imagej script

/*
  
This is a script made in imageJ for segmenting human body parts from infrared images. 
After segmentation (based on morphology and signal intensity), several measurements are performed, such as antropometrical variables (eg.limb width) and temperature (siganl intensity) of different body segments. 

Date of start: 01.06.2018
Last edition: 01.06.2018

coded by Vasco Fachada
supervised by Mika Silvennoinen
project:  
*/





start = getTime(); 





//Batch open image data - waiting
//setBatchMode("hide");


//setting and calibration
rename("original");
run("Duplicate...", "title=bin_original");

//Binarizing and cropping
run("Subtract Background...", "rolling=90");
setThreshold(0, 46);
run("Convert to Mask");
run("Invert");
run("Create Selection");
run("Enlarge...", "enlarge=15");
selectWindow("original");
run("Restore Selection");
run("Crop");
run("Duplicate...", "title=stk_seg_masks");
run("RGB Color");
selectWindow("bin_original");
run("Crop");
 
//skeletonizing
run("Duplicate...", "title=skeletoid");
run("Select None");
run("Skeletonize");
run("Dilate");

//making quadrants and classinfying according to body segment
selectWindow("skeletoid");

	//head
run("Duplicate...", "title=skeletoid_head");
setBackgroundColor(255, 255, 255); 

getDimensions(width, height, channels, slices, frames);
x_local=(width/2)-(20/2);
y_local=(height*0.05);
makeRectangle(x_local, y_local, 20, 20, 10);
run("Clear Outside");
run("Select None");
run("Create Selection");
List.setMeasurements;
headSeed_x=List.getValue("X");
headSeed_y=List.getValue("Y");
selectWindow("original");
run("Restore Selection");
run("Level Sets", "method=[Active Contours] use_level_sets grey_value_threshold=1 distance_threshold=0.05 advection=5 propagation=0.50 curvature=0.40 grayscale=5 convergence=0.0050 region=outside");
selectWindow("Segmentation of original");
rename("stk_head");
run("Create Selection"); 
selectWindow("original");
run("Select None");
selectWindow("stk_head");
run("Select None");
run("Invert");
run("Restore Selection");
run("RGB Color");
setForegroundColor(255, 0, 229);
head_color = getValue("rgb.foreground");
print (head_color);
run("Fill", "slice");
run("Select None");




	
	//feft foot - "lO"
selectWindow("skeletoid");
run("Duplicate...", "title=skeletoid_lFoot");
setBackgroundColor(255, 255, 255); 

getDimensions(width, height, channels, slices, frames);
x_local=(width/2)+(20/2);
y_local=(height*0.90);
makeRectangle(x_local, y_local, 20, 20, 10);
run("Clear Outside");
run("Select None");
run("Create Selection");
List.setMeasurements;
lFootSeed_x=List.getValue("X");
lFootSeed_y=List.getValue("Y");
selectWindow("original");
run("Restore Selection");
run("Level Sets", "method=[Active Contours] use_level_sets grey_value_threshold=1 distance_threshold=0.05 advection=5 propagation=0.50 curvature=0.40 grayscale=5 convergence=0.0050 region=outside");
selectWindow("Segmentation of original");
rename("stk_lFoot");
run("Create Selection"); 
selectWindow("original");
run("Select None");
selectWindow("stk_lFoot");
run("Select None");
run("Invert");
run("Restore Selection");
run("RGB Color");
setForegroundColor(255, 0, 0);
lFoot_color = getValue("rgb.foreground");
print (lFoot_color);
run("Fill", "slice");
run("Select None");



//Assembling final images with different segments
run("Images to Stack", "name=seg_masks title=stk keep");
run("Z Project...", "projection=[Standard Deviation]");
rename("just_masks_");
selectWindow("seg_masks");
run("Z Project...", "start=2 projection=[Standard Deviation]");
rename("just_masks");
run("Images to Stack", "method=[Copy (center)] name=mont title=just_masks keep");
run("Make Montage...", "columns=2 rows=1 scale=1 last=2");
run("In [+]");
run("In [+]");
//setBatchMode("show");






Dialog.create("SEGMENTATION COMPLETED");
items = newArray("Yes, this is good enough!", "Not really, I want to edit");
Dialog.addRadioButtonGroup("Are you satisfied with the current segmentation results? \n \n", items, 2, 1, "Yes, this is good enough!");
Dialog.show;
print("Choice: "+Dialog.getRadioButton);


Dialog.create(head_color);


items = newArray(head_color, lFoot_color, "Paris", "Tokyo");
Dialog.addChoice("label", items, "Paris");
Dialog.show;

//Selecting the body segment to edit
setTool("dropper");
waitForUser("Segment selection", "click on the segment you want to edit, then press 'OK'.");
current_foreground = getValue("rgb.foreground");
if (current_foreground==head_color){
	showMessage("this is the head");
	setTool("Paintbrush Tool");
	run("Paintbrush Tool Options...", "brush=2");
	selectWindow("just_masks_");
	run("Duplicate...", "title=just_masks_temp");
	selectWindow("just_masks_temp");
	run("Set... ", "zoom=600 x="+(headSeed_x)+" y="+(headSeed_y)); 
	waitForUser("Editing Segment", "Press 'OK' after you finished your editing.");
	doWand(headSeed_x, headSeed_y);
	selectWindow("stk_head");
	doWand(headSeed_x, headSeed_y);
	setBackgroundColor(0, 0, 0);
	run("Clear", "slice");
	run("Restore Selection");
	setForegroundColor(255, 0, 229);
	run("Fill", "slice");}
	
else if (current_foreground==lFoot_color){
	showMessage("this is the left foot")}
else if (type==10){
      print("point selection")}
else{
      print("line selection")}

 


x=100; y=200; 
  call("ij.gui.WaitForUserDialog.setNextLocation",x,y); 
  waitForUser("DONE!!!!!!! It took "+(getTime()-start)/1000/60+" MINUTES or "+(getTime()-start)/1000/60/60+" HOURS... This means you need to upgrade this machine ;)"); 

/*
while (nImages>0) { 
         selectImage(nImages); 
         close(); 
}
*/