package com.elphel.imagej.calibration.hardware;
import java.io.IOException;
import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.Properties;
import java.util.Set;
import java.util.concurrent.atomic.AtomicInteger;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import org.apache.commons.io.IOUtils;
import org.w3c.dom.Document;
import org.xml.sax.SAXException;
//import org.xml.sax.SAXParseException;
import com.elphel.imagej.calibration.MatchSimulatedPattern;
import com.elphel.imagej.calibration.UVLEDandLasers;
import com.elphel.imagej.common.WindowTools;
import com.elphel.imagej.jp4.JP46_Reader_camera;
import ij.IJ;
import ij.ImagePlus;
import ij.Prefs;
import ij.gui.GenericDialog;
import ij.io.FileSaver;
import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
public class CamerasInterface{
// JP46_Reader_camera JP4_INSTANCE= new JP46_Reader_camera(false);
public LaserPointersHardware laserPointers=null;
private int masterSubCamera=0; // "master" camera index of IP in the list
private int masterPort= 0; // "master" camera port (0..3) to apply trigger to
private JP46_Reader_camera [] jp4_Instances=null;
private String [] resetURLs=null;
private String [] imageURLs=null;
private String [] metaURLs=null;
private String triggerURL="";
private boolean [] flipImages=null;
private ImagePlus [] images= null; // to reuse same instances
private ImagePlus [] imagesIP= null;
// TODO: when saving/restoring save cameraSubnet, iBaseIP, cameraIPs, so any IPs are OK through config, generate - sequential
private String cameraSubnet="192.168.0.";
private int iBaseIP=236;
private String [] cameraIPs = null; // since nc393 port is a part of cameraIPs[]
private int [] channelIPPort = null; // index in camareIPs (each IP/port combination) for each individual sensor
private int imgsrvPort=8081;
private String resetURLcmd="towp/save/pointers"; // advance buffer, next time will wait for the next frame acquired
// will return XML, just "trig" - 1x1 GIF
private String triggerURLcmd="trig/pointers"; // TRIG=4 should be set in advance, this command will set in single-shot trigger mode
private String imageURLcmd="torp/wait/bimg"; // will wait if needed. If repeated (as when reading Exif)- won't wait
private String metaURLcmd="torp/wait/meta"; // will get XML, including timestamp
private String lastTimestamp="";
public int debugLevel=2;
private double lastTemperature=Double.NaN;
private int colorMode=5; // JP4
private boolean noWait= true; // when false, IRQ_SMART=3 and the frame is available only 1 frame later, when true IRQ_SMART=6, frame is available after compression end
private boolean nc393 = false;
private int debugSensorNumber=-1; // increase debug level for this particular sensor
private int JPEGquality=99; // JPEG quality
private boolean cameraAutoExposure = false;
private boolean cameraAutoWhiteBalance =false;
private String cameraExtraURLCommon = ""; // (should start with "&")
private boolean setupTriggerMode= false;
private boolean externalTriggerCabling=false;
private boolean noCabling= false; // for single camera
private double cameraExposure= 5.0;
private double scaleExposureForLasers= 0.4;
private double scaleExposureForHeadLasers= 0.05;
private double cameraAutoExposureMax= 30.0; //Maximal autoexposure value
private double cameraGain = 2.0;
private double cameraRScale =1.25;
private double cameraBScale =1.5;
private double cameraGScale =1.0;
private double [] cameraExposureCorr=null; // per-camera exposure correction1
private double [] cameraGainCorr = null; // per-camera gain correction;
private double [] cameraRScaleCorr = null; // per-camera R/G scale correction;
private double [] cameraBScaleCorr = null; // per-camera B/G scale correction;
private double [] cameraGScaleCorr = null; // per-camera GB/G scale correction;
private String [] cameraExtraURL = null; // per-camera extra URL (should start with "&")
// these are initialized after being null, when the cameras are probed
private int [] cameraFrameNumber=null;
private boolean [] triggeredMode= null; // true - triggered, false - free running
private boolean [][] sensorPresent= null; // probe which sensors (of 3) are detected per system board (NC393 - per board/port)
// TODO - try if skipping setting TRIG_PERIOD=0, IRQ_SMART=6 (when they are already set) will fix hanging
private int [] triggerPeriod= null;
private int [] cameraMasterPort= null;
private int [] irqSmart= null;
private int [] motorsPosition= null; // motors steps when the images were acquired (for null)
private long startTime=System.nanoTime();
private long lastTime=startTime;
private long thisTime=startTime;
public boolean reportTiming=false;
public int cameraBootTimeSeconds=100;
public int connectionTimeoutMilliseconds=3000;
public boolean is_10398 = false;
private void printTiming(String title){
if (this.reportTiming) {
this.thisTime=System.nanoTime();
System.out.println(title+ " done at "+IJ.d2s(0.000000001*(this.thisTime-this.startTime),3)+
" (+"+IJ.d2s(0.000000001*(this.thisTime-this.lastTime),3)+") sec");
this.lastTime=this.thisTime;
}
}
private void printTimingInit(){
this.startTime=System.nanoTime();
this.lastTime=this.startTime;
this.thisTime=this.startTime;
}
private int [][] channelMap_23_393={ // ip index, channel number, port
{0,0,3},{0,0,2},{0,0,0},{0,0,1},{1,0,3},{1,0,2},{1,0,0},{1,0,1},
{0,1,3},{0,1,2},{0,1,0},{0,1,1},{1,1,3},{1,1,2},{1,1,0},{1,1,1},
{0,2,3},{0,2,2},{0,2,0},{0,2,1},{1,2,3},{1,2,2},{1,2,0},{1,2,1},
{2,0,2},{2,0,3}};
private int [][] channelMap21={ // ip index, channel number
{0,1,0},{0,0,0},{0,2,0},
{1,1,0},{1,0,0},{1,2,0},
{2,1,0},{2,0,0},{2,2,0},
{3,1,0},{3,0,0},{3,2,0},
{4,1,0},{4,0,0},{4,2,0},
{5,1,0},{5,0,0},{5,2,0},
{6,1,0},{6,0,0},{6,2,0}};
private int [][] channelMap1={ // ip index, channel number
// {0,-1}}; // negative channel - single camera
{0,0,0}}; // Try with 0
private int [][] channelMap2={ // ip index, channel number
{0,0,0},{0,1,0}};
private int [][] channelMap3={ // ip index, channel number
// {0,-1}}; // negative channel - single camera
{0,0,0},{1,0,0},{2,0,0}};
private int [][] channelMap=null;
public int maxNumberOfThreads=100;
/**
* Initialize JP46_Reader_camera instances, one per sub-camera
*/
public CamerasInterface(int size, LaserPointersHardware laserPointers){
this.laserPointers=laserPointers;
initDefaultMap(size);
initIPs();
initJP4();
initCamParsDefaultArrays(this.cameraIPs.length);
}
public CamerasInterface(int size){
initDefaultMap(size);
initIPs();
initJP4();
initCamParsDefaultArrays(this.cameraIPs.length);
}
public void setNumberOfThreads(int n){
this.maxNumberOfThreads=n;
}
public int getSubCamera (int channelNumber){
return ((channelNumber>=0)&& (channelNumber<this.channelMap.length))?this.channelMap[channelNumber][0]:-1;
}
public int getSubChannel (int channelNumber){
return ((channelNumber>=0)&& (channelNumber<this.channelMap.length))?this.channelMap[channelNumber][1]:-1;
}
public int getSensorPort (int channelNumber){
return ((channelNumber>=0)&& (channelNumber<this.channelMap.length))?this.channelMap[channelNumber][2]:-1;
}
public boolean is14Mpix() {
return this.is_10398;
}
// not used anywhere
public int getChannel (int subCam, int subChn){
return getChannel (subCam, subChn, 0); // for compatibility with 353
}
public int getChannel (int subCam, int subChn, int port){
for (int channelNumber=0;channelNumber<this.channelMap.length;channelNumber++)
if ((this.channelMap[channelNumber][0]==subCam) &&
(this.channelMap[channelNumber][1]==subChn) &&
(this.channelMap[channelNumber][2]==port)) return channelNumber;
return -1;
}
private void initJP4(){
this.jp4_Instances=new JP46_Reader_camera[this.cameraIPs.length];
this.resetURLs=new String [this.cameraIPs.length];
this.imageURLs=new String [this.cameraIPs.length];
this.metaURLs= new String [this.cameraIPs.length];
// this.triggerURL is already defined
// this.triggerURL="http://"+this.cameraIPs[this.masterSubCamera]+":"+(this.imgsrvPort+this.masterPort)+"/"+triggerURLcmd;
this.images= new ImagePlus[this.channelMap.length];
this.imagesIP= new ImagePlus[this.cameraIPs.length];
for (int i=0; i<this.cameraIPs.length;i++){
this.jp4_Instances[i]=new JP46_Reader_camera(false);// invisible
// this.jp4_Instances[i].camera_url="http://"+this.cameraIPs[i]+":"+this.imgsrvPort+"/";
this.jp4_Instances[i].camera_url="http://"+this.cameraIPs[i]+"/";
this.jp4_Instances[i].camera_img= this.imageURLcmd; // not currently used
this.jp4_Instances[i].camera_img_new=this.imageURLcmd; //"torp/wait/" will survive, only "towp/wait/" is removed for Exif re-read
this.jp4_Instances[i].ABSOLUTELY_SILENT=true;
// this.resetURLs[i]="http://"+this.cameraIPs[i]+":"+this.imgsrvPort+"/"+resetURLcmd;
// this.imageURLs[i]="http://"+this.cameraIPs[i]+":"+this.imgsrvPort+"/"+this.imageURLcmd;
// this.metaURLs[i]= "http://"+this.cameraIPs[i]+":"+this.imgsrvPort+"/"+metaURLcmd;
this.resetURLs[i]="http://"+this.cameraIPs[i]+"/"+resetURLcmd;
this.imageURLs[i]="http://"+this.cameraIPs[i]+"/"+this.imageURLcmd;
this.metaURLs[i]= "http://"+this.cameraIPs[i]+"/"+metaURLcmd;
this.imagesIP[i]= null;
}
for (int i=0; i<this.images.length;i++) this.images[i]= null;
}
private void initCamParsDefaultArrays(int num){
this.cameraExposureCorr=new double[num];
this.cameraGainCorr= new double[num];
this.cameraRScaleCorr= new double[num];
this.cameraBScaleCorr= new double[num];
this.cameraGScaleCorr= new double[num];
this.cameraExtraURL= new String[num];
for (int i=0; i<num;i++){
this.cameraExposureCorr[i]=1.0;
this.cameraGainCorr[i]= 1.0;
this.cameraRScaleCorr[i]= 1.0;
this.cameraBScaleCorr[i]= 1.0;
this.cameraGScaleCorr[i]= 1.0;
this.cameraExtraURL[i]= "";
}
}
/**
* Initialize cameraIPs from subNet and baseIP (sequentially)
*/
private void initIPs(){
ArrayList<Integer> ip_ports_list= new ArrayList<Integer>();
for (int i=0;i<this.channelMap.length;i++) {
Integer ip_port=(this.channelMap[i][0]<<2) + this.channelMap[i][2];
if (!ip_ports_list.contains(ip_port)) ip_ports_list.add(ip_port);
}
Collections.sort(ip_ports_list);
this.cameraIPs = new String [ip_ports_list.size()];
this.channelIPPort = new int [this.channelMap.length];
for (int i = 0; i<this.cameraIPs.length; i++){
int ip_index= ip_ports_list.get(i)>>2;
int sensor_port = ip_ports_list.get(i) & 3;
this.cameraIPs[i] = this.cameraSubnet+(this.iBaseIP + ip_index) + ":"+ (this.imgsrvPort+sensor_port);
for (int j = 0; j<this.channelMap.length; j++){
if ((this.channelMap[j][0] == ip_index) && (this.channelMap[j][2] == sensor_port)) {
this.channelIPPort[j] = i;
}
}
}
this.triggerURL="http://"+this.cameraSubnet+(this.iBaseIP+this.masterSubCamera)+":"+
(this.imgsrvPort+ (this.masterPort & 3))+"/"+triggerURLcmd;
if (this.debugLevel>2) System.out.println("DEBUG393: initIPs(): this.triggerURL ="+this.triggerURL);
}
/*
//pre nc393
private void initIPs(){
if (this.debugLevel>2) System.out.println("initIPs(): this.iBaseIP=" + this.iBaseIP );
int size=0;
for (int i=0;i<this.channelMap.length;i++) if (this.channelMap[i][0]>size) size=this.channelMap[i][0];
size++;
this.cameraIPs=new String [size];
for (int i=0;i<size;i++) this.cameraIPs[i]=this.cameraSubnet+(this.iBaseIP+i);
// this.masterSubCamera=0;
}
*/
/**
* Initialize default subcamera map
* @param size number of subcameras
*/
private void initDefaultMap(int size){
this.channelMap=new int [size][];
this.flipImages=new boolean[size];
int []port_seq={1,0,2,3};
this.masterSubCamera=0;
this.masterPort=0;
if (this.nc393){
this.imgsrvPort=2323;
this.resetURLcmd="towp/save/pointers"; // advance buffer, next time will wait for the next frame acquired
this.imageURLcmd="torp/wait/timestamp_name/bimg"; // will wait if needed. If repeated (as when reading Exif)- won't wait
this.metaURLcmd="torp/wait/meta"; // will get XML, including timestamp
if (size == 26) {
for (int i=0;i<size;i++){
this.channelMap[i]=channelMap_23_393[i].clone();
this.flipImages[i]=false;
}
this.masterSubCamera = 2;
this.masterPort=2;
} else for (int i=0;i<size;i++){
this.flipImages[i]=false;
this.channelMap[i]=new int[3];
this.channelMap[i][0]= i >> 2;
this.channelMap[i][1]= 0;
if (size <4) {
this.channelMap[i][2]= i;
} else {
this.channelMap[i][2]= port_seq[i & 3];
}
}
} else {
if (size==1) { // single camera - old lens focusing
this.channelMap[0]=channelMap1[0].clone();
this.flipImages[0]=true;
} else if (size==2){ // New lens focusing machine
this.channelMap[0]=channelMap2[0].clone();
this.flipImages[0]=true; // main sensor under test
this.channelMap[1]=channelMap2[1].clone();
this.flipImages[1]=false; // extra sensor for location
} else if (size==3){
for (int i=0;i<size;i++){
this.flipImages[i]=false;
int i0=((i>=this.channelMap3.length)?(this.channelMap3.length-1):i);
// this.channelMap[i]=this.channelMap21[i0].clone();
this.channelMap[i]=this.channelMap3[i0].clone();
}
} else for (int i=0;i<size;i++){
this.flipImages[i]=false;
int i0=((i>=this.channelMap21.length)?(this.channelMap21.length-1):i);
this.channelMap[i]=this.channelMap21[i0].clone();
}
}
}
public void setProperties(String prefix,Properties properties){
properties.setProperty(prefix+"cameraSubnet",this.cameraSubnet);
properties.setProperty(prefix+"iBaseIP",this.iBaseIP+"");
properties.setProperty(prefix+"masterSubCamera",this.masterSubCamera+"");
properties.setProperty(prefix+"masterPort",this.masterPort+"");
properties.setProperty(prefix+"cameraBootTimeSeconds",this.cameraBootTimeSeconds+"");
properties.setProperty(prefix+"connectionTimeoutMilliseconds",this.connectionTimeoutMilliseconds+"");
properties.setProperty(prefix+"imgsrvPort",this.imgsrvPort+"");
properties.setProperty(prefix+"resetURLcmd",this.resetURLcmd);
properties.setProperty(prefix+"triggerURLcmd",this.triggerURLcmd);
properties.setProperty(prefix+"imageURLcmd",this.imageURLcmd);
properties.setProperty(prefix+"metaURLcmd",this.metaURLcmd);
properties.setProperty(prefix+"channelMap.length",this.channelMap.length+"");
for (int i=0;i<this.channelMap.length;i++) {
properties.setProperty(prefix+"channelMap_"+i+"_IPindex", this.channelMap[i][0]+"");
properties.setProperty(prefix+"channelMap_"+i+"_subchannel",this.channelMap[i][1]+"");
properties.setProperty(prefix+"channelMap_"+i+"_port", this.channelMap[i][2]+"");
properties.setProperty(prefix+"flipImages_"+i ,this.flipImages[i]?"1":"0");
}
properties.setProperty(prefix+"cameraIPs.length",this.cameraIPs.length+"");
properties.setProperty(prefix+"colorMode",this.colorMode+"");
properties.setProperty(prefix+"noWait",this.noWait+"");
properties.setProperty(prefix+"nc393",this.nc393+"");
properties.setProperty(prefix+"debugSensorNumber",this.debugSensorNumber+"");
properties.setProperty(prefix+"JPEGquality",this.JPEGquality+"");
properties.setProperty(prefix+"cameraAutoExposure",this.cameraAutoExposure+"");
properties.setProperty(prefix+"cameraAutoWhiteBalance",this.cameraAutoWhiteBalance+"");
properties.setProperty(prefix+"cameraExtraURLCommon","<![CDATA["+this.cameraExtraURLCommon+"]]>");
properties.setProperty(prefix+"setupTriggerMode",this.setupTriggerMode+"");
properties.setProperty(prefix+"externalTriggerCabling",this.externalTriggerCabling+"");
properties.setProperty(prefix+"noCabling",this.noCabling+"");
properties.setProperty(prefix+"cameraExposure",this.cameraExposure+"");
properties.setProperty(prefix+"scaleExposureForLasers",this.scaleExposureForLasers+"");
properties.setProperty(prefix+"scaleExposureForHeadLasers",this.scaleExposureForHeadLasers+"");
properties.setProperty(prefix+"cameraAutoExposureMax",cameraAutoExposureMax+"");
properties.setProperty(prefix+"cameraGain",this.cameraGain+"");
properties.setProperty(prefix+"cameraRScale",this.cameraRScale+"");
properties.setProperty(prefix+"cameraBScale",this.cameraBScale+"");
properties.setProperty(prefix+"cameraGScale",this.cameraGScale+"");
for (int i=0;i<this.cameraIPs.length;i++){
properties.setProperty(prefix+"cameraIPs_"+i,this.cameraIPs[i]+"");
properties.setProperty(prefix+"cameraExposureCorr_"+i,this.cameraExposureCorr[i]+"");
properties.setProperty(prefix+"cameraGainCorr_"+i, this.cameraGainCorr[i]+"");
properties.setProperty(prefix+"cameraRScaleCorr_"+i, this.cameraRScaleCorr[i]+"");
properties.setProperty(prefix+"cameraBScaleCorr_"+i, this.cameraBScaleCorr[i]+"");
properties.setProperty(prefix+"cameraGScaleCorr_"+i, this.cameraGScaleCorr[i]+"");
properties.setProperty(prefix+"cameraExtraURL_"+i, "<![CDATA["+this.cameraExtraURL[i]+"]]>");
}
}
public void getProperties(String prefix,Properties properties){
if (properties.getProperty(prefix+"channelMap.length")!=null) {
// next initializes default values, so it should be before reading them from saved properties
initDefaultMap (Integer.parseInt(properties.getProperty(prefix+"channelMap.length")));
this.flipImages=new boolean[this.channelMap.length];
for (int i=0;i<this.channelMap.length;i++) {
if (properties.getProperty(prefix+"channelMap_"+i+"_IPindex")!=null)
this.channelMap[i][0]=Integer.parseInt(properties.getProperty(prefix+"channelMap_"+i+"_IPindex"));
if (properties.getProperty(prefix+"channelMap_"+i+"_subchannel")!=null)
this.channelMap[i][1]=Integer.parseInt(properties.getProperty(prefix+"channelMap_"+i+"_subchannel"));
if (properties.getProperty(prefix+"channelMap_"+i+"_port")!=null)
this.channelMap[i][2]=Integer.parseInt(properties.getProperty(prefix+"channelMap_"+i+"_port"));
if (properties.getProperty(prefix+"flipImages_"+i)!=null)
this.flipImages[i]=(Integer.parseInt(properties.getProperty(prefix+"flipImages_"+i))>0);
}
}
int numCams=0;
if (properties.getProperty(prefix+"cameraIPs.length")!=null) {
numCams=Integer.parseInt(properties.getProperty(prefix+"cameraIPs.length"));
this.cameraIPs=new String[numCams];
for (int i=0;i<numCams;i++) {
if (properties.getProperty(prefix+"cameraIPs_"+i)!=null)
this.cameraIPs[i]=properties.getProperty(prefix+"cameraIPs_"+i);
}
}
initCamParsDefaultArrays(numCams);
if (properties.getProperty(prefix+"cameraSubnet")!=null)
this.cameraSubnet=properties.getProperty(prefix+"cameraSubnet");
if (properties.getProperty(prefix+"iBaseIP")!=null)
this.iBaseIP=Integer.parseInt(properties.getProperty(prefix+"iBaseIP"));
if (properties.getProperty(prefix+"masterSubCamera")!=null)
this.masterSubCamera=Integer.parseInt(properties.getProperty(prefix+"masterSubCamera"));
if (properties.getProperty(prefix+"masterPort")!=null)
this.masterPort=Integer.parseInt(properties.getProperty(prefix+"masterPort"));
if (properties.getProperty(prefix+"cameraBootTimeSeconds")!=null)
this.cameraBootTimeSeconds=Integer.parseInt(properties.getProperty(prefix+"cameraBootTimeSeconds"));
if (properties.getProperty(prefix+"connectionTimeoutMilliseconds")!=null)
this.connectionTimeoutMilliseconds=Integer.parseInt(properties.getProperty(prefix+"connectionTimeoutMilliseconds"));
if (properties.getProperty(prefix+"imgsrvPort")!=null)
this.imgsrvPort=Integer.parseInt(properties.getProperty(prefix+"imgsrvPort"));
if (properties.getProperty(prefix+"resetURLcmd")!=null)
this.resetURLcmd=properties.getProperty(prefix+"resetURLcmd");
if (properties.getProperty(prefix+"triggerURLcmd")!=null)
this.triggerURLcmd=properties.getProperty(prefix+"triggerURLcmd");
if (properties.getProperty(prefix+"imageURLcmd")!=null)
this.imageURLcmd=properties.getProperty(prefix+"imageURLcmd");
if (properties.getProperty(prefix+"metaURLcmd")!=null)
this.metaURLcmd=properties.getProperty(prefix+"metaURLcmd");
// both defaults were here
if (properties.getProperty(prefix+"colorMode")!=null)
this.colorMode=Integer.parseInt(properties.getProperty(prefix+"colorMode"));
if (properties.getProperty(prefix+"debugSensorNumber")!=null)
this.debugSensorNumber=Integer.parseInt(properties.getProperty(prefix+"debugSensorNumber"));
if (properties.getProperty(prefix+"JPEGquality")!=null)
this.JPEGquality=Integer.parseInt(properties.getProperty(prefix+"JPEGquality"));
if (properties.getProperty(prefix+"noWait")!=null)
this.noWait=Boolean.parseBoolean(properties.getProperty(prefix+"noWait"));
if (properties.getProperty(prefix+"nc393")!=null)
this.nc393=Boolean.parseBoolean(properties.getProperty(prefix+"nc393"));
if (properties.getProperty(prefix+"cameraAutoExposure")!=null)
this.cameraAutoExposure=Boolean.parseBoolean(properties.getProperty(prefix+"cameraAutoExposure"));
if (properties.getProperty(prefix+"cameraAutoWhiteBalance")!=null)
this.cameraAutoWhiteBalance=Boolean.parseBoolean(properties.getProperty(prefix+"cameraAutoWhiteBalance"));
if (properties.getProperty(prefix+"cameraExtraURLCommon")!=null) {
this.cameraExtraURLCommon=properties.getProperty(prefix+"cameraExtraURLCommon");
if ((this.cameraExtraURLCommon.length()>10) && this.cameraExtraURLCommon.substring(0,9).equals("<![CDATA["))
this.cameraExtraURLCommon=this.cameraExtraURLCommon.substring(9,this.cameraExtraURLCommon.length()-3);
}
if (properties.getProperty(prefix+"setupTriggerMode")!=null)
this.setupTriggerMode=Boolean.parseBoolean(properties.getProperty(prefix+"setupTriggerMode"));
if (properties.getProperty(prefix+"externalTriggerCabling")!=null)
this.externalTriggerCabling=Boolean.parseBoolean(properties.getProperty(prefix+"externalTriggerCabling"));
if (properties.getProperty(prefix+"noCabling")!=null)
this.noCabling=Boolean.parseBoolean(properties.getProperty(prefix+"noCabling"));
if (properties.getProperty(prefix+"cameraExposure")!=null)
this.cameraExposure=Double.parseDouble(properties.getProperty(prefix+"cameraExposure"));
if (properties.getProperty(prefix+"scaleExposureForLasers")!=null)
this.scaleExposureForLasers=Double.parseDouble(properties.getProperty(prefix+"scaleExposureForLasers"));
if (properties.getProperty(prefix+"scaleExposureForHeadLasers")!=null)
this.scaleExposureForHeadLasers=Double.parseDouble(properties.getProperty(prefix+"scaleExposureForHeadLasers"));
if (properties.getProperty(prefix+"cameraAutoExposureMax")!=null)
this.cameraAutoExposureMax=Double.parseDouble(properties.getProperty(prefix+"cameraAutoExposureMax"));
if (properties.getProperty(prefix+"cameraGain")!=null)
this.cameraGain=Double.parseDouble(properties.getProperty(prefix+"cameraGain"));
if (properties.getProperty(prefix+"cameraRScale")!=null)
this.cameraRScale=Double.parseDouble(properties.getProperty(prefix+"cameraRScale"));
if (properties.getProperty(prefix+"cameraBScale")!=null)
this.cameraBScale=Double.parseDouble(properties.getProperty(prefix+"cameraBScale"));
if (properties.getProperty(prefix+"cameraGScale")!=null)
this.cameraGScale=Double.parseDouble(properties.getProperty(prefix+"cameraGScale"));
for (int i=0;i<numCams;i++) {
if (properties.getProperty(prefix+"cameraExposureCorr_"+i)!=null)
this.cameraExposureCorr[i]=Double.parseDouble(properties.getProperty(prefix+"cameraExposureCorr_"+i));
if (properties.getProperty(prefix+"cameraGainCorr_"+i)!=null)
this.cameraGainCorr[i]=Double.parseDouble(properties.getProperty(prefix+"cameraGainCorr_"+i));
if (properties.getProperty(prefix+"cameraRScaleCorr_"+i)!=null)
this.cameraRScaleCorr[i]=Double.parseDouble(properties.getProperty(prefix+"cameraRScaleCorr_"+i));
if (properties.getProperty(prefix+"cameraBScaleCorr_"+i)!=null)
this.cameraBScaleCorr[i]=Double.parseDouble(properties.getProperty(prefix+"cameraBScaleCorr_"+i));
if (properties.getProperty(prefix+"cameraGScaleCorr_"+i)!=null)
this.cameraGScaleCorr[i]=Double.parseDouble(properties.getProperty(prefix+"cameraGScaleCorr_"+i));
if (properties.getProperty(prefix+"cameraExtraURL_"+i)!=null) {
this.cameraExtraURL[i]=properties.getProperty(prefix+"cameraExtraURL_"+i);
if ((this.cameraExtraURL[i].length()>10) && this.cameraExtraURL[i].substring(0,9).equals("<![CDATA["))
this.cameraExtraURL[i]=this.cameraExtraURL[i].substring(9,this.cameraExtraURL[i].length()-3);
}
}
initIPs(); // was missing here?
initJP4();
}
public boolean showDialog(String title, int numCams, boolean askRegenerate) { // numCams<=0 -> do not initialize number
if (numCams>0){
// initDefaultMap(1);
initDefaultMap(numCams);
initIPs();
initCamParsDefaultArrays(this.cameraIPs.length);
initJP4();
}
//http://192.168.0.223/parsedit.php?title=PHASES&SENSOR_PHASE&MULTI_PHASE1&MULTI_PHASE2&MULTI_PHASE3&DEBUG&CABLE_TIM&FPGA_TIM0&FPGA_TIM1&DLY359_P1&DLY359_P2&DLY359_P3&DLY359_C1&DLY359_C2&DLY359_C3&SENSOR&FRAME_SIZE=@&refresh
//http://192.168.0.228/parsedit.php?immediate&EXPOS=25000*0&AUTOEXP_ON=0*0&WB_EN=0*0
//http://192.168.0.221/parsedit.php?immediate&EXPOS=25000*0&AUTOEXP_ON=0*0&WB_EN=0*0&COLOR=1*0&GAINR=0x20000*0&GAING=0x20000*0&GAINB=0x36666*0&GAINGB=0x20000*0
//http://192.168.0.221/parsedit.php?title=PHASES&SENSOR_PHASE&MULTI_PHASE1&MULTI_PHASE2&MULTI_PHASE3&FRAME_SIZE=@
//http://192.168.0.222/parsedit.php?title=day&immediate&EXPOS=20000*0&AUTOEXP_ON=0*0&WB_EN=0*0&COLOR=1*0&GAINR=0x270a4*0&GAING=0x20000*0&GAINB=0x2999a*0&GAINGB=0x20000*0
//http://192.168.0.236/parsedit.php?title=night&immediate&EXPOS=13000*0&AUTOEXP_ON=0*0&WB_EN=0*0&COLOR=1*0&GAINR=0x1fb35*0&GAING=0x20000*0&GAINB=0x3961c*0&GAINGB=0x20000*0
//http://192.168.0.221/parsedit.php?title=bright-day&immediate&EXPOS=10000*0&AUTOEXP_ON=0*0&WB_EN=0*0&COLOR=1*0&GAINR=0x270a4*0&GAING=0x20000*0&GAINB=0x2999a*0&GAINGB=0x20000*0
//http://192.168.0.221/parsedit.php?immediate&TRIG&TRIG_PERIOD
GenericDialog gd = new GenericDialog(title);
gd.addCheckbox ("NC393 (unchecked - nc353)", this.nc393);
gd.addStringField ("Subnet of the cameras (3 first of the four IPv4 address ending with '.')",this.cameraSubnet,12);
gd.addNumericField("Last byte of the first sub-camera IP address)",this.iBaseIP,0);
gd.addNumericField("Camera boot time",this.cameraBootTimeSeconds,0,3,"sec");
gd.addNumericField("Network connection timeout",this.connectionTimeoutMilliseconds,0,3,"ms");
gd.addNumericField("Index (in IP table) of the master camera (used for triggering)",this.masterSubCamera,0);
gd.addNumericField("Master (used for triggering), normally lowest connected port (0..3)",this.masterPort,0);
gd.addNumericField("Image server port number)",this.imgsrvPort,0);
gd.addStringField ("Image server command to reset image buffer",this.resetURLcmd,25);
gd.addStringField ("Image server command to trigger acquisition",this.triggerURLcmd,25);
gd.addStringField ("Image server command to acquire image (waits for the new one after reset)",this.imageURLcmd,25);
gd.addStringField ("Image server command to receive XML metadata (with timestamp)",this.metaURLcmd,25);
gd.addMessage("Configure each sub-camera - which IP index and channel does it use.");
if (askRegenerate) gd.addMessage("You may change number of subcameras and press REGENERATE below");
for (int i=0; i< this.channelMap.length;i++){
gd.addMessage("---------------------------------------------------------");
gd.addNumericField("Subcamera "+(i+1)+" IP index (starting from 0)", this.channelMap[i][0],0);
gd.addNumericField("Subcamera "+(i+1)+" port (0..3)", this.channelMap[i][2],0);
gd.addNumericField("Subcamera "+(i+1)+" channel (0,1 or 2)", this.channelMap[i][1],0);
gd.addCheckbox("Subcamera "+(i+1)+" - used mirror", this.flipImages[i]);
}
gd.addMessage("---------------------------------------------------------");
if (askRegenerate) {
gd.addCheckbox ("Individually overwrite IP addresses",false);
gd.addNumericField("Number of subcameras (need to press REGENERATE button to change)", this.channelMap.length, 0);
gd.enableYesNoCancel("OK", "REGENERATE");
}
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return false;
this.nc393= gd.getNextBoolean();
this.cameraSubnet= gd.getNextString();
if (!this.cameraSubnet.endsWith(".")) this.cameraSubnet += ".";
int bip= (int) gd.getNextNumber();
if ((bip>0) && (bip<255) && (bip!=this.iBaseIP)){
this.iBaseIP=bip;
initIPs();
}
this.cameraBootTimeSeconds=(int) gd.getNextNumber();
this.connectionTimeoutMilliseconds=(int) gd.getNextNumber();
this.masterSubCamera= (int) gd.getNextNumber(); // should be after initIPs()!
this.masterPort= (int) gd.getNextNumber(); // should be after initIPs()!
this.imgsrvPort= (int) gd.getNextNumber();
this.resetURLcmd= gd.getNextString();
this.triggerURLcmd= gd.getNextString();
this.imageURLcmd= gd.getNextString();
this.metaURLcmd= gd.getNextString();
for (int i=0; i< this.channelMap.length;i++){
this.channelMap[i][0]=(int) gd.getNextNumber();
this.channelMap[i][2]=(int) gd.getNextNumber();
this.channelMap[i][1]=(int) gd.getNextNumber();
this.flipImages[i]= gd.getNextBoolean();
}
if (askRegenerate) {
boolean overwriteIPs=gd.getNextBoolean();
int newSubCams=(int) gd.getNextNumber();
// if (!gd.wasOKed() &&(newSubCams!=this.channelMap.length)) {
if (!gd.wasOKed()) { // regenerate always if pressed, even if number is the same
// initDefaultMap(newSubCams);
// initIPs();
int [][] backupMap=this.channelMap;
if (!showDialog(title, newSubCams, false)) {
this.channelMap=backupMap;
return false; // channelMap is restored, but some other fields may be broken
}
}
if (overwriteIPs && !editSubCamerasIPs()) return false;
}
return true;
}
/**
* Wait for camera to boot
* @param chn - camera channel number (0)
* @return -1 if camera is not yet set to trigger mode, else - last frame number acquired
* throws on timeout
*/
public int getCurrentFrameNumberWithTimeout(int chn, boolean showStatus, AtomicInteger stopRequested){
long startTime=System.nanoTime();
double dTimeOut=1E9* this.cameraBootTimeSeconds;
long endTime=startTime+(long) dTimeOut;
while (true){
if (probeCameraState(chn, showStatus, true,this.connectionTimeoutMilliseconds)){
if (showStatus) IJ.showProgress(0.0);
if (!this.triggeredMode[chn]) return -1;
if (this.triggerPeriod[chn]>1) return -1; // trigger period is not set to 1 - not yet programmed
return this.cameraFrameNumber[chn];
}
long time=System.nanoTime();
if (time>endTime){
if (showStatus) IJ.showProgress(0.0);
throw new IllegalArgumentException ("Timeout while waiting for the camera #"+chn+" to respond");
}
if (stopRequested.get()>0) {
System.out.println("User requested stop");
if (showStatus) IJ.showProgress(0.0);
throw new IllegalArgumentException ("Waiting for camera #"+chn+" aborted by user request");
}
if (showStatus) IJ.showProgress((time-startTime)/dTimeOut);
}
}
public String getSerialNumber(int chn, int EEPROM_chn){
String [] ser_mod = getSerialNumberModel(chn, EEPROM_chn);
if ((ser_mod==null) || (ser_mod.length < 1)) return null;
return ser_mod[0];
}
public String getModelNumber(int chn, int EEPROM_chn){
String [] ser_mod = getSerialNumberModel(chn, EEPROM_chn);
if ((ser_mod==null) || (ser_mod.length < 2)) return null;
return ser_mod[1];
}
public String [] getSerialNumberModel(int chn, int EEPROM_chn){
int colon_index = this.cameraIPs[chn].indexOf(":");
int sensor_port = Integer.parseInt(this.cameraIPs[chn].substring(colon_index+1)) - this.imgsrvPort;
String ip=this.cameraIPs[chn].substring(0, colon_index);
// String url="http://"+this.cameraIPs[chn]+"/i2c.php?cmd=fromEEPROM0&EEPROM_chn="+EEPROM_chn;
// ip = "192.168.0.236";
String url="http://"+ip+"/i2c.php?cmd=fromEEPROM" + sensor_port+ "&EEPROM_chn="+EEPROM_chn;
Document dom=null;
String serial=null;
String model=null;
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
InputStream in = new URL( url ).openStream();
byte[] bytes = new byte[0];
try {
bytes = IOUtils.toByteArray(in);
} finally {
IOUtils.closeQuietly(in); // always gets here
}
for (byte b:bytes) {
if (b < 0) {
String msg="Sensor EEPROM is not initialized. Use bootblock393 to initialize it. Will throw now";
IJ.showMessage("Error",msg);
System.out.println(msg);
throw new IllegalArgumentException ("SAX error");
// return null;
}
}
dom = db.parse(url);
if (!dom.getDocumentElement().getNodeName().equals("board")) {
String msg="Root element: expected 'board', got \"" + dom.getDocumentElement().getNodeName()+"\"";
IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg);
}
serial=(dom.getDocumentElement().getElementsByTagName("serial").item(0).getChildNodes().item(0)).getNodeValue();
// remove opening and closing "
if (serial==null){
String msg="Could not read tag <serial>";
IJ.showMessage("Error",msg);
System.out.println(msg);
return null;
}
if (serial.startsWith("\"")){
serial=serial.substring(1, serial.length()-1);
}
model=(dom.getDocumentElement().getElementsByTagName("model").item(0).getChildNodes().item(0)).getNodeValue();
if (model !=null){
if (model.startsWith("\"")){
model=model.substring(1, model.length()-1);
}
}
} catch(MalformedURLException e){
String msg="Please check the URL:" + e.toString();
IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg);
} catch(IOException e1){
String msg = e1.getMessage();
if (msg==null || msg.equals("")) msg = ""+e1;
IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg);
}catch(ParserConfigurationException pce) {
pce.printStackTrace();
throw new IllegalArgumentException ("PCE error");
}catch(SAXException se) {
se.printStackTrace();
throw new IllegalArgumentException ("SAX error");
// }catch (SAXParseException spe) {
}
this.is_10398 = "10398".equals(model);
return new String[] {serial, model};
}
public double getSensorTemperature(int chn, int EEPROM_chn){
// Need to configure camera to be able to read temperature
if (sensorPresent==null) { // cameras were not probed/configured
probeCameraState(); // testing detection
printTiming("=== probeCameraState()");
setupCameraAcquisition();
printTiming("=== setupCameraAcquisition()");
}
if (!this.sensorPresent[chn][0] && !this.sensorPresent[chn][1] && !this.sensorPresent[chn][2]) EEPROM_chn=0; // no 10359 - null pointer while "lens center" if first
int colon_index = this.cameraIPs[chn].indexOf(":");
int sensor_port = Integer.parseInt(this.cameraIPs[chn].substring(colon_index+1)) - this.imgsrvPort;
String ip=this.cameraIPs[chn].substring(0, colon_index);
// String url="http://"+this.cameraIPs[chn]+"/i2c.php?cmd=fromEEPROM0&EEPROM_chn="+EEPROM_chn;
String url="http://"+ip+"/i2c.php?cmd=fromEEPROM"+ sensor_port +"&EEPROM_chn="+EEPROM_chn;
this.lastTemperature=Double.NaN;
Document dom=null;
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
dom = db.parse(url);
if (!dom.getDocumentElement().getNodeName().equals("board")) {
String msg="Root element: expected 'board', got \"" + dom.getDocumentElement().getNodeName()+"\"";
IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg);
}
String sTemperature=null;
if ((dom.getDocumentElement().getElementsByTagName("sensorTemperature").item(0))!=null){
sTemperature=(dom.getDocumentElement().getElementsByTagName("sensorTemperature").item(0).getChildNodes().item(0)).getNodeValue();
}else{
sTemperature= "0.0";
}
// remove opening and closing "
if (sTemperature==null){
String msg="Could not read sensor temperature";
// IJ.showMessage("Error",msg);
System.out.println("Warning: "+msg);
return Double.parseDouble(sTemperature);
}
this.lastTemperature= Double.parseDouble(sTemperature);
} catch(MalformedURLException e){
String msg="Please check the URL:" + e.toString();
IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg);
} catch(IOException e1){
String msg = e1.getMessage();
if (msg==null || msg.equals("")) msg = ""+e1;
IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg);
}catch(ParserConfigurationException pce) {
pce.printStackTrace();
throw new IllegalArgumentException ("PCE error");
}catch(SAXException se) {
se.printStackTrace();
throw new IllegalArgumentException ("SAX error");
}
return this.lastTemperature;
}
// private int [] motors= null; // motors steps when the images were acquired (for null)
public int [] getMotorsPosition() {return this.motorsPosition;} // may be null
public void setMotorsPosition (int [] position) {this.motorsPosition=position;}
public void resetInitialization(){
System.out.println("resetInitialization()");
this.sensorPresent=null;
}
public int probeCameraState(){
int numOnline=0;
int numSensors=0;
int numChn=this.cameraIPs.length;
initCameraArrays(numChn);
/*
this.cameraFrameNumber=new int[numChn];
this.triggeredMode=new boolean[numChn];
this.sensorPresent=new boolean[numChn][];
// TODO - try if skipping setting TRIG_PERIOD=0, IRQ_SMART=6 (when they are already set) will fix hanging
this.triggerPeriod=new int[numChn];
this.irqSmart= new int[numChn];
*/
for (int chn=0;chn<numChn;chn++){
this.cameraFrameNumber[chn]=-1;
this.triggeredMode[chn]=false;
this.sensorPresent[chn]=null; // camera did not respond, {false,false,false} - single camera (no 10359)
if (this.debugLevel>1) System.out.println("Probing camera "+chn+" ("+this.cameraIPs[chn]+")...");
IJ.showStatus("Probing camera "+chn+" ("+this.cameraIPs[chn]+")...");
if (probeCameraState(chn)) {
numOnline++;
printTiming("===== probing channel "+chn);
boolean single_no_mux= (!this.sensorPresent[chn][0] && !this.sensorPresent[chn][1] && !this.sensorPresent[chn][2]);
if (this.debugLevel>1) System.out.println("Frame number: "+this.cameraFrameNumber[chn]+
", Trigger mode:"+(this.triggeredMode[chn]?"ex":"in")+"ternal, "+
" sensors attached:"+(this.sensorPresent[chn][0]?"1 ":"")+(this.sensorPresent[chn][1]?"2 ":"")+(this.sensorPresent[chn][2]?"3 ":"")+
(single_no_mux?"single-sensor, no multiplexer":"") +
(" Master port "+this.cameraMasterPort[chn])
);
for (int i=0;i<this.sensorPresent[chn].length;i++) if (this.sensorPresent[chn][i]) numSensors++;
if (single_no_mux) numSensors++;
} else {
if (this.debugLevel>1) System.out.println("Camera did not respond");
}
}
IJ.showStatus("Found "+numOnline+" camera IP, "+numSensors+" sensors");
if (this.debugLevel>1) System.out.println("Found "+numOnline+" camera IP, "+numSensors+" sensors");
return numOnline;
}
public void initCameraArrays(int numChn){
if (this.debugLevel>1) System.out.println("initCameraArrays("+numChn+")");
this.cameraFrameNumber=new int[numChn];
this.triggeredMode= new boolean[numChn];
this.sensorPresent= new boolean[numChn][];
// TODO - try if skipping setting TRIG_PERIOD=0, IRQ_SMART=6 (when they are already set) will fix hanging
this.triggerPeriod= new int[numChn];
this.irqSmart= new int[numChn];
this.cameraMasterPort= new int[numChn]; // not sure if will use it - master port for each camera:port
}
public boolean probeCameraState(
int chn){
return probeCameraState(chn, false, false,0);
}
public boolean probeCameraState(
int chn,
boolean showStatus,
boolean doNotThrow,
int timeout // ms
){
//http://192.168.0.221/parsedit.php?immediate&TRIG&TRIG_PERIOD&FRAME
String url;
int colon_index = this.cameraIPs[chn].indexOf(":");
int sensor_port = Integer.parseInt(this.cameraIPs[chn].substring(colon_index+1)) - this.imgsrvPort;
String ip=this.cameraIPs[chn].substring(0, colon_index);
if (this.nc393){
// url="http://"+this.cameraIPs[chn]+"/parsedit.php?immediate&TRIG&TRIG_PERIOD&SENS_AVAIL&FRAME";
url="http://"+ip+"/parsedit.php?sensor_port="+sensor_port+"&immediate&TRIG&TRIG_PERIOD&SENS_AVAIL&FRAME&TRIG_MASTER";
} else {
// url="http://"+this.cameraIPs[chn]+"/parsedit.php?immediate&TRIG&TRIG_PERIOD&IRQ_SMART&SENS_AVAIL&FRAME";
url="http://"+ip+"/parsedit.php?immediate&TRIG&TRIG_PERIOD&IRQ_SMART&SENS_AVAIL&FRAME";
}
if (this.debugLevel>1) System.out.println("url="+url);
Document dom=null;
if ((this.cameraFrameNumber==null) || ((this.cameraFrameNumber.length<(chn+1)))) initCameraArrays(chn+1);
// did not find yet - why cameraFrameNumber is not null, but sensorPresent is? Added next lines until find
if ((this.triggeredMode==null) || ((this.triggeredMode.length<(chn+1)))) initCameraArrays(chn+1);
if ((this.sensorPresent==null) || ((this.sensorPresent.length<(chn+1)))) initCameraArrays(chn+1);
if ((this.triggerPeriod==null) || ((this.triggerPeriod.length<(chn+1)))) initCameraArrays(chn+1);
if (!this.nc393) {
if ((this.irqSmart==null) || ((this.irqSmart.length<(chn+1)))) initCameraArrays(chn+1);
} else {
if ((this.cameraMasterPort==null) || ((this.cameraMasterPort.length<(chn+1)))) initCameraArrays(chn+1);
}
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
if (timeout<=0){
dom = db.parse(url);
} else {
URL uUrl = new URL(url);
URLConnection con = uUrl.openConnection();
con.setConnectTimeout(timeout);//The timeout in mills
dom = db.parse(con.getInputStream());
}
if (!dom.getDocumentElement().getNodeName().equals("parameters")) {
String msg="Root element: expected 'parameters', got \"" + dom.getDocumentElement().getNodeName()+"\"";
if (showStatus) IJ.showStatus(msg);
if (doNotThrow) return false;
IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg);
}
// String sNode;
if (this.triggeredMode==null) System.out.println("this.triggeredMode==null");
if (this.triggeredMode.length<(chn+1)) System.out.println("this.triggeredMode.length="+this.triggeredMode.length+" chn="+chn);
this.triggeredMode[chn]= (Integer.parseInt((dom.getDocumentElement().getElementsByTagName("TRIG").item(0).getChildNodes().item(0)).getNodeValue())==4);
int sensAvail= Integer.parseInt((dom.getDocumentElement().getElementsByTagName("SENS_AVAIL").item(0).getChildNodes().item(0)).getNodeValue());
if (this.sensorPresent==null) System.out.println("sensorPresent==null");
if (this.sensorPresent.length<(chn+1)) System.out.println("sensorPresent="+this.sensorPresent.length+" chn="+chn);
this.sensorPresent[chn]=new boolean[3];
for (int i=0;i<this.sensorPresent[chn].length;i++) this.sensorPresent[chn][i]=(sensAvail & (1<<i))!=0;
this.triggerPeriod[chn]= Integer.parseInt((dom.getDocumentElement().getElementsByTagName("TRIG_PERIOD").item(0).getChildNodes().item(0)).getNodeValue());
if (!this.nc393) {
this.irqSmart[chn]= Integer.parseInt((dom.getDocumentElement().getElementsByTagName("IRQ_SMART").item(0).getChildNodes().item(0)).getNodeValue());
this.cameraMasterPort[chn]= sensor_port;
} else {
this.cameraMasterPort[chn]= Integer.parseInt((dom.getDocumentElement().getElementsByTagName("TRIG_MASTER").item(0).getChildNodes().item(0)).getNodeValue());
}
this.cameraFrameNumber[chn]= Integer.parseInt((dom.getDocumentElement().getElementsByTagName("FRAME").item(0).getChildNodes().item(0)).getNodeValue());
} catch(MalformedURLException e){
String msg="Please check the URL:" + e.toString();
IJ.showMessage("Error",msg);
if (showStatus) IJ.showStatus(msg);
if (doNotThrow) return false;
throw new IllegalArgumentException (msg);
} catch(IOException e1){
String msg = e1.getMessage();
if (msg==null || msg.equals("")) msg = ""+e1;
msg="Camera "+chn+" ("+this.cameraIPs[chn]+") did not respond: "+msg; // "Connection refused"
if (showStatus) IJ.showStatus(msg);
if (doNotThrow) return false;
IJ.showMessage("Error",msg);
System.out.println(msg);
return false;
}catch(ParserConfigurationException pce) {
pce.printStackTrace();
String msg="PCE error "+pce.getMessage();
if (showStatus) IJ.showStatus(msg);
if (doNotThrow) return false;
throw new IllegalArgumentException (msg);
}catch(SAXException se) {
se.printStackTrace();
String msg="SAX error "+se.getMessage();
if (showStatus) IJ.showStatus(msg);
if (doNotThrow) return false;
throw new IllegalArgumentException (msg);
}
return true;
}
public boolean setupCameraAcquisition(){
return setupCameraAcquisition(Double.NaN);
}
public boolean setupCameraAcquisition(final double exposureScale){
// final boolean mp14 = is14Mpix();
final int ipLength=this.resetURLs.length;
final boolean [] results=new boolean[ipLength];
for (int chn=0;chn<ipLength;chn++) results[chn]=(this.sensorPresent[chn]!=null);
final Thread[] threads = newThreadArray(this.maxNumberOfThreads);
final AtomicInteger chnAtomic = new AtomicInteger(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
@Override
public void run() {
for (int chn=chnAtomic.getAndIncrement(); chn<ipLength;chn=chnAtomic.getAndIncrement()) if (results[chn]){
results[chn]=setupCameraAcquisition(chn,exposureScale);
}
}
};
}
startAndJoin(threads);
if (Double.isNaN(exposureScale)){ // full init
int nRepeat=this.setupTriggerMode?4:1;
int sleep_ms = 1000;
if (is14Mpix()) {
nRepeat=this.setupTriggerMode?4:2; // FIXME: Modified for 14Mpix
sleep_ms = 2000;
}
if (this.nc393) nRepeat++; // is it needed?
for (int i=0;i<nRepeat;i++){
if (this.debugLevel>0) System.out.println((i+1)+" of "+nRepeat+": Triggering cameras to give parameters a chance to propagate");
trigger();
try
{
Thread.sleep( sleep_ms ); // ms // FIXME: Modified for 14Mpix
}
catch ( InterruptedException e )
{
System.out.println( "awakened prematurely" );
}
}
} else if (is14Mpix()) {
try
{
Thread.sleep( 2000 ); // ms // FIXME: Modified for 14Mpix
}
catch ( InterruptedException e )
{
System.out.println( "awakened prematurely" );
}
trigger();
}
boolean result=true;
for (int chn=0;chn<ipLength;chn++) if (this.sensorPresent[chn]!=null) result &=results[chn];
return result;
}
public boolean setupCameraAcquisitionNoTHreads(double exposureScale){
boolean result=true;
for (int chn=0;chn<this.cameraIPs.length;chn++) if (this.sensorPresent[chn]!=null){
result&=setupCameraAcquisition(chn,exposureScale);
}
// trigger ?
if (Double.isNaN(exposureScale)){ // just a hack - if exposureScale is non-NaN only update exposure
trigger();
//sleep (1000);
for ( long endTime=System.nanoTime()+(1000000000);endTime<System.nanoTime(););
}
return result;
}
// TODO: issue several TRIG pulses after setting parameters?
public boolean setupCameraAcquisition(int chn, double exposureScale){
int colon_index = this.cameraIPs[chn].indexOf(":");
int sensor_port = Integer.parseInt(this.cameraIPs[chn].substring(colon_index+1)) - this.imgsrvPort;
String ip=this.cameraIPs[chn].substring(0, colon_index);
boolean isMasterSubcamera = ip.equals(this.cameraSubnet+(this.iBaseIP+this.masterSubCamera));
boolean isMasterPort = (this.cameraMasterPort[chn] == sensor_port); // for 353 should always be master port
if (isMasterSubcamera && (this.cameraMasterPort[chn] != this.masterPort)){
System.out.println("Master port mismatch for camera "+ip+" (master) - parameters master port = "+
this.masterPort+", camera responded with "+this.cameraMasterPort[chn] );
}
if (this.debugLevel>1) System.out.println("DEBUG393: chn="+chn+" sensor_port="+sensor_port+" ip= "+ip+" isMasterSubcamera="+isMasterSubcamera+ " isMasterPort="+isMasterPort);
boolean exposureOnly=!Double.isNaN(exposureScale);
int minExposure=10; // usec
int maxExposure=1000000; //usec
int minGain=(int) (0x10000*1.0);
int maxGain=(int) (0x10000*15.75);
int minScale=0;
int maxScale=(int) (0x10000*4.0);
int exposure= (int) (Math.round(1000*this.cameraExposure*this.cameraExposureCorr[chn])*(exposureOnly?exposureScale:1.0));
int autoExposureMax= (int) (Math.round(1000*this.cameraAutoExposureMax*this.cameraExposureCorr[chn]));
int gain= (int) (Math.round(0x10000*this.cameraGain*this.cameraGainCorr[chn]));
int rScale= (int) (Math.round(0x10000*this.cameraRScale*this.cameraRScaleCorr[chn]));
int bScale= (int) (Math.round(0x10000*this.cameraBScale*this.cameraBScaleCorr[chn]));
int gScale= (int) (Math.round(0x10000*this.cameraGScale*this.cameraGScaleCorr[chn]));
int autoExp= this.cameraAutoExposure?1:0;
int autoWB= this.cameraAutoWhiteBalance?1:0;
String extraURL="";
if (this.cameraExtraURLCommon.length()>0){
extraURL+=(this.cameraExtraURLCommon.substring(0,1).equals("&"))?"":"&"+this.cameraExtraURLCommon;
}
if (this.cameraExtraURL[chn].length()>0){
extraURL+=(this.cameraExtraURL[chn].substring(0,1).equals("&"))?"":"&"+this.cameraExtraURL[chn];
}
if (exposure<minExposure) exposure=minExposure; else if (exposure>maxExposure) exposure=maxExposure;
if (autoExposureMax<minExposure) autoExposureMax=minExposure; else if (autoExposureMax>maxExposure) autoExposureMax=maxExposure;
if (gain<minGain) gain= minGain ; else if (gain> maxGain) gain= maxGain;
if (rScale<minScale) rScale= minScale ; else if (rScale> maxScale) rScale= maxScale;
if (bScale<minScale) bScale= minScale ; else if (bScale> maxScale) bScale= maxScale;
if (gScale<minScale) gScale= minScale ; else if (gScale> maxScale) gScale= maxScale;
String triggerMode="";
if (this.nc393) {
if (isMasterPort) {
/*
* P_TRIG_OUT (outputs):
* off: 0x00000
* external: 0x02000
* internal: 0x20000
* both: 0x22000
* P_TRIG_IN (inputs):
* off: 0x00000
* external: 0x80000
* internal: 0x08000
* both: 0x88000
*/
if (this.setupTriggerMode){
triggerMode+="&TRIG_CONDITION="+(this.noCabling?(0):(this.externalTriggerCabling?"0x80000":"0x08000"))+"*0"+
"&TRIG_OUT="+(this.noCabling?(0):(this.externalTriggerCabling?"0x02000":"0x20000"))+"*0"+
"&TRIG=4*3";
}
if ((this.triggerPeriod[chn]>1) || this.setupTriggerMode) {
triggerMode+="&TRIG_PERIOD=0*1"; // just stop it if it wasn't already, imgsrv /trig does not set it, only FPGA register
}
}
}else {
if (this.setupTriggerMode){
triggerMode+="&TRIG_CONDITION="+(this.noCabling?(0):(this.externalTriggerCabling?"0x200000":"0x20000"))+"*0"+
"&TRIG_OUT="+(this.noCabling?(0):(this.externalTriggerCabling?"0x800000":"0x80000"))+"*0"+
"&TRIG=4*3";
}
if ((this.triggerPeriod[chn]>1) || this.setupTriggerMode){
triggerMode+="&TRIG_PERIOD=1*0"; // just imgsrv /trig does not set it, only FPGA register
}
}
String url="http://"+ip+"/parsedit.php?immediate";
if (this.nc393) {
url += "&sensor_port="+sensor_port;
}
url+="&EXPOS="+exposure+"*0"; // always
if (!exposureOnly){
if (!this.nc393) {
if (this.irqSmart[chn]!=(this.noWait?6:3)){
url+="&IRQ_SMART="+(this.noWait?6:3)+"*0";
}
}
url+="&COLOR="+this.colorMode+"*"+(this.nc393?"1":"0")+
"&QUALITY="+this.JPEGquality+"*0"+
"&EXPOS="+exposure+"*0"+
"&AUTOEXP_EXP_MAX="+autoExposureMax+"*0"+
"&AUTOEXP_ON="+autoExp+"*0"+
"&GAING="+gain+"*0"+
"&RSCALE="+rScale+"*0"+
"&BSCALE="+bScale+"*0"+
"&GSCALE="+gScale+"*0"+ // GB/G ratio
"&WB_EN="+autoWB+"*0"+
"&DAEMON_EN_TEMPERATURE=1"+"*0"+
triggerMode+ // needed here?
"&FRAME"+
extraURL;
}
// if (this.debugLevel>2) {
if (this.debugLevel>1) { // temporary - debugging
System.out.println("Setting camera "+chn+", URL="+url);
}
Document dom=null;
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
dom = db.parse(url);
if (!dom.getDocumentElement().getNodeName().equals("parameters")) {
String msg="Root element: expected 'parameters', got \"" + dom.getDocumentElement().getNodeName()+"\"";
IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg);
}
// String sNode;
if (!exposureOnly) this.cameraFrameNumber[chn]= Integer.parseInt((dom.getDocumentElement().getElementsByTagName("FRAME").item(0).getChildNodes().item(0)).getNodeValue());
} catch(MalformedURLException e){
String msg="Please check the URL:" + e.toString();
IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg);
} catch(IOException e1){
String msg = e1.getMessage();
if (msg==null || msg.equals("")) msg = ""+e1;
msg="Camera "+chn+" ("+this.cameraIPs[chn]+") did not respond\n"+msg;
IJ.showMessage("Error",msg);
System.out.println(msg);
return false;
}catch(ParserConfigurationException pce) {
pce.printStackTrace();
throw new IllegalArgumentException ("PCE error");
}catch(SAXException se) {
se.printStackTrace();
throw new IllegalArgumentException ("SAX error");
}
return true;
}
private boolean editSubCamerasIPs() {
GenericDialog gd = new GenericDialog("Edit IPs/hosts and ports of the sub cameras");
for (int i=0;i<this.cameraIPs.length;i++){
gd.addStringField(i+": IP address/host:sensor port of the subcamera",this.cameraIPs[i],25);
}
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return false;
for (int i=0;i<this.cameraIPs.length;i++){
this.cameraIPs[i]=gd.getNextString();
}
initJP4(); // initialize JP46_Reader_camera class instances
/// initCamParsDefaultArrays(this.cameraIPs.length); - probably not needed as number of cameras is not changed
return true;
}
public boolean editCameraSettings(String title){
GenericDialog gd = new GenericDialog("title");
gd.addCheckbox ("NC393 (unchecked - nc353)", this.nc393);
gd.addNumericField("Camera exposure",this.cameraExposure,2,8,"ms");
gd.addNumericField("Scale camera exposure for target laser detection (4 lasers)",100*this.scaleExposureForLasers,1,5,"%");
gd.addNumericField("Scale camera exposure for optical head laser detection (2 lasers)",100*this.scaleExposureForHeadLasers,1,5,"%");
gd.addCheckbox ("Enable autoexposure", this.cameraAutoExposure);
gd.addNumericField("Maximal automatic exposure",this.cameraAutoExposureMax,2,8,"ms");
gd.addNumericField("Analog gain (2.0 recommended)",this.cameraGain,3,6,"x");
gd.addNumericField("Red-to-green color balance",this.cameraRScale,3,6,"x");
gd.addNumericField("Blue-to-green color balance",this.cameraBScale,3,6,"x");
gd.addNumericField("Green(blue row) to green (red row) color balance",this.cameraGScale,3,6,"x");
// TODO: Make one-time WB by averaging scales from all channels
gd.addCheckbox ("Enable auto white balance", this.cameraAutoWhiteBalance);
gd.addNumericField("Color mode (JP4=5)",this.colorMode,0,6,"");
gd.addNumericField("Compression quality",this.JPEGquality,0,6,"%");
gd.addCheckbox ("No wait for the next frame sync (IRQ_SMART=6, unchecked - IRQ_SMART=3)", this.noWait);
gd.addCheckbox ("Setup trigger mode", this.setupTriggerMode);
gd.addCheckbox ("Use external trigger wiring", this.externalTriggerCabling);
gd.addCheckbox ("Use internal FPGA trigger (no cables, for single camera)", this.noCabling);
// this.setupTriggerMode
// this.externalTriggerCabling
gd.addStringField ("Extra URL for all sub-cameras",this.cameraExtraURLCommon,40);
for (int i=0;i<this.cameraIPs.length;i++){
gd.addMessage("\n"+i+": camera "+this.cameraIPs[i]+" :");
gd.addNumericField(" Exposure correction ",this.cameraExposureCorr[i],2,8,"x");
gd.addNumericField(" Gain correction ",this.cameraGainCorr[i],2,8,"x");
gd.addNumericField(" R/G correction ",this.cameraRScaleCorr[i],2,8,"x");
gd.addNumericField(" B/G correction ",this.cameraBScaleCorr[i],2,8,"x");
gd.addNumericField(" G(B)/G(R) correction",this.cameraGScaleCorr[i],2,8,"x");
gd.addStringField (" Extra URL string ",this.cameraExtraURL[i],40);
}
gd.addNumericField("Debug sensor number (<0 - none)",this.debugSensorNumber,0,6,"");
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return false;
this.nc393= gd.getNextBoolean();
this.cameraExposure= gd.getNextNumber();
this.scaleExposureForLasers= 0.01*gd.getNextNumber();
this.scaleExposureForHeadLasers=0.01*gd.getNextNumber();
this.cameraAutoExposure= gd.getNextBoolean();
this.cameraAutoExposureMax= gd.getNextNumber();
this.cameraGain= gd.getNextNumber();
this.cameraRScale= gd.getNextNumber();
this.cameraBScale= gd.getNextNumber();
this.cameraGScale= gd.getNextNumber();
this.cameraAutoWhiteBalance= gd.getNextBoolean();
this.colorMode= (int) gd.getNextNumber();
this.JPEGquality= (int) gd.getNextNumber();
this.noWait= gd.getNextBoolean();
this.setupTriggerMode= gd.getNextBoolean();
this.externalTriggerCabling= gd.getNextBoolean();
this.noCabling= gd.getNextBoolean();
this.cameraExtraURLCommon= gd.getNextString();
for (int i=0;i<this.cameraIPs.length;i++){
this.cameraExposureCorr[i]= gd.getNextNumber();
this.cameraGainCorr[i]= gd.getNextNumber();
this.cameraRScaleCorr[i]= gd.getNextNumber();
this.cameraBScaleCorr[i]= gd.getNextNumber();
this.cameraGScaleCorr[i]= gd.getNextNumber();
this.cameraExtraURL[i]= gd.getNextString();
}
this.debugSensorNumber= (int) gd.getNextNumber();
return true;
}
public void resetCameras(){
resetCameras(selectAllSubcameras());
}
public double[] timestampCameras(){
return timestampCameras(selectAllSubcameras());
}
public void resetIPs(){
resetIPs(selectAllIPs());
}
public double[] timestampIPs(){
return timestampIPs(selectAllIPs());
}
public boolean [] selectAllSubcameras(){
boolean [] all= new boolean[this.channelMap.length];
for (int i=0;i<all.length;i++) all[i]=true;
return all;
}
public boolean [] selectNoneSubcameras(){
boolean [] all= new boolean[this.channelMap.length];
for (int i=0;i<all.length;i++) all[i]=false;
return all;
}
public boolean [] selectAllIPs(){
boolean [] all= new boolean[this.cameraIPs.length];
for (int i=0;i<all.length;i++) all[i]=true;
return all;
}
public boolean [] selectIPs(boolean [] selectCameras){
boolean [] IPs= new boolean[this.cameraIPs.length];
for (int i=0;i<IPs.length;i++) IPs[i]=false;
for (int i=0;i<selectCameras.length;i++) if (i<this.channelMap.length) {
// IPs[this.channelMap[i][0]]=true;
IPs[this.channelIPPort[i]] = true; // since NC393
}
return IPs;
}
public void trigger(){
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
String url=this.triggerURL;
if (this.debugLevel>2) System.out.println(">>> trigger:" + url );
db.parse(url); // should be some XML (currently discarded)
} catch(MalformedURLException e){
System.out.println("Please check the URL:" + e.toString() );
return;
} catch(IOException e1){
IJ.showStatus("");
String error = e1.getMessage();
if (error==null || error.equals("")) error = ""+e1;
IJ.showMessage("trigger() ERROR", ""+error);
return;
}catch(ParserConfigurationException pce) {
pce.printStackTrace();
return;
}catch(SAXException se) {
se.printStackTrace();
return;
}
}
public double[] timestampCameras(boolean [] selection){
double [] ts_ip=timestampIPs(selectIPs(selection));
double [] ts=new double [selection.length];
for (int i=0;i<ts.length;i++){
ts[i]=0.0;
if (i<this.channelMap.length) ts[i]=ts_ip[this.channelMap[i][0]];
}
return ts;
}
public double[] timestampIPs(boolean [] ipSelection){
final Thread[] threads = newThreadArray(this.maxNumberOfThreads);
final AtomicInteger ipIndexAtomic = new AtomicInteger(0);
final int ipLength=this.resetURLs.length;
final int debugLevel=this.debugLevel;
final String [] metaURLs=this.metaURLs;
final double [] ts= new double[this.cameraIPs.length];
for (int i=0;i<ts.length;i++) ts[i]=0.0;
//TODO: Multithread the next cycle (per-sensor)
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
@Override
public void run() {
for (int ipIndex=ipIndexAtomic.getAndIncrement(); ipIndex<ipLength;ipIndex=ipIndexAtomic.getAndIncrement()){
// for (int ipIndex=0;ipIndex<this.resetURLs.length;ipIndex++) if ((ipIndex<ipSelection.length) && ipSelection[ipIndex]){
try {
Document dom=null;
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
String url=metaURLs[ipIndex];
// if (debugLevel>2) System.out.println("timestampIPs:" + url );
if (debugLevel>0) System.out.println("timestampIPs:" + url );
dom = db.parse(url);
if (!dom.getDocumentElement().getNodeName().equals("meta")) {
System.out.println("Root element: expected 'meta', got'" + dom.getDocumentElement().getNodeName()+"'");
IJ.showMessage("Error","Root element: expected 'meta', got'" + dom.getDocumentElement().getNodeName()+"'");
continue;
}
if (dom.getDocumentElement().getElementsByTagName("frame").getLength()==0) {
String sError="reading timestamp failed. Do you have camera firmware version >=8.1.1.1?";
System.out.println("ERROR: "+sError );
IJ.showMessage("Error",sError);
continue;
}
ts[ipIndex]=Double.parseDouble(
(dom.getDocumentElement().getElementsByTagName("timestamp").item(0).getChildNodes().item(0)).getNodeValue());
} catch(MalformedURLException e){
System.out.println("Please check the URL:" + e.toString() );
continue;
} catch(IOException e1){
IJ.showStatus("");
String error = e1.getMessage();
if (error==null || error.equals("")) error = ""+e1;
IJ.showMessage("timestampIPs() ERROR", ""+error);
continue;
}catch(ParserConfigurationException pce) {
pce.printStackTrace();
continue;
}catch(SAXException se) {
se.printStackTrace();
continue;
}
}
}
};
}
startAndJoin(threads);
return ts;
}
public void resetCameras(boolean [] selection){
if (this.debugLevel>2) {
System.out.println("resetCameras(...)");
for (int ii=0;ii<this.cameraIPs.length;ii++)System.out.println(ii+": "+this.cameraIPs[ii]);
}
resetIPs(selectIPs(selection));
}
public void resetIPs(boolean [] ipSelection){
final Thread[] threads = newThreadArray(this.maxNumberOfThreads);
final AtomicInteger ipIndexAtomic = new AtomicInteger(0);
final int ipLength=this.resetURLs.length;
final int debugLevel=this.debugLevel;
final String [] resetURLs=this.resetURLs;
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
@Override
public void run() {
for (int ipIndex=ipIndexAtomic.getAndIncrement(); ipIndex<ipLength;ipIndex=ipIndexAtomic.getAndIncrement()){
String url="";
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
url=resetURLs[ipIndex];
if (debugLevel>2) System.out.println("--- resetURLs:" + url );
// if (debugLevel>1) System.out.println("--- resetURLs:" + url );
db.parse(url); // should be some XML (currently discarded)
} catch(MalformedURLException e){
System.out.println("Please check the URL:" + e.toString() );
continue;
} catch(IOException e1){
IJ.showStatus("");
String error = e1.getMessage();
if (error==null || error.equals("")) error = ""+e1;
IJ.showMessage("resetIPs() ERROR", url+"\n"+error);
continue;
}catch(ParserConfigurationException pce) {
pce.printStackTrace();
continue;
}catch(SAXException se) {
se.printStackTrace();
continue;
}
}
}
};
}
startAndJoin(threads);
}
// public boolean preTrigger() { // mt9f002 fails if more than 1-3 sec between triggers
// return true;
// }
public ImagePlus [] getImages(final boolean [] acquire, boolean resetAndTrigger, final boolean show){
final boolean [] acquireIPs=selectIPs(acquire);
if (this.debugLevel>2) {
System.out.println("getImages(...) 2");
for (int ii=0;ii<this.cameraIPs.length;ii++)System.out.println(ii+": "+this.cameraIPs[ii]);
}
if (resetAndTrigger) {
if (is14Mpix()) {
try { // FIXME: Make conditional for 14MPix
Thread.sleep(2000);
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
resetCameras();
trigger();
}
final double [] timestamps= timestampIPs(acquireIPs);
if (this.debugLevel>2) System.out.println("getImages(): this.imagesIP.length=" + this.imagesIP.length);
final Thread[] threads = newThreadArray(this.maxNumberOfThreads);
final AtomicInteger ipIndexAtomic = new AtomicInteger(0);
final int ipLength=this.resetURLs.length;
final int debugLevel=this.debugLevel;
final String [] imageURLs=this.imageURLs;
final ImagePlus [] imagesIP=this.imagesIP;
final JP46_Reader_camera [] jp4_Instances=this.jp4_Instances;
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
@Override
public void run() {
for (int ipIndex=ipIndexAtomic.getAndIncrement(); ipIndex<ipLength;ipIndex=ipIndexAtomic.getAndIncrement()){
// for (int i=0;i<this.imagesIP.length;i++){
if (debugLevel>1/*2*/) System.out.println("getImages()3: ipIndex="+ipIndex+" acquireIPs.length=" +acquireIPs.length+
((ipIndex<acquireIPs.length)? (" acquireIPs[ipIndex]="+acquireIPs[ipIndex]):""));
if ((ipIndex<acquireIPs.length) && acquireIPs[ipIndex]) {
if (debugLevel>2) System.out.println("getImages:" + imageURLs[ipIndex] );
if ((debugLevel>3) &&(imagesIP[ipIndex]!=null) && show){
System.out.println("=============== old image ==========");
jp4_Instances[ipIndex].listImageProperties(imagesIP[ipIndex]);
}
imagesIP[ipIndex]=jp4_Instances[ipIndex].openURL( // gains inside were OK
imageURLs[ipIndex],
"",
true, //scale
imagesIP[ipIndex],
false); //show); // show image
imagesIP[ipIndex].setProperty("timestamp", IJ.d2s(timestamps[ipIndex],6));
imagesIP[ipIndex].setProperty("MIRRORED","NO");
if (debugLevel>2) {
jp4_Instances[ipIndex].listImageProperties(imagesIP[ipIndex],true); // to console - properties old - fixed
}
if (show){
imagesIP[ipIndex].updateAndDraw(); /// Redisplays final image
if (debugLevel>2){
System.out.println("=============== new image ==========");
jp4_Instances[ipIndex].listImageProperties(imagesIP[ipIndex]);
}
}
}
}
}
};
}
startAndJoin(threads);
//TODO: Multithread the next cycle (per-sensor)
final ImagePlus [] images=this.images;
final int [][] channelMap = this.channelMap;
final int [] channelIPPort = this.channelIPPort;
final AtomicInteger imageIndexAtomic = new AtomicInteger(0);
final int [] motorsPosition=this.motorsPosition;
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
@Override
public void run() {
// Next calls do not require image acquisition, so default settings for the new instance are OK
JP46_Reader_camera jp4_Instance= new JP46_Reader_camera(false);
for (int imageIndex=imageIndexAtomic.getAndIncrement(); imageIndex<images.length;imageIndex=imageIndexAtomic.getAndIncrement())
if ((imageIndex<acquire.length) && acquire[imageIndex]){
// for (int i=0;i<this.images.length;i++) if ((i<acquire.length) && acquire[i]) {
// int iIP=channelMap[imageIndex][0];
int iIP=channelIPPort[imageIndex]; // index in composite images (per ip/port)
if (sensorPresent[iIP]==null) { // system board for this channel did not respond null pointer - check cameras were detected
images[imageIndex]=null;
continue;
}
boolean singleSensor=true;
for (int s=0;s<sensorPresent[iIP].length;s++) singleSensor&= !sensorPresent[iIP][s];
if (singleSensor){ // no 10359 multiplexor
if (debugLevel>1) System.out.println("DEBUG393: demuxing single sensor imageIndex="+imageIndex+" iIP="+iIP);
images[imageIndex]=jp4_Instance.demuxClone(imagesIP[iIP]);
} else {
int subCam=channelMap[imageIndex][1];
if (!sensorPresent[iIP][subCam]){ // requested sensor does not exist
images[imageIndex]=null;
continue;
}
// skip missing channels, then demux
for (int s=0;s<channelMap[imageIndex][1];s++) if (!sensorPresent[iIP][s]) subCam--;
if (debugLevel>1) System.out.println("DEBUG393: demuxing imageIndex="+imageIndex+" iIP="+iIP+" subCam="+subCam);
images[imageIndex]=jp4_Instance.demuxImage(imagesIP[iIP],subCam);
}
// this.images[i]=this.jp4_Instances[j].demuxImageOrClone(this.imagesIP[j],this.channelMap[i][1]);
if (images[imageIndex]==null) continue;
if (debugLevel>2) jp4_Instance.listImageProperties(images[imageIndex]);
if (debugLevel>2) jp4_Instance.encodeProperiesToInfo(images[imageIndex]);
if (debugLevel>2) {
jp4_Instance.listImageProperties(images[imageIndex]);
jp4_Instance.decodeProperiesFromInfo(images[imageIndex]);
jp4_Instance.listImageProperties(images[imageIndex]);
}
String title=IJ.d2s(timestamps[iIP],6).replace('.','_')+String.format("-%02d.tiff", imageIndex); // sensor number
images[imageIndex].setTitle(title);
if (flipImages[imageIndex]) { // this is only for physical mirror
flipKeepBayer(images[imageIndex]);
if (debugLevel>2){
System.out.println("=============== flipKeepBayer ==========");
jp4_Instance.listImageProperties(images[imageIndex]);
}
if (show) images[imageIndex].updateAndDraw();
}
images[imageIndex].setProperty("channel", String.format("%02d", imageIndex));
images[imageIndex].setProperty("subcamera",""+getSubCamera(imageIndex));
images[imageIndex].setProperty("sensor_port",""+getSensorPort(imageIndex));
images[imageIndex].setProperty("subchannel", ""+getSubChannel(imageIndex));
// private int [] motorsPosition= null; // motors steps when the images were acquired (for null)
if (motorsPosition!=null) for (int m=0;m<motorsPosition.length;m++ ) {
images[imageIndex].setProperty("MOTOR"+(m+1), ""+motorsPosition[m]);
}
jp4_Instance.encodeProperiesToInfo(images[imageIndex]);
}
}
};
}
startAndJoin(threads);
return this.imagesIP;
}
// should be already triggered!
public ImagePlus [] getImages(
UVLEDandLasers uvLEDandLasers, // or null - not null only for adjustment machine lasers
boolean [] pre_acquire,
boolean [] pre_lasers,
boolean resetAndTrigger,
final boolean show){
// this.reportTiming=this.debugLevel>1; // Need to be set by caller
printTimingInit();
// long startTime = System.nanoTime();
final int debugLevel=this.debugLevel;
final boolean opticalHeadLasersMode=(uvLEDandLasers!=null);
// boolean [] lasers2={true,true};
final boolean [] lasers=opticalHeadLasersMode?pre_acquire:pre_lasers;
if (this.sensorPresent==null) { // cameras were not probed/configured
probeCameraState(); // testing detection
printTiming("=== probeCameraState()");
setupCameraAcquisition();
printTiming("=== setupCameraAcquisition()");
}
boolean [] acquire= new boolean[this.channelMap.length];
for (int i=0;i<acquire.length;i++) {
acquire[i]= ((i<pre_acquire.length) && pre_acquire[i]) || ((lasers!=null) && (i<lasers.length) && lasers[i]);
}
boolean [] opticalHeadLasersInitial=null;
int[] opticalHeadSequence={0,1,2};
final boolean [][] headLaserWasOn={{false,true,false},{false,false,true}};
if (opticalHeadLasersMode){
opticalHeadLasersInitial=uvLEDandLasers.getLasers();
} else if ((lasers!=null) && (this.laserPointers!=null)) {
if (this.debugLevel>2) System.out.println("************ turning lasers off *************");
this.laserPointers.setLasers(0);// turn off all lasers
//lasersSequence
if (this.debugLevel>2) {
System.out.println("getImages(...) 1");
for (int ii=0;ii<this.cameraIPs.length;ii++)System.out.println(ii+": "+this.cameraIPs[ii]);
}
}
if ((lasers==null) && !opticalHeadLasersMode) {
getImages(acquire, resetAndTrigger, show); // get images w/o lasers, flip if needed
printTiming("=== Image acquisition");
return this.imagesIP;
}
//scaleExposureForLasers
// reduce exposure for lasers (both 4 and 2)
final double scaleExposureForLasers=opticalHeadLasersMode?
(((this.scaleExposureForHeadLasers>0.0) && (this.scaleExposureForHeadLasers<1.0))?this.scaleExposureForHeadLasers:0.0):
(((this.scaleExposureForLasers>0.0) && (this.scaleExposureForLasers<1.0))?this.scaleExposureForLasers:0.0);
if (scaleExposureForLasers>0) setupCameraAcquisition(scaleExposureForLasers);
final boolean [] lasersIPs= selectIPs(opticalHeadLasersMode?acquire:lasers);
final int [] sequence=opticalHeadLasersMode?opticalHeadSequence:this.laserPointers.getSequence();
if (debugLevel>2) for (int i=0;i<sequence.length;i++) System.out.println(String.format("Laser sequence[%d]=0x%x", i,sequence[i]));
final ImagePlus [][] laserImagesIP=new ImagePlus[sequence.length-1][this.imagesIP.length];
if (this.debugLevel>2) System.out.println("this.imagesIP.length="+this.imagesIP.length+" sequence.length="+sequence.length);
final String [] imageURLs=this.imageURLs;
final JP46_Reader_camera [] jp4_Instances=this.jp4_Instances;
final Thread[] threads = newThreadArray(this.maxNumberOfThreads);
final AtomicInteger ipIndexAtomic = new AtomicInteger(0);
for (int nSeqNum=1; nSeqNum<sequence.length;nSeqNum++){
if (opticalHeadLasersMode) {
boolean [] bLasers={(sequence[nSeqNum]&1)!=0,(sequence[nSeqNum]&2)!=0};
uvLEDandLasers.setLasersAndUV(bLasers,null,null);
if (debugLevel>2) System.out.println("uvLEDandLasers.setLasersAndUV("+bLasers[0]+","+bLasers[1]+")");
} else {
this.laserPointers.setLasers (sequence[nSeqNum]);// turn on selected laser
if (debugLevel>2) System.out.println(String.format("this.laserPointers.setLasers (0x%x)", sequence[nSeqNum]));
}
resetIPs(selectIPs(lasersIPs)); // flush buffer
if (is14Mpix()) {
try { // FIXME: Make conditional for 14MPix
Thread.sleep(2000);
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
trigger(); // trigger cameras
ipIndexAtomic.set(0);
final int fnSeqNum=nSeqNum;
final boolean reportTiming=this.reportTiming;
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
@Override
public void run() {
for (int ipIndex=ipIndexAtomic.getAndIncrement(); ipIndex<lasersIPs.length;ipIndex=ipIndexAtomic.getAndIncrement()){
long st=System.nanoTime();
if (debugLevel>1) {
System.out.println("image url["+ipIndex+"]="+imageURLs[ipIndex]);
}
laserImagesIP[fnSeqNum-1][ipIndex]=jp4_Instances[ipIndex].openURL(
imageURLs[ipIndex],
"",
true, //scale
null, // new image, nothing to reuse
false); // show image no timestamps here
if (reportTiming){
System.out.println("==== "+imageURLs[ipIndex]+ " opened in "+IJ.d2s(0.000000001*(System.nanoTime()-st),3)+" sec");
}
laserImagesIP[fnSeqNum-1][ipIndex].setProperty("MIRRORED","NO");
// laserImagesIP[fnSeqNum-1][ipIndex].setTitle("raw"+fnSeqNum); //FIXME:Debugging
// laserImagesIP[fnSeqNum-1][ipIndex].show(); //FIXME:Debugging
}
}
};
}
startAndJoin(threads);
printTiming("=== Image # "+nSeqNum+" acquisition");
}
// acquire no-laser image after all others are acquired, so the camera is completely still at that time
if (opticalHeadLasersMode) {
boolean [] bLasers={(sequence[0]&1)!=0,(sequence[0]&2)!=0};
uvLEDandLasers.setLasersAndUV(bLasers,null,null);
if (debugLevel>2) System.out.println("uvLEDandLasers.setLasersAndUV("+bLasers[0]+","+bLasers[1]+")");
} else {
this.laserPointers.setLasers (sequence[0]);// turn on selected laser
if (debugLevel>2) System.out.println(String.format("this.laserPointers.setLasers (0x%x)", sequence[0]));
}
// this.laserPointers.setLasers (0);// turn off all lasers
if (scaleExposureForLasers>0.0) setupCameraAcquisition(1.0);
getImages(acquire, resetAndTrigger, show); // get images w/o lasers, flip if needed
printTiming("=== Final (no-laser) image # 0 acquired");
if (opticalHeadLasersMode) {
uvLEDandLasers.setLasersAndUV(opticalHeadLasersInitial,null,null);
if (debugLevel>2) System.out.println("Restoring lasers: uvLEDandLasers.setLasersAndUV("+opticalHeadLasersInitial[0]+","+opticalHeadLasersInitial[1]+")");
}
// now demux images (if composite) and process laser spots
// for (int sensorNum=0;sensorNum<this.images.length;sensorNum++) if (this.images[sensorNum]!=null){
// final MatchSimulatedPattern matchSimulatedPattern = new MatchSimulatedPattern();
// final ImagePlus imp_pointed=null;
final int bayerG1=0;
final int bayerG2=3;
final int bayerR=1;
final int bayerB=2;
final boolean useOther=laserPointers.laserPointer.useOther;
final boolean otherGreen=laserPointers.laserPointer.otherGreen;
final int [][] channelMap=this.channelMap;
final int [] channelIPPort = this.channelIPPort;
final ImagePlus [] images=this.images;
final boolean [] flipImages=this.flipImages;
final LaserPointersHardware laserPointers=this.laserPointers;
final boolean [][] sensorPresent=this.sensorPresent;
final int debugSensorNumber=this.debugSensorNumber;
printTiming("=== Acquisition done, starting multi-threaded laser pointer location processing");
//TODO: Multithread the next cycle (per-sensor)
final AtomicInteger sensorNumAtomic = new AtomicInteger(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
@Override
public void run() {
// Next calls do not require image acquisition, so default settings for the new instance are OK
JP46_Reader_camera jp4_Instance= new JP46_Reader_camera(false);
MatchSimulatedPattern matchSimulatedPattern = new MatchSimulatedPattern();
for (int sensorNum=sensorNumAtomic.getAndIncrement(); sensorNum<lasers.length;sensorNum=sensorNumAtomic.getAndIncrement()) // null pointer
if (lasers[sensorNum] && (images[sensorNum]!=null)){
// for (int sensorNum=0;sensorNum<lasers.length;sensorNum++) if (lasers[sensorNum] && (this.images[sensorNum]!=null)){ // lasers - here sensors to use lasers for
// int iIP=channelMap[sensorNum][0];
int iIP=channelIPPort[sensorNum]; // index in composite images (per ip/port)
double saturationRed=255.0;
if (images[sensorNum].getProperty("saturation_0")!=null) saturationRed=Double.parseDouble((String)images[sensorNum].getProperty("saturation_0"));
if (scaleExposureForLasers>0) saturationRed*=scaleExposureForLasers; // scaled to reduced exposure time
double[][] backgroundBayer =matchSimulatedPattern.splitBayer (images[sensorNum], null, true); // full window
double[][] pointedBayer;
double [][] pontersXY=null;
// int iIP=this.channelMap[sensorNum][0];
int len=backgroundBayer[bayerG1].length;
double [][] greens=useOther?(new double [sequence.length][]):null;
double [][] reds= new double [sequence.length][];
if (useOther){
greens[0]=otherGreen?(new double[len]):backgroundBayer[bayerB];
if (otherGreen) for (int j=0; j<len;j++) greens[0][j]=0.5*(backgroundBayer[bayerG1][j]+backgroundBayer[bayerG2][j]);
}
reds[0]=backgroundBayer[bayerR]; // no need to clone?
if (debugLevel>2) System.out.println("getImages (): sensorNum="+sensorNum+", iIP="+iIP+" sequence.length="+sequence.length);
// if ((debugLevel>1) && (sensorNum==13)) System.out.println("getImages (): sensorNum="+sensorNum+", iIP="+iIP+" sequence.length="+sequence.length);
boolean singleSensor=true;
for (int s=0;s<sensorPresent[iIP].length;s++) singleSensor&= !sensorPresent[iIP][s];
ImagePlus imp_pointed=null;
for (int nSeqNum=1; nSeqNum<sequence.length; nSeqNum++){
if (debugLevel>2) System.out.println("getImages(): sensorNum="+sensorNum+", iIP="+iIP+" nSeqNum="+nSeqNum+" this.channelMap["+sensorNum+"][1]="+channelMap[sensorNum][1]);
// here we are processing only same sensors that produced no-laser images, no need to check if they exist again
if (singleSensor){ // no 10359 multiplexor
//imp_pointed=jp4_Instances[iIP].demuxClone(laserImagesIP[nSeqNum-1][iIP]);
imp_pointed=jp4_Instance.demuxClone(laserImagesIP[nSeqNum-1][iIP]);
} else {
int subCam=channelMap[sensorNum][1];
// skip missing channels, then demux
for (int s=0;s<channelMap[sensorNum][1];s++) if (!sensorPresent[iIP][s]) subCam--;
//imp_pointed=jp4_Instances[iIP].demuxImage(laserImagesIP[nSeqNum-1][iIP],subCam);
if (laserImagesIP[nSeqNum-1][iIP]==null){
System.out.println("getImages(): laserImagesIP["+(nSeqNum-1)+"]["+iIP+"]==null");
}
imp_pointed=jp4_Instance.demuxImage(laserImagesIP[nSeqNum-1][iIP],subCam);
}
imp_pointed.setTitle(imp_pointed.getTitle()+"_"+sensorNum);
if (flipImages[sensorNum]) {
flipKeepBayer(imp_pointed);
if (show) imp_pointed.updateAndDraw();
}
pointedBayer=matchSimulatedPattern.splitBayer (imp_pointed, null, true);
if (useOther){
greens[nSeqNum]=otherGreen?(new double[len]):pointedBayer[bayerB];
if (otherGreen) for (int j=0; j<len;j++) greens[nSeqNum][j]=0.5*(pointedBayer[bayerG1][j]+pointedBayer[bayerG2][j]);
}
reds[nSeqNum]=pointedBayer[bayerR].clone();
}
//minimalIntensity scaleExposureForLasers>0 saturationRed
pontersXY=laserPointers.laserPointer.getPointerXY( // returns x,y pair or null if pointer not detected
opticalHeadLasersMode,
saturationRed,
scaleExposureForLasers, //>0.0,
greens, // combined Bayer greens for each image, starting with no-laser
reds, // red Bayer component for each image, starting with no-laser
opticalHeadLasersMode?headLaserWasOn:laserPointers.laserWasOn(), // array specifying which image should have pointer on, for each laser
imp_pointed.getWidth(),// image width in pixels
imp_pointed.getTitle(), // String title,
debugLevel+ ((sensorNum==debugSensorNumber)?1:0) // debug level (normal == 1)
// debugLevel
);
int pointersDetected=0;
if (!opticalHeadLasersMode){
for (int nPointer=0; nPointer<laserPointers.getNumberOfLasers();nPointer++){
if (pontersXY[nPointer]!=null){
if (debugLevel>1) System.out.println("image:"+sensorNum+" pointer #"+(nPointer+1)+
", X="+pontersXY[nPointer][0]+", Y="+pontersXY[nPointer][1]);
images[sensorNum].setProperty("POINTER_X_"+nPointer, IJ.d2s(pontersXY[nPointer][0],1));
images[sensorNum].setProperty("POINTER_Y_"+nPointer, IJ.d2s(pontersXY[nPointer][1],1));
if ((laserPointers.laserPointer.laserUVMap!=null) && (laserPointers.laserPointer.laserUVMap[nPointer]!=null)) {
images[sensorNum].setProperty("POINTER_U_"+nPointer, IJ.d2s(laserPointers.laserPointer.laserUVMap[nPointer][0],1));
images[sensorNum].setProperty("POINTER_V_"+nPointer, IJ.d2s(laserPointers.laserPointer.laserUVMap[nPointer][1],1));
}
pointersDetected++;
}
}
if ((pointersDetected>0) && (debugLevel>0)) {
System.out.println("image:"+sensorNum+" - "+pointersDetected+" pointer"+((pointersDetected>1)?"s":"")+" detected");
}
} else {
for (int nPointer=0; nPointer<2;nPointer++){
if (pontersXY[nPointer]!=null){
if (debugLevel>1) System.out.println("image:"+sensorNum+" pointer #"+(nPointer+1)+
", X="+pontersXY[nPointer][0]+", Y="+pontersXY[nPointer][1]);
images[sensorNum].setProperty("HEAD_POINTER_X_"+nPointer, IJ.d2s(pontersXY[nPointer][0],1));
images[sensorNum].setProperty("HEAD_POINTER_Y_"+nPointer, IJ.d2s(pontersXY[nPointer][1],1));
pointersDetected++;
}
}
}
images[sensorNum].setProperty("HEAD_POINTERS", pointersDetected+"");
//jp4_Instances[iIP].encodeProperiesToInfo(images[sensorNum]);
jp4_Instance.encodeProperiesToInfo(images[sensorNum]);
}
}
};
}
startAndJoin(threads);
// this.laserPointers.setLasers (0);// turn off all lasers
printTiming("=== Image acquisition/laser pointers location");
return this.imagesIP;
}
public double [][] getHeadPointers(ImagePlus imp){
if (imp.getProperty("HEAD_POINTERS")==null) return null;
int numHeadPointers=Integer.parseInt((String) imp.getProperty("HEAD_POINTERS"));
double [][] headPointers=new double[numHeadPointers][];
for (int n=0;n<headPointers.length;n++){
if ((imp.getProperty("HEAD_POINTER_X_"+n)!=null) && (imp.getProperty("HEAD_POINTER_Y_"+n)!=null)){
headPointers[n]=new double[2];
headPointers[n][0]=Double.parseDouble((String)imp.getProperty("HEAD_POINTER_X_"+n));
headPointers[n][1]=Double.parseDouble((String)imp.getProperty("HEAD_POINTER_Y_"+n));
} else headPointers[n]=null;
}
return headPointers;
}
// return array of last acquired images
public ImagePlus [] getImages(){
return this.images;
}
public ImagePlus [] getImages(int numberOfPointers){ // return images with at least this number of pointers detected
ImagePlus [] filteredImages=this.images.clone();
for (int i=0;i<filteredImages.length;i++) if (getNumberOfPointers(i)<numberOfPointers) filteredImages[i]=null;
return filteredImages;
}
public int getNumberOfPointers (int sensorNum){
return getNumberOfPointers (this.images[sensorNum]);
}
public int getNumberOfPointers (ImagePlus imp){
if (imp==null) return 0;
if (imp.getProperty("POINTERS")!=null) return Integer.parseInt((String) imp.getProperty("POINTERS"));
else return 0;
}
public int saveImages(boolean [] selection, String directory, boolean updateStatus){
int numImg=0;
boolean notYetPrinted=true;
for (int i=0;(i<this.channelMap.length) && ((selection==null) || (i<selection.length));i++)
if ((this.images[i]!=null) && ((selection==null) || selection[i])){
FileSaver fs=new FileSaver(this.images[i]);
String path=directory+Prefs.getFileSeparator()+this.images[i].getTitle();
if (updateStatus) IJ.showStatus("Saving "+path);
if (this.debugLevel>0){
if (this.debugLevel>1) System.out.println("Saving "+path); // was >0
else if (notYetPrinted) {
System.out.println("Saving "+path+ " (and other with the same timestamp)" ); // was >0
notYetPrinted=false;
}
}
fs.saveAsTiff(path);
numImg++;
}
return numImg;
}
/*
imp_psf = new ImagePlus(filePaths[dirNum][fileNum][1], stack);
// if (DEBUG_LEVEL>1) imp_psf.show();
if (DEBUG_LEVEL>1) System.out.println("Saving result to"+filePaths[dirNum][fileNum][1]+ " at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
FileSaver fs=new FileSaver(imp_psf);
fs.saveAsTiffStack(filePaths[dirNum][fileNum][1]);
*/
/**
* FLips image vertically and crops by one pixel at the top and bottom (to preserve Bayer pattern)
* @param imp
* @return
*/
public ImagePlus flipAndCrop(ImagePlus imp){
String title=imp.getTitle();
imp.setTitle(title+"-original");
ImageProcessor ip=imp.getProcessor();
ip.setRoi(0,1,ip.getWidth(),ip.getHeight()-2);
ImageProcessor ip2=ip.crop();
ip2.flipVertical();
ImagePlus imp_new=new ImagePlus(title,ip2);
// copy all properties and add "MIRRORED=Y"
Set<Object> imp_set;
Properties imp_prop;
Iterator<Object> itr;
String str;
imp_prop=imp.getProperties();
if (imp_prop!=null) {
imp_set=imp_prop.keySet();
itr=imp_set.iterator();
while(itr.hasNext()) {
str = (String) itr.next();
imp_new.setProperty(str,imp_prop.getProperty(str));
}
}
imp_new.setProperty("MIRRORED","YES");
return imp_new;
}
public ImagePlus flipKeepBayer(ImagePlus imp){
ImageProcessor ip=imp.getProcessor();
float [] pixels=(float[]) ip.getPixels();
float [] new_pixels=new float[pixels.length];
int width=ip.getWidth();
int height=ip.getHeight();
for (int i=1;i<height-1;i++) for (int j=0;j<width;j++){
new_pixels[i*width+j]=pixels[(height-i)*width+j];
}
for (int j=0;j<width;j++) new_pixels[j]=new_pixels[2*width+j]; // copy second line to 0
ip.setPixels(new_pixels);
imp.setProperty("MIRRORED","YES");
return imp;
}
public ImagePlus flipKeepBayerNew(ImagePlus imp){
float [] pixels=(float []) imp.getProcessor().getPixels();
float [] new_pixels=new float[pixels.length];
int width=imp.getWidth();
int height=imp.getHeight();
for (int i=1;i<height-1;i++) for (int j=0;j<width;j++){
new_pixels[i*width+j]=pixels[(height-i)*width+j];
}
for (int j=0;j<width;j++) new_pixels[j]=new_pixels[2*width+j]; // copy second line to 0
ImageProcessor ip=new FloatProcessor(imp.getWidth(), imp.getHeight());
ip.setPixels(new_pixels);
ip.resetMinAndMax();
ImagePlus imp_flipped= new ImagePlus(imp.getTitle()+"-flipped", ip);
imp_flipped.setProperty("MIRRORED","YES");
return imp_flipped;
}
// in detection mode - reduce exp
public void test1(boolean useLasers) {
getImages(
null, // UVLEDLasers
selectAllSubcameras(),
(useLasers?selectAllSubcameras():null),
true,
this.debugLevel>1); // reset and trigger
if (this.debugLevel>1) {
if (this.debugLevel>2) System.out.println("++++++++++++++++++ Image Properies ++++++++++++++++++++++++++++");
for (int i=0;i<this.images.length;i++) if (this.images[i]!=null) {
// int j=this.channelMap[i][0];
int j=channelIPPort[i]; // sincer NC393 adder port
if (this.debugLevel>2) {
System.out.println("Image #"+i);
this.jp4_Instances[j].listImageProperties(this.images[i]);
}
if ((this.debugLevel>2) || (getNumberOfPointers (i)>0)) {
this.images[i].show();
this.images[i].updateAndDraw();
}
}
}
}
public void acquire(String directory, boolean useLasers, boolean updateStatus) {
getImages(
null, // UVLEDLasers
selectAllSubcameras(),
(useLasers?selectAllSubcameras():null),
true,
this.debugLevel>1); // reset and trigger
int numImg=saveImages(selectAllSubcameras(), directory, updateStatus);
if (this.debugLevel>1) System.out.println("Saved "+numImg+" images.");
}
public ImagePlus acquireSingleImage (boolean useLasers, boolean updateStatus){
getImages(
null, // UVLEDLasers
selectAllSubcameras(),
(useLasers?selectAllSubcameras():null),
true,
this.debugLevel>1); // reset and trigger
this.lastTimestamp=(String) this.images[0].getProperty("timestamp");
return this.images[0];
}
public ImagePlus [] acquireSeveralImages (boolean useLasers, boolean updateStatus){
getImages(
null, // UVLEDLasers
selectAllSubcameras(),
(useLasers?selectAllSubcameras():null),
true,
this.debugLevel>1); // reset and trigger
this.lastTimestamp=(String) this.images[0].getProperty("timestamp");
return this.images;
}
public ImagePlus acquireSingleImage (UVLEDandLasers uvLEDLasers, boolean updateStatus){
getImages(
uvLEDLasers, // UVLEDLasers
selectAllSubcameras(),
null,
true,
this.debugLevel>1); // reset and trigger
this.lastTimestamp=(String) this.images[0].getProperty("timestamp");
return this.images[0];
}
public String getLastTimestampUnderscored(){
return this.lastTimestamp.replace('.','_');
}
/* Create a Thread[] array as large as the number of processors available.
* From Stephan Preibisch's Multithreading.java class. See:
* http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
*/
private Thread[] newThreadArray(int maxCPUs) {
int n_cpus = Runtime.getRuntime().availableProcessors();
if (n_cpus>maxCPUs)n_cpus=maxCPUs;
return new Thread[n_cpus];
}
/* Start all given threads and wait on each of them until all are done.
* From Stephan Preibisch's Multithreading.java class. See:
* http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
*/
private static void startAndJoin(Thread[] threads)
{
for (int ithread = 0; ithread < threads.length; ++ithread)
{
threads[ithread].setPriority(Thread.NORM_PRIORITY);
threads[ithread].start();
}
try
{
for (int ithread = 0; ithread < threads.length; ++ithread)
threads[ithread].join();
} catch (InterruptedException ie)
{
throw new RuntimeException(ie);
}
}
}