColorCell> colors256;
- int[] red, green, blue;
- int[] indexes;
+ private boolean capturing;
+ private boolean looping;
+ private int delayTime100ths = -1;
+ private int bitsPerPixel = 1;
+
+ private int byteCount;
+
/**
* we allow for animated GIF by being able to re-enter the code with
different
* parameters held in params
@@ -139,26 +143,19 @@
isTransparent = true;
}
- //floydSteinberg = false;
-
- logging = true;
-
interlaced = (Boolean.TRUE == params.get("interlaced"));
- if (interlaced
- || params.containsKey("captureRootExt") // file0000.gif
- || !params.containsKey("captureMode")) // animated gif
+ if (params.containsKey("captureRootExt") // file0000.gif
+ || !params.containsKey("captureMode")) // animated gif
return;
+ interlaced = false;
+ capturing = true;
try {
byteCount = ((Integer) params.get("captureByteCount")).intValue();
} catch (Exception e) {
// ignore
}
- int imode = "maec".indexOf(((String) params.get("captureMode")).substring(
- 0, 1));
-
- if (logging)
- System.out.println("GIF capture mode " + imode);
- switch (imode) {
+ switch ("maec"
+ .indexOf(((String) params.get("captureMode")).substring(0, 1))) {
case 0: //"movie"
params.put("captureMode", "add");
addImage = false;
@@ -183,15 +180,41 @@
}
}
+ @Override
+ protected void generate() throws IOException {
+ if (addHeader)
+ writeHeader();
+ addHeader = false; // only one header
+ if (addImage) {
+ createPalette();
+ writeGraphicControlExtension();
+ if (delayTime100ths >= 0 && looping)
+ writeNetscapeLoopExtension();
+ writeImage();
+ }
+ }
+
+ @Override
+ protected void close() {
+ if (addTrailer) {
+ writeTrailer();
+ } else {
+ doClose = false;
+ }
+ if (capturing)
+ params.put("captureByteCount", Integer.valueOf(byteCount));
+ }
+
+ ////////////// 256-color quantization //////////////
+
private class ColorItem {
int rgb;
P3 lab;
- int count;
ColorItem(int rgb) {
this.rgb = rgb;
- lab = toXYZ(rgb);
+ lab = toLAB(rgb);
}
@Override
@@ -200,72 +223,18 @@
}
}
- protected class ColorVector extends Lst<ColorItem> {
-
- private Lst<ColorCell> boxes;
-
- void indexColors() {
- // goal is to create an index set and and to generate rgb errors for
each color
- boxes = new Lst<ColorCell>();
- // start with just two boxes -- fixed background color and all others
- ColorCell cc = new ColorCell(0);
- cc.addItem(new ColorItem(backgroundColor));
- boxes.addLast(cc);
- cc = new ColorCell(1);
- for (int i = size(); --i >= 0;) {
- ColorItem c = get(i);
- if (c.rgb != backgroundColor)
- cc.addItem(c);
- }
- boxes.addLast(cc);
- int n;
- while ((n = boxes.size()) < 256 && splitBoxes()) {
- // loop
- }
- clear();
- colorMap = new Hashtable<Integer, ColorCell>();
- colors256 = new Hashtable<Integer, ColorCell>();
- for (int i = 0; i < n; i++)
- addLast(boxes.get(i).average());
- for (int i = 0; i < n; i++)
- boxes.get(i).setErrors();
- }
-
- private boolean splitBoxes() {
- int n = boxes.size();
- float maxVol = 0;
- int imax = -1;
- for (int i = n; --i >= 1;) {
- float v = boxes.get(i).getVolume();
- if (v > maxVol) {
- maxVol = v;
- imax = i;
- }
- }
- if (imax < 0)
- return false;
- boxes.get(imax).splitBox(boxes);
- return true;
- }
-
- }
-
private class ColorCell {
protected int index;
// counts here are counts of color occurances for this grouped set.
// ints here allow for 2147483647/0x100 = count of 8388607 for THIS
average color, which should be fine.
- private P3 xyz;
+ protected P3 lab;
// min and max based on 0 0 0 for this rgb
- private float maxr = Integer.MAX_VALUE, minr = -Integer.MAX_VALUE,
- maxg = Integer.MAX_VALUE, ming = -Integer.MAX_VALUE,
- maxb = Integer.MAX_VALUE, minb = -Integer.MAX_VALUE;
- private float rmaxr = -Integer.MAX_VALUE, rminr = Integer.MAX_VALUE,
- rmaxg = -Integer.MAX_VALUE, rming = Integer.MAX_VALUE,
- rmaxb = -Integer.MAX_VALUE, rminb = Integer.MAX_VALUE;
- private float maxre = Integer.MAX_VALUE, minre = -Integer.MAX_VALUE,
- maxge = Integer.MAX_VALUE, minge = -Integer.MAX_VALUE,
- maxbe = Integer.MAX_VALUE, minbe = -Integer.MAX_VALUE;
- private ColorCell nextr, prevr, nextg, prevg, nextb, prevb;
+// private float maxr = Integer.MAX_VALUE, minr = -Integer.MAX_VALUE,
+// maxg = Integer.MAX_VALUE, ming = -Integer.MAX_VALUE,
+// maxb = Integer.MAX_VALUE, minb = -Integer.MAX_VALUE;
+// private float rmaxr = -Integer.MAX_VALUE, rminr = Integer.MAX_VALUE,
+// rmaxg = -Integer.MAX_VALUE, rming = Integer.MAX_VALUE,
+// rmaxb = -Integer.MAX_VALUE, rminb = Integer.MAX_VALUE;
int rgb;
Lst<ColorItem> lst;
private float volume;
@@ -280,403 +249,482 @@
return volume;
if (lst.size() < 2)
return -1;
- float d;
- rmaxr = -Integer.MAX_VALUE;
- rminr = Integer.MAX_VALUE;
- rmaxg = -Integer.MAX_VALUE;
- rming = Integer.MAX_VALUE;
- rmaxb = -Integer.MAX_VALUE;
- rminb = Integer.MAX_VALUE;
+ //if (true)
+ //return lst.size();
+ //float d;
+ float maxx = -Integer.MAX_VALUE;
+ float minx = Integer.MAX_VALUE;
+ float maxy = -Integer.MAX_VALUE;
+ float miny = Integer.MAX_VALUE;
+ float maxz = -Integer.MAX_VALUE;
+ float minz = Integer.MAX_VALUE;
int n = lst.size();
for (int i = n; --i >= 0;) {
P3 xyz = lst.get(i).lab;
- if (xyz.x < rminr)
- rminr = xyz.x;
- if (xyz.y < rming)
- rming = xyz.y;
- if (xyz.z < rminb)
- rminb = xyz.z;
- if (xyz.x > rmaxr)
- rmaxr = xyz.x;
- if (xyz.y > rmaxg)
- rmaxg = xyz.y;
- if (xyz.z > rmaxb)
- rmaxb = xyz.z;
+ if (xyz.x < minx)
+ minx = xyz.x;
+ if (xyz.y < miny)
+ miny = xyz.y;
+ if (xyz.z < minz)
+ minz = xyz.z;
+ if (xyz.x > maxx)
+ maxx = xyz.x;
+ if (xyz.y > maxy)
+ maxy = xyz.y;
+ if (xyz.z > maxz)
+ maxz = xyz.z;
}
- return volume = ((d = (rmaxr - rminr)/RFACTOR) * d + (d = rmaxg - rming)
* d + (d = rmaxb
- - rminb)
- * d);
+ float dx = (maxx - minx);
+ float dy = (maxy - miny);
+ float dz = (maxz - minz);
+ return volume = dx * dx + dy * dy + dz * dz;
}
- void setErrors() {
- if (nextr != null)
- maxre = ((nextr.minr + maxr) / 2) - xyz.x;
- if (nextg != null)
- maxge = ((nextg.ming + maxg) / 2) - xyz.y;
- if (nextb != null)
- maxbe = ((nextb.minb + maxb) / 2) - xyz.z;
- if (prevr != null)
- minre = ((prevr.maxr + minr) / 2) - xyz.x;
- if (prevg != null)
- minge = ((prevg.maxg + ming) / 2) - xyz.y;
- if (prevb != null)
- minbe = ((prevb.maxb + minb) / 2) - xyz.z;
- }
-
void addItem(ColorItem c) {
lst.addLast(c);
}
- ColorItem average() {
+ /**
+ * Set the average L*a*b value for this box
+ *
+ * @return RGB point
+ *
+ */
+ protected P3 setColor() {
int count = lst.size();
- xyz = new P3();
+ lab = new P3();
for (int i = count; --i >= 0;) {
- ColorItem c = lst.get(i);
- colorMap.put(Integer.valueOf(c.rgb), this);
- xyz.add(c.lab);
+ lab.add(lst.get(i).lab);
}
- xyz.scale(1f / count);
- P3 ptrgb = toRGB(xyz);
+ lab.scale(1f / count);
+ P3 ptrgb = toRGB(lab);
rgb = CU.colorPtToFFRGB(ptrgb);
- red[index] = (int) ptrgb.x;
- green[index] = (int) ptrgb.y;
- blue[index] = (int) ptrgb.z;
- /*
- for (int i = size(); --i >= 0;) {
- int rgb = get(i).rgb;
- r = (rgb & 0xFCFCFC)>> 2;
- System.out.println("draw id 'd"+index+"_"+i+"' width 0.5 " +
CU.colorPtFromInt(r, null) + " color "+CU.colorPtFromInt(rgb, null)+"");
- }
- r = (rgb & 0xFCFCFC)>> 2;
- System.out.println("draw id 'c"+index+"' width 1.0 " +
CU.colorPtFromInt(r, null) + " color "+CU.colorPtFromInt(rgb, null)+"");
-
- */
- colors256.put(Integer.valueOf(rgb), this);
- System.out.println(index + " " + Integer.toHexString(rgb) + " " + ptrgb
+ " " + xyz + " " + (maxr - minr)+ " " + (maxg - ming) + " " + (maxb-minb));
- return new ColorItem(rgb);
+ //for (int i = 0; i < count; i++) {
+ // drawPt(index, i+1, lst.get(i).rgb, false);
+ // }
+
+ // drawPt(index, 0, rgb, true);
+ // System.out.println("boundbox corners { " + Math.max(minr, 0) + "
"
+ // + Math.max(ming, 0) + " " + Math.max(minb, 0) + "}{ "
+ // + Math.min(maxr, 100) + " " + Math.min(maxg, 100) + " "
+ // + Math.min(maxb, 100) + "}");
+ // System.out.println("draw d" + index + " boundbox color "
+ // + CU.colorPtFromInt(rgb, null) + " mesh nofill");
+ // System.out.println("//" + index + " " + volume);
+
+ //System.out.println(index + " " + Integer.toHexString(rgb) + " " +
ptrgb + " " + xyz + " " + (maxr - minr)+ " " + (maxg - ming) + " " +
(maxb-minb));
+ return ptrgb;
}
- private float[] ar, ag, ab;
-
/**
* use median_cut algorithm to split the box, creating a doubly linked
list.
*
* Paul Heckbert, MIT thesis COLOR IMAGE QUANTIZATION FOR FRAME BUFFER
* DISPLAY https://www.cs.cmu.edu/~ph/ciq_thesis
*
+ * except, as in GIMP, we use mean, not median here.
+ *
* @param boxes
+ * @return true if split
*/
- protected void splitBox(Lst<ColorCell> boxes) {
+ protected boolean splitBox(Lst<ColorCell> boxes) {
int n = lst.size();
if (n < 2)
- return;
+ return false;
int newIndex = boxes.size();
ColorCell newBox = new ColorCell(newIndex);
boxes.addLast(newBox);
- for (int i = 0; i < 3; i++)
- getArray(i);
- float ranger = (ar[n - 1] - ar[0]) / RFACTOR;
- float rangeg = ag[n - 1] - ag[0];
- float rangeb = ab[n - 1] - ab[0];
- int mode = (ranger >= rangeg ? (ranger >= rangeb ? 0 : 2)
- : rangeg >= rangeb ? 1 : 2);
- float[] a = (mode == 0 ? ar : mode == 1 ? ag : ab);
- int median = n / 2;
- float val = a[median];
- int dir = (val == a[0] ? 1 : -1);
- while (median >= 0 && median < n && a[median] == val) {
- median += dir;
+ float[][] ranges = new float[3][3];
+ for (int ic = 0; ic < 3; ic++) {
+ float low = Float.MAX_VALUE;
+ float high = -Float.MAX_VALUE;
+ for (int i = lst.size(); --i >= 0;) {
+ P3 lab = lst.get(i).lab;
+ float v = (ic == 0 ? lab.x : ic == 1 ? lab.y : lab.z);
+ if (low > v)
+ low = v;
+ if (high < v)
+ high = v;
+ }
+ ranges[0][ic] = low;
+ ranges[1][ic] = high;
+ ranges[2][ic] = high - low;
}
- if (dir == -1)
- median++;
- val = a[median];
- newBox.nextr = nextr;
- newBox.nextg = nextg;
- newBox.nextb = nextb;
- newBox.prevr = prevr;
- newBox.prevg = prevg;
- newBox.prevb = prevb;
- newBox.minr = minr;
- newBox.ming = ming;
- newBox.minb = minb;
- newBox.maxr = maxr;
- newBox.maxg = maxg;
- newBox.maxb = maxb;
- //System.out.println("split " + index + " " + newBox.index);
+ float[] r = ranges[2];
+ int mode = (r[0] >= r[1] ? (r[0] >= r[2] ? 0 : 2)
+ : r[1] >= r[2] ? 1 : 2);
+ // NOTE: GIMP does not use median! uses mean instead;
+
+ // int median = n / 2;
+ // float val = a[median];
+ // int dir = (val == a[0] ? 1 : -1);
+ // while (median >= 0 && median < n && a[median] == val) {
+ // median += dir;
+ // }
+ // if (dir == -1)
+ // median++;
+ // val = a[median];
+
+ float val = ranges[0][mode] + ranges[2][mode] / 2;
+
+// newBox.minr = minr;
+// newBox.ming = ming;
+// newBox.minb = minb;
+// newBox.maxr = maxr;
+// newBox.maxg = maxg;
+// newBox.maxb = maxb;
volume = 0;
+
switch (mode) {
case 0:
for (int i = lst.size(); --i >= 0;)
if (lst.get(i).lab.x >= val)
newBox.addItem(lst.remove(i));
- newBox.prevr = this;
- nextr = newBox;
- maxr = val - DELTA;
- newBox.minr = val;
+// maxr = val - 0.001f;
+// newBox.minr = val;
break;
case 1:
for (int i = lst.size(); --i >= 0;)
if (lst.get(i).lab.y >= val)
newBox.addItem(lst.remove(i));
- newBox.prevg = this;
- nextg = newBox;
- maxg = val - DELTA;
- newBox.ming = val;
+// maxg = val - 0.001f;
+// newBox.ming = val;
break;
case 2:
for (int i = lst.size(); --i >= 0;)
if (lst.get(i).lab.z >= val)
newBox.addItem(lst.remove(i));
- newBox.prevb = this;
- nextb = newBox;
- maxb = val - DELTA;
- newBox.minb = val;
+// maxb = val - 0.001f;
+// newBox.minb = val;
break;
}
- System.out.println(this + " -"+mode+"-> " + newBox +" " + lst.size() +
"/" + newBox.lst.size());
+ return true;
}
- /**
- * Get sorted array of unique component entries
- *
- * @param ic
- * 0(red) 1(green) 2(blue)
- */
- private void getArray(int ic) {
- float[] a = new float[lst.size()];
- for (int i = a.length; --i >= 0;) {
- P3 xyz = lst.get(i).lab;
- a[i] = (ic == 0 ? xyz.x : ic == 1 ? xyz.y : xyz.z);
- }
- Arrays.sort(a);
- switch (ic) {
- case 0:
- ar = a;
- break;
- case 1:
- ag = a;
- break;
- case 2:
- ab = a;
- }
- }
-
- /**
- *
- * Find nearest cell; return errors in [x y z]
- *
- * @param xyz
- * @param err
- * @return color cell
- *
- */
- ColorCell findCell(P3 xyz, P3 err) {
- err.sub2(xyz, this.xyz);
- //System.out.println(Integer.toHexString(rgb) + " " + this + " " +
PT.toJSON(null, err));
- if (err.x > maxre && nextr != null)
- return nextr.findCell(xyz, err);
- if (err.x < minre && prevr != null)
- return prevr.findCell(xyz, err);
- if (err.y > maxge && nextg != null)
- return nextg.findCell(xyz, err);
- if (err.y < minge && prevg != null)
- return prevg.findCell(xyz, err);
- if (err.z > maxbe && nextb != null)
- return nextb.findCell(xyz, err);
- if (err.z < minbe && prevb != null)
- return prevb.findCell(xyz, err);
- return this; // in this box or best we can do
- }
-
@Override
public String toString() {
return index + " " + Integer.toHexString(rgb);
}
}
-/*
- float RFACTOR = 3.6f;
- float DELTA = 0.001f;
-
- P3 toRGB(P3 xyz) {
- return CU.hslToRGB(xyz);
- }
-
- P3 toXYZ(int rgb) {
- return CU.rgbToHSL(CU.colorPtFromInt(rgb, new P3()), false);
- }
-*/
-
- float RFACTOR = 1;
- float DELTA = 1;
- P3 toRGB(P3 xyz) {
- return P3.new3(clamp(xyz.x), clamp(xyz.y), clamp(xyz.z));
- }
-
- P3 toXYZ(int rgb) {
- return CU.colorPtFromInt(rgb, new P3());
- }
-
- @Override
- protected void generate() throws IOException {
- if (addHeader)
- writeHeader();
- addHeader = false; // only one header
- if (addImage) {
- createColorTable();
- writeGraphicControlExtension();
- if (delayTime100ths >= 0 && looping)
- writeNetscapeLoopExtension();
- writeImage();
- }
- }
-
- @Override
- protected void close() {
- if (addTrailer) {
- writeTrailer();
- } else {
- doClose = false;
- }
- params.put("captureByteCount", Integer.valueOf(byteCount));
- }
-
/**
- * includes logical screen descriptor
+ * Generate a palette and quantize all colors into it.
*
- * @throws IOException
*/
- private void writeHeader() throws IOException {
- putString("GIF89a");
- putWord(width);
- putWord(height);
- putByte(0); // no global color table -- using local instead
- putByte(0); // no background
- putByte(0); // no pixel aspect ratio given
- }
-
- /**
- * generates a 256-color or fewer color table consisting of a set of red,
- * green, blue arrays and a hash table pointing to a color index; adapts to
- * situations where more than 256 colors are present.
- *
- */
- private void createColorTable() {
- ColorVector colors = getColors();
- int nTotal = colors.size();//colors256.size();
- setBitsPerPixel(nTotal);
- colors.indexColors();
- ditherPixels();
- }
-
- private void setBitsPerPixel(int nTotal) {
+ private void createPalette() {
+ Lst<ColorItem> colors = new Lst<ColorItem>();
+ Map<Integer, ColorItem> ciHash = new Hashtable<Integer, ColorItem>();
+ for (int i = 0, n = pixels.length; i < n; i++) {
+ int rgb = pixels[i];
+ Integer key = Integer.valueOf(rgb);
+ ColorItem item = ciHash.get(key);
+ if (item == null) {
+ item = new ColorItem(rgb);
+ ciHash.put(key, item);
+ colors.addLast(item);
+ }
+ }
+ ciHash = null;
+ int nTotal = colors.size();
+ System.out.println("GIF total image colors: " + nTotal);
bitsPerPixel = (nTotal <= 2 ? 1 : nTotal <= 4 ? 2 : nTotal <= 16 ? 4 : 8);
- int mapSize = 1 << bitsPerPixel;
- red = new int[mapSize];
- green = new int[mapSize];
- blue = new int[mapSize];
+ palette = new P3[1 << bitsPerPixel];
+ quantizeColors(colors);
}
/**
- * Generate a list of all unique colors in the image.
- *
- * @return the vector
+ * Quantize colors by generating a set of boxes containing all colors.
+ * Start with just two boxes -- fixed background color and all others.
+ * Keep splitting boxes while there are fewer than 256 and some with
+ * multiple colors in them.
+ *
+ * It is possible that we will end up with fewer than 256 colors.
+ *
+ * @param colors
*/
- private ColorVector getColors() {
- int n = pixels.length;
- errors = new P3[n];
- pixelsLab = new P3[n];
- indexes = new int[n];
- ColorVector colorVector = new ColorVector();
- Map<Integer, ColorItem> ciHash = new Hashtable<Integer, ColorItem>();
- int nColors = 0;
+ private void quantizeColors(Lst<ColorItem> colors) {
+ Map<Integer, ColorCell> colorMap = new Hashtable<Integer, ColorCell>();
+ Lst<ColorCell> boxes = new Lst<ColorCell>();
+ ColorCell cc = new ColorCell(0);
+ cc.addItem(new ColorItem(backgroundColor));
+ boxes.addLast(cc);
+ boxes.addLast(cc = new ColorCell(1));
+ for (int i = colors.size(); --i >= 0;) {
+ ColorItem c = colors.get(i);
+ if (c.rgb != backgroundColor)
+ cc.addItem(c);
+ }
+ colors.clear();
+ int n;
+ while ((n = boxes.size()) < 256) {
+ float maxVol = 0;
+ ColorCell maxCell = null;
+ for (int i = n; --i >= 1;) {
+ ColorCell b = boxes.get(i);
+ float v = b.getVolume();
+ if (v > maxVol) {
+ maxVol = v;
+ maxCell = b;
+ }
+ }
+ if (maxCell == null || !maxCell.splitBox(boxes))
+ break;
+ }
for (int i = 0; i < n; i++) {
- pixelsLab[i] = toXYZ(pixels[i]);
- nColors += addColor(colorVector, ciHash, i);
+ ColorCell b = boxes.get(i);
+ palette[i] = b.setColor();
+ colorMap.put(Integer.valueOf(b.rgb), b);
}
- ciHash = null;
- //colorVector.sort();
- System.out.println("# total image colors = " + nColors);
- // dont sort by frequency
- return colorVector;
+ System.out.println("GIF final color count: " + boxes.size());
+ quantizePixels(colorMap, boxes);
}
- private int addColor(ColorVector colorVector, Map<Integer, ColorItem> ciHash,
- int pt) {
- int rgb = pixels[pt];
- Integer key = Integer.valueOf(rgb);
- ColorItem item = ciHash.get(key);
- if (item == null) {
- item = new ColorItem(rgb);
- ciHash.put(key, item);
- colorVector.addLast(item);
- return 1;
- }
- item.count++;
- return 0;
- }
-
/**
*
- * Idea is to find the closest known color and then spread out the error over
- * four pixels
+ * Assign all colors to their closest approximation and
+ * change pixels[] array to index values.
*
+ * Floyd-Steinberg dithering, with error limiting to 75%. Finds the closest
+ * known color and then spreads out the error over four leading pixels.
+ *
+ * @param colorMap
+ * @param boxes
+ *
*/
- private void ditherPixels() {
- P3 xyz = new P3();
+ private void quantizePixels(Map<Integer, ColorCell> colorMap, Lst<ColorCell>
boxes) {
+ P3[] pixelErr = new P3[pixels.length];
+ P3 err = new P3();
+ P3 lab;
+ int rgb;
for (int i = 0, p = 0; i < height; ++i) {
boolean notLastRow = (i != height - 1);
for (int j = 0; j < width; ++j, p++) {
- int rgb = getRGB(p, xyz);
- try {
- ColorCell app = colors256.get(Integer.valueOf(rgb));
- if (app == null) {
- P3 err = new P3();
- app = colorMap.get(Integer.valueOf(pixels[p]));
- if (floydSteinberg) {
- app = app.findCell(xyz, err);
- colorMap.put(Integer.valueOf(rgb), app);
- boolean notLastCol = (j < width - 1);
+ if (pixelErr[p] == null) {
+ lab = null;
+ rgb = pixels[p];
+ } else {
+ lab = toLAB(pixels[p]);
+ err = pixelErr[p]; // it does not matter that we repurpose errors[p]
here.
+ err.x = clamp(err.x, -75, 75);
+ err.y = clamp(err.y, -75, 75);
+ err.z = clamp(err.z, -75, 75);
+ lab.add(err);
+ rgb = CU.colorPtToFFRGB(toRGB(lab));
+ }
+ ColorCell app = colorMap.get(Integer.valueOf(rgb));
+ if (app == null) {
+ if (lab == null)
+ lab = toLAB(pixels[p]);
+ // find nearest cell
+ float maxerr = Float.MAX_VALUE;
+ // skip 0 0 0
+ for (int ib = boxes.size(); --ib >= 1;) {
+ ColorCell b = boxes.get(ib);
+ err.sub2(lab, b.lab);
+ float d = err.lengthSquared();
+ if (d < maxerr) {
+ maxerr = d;
+ app = b;
+ }
+ }
+ err.sub2(lab, app.lab);
+
+ if (floydSteinberg) {
+ // dither
+ boolean notLastCol = (j < width - 1);
+ if (notLastCol)
+ addError(err, 7, pixelErr, p + 1);
+ if (notLastRow) {
+ if (j > 0)
+ addError(err, 3, pixelErr, p + width - 1);
+ addError(err, 5, pixelErr, p + width);
if (notLastCol)
- addError(err, 7, p + 1);
- if (notLastRow) {
- if (j > 0)
- addError(err, 3, p + width - 1);
- addError(err, 5, p + width);
- if (notLastCol)
- addError(err, 1, p + width + 1);
- }
+ addError(err, 1, pixelErr, p + width + 1);
}
}
- indexes[p] = app.index;
- } catch (Throwable e) {
- System.out.println("GIF error: " + e);
}
+ pixels[p] = app.index;
}
}
}
- private int getRGB(int p, P3 xyz) {
- P3 err = errors[p];
- xyz.setT(pixelsLab[p]);
- if (err == null)
- return pixels[p];
- xyz.add(err);
- return CU.colorPtToFFRGB(toRGB(xyz));
- }
-
- private void addError(P3 err, int f, int p) {
- P3 errp = errors[p];
+ private void addError(P3 err, int f, P3[] pixelErr, int p) {
+ if (pixels[p] == backgroundColor)
+ return;
+ P3 errp = pixelErr[p];
if (errp == null)
- errp = errors[p] = new P3();
+ errp = pixelErr[p] = new P3();
errp.scaleAdd2(f / 16f, err, errp);
}
- int clamp(float c) {
- return (int) Math.floor(c < 0 ? 0 : c > 255 ? 255 : c);
+ // protected void drawPt(int index, int i, int rgb, boolean isMain) {
+ // P3 pt = toLAB(rgb);
+ // System.out.println("draw id 'd" + index + "_" + i + "' width "
+ // + (isMain ? 1.0 : 0.2) + " " + pt + " color "
+ // + CU.colorPtFromInt(rgb, null) + " '" + index + "'");
+ // }
+
+ ///////////////////////// CIE L*a*b / XYZ / sRGB conversion methods /////////
+
+
+ // these could be static, but that just makes for more JavaScript code
+
+ protected P3 toLAB(int rgb) {
+ P3 lab = CU.colorPtFromInt(rgb, null);
+ rgbToXyz(lab, lab);
+ xyzToLab(lab, lab);
+ // normalize to 0-100
+ lab.y = (lab.y + 86.185f) / (98.254f + 86.185f) * 100f;
+ lab.z = (lab.z + 107.863f) / (94.482f + 107.863f) * 100f;
+ return lab;
}
+ protected P3 toRGB(P3 lab) {
+ P3 xyz = P3.newP(lab);
+ // normalized to 0-100
+ xyz.y = xyz.y / 100f * (98.254f + 86.185f) - 86.185f;
+ xyz.z = xyz.z / 100f * (94.482f + 107.863f) - 107.863f;
+ labToXyz(xyz, xyz);
+ return xyzToRgb(xyz, xyz);
+ }
+
+ private static M3 xyz2rgb;
+ private static M3 rgb2xyz;
+
+ static {
+ rgb2xyz = M3.newA9(new float[] { 0.4124f, 0.3576f, 0.1805f, 0.2126f,
+ 0.7152f, 0.0722f, 0.0193f, 0.1192f, 0.9505f });
+
+ xyz2rgb = M3.newA9(new float[] { 3.2406f, -1.5372f, -0.4986f, -0.9689f,
+ 1.8758f, 0.0415f, 0.0557f, -0.2040f, 1.0570f });
+ }
+
+ private P3 rgbToXyz(P3 rgb, P3 xyz) {
+ // http://en.wikipedia.org/wiki/CIE_1931_color_space
+ // http://rsb.info.nih.gov/ij/plugins/download/Color_Space_Converter.java
+ if (xyz == null)
+ xyz = new P3();
+ xyz.x = srgb(rgb.x);
+ xyz.y = srgb(rgb.y);
+ xyz.z = srgb(rgb.z);
+ rgb2xyz.rotate(xyz);
+ return xyz;
+ }
+
+ private float srgb(float x) {
+ x /= 255;
+ return (float) (x <= 0.04045 ? x / 12.92 : Math.pow(((x + 0.055) / 1.055),
+ 2.4)) * 100;
+ }
+
+ private P3 xyzToRgb(P3 xyz, P3 rgb) {
+ // http://en.wikipedia.org/wiki/CIE_1931_color_space
+ // http://rsb.info.nih.gov/ij/plugins/download/Color_Space_Converter.java
+ if (rgb == null)
+ rgb = new P3();
+ rgb.setT(xyz);
+ rgb.scale(0.01f);
+ xyz2rgb.rotate(rgb);
+ rgb.x = clamp(sxyz(rgb.x), 0, 255);
+ rgb.y = clamp(sxyz(rgb.y), 0, 255);
+ rgb.z = clamp(sxyz(rgb.z), 0, 255);
+ return rgb;
+ }
+
+ private float sxyz(float x) {
+ return (float) (x > 0.0031308f ? (1.055 * Math.pow(x, 1.0 / 2.4)) - 0.055
+ : x * 12.92) * 255;
+ }
+
+ private P3 xyzToLab(P3 xyz, P3 lab) {
+ // http://en.wikipedia.org/wiki/Lab_color_space
+ // http://rsb.info.nih.gov/ij/plugins/download/Color_Space_Converter.java
+ // Lab([0..100], [-86.185..98.254], [-107.863..94.482])
+ // XYZn = D65 = {95.0429, 100.0, 108.8900};
+ if (lab == null)
+ lab = new P3();
+ float x = flab(xyz.x / 95.0429f);
+ float y = flab(xyz.y / 100);
+ float z = flab(xyz.z / 108.89f);
+ lab.x = (116 * y) - 16;
+ lab.y = 500 * (x - y);
+ lab.z = 200 * (y - z);
+ return lab;
+ }
+
+ private float flab(float t) {
+ return (float) (t > 8.85645168E-3 /* (24/116)^3 */? Math.pow(t,
+ 0.333333333) : 7.78703704 /* 1/3*116/24*116/24 */* t + 0.137931034 /*
16/116 */
+ );
+ }
+
+ private P3 labToXyz(P3 lab, P3 xyz) {
+ // http://en.wikipedia.org/wiki/Lab_color_space
+ // http://rsb.info.nih.gov/ij/plugins/download/Color_Space_Converter.java
+ // XYZn = D65 = {95.0429, 100.0, 108.8900};
+ if (xyz == null)
+ xyz = new P3();
+
+ xyz.setT(lab);
+ float y = (xyz.x + 16) / 116;
+ float x = xyz.y / 500 + y;
+ float z = y - xyz.z / 200;
+ xyz.x = fxyz(x) * 95.0429f;
+ xyz.y = fxyz(y) * 100;
+ xyz.z = fxyz(z) * 108.89f;
+
+ return xyz;
+ }
+
+ private float fxyz(float t) {
+ return (float) (t > 0.206896552 /* (24/116) */? t * t * t
+ : 0.128418549 /* 3*24/116*24/116 */* (t - 0.137931034 /* 16/116 */));
+ }
+
+ private float clamp(float c, float min, float max) {
+ return Math.round(c < min ? min : c > max ? max : c);
+ }
+
+ //static {
+ // P3 x;
+ // x = rgbToXyz(P3.new3(0,0,0), null);
+ // System.out.println("xyz="+x);
+ // x = xyzToLab(x, x);
+ // System.out.println("lab="+x);
+ // x = labToXyz(x, x);
+ // System.out.println(x);
+ // x = xyzToRgb(x, x);
+ // System.out.println(x);
+ //
+ // x = rgbToXyz(P3.new3(254,1,253), null);
+ // System.out.println("xyz="+x);
+ // x = xyzToLab(x, x);
+ // System.out.println("lab="+x);
+ // x = labToXyz(x, x);
+ // System.out.println(x);
+ // x = xyzToRgb(x, x);
+ // System.out.println(x);
+ //
+ // System.out.println(toRGB(toLAB(CU.colorPtToFFRGB(P3.new3(200,100,50)))));
+ //}
+
+ ///////////////////////// GifEncoder writing methods ////////////////////////
+
+ /**
+ * includes logical screen descriptor
+ *
+ * @throws IOException
+ */
+ private void writeHeader() throws IOException {
+ putString("GIF89a");
+ putWord(width);
+ putWord(height);
+ putByte(0); // no global color table -- using local instead
+ putByte(0); // no background
+ putByte(0); // no pixel aspect ratio given
+ }
+
private void writeGraphicControlExtension() {
if (isTransparent || delayTime100ths >= 0) {
putByte(0x21); // graphic control extension
@@ -763,10 +811,13 @@
int packedFields = 0x80 | (interlaced ? 0x40 : 0) | (bitsPerPixel - 1);
putByte(packedFields);
int colorMapSize = 1 << bitsPerPixel;
+ P3 p = new P3();
for (int i = 0; i < colorMapSize; i++) {
- putByte(red[i]);
- putByte(green[i]);
- putByte(blue[i]);
+ if (palette[i] != null)
+ p = palette[i];
+ putByte((int) p.x);
+ putByte((int) p.y);
+ putByte((int) p.z);
}
putByte(initCodeSize = (bitsPerPixel <= 1 ? 2 : bitsPerPixel));
compress();
@@ -786,7 +837,7 @@
private int nextPixel() {
if (countDown-- == 0)
return EOF;
- int colorIndex = indexes[curpt];
+ int colorIndex = pixels[curpt];
// Bump the current X position
++curx;
if (curx == width) {
@@ -1072,4 +1123,5 @@
bufPt = 0;
}
}
+
}
Modified: trunk/Jmol/src/javajs/util/OC.java
===================================================================
--- trunk/Jmol/src/javajs/util/OC.java 2014-11-08 17:41:04 UTC (rev 20093)
+++ trunk/Jmol/src/javajs/util/OC.java 2014-11-09 22:12:09 UTC (rev 20094)
@@ -8,6 +8,7 @@
import java.io.OutputStreamWriter;
+
import javajs.J2SIgnoreImport;
import javajs.api.BytePoster;
@@ -72,8 +73,7 @@
os = null;
}
this.os = os;
- isLocalFile = (fileName != null && !(fileName.startsWith("http://";) ||
fileName
- .startsWith("https://";)));
+ isLocalFile = (fileName != null && !isRemote(fileName));
if (asWriter && !isBase64 && os != null)
bw = new BufferedWriter(new OutputStreamWriter(os));
return this;
@@ -343,4 +343,34 @@
return bytePoster.postByteArray(fileName, bytes);
}
+ public final static String[] urlPrefixes = { "http:", "https:", "sftp:",
"ftp:",
+ "file:" };
+ // note that SFTP is not supported
+ public final static int URL_LOCAL = 4;
+
+ public static boolean isRemote(String fileName) {
+ if (fileName == null)
+ return false;
+ int itype = urlTypeIndex(fileName);
+ return (itype >= 0 && itype != URL_LOCAL);
+ }
+
+ public static boolean isLocal(String fileName) {
+ if (fileName == null)
+ return false;
+ int itype = urlTypeIndex(fileName);
+ return (itype < 0 || itype == URL_LOCAL);
+ }
+
+ public static int urlTypeIndex(String name) {
+ if (name == null)
+ return -2; // local unsigned applet
+ for (int i = 0; i < urlPrefixes.length; ++i) {
+ if (name.startsWith(urlPrefixes[i])) {
+ return i;
+ }
+ }
+ return -1;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/awtjs2d/JSFile.java
===================================================================
--- trunk/Jmol/src/org/jmol/awtjs2d/JSFile.java 2014-11-08 17:41:04 UTC (rev
20093)
+++ trunk/Jmol/src/org/jmol/awtjs2d/JSFile.java 2014-11-09 22:12:09 UTC (rev
20094)
@@ -4,9 +4,9 @@
import javajs.api.GenericFileInterface;
import javajs.util.AjaxURLConnection;
+import javajs.util.OC;
import javajs.util.PT;
-import org.jmol.viewer.FileManager;
import org.jmol.viewer.Viewer;
/**
@@ -29,7 +29,7 @@
JSFile(String name) {
this.name = name.replace('\\','/');
fullName = name;
- if (!fullName.startsWith("/") && FileManager.urlTypeIndex(name) < 0)
+ if (!fullName.startsWith("/") && OC.urlTypeIndex(name) < 0)
fullName = Viewer.jsDocumentBase + "/" + fullName;
fullName = PT.rep(fullName, "/./", "/");
name = name.substring(name.lastIndexOf("/") + 1);
Modified: trunk/Jmol/src/org/jmol/io/JmolUtil.java
===================================================================
--- trunk/Jmol/src/org/jmol/io/JmolUtil.java 2014-11-08 17:41:04 UTC (rev
20093)
+++ trunk/Jmol/src/org/jmol/io/JmolUtil.java 2014-11-09 22:12:09 UTC (rev
20094)
@@ -34,6 +34,7 @@
import javajs.api.GenericZipTools;
import javajs.api.GenericBinaryDocument;
import javajs.util.LimitedLineReader;
+import javajs.util.OC;
import javajs.util.Rdr;
import javajs.util.Lst;
import javajs.util.PT;
@@ -52,7 +53,6 @@
import org.jmol.api.JmolZipUtilities;
import org.jmol.util.Escape;
import org.jmol.util.Logger;
-import org.jmol.viewer.FileManager;
import org.jmol.viewer.Viewer;
public class JmolUtil implements JmolZipUtilities {
@@ -695,7 +695,7 @@
return "" + ret;
image = (vwr.isJS ? ret : apiPlatform.createImage(ret));
} else if (vwr.isJS) {
- } else if (FileManager.urlTypeIndex(fullPathName) >= 0) {
+ } else if (OC.urlTypeIndex(fullPathName) >= 0) {
try {
image = apiPlatform.createImage(new URL((URL) null, fullPathName,
null));
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-11-08 17:41:04 UTC
(rev 20093)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-11-09 22:12:09 UTC
(rev 20094)
@@ -479,16 +479,16 @@
}
Map<String, Object> params = vwr.captureParams;
String type = (params == null ? "GIF" : (String) params.get("type"));
- float endTime = 10; // ten seconds by default
+ float endTime = 0; // indefinitely by default
int mode = 0;
int slen = e.slen;
- boolean isTransparent = (tokAt(e.slen - 1) == T.translucent);
- if (isTransparent)
- slen--;
String fileName = "";
boolean looping = !vwr.am.animationReplayMode.name().equals("ONCE");
int i = 1;
int tok = tokAt(i);
+ boolean isTransparent = (tok == T.translucent);
+ if (isTransparent)
+ tok = tokAt(++i);
switch (tok == T.nada ? (tok = T.end) : tok) {
case T.string:
fileName = e.optParameterAsString(i++);
@@ -511,8 +511,14 @@
} else {
type = "GIF";
}
- boolean streaming = (fileName.indexOf("0000.") !=
fileName.lastIndexOf(".") - 4);
+ if (isTransparent)
+ type += "T";
+ boolean streaming = (fileName.indexOf("0000.") !=
fileName.lastIndexOf(".") - 4);
boolean isRock = false;
+ if (tokAt(i) == T.loop) {
+ looping = true;
+ tok = tokAt(++i);
+ }
switch (tokAt(i)) {
case T.rock:
isRock = true;
@@ -540,15 +546,13 @@
boolean wf = vwr.g.waitForMoveTo;
s = "set waitformoveto true;" + PT.rep(s, "Y", axis)
+ ";set waitformoveto " + wf;
- s = "capture " + PT.esc(fileName) + " -1"
- + (isTransparent ? " transparent;" : ";") + s + ";capture end;";
+ s = "capture " + (isTransparent ? "transparent " : "") +
PT.esc(fileName) + " LOOP;"
+ + s + ";capture end;";
e.cmdScript(0, null, s);
return;
case T.decimal:
case T.integer:
endTime = floatParameter(i++);
- if (endTime < 0)
- looping = true;
break;
}
if (chk)
@@ -584,13 +588,11 @@
params.put("type", type);
Integer c = Integer.valueOf(vwr.getBackgroundArgb());
params.put("backgroundColor", c);
- if (isTransparent)
- params.put("transparentColor", c);
params.put("fileName", fileName);
params.put("quality", Integer.valueOf(-1));
params.put(
"endTime",
- Long.valueOf(endTime < 0 ? -1 : System.currentTimeMillis()
+ Long.valueOf(endTime <= 0 ? -1 : System.currentTimeMillis()
+ (long) (endTime * 1000)));
params.put("captureMode", T.nameOf(mode).toLowerCase());
params.put("captureLooping", looping ? Boolean.TRUE : Boolean.FALSE);
@@ -6019,7 +6021,7 @@
} else if (PT.isOneOf(type, ";ZIP;ZIPALL;SPT;STATE;")) {
pt++;
break;
- } else if (!isCoord){
+ } else if (!isCoord) {
type = "(image)";
}
}
@@ -6105,6 +6107,8 @@
|| type.equals("FRAME") || type.equals("VIBRATION")) {
type = (fileName != null && fileName.indexOf(".") >= 0 ? fileName
.substring(fileName.lastIndexOf(".") + 1).toUpperCase() : "JPG");
+ if (PT.isOneOf(type, ";PNGJ;PNGT;GIFT;"))
+ fileName = fileName.substring(0, fileName.length() - 1);
}
if (type.equals("MNU")) {
type = "MENU";
@@ -6291,7 +6295,8 @@
}
} else {
if (fileName != null
- && (bytes = data = vwr.createZip(fileName, v.size() == 1 ?
"BINARY" : "ZIPDATA", v)) == null)
+ && (bytes = data = vwr.createZip(fileName,
+ v.size() == 1 ? "BINARY" : "ZIPDATA", v)) == null)
e.evalError("#CANCELED#", null);
}
} else if (data == "SPT") {
@@ -6378,11 +6383,6 @@
params = new Hashtable<String, Object>();
if (fileName != null)
params.put("fileName", fileName);
- if (type.equals("GIFT")) {
- params.put("transparentColor",
- Integer.valueOf(vwr.getBackgroundArgb()));
- type = "GIF";
- }
params.put("backgroundColor",
Integer.valueOf(vwr.getBackgroundArgb()));
params.put("type", type);
if (bytes instanceof String && quality == Integer.MIN_VALUE)
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2014-11-08 17:41:04 UTC
(rev 20093)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2014-11-09 22:12:09 UTC
(rev 20094)
@@ -397,7 +397,7 @@
.appendSB(Base64.getBase64(bytes)).toString();
}
}
- int iurl = urlTypeIndex(name);
+ int iurl = OC.urlTypeIndex(name);
boolean isURL = (iurl >= 0);
String post = null;
if (isURL && (iurl = name.indexOf("?POST?")) >= 0) {
@@ -930,30 +930,6 @@
// JSmol will call that from awtjs2d.Platform.java asynchronously
}
- public final static int URL_LOCAL = 4;
- private final static String[] urlPrefixes = { "http:", "https:", "sftp:",
"ftp:",
- "file:" };
-
- public static int urlTypeIndex(String name) {
- if (name == null)
- return -2; // local unsigned applet
- for (int i = 0; i < urlPrefixes.length; ++i) {
- if (name.startsWith(urlPrefixes[i])) {
- return i;
- }
- }
- return -1;
- }
-
- public static boolean isLocal(String fileName) {
- if (fileName == null)
- return false;
- int itype = urlTypeIndex(fileName);
- return (itype < 0 || itype == URL_LOCAL);
- }
-
-
-
/**
* [0] and [2] may return same as [1] in the
* case of a local unsigned applet.
@@ -987,7 +963,7 @@
if (appletDocumentBaseURL == null) {
// This code is for the app or signed local applet
// -- no local file reading for headless
- if (urlTypeIndex(name) >= 0 || vwr.haveAccess(ACCESS.NONE)
+ if (OC.urlTypeIndex(name) >= 0 || vwr.haveAccess(ACCESS.NONE)
|| vwr.haveAccess(ACCESS.READSPT) && !name.endsWith(".spt")
&& !name.endsWith("/")) {
try {
@@ -1025,7 +1001,7 @@
names[0] = pathForAllFiles + names[1];
Logger.info("FileManager substituting " + name0 + " --> " + names[0]);
}
- if (isFullLoad && (file != null || urlTypeIndex(names[0]) == URL_LOCAL)) {
+ if (isFullLoad && (file != null || OC.urlTypeIndex(names[0]) ==
OC.URL_LOCAL)) {
String path = (file == null ? PT.trim(names[0].substring(5), "/")
: names[0]);
int pt = path.length() - names[1].length() - 1;
@@ -1203,7 +1179,7 @@
for (int iFile = 0; iFile < nFiles; iFile++) {
String name0 = fileNames.get(iFile);
String name = name0;
- if (isLocal == isLocal(name)) {
+ if (isLocal == OC.isLocal(name)) {
int pt = (noPath ? -1 : name.indexOf("/" + dataPath + "/"));
if (pt >= 0) {
name = name.substring(pt + 1);
@@ -1323,6 +1299,8 @@
@Override
public String postByteArray(String fileName, byte[] bytes) {
+ // in principle, could have sftp or ftp here
+ // but sftp is not implemented
Object ret = getBufferedInputStreamOrErrorMessageFromName(fileName, null,
false,
false, bytes, false, true);
if (ret instanceof String)
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-08 17:41:04 UTC
(rev 20093)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-09 22:12:09 UTC
(rev 20094)
@@ -15,7 +15,7 @@
TODO: design and implement sidechain mutation -- MUTATE command ?
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.8_2014.11.08"
+Jmol.___JmolVersion="14.3.8_2014.11.09"
new feature: CAPTURE "filename0000.png"
-- captures set of PNG files
@@ -25,13 +25,18 @@
-- captures set of GIF files
-- 0000 IS required in order to distinguish this from animated GIF
-code: code clean-up in GData, Graphics3D, and Export3D
-code: modifications to GIF writer. Not really satisfying; still using HSL
-code: PDB reader CONECT efficiency
+bug fix: GIF writer not properly handling large numbers of colors
+ -- use of CIE L*a*b gives GIMP-like color quantification
+bug fix: WRITE command should remove "t" or "j" in WRITE xxx.PNGJ, WRITE
xxx.PNGT, WRITE xxx.GIFT
+ -- specifically when no PNGJ, GIFT, or PNGT designation is made.
+
bug fix: PDB reader limited to 20 connections per atom
+code: code clean-up in GData, Graphics3D, and Export3D
+code: PDB reader CONECT efficiency
+
JmolVersion="14.3.8_2014.10.27"
bug fix: up-arrow in console may not return command if contains unicode
Modified: trunk/Jmol/src/org/jmol/viewer/OutputManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2014-11-08 17:41:04 UTC
(rev 20093)
+++ trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2014-11-09 22:12:09 UTC
(rev 20094)
@@ -168,7 +168,7 @@
OC outTemp = getOutputChannel(null, null);
getWrappedState(fileName, scripts, image, outTemp);
stateData = outTemp.toByteArray();
- } else if (rgbbuf == null && !asBytes) {
+ } else if (rgbbuf == null && !asBytes &&
!params.containsKey("captureMode")) {
stateData = ((String) getWrappedState(null, scripts, image, null))
.getBytes();
}
@@ -176,11 +176,12 @@
params.put("pngAppData", stateData);
params.put("pngAppPrefix", "Jmol Type");
}
- if (type.equals("PNGT"))
- params.put("transparentColor",
- Integer.valueOf(vwr.getBackgroundArgb()));
- type = "PNG";
}
+ if (type.equals("PNGT") || type.equals("GIFT")) {
+ params.put("transparentColor",
+ Integer.valueOf(vwr.getBackgroundArgb()));
+ type = type.substring(0, 3);
+ }
if (comment != null)
params.put("comment", comment.length() == 0 ? Viewer.getJmolVersion()
: comment);
@@ -191,7 +192,6 @@
if (isOK) {
if (params.containsKey("captureMsg") &&
!params.containsKey("captureSilent"))
vwr.prompt((String) params.get("captureMsg"), "OK", null, true);
-
if (asBytes)
bytes = out.toByteArray();
else if (params.containsKey("captureByteCount"))
@@ -365,7 +365,7 @@
}
if (fullPath != null)
fullPath[0] = fileName;
- String localName = (FileManager.isLocal(fileName) ? fileName : null);
+ String localName = (OC.isLocal(fileName) ? fileName : null);
try {
return openOutputChannel(privateKey, localName, false, false);
} catch (IOException e) {
@@ -647,7 +647,7 @@
return null;
params.put("fileName", fileName);
// JSmol/HTML5 WILL produce a localName now
- if (FileManager.isLocal(fileName))
+ if (OC.isLocal(fileName))
localName = fileName;
int saveWidth = vwr.dimScreen.width;
int saveHeight = vwr.dimScreen.height;
@@ -908,7 +908,7 @@
Lst<String> newFileNames = new Lst<String>();
for (int iFile = 0; iFile < nFiles; iFile++) {
String name = fileNames.get(iFile);
- boolean isLocal = !vwr.isJS && FileManager.isLocal(name);
+ boolean isLocal = !vwr.isJS && OC.isLocal(name);
String newName = name;
// also check that somehow we don't have a local file with the same name
as
// a fixed remote file name (because someone extracted the files and
then used them)
Modified: trunk/Jmol/src/org/jmol/viewer/OutputManagerAwt.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/OutputManagerAwt.java 2014-11-08
17:41:04 UTC (rev 20093)
+++ trunk/Jmol/src/org/jmol/viewer/OutputManagerAwt.java 2014-11-09
22:12:09 UTC (rev 20094)
@@ -85,7 +85,7 @@
OC openOutputChannel(double privateKey, String fileName,
boolean asWriter, boolean asAppend)
throws IOException {
- boolean isLocal = FileManager.isLocal(fileName);
+ boolean isLocal = OC.isLocal(fileName);
if (asAppend && isLocal && fileName.indexOf("JmolLog_") < 0)
asAppend = false;
return (fileName != null && !vwr.haveAccess(ACCESS.ALL)
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
