import ij.*;

import ij.process.*;

import ij.process.StackProcessor.*;

import ij.gui.*;

import ij.plugin.*;



import java.awt.*;

import java.awt.event.*;

import java.awt.image.*;

import java.util.*;

import ij.plugin.filter.PlugInFilter;

import ij.measure.*;

import ij.text.*;

import ij.plugin.frame.*;

import ij.plugin.filter.Analyzer;





public class Cell_Counter implements PlugInFilter{

  int type1Count, type2Count, type3Count, type4Count, totalCount;

  ImagePlus img, img2;

  int type;

  ResultsTable rt;

  Analyzer an;



  public int setup(String arg, ImagePlus img){

    this.img=img;

    reset();

    return DOES_ALL;

  } // end of setup



  public void run(ImageProcessor ipp) {

    ImagePlus imp1 = WindowManager.getCurrentImage();

    if (imp1==null){

      IJ.showMessage("You need an image...");

    } // no image...

    else if (imp1.getStackSize() == 1) {

      ImageProcessor ip = imp1.getProcessor();

      ip.setRoi(null);

      ip = ip.crop();

      ImagePlus img = new ImagePlus("Counter Window - "+imp1.getTitle(), ip);

      CustomCanvas cc = new CustomCanvas(img);

      new CustomWindow(img, cc);

      img2 = WindowManager.getCurrentImage();

      resultSetup();

    } // making the counter window

    else if (imp1.getStackSize() > 1){

      ImageStack stack = imp1.getStack();

      int size = stack.getSize();

      ImageStack stack2 = imp1.createEmptyStack();

      for (int i = 1; i <= size; i++){

	ImageProcessor ip = stack.getProcessor(i);

        ip.setRoi(null);

        ip = ip.crop();

	stack2.addSlice(stack.getSliceLabel(i), ip);

      }

      CustomCanvas cc = new CustomCanvas(img);

      new CustomStackWindow(img, cc);

      img2 = WindowManager.getCurrentImage();

      resultSetup();

    } // Stacks supported

  } // end of run



  public void resultSetup(){

    IJ.setColumnHeadings("Active Type\t Type 1\tType 2\tType 3\tType 4\tTotal");

  } // the result table



  void reset(){

    type1Count = 0;

    type2Count = 0;

    type3Count = 0;

    type4Count = 0;

    totalCount = 0;

  } // end of results reset



  void report(){

    IJ.write("Type 1: "+type1Count);

    IJ.write("Type 2: "+type2Count);

    IJ.write("Type 3: "+type3Count);

    IJ.write("Type 4: "+type4Count);

    IJ.write("Total:  "+totalCount);

  } // end of result report method



  class CustomCanvas extends ImageCanvas {

    CustomCanvas(ImagePlus imp) {

      super(imp);

    }



    public void mousePressed(MouseEvent e) {

        if (Toolbar.getToolId()==Toolbar.MAGNIFIER) {

	super.mousePressed(e);

	return;

      }

      int x = offScreenX(e.getX());

      int y = offScreenY(e.getY());

      if (Toolbar.getToolId()!=Toolbar.CROSSHAIR) 

           Toolbar.getInstance().setTool(Toolbar.CROSSHAIR);

      if (type == 1){ // button 1

	 type1Count++;

	 totalCount++;

	 IJ.setForegroundColor(255,255,255);

	 img2.setRoi(x-4,y-4,9,9);

	 IJ.run("Fill", "slice");

	 IJ.write(type+"\t"+type1Count+"\t"+type2Count+"\t"+type3Count+"\t"+type4Count+"\t"+totalCount);

      }

      if (type == 2){ // button 2

	 type2Count++;

	 totalCount++;

	 IJ.setForegroundColor(0,255,0);

	 img2.setRoi(x-4,y-4,9,9);

	 IJ.run("Fill", "slice");

	 IJ.write(type+"\t"+type1Count+"\t"+type2Count+"\t"+type3Count+"\t"+type4Count+"\t"+totalCount);

      }

      if (type == 3){ // button 3

	 type3Count++;

	 totalCount++;

	 IJ.setForegroundColor(0,0,255);

	 img2.setRoi(x-4,y-4,9,9);

	 IJ.run("Fill", "slice");

	 IJ.write(type+"\t"+type1Count+"\t"+type2Count+"\t"+type3Count+"\t"+type4Count+"\t"+totalCount);

      }

      if (type == 4){ // button4

	 type4Count++;

	 totalCount++;

	 IJ.setForegroundColor(255,255,0);

	 img2.setRoi(x-4,y-4,9,9);

	 IJ.run("Fill", "slice");

	 IJ.write(type+"\t"+type1Count+"\t"+type2Count+"\t"+type3Count+"\t"+type4Count+"\t"+totalCount);

      }

      if (type ==5){ // button 5

	 return;

      }

      return;

    }

  } // end of customcanvas





  class CustomWindow extends ImageWindow implements ActionListener {

    private Button button1, button2, button3, button4, button5;

    CustomWindow(ImagePlus imp, ImageCanvas ic) {

      super(imp, ic);

      addPanel();

    }

    void addPanel() {

      Panel panel = new Panel();

      panel.setLayout(new BorderLayout());

      Panel buttonPanel = new Panel();

      button1 = new Button(" Type 1 ");

      button1.addActionListener(this);

      buttonPanel.add(button1);

      button2 = new Button(" Type 2 ");

      button2.addActionListener(this);

      buttonPanel.add(button2);

      button3 = new Button(" Type 3 ");

      button3.addActionListener(this);

      buttonPanel.add(button3);

      button4 = new Button(" Type 4 ");

      button4.addActionListener(this);

      buttonPanel.add(button4);

      button5 = new Button(" Results ");

      button5.addActionListener(this);

      buttonPanel.add(button5);

      add(BorderLayout.NORTH, buttonPanel);

      add(panel);

      pack();

    }



    public void actionPerformed(ActionEvent e) {

      Object b = e.getSource();

      if (b==button1) type = 1;

      else if (b==button2) type = 2;

      else if (b==button3) type = 3;

      else if (b==button4) type = 4;

      else if (b==button5){

	report();

	reset();

      }

    }

  }// end of Custom Window adding the buttons



  class CustomStackWindow extends StackWindow implements ActionListener {

    private Button button1, button2, button3, button4, button5;

    CustomStackWindow(ImagePlus imp, ImageCanvas ic) {

      super(imp, ic);

      addPanel();

    }

    void addPanel() {

      Panel panel = new Panel();

      panel.setLayout(new BorderLayout());

      Panel buttonPanel = new Panel();

      button1 = new Button(" Type 1 ");

      button1.addActionListener(this);

      buttonPanel.add(button1);

      button2 = new Button(" Type 2 ");

      button2.addActionListener(this);

      buttonPanel.add(button2);

      button3 = new Button(" Type 3 ");

      button3.addActionListener(this);

      buttonPanel.add(button3);

      button4 = new Button(" Type 4 ");

      button4.addActionListener(this);

      buttonPanel.add(button4);

      button5 = new Button(" Results ");

      button5.addActionListener(this);

      buttonPanel.add(button5);

      add(BorderLayout.NORTH, buttonPanel);

      add(panel);

      pack();

    }



    public void actionPerformed(ActionEvent e) {

      Object b = e.getSource();

      if (b==button1) type = 1;

      else if (b==button2) type = 2;

      else if (b==button3) type = 3;

      else if (b==button4) type = 4;

      else if (b==button5){

	report();

	reset();

      }

    }

  }// end of Custom Window adding the buttons

}// end of Counter Class


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