// Action Bar description file :Kalensbar
//Added OJ prefs 12/2/14 KB

run("Action Bar","/plugins/ActionBar/_Kalensbar.txt");
exit();
<startupAction>
run("Action Bar","/plugins/ActionBar/_Kalensbar.txt");
</startupAction>

<sticky>
<line>
<button>
label=Close this bar
icon=noicon
arg=<close>
</line>

<line>
<button>
	label=Prev Object
	icon=noicon
	arg=<macro>
	
	if ( ojSelectedObject()!=0 && ojImageLink()!=0 ){
	
	ojnum=ojSelectedObject();
		//Real OJnum
		currentImage=ojImageLink();
		ojnum=ojnum-ojFirstObject(currentImage)+1;
		
		if (ojnum!=1){
			ojnum=ojnum-1;
		}
		goToOjnumAll(ojnum);
		
	}
</macro>
</line>


<line>
<button>
	label=Center Current Object
	icon=noicon
	arg=<macro>
	if (ojSelectedObject()!=0 && ojImageLink()!=0){
	
	
	currentImage=ojImageLink();
	ojnum=ojSelectedObject();
	
	
		if (ojnum==ojNObjects()){
			ojnum=ojFirstObject(currentImage);
		}else if (currentImage<ojNImages()){
			if (ojnum==ojFirstObject(currentImage+1)) {
				ojnum=ojFirstObject(currentImage);
			} 	
		} 
		
		
		ojnum=ojnum-ojFirstObject(currentImage)+1;
		//The prev line just makes the numbers come out right. 
		
		goToOjnumAll(ojnum);
	}


</macro>

</line>


<line>
<button>
	label= Next Obj
	icon=noicon
	arg=<macro>
	if (ojSelectedObject()!=0 && ojImageLink()!=0){
	
	
	currentImage=ojImageLink();
	ojnum=ojSelectedObject();
	
	
		if (ojnum==ojNObjects()){
			ojnum=ojFirstObject(currentImage);
		}else if (currentImage<ojNImages()){
			if (ojnum+1==ojFirstObject(currentImage+1)) {
				ojnum=ojFirstObject(currentImage);
			} 	
		} 
		
		
		ojnum=ojnum-ojFirstObject(currentImage)+1;
		//This addition actually increments the location. The prev line just makes the numbers come out right. 
		ojnum=ojnum+1;
		goToOjnumAll(ojnum);
	}


</macro>

</line>

<line>
<button>
	label= Prev Image
	icon=noicon
	arg=<macro>

	//boolean for turning current images channels on or off on subsequent or prev iamges
	lockChannelChoice=call("ij.Prefs.get","marker.lockChannelChoice",true);

	
	if (ojImageLink()!=0){
	
	
	n=ojImageLink();
    getLocationAndSize(x, y, width, height);

		if (n>1){
			n=n-1;
		}else{
			n=ojNImages();
		}	
		
		while (ojGetImageValue(n, "ID")==0){
			
			if (n>1){
				n=n-1;
			}else{
				n=ojNImages();
			}	
		}

		Stack.getActiveChannels(activeChan);	
		
		
		
		ojShowImage(n);
		setLocation(x, y);


		if(lockChannelChoice==true)
			Stack.setActiveChannels(activeChan);


		


}

</macro>

</line>


<line>
<button>
	label= Next image
	icon=noicon
	arg=<macro>

	//boolean for turning current images channels on or off on subsequent or prev iamges
	lockChannelChoice=call("ij.Prefs.get","marker.lockChannelChoice",true);

	
if (ojImageLink()!=0){
	n=ojImageLink();
    getLocationAndSize(x, y, width, height);

		if (n<ojNImages()){
			n=n+1;
		}else{
			n=1;
		}	
		
		while (ojGetImageValue(n, "ID")==0){
			if (n<ojNImages()){
				n=n+1;
			}else{
				n=1;
			}	
		}
		
		Stack.getActiveChannels(activeChan);	
		
				
		ojShowImage(n);
		setLocation(x, y);

		if(lockChannelChoice==true)
			Stack.setActiveChannels(activeChan);
}
</macro>
</line>


//imageJ array is zero ordered FYI
<line>
<button>
	label= Ch1
	icon=noicon
	arg=<macro>	
	Stack.getActiveChannels(activeChan);	
	activateChan=toString(activeChan,0);

	if (substring(activeChan,0,1)=="1"){
	   temp="0"+substring(activeChan,1);
     	   Stack.setActiveChannels(temp);
	} else {
	   temp="1"+substring(activeChan,1);
	   Stack.setActiveChannels(temp);	
	}	
</macro>
</line>

<line>
<button>
	label= Ch2
	icon=noicon
	arg=<macro>	
	Stack.getActiveChannels(activeChan);
	if (substring(activeChan,1,2)=="1"){
     	   Stack.setActiveChannels(substring(activeChan,0,1)+"0"+substring(activeChan,2));
	} else {
  	   Stack.setActiveChannels(substring(activeChan,0,1)+"1"+substring(activeChan,2));
	}	
</macro>
</line>

<line>
<button>
	label= Ch3
	icon=noicon
	arg=<macro>	
	Stack.getActiveChannels(activeChan);
	if (substring(activeChan,2,3)=="1"){
     	   Stack.setActiveChannels(substring(activeChan,0,2)+"0"+substring(activeChan,3));
	} else {
	   Stack.setActiveChannels(substring(activeChan,0,2)+"1"+substring(activeChan,3));	
	}	
</macro>
</line>
<line>

<button>

	label= Add Note
	icon=noicon
	arg=<macro>
if (ojSelectedObject()!=0){	
	ojnum=ojSelectedObject();
	row=ojIndexToRow(ojnum);
	orig=ojResultString("Notes",row);
	width=512; height=512;
	ojNumOnImage=ojnum-ojFirstObject(ojOwnerIndex(ojnum))+1;
	
	Dialog.create("Notes on Marker Number: "+ojNumOnImage);
	if (orig == "") {
		Dialog.addString("Notes on Marker Number: "+ojNumOnImage, "Write Your Note",75);
	} else  {
		Dialog.addString("Notes on Marker Number: "+ojNumOnImage, orig,75);
	}
	  Dialog.show();
  	value = Dialog.getString();
	ojSetResult("Notes",row, value);
	
}
</macro>
</line>

<line>

<button>

	label= Toggle Bookmark / Unsure
	icon=noicon
	arg=<macro>	
if (ojSelectedObject()!=0){
	
	n=ojSelectedObject();
	row=ojIndexToRow(n);
	ojNumOnImage=n-ojFirstObject(ojOwnerIndex(n))+1;
	
	booktest=ojResult("Bookmarked", row);
	if (booktest==1){
		ojSetResult("Bookmarked", row, 0);
		showMessage("Removed Bookmark for Marker Number: "+ ojNumOnImage);
	} else {
		ojSetResult("Bookmarked", row, 1);
		showMessage("Added Bookmark for Marker Number: "+ojNumOnImage);
	}
}
</macro>
</line>
















<line>
<button>

	label=Toggle Pan
	icon=noicon
	arg=<macro>	
	ojSetTool("hand");
</macro>
</line>

<line>
<button>
	label=Apply Zoom
	icon=noicon
	arg=<macro>	
if (ojSelectedObject()!=0 && ojImageLink()!=0){
		currentimage=ojImageLink();
		ojnum=ojSelectedObject();
		if (ojnum>=ojFirstObject(currentimage) && ojnum<=ojLastObject(currentimage)){
			ojnum=ojnum-ojFirstObject(currentimage)+1;
			
		}else{
			ojnum=1;
		}
		goToOjnumAll(ojnum);
}
</macro>
</line>

<line>
<button>
	label=Save Project
	icon=noicon
	arg=<macro>	
		ojSaveProject();
		showMessage("Project Saved");
		
</macro>
</line>

<line>
<button>
	label=Insert Landmarks
	icon=noicon
	arg=run("Action Bar","/plugins/ActionBar/Insert_New_Landmarks.txt");
	
</line>

<line>
<button>
	label=Turn on Synapse History View
	icon=noicon
	arg=<macro>	

		markers = newArray("Landmark","SpineWithPSD","InhibitoryShaft","SpineWithInhibitorySynapse","NudeSpine","Nothing"); 
		nOld=-1;
		truthtest=true;
		while(truthtest){	
			
			n=ojSelectedObject();
			
				if(n!=nOld&&n>0){
			
					imageNum=ojImageLink();
					first=ojFirstObject(imageNum);
										
					numToAdd=n-first;
					size=ojNImages();
					type=Array.fill(newArray(size),-1);//starts everything as minus 1 so I can tell if any markers are undefined		
					Session_Number=newArray(size);//id of sessions
					Synapse_Type=newArray(size);
					Notes_on_session=newArray(size);
					for(i=1;i<=ojNImages();i++){
						first=ojFirstObject(i);
						numOnImage=numToAdd+first;
						Session_Number[i-1]=d2s(i,0);
						if(numOnImage<=ojLastObject(i)){
						
							for(markTypeNum=0;markTypeNum<6;markTypeNum++){ 
								column=markers[markTypeNum]+"_X"; 
								if( ojResult(column,ojIndexToRow(numOnImage)) >0) 
									type[i-1]=markTypeNum; 
							} 
							
							temp=ojResultString("Notes",ojIndexToRow(numOnImage));
						}else{
							temp="";
						}
			
						if(type[i-1]==-1)
							Synapse_Type[i-1]="No marker";
						else
							Synapse_Type[i-1]=markers[type[i-1]];
							
						
						
						if(temp!="")
					 	   Notes_on_session[i-1]=temp;
					    else
					   	   Notes_on_session[i-1]="_______";
					}
					
					numToAdd=numToAdd+1;
					Synapse_ID=Array.fill(newArray(size),numToAdd);
					Array.show("History of Selected Synapse: ", Session_Number,Synapse_ID,Synapse_Type,Notes_on_session); 
					nOld=n;
				}
				wait(500);
		}		
</macro>
</line>



<line>
<button>
	label=Highlight dynamic synapses
	icon=noicon
	arg=<macro>	

	total=ojLastObject(1);
	dynamicCheck=Array.fill(newArray(total),0);
	nImage=ojNImages();
	dynamicCount=0;
	
	var markers = newArray("Landmark","SpineWithPSD","InhibitoryShaft","SpineWithInhibitorySynapse","NudeSpine","Nothing"); 
	for(n=1;n<=total;n++){	
		orig=newArray(7);

		for(c=0;c<6;c++){		
			cTitle=markers[c]+"_X";
			if(ojResult(cTitle,n)>0)
				orig[c]=1;
			else
				orig[c]=0;	
		}

		for(i=1;i<=nImage;i++){
			compare=newArray(7);	
			first=ojFirstObject(i)-1;
			for(c=0;c<6;c++){		
				cTitle=markers[c]+"_X";
				if(ojResult(cTitle,n+first)>0)
					check=1;
				else
					check=0;	
					
				if(orig[c]!=check){
					dynamicCheck[n-1]=1;
					break;
				}
								
			}	

			if(dynamicCheck[n-1]==1){
					dynamicCount++;
					break;
			}	
				
		}	
	}

//get row indexes of dynamics
	dynNums=newArray(dynamicCount);
	counter=0;
	for(i=0;i<lengthOf(dynamicCheck);i++){
		if(dynamicCheck[i]==1){
			dynNums[counter]=i+1;
			counter++;
		}
	}

	rowArray=newArray(lengthOf( dynNums )*nImage);	
	counter=0;
	
	for(i=0;i<lengthOf( dynNums );i++){
			rowArray[counter]=dynNums[i];
			counter++;
			for(j=2;j<=nImage;j++){
				rowArray[counter]=dynNums[i]+ojFirstObject(j)-1;
				counter++;
			}
	}

// make all false then turn dynamic true
	for (i=0; i<ojNObjects(); i++){
		ojQualify(i, false);
	}

	for (i=0; i<lengthOf(rowArray); i++){
		ojQualify(rowArray[i], true);
	}

</macro>
</line>

<line>
<button>
	label=Highlight All Synapses
	icon=noicon
	arg=<macro>	

	for (i=0; i<ojNObjects(); i++){
		ojQualify(i, true);
	}
		
</macro>
</line>





<line>
<button>
	label=Copy marks from one session to another
	icon=noicon
	arg=run("Action Bar","/plugins/ActionBar/Copy_Paste_Between_ojj_files.txt");	
</line>

<line>
<button>
	label=Edit ObjectJ Settings
	icon=noicon
	arg=<macro>	
	
	var markerSize = call("ij.Prefs.get","marker.Size",0);
	var markerMultiplier = call("ij.Prefs.get","marker.Multiplier",0);
	var fontSize = call("ij.Prefs.get","font.Size",0);
	var markerChoice=call("ij.Prefs.get","marker.channelMustBeActive",true);
	var lockChannelChoice=call("ij.Prefs.get","marker.lockChannelChoice",true);


	if (markerSize == 0) {
		showMessage("Run ObjectJ or check your version first because there is something fishy going on here");
	
	}else{
		Dialog.create("ObjectJ Preferences");
		
		Dialog.addString("Set the default size of markers here (16): ", markerSize);
		Dialog.addString("Set the default font size of marker labels (16): ",fontSize);
		Dialog.addString("This number adjusts how much larger a selected marker becomes (1.5): ", markerMultiplier);
		Dialog.addCheckbox("Hide markers when the channel they are on is off", markerChoice)
		Dialog.addCheckbox("Keep same channels on or off when using prev or next object buttons", lockChannelChoice)
		Dialog.show();

		markerSize = Dialog.getString();
		fontSize = Dialog.getString();	
		markerMultiplier = Dialog.getString();
		markerChoice=Dialog.getCheckbox();
		lockChannelChoice=Dialog.getCheckbox();
			
		call("ij.Prefs.set","marker.Size",parseInt(markerSize));
		call("ij.Prefs.set","marker.Multiplier",parseFloat(markerMultiplier));
		call("ij.Prefs.set","font.Size",fontSize);
		call("ij.Prefs.set","marker.channelMustBeActive",markerChoice);
		call("ij.Prefs.set","marker.lockChannelChoice",lockChannelChoice);
		call("ij.Prefs.savePreferences");
	    ojUpdateMarkers(true);
	    
	    if (ojImageLink()>0){
	    	currentImage=ojImageLink();
	    	getLocationAndSize(x, y, width, height);
	    	Stack.getPosition(channel, slice, frame);
	    	flag=getBoolean("Do you want to close the current ObjectJ Image and try to show these settings? You may have to close and reopen the project if this doesn't work. ");
	    	
	    	if (	flag){
	    			close();
	    			ojShowImage(currentImage);
	    	    	setLocation(x, y);
	    			Stack.setPosition(channel, slice, frame);
	    	}

	    
	    
	    }
	    
	}
</macro>
</line>








</sticky>


<codeLibrary>



function ojQualifyApply(rowArray,flag){	
			for (i=0; i<lengthOf(rowArray); i++){
				if(rowArray[i]>0){
					ojQualify(rowArray[i], flag);
				}
			}
		}



function goToOjnumAll(ojnum){

        currentimage=ojImageLink();
		firstoncurrentimage=ojFirstObject(currentimage);
		zoom=getZoom();
		
		totalimages=ojNImages();
		for (n=1; n<=totalimages; n=n+1){
			if(n != currentimage){
				if(ojGetImageValue(n, "ID")!=0){
					ojShowImage(n);
					firstonimage=ojFirstObject(n);
					ojToShow=ojnum+firstonimage-1;
					
					if (ojToShow<=ojLastObject(n)) {
						ojShowObject(ojToShow);
						yoj=ojYPos(1);
						xoj=ojXPos(1);
						ojZoom(zoom,xoj,yoj);
					}
				}
			
			}
		// To return the view to the start
		}
			
		ojShowImage(currentimage);
		ojShowObject(ojnum+firstoncurrentimage-1);
		yoj=ojYPos(1);
		xoj=ojXPos(1);
		ojZoom(zoom,xoj,yoj);
			
}

</codeLibrary>