// 
// Script to test Autofocus alogrithms by testing them against the existing autofocus 
// Prashanth
//

import java.io.FileWriter;
import java.io.IOException;
import javax.swing.JTextField;
import javax.swing.JLabel;
import javax.swing.JFrame;
import java.awt.Container;
import java.awt.FlowLayout;
import java.lang.Math;
import mmcorej.StrVector;
import org.micromanager.api.Autofocus;
import org.micromanager.api.AcquisitionOptions;


// Force load of the java plugin if not installed
//acq.installAutofocusPlugin("Autofocus_"); 

int 	maxDisplacement 				= 			30;
int	numTests		  					= 			11;
String 	outputfilePath 				= 			"C://projects//micromanager1.3//DeviceAdapters//SimpleAF//autofocus_output.txt";
// file locations for storing the output sequence
acqName = "test-af-visual";
rootDirName = "C:/acquisitionData";
// general parameters for autofocus tests
numFrames = 3;
String[] channels = {"AF-Channel"};
Color[] colors = {Color.GRAY};
numSlices = 1;
intervalMs = 1000;
exposure = 10;

try
{
	Autofocus af = gui.getAutofocus();
	String autofocusname = mmc.getProperty("Core",mmc.getDevicePropertyNames("Core").get(0));
	String ZStage = mmc.getFocusDevice();
	//gui.message(ZStage);
	FileWriter writer = new FileWriter(outputfilePath,true);	// Which file to write that data into
	double manualFocus = mmc.getPosition(ZStage);		// Enter the point of manual focus here
	
	String Mesg = autofocusname+" test - All measurements of errors and error statistics in microns, \n---------------------------------------------------------------------------------------------";
   Mesg += "\nManual best focus is : "+((double)Math.round(manualFocus*1000)/1000)
				+"\n";
	Double [] displacements = new Double[numTests];
	double step			  = (2*(double)maxDisplacement)/(double)numTests;
	Double [] err = new Double[numTests];
	boolean addoneFlag = false;
	double displacement;
	// Calculate the standard deviation
	Double [] residuals = new Double[numTests];
	Double sd = 0;
	// Calculate mean error
	Double signedmean = 0;
	// Calculate minimum error and maximum error
	Double minerror = 500000000.0;
   Double maxerror = -50000000.0;
	// Create the displacement array that the script willl have to run
	for(int i = 0; i < numTests; ++i)
	{
		displacement = (manualFocus - maxDisplacement) + i*(step);
		if(displacement == 0 || addoneFlag)
		{
			displacement = ((i+1)*step -maxDisplacement);
			addoneFlag = true;
		}
		displacements[i] = displacement;
		double z_stagedispfrombest = (- maxDisplacement) + i*(step);
		mmc.setPosition(ZStage,(displacement));
		double start = System.currentTimeMillis();
		af.fullFocus();
		String valfull = "Not-Initialized";
		StrVector properties = mmc.getDevicePropertyNames(autofocusname);
		for (int i=0; i<properties.size(); i++) 
		{
	 		//String Mesg;
    		String prop = properties.get(i);
			if(prop.equals("Total Number of images acquired by autofocus"))
	 		{
				valfull = mmc.getProperty(autofocusname, prop);					
    			
			}
		}
		af.incrementalFocus();
		double stop = System.currentTimeMillis();
		String valinc = "Not-Initialized";
		StrVector properties = mmc.getDevicePropertyNames(autofocusname);
		for (int i=0; i<properties.size(); i++) 
		{
	 		//String Mesg;
    		String prop = properties.get(i);
			if(prop.equals("Total Number of images acquired by autofocus"))
	 		{
				valinc = mmc.getProperty(autofocusname, prop);	
			}
		}
		//gui.autofocus(); 
		
		double pos = mmc.getPosition(ZStage);
		err[i] = pos - manualFocus;
		Mesg+="z-displacement : "+((float)Math.round((z_stagedispfrombest)*1000)/1000)+" mic "+
				//"("+(float)(Math.round(z_stagedispfrombest*1000)/1000)+" units)"+
				"\tz-error : "+((double)Math.round((err[i]*1000))/1000)+" mic "+
				"\tz-autofocus : "+(double)((double)Math.round(pos*1000)/1000)+" mic"+
				//"( "+(float)(Math.round(pos*1000)/1000)+" units) "+
				"\tTime Taken : "+((double)(stop-start)/1000)+" secs"+
				"\tImages taken : "+valfull+"/"+valinc+"\n";

	}
	
	for(int i = 0; i < numTests; ++i)
	{
		signedmean += err[i]/numTests;
	}
	
	for(int i = 0; i < numTests; i++)
	{
			if(err[i] < minerror)
				minerror = err[i];
			if(err[i] > maxerror)
				maxerror = err[i];		
	}


   Mesg += "Run report : ("+autofocusname+")\n************\n";
	Mesg += "Average focus : "+(signedmean + manualFocus)+"\n";
	Mesg += "Mean error : "+(signedmean)+" microns \n";
	Mesg += "Highest Focus Point : "+((manualFocus - minerror))+" \n";
	Mesg += "Lowest Focus Point : "+((manualFocus - maxerror))+" \n";
	Mesg += "Span of the autofocus values is : "+((((double)Math.round((maxerror - minerror)*1000)))/1000)+" microns \n";
	Double meanfocus = manualFocus + signedmean;
	// Find maximum deviation from mean focus
	Double maxdeviation  = -1000000;
	double maxdeviationPos = 0;
	for(int i = 0; i < numTests; i++)
	{
			if(Math.abs((manualFocus+err[i]) - meanfocus) > maxdeviation)
			{
				maxdeviation = (manualFocus+err[i]) - meanfocus;
				maxdeviationPos = manualFocus+err[i];
			}		
	}
	Mesg += "Maximum deviation from mean computed focus is : "+maxdeviation+" microns \n";
	
	
	

	for(int i = 0; i < numTests; ++i)
	{	
		residuals[i] = (err[i] - signedmean)*(err[i] - signedmean);
	}
	for(int i = 0; i < numTests; ++i)
	{
		sd += residuals[i]/numTests;
	}
	sd = Math.sqrt(sd);
	Mesg += "The standard deviation of the errors (calculated with the signed mean) is : "+(sd)+" microns \n\n\n";
	//Mesg += "The lowest AF value observed was "+lowest+" , and the highest AF value observed was "+highest+" span being "+(highest - lowest);
	Mesg+= "Properties for the device are: \n";
	//String autofocusname = mmc.getProperty("Core",mmc.getDevicePropertyNames("Core").get(0));
	StrVector properties = mmc.getDevicePropertyNames(autofocusname);
	//properties = mmc.getDevicePropertyNames(getProperty(properties.get(0));
	for (int i=0; i<properties.size(); i++) 
	{
	 //String Mesg;
    	String prop = properties.get(i);
	 	String val = mmc.getProperty(autofocusname, prop);
    	Mesg += "\tProperty Name : \t" + prop + "\n\tProperty value: \t" + val + "\n";
	}
	gui.message(Mesg);
	writer.append(Mesg);
	writer.flush();
	writer.close();
	gui.closeAllAcquisitions();
	// Displaying the autofocus images at the key points
	// 1st at manual best focus
	// 2nd at average computed focus
	//3rd at worst computed focus i.e maximum deviation from mean
	gui.openAcquisition(acqName, rootDirName, numFrames, channels.length, numSlices);
	for (int i=0; i<colors.length; i++)
   	gui.setChannelColor(acqName, i, colors[i]);
	for (int i=0; i<channels.length; i++)
   	gui.setChannelName(acqName, i, channels[i]);
	for (int i=0; i<numFrames; i++) 
	{
		if(i == 0)
		{
			// Go to manual best focus
			mmc.setPosition(ZStage,manualFocus);			
		}
		if(i == 1)
		{
			double averageFocalPlane = signedmean + manualFocus;
			// Go to the mean focus plane
			mmc.setPosition(ZStage,averageFocalPlane);
		}
		if(i == 2)
		{
			// Go to the worst focus plane
			mmc.setPosition(ZStage,maxdeviationPos);
		}
			mmc.setExposure(exposure);
   	
       	gui.snapAndAddImage(acqName, i, 0, 0);   
   	// set channel contrast based on the first frame
   	if (i==0) 
		{
      	gui.setContrastBasedOnFrame(acqName, i, 0);
   	}
   	gui.sleep(intervalMs);
	}
	double averageFocalPlane = signedmean + manualFocus;
	// Go to the mean focus plane
	mmc.setPosition(ZStage,averageFocalPlane);


}
catch(Exception e)
{
	e.printStackTrace();
}