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ColorMIP_Mask_Search.java
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ColorMIP_Mask_Search.java
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import ij.*;
import ij.io.*;
import ij.plugin.filter.*;
import ij.process.*;
import ij.gui.*;
import java.io.*;
import java.util.Arrays;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import java.util.*;
public class ColorMIP_Mask_Search implements PlugInFilter
{
ImagePlus imp, imp2;
ImageProcessor ip1, nip1, ip2, ip3, ip4, ip5, ip6, ip33;
int pix1=0, CheckPost,UniqueLineName=0,IsPosi;
int pix3=0,Check=0,arrayPosition=0,dupdel=1,FinalAdded=1,enddup=0;;
ImagePlus newimp, newimpOri;
String linename,LineNo, LineNo2,preLineNo="A",FullName,LineName,arrayName,PostName;
String args [] = new String[10],PreFullLineName,ScorePre,TopShortLinename;
ExecutorService m_executor;
boolean DUPlogon;
public class SearchResult{
String m_name;
int m_sid;
long m_offset;
byte[] m_pixels;
byte[] m_colocs;
ImageProcessor m_iporg;
ImageProcessor m_ipcol;
SearchResult(String name, int sid, long offset, byte[] pxs, byte[] coloc, ImageProcessor iporg, ImageProcessor ipcol){
m_name = name;
m_sid = sid;
m_offset = offset;
m_pixels = pxs;
m_colocs = coloc;
m_iporg = iporg;
m_ipcol = ipcol;
}
}
public int setup(String arg, ImagePlus imp)
{
IJ.register (ColorMIP_Mask_Search.class);
if (IJ.versionLessThan("1.32c")){
IJ.showMessage("Error", "Please Update ImageJ.");
return 0;
}
// IJ.log(" wList;"+String.valueOf(wList));
this.imp = imp;
if(imp.getType()!=ImagePlus.COLOR_RGB){
IJ.showMessage("Error", "Plugin requires RGB image");
return 0;
}
return DOES_RGB;
// IJ.log(" noisemethod;"+String.valueOf(ff));
}
public String getZeroFilledNumString(int num, int digit) {
String stri = Integer.toString(num);
if (stri.length() < digit) {
String zeros = "";
for (int i = digit - stri.length(); i > 0; i--)
zeros += "0";
stri = zeros + stri;
}
return stri;
}
public String getZeroFilledNumString(double num, int decimal_len, int fraction_len) {
String strd = String.format("%."+fraction_len+"f", num);
int decdigit = strd.length()-(fraction_len+1);
if (decdigit < decimal_len) {
String zeros = "";
for (int i = decimal_len - decdigit; i > 0; i--)
zeros += "0";
strd = zeros + strd;
}
return strd;
}
public void run(ImageProcessor ip){
int wList [] = WindowManager.getIDList();
if (wList==null || wList.length<2) {
IJ.showMessage("There should be at least two windows open");
return;
}
int imageno = 0; int SingleSliceMIPnum=0; int MultiSliceStack=0;
String titles [] = new String[wList.length];
int slices [] = new int[wList.length];
for (int i=0; i<wList.length; i++) {
ImagePlus imp = WindowManager.getImage(wList[i]);
if (imp!=null){
titles[i] = imp.getTitle();//Mask.tif and Data.tif
slices[i] = imp.getStackSize();
if(slices[i]>1){
titles[i] = titles[i]+" ("+slices[i]+") slices";
MultiSliceStack = i;
}else{
titles[i] = titles[i]+" ("+slices[i]+") slice";
SingleSliceMIPnum = i;
}
imageno = imageno +1;
}else
titles[i] = "";
}
String[] negtitles = new String[titles.length+1];
negtitles[0] = "none";
System.arraycopy(titles, 0, negtitles, 1, titles.length);
/////Dialog//////////////////////////////////////////////
int Mask=(int)Prefs.get("Mask.int",0);
boolean mirror_mask=(boolean)Prefs.get("mirror_mask.boolean",false);
int NegMask=(int)Prefs.get("NegMask.int",0);
boolean mirror_negmask=(boolean)Prefs.get("mirror_negmask.boolean",false);
int datafile=(int)Prefs.get("datafile.int",1);
int Thres=(int)Prefs.get("Thres.int",100);
double pixThres=(double)Prefs.get("pixThres.double",10);
int dupline=(int)Prefs.get("dupline.int",2);
int colormethod=(int)Prefs.get("colormethod.int",1);
double pixflu=(double)Prefs.get("pixflu.double",2);
int xyshift=(int)Prefs.get("xyshift.int",0);
boolean logon=(boolean)Prefs.get("logon.boolean",false);
int Thresm=(int)Prefs.get("Thresm.int",50);
int NegThresm=(int)Prefs.get("NegThresm.int",50);
boolean logNan=(boolean)Prefs.get("logNan.boolean",false);
int labelmethod=(int)Prefs.get("labelmethod.int",0);
boolean DUPlogon=(boolean)Prefs.get("DUPlogon.boolean",false);
boolean GCON=(boolean)Prefs.get("GCON.boolean",false);
boolean ShowCo=(boolean)Prefs.get("ShowCo.boolean",false);
int NumberSTint=(int)Prefs.get("NumberSTint.int",0);
int threadNum=(int)Prefs.get("threadNum.int",8);
if(datafile >= imageno){
int singleslice=0; int Maxsingleslice=0; int MaxStack=0;
for(int isliceSearch=0; isliceSearch<wList.length; isliceSearch++){
singleslice=slices[isliceSearch];
if(singleslice>Maxsingleslice){
Maxsingleslice=singleslice;
MaxStack=isliceSearch;
}
}
datafile=MaxStack;
}
if(Mask >= imageno){
int singleslice=0; int isliceSearch=0;
while(singleslice!=1){
singleslice=slices[isliceSearch];
isliceSearch=isliceSearch+1;
if(isliceSearch>imageno){
IJ.showMessage("Need to be a single slice open");
return;
}
}
Mask=isliceSearch-1;
}
if(NegMask >= imageno+1)
NegMask = 0;
ImagePlus impMask = WindowManager.getImage(wList[Mask]);
int MaskSliceNum = impMask.getStackSize();
ImagePlus impData = WindowManager.getImage(wList[datafile]);
int DataSliceNum = impData.getStackSize();
if(MaskSliceNum!=1){
Mask=SingleSliceMIPnum;
}
if(DataSliceNum==1){
datafile=MultiSliceStack;
}
// IJ.log("mask; "+String.valueOf(Mask)+"datafile; "+String.valueOf(datafile)+"imageno; "+String.valueOf(imageno)+"wList.length; "+String.valueOf(wList.length));
if(labelmethod>1)
labelmethod=1;
GenericDialog gd = new GenericDialog("ColorMIP_3D_Mask search");
gd.addChoice("Mask", titles, titles[Mask]); //Mask
gd.addSlider("1.Threshold for mask", 0, 255, Thresm);
gd.setInsets(0, 340, 0);
gd.addCheckbox("1.Add mirror search", mirror_mask);
gd.setInsets(20, 0, 0);
gd.addChoice("Negative Mask", negtitles, negtitles[NegMask]); //Negative Mask
gd.addSlider("2.Threshold for negative mask", 0, 255, NegThresm);
gd.setInsets(0, 340, 0);
gd.addCheckbox("2.Add mirror search", mirror_negmask);
gd.setInsets(20, 0, 0);
gd.addChoice("Data for the ColorMIP", titles, titles[datafile]); //Data
//gd.addNumericField("Threshold", slicenumber,0);
gd.addSlider("3.Threshold for data", 0, 255, Thres);
gd.addMessage("");
// gd.addSlider("100x % of Positive PX Threshold", (double) 0, (double) 10000, pixThres);
gd.addNumericField("% of Positive PX Threshold 0-100 %", pixThres, 2);
gd.addSlider("Pix Color Fluctuation, 1.18 per slice", 0, 20, pixflu);
String[] dupnumstr = new String[11];
for (int i = 0; i < dupnumstr.length; i++)
dupnumstr[i] = Integer.toString(i);
gd.addChoice("Duplicated line numbers; (only for GMR & VT), 0 = no check", dupnumstr, dupnumstr[dupline]); //Mask
gd.setInsets(20, 0, 0);
gd.addNumericField("Thread", threadNum, 0);
//gd.setInsets(0, 372, 0);
//gd.addCheckbox("Show Duplication log",DUPlogon);
//gd.setInsets(0, 362, 5);
//String [] ColorDis = {"Combine", "Two windows"};
//gd.addRadioButtonGroup("Result windows", ColorDis, 1, 2, ColorDis[colormethod]);
//gd.setInsets(0, 362, 5);
//String [] labelmethodST = {"overlap value", "overlap value + line name"};
//gd.addRadioButtonGroup("Slice sorting method; ", labelmethodST, 1, 2, labelmethodST[labelmethod]);
gd.setInsets(0, 362, 5);
String [] shitstr = {"0px ", "2px ", "4px "};
gd.addRadioButtonGroup("XY Shift: ", shitstr, 1, 3, shitstr[xyshift/2]);
gd.setInsets(0, 362, 5);
String [] NumberST = {"%", "absolute value"};
gd.addRadioButtonGroup("Scoring method; ", NumberST, 1, 2, NumberST[NumberSTint]);
gd.setInsets(20, 372, 0);
gd.addCheckbox("Show log",logon);
gd.setInsets(20, 372, 0);
gd.addCheckbox("Clear memory before search. Slow at beginning but fast search",GCON);
gd.setInsets(20, 372, 0);
gd.addCheckbox("Co-localized stack shown (more memory needs)",ShowCo);
gd.showDialog();
if(gd.wasCanceled()){
return;
}
Mask = gd.getNextChoiceIndex(); //Mask
Thresm=(int)gd.getNextNumber();
mirror_mask = gd.getNextBoolean();
NegMask = gd.getNextChoiceIndex(); //Negative Mask
NegThresm=(int)gd.getNextNumber();
mirror_negmask = gd.getNextBoolean();
datafile = gd.getNextChoiceIndex(); //Color MIP
Thres=(int)gd.getNextNumber();
pixThres=(double)gd.getNextNumber();
pixflu=(double)gd.getNextNumber();
dupline=Integer.parseInt(dupnumstr[gd.getNextChoiceIndex()]);
DUPlogon = false;
threadNum = (int)gd.getNextNumber();
xyshift=Integer.parseInt( ((String)gd.getNextRadioButton()).substring(0,1) );
String thremethodSTR="Two windows";
String labelmethodSTR="overlap value + line name";
String ScoringM=(String)gd.getNextRadioButton();
logon = gd.getNextBoolean();
GCON = gd.getNextBoolean();
ShowCo = gd.getNextBoolean();
if(GCON==true)
System.gc();
if(logon==true){
GenericDialog gd2 = new GenericDialog("log option");
gd2.addCheckbox("Show NaN",logNan);
gd2.showDialog();
if(gd2.wasCanceled()){
return;
}
String logmethodSTR=(String)gd2.getNextRadioButton();
logNan = gd2.getNextBoolean();
Prefs.set("logNan.boolean",logNan);
}//if(logon==true){
colormethod=1;
if(thremethodSTR=="Combine")
colormethod=0;
if(labelmethodSTR=="overlap value")
labelmethod=0;//on top
if(labelmethodSTR=="overlap value + line name")
labelmethod=1;
if(ScoringM=="%")
NumberSTint=0;
else
NumberSTint=1;
Prefs.set("Mask.int", Mask);
Prefs.set("mirror_mask.boolean", mirror_mask);
Prefs.set("mirror_negmask.boolean", mirror_negmask);
Prefs.set("Thresm.int", Thresm);
Prefs.set("NegMask.int", NegMask);
Prefs.set("NegThresm.int", NegThresm);
Prefs.set("pixThres.double", pixThres);
Prefs.set("Thres.int", Thres);
Prefs.set("datafile.int",datafile);
Prefs.set("colormethod.int",colormethod);
Prefs.set("pixflu.double", pixflu);
Prefs.set("xyshift.int",xyshift);
Prefs.set("logon.boolean",logon);
Prefs.set("labelmethod.int",labelmethod);
Prefs.set("DUPlogon.boolean",DUPlogon);
Prefs.set("dupline.int",dupline);
Prefs.set("GCON.boolean",GCON);
Prefs.set("ShowCo.boolean",ShowCo);
Prefs.set("NumberSTint.int",NumberSTint);
Prefs.set("threadNum.int",threadNum);
double pixfludub=pixflu/100;
// IJ.log(" pixfludub;"+String.valueOf(pixfludub));
final double pixThresdub = pixThres/100;///10000
// IJ.log(" pixThresdub;"+String.valueOf(pixThresdub));
///////
ImagePlus imask = WindowManager.getImage(wList[Mask]); //Mask
ImagePlus inegmask = NegMask > 0 ? WindowManager.getImage(wList[NegMask-1]) : null; //Negative Mask
titles[Mask] = imask.getTitle();
if (inegmask != null) negtitles[NegMask] = inegmask.getTitle();
ImagePlus idata = WindowManager.getImage(wList[datafile]); //Data
ip1 = imask.getProcessor(); //Mask
nip1 = NegMask > 0 ? inegmask.getProcessor() : null; //Negative Mask
int slicenumber = idata.getStackSize();
int width = imask.getWidth();
int height = imask.getHeight();
if(IJ.escapePressed())
return;
IJ.showProgress(0.0);
// IJ.log("maxvalue; "+maxvalue2+" gap; "+gap);
final ImageStack st3 = idata.getStack();
int posislice = 0;
double posipersent2 = 0;
double pixThresdub2 = 0;
final ColorMIPMaskCompare cc = new ColorMIPMaskCompare (ip1, Thresm, mirror_mask, nip1, NegThresm, mirror_negmask, Thres, pixfludub, xyshift);
m_executor = Executors.newFixedThreadPool(threadNum);
final int maskpos_st = cc.getMaskStartPos()*3;
final int maskpos_ed = cc.getMaskEndPos()*3;
final int stripsize = maskpos_ed-maskpos_st+3;
long start, end;
start = System.nanoTime();
//IJ.log(" masksize;"+String.valueOf(masksize));
ArrayList<String> srlabels = new ArrayList<String>();
ArrayList<String> finallbs = new ArrayList<String>();
HashMap<String, SearchResult> srdict = new HashMap<String, SearchResult>(1000);
final int fslicenum = slicenumber;
final int fthreadnum = threadNum;
final boolean fShowCo = ShowCo;
final boolean flogon = logon;
final boolean flogNan = logNan;
final int fNumberSTint = NumberSTint;
final int flabelmethod = labelmethod;
if (st3.isVirtual()) {
final VirtualStack vst = (VirtualStack)st3;
if (vst.getDirectory() == null) {
IJ.log("Virtual Stack (stack)");
final FileInfo fi = idata.getOriginalFileInfo();
if (fi.directory.length()>0 && !(fi.directory.endsWith(Prefs.separator)||fi.directory.endsWith("/")))
fi.directory += Prefs.separator;
final String datapath = fi.directory + fi.fileName;
final long size = fi.width*fi.height*fi.getBytesPerPixel();
final List<Callable<ArrayList<SearchResult>>> tasks = new ArrayList<Callable<ArrayList<SearchResult>>>();
for (int ithread = 0; ithread < threadNum; ithread++) {
final int ftid = ithread;
final int f_th_snum = fslicenum/fthreadnum;
tasks.add(new Callable<ArrayList<SearchResult>>() {
public ArrayList<SearchResult> call() {
ArrayList<SearchResult> out = new ArrayList<SearchResult>();
RandomAccessFile f = null;
try {
f = new RandomAccessFile(datapath, "r");
for (int slice = fslicenum/fthreadnum*ftid+1, count = 0; slice <= fslicenum && count < f_th_snum; slice++, count++) {
byte [] impxs = new byte[(int)size];
byte [] colocs = null;
if (fShowCo) colocs = new byte[(int)size];
if (ftid == 0)
IJ.showProgress((double)slice/(double)f_th_snum);
long loffset = fi.getOffset() + (slice-1)*(size+fi.gapBetweenImages) + maskpos_st;
f.seek(loffset);
f.read(impxs, maskpos_st, stripsize);
linename=st3.getSliceLabel(slice);
ColorMIPMaskCompare.Output res = cc.runSearch(impxs, colocs);
int posi = res.matchingPixNum;
double posipersent = res.matchingPct;
if(posipersent<=pixThresdub){
if (flogon==true && flogNan==true)
IJ.log("NaN");
}else if(posipersent>pixThresdub){
loffset = fi.getOffset() + (slice-1)*(size+fi.gapBetweenImages);
double posipersent3=posipersent*100;
double pixThresdub3=pixThresdub*100;
posipersent3 = posipersent3*100;
posipersent3 = Math.round(posipersent3);
double posipersent2 = posipersent3 /100;
pixThresdub3 = pixThresdub3*100;
pixThresdub3 = Math.round(pixThresdub3);
if(flogon==true && flogNan==true)// sort by name
IJ.log("Positive linename; "+linename+" "+String.valueOf(posipersent2));
String title="";
if(fNumberSTint==0){
String numstr = getZeroFilledNumString(posipersent2, 3, 2);
title = (flabelmethod==0 || flabelmethod==1) ? numstr+"_"+linename : linename+"_"+numstr;
}
else if(fNumberSTint==1){
String posiST=getZeroFilledNumString(posi, 4);
title = (flabelmethod==0 || flabelmethod==1) ? posiST+"_"+linename : linename+"_"+posiST;
}
out.add(new SearchResult(title, slice, loffset, impxs, colocs, null, null));
if (ftid == 0)
IJ.showStatus("Number of Hits (estimated): "+out.size()*fthreadnum);
}
}
f.close();
} catch (IOException e) {
e.printStackTrace();
} finally {
try { if (f != null) f.close(); }
catch (IOException e) { e.printStackTrace(); }
}
return out;
}
});
}
try {
List<Future<ArrayList<SearchResult>>> taskResults = m_executor.invokeAll(tasks);
for (Future<ArrayList<SearchResult>> future : taskResults) {
for (SearchResult r : future.get()) {
srlabels.add(r.m_name);
srdict.put(r.m_name, r);
posislice=posislice+1;
}
}
} catch (Exception e) {
e.printStackTrace();
}
} else {
IJ.log("Virtual Stack (directory)");
String dirtmp = vst.getDirectory();
if (dirtmp.length()>0 && !(dirtmp.endsWith(Prefs.separator)||dirtmp.endsWith("/")))
dirtmp += Prefs.separator;
final String directory = dirtmp;
final long size = width*height*3;
final List<Callable<ArrayList<SearchResult>>> tasks = new ArrayList<Callable<ArrayList<SearchResult>>>();
for (int ithread = 0; ithread < threadNum; ithread++) {
final int ftid = ithread;
final int f_th_snum = fslicenum/fthreadnum;
tasks.add(new Callable<ArrayList<SearchResult>>() {
public ArrayList<SearchResult> call() {
ArrayList<SearchResult> out = new ArrayList<SearchResult>();
for (int slice = fslicenum/fthreadnum*ftid+1, count = 0; slice <= fslicenum && count < f_th_snum; slice++, count++) {
byte [] impxs = new byte[(int)size];
byte [] colocs = null;
if (fShowCo) colocs = new byte[(int)size];
String datapath = directory + vst.getFileName(slice);
if (ftid == 0)
IJ.showProgress((double)slice/(double)f_th_snum);
try {
RandomAccessFile f = new RandomAccessFile(datapath, "r");
TiffDecoder tfd = new TiffDecoder(directory, vst.getFileName(slice));
if (tfd == null) continue;
FileInfo[] fi_list = tfd.getTiffInfo();
if (fi_list == null) continue;
long loffset = fi_list[0].getOffset();
f.seek(loffset+(long)maskpos_st);
f.read(impxs, maskpos_st, stripsize);
String linename = st3.getSliceLabel(slice);
ColorMIPMaskCompare.Output res = cc.runSearch(impxs, colocs);
int posi = res.matchingPixNum;
double posipersent = res.matchingPct;
if(posipersent<=pixThresdub){
if (flogon==true && flogNan==true)
IJ.log("NaN");
}else if(posipersent>pixThresdub){
double posipersent3=posipersent*100;
double pixThresdub3=pixThresdub*100;
posipersent3 = posipersent3*100;
posipersent3 = Math.round(posipersent3);
double posipersent2 = posipersent3 /100;
pixThresdub3 = pixThresdub3*100;
pixThresdub3 = Math.round(pixThresdub3);
if(flogon==true && flogNan==true)// sort by name
IJ.log("Positive linename; "+linename+" "+String.valueOf(posipersent2));
String title="";
if(fNumberSTint==0){
String numstr = getZeroFilledNumString(posipersent2, 3, 2);
title = (flabelmethod==0 || flabelmethod==1) ? numstr+"_"+linename : linename+"_"+numstr;
}
else if(fNumberSTint==1) {
String posiST=getZeroFilledNumString(posi, 4);
title = (flabelmethod==0 || flabelmethod==1) ? posiST+"_"+linename : linename+"_"+posiST;
}
out.add(new SearchResult(title, slice, loffset, impxs, colocs, null, null));
if (ftid == 0)
IJ.showStatus("Number of Hits (estimated): "+out.size()*fthreadnum);
}
f.close();
} catch (IOException e) {
continue;
}
}
return out;
}
});
}
try {
List<Future<ArrayList<SearchResult>>> taskResults = m_executor.invokeAll(tasks);
for (Future<ArrayList<SearchResult>> future : taskResults) {
for (SearchResult r : future.get()) {
srlabels.add(r.m_name);
srdict.put(r.m_name, r);
posislice=posislice+1;
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
} else {
final List<Callable<ArrayList<SearchResult>>> tasks = new ArrayList<Callable<ArrayList<SearchResult>>>();
for (int ithread = 0; ithread < threadNum; ithread++) {
final int ftid = ithread;
final int f_th_snum = fslicenum/fthreadnum;
tasks.add(new Callable<ArrayList<SearchResult>>() {
public ArrayList<SearchResult> call() {
ArrayList<SearchResult> out = new ArrayList<SearchResult>();
for (int slice = fslicenum/fthreadnum*ftid+1, count = 0; slice <= fslicenum && count < f_th_snum; slice++, count++) {
if (ftid == 0)
IJ.showProgress((double)slice/(double)f_th_snum);
ColorProcessor ipnew = null;
if (fShowCo) ipnew = new ColorProcessor(width, height);
ImageProcessor ip3 = st3.getProcessor(slice);
String linename = st3.getSliceLabel(slice);
ColorMIPMaskCompare.Output res = cc.runSearch(ip3, ipnew);
int posi = res.matchingPixNum;
double posipersent = res.matchingPct;
if(posipersent<=pixThresdub){
if (flogon==true && flogNan==true)
IJ.log("NaN");
}else if(posipersent>pixThresdub){
double posipersent3=posipersent*100;
double pixThresdub3=pixThresdub*100;
posipersent3 = posipersent3*100;
posipersent3 = Math.round(posipersent3);
double posipersent2 = posipersent3 /100;
pixThresdub3 = pixThresdub3*100;
pixThresdub3 = Math.round(pixThresdub3);
if(flogon==true && flogNan==true)// sort by name
IJ.log("Positive linename; "+linename+" "+String.valueOf(posipersent2));
String title="";
if(fNumberSTint==0){
String numstr = getZeroFilledNumString(posipersent2, 3, 2);
title = (flabelmethod==0 || flabelmethod==1) ? numstr+"_"+linename : linename+"_"+numstr;
}
else if(fNumberSTint==1) {
String posiST=getZeroFilledNumString(posi, 4);
title = (flabelmethod==0 || flabelmethod==1) ? posiST+"_"+linename : linename+"_"+posiST;
}
out.add(new SearchResult(title, slice, 0L, null, null, ip3, ipnew));
if (ftid == 0)
IJ.showStatus("Number of Hits (estimated): "+out.size()*fthreadnum);
}
}
return out;
}
});
}
try {
List<Future<ArrayList<SearchResult>>> taskResults = m_executor.invokeAll(tasks);
for (Future<ArrayList<SearchResult>> future : taskResults) {
for (SearchResult r : future.get()) {
srlabels.add(r.m_name);
srdict.put(r.m_name, r);
posislice=posislice+1;
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
IJ.showStatus("Number of Hits: "+String.valueOf(posislice));
IJ.log(" positive slice No.;"+String.valueOf(posislice));
int PositiveSlices=posislice;
String OverlapValueLineArray [] = new String [posislice];
for(int format=0; format<posislice; format++)
OverlapValueLineArray [format]="0";
String LineNameArray [] = new String[posislice];
if(posislice>0){// if result is exist
int posislice2=posislice;
if(posislice==1)
dupline=0;
String linenameTmpo;
for(int CreateLineArray=0; CreateLineArray<posislice; CreateLineArray++){
linenameTmpo = srlabels.get(CreateLineArray);
int GMRPosi=(linenameTmpo.indexOf("GMR"));
int RPosi=(linenameTmpo.indexOf("R"));
int VTPosi=(linenameTmpo.indexOf("VT"));
if(RPosi!=-1 && GMRPosi==-1){// it is R
int UnderS2=(linenameTmpo.indexOf("_", RPosi ));// end of line number
LineNo=linenameTmpo.substring(RPosi, UnderS2);// GMR_01A02
}else if(GMRPosi!=-1){// it is GMR
int UnderS1=(linenameTmpo.indexOf("_", GMRPosi+1));
int UnderS2=(linenameTmpo.indexOf("_", UnderS1+1 ));// end of line number
LineNo=linenameTmpo.substring(GMRPosi, UnderS2);// GMR_01A02
}else if(VTPosi!=-1){//if VT
int UnderS1=(linenameTmpo.indexOf("_", VTPosi+1));
LineNo=linenameTmpo.substring(VTPosi, UnderS1);// VT00002
}
String posipersent2ST;
if(labelmethod==0 || labelmethod==1){// on top score
int UnderS0=(linenameTmpo.indexOf("_"));
posipersent2ST = linenameTmpo.substring(0, UnderS0);// VT00002
}else{
int UnderS0=(linenameTmpo.lastIndexOf("_"));
posipersent2ST = linenameTmpo.substring(UnderS0, linenameTmpo.length());// VT00002
}
//posipersent2= Double.parseDouble(posipersent2ST);
LineNameArray[CreateLineArray]=LineNo+","+posipersent2ST+","+linenameTmpo;
// IJ.log("linenameTmpo;dcstack "+linenameTmpo);
}
Arrays.sort(LineNameArray, Collections.reverseOrder());
//// duplication check and create top n score line list ////////////////////////////////////
if(dupline!=0){
// LineNameArray[posislice]="Z,0,Z";
//// scan complete line name list and copy the list to new positive list //////////////
String[] FinalPosi = new String [posislice];
int duplicatedLine=0;
for(int LineInt=0; LineInt<posislice; LineInt++)
if(DUPlogon==true)
IJ.log(LineInt+" "+LineNameArray[LineInt]);
for(int Fposi=0; Fposi<=posislice; Fposi++){
//////// pre line name ///////////////////////////
if(Fposi>0){
String arrayNamePre=LineNameArray[Fposi-1];
arrayPosition=0;
for (String retval: arrayNamePre.split(",")){
args[arrayPosition]=retval;
arrayPosition=arrayPosition+1;
}
preLineNo = args[0];// LineNo
}
///// current line name //////////////////////////
if(Fposi<posislice){
String arrayName=LineNameArray[Fposi];
// IJ.log("Original array; "+arrayName);
arrayPosition=0;
for (String retval: arrayName.split(",")){
args[arrayPosition]=retval;
arrayPosition=arrayPosition+1;
}
LineNo2 = args[0];// LineNo
linename = args[2];//linename
}
if(Fposi==0)
preLineNo=LineNo2;
if(Fposi==posislice)
LineNo2="End";
// IJ.log("LineNo 662; "+LineNo2+" preLineNo; "+preLineNo+ " duplicatedLine; "+duplicatedLine); // Sort OK!
Check=-1;
Check=(LineNo2.indexOf(preLineNo));
// IJ.log("Check; "+Check);
if(Check!=-1 && Fposi!=0){
duplicatedLine=duplicatedLine+1;
// IJ.log("Duplicated");
}
if(Check==-1 && duplicatedLine>dupline-1){// end of duplication, at next new file name
if(DUPlogon==true){
IJ.log("");
IJ.log("Line Duplication; "+String.valueOf(duplicatedLine+1));
}
String [] Battle_Values = new String [duplicatedLine+1];
for(int dupcheck=1; dupcheck<=duplicatedLine+1; dupcheck++){
arrayName=LineNameArray[Fposi-dupcheck];
arrayPosition=0;
for (String retval: arrayName.split(",")){
args[arrayPosition]=retval;
arrayPosition=arrayPosition+1;
}
Battle_Values [dupcheck-1] = args[1]+","+args[2];//score + fullname
if(DUPlogon==true)
IJ.log("Overlap_Values; "+Battle_Values [dupcheck-1]);
}//for(int dupcheck=1; dupcheck<=duplicatedLine+1; dupcheck++){
// Collections.reverse(Ints.asList(Battle_Values));
Arrays.sort(Battle_Values, Collections.reverseOrder());
for(int Endvalue=0; Endvalue<dupline; Endvalue++){// scan from top value to the border
for(int dupcheck=1; dupcheck<=duplicatedLine+1; dupcheck++){
arrayPosition=0;
for (String retval: LineNameArray[Fposi-dupcheck].split(",")){
args[arrayPosition]=retval;
arrayPosition=arrayPosition+1;
}
String OverValue = args[1];//posipersent2
LineName = args[0];//posipersent2
FullName = args[2];//posipersent2
arrayPosition=0;
for (String retval: Battle_Values[Endvalue].split(",")){
args[arrayPosition]=retval;
arrayPosition=arrayPosition+1;
}
String TopValue = args[0];//posipersent2
String FullNameBattle = args[1];//posipersent2
int BattleCheck=(FullNameBattle.indexOf(FullName));
// IJ.log("OverValue; "+OverValue+" TopValue; "+TopValue);
// IJ.log("FullNameBattle; "+FullNameBattle+" FullName; "+FullName);
double OverValueDB = Double.parseDouble(OverValue);
double OverValueBV = Double.parseDouble(TopValue);
if(OverValueBV==OverValueDB && BattleCheck!=-1){
// IJ.log("OverValueSlice1; "+LineNameArray[Fposi-dupcheck]);
if(labelmethod==0)// Sort by value
LineNameArray[Fposi-dupcheck]="10000000,10000000,100000000";//delete positive overlap array for negative overlap list
if(labelmethod==1){// Sort by value and line
if(Endvalue==0){// highest value
if(DUPlogon==true)
IJ.log(1+UniqueLineName+" UniqueLineName; "+FullName);
OverlapValueLineArray[UniqueLineName]=FullName+","+LineName;
UniqueLineName=UniqueLineName+1;
}
}
// IJ.log("OverValueSlice2; "+LineNameArray[Fposi-dupcheck]);
// PositiveSlices=PositiveSlices-1;
}
}//for(int dupcheck=1; dupcheck<=duplicatedLine+1; dupcheck++){
}// for(int Endvalue=0; Endvalue<dupline; Endvalue++){// scan from top value to the border
duplicatedLine=0; Check=2;
}//if(preLineNo!=LineNo && duplicatedLine>dupline-1){// end of duplication, at next new file name
int initialNo=Fposi-duplicatedLine-1;
if(initialNo>0 && Check==-1 && duplicatedLine<=dupline-1){//&& CheckPost==-1
for(int dupwithinLimit=1; dupwithinLimit<=duplicatedLine+1; dupwithinLimit++){
if(DUPlogon==true){
IJ.log("");
IJ.log("dupwithinLimit; "+LineNameArray[Fposi-dupwithinLimit]+" dupwithinLimit; "+dupwithinLimit+" duplicatedLine; "+duplicatedLine);
}
if(labelmethod==0)// Sort by value
LineNameArray[Fposi-dupwithinLimit]="10000000,10000000,100000000";// delete positive files within duplication limit from negative list
else if (labelmethod==1){// Sort by value and line
arrayName=LineNameArray[Fposi-dupwithinLimit];
arrayPosition=0;
for (String retval: arrayName.split(",")){
args[arrayPosition]=retval;
arrayPosition=arrayPosition+1;
}
LineName = args[0];//posipersent2
String ScoreCurrent= args[1];
FullName = args[2];//posipersent2
if(dupwithinLimit==2){/// 2nd file
double CurrentScore = Double.parseDouble(ScoreCurrent);
double PreScore = Double.parseDouble(ScorePre);
if(DUPlogon==true)
IJ.log("CurrentScore; "+CurrentScore+" PreScore; "+PreScore);
if(CurrentScore>PreScore){
if(DUPlogon==true)
IJ.log(1+UniqueLineName-1+" UniqueLineName; "+FullName);
OverlapValueLineArray[UniqueLineName-1]=FullName+","+LineName;
LineNameArray[Fposi-dupwithinLimit+1]=LineName+","+ScoreCurrent+","+FullName;
LineNameArray[Fposi-dupwithinLimit]=LineName+","+ScorePre+","+PreFullLineName;
}else{
if(DUPlogon==true)
IJ.log(1+UniqueLineName-1+" UniqueLineName; "+PreFullLineName);
// OverlapValueLineArray[UniqueLineName]=PreFullLineName+","+LineName;
}
}//if(dupwithinLimit==2){
if(dupwithinLimit==1){
arrayName=LineNameArray[Fposi-dupwithinLimit-1];
arrayPosition=0;
for (String retval: arrayName.split(",")){
args[arrayPosition]=retval;
arrayPosition=arrayPosition+1;
}
String PreSLineName = args[0];//posipersent2
ScorePre= ScoreCurrent;
PreFullLineName = FullName;//posipersent2
int PreCheck=(LineName.indexOf(PreSLineName));
if(PreCheck==-1 && DUPlogon==true)
IJ.log(1+UniqueLineName+" UniqueLineName; "+FullName);
OverlapValueLineArray[UniqueLineName]=FullName+","+LineName;
UniqueLineName=UniqueLineName+1;
// LineNameArray[Fposi-dupwithinLimit]="0";
}//if(dupwithinLimit==1){
}//else if (labelmethod==2){// Sort by value and line
// PositiveSlices=PositiveSlices-1;
}
duplicatedLine=0;
}//if(initialNo!=0 && preLineNo!=LineNo && duplicatedLine<=dupline-1){
if(initialNo<=0 && Check==-1 && duplicatedLine<=dupline-1 && Fposi>0){// && CheckPost==-1
for(int dupwithinLimit=1; dupwithinLimit<=duplicatedLine+1; dupwithinLimit++){
if(DUPlogon==true){
IJ.log("");
IJ.log("dupwithinLimit start; "+LineNameArray[Fposi-dupwithinLimit]);
}
if(labelmethod==0)// Sort by value
LineNameArray[Fposi-dupwithinLimit]="10000000,10000000,100000000";// delete positive files within duplication limit from negative list
else if (labelmethod==1){// Sort by value and line
arrayName=LineNameArray[Fposi-dupwithinLimit];
arrayPosition=0;
for (String retval: arrayName.split(",")){
args[arrayPosition]=retval;
arrayPosition=arrayPosition+1;
}
LineName = args[0];//posipersent2
FullName = args[2];//posipersent2
if(dupwithinLimit==1){
if(DUPlogon==true)
IJ.log(1+UniqueLineName+" UniqueLineName; "+FullName);
OverlapValueLineArray[UniqueLineName]=FullName+","+LineName;
UniqueLineName=UniqueLineName+1;
// LineNameArray[Fposi-dupwithinLimit]="0";
}
}
// PositiveSlices=PositiveSlices-1;
}
duplicatedLine=0;
}//if(initialNo<=0 && Check==-1 && duplicatedLine<=dupline-1 && Fposi>0){
// preLineNo=LineNo2;
}//for(int Fposi=0; Fposi<posislice; Fposi++){
Arrays.sort(LineNameArray, Collections.reverseOrder());// negative list
}// if(dupline!=0){
if (labelmethod==1)
Arrays.sort(OverlapValueLineArray, Collections.reverseOrder());// top value list
else
UniqueLineName=posislice2-1;
// for(int overarray=0; overarray<UniqueLineName; overarray++){
// IJ.log("OverlapValueLineArray; "+OverlapValueLineArray[overarray]);
// }