/**
** -----------------------------------------------------------------------------**
** JP46_Reader_camera.java
**
** Reads Elphel Camera JP46 files into ImageJ, un-applying gamma and gains
**
** Copyright (C) 2010 Elphel, Inc.
**
** -----------------------------------------------------------------------------**
**
** JP46_Reader.java is free software: you can redistribute it and/or modify
** it under the terms of the GNU General Public License as published by
** the Free Software Foundation, either version 3 of the License, or
** (at your option) any later version.
**
** This program is distributed in the hope that it will be useful,
** but WITHOUT ANY WARRANTY; without even the implied warranty of
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
** GNU General Public License for more details.
**
** You should have received a copy of the GNU General Public License
** along with this program. If not, see <http://www.gnu.org/licenses/>.
** -----------------------------------------------------------------------------**
**
*/
import java.awt.Button;
import java.awt.Frame;
import java.awt.GridLayout;
import java.awt.Image;
import java.awt.Panel;
import java.awt.Rectangle;
import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.BufferedInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.RandomAccessFile;
import java.io.StringReader;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
import java.util.Iterator;
import java.util.Properties;
import java.util.Set;
import javax.swing.JFileChooser;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import org.w3c.dom.Document;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.Prefs;
import ij.WindowManager;
import ij.gui.GUI;
import ij.gui.GenericDialog;
import ij.io.FileInfo;
import ij.io.OpenDialog;
import ij.plugin.frame.PlugInFrame;
import ij.process.ImageConverter;
import ij.process.ImageProcessor;
import ij.text.TextWindow;
/* This plugin opens images in Elphel JP4/JP46 format (opens as JPEG, reads MakerNote and converts). */
public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
/**
*
*/
private static final long serialVersionUID = 390855361964415147L;
Panel panel1;
Panel confpanel;
Frame instance;
String arg;
static File dir;
public String camera_url = "http://192.168.0.236:8081/";
public String camera_img = "bimg";
public String camera_img_new = "towp/wait/bimg"; // will always wait for the next image (repetitive acquisitions get new images)
public String camera_jp46settings = "";
public boolean IS_SILENT=true;
public boolean ABSOLUTELY_SILENT=false;
public boolean demux=true;
public String imageTitle="cameraImage";
private int ExifOffset=0x0c;
public JP46_Reader_camera() {
super("JP46 Reader Camera");
if (IJ.versionLessThan("1.39t")) return;
if (instance!=null) {
instance.toFront();
return;
}
instance = this;
addKeyListener(IJ.getInstance());
panel1 = new Panel();
panel1.setLayout(new GridLayout(6, 1, 50, 5));
addButton("Open JP4/JP46...",panel1);
addButton("Open JP4/JP46 from camera",panel1);
addButton("Configure...",panel1);
addButton("Show image properties",panel1);
addButton("Decode image info to properties",panel1);
addButton("Split Bayer",panel1);
add(panel1);
pack();
GUI.center(this);
setVisible(true);
}
public JP46_Reader_camera(boolean showGUI) {
super("JP46 Reader Camera");
if (IJ.versionLessThan("1.39t")) return;
if (instance!=null) {
instance.toFront();
return;
}
instance = this;
addKeyListener(IJ.getInstance());
panel1 = new Panel();
panel1.setLayout(new GridLayout(6, 1, 50, 5));
addButton("Open JP4/JP46...",panel1);
addButton("Open JP4/JP46 from camera",panel1);
addButton("Configure...",panel1);
addButton("Show image properties",panel1);
addButton("Decode image info to properties",panel1);
addButton("Split Bayer",panel1);
add(panel1);
pack();
GUI.center(this);
setVisible(showGUI);
}
void addButton(String label, Panel panel) {
Button b = new Button(label);
b.addActionListener(this);
b.addKeyListener(IJ.getInstance());
panel.add(b);
}
@Override
public void actionPerformed(ActionEvent e) {
String label = e.getActionCommand();
/* nothing */
if (label==null) return;
/* button */
if (label.equals("Open JP4/JP46...")) {
read_jp46(arg,true);
}else if (label.equals("Open JP4/JP46 (no scale)...")) {
read_jp46(arg,false);
}else if (label.equals("Configure...")) {
showConfigDialog(); // open configure dialog
}else if (label.equals("Open JP4/JP46 from camera")) {
openURL(camera_url + camera_img_new + camera_jp46settings, arg, true);
}else if (label.equals("Open JP4/JP46 from camera (no scale)")) {
openURL(camera_url + camera_img_new + camera_jp46settings, arg, false);
}else if (label.equals("Show image properties")) {
ImagePlus imp_sel = WindowManager.getCurrentImage();
if (imp_sel==null){
IJ.showMessage("Error","No images selected");
return;
}
listImageProperties (imp_sel);
}
else if (label.equals("Decode image info to properties")) {
ImagePlus imp_sel = WindowManager.getCurrentImage();
if (imp_sel==null){
IJ.showMessage("Error","No images selected");
return;
}
decodeProperiesFromInfo(imp_sel);
listImageProperties (imp_sel);
}
else if (label.equals("Split Bayer")) {
ImagePlus imp_sel = WindowManager.getCurrentImage();
if (imp_sel==null){
IJ.showMessage("Error","No images selected");
return;
}
splitShowBayer(imp_sel);
}
IJ.showStatus("DONE");
}
public void splitShowBayer(ImagePlus imp){
float [] pixels= (float[]) imp.getProcessor().getPixels();
int height=imp.getHeight();
int width= imp.getWidth();
int halfHeight=height/2;
int halfWidth=width/2;
float [][] bayerPixels=new float[4][halfHeight * halfWidth];
for (int iy=0;iy<halfHeight;iy++) for (int ix=0;ix<halfWidth;ix++){
int oIndex=iy*halfWidth+ix;
int iIndex=iy*2*width+ix*2;
bayerPixels[0][oIndex]=pixels[iIndex];
bayerPixels[1][oIndex]=pixels[iIndex+1];
bayerPixels[2][oIndex]=pixels[iIndex+width];
bayerPixels[3][oIndex]=pixels[iIndex+width+1];
}
ImageStack array_stack=new ImageStack(halfWidth,halfHeight);
for (int i=0;i<4;i++) array_stack.addSlice("chn-"+i, bayerPixels[i]);
ImagePlus imp_stack = new ImagePlus(imp.getTitle()+"-BAYER", array_stack);
imp_stack.getProcessor().resetMinAndMax();
imp_stack.show();
}
public void read_jp46(String arg, boolean scale) {
JFileChooser fc=null;
//try {fc = new JFileChooser();}
fc = new JFileChooser();
//catch (Throwable e) {IJ.error("This plugin requires Java 2 or Swing."); return;}
fc.setMultiSelectionEnabled(true);
if (dir==null) {
String sdir = OpenDialog.getDefaultDirectory();
if (sdir!=null)
dir = new File(sdir);
}
if (dir!=null)
fc.setCurrentDirectory(dir);
int returnVal = fc.showOpenDialog(IJ.getInstance());
if (returnVal!=JFileChooser.APPROVE_OPTION)
return;
File[] files = fc.getSelectedFiles();
if (files.length==0) { // getSelectedFiles does not work on some JVMs
files = new File[1];
files[0] = fc.getSelectedFile();
}
String path = fc.getCurrentDirectory().getPath()+Prefs.getFileSeparator();
dir = fc.getCurrentDirectory();
for (int i=0; i<files.length; i++) {
open(path, files[i].getName(), arg, scale);
}
}
public boolean showConfigDialog() {
GenericDialog gd = new GenericDialog("Configure");
gd.addStringField ("Image title: ", getTitle(), 20);
gd.addStringField("Camera Address: ", getURL(), 20);
gd.addStringField("Image: ", camera_img, 20);
gd.addStringField("Image (new): ", camera_img_new, 20);
gd.addStringField("JP46 Parameters: ", camera_jp46settings, 50);
gd.addCheckbox("Demux composite frame? ", demux);
gd.addCheckbox("Silent? ", IS_SILENT);
// gd.addCheckbox("JP4 (not JP46)? ", IS_JP4);
confpanel = new Panel();
gd.addPanel(confpanel);
addButton("Open JP4/JP46 (no scale)...", confpanel);
addButton("Open JP4/JP46 from camera (no scale)", confpanel);
//Vector textfields = gd.getStringFields();
//((TextField)fields.elementAt(0)).SetWidth = 20;
gd.showDialog();
if (gd.wasCanceled()) return false;
setTitle(gd.getNextString());
setURL (gd.getNextString());
camera_img = gd.getNextString();
camera_img_new = gd.getNextString();
camera_jp46settings = gd.getNextString();
demux=gd.getNextBoolean();
IS_SILENT=gd.getNextBoolean();
return true;
}
public ImagePlus open(String directory, String fileName, String arg, boolean scale) {
return open(directory, fileName, arg, scale, null,true);
}
public ImagePlus open(String directory, String fileName, String arg, boolean scale, ImagePlus imp_src) {
return open(directory, fileName, arg, scale, imp_src,true);
}
public ImagePlus open(
String directory,
String fileName,
String arg,
boolean scale,
ImagePlus imp_src,
boolean showImage) {
long[] ElphelMakerNote=null;
ImagePlus imp = null;
boolean reuse_imp=false;
boolean showDemux=showImage && demux;
if (demux) showImage=false;
double [] xtraExif=new double[1]; // ExposureTime
try {
imp = openJpegOrGif(directory, fileName);
if (imp == null) {
IJ.showMessage("JP46 Reader Error", "Could not open "+directory+"" + fileName + " as JPEG/JP46");
} else {
if ((imp_src==null)&& showImage) imp.show(); /* Shows before re-ordering*/
ElphelMakerNote = readElphelMakerNote(directory, fileName, 16,xtraExif); /* after or 8.2.2 */
if (ElphelMakerNote==null) ElphelMakerNote = readElphelMakerNote(directory, fileName, 14,xtraExif); /* after or 8.0.8.32 */
if (ElphelMakerNote==null) ElphelMakerNote = readElphelMakerNote(directory, fileName, 12,xtraExif); /* after or 8.0.7.3 */
if (ElphelMakerNote==null) ElphelMakerNote = readElphelMakerNote(directory, fileName, 8 ,xtraExif); /* before 8.0.7.3 */
}
} catch (IOException e) {
IJ.showStatus("");
String error = e.getMessage();
if (error==null || error.equals("")) error = ""+e;
IJ.showMessage("JP46 Reader", ""+error);
return null;
}
if (imp!=null) {
reuse_imp=jp46Reorder(imp, ElphelMakerNote, scale, imp_src);
if (reuse_imp) {
imp=imp_src;
} else if ((imp_src!=null)&& showImage) { /* tried to reuse, but wrong size */
imp.show(); /* never did that before */
}
if ((xtraExif!=null) && !Double.isNaN(xtraExif[0])){
imp.setProperty("EXPOSURE", String.format("%f",xtraExif[0]));
}
if (showImage) imp.updateAndDraw(); /* Redisplays final image*/
if (showDemux) {
if (!this.ABSOLUTELY_SILENT) System.out.println("demuxing...");
ImagePlus imp_0 = demuxImage(imp, 0); if (imp_0!=null) imp_0.show();
ImagePlus imp_1 = demuxImage(imp, 1); if (imp_1!=null) imp_1.show();
ImagePlus imp_2 = demuxImage(imp, 2); if (imp_2!=null) imp_2.show();
if ((imp_0==null) && (imp_0==null) && (imp_0==null)) imp.show(); // Show original image if demux failed (single original)
}
return imp;
}
return null;
}
public ImagePlus openURL(ImagePlus imp_src) {
if (imp_src==null) return openURL(camera_url + camera_img_new + camera_jp46settings, arg, true);
return openURL(camera_url + camera_img_new + camera_jp46settings, arg, true, imp_src,true);
}
public ImagePlus openURL() {
return openURL(camera_url + camera_img_new + camera_jp46settings, arg, true);
}
public ImagePlus openURL(String url, String arg, boolean scale) {
return openURL(url, arg, scale, null,true);
}
public ImagePlus openURL(
String url,
String arg,
boolean scale,
ImagePlus imp_src,
boolean showImage) {
long[] ElphelMakerNote=null;
ImagePlus imp = null;
boolean reuse_imp=false;
boolean showDemux=showImage && demux;
if (demux) showImage=false;
double [] xtraExif=new double[1]; // ExposureTime
// System.out.println("imp_src is "+((imp_src!=null)?"not ":"")+"null");
try {
imp = openJpegOrGifUsingURL(url);
if (imp == null) {
IJ.showMessage("JP46 Reader Error", "Could not open the URL: " + url + " as JPEG/JP46");
} else {
if ((imp_src==null) && showImage) {
// System.out.println("show() 1");
imp.show(); /* Shows before re-ordering*/
}
/// get rid of the "/towp/wait" if any - there is a chance to re-read the same image
ElphelMakerNote = readElphelMakerNoteURL(url.replaceFirst("/towp/wait",""), 16,xtraExif); /* after or 8.2.2 */
if (ElphelMakerNote==null) ElphelMakerNote = readElphelMakerNoteURL(url.replaceFirst("/towp/wait",""), 14,xtraExif); /* after or 8.0.8.32 */
if (ElphelMakerNote==null) ElphelMakerNote = readElphelMakerNoteURL(url.replaceFirst("/towp/wait",""), 12,xtraExif); /* after or 8.0.7.3 */
if (ElphelMakerNote==null) ElphelMakerNote = readElphelMakerNoteURL(url.replaceFirst("/towp/wait",""), 8 ,xtraExif ); /* before 8.0.7.3 */
}
} catch (IOException e) {
IJ.showStatus("");
String error = e.getMessage();
if (error==null || error.equals(""))
error = ""+e;
IJ.showMessage("JP46 Reader", ""+error);
return null;
}
if (imp!=null) {
reuse_imp=jp46Reorder(imp, ElphelMakerNote, scale, imp_src);
if (reuse_imp) {
imp=imp_src;
} else if ((imp_src!=null) && showImage) { /* tried to reuse, but wrong size */
// System.out.println("show() 2");
imp.show(); /* never did that before */
}
if ((xtraExif!=null) && !Double.isNaN(xtraExif[0])){
imp.setProperty("EXPOSURE", String.format("%f",xtraExif[0]));
}
if (showImage) imp.updateAndDraw(); /* Redisplays final image*/
if (showDemux) {
if (!this.ABSOLUTELY_SILENT) System.out.println("demuxing...");
ImagePlus imp_0 = demuxImage(imp, 0); if (imp_0!=null) imp_0.show();
ImagePlus imp_1 = demuxImage(imp, 1); if (imp_1!=null) imp_1.show();
ImagePlus imp_2 = demuxImage(imp, 2); if (imp_2!=null) imp_2.show();
if ((imp_0==null) && (imp_0==null) && (imp_0==null)) imp.show(); // Show original image if demux failed (single original)
}
return imp;
}
return null;
}
boolean jp46Reorder(ImagePlus imp, long[] MakerNote, boolean scale) {
return jp46Reorder(imp, MakerNote, scale, null);
}
void swapArrayElements (double[]arr,int i, int j) {
double tmp=arr[i];
arr[i]=arr[j];
arr[j]=tmp;
}
void swapArrayElements (long[]arr,int i, int j) {
long tmp=arr[i];
arr[i]=arr[j];
arr[j]=tmp;
}
boolean jp46Reorder(ImagePlus imp, long[] MakerNote, boolean scale, ImagePlus imp_src) {
// int MARGIN=2; // 2 pixels in JP4/JP46 mode around WOI
double[] gains= new double[4];
double[] blacks= new double[4];
double[] blacks256= new double[4];
double[] gammas= new double[4];
long [] gamma_scales= new long[4]; /* now not used, was scale _after_ gamma is applied, 0x400(default) corresponds to 1.0 */
int i;
double[][] rgammas=new double[4][];
double min_gain;
long WOI_LEFT,WOI_WIDTH,WOI_TOP,WOI_HEIGHT,BAYER_MODE,DCM_HOR,DCM_VERT,BIN_HOR,BIN_VERT;
long COLOR_MODE=0;
long FLIPH=0;
long FLIPV=0;
long HEIGHT1=0;
long HEIGHT2=0;
long HEIGHT3=0;
long BLANK1=0;
long BLANK2=0;
boolean FLIPH1=false;
boolean FLIPV1=false;
boolean FLIPH2=false;
boolean FLIPV2=false;
boolean FLIPH3=false;
boolean FLIPV3=false;
boolean COMPOSITE=false;
boolean PORTRAIT=false;
boolean YTABLEFORC=false;
long QUALITY=0;
long CQUALITY=0;
long CORING_INDEX_Y=0;
long CORING_INDEX_C=0;
double [] satValue={255.0, 255.0, 255.0, 255.0};
if (MakerNote !=null) {
for (i=0;i<4;i++) { /* r,g,gb,b */
gains[i]= MakerNote[i]/65536.0;
blacks[i]=(MakerNote[i+4]>>24)/256.0;
gammas[i]=((MakerNote[i+4]>>16)&0xff)/100.0;
gamma_scales[i]=MakerNote[i+4] & 0xffff;
imp.setProperty("gains_"+i,String.format("%f",gains[i]));
imp.setProperty("blacks_"+i,String.format("%f",blacks[i]));
imp.setProperty("gammas_"+i,String.format("%f",gammas[i]));
imp.setProperty("gamma_scales_"+i,String.format("%d",gamma_scales[i]));
}
IJ.showStatus("R=" +(0.001*((int)(1000*gains[0])))+
" G=" +IJ.d2s(gains[1],3)+
" Gb="+IJ.d2s(gains[2],3)+
" B=" +IJ.d2s(gains[3],3)+
" Gamma[0]="+IJ.d2s(gammas[0],3)+
" Black[0]="+((int) (256*blacks[0])));
String info=new String();
info+="Gain\t"+ IJ.d2s(gains[0],3) + "\t"+ IJ.d2s(gains[1],3) + "\t"+ IJ.d2s(gains[2],3) + "\t"+ IJ.d2s(gains[3],3) + "\n"+
"Gamma\t"+IJ.d2s(gammas[0],3) + "\t"+IJ.d2s(gammas[1],3) + "\t"+IJ.d2s(gammas[2],3) + "\t"+IJ.d2s(gammas[3],3) + "\n"+
"Black\t"+IJ.d2s(blacks[0],3) + "\t"+IJ.d2s(blacks[1],3) + "\t"+IJ.d2s(blacks[2],3) + "\t"+IJ.d2s(blacks[3],3) + "\n";
if (MakerNote.length>=14) {
COMPOSITE= ((MakerNote[10] & 0xc0000000)!=0);
if (COMPOSITE) {
HEIGHT1= MakerNote[11] & 0xffff;
BLANK1= (MakerNote[11]>>16) & 0xffff;
HEIGHT2= MakerNote[12] & 0xffff;
BLANK2= (MakerNote[12]>>16) & 0xffff;
// HEIGHT3=(( MakerNote[9]>>16)+2*MARGIN) - HEIGHT1-BLANK1-HEIGHT2-BLANK2;
HEIGHT3=( MakerNote[9]>>16) - HEIGHT1-BLANK1-HEIGHT2-BLANK2;
FLIPH1= (((MakerNote[10] >> 24) & 1)!=0); // Same value as FLIP_H
FLIPV1= (((MakerNote[10] >> 25) & 1)!=0); // Same value as FLIP_V
FLIPH2= (((MakerNote[10] >> 26) & 1)!=0);
FLIPV2= (((MakerNote[10] >> 27) & 1)!=0);
FLIPH3= (((MakerNote[10] >> 28) & 1)!=0);
FLIPV3= (((MakerNote[10] >> 29) & 1)!=0);
}
PORTRAIT= (((MakerNote[13] >> 7) & 1)!=0);
YTABLEFORC=(((MakerNote[13] >> 15) & 1)!=0);
QUALITY= (MakerNote[13] & 0x7f);
CQUALITY= ((MakerNote[13]>>8) & 0x7f);
if (CQUALITY==0) CQUALITY=QUALITY;
CORING_INDEX_Y= ((MakerNote[13]>>16) & 0x7f);
CORING_INDEX_C= ((MakerNote[13]>>24) & 0x7f);
if (CORING_INDEX_C==0) CORING_INDEX_C=CORING_INDEX_Y;
}
if (MakerNote.length>=12) {
WOI_LEFT= MakerNote[8]&0xffff;
WOI_WIDTH= MakerNote[8]>>16;
WOI_TOP= MakerNote[9]&0xffff;
WOI_HEIGHT= MakerNote[9]>>16;
FLIPH= MakerNote[10] & 1;
FLIPV= (MakerNote[10]>> 1) & 1;
BAYER_MODE=(MakerNote[10]>> 2) & 3;
COLOR_MODE=(MakerNote[10]>> 4) & 0x0f;
DCM_HOR= (MakerNote[10]>> 8) & 0x0f;
DCM_VERT= (MakerNote[10]>>12) & 0x0f;
BIN_HOR= (MakerNote[10]>>16) & 0x0f;
BIN_VERT= (MakerNote[10]>>20) & 0x0f;
info+="WOI_LEFT\t" + WOI_LEFT+"\t\t\t\n"+
"WOI_WIDTH\t"+ WOI_WIDTH+"\t\t\t\n"+
"WOI_TOP\t" + WOI_TOP+"\t\t\t\n"+
"WOI_HEIGHT\t"+ WOI_HEIGHT+"\t\t\t\n"+
"FLIP_HOR\t"+ (FLIPH!=0)+"\t\t\t\n"+
"FLIP_VERT\t"+ (FLIPV!=0)+"\t\t\t\n"+
"BAYER_MODE\t"+ BAYER_MODE+"\t\t\t\n"+
"COLOR_MODE\t"+ COLOR_MODE+"\t"+ ((COLOR_MODE==2)?"JP46":((COLOR_MODE==5)?"JP4":((COLOR_MODE==0)?"MONO":"OTHER"))) +"\t\t\n"+
"DECIM_HOR\t"+ DCM_HOR+"\t\t\t\n"+
"DECIM_VERT\t"+ DCM_VERT+"\t\t\t\n"+
"BIN_HOR\t"+ BIN_HOR+"\t\t\t\n"+
"BIN_VERT\t"+ BIN_VERT+"\t\t\t\n";
imp.setProperty("WOI_LEFT", String.format("%d",WOI_LEFT));
imp.setProperty("WOI_WIDTH", String.format("%d",WOI_WIDTH));
imp.setProperty("WOI_TOP", String.format("%d",WOI_TOP));
imp.setProperty("WOI_HEIGHT",String.format("%d",WOI_HEIGHT));
imp.setProperty("FLIPH", String.format("%d",FLIPH));
imp.setProperty("FLIPV", String.format("%d",FLIPV));
imp.setProperty("BAYER_MODE",String.format("%d",BAYER_MODE));
imp.setProperty("COLOR_MODE",((COLOR_MODE==2)?"JP46":((COLOR_MODE==5)?"JP4":((COLOR_MODE==0)?"MONO":"OTHER"))));
imp.setProperty("DCM_HOR", String.format("%d",DCM_HOR));
imp.setProperty("DCM_VERT", String.format("%d",DCM_VERT));
imp.setProperty("BIN_HOR", String.format("%d",BIN_HOR));
imp.setProperty("BIN_VERT", String.format("%d",BIN_VERT));
}
if (MakerNote.length>=14) {
info+="COMPOSITE\t" + COMPOSITE+"\t\t\t\n";
info+="ORIENTATION\t" + (PORTRAIT?"PORTRAIT":"LANDSCAPE" )+"\t\t\t\n";
info+="JPEG quality\t" + QUALITY+"\t"+((CQUALITY!=QUALITY)?("("+CQUALITY+")"):"")+"\t"+(YTABLEFORC? "Color use Y table":"")+"\t\n";
info+="Coring index\t" + CORING_INDEX_Y+"\t"+((CORING_INDEX_C!=CORING_INDEX_Y)?("("+CORING_INDEX_C+")"):"")+"\t\t\n";
imp.setProperty("COMPOSITE",String.format("%d",COMPOSITE?1:0));
imp.setProperty("ORIENTATION",(PORTRAIT?"PORTRAIT":"LANDSCAPE" ));
imp.setProperty("QUALITY",String.format("%d",QUALITY)); //not full
imp.setProperty("CORING_INDEX_Y",String.format("%d",CORING_INDEX_Y));
imp.setProperty("CORING_INDEX_C",String.format("%d",CORING_INDEX_C));
}
if (MakerNote.length>=16) {
long [] iTemps={
(MakerNote[14]>> 0) & 0xffff,
(MakerNote[14]>>16) & 0xffff,
(MakerNote[15]>> 0) & 0xffff,
(MakerNote[15]>>16) & 0xffff};
for (i=0;i<iTemps.length;i++) if (iTemps[i]!=0xffff){
double temperature=(iTemps[i]&0xfff)/16.0;
if (i==0) info+="SYSTEM TEMPERATURE\t" + temperature+"\t\t\t\n";
else info+="SFE "+i+" TEMPERATURE\t" + temperature+"\t\t\t\n";
imp.setProperty("TEMPERATURE_"+i,""+temperature);
}
}
if (COMPOSITE) {
info+="SUB_FRAMES\t- 1 -\t- 2 -\t- 3 -\t\n";
info+="HEIGHTS\t"+HEIGHT1+"\t"+HEIGHT2+"\t"+HEIGHT3+"\t\n";
info+="BLANK_ROWS\t" +BLANK1+"\t"+BLANK2+"\t\t\n";
info+="FLIPH\t"+FLIPH1+"\t"+FLIPH2+"\t"+FLIPH3+"\t\n";
info+="FLIPV\t"+FLIPV1+"\t"+FLIPV2+"\t"+FLIPV3+"\t\n";
imp.setProperty("HEIGHT1",String.format("%d",HEIGHT1));
imp.setProperty("HEIGHT2",String.format("%d",HEIGHT2));
imp.setProperty("HEIGHT3",String.format("%d",HEIGHT3));
imp.setProperty("BLANK_ROWS1",String.format("%d",BLANK1));
imp.setProperty("BLANK_ROWS2",String.format("%d",BLANK2));
imp.setProperty("FLIPH1",FLIPH1?"1":"0");
imp.setProperty("FLIPH2",FLIPH2?"1":"0");
imp.setProperty("FLIPH3",FLIPH3?"1":"0");
imp.setProperty("FLIPV1",FLIPV1?"1":"0");
imp.setProperty("FLIPV2",FLIPV2?"1":"0");
imp.setProperty("FLIPV3",FLIPV3?"1":"0");
}
if (!IS_SILENT) new TextWindow(imp.getTitle()+" info", "Parameter\tRed\tGreen(R)\tGreen(B)\tBlue",info, 400, COMPOSITE?(600):((MakerNote.length>=12)?600:160));
//tw.setLocation(0,0);
// If there are FLIPH, FLIPV - swap gains, gammas, blacks accordingly. later the images will be also flipped
if (FLIPV!=0) {
swapArrayElements (gains, 1, 3);
swapArrayElements (gains, 0, 2);
swapArrayElements (blacks, 1, 3);
swapArrayElements (blacks, 0, 2);
swapArrayElements (gammas, 1, 3);
swapArrayElements (gammas, 0, 2);
swapArrayElements (gamma_scales,1, 3);
swapArrayElements (gamma_scales,0, 2);
}
if (FLIPH!=0) {
swapArrayElements (gains, 1, 0);
swapArrayElements (gains, 3, 2);
swapArrayElements (blacks, 1, 0);
swapArrayElements (blacks, 3, 2);
swapArrayElements (gammas, 1, 0);
swapArrayElements (gammas, 3, 2);
swapArrayElements (gamma_scales,1, 0);
swapArrayElements (gamma_scales,3, 2);
}
for (i=0;i<4;i++) rgammas[i]=elphel_gamma_calc (gammas[i], blacks[i], gamma_scales[i]);
} else {
IJ.showMessage("WARNING", "MakerNote not found");
}
/**adjusting gains to have the result picture in the range 0..256 */
min_gain=2.0*gains[0];
for (i=0;i<4;i++) {
if (min_gain > gains[i]*(1.0-blacks[i])) min_gain = gains[i]*(1.0-blacks[i]);
System.out.println("gains["+i+"]="+gains[i]+" min_gain="+min_gain);
}
imp.setProperty("GAIN",String.format("%f",min_gain)); // common gain
for (i=0;i<4;i++) gains[i]/=min_gain;
for (i=0;i<4;i++) blacks256[i]=256.0*blacks[i];
for (i=0;i<4;i++) {
System.out.println("scaled gains["+i+"]="+gains[i]);
}
for (i=0;i<4;i++) {
if (MakerNote !=null) {
if (scale) satValue[i]=((rgammas[i][255])-blacks256[i])/gains[i];
else satValue[i]=((rgammas[i][255])-blacks256[i]);
} else satValue[i]=255.0;
imp.setProperty("saturation_"+i,String.format("%f",satValue[i]));
System.out.println("scaled gains["+i+"]="+gains[i]+" satValue["+i+"]="+satValue[i]);
}
// swap satValue to match FLIPH,FLIPV again
if (FLIPV!=0) {
swapArrayElements (satValue, 1, 3);
swapArrayElements (satValue, 0, 2);
}
if (FLIPH!=0) {
swapArrayElements (satValue, 1, 0);
swapArrayElements (satValue, 3, 2);
}
for (i=0;i<4;i++) {
imp.setProperty("saturation_"+i,String.format("%f",satValue[i]));
//System.out.println("saturation_"+i+"\t"+String.format("%f",satValue[i]));
}
ImageProcessor ip = imp.getProcessor();
// if (FLIPH!=0) ip.flipHorizontal(); /* To correct Bayer */
// if (FLIPV!=0) ip.flipVertical(); /* To correct Bayer */
int width = ip.getWidth();
int height = ip.getHeight();
int yb,y,xb,x,offset,nb,xbyr,ybyr;
float [] pixels = (float[])ip.getPixels();
float [][] macroblock=new float[16][16];
float [] pixels1= null;
boolean IS_JP4=(COLOR_MODE==5);
boolean IS_JP46=(COLOR_MODE==2);
if (IS_JP4) pixels1= pixels.clone(); ///JP4 mode
boolean use_imp_src= (imp_src!=null) && (imp_src.getWidth()==imp.getWidth()) && (imp_src.getHeight()==imp.getHeight());
ImageProcessor ip_src= use_imp_src? imp_src.getProcessor():ip;
if (ip_src==null) {
ip_src=ip;
use_imp_src=false;
}
for (yb=0;yb<(height>>4); yb++) for (xb=0;xb<(width>>4); xb++) { /* iterating macroblocks */
if (IS_JP4) {
for (nb=0; nb<4;nb++) {
xbyr=nb & 1;
ybyr=(nb>>1) & 1;
for (y=0;y<8;y++) {
offset=((yb<<4)+y)*width+ (nb<<3) +((xb>=(width>>5))?(((xb<<5)-width)+(width<<3)):(xb<<5));
for (x=0;x<8;x++) {
macroblock[(y<<1) | ybyr][(x<<1) | xbyr]=pixels1[offset+x];
}
}
}
} else if (IS_JP46) {
for (y=0;y<16;y++) {
offset=((yb<<4)+y)*width+(xb<<4);
for (x=0;x<16;x++) {
macroblock[((y<<1)&0xe) | ((y>>3) & 0x1)][((x<<1)&0xe) | ((x>>3) & 0x1)]=pixels[offset+x];
}
}
} else { /// mono and other non-processed
for (y=0;y<16;y++) {
offset=((yb<<4)+y)*width+(xb<<4);
for (x=0;x<16;x++) {
macroblock[y][x]=pixels[offset+x];
}
}
}
/* apply gammas here */
if (MakerNote !=null) {
if (scale) {
for (y=0;y<16;y+=2) for (x=0;x<16;x+=2) {
i=(int) macroblock[y ][x ]; if (i<0) i=0 ; else if (i>255) i=255;
macroblock[y ][x ]= (float) (((rgammas[1][i])-blacks256[1])/gains[1]);
i=(int) macroblock[y ][x+1]; if (i<0) i=0 ; else if (i>255) i=255;
macroblock[y ][x+1]= (float) (((rgammas[0][i])-blacks256[0])/gains[0]);
i=(int) macroblock[y+1][x ]; if (i<0) i=0 ; else if (i>255) i=255;
macroblock[y+1][x ]= (float) (((rgammas[3][i])-blacks256[3])/gains[3]);
i=(int) macroblock[y+1][x+1]; if (i<0) i=0 ; else if (i>255) i=255;
macroblock[y+1][x+1]= (float) (((rgammas[2][i])-blacks256[2])/gains[2]);
}
} else {
for (y=0;y<16;y+=2) for (x=0;x<16;x+=2) {
i=(int) macroblock[y ][x ]; if (i<0) i=0 ; else if (i>255) i=255;
macroblock[y ][x ]= (float) ((rgammas[1][i])-blacks256[1]);
i=(int) macroblock[y ][x+1]; if (i<0) i=0 ; else if (i>255) i=255;
macroblock[y ][x+1]= (float) ((rgammas[0][i])-blacks256[0]);
i=(int) macroblock[y+1][x ]; if (i<0) i=0 ; else if (i>255) i=255;
macroblock[y+1][x ]= (float) ((rgammas[3][i])-blacks256[3]);
i=(int) macroblock[y+1][x+1]; if (i<0) i=0 ; else if (i>255) i=255;
macroblock[y+1][x+1]= (float) ((rgammas[2][i])-blacks256[2]);
}
}
}
if (ip_src==null) System.out.println("ip_src is null");
// else if (ip_src.setf==null) System.out.println("ip_src.setf is null");
for (y=0;y<16;y++) {
offset=(yb<<4)+y;
for (x=0;x<16;x++) {
ip_src.setf((xb<<4)+ x, offset, macroblock[y][x]); // here null pointer if image was closed
}
}
}
if (FLIPH!=0) ip_src.flipHorizontal(); /* To correct Bayer */
if (FLIPV!=0) ip_src.flipVertical(); /* To correct Bayer */
/* Is it needed here ? */
/* imp.draw();
imp.show(); **/
if (use_imp_src) copyProperties (imp, imp_src);
return use_imp_src;
}
/* reverses gamma calculations in the camera
returns double[] table , in the range 0.0..255.996
*/
double [] elphel_gamma_calc (double gamma, double black, long gamma_scale) {
int i;
double x, black256 ,k;
int[] gtable = new int[257];
double[] rgtable =new double[256];
int ig;
black256=black*256.0;
k=1.0/(256.0-black256);
if (gamma < 0.13) gamma=0.13;
if (gamma >10.0) gamma=10.0;
for (i=0; i<257; i++) {
x=k*(i-black256);
if (x < 0.0 ) x=0.0;
ig= (int) (0.5+65535.0*Math.pow(x,gamma));
ig=(ig* (int) gamma_scale)/0x400;
if (ig > 0xffff) ig=0xffff;
gtable[i]=ig;
}
/* now gtable[] is the same as was used in the camera */
/* FPGA was using linear interpolation between elements of the gamma table, so now we'll reverse that process */
// double[] rgtable =new double[256];
int indx=0;
double outValue;
for (i=0; i<256; i++ ) {
outValue=128+(i<<8);
while ((gtable[indx+1]<outValue) && (indx<256)) indx++;
if (indx>=256) rgtable[i]=65535.0/256;
else if (gtable[indx+1]==gtable[indx]) rgtable[i]=i;
else rgtable[i]=indx+(1.0*(outValue-gtable[indx]))/(gtable[indx+1] - gtable[indx]);
}
return rgtable;
}
long[] readElphelMakerNote(String directory, String fileName, int len, double [] xtraExif) throws IOException {
byte [] sig= {(byte) 0x92 ,0x7c, /* MakerNote*/
0x00 ,0x04, /* type (long)*/
0x00 ,0x00 ,0x00 ,0x08 }; /* number*/
/* should always read all MakerNote - verify that format did not change (edit here when it does). */
sig[7]=(byte) (len & 0xff);
sig[6]=(byte) ((len>>8) & 0xff);
sig[5]=(byte) ((len>>16) & 0xff);
sig[4]=(byte) ((len>>24) & 0xff);
RandomAccessFile in = new RandomAccessFile(directory + fileName, "r");
byte[] head = new byte[4096]; /* just read the beginning of the file */
in.readFully(head);
in.close(); // was no close()! -? "too many open files"
if ((head[this.ExifOffset]!=0x4d) || (head[this.ExifOffset+1]!=0x4d)) {
IJ.showMessage("JP46 Reader", "Exif Header not found in " + directory + fileName);
return null;
}
/* search for MakerNote */
long [] note=getExifData (sig, head, len);
if (xtraExif!=null){
if (xtraExif.length>0){ // get exposure time
byte [] exposureTime={
(byte) 0x82,(byte) 0x9a,0x00,0x05,
0x00,0x00,0x00,0x01};
long [] nomDenom=getExifData (exposureTime, head, 2);
if (nomDenom==null) xtraExif[0]=Double.NaN;
else {
xtraExif[0]=(1.0*nomDenom[0])/nomDenom[1];
}
}
}
return note;
}
long[] readElphelMakerNoteURL(String url, int len, double [] xtraExif) throws IOException {
URL camURL = null;
URLConnection urlConn = null;
byte[] data = new byte[4096];
// System.out.println("loading exif from: " + url);
try {
camURL = new URL(url);
urlConn = camURL.openConnection();
int contentLength = 4096; /* just read the beginning of the file */ //urlConn.getContentLength();
//inStream = new InputStreamReader(urlConn.getInputStream());
int bytesRead = 0;
int offset = 0;
InputStream raw = urlConn.getInputStream();
InputStream in = new BufferedInputStream(raw);
while (offset < contentLength) {
bytesRead = in.read(data, offset, data.length - offset);
if (bytesRead == -1)
break;
offset += bytesRead;
}
in.close();
} catch(MalformedURLException e){
System.out.println("Please check the URL:" + e.toString() );
} catch(IOException e1){
System.out.println("Can't read from the Internet: "+ e1.toString() );
}
byte [] sig= {(byte) 0x92 ,0x7c, /* MakerNote*/
0x00 ,0x04, /* type (long)*/
0x00 ,0x00 ,0x00 ,0x08 }; /* number*/
/* should always read all MakerNote - verify that format did not change (edit here when it does). */
sig[7]=(byte) (len & 0xff);
sig[6]=(byte) ((len>>8) & 0xff);
sig[5]=(byte) ((len>>16) & 0xff);
sig[4]=(byte) ((len>>24) & 0xff);
//in = new RandomAccess(RandomAccessFactory.createRO(camURL), "r");
byte[] head = new byte[4096]; /* just read the beginning of the file */
head = data;
//in.readFully(head);
if ((head[this.ExifOffset] != 0x4d) || (head[this.ExifOffset+1] != 0x4d)) {
IJ.showMessage("JP46 Reader", "Exif Header not found in " + url);
return null;
}
/* search for MakerNote */
// return getExifData (sig, head, len);
long [] note=getExifData (sig, head, len);
if (xtraExif!=null){
if (xtraExif.length>0){ // get exposure time
byte [] exposureTime={
(byte) 0x82,(byte) 0x9a,0x00,0x05,
0x00,0x00,0x00,0x01};
long [] nomDenom=getExifData (exposureTime, head, 2);
if (nomDenom==null) xtraExif[0]=Double.NaN;
else {
xtraExif[0]=(1.0*nomDenom[0])/nomDenom[1];
}
}
}
return note;
}
long [] getExifData (byte [] sig, byte [] head, int len){
/* search for sig array */
int i = this.ExifOffset + 2;
boolean match=false;
for (i = this.ExifOffset + 2; i < (head.length - sig.length); i++ ) {
match=true;
for (int j=0;j<sig.length;j++)if (head[i+j]!=sig[j]){
match=false;
break;
}
if (match) break;
}
i += sig.length;
if (i >= (head.length-4)) {
/* IJ.showMessage("JP46 Reader", "MakerNote tag not found in "+directory + fileName+ ", finished at offset="+i); // re-enable with DEBUG_LEVEL*/
return null;
}
int offs=this.ExifOffset+(((head[i]<<24) & 0xff000000) |((head[i+1]<<16) & 0xff0000)| ((head[i+2]<<8) & 0xff00) | (head[i+3] & 0xff));
// IJ.showMessage("JP46 Reader Debug", "MakerNote starts at offset "+offs);
if (offs > (head.length-len) ) {
IJ.showMessage("JP46 Reader", "Error: data (i.e.MakerNote) starts too far - at offset "+offs+", while we read only "+ head.length+ "bytes");
return null;
}
long[] note=new long[len];
for (i=0; i<len; i++) note[i]=((head[offs+(i<<2)]&0xff) << 24) | ((head[offs+(i<<2)+1]&0xff) << 16) | ((head[offs+(i<<2)+2]&0xff) << 8) | (head[offs+(i<<2)+3]&0xff);
return note;
}
/* Modified from Opener.java */
ImagePlus openJpegOrGif(String dir, String name) {
ImagePlus imp = null;
Image img = Toolkit.getDefaultToolkit().createImage(dir+name);
if (img!=null) {
try {
imp = new ImagePlus(name, img);
} catch (IllegalStateException e) {
return null; // error loading image
}
if (imp.getType()==ImagePlus.COLOR_RGB) {
checkGrayJpegTo32Bits(imp);
}
IJ.showStatus("Converting to 32-bits");
new ImageConverter(imp).convertToGray32();
FileInfo fi = new FileInfo();
fi.fileFormat = FileInfo.GIF_OR_JPG;
fi.fileName = name;
fi.directory = dir;
imp.setFileInfo(fi);
}
return imp;
}
@Override
public void setTitle (String title) {
imageTitle=title;
}
@Override
public String getTitle () {
return imageTitle;
}
public void setURL (String url) {
camera_url=url;
}
public String getURL () {
return camera_url;
}
ImagePlus openJpegOrGifUsingURL (String cameraurl) {
URL url = null;
ImagePlus imp = null;
Image img = null;
/* Validate URL */
try {
url = new URL(cameraurl);
} catch (MalformedURLException e) {
System.out.println("Bad URL: " + cameraurl);
return null;
}
img = Toolkit.getDefaultToolkit().createImage(url);
if (!this.ABSOLUTELY_SILENT) System.out.println("loading image from: " + url);
// imp = new ImagePlus("test", img);
imp = new ImagePlus(imageTitle, img);
if (imp.getType() == ImagePlus.COLOR_RGB) {
checkGrayJpegTo32Bits(imp);
}
IJ.showStatus("Converting to 32-bits");
new ImageConverter(imp).convertToGray32();
FileInfo fi = new FileInfo();
fi.fileFormat = FileInfo.GIF_OR_JPG;
fi.fileName = "aquired from camera";
fi.directory = cameraurl;
imp.setFileInfo(fi);
return imp;
}
public static void checkGrayJpegTo32Bits(ImagePlus imp) {
ImageProcessor ip = imp.getProcessor();
int width = ip.getWidth();
int height = ip.getHeight();
int[] pixels = (int[])ip.getPixels();
int c,r,g,b,offset;
for (int y=0; y<(height-8); y++) {
offset = y*width;
for (int x=0; x<(width-8); x++) {
c = pixels[offset+x];
r = (c&0xff0000)>>16;
g = (c&0xff00)>>8;
b = c&0xff;
if (!((r==g)&&(g==b))) {
IJ.error("Warning: color image");
return;
}
}
}
IJ.showStatus("Converting to 32-bits");
new ImageConverter(imp).convertToGray32();
}
/* =====Other methods =================================================================== */
/* ======================================================================== */
public void listImageProperties (ImagePlus imp) {
listImageProperties (imp,false);
}
public void listImageProperties (ImagePlus imp, boolean toConsole) {
StringBuffer sb = new StringBuffer();
Set<Object> jp4_set;
Properties jp4_prop;
Iterator<Object> itr;
String str;
jp4_prop=imp.getProperties();
if (jp4_prop!=null) {
jp4_set=jp4_prop.keySet();
itr=jp4_set.iterator();
while(itr.hasNext()) {
str = (String) itr.next();
sb.append(str+"\t"+jp4_prop.getProperty(str)+"\n");
// System.out.println(str + "=\t" +jp4_prop.getProperty(str));
}
}
if (toConsole){
System.out.println(imp.getTitle()+" properties\n"+sb.toString());
} else {
new TextWindow(imp.getTitle()+" properties", "name\tvalue", sb.toString(),400,800);
}
}
/* ======================================================================== */
public double fracOverExposed(double [] map, // map of overexposed pixels 0.0 - 0K, >0 (==1.0) - overexposed
int mapWidth, // width of the map
int x0, // X of the top left corner of the selection
int y0, // Y of the top left corner of the selection
int width, // selection width
int height){ // selection height
int index,i,j;
int y1=y0+height;
int over=0;
for (i=y0;i<y1;i++) {
index=i*mapWidth+x0;
for (j=0;j<width;j++) if (map[index++]>0.0) over++;
}
return (1.0*over)/width/height;
}
// returns 1.0 if there is overexposed pixel, 0.0 - if OK
/* ======================================================================== */
public double [] overexposedMap (ImagePlus imp) {
return overexposedMap (imp, 0.999);
}
public double [] overexposedMap (ImagePlus imp, double relativeThreshold) {
double [] satValues=new double[4];
boolean noProperties=false;
int i,j,index;
for (i=0;i<4;i++) {
//protect from Double.valueOf(null), move to a function
if (imp.getProperty("saturation_"+i)!=null) satValues[i]= Double.valueOf((String) imp.getProperty("saturation_"+i)).doubleValue();
else {
noProperties=true;
break;
}
}
if (noProperties) return null;
//0 - red, 1,2 - green (use Math.min()), 3 - blue
for (i=0;i<4;i++) satValues[i]*=relativeThreshold;
ImageProcessor ip=imp.getProcessor();
int width=imp.getWidth();
float []pixels=(float[]) ip.getPixels();
double [] overexposed= new double [pixels.length];
for (index=0;index<overexposed.length;index++){
i=(index / width) % 2;
j=1-((index % width) % 2);
overexposed[index]=(pixels[index]>=satValues[i*2+j])?1.0:0.0;
}
return overexposed;
}
public ImagePlus demuxImageOrClone(ImagePlus imp, int numImg) {
ImagePlus imp_new=demuxImage(imp, numImg);
if (imp_new!=null) return imp_new;
return demuxClone(imp);
}
public ImagePlus demuxClone(ImagePlus imp) {
ImageProcessor ip=imp.getProcessor().duplicate();
ImagePlus imp_new=new ImagePlus(imp.getTitle()+"-dup",ip);
Set<Object> jp4_set;
Properties jp4_prop;
Iterator<Object> itr;
String str;
jp4_prop=imp.getProperties();
if (jp4_prop!=null) {
jp4_set=jp4_prop.keySet();
itr=jp4_set.iterator();
while(itr.hasNext()) {
str = (String) itr.next();
imp_new.setProperty(str,jp4_prop.getProperty(str));
}
}
return imp_new;
}
public ImagePlus demuxImage(ImagePlus imp, int numImg) {
int width= imp.getWidth();
// int height=imp.getHeight();
int FLIPGV,FLIPGH;
int [] FLIPV= new int[3];
int [] FLIPH= new int[3];
int [] HEIGHTS=new int[3];
int [] BLANKS= new int[2];
Object timestamp=null;
if (imp.getProperty("FLIPV")!=null) FLIPGV= Integer.valueOf((String) imp.getProperty("FLIPV")).intValue(); else return null;
if (imp.getProperty("FLIPH")!=null) FLIPGH= Integer.valueOf((String) imp.getProperty("FLIPH")).intValue(); else return null;
int i;
for (i=1;i<=3;i++) {
if (imp.getProperty("FLIPV"+i)!=null) FLIPV[i-1]= Integer.valueOf((String) imp.getProperty("FLIPV"+i)).intValue(); else return null;
if (imp.getProperty("FLIPH"+i)!=null) FLIPH[i-1]= Integer.valueOf((String) imp.getProperty("FLIPH"+i)).intValue(); else return null;
if (imp.getProperty("HEIGHT"+i)!=null) HEIGHTS[i-1]= Integer.valueOf((String) imp.getProperty("HEIGHT"+i)).intValue(); else return null;
}
for (i=1;i<=2;i++) {
if (imp.getProperty("BLANK_ROWS"+i)!=null) BLANKS[i-1]= Integer.valueOf((String) imp.getProperty("BLANK_ROWS"+i)).intValue(); else return null;
}
timestamp=imp.getProperty("timestamp");
if (timestamp!=null);
/*
System.out.println("FLIPV="+FLIPGV+" FLIPH="+FLIPGH);
for (i=0;i<3;i++) System.out.println("FLIPV["+i+"]= "+FLIPV[i]+" FLIPH["+i+"]= "+FLIPH[i]);
for (i=0;i<3;i++) System.out.println("HEIGHTS["+i+"]="+HEIGHTS[i]);
for (i=0;i<2;i++) System.out.println("BLANKS["+i+"]= "+BLANKS[i]);
*/
Rectangle [] r = new Rectangle[3];
r[0]=new Rectangle(0, 0, width,HEIGHTS[0]);
r[1]=new Rectangle(0, HEIGHTS[0]+BLANKS[0], width,HEIGHTS[1]);
r[2]=new Rectangle(0, HEIGHTS[0]+BLANKS[0]+HEIGHTS[1]+BLANKS[1],width,HEIGHTS[2]);
// assuming that (HEIGHTS[1]==0) && (HEIGHTS[2]!=0) == false
if (FLIPGV!=0){
if (HEIGHTS[1]>0) {
if (HEIGHTS[2]>0) {
Rectangle r_tmp=r[0];
r[0]=r[2];
r[2]=r_tmp;
} else {
Rectangle r_tmp=r[0];
r[0]=r[1];
r[1]=r_tmp;
}
}
}
if (FLIPGV>0) for (i=0;i<3;i++) FLIPV[i]=1-FLIPV[i];
if (FLIPGH>0) for (i=0;i<3;i++) FLIPH[i]=1-FLIPH[i];
// for (i=0;i<3;i++) System.out.println("Final: FLIPV["+i+"]= "+FLIPV[i]+" FLIPH["+i+"]= "+FLIPH[i]);
// if needed, we'll cut one pixel line. later can modify to add one extra, but then we need to duplicate the pre-last one (same Bayer),
// not just add zeros - later before sliding FHT the two border lines are repeated for 16 times to reduce border effects.
for (i=0;i<3;i++) {
// System.out.println("before r["+i+"].x= "+r[i].x+" r["+i+"].width= "+r[i].width);
// System.out.println("before r["+i+"].y= "+r[i].y+" r["+i+"].height= "+r[i].height);
if (((r[i].height & 1)==0 ) & (((r[i].y+FLIPV[i])&1)!=0)) r[i].height-=2;
r[i].height &=~1;
if (((r[i].y+FLIPV[i])&1)!=0) r[i].y+=1;
if (((r[i].width & 1)==0 ) & (((r[i].x+FLIPH[i])&1)!=0)) r[i].width-=2;
r[i].width &=~1;
if (((r[i].x+FLIPH[i])&1)!=0) r[i].x+=1;
// System.out.println("after r["+i+"].x= "+r[i].x+" r["+i+"].width= "+r[i].width);
// System.out.println("after r["+i+"].y= "+r[i].y+" r["+i+"].height= "+r[i].height);
}
if (r[numImg].height<=0) return null;
// ImageProcessor ip=imp.getProcessor();
// ip.setRoi(r[numImg]);
// ImageProcessor ip_individual=ip.crop().duplicate(); //java.lang.NegativeArraySizeException
/*
* When using in multithreaded with (probably) the same composite image
Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970912
at ij.process.FloatProcessor.crop(FloatProcessor.java:706)
at JP46_Reader_camera.demuxImage(JP46_Reader_camera.java:1104)
at CalibrationHardwareInterface$CamerasInterface$4.run(CalibrationHardwareInterface.java:1101)
*/
// ImageProcessor ip=imp.getProcessor();
// ip.setRoi(r[numImg]);
ImageProcessor ip_individual=imp.getProcessor().duplicate(); //java.lang.NegativeArraySizeException
ip_individual.setRoi(r[numImg]);
ip_individual=ip_individual.crop();
if (FLIPH[numImg]!=0) ip_individual.flipHorizontal();
if (FLIPV[numImg]!=0) ip_individual.flipVertical();
ImagePlus imp_result=new ImagePlus(imp.getTitle()+"-"+numImg,ip_individual);
//copy all defined properties of the composite image
Set<Object> jp4_set;
Properties jp4_prop;
Iterator<Object> itr;
String str;
jp4_prop=imp.getProperties();
if (jp4_prop!=null) {
jp4_set=jp4_prop.keySet();
itr=jp4_set.iterator();
while(itr.hasNext()) {
str = (String) itr.next();
imp_result.setProperty(str,jp4_prop.getProperty(str));
}
}
// Replaced by copying all properties from the composite image
/*
for (i=0;i<4;i++) {
//protect from Double.valueOf(null), move to a function
if (imp.getProperty("saturation_"+i)!=null) {
imp_result.setProperty("saturation_"+i, imp.getProperty("saturation_"+i));
}
}
if (timestamp!=null)imp_result.setProperty("timestamp", timestamp);
*/
// fill in meta data
return imp_result;
}
public void copyProperties (ImagePlus imp_src,ImagePlus imp_dst){
// copy all the properties to the new image
Set<Object> set;
Properties prop;
Iterator<Object> itr;
String str;
prop=imp_src.getProperties();
if (prop!=null) {
set=prop.keySet();
itr=set.iterator();
while(itr.hasNext()) {
str = (String) itr.next();
imp_dst.setProperty(str,prop.getProperty(str));
}
}
}
public ImagePlus encodeProperiesToInfo(ImagePlus imp){
String info="<?xml version=\"1.0\" encoding=\"UTF-8\"?><properties>";
Set<Object> jp4_set;
Properties jp4_prop;
Iterator<Object> itr;
String str;
jp4_prop=imp.getProperties();
if (jp4_prop!=null) {
jp4_set=jp4_prop.keySet();
itr=jp4_set.iterator();
while(itr.hasNext()) {
str = (String) itr.next();
// if (!str.equals("Info")) info+="<"+str+">\""+jp4_prop.getProperty(str)+"\"</"+str+">";
if (!str.equals("Info")) info+="<"+str+">"+jp4_prop.getProperty(str)+"</"+str+">";
}
}
info+="</properties>\n";
imp.setProperty("Info", info);
return imp;
}
public boolean decodeProperiesFromInfo(ImagePlus imp){
if (imp.getProperty("Info")==null) return false;
String xml= (String) imp.getProperty("Info");
DocumentBuilder db=null;
try {
db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
} catch (ParserConfigurationException e) {
return false;
}
InputSource is = new InputSource();
is.setCharacterStream(new StringReader(xml));
Document doc = null;
try {
doc = db.parse(is);
} catch (SAXException e) {
return false;
} catch (IOException e) {
return false;
}
NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
for (int i=0;i<allNodes.getLength();i++) {
String name= allNodes.item(i).getNodeName();
String value=allNodes.item(i).getFirstChild().getNodeValue();
imp.setProperty(name, value);
}
return true;
}
/**
* Main method for debugging.
*
* For debugging, it is convenient to have a method that starts ImageJ, loads an
* image and calls the plugin, e.g. after setting breakpoints.
* Grabbed from https://github.com/imagej/minimal-ij1-plugin
* @param args unused
*/
public static void main(String[] args) {
// set the plugins.dir property to make the plugin appear in the Plugins menu
Class<?> clazz = Aberration_Calibration.class;
String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();
String pluginsDir = url.substring(5, url.length() - clazz.getName().length() - 6);
System.setProperty("plugins.dir", pluginsDir);
// start ImageJ
new ImageJ();
// run the plugin
IJ.runPlugIn(clazz.getName(), "");
}
}