import ij.*;
import ij.measure.*;
import ij.plugin.*;
import ij.util.*;
import ij.process.*;
import ij.plugin.filter.*;
import java.util.*;
import ij.gui.*;

public class ResultsAndText_gj implements PlugIn, Measurements {
	String readme= 
		   "This plug-in extends ResultsTable and TextPanel functions."
		+"\nThe Analyzer.ResultsTable is usually the pivot of an analysis process and"
		+"\n can be displayed on the IJ system TextPanel."
		+"\n "		
		+"\nFile>SaveAs>measurements"
		+"\n  saves the textpanel including text written by a plugin via IJ.write;"
		+"\n  it does not save the resultsTable."
		+"\n "
		+"\nAnalyze>Clear Results"
		+"\n  clears both the textpanel and resultsTable."
		+"\n "
		+"\nThis ResultsAndText plugin provides additional functions:"
		+"\n*  TextPanel clear to headings/noheadings without clearing of ResultsTable"
		+"\n "
		+"\n*  selective ResultsTable list,"
		+"\n	{eg after a (large) ResultsTable generated by analyzeParticles"
		+"\n	 used with Display Results unchecked or"
		+"\n	 ResultsTable columns extended post table creation}"
		+"\n"
		+"\n*  save ResultsTable to a float image," 
		+"\n*  restore from the current float image"
		+"\n	      this version does not support row labels"
		+"\nThese functions allow checkpointing and restart or"
		+"\n  remote pickup of a multiphase analysis process"
		+"\n  where details (eg tracking data from extended analyzeParticles)"
		+"\n  can be saved/restored for continuing or remote analysis."
		+"\n  arg==\"about\":  displays this message"
		+"\n  arg==null:  runs a demonstration sequence"
		+"\n  arg==\"install\":  installs plugin options"
		+GJx.sign
		;
	public static final int CLEAR_HEAD=2,CLEAR=ParticleAnalyzer.CLEAR_WORKSHEET;//64
	
	public void run(String arg) {
		StringTokenizer st=new StringTokenizer(arg);
		String verb="";
		char action='0';
		if (st.countTokens()>0)verb=st.nextToken();
		if (verb.length()==1)action=verb.charAt(0);
		else{
			String verbs="c clear,h heading,m measurements, r reset,l list,s save,t restore"
				+",a about,d readme,x concatReadme,i install,u uninstall";
			int n=verbs.indexOf(verb);
			if(n>1)action=verbs.charAt(n-2);
		}
		//IJ.write(""+action);
		switch (action){
			case 'c':{IJ.setColumnHeadings("");
				break;}
			case 'h':{IJ.setColumnHeadings(Analyzer.getResultsTable().getColumnHeadings());
						IJ.write(" ");//headings dont appear unless a line is written
				break;}
			case 'm':{new MeasurementsWriter().run("");
				break;}
			case 'r':{Analyzer.getResultsTable().reset();
				break;}
			case 'l':{new ResultsList(arg);
				break;}
			case 's':{new ResultsTable_Image("put");
				break;}
			case 't':{new ResultsTable_Image("get");
					 // new ResultsList("list");
				break;}
			case 'a':{if(!IJ.showMessageWithCancel("About ResultsAndText_gj",readme))return;
				break;}
			case 'd':{GJx.writeAbout("About ResultsAndText_gj",readme);
				break;}
			case 'x':{GJx.writeAbout("About ResultsAndText_gj",readme,false);
				break;}
			case 'i':{if(!IJ.showMessageWithCancel
						("ResultsAndText_gj","InstallPluginsGJ"))return;
					(new InstallPluginsGJ()).run("");
				break;}
			case 'u':{if(!IJ.showMessageWithCancel
						("ResultsAndText_gj","UNInstallPluginsGJ"))return;
					(new InstallPluginsGJ()).run("un");
				break;}
			default:
			case '0':{
			
				if(!IJ.showMessageWithCancel("About ResultsAndText_gj",readme))return;
				if(!IJ.showMessageWithCancel("ResultsAndText_gj"
				,"ResultsAndText\n Demonstration\n"
				+"\n before running, it best to ensure\n30+ lines are visible in worksheet textpanel"))
					return;
				IJ.showMessage("clear IJ textPanel &"
					+"\nclear Analyzer.ResultsTable");
				IJ.setColumnHeadings("");
				Analyzer.getResultsTable().reset();
				IJ.showMessage("generate Analyzer.ResultsTable entries"
					+"\nclear Textpanel\nlist ResultsTable\n  no headings");
				testResults(31);
				new ResultsList(CLEAR);
				IJ.showMessage("clear Textpanel\n list ResultsTable with headings"
					+"\nsave ResultsTable in image"
					+"\n  if saved	ResultsTable_image is already current,"
					+"\n	then will restore ResultsTable");
				new ResultsList(CLEAR_HEAD);
				new ResultsTable_Image();// no GRAY32 so write
				IJ.showMessage("restore ResultsTable from image");			
				new ResultsTable_Image();// GRAY32 image current so read			
				IJ.showMessage("ResultsTable_list with headings");
				new ResultsList(CLEAR_HEAD);
				IJ.showMessage("display About on textpanel worksheet");
				GJx.writeAbout("About ResultsAndText_gj",readme);
				if(!IJ.showMessageWithCancel("ResultsAndText_gj","InstallPluginsGJ"))return;
				(new InstallPluginsGJ()).run();
				}
			}
	}
	ResultsTable testResults(int n){
		ResultsTable rt=Analyzer.getResultsTable();
		rt.reset();
		String[] headings={"","x","x^2","logX"};
		int[]cols={1,2,3};
		for(int i=0;i<headings.length;i++)rt.setHeading(i,headings[i]);
		for(int i=0;i<n;i++){
			rt.incrementCounter();
			rt.setValue(cols[0],i,i);
			rt.setValue(cols[1],i,i*i);
			rt.setValue(cols[2],i,(i==0)?0:Math.log(i));
		}
		return rt;
	}
}
class ResultsList{
	ResultsTable rt;
	int rCount;
	static int to_res=0,from_res=0;
	boolean arg_set=false;
	private int options;
	private static int CLEAR=ParticleAnalyzer.CLEAR_WORKSHEET//64
		,FROMFIRST=1,CLEAR_HEAD=2,SELECTCOLS=4,staticOptions = CLEAR;
	static boolean[]dCols;
	int[]colIs;
	static int nCols=0;
	static String pHeadings;
	
	ResultsList(){this("",-1);}
	ResultsList(int options){this("",options);}
	ResultsList(String arg){this(arg,-1);}
	ResultsList(String arg,int options){this.options=options;
		if (arg!=null && arg!=""){
			StringTokenizer st=new StringTokenizer(arg);
			if(st.hasMoreTokens())st.nextToken();
			if(st.hasMoreTokens()){
				String opt=st.nextToken();
				this.options|=opt.charAt(0)!='h'?CLEAR:CLEAR_HEAD;
				String rem=arg.substring(arg.indexOf(opt)+opt.length());
				int[]iargs = s2ints(rem);
				if (iargs.length>0){to_res=iargs[0];arg_set=true;}
				if (iargs.length>1)from_res=iargs[1];
				}}
		rt = Analyzer.getResultsTable();
		if (rt==null)if(!IJ.showMessageWithCancel("setup","null ResultsTable?"))return;
		rCount=rt.getCounter();
		if(rCount==0)if(!IJ.showMessageWithCancel("setup","empty ResultsTable?"))return;
		if((this.options>=0) && (this.options&FROMFIRST)!=0){to_res=1;from_res=rCount;}
		else{to_res=rCount;from_res=0;}
		if(this.options<0)if(!showDialog())return;
		boolean selectCols=false;
		if((this.options&SELECTCOLS)!=0)selectCols=true;
		int rCount=rt.getCounter();
		int n0,n1,n2,n3;
		if((this.options&FROMFIRST)>0){//"from n to m"}
			n0=to_res-1;n1=from_res;n2=0;n3=0;
			if(n1>rCount)n1=rCount;
			if(n1<0)n1=0;}
		else{//{"first n, last m",
			n1=to_res;n2=rCount-from_res;n0=0;n3=rCount;
			if(n1>rCount)n1=rCount;
			if(n2<=n1)n2=n1+1;}
		if((this.options & CLEAR)>0)IJ.setColumnHeadings("");
		if((this.options & CLEAR_HEAD)>0)
			IJ.setColumnHeadings(selectCols?getColumnHeadings(rt):rt.getColumnHeadings());
		//IJ.write(""+this.options+","+n0+","+n1+","+n2+","+n3+rt+colIs);
		//IJ.showMessage("options:"+this.options);	
		for (int i=n0;i<n1;i++){if(IJ.spaceBarDown())break;
			IJ.write(selectCols?getRowAsString(rt,colIs,i):rt.getRowAsString(i));}
		if((this.options&FROMFIRST)==0 && n2<n3)
			{IJ.write("...");
			for (int i=n2;i<n3;i++){if(IJ.spaceBarDown())break;
				IJ.write(selectCols?getRowAsString(rt,colIs,i):rt.getRowAsString(i));}}
	}
	boolean getListCols(StringTokenizer st,int nCols){
		String headings=rt.getColumnHeadings();
		if(pHeadings==null || !pHeadings.equals(headings)){
			dCols = new boolean[nCols];
			for(int i=0;i<nCols;i++)dCols[i]=true;
			colIs=new int[nCols];
			pHeadings=headings;
			}
		st.nextToken();
		int i=0,jm=0,jp=0;
		boolean all=true;
		while(i<nCols){
			GenericDialog gd = new GenericDialog("ResultsTable_list",IJ.getInstance());
			gd.addMessage(""+nCols+" columns titled:");
			do{	jm++;
				String cH=st.nextToken();
				gd.addCheckbox(cH,dCols[i]);
				colIs[i++]=rt.getColumnIndex(cH);}
					while(i<nCols && i%gd.MAX_ITEMS!=0);//gd.MAX_ITEMS==20
			gd.showDialog();
			if (gd.wasCanceled())return false;
			for(int j=jp;j<jm;j++){
				if(gd.getNextBoolean()){dCols[j]=true;
					}
				else {dCols[j]=false;all=false;}}
			jp=jm;
		}
		if(all==true)options&=~SELECTCOLS;
		return true;
	}
	String getColumnHeadings(ResultsTable rt){
		StringTokenizer st = new StringTokenizer(rt.getColumnHeadings(), "\t");
		int nCols = st.countTokens()-1;
		String s="   \t";st.nextToken();
		for (int i=0;i<nCols;i++){
			if(dCols[i])s+="\t"+st.nextToken();
			else st.nextToken();}
		return s;
	}	
	String getRowAsString(ResultsTable rt,int[]colIs,int r){String s=""+(r+1);
		for (int i=0;i<colIs.length;i++)
			if(dCols[i])s+="\t"+IJ.d2s(rt.getValue(colIs[i],r),Analyzer.precision);
		return s;
	}
	public boolean showDialog() {
		options = staticOptions;
		String[]choices ={"no, dont clear","without headings","with headings"};
		String[]choicen ={"first n rows, last m rows","from row n to m"};
		GenericDialog gd = new GenericDialog("ResultsTable_list", IJ.getInstance());
		gd.addChoice("Clear Worksheet first",choices,choices[2]);
		gd.addMessage("terminates if spaceBarDown");
		gd.addChoice("display Results rows ",choicen,choicen[((options&FROMFIRST)!=0)?1:0]);
		gd.addNumericField("n:",to_res, 0);
		gd.addNumericField("m:", from_res, 0);
		StringTokenizer st = new StringTokenizer(rt.getColumnHeadings(), "\t");
		int nCols = st.countTokens()-1;
		gd.addCheckbox("select from "+nCols+" columns",(options&SELECTCOLS)>0);
		gd.showDialog();
		if (gd.wasCanceled())return false;
		switch (gd.getNextChoiceIndex()){
			case 0:{options&=~CLEAR;break;}
			case 1:{options|=CLEAR;break;}
			case 2:{options|=CLEAR_HEAD;break;}} 
		if((gd.getNextChoiceIndex())==1)options|=FROMFIRST;else options &=~FROMFIRST;
		to_res = (int)gd.getNextNumber();
		from_res = (int)gd.getNextNumber();
		if (gd.invalidNumber()) {
			IJ.error("invalid number");
			return false;}
		if(gd.getNextBoolean())options|=SELECTCOLS;else options&=~SELECTCOLS;
		staticOptions=options;
		if((options&SELECTCOLS)!=0){
			if(getListCols(st,nCols))options |= CLEAR_HEAD;
			else return false;}
		staticOptions=options;
		return true;
	}
	public int[] s2ints(String s) {
		StringTokenizer st = new StringTokenizer(s, ", \t");
		int nInts = st.countTokens();
		int[] ints = new int[nInts];
		for(int i=0; i<nInts; i++) {
			try {ints[i] = Integer.parseInt(st.nextToken());}
			catch (NumberFormatException e) {IJ.write(""+e); return null;}}
		return ints;
	}
}
/**
* saves/restores ResultsTable to/from Image   ( not displayed textPanel contents
*/
class ResultsTable_Image{
	ResultsTable rt;
	int rCount;
	String headings;
	StringTokenizer st;
	int nCols;
    ImagePlus imp;
    boolean debug=false;

	ResultsTable_Image(){run("");}
	ResultsTable_Image(String arg){run(arg);}
	public void run(String arg){
	    rt = Analyzer.getResultsTable();
	    if (rt==null)IJ.showMessageWithCancel("setup","null ResultsTable?");
	    rCount=rt.getCounter();
	    imp = WindowManager.getCurrentImage();
		if (imp==null || (arg=="put" || imp.getType()!=ImagePlus.GRAY32))
			put();			
		else if (arg=="get" || imp.getType()==ImagePlus.GRAY32)
			get();
	}
			 
	int nCols(ResultsTable rt){int nCols=0;
		for(int i=0;i<ResultsTable.MAX_COLUMNS;i++){
			float[]col= rt.getColumn(i);
			if (col!=null)nCols++;}
		return nCols;
	}
	int[] getColumns(ResultsTable rt){int[]cols =new int[nCols(rt)];
		int n=0;
		for(int i=0;i<ResultsTable.MAX_COLUMNS;i++){
			float[]col= rt.getColumn(i);
			if (col!=null)cols[n++]=i;}
		return cols;
	}
	public boolean put(){
		if(rCount==0)if(!IJ.showMessageWithCancel("setup","empty ResultsTable?"))return false;
		String s= rt.getColumnHeadings();
		StringTokenizer st = new StringTokenizer(s, ", \t");
		int nCols = st.countTokens();
		int nc=nCols(rt);
		if (nCols!=nc)IJ.showMessageWithCancel("putResultsTable_Image",""+nCols+" vs "+nc);
		int[]cols=getColumns(rt);
		float[]fColHdr=new float[16];
		int nCHRows=16;//# of Trailer rows for column headings
		FloatProcessor ip= new FloatProcessor(nCols,rCount+nCHRows);
		float[]array=(float[])ip.getPixels();
		if (array==null)if(!IJ.showMessageWithCancel("ResultsTable","no array?"))return false;
		int h=rCount+nCHRows;
		for(int i=0;i<nCols;i++){
			int y=i;
			float[]col= rt.getColumn(cols[i]);
			for(int j=0;j<rCount;j++){
				array[y]=col[j];
				y+=nCols;}}
		for(int i=0;i<nCols;i++){
			int y=i+rCount*nCols;
			int c=cols[i];
			array[y]=c;
			String colHdr=st.nextToken();
			float[]fs=StringFloat.encode(colHdr);
			int fsl=fs.length; if (fsl>8)fsl=8;
			y+=nCols;array[y]=fsl;
			for(int j=0;j<fsl;j++){ y+=nCols;array[y]=fs[j];}}
		array[array.length-1]=StringFloat.encode("*GJ*")[0];//last row hdr tag
		array[array.length-2]=1;//version # 1
		array[array.length-3]=nCHRows;
		//IJ.write("ResultsTable image column hdrs written");
		imp = new ImagePlus("ResultsTable_Image",ip);
		imp.setProperty("headings",rt.getColumnHeadings());// not really used
		imp.show();
		return true;
	}
	public boolean get(){
		if (imp==null)
			{IJ.noImage(); return false;}
		if(imp.getType()!=ImagePlus.GRAY32)
			if(!IJ.showMessageWithCancel("ResultsTable","not GRAY32"))return false;
		if(rCount!=0)
			if(!IJ.showMessageWithCancel("ResultsTable"
							,"overwrite "+rCount+" results with ResultsTable_image?"))
				return false;
		rt.reset();
		FloatProcessor ip= (FloatProcessor)imp.getProcessor();
		float[] array = (float[])ip.getPixels();
		int nCols,h;
		nCols = ip.getWidth();
		h = ip.getHeight();
		if(array[array.length-1]!=StringFloat.encode("*GJ*")[0])
			if(!IJ.showMessageWithCancel("getResultsTable_Image","no tag"))
				return false;//last row tag
		if(array[array.length-2]!=1)
			if(!IJ.showMessageWithCancel("getResultsTable_Image"
					,"written by different version"))
				return false;//last row tag
		int nCHRows=(int)array[array.length-3];
		rCount=h-nCHRows;
		int[]cols=new int[nCols];
		int[]colL=new int[nCols];
		for(int i=0;i<nCols;i++){
			cols[i]=(int)array[rCount*nCols+i];
			colL[i]=(int)array[(rCount+1)*nCols+i];
			float[]fCHdr=new float[colL[i]];
			for(int j=0;j<colL[i];j++)fCHdr[j]=array[(rCount+2+j)*nCols+i];
			rt.setHeading(i,StringFloat.decode(fCHdr));}
		for(int y=0;y<rCount;y++){
			rt.incrementCounter();
			int yb = y * nCols;
			for(int x=0;x<nCols;x++)if(array[yb +x]!=-808080)rt.setValue(x,y,array[yb +x]);}
		IJ.write(rt.getColumnHeadings());
		IJ.write(rt.getRowAsString(0));
		IJ.write(rt.getRowAsString(rCount-1));
		IJ.write("\nResultsTable "+nCols+"x"+rCount+" loaded.");
		return true;
	}
}
class StringFloat{
	static float[] encode(String string){
		char[] chs=string.toCharArray();
		float[] f = new float[(chs.length+3)/4];
		for(int i=0;i<f.length;i++){f[i]=ch4ToFloat(chs,i*4);}
		return f;
	}
	static float ch4ToFloat(char[]chs,int n){
		//IJ.write("n:"+n+"\t"+chs.length);
		int r=chs[n];
		for(int i=1;i<4;i++){if(n+i>=chs.length)r<<=8;else r=(r<<8)+chs[n+i];}
		return Float.intBitsToFloat(r);
	}
	static String decode(float[] fs){int p=0;
		char[] chs=new char[fs.length*4];
		char[]ch4;
		for(int i=0;i<fs.length;i++){
			ch4=floatToCh4(fs[i]);
			for(int j=0;j<4;j++)chs[p++]=ch4[j];}
		int n=0;while(n<chs.length && chs[n]!=0)n++;
		return new String(chs,0,n);
	}
	static char[]floatToCh4(float f){
		char[]chs=new char[4];
		int n=Float.floatToIntBits(f);
		//IJ.write(""+Integer.toHexString(n));
		for(int i=0;i<4;i++){chs[i]=(char) ((n>>8*(3-i))&0xff);
			//IJ.write(""+chs[i]+"["+Integer.toHexString((n>>8*(3-i))&0xff) );
			}		
		return chs;
	}
}
class GJx{
	public static String sign=""
+"\n \nwritten by"
+"\nGreg Joss,			   1st March 2001 last modified 9th March 2001"
+"\nDepartment of Biological Sciences, Phone: (61)(2) 9850 8212 Fax: 9850 8245"
+"\nMacquarie University,	       Email: gjoss@rna.bio.mq.edu.au"
+"\nNorth Ryde, (Sydney,) NSW 2109, Australia"
+"\n \nAll comments, criticisms, suggestions, feedback or bug reports"
+"\n  would be gratefully received and appreciated."
;
	public static void writeAbout(String title, String readme) {writeAbout(title,readme,true);}
	public static void writeAbout(String title, String readme, boolean clear) {
		if (clear)IJ.setColumnHeadings("");
		IJ.write(title+'\n'+readme);
	}
}
    /** Adds a plugin based command to the end of a specified menu.
    * @param plugin    the plugin name (e.g. "Inverter_", "Inverter_("about")")
    * @param menuCode  PLUGINS_MENU, IMPORT_MENU or SAVE_AS_MENU
    * @param command	the menu item label
    * @param command	 the keyboard shortcut (e.g. "y", "Y", "F1")
    * @param ij     ImageJ (the action listener)
    *
    * @return	 returns an error code(NORMAL_RETURN,SHORTCUT_IN_USE_ERROR,etc.)
    */
//public //'public' requires separate source file
class InstallPluginsGJ {
	ImageJ ij;
	public void run(){run("");}
	public void run(String arg) {
		if (arg=="about"){IJ.showMessage("Install_GJ_Plugins","all is Trivial");return;}
		String[][] ps =
 {{"-","-",""}
,{"ResultsAndText_gj(\"reset\")"	,"Results reset"				,"F1"}
,{"ResultsAndText_gj(\"list\")" 	,"Results list" 				,"F2"}
,{"ResultsAndText_gj(\"save\")" 	,"Results save" 				,"F3"}
,{"ResultsAndText_gj(\"restore\")"	,"Results restore"				,"F4"}
,{"-","-",""}
,{"ResultsAndText_gj(\"clear\")"	,"Worksheet clear"				,"F5"}
,{"ResultsAndText_gj(\"heading\")"	,"Worksheet clear to headings"	,"F6"}
,{"ResultsAndText_gj(\"measurements\")" ,"Worksheet saved as measurements"	,"F7"}
,{"-","-",""}
,{"ResultsAndText_gj(\"about\")"	,"ResultsAndText about" 		,""}
,{"ResultsAndText_gj(\"readme\")"	,"ResultsAndText readme"		,""}
,{"ResultsAndText_gj(\"\")"			,"ResultsAndText demonstration" ,""}
,{"ResultsAndText_gj(\"x\")"		,"ResultsAndText install plugins",""}
,{"ResultsAndText_gj(\"u\")"		,"ResultsAndText uninstall"		,""}
,{"-","-",""}
};
	String[]rets={"NORMAL_RETURN","COMMAND_IN_USE","INVALID_SHORTCUT"
				,"SHORTCUT_IN_USE","NOT_INSTALLED","COMMAND_NOT_FOUND"};

		if (arg=="un"){int n=0;
			for (int i=0; i<ps.length;i++){
				int ret=Menus.uninstallPlugin(ps[i][1]);
				if (ret==0)n++;
				IJ.write(""+rets[-ret]+'\t'+ps[i][2]);}
			IJ.write(""+n+"/"+ps.length+" commands unInstalled.\nRESTART IJ");
			return;
		}
		ij=IJ.getInstance();
		IJ.setColumnHeadings("return\tsh\tplugin			\tcommand GJ");
		IJ.write("return       \tsh\tplugin			   \tcommand GJ\n");
		IJ.write("\nInstall_GJ_Plugins");
		char p=Menus.PLUGINS_MENU;
		int n=0;
		for (int i=0; i<ps.length;i++){
			int ret=Menus.installPlugin(ps[i][0],p,ps[i][1],ps[i][2],ij);
			if (ret==0)n++;
			IJ.write(""+rets[-ret]+'\t'+ps[i][2]+'\t'+ps[i][0]+'\t'+ps[i][1]);
		}
		IJ.write(""+n+"/"+ps.length+" commands installed.\n");
		String[]pr={
		 "ResultsAndText_gj"
		};
		for (int i=0; i<pr.length;i++){
			IJ.runPlugIn(pr[i],"concatReadme");
			IJ.write("____________________________\n ");
		}	
	}
}