/*
   MRI Opera export tools
  
   The tool stitches images from the Opera Phenix HCS System.
   It reads the ``Index.idx.xml`` file to pre-arrange the images and then
   stitches and fuses them using the ``Grid/Collection stitching``-plugin.

   Images are stitched by plane and channel. Z-stacks and multi-channel images can
   optionally be created. Projections can also be created.
    
   (c) 2021-2022, INSERM
   
   written by Volker Baecker and Léo Tellez-Arenas at Montpellier Ressources Imagerie, Biocampus Montpellier, INSERM, CNRS, University of Montpellier (www.mri.cnrs.fr)
*/

var helpURL = "https://github.com/MontpellierRessourcesImagerie/imagej_macros_and_scripts/wiki/MRI_Opera_export_tools";
var _OPERA_INDEX_FILE = "";
var _BYTES_TO_READ = 100000000;
var _MAX_NB_CHANNELS = 7;
var _CHANNEL_PER_ROW_IN_DIALOG = 2;

var _CHANNELS_DEFINED = false;
var _NB_CHANNELS = -1;
var _CHANNELS_NAMES = newArray(0);

var _WELLS_DEFINED = false;
var _WELLS = newArray(0);
var _SELECTED_WELLS = newArray(0);
var _WELLS_NAMES = newArray(0);
var _WELLS_NAMES_FILE = "wellNames.txt"
var _EXPORT_ALL = true;

var _ASSEMBLING_BASE = newArray("Stitching", "Montage");
var _PADDING = 0;
var _MONTAGE = false; // true: Image are sampled and must be assembled || false: Image must be stitched
var _STITCHING_BASE = newArray("Z-Slice","Max Intensity Projection");
var _STITCH_ON_PROJECTION = false;
var _ZSLICE = 0;
var _CHANNEL = 1; // Starts at 1
var _RANDOM_SAMPLED = false; // In case the wells were randomly sampled at different positions, and no stitching is required.

var _EXPORT_Z_STACK_FIELDS = true;
var _EXPORT_Z_STACK_FIELDS_COMPOSITE = false;
var _EXPORT_PROJECTION_FIELDS = true;
var _EXPORT_PROJECTION_FIELDS_COMPOSITE = false;
var _EXPORT_Z_STACK_MOSAIC = true;
var _EXPORT_Z_STACK_MOSAIC_COMPOSITE = false;
var _EXPORT_PROJECTION_MOSAIC = true;
var _EXPORT_PROJECTION_MOSAIC_COMPOSITE = false;
var _EXPORT_PROJECTION_MOSAIC_RGB = true;
var _EXPORT_RGB_CHANNEL = newArray(_MAX_NB_CHANNELS);

var _FUSION_COMPUTE_OVERLAP = true;
var _FUSION_METHODS = newArray("Linear_Blending", "Average", "Median", "Max_Intensity", "Min_Intensity", "random");
var _FUSION_METHOD = "Linear_Blending";
var _FUSION_REGRESSION_THRESHOLD = 0.30;
var _FUSION_DISPLACEMENT_THRESHOLD = 2.5;
var _FUSION_ABS_DISPLACEMENT_THRESHOLD = 3.5;

var _CORRECT_INDEX_FLAT_FIELD = false;
var _CORRECT_NORMALIZE = false;
var _CORRECT_PSEUDO_FLAT_FIELD_RADIUS = 0;
var _CORRECT_ROLLING_BALL_RADIUS = 0;
var _CORRECT_FIND_AND_SUB_BACK_RADIUS = 0;
var _CORRECT_FIND_AND_SUB_BACK_OFFSET = 3;
var _CORRECT_FIND_AND_SUB_BACK_ITERATIONS = 1;
var _CORRECT_FIND_AND_SUB_BACK_SKIP = 0.3;

var _COLORS = newArray("Red", "Green", "Blue", "Cyan", "Magenta", "Yellow", "Grays");
var _COLORS_SELECTED = newArray("Blue", "Green", "Red", "Cyan", "Magenta", "Yellow", "Grays");

var _CUSTOM_OUTPUT_FOLDER = "";

	
launchExport();
exit();

macro "Opera export tools help (f4) Action Tool - CdedD62CdddD72CdedL8292CeeeLa2b2Ca9aD43C555D53C434L6373C555L8393C666Da3C555Lb3c3C666Dd3Ca9aDe3C888D44C666D54C555D64C434L7494C555Da4C434Db4C666Lc4d4C989De4L4555C877D65C434D75C877D85C555D95C877Da5C555Db5CbbbDc5Ca9aLd5e5C989D46C877D56C666D66C434D76C989D86C877L96a6C666Db6C989Dc6C877Dd6Ca9aDe6CdddL1737Ca9aD47C666L5787C888L97a7C989Lb7d7CdddDe7CdedD08C989L1828CdddL3868CdedL78a8CeeeLb8c8CdedDd8CeeeDe8CdddD09C888L1929CdddD39CdedD49CdddD59CdedL6999CeeeLa9d9CdddD0aC989L1a2aCdddD3aCeeeL4a5aLbacaCdedDdaCeeeDeaCdedD0bC666L1b2bCbbbD3bCdddD4bCbbbL5b7bCa9aD8bC989D9bC888LabbbC666LcbdbCbbbDebCdddD1cC888D2cC666L3c5cC989D6cCa9aD7cCbbbL8c9cCdddDacCdedDbcCeeeDcc"{
	run('URL...', 'url='+helpURL);
}

macro "Opera export tools help [f4]" {
	run('URL...', 'url='+helpURL);
}

macro "Set index file (f5) Action Tool - C666D12C000L2262CaaaD72C444D13C333D23CcccL3353C888D63C000D73C444L83c3C666Dd3C444L1424CaaaD74C444L84b4C333Dc4C000Dd4C444L1525CcccDc5C000Dd5C444L1626L1727CbbbD37C444L47d7C555De7C444L1828C666D38C111D48C444L58c8C111Dd8C555De8C444L1929C222D39C888D49C111Dd9C888De9C444D1aC222D2aC000D3aCcccD4aCdddDcaC000DdaCdddDeaC444D1bC000L2b3bC888DcbC111DdbC444D1cC000D2cC333D3cCcccL4cbcC444DccC555DdcC666D1dC000L2dcdC888Ddd" {
	setIndexFile();
}

macro "set index-file [f5]" {
	setIndexFile();
}

macro "Select wells (f6) Action Tool - C111D22C000L3242CcccL5262C000L7282CcccL92a2C000Lb2c2C111Dd2C000L2343CcccL5363C000L7383CcccL93a3C000Lb3d3L2444CcccL5464C000L7484CcccL94a4C000Lb4d4CcccL2545L7585Lb5d5L2646L7686Lb6d6C000L2747CcccL5767C000L7787CcccL97a7C000Lb7d7L2848CcccL5868C000L7888CcccL98a8C000Lb8d8CcccL2949L7989Lb9d9L2a4aL7a8aLbadaC000L2b4bCcccL5b6bC000L7b8bCcccL9babC000LbbdbL2c4cCcccL5c6cC000L7c8cCcccL9cacC000LbcdcC111D2dC000L3d4dCcccL5d6dC000L7d8dCcccL9dadC000LbdcdC111Ddd" {
	selectWells();
}

macro "select wells [f6]" {
	selectWells();
}

macro "Rename wells (f7) Action Tool - C000T6b12T"{
	renameWells();
}

macro "rename wells [f7]"{
	renameWells();
}

macro "Set options (f8) Action Tool - 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" {
	setOptions();	
}

macro "set options [f8]" {
	setOptions();
}

macro "Set correction options (f9) Action Tool - C555D60C000L7080C555D90CeeeD21C888D31CaaaD41CcccD51C000D61C111L7181C000D91CcccDa1C999Db1C888Dc1CdddDd1D12C111D22C000L3242C111D52C000D62C777L7282C000D92C111Da2C000Lb2c2C111Dd2CeeeDe2C888D13C000D23C444D33C333D43C000D53C222D63CeeeL7383C333D93C000Da3C444Lb3c3C000Dd3C999De3D14C000D24C444D34CeeeD54C333Dc4C000Dd4CaaaDe4CdddD15C111D25C000D35C777D65C222L7585C777D95CeeeDb5C000Dc5C111Dd5CcccDe5C666D06C000L1626C333D36C777D56C000L6696C777Da6C222Dc6C000Ld6e6C555Df6C000D07C111D17C777D27CeeeD37C222D57C000D67CcccL7787C000D97C222Da7CeeeDc7C777Dd7C111De7C000Df7D08C222D18C888D28CeeeD38C222D58C000D68CcccL7888C000D98C222Da8CeeeDc8C777Dd8C111De8C000Df8C444D09C000L1929C333D39C777D59C000L6999C888Da9C333Dc9C000Ld9e9C555Df9CbbbD1aC111D2aC000D3aCeeeD4aC777D6aC222L7a8aC888D9aC000DcaC111DdaCcccDeaCaaaD1bC000D2bC333D3bCeeeDabC444DcbC000DdbC999DebD1cC000D2cC444L3c4cC000D5cC333D6cCeeeL7c8cC222D9cC000DacC333DbcC444DccC000DdcC888DecCeeeD1dC111D2dC000L3d4dC111D5dC000D6dC777D7dC888D8dC000D9dC111DadC000LbdcdC111DddCdddDedD2eC888D3eC999D4eCdddD5eC000D6eC111D7eC222D8eC000D9eCbbbDaeCaaaDbeC888DceCeeeDdeC666D6fC000L7f8fC444D9f" {
	setCorrectionOptions();
}

macro "set correction options [f9]" {
	setCorrectionOptions();
}

macro "Launch export (f10) Action Tool - CbbbD61C444L7181CcccD91CaaaD52C000D62C555L7282C000D92CaaaDa2CcccD43C000D53CaaaD63D93C000Da3CcccDb3C555D44C444D54CdddL7484C444Da4C555Db4C111D45C999D55CdddD65C000L7585CeeeD95C999Da5C111Db5C000D46CcccD56CdddD66C000L7686CeeeD96CcccDa6C000Db6D47CcccD57CeeeL7787CcccDa7C000Db7D48CcccD58Da8C000Db8D49CcccD59Da9C000Db9C666D3aC000D4aCeeeD5aDaaC000DbaC666DcaCdddD2bC000D3bC111D4bC444L5babC111DbbC000DcbCdddDdbD2cC444L3cccCdddDdcCeeeD5dC444D6dCaaaL7d8dC444D9dCeeeDadC777D6eC000L7e8eC777D9eCbbbL7f8f" {
	launchExport();
}

macro "launch export [f10]" {
	launchExport();
}

function launchExport() {
	print("3, 2, 1, go...");
	
	macrosDir = getDirectory("macros");
	script = File.openAsString(macrosDir + "/toolsets/opera_export_tools.py");
	options = getOptions();
	
	setBatchMode(true);
	baseDir = File.getDirectory(_OPERA_INDEX_FILE);
	getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
	dir = File.getParent(baseDir);
	file = File.open(dir + "/" + year + "-" + IJ.pad(month+1,2) + "-" + IJ.pad(dayOfMonth, 2) + "_"+hour+"_"+minute+"_"+second+"_options.txt");
	print(file, options);
	File.close(file);
	if(_CORRECT_INDEX_FLAT_FIELD)	prepareFlatfieldFolder();
	call("ij.plugin.Macro_Runner.runPython", script, options); 
	setBatchMode(false);
	
	print("The eagle has landed!!!");
}

function getOptions(){
	_OPERA_INDEX_FILE = getIndexFile();

	loadWellNames();
	
	options = "--wells=";
	if (_EXPORT_ALL) options = options + "all";
	else {
		for (i = 0; i < _WELLS.length; i++) {
			if (!_SELECTED_WELLS[i]) continue;
			options = options + _WELLS[i];			
		}
	}
	//Base for Stitching
	options = options + " --slice=" + _ZSLICE;
	options = options + " --channel=" + _CHANNEL;
	if (_STITCH_ON_PROJECTION) options = options + " --stitchOnMIP";
	// Making a montage of randomly sampled fields
	options += " --padding=" + _PADDING;
	if (_MONTAGE) options += " --montage";
	//Export Options
	if(_EXPORT_Z_STACK_FIELDS) options = options+ " --zStackFields";
	if(_EXPORT_Z_STACK_FIELDS_COMPOSITE) options = options+ " --zStackFieldsComposite";
	if(_EXPORT_PROJECTION_FIELDS) options = options+ " --projectionFields";
	if(_EXPORT_PROJECTION_FIELDS_COMPOSITE) options = options+ " --projectionFieldsComposite";
	
	if(_EXPORT_Z_STACK_MOSAIC) options = options+ " --zStackMosaic";
	if(_EXPORT_Z_STACK_MOSAIC_COMPOSITE) options = options+ " --zStackMosaicComposite";
	if(_EXPORT_PROJECTION_MOSAIC) options = options+ " --projectionMosaic";
	if(_EXPORT_PROJECTION_MOSAIC_COMPOSITE) options = options+ " --projectionMosaicComposite";
	if(_EXPORT_PROJECTION_MOSAIC_RGB) options = options+ " --projectionMosaicRGB";
	
	tmp = "";
	channelSelected = false;
	if(_NB_CHANNELS==-1){
		channelName = getChannelsFromIndex();
		_NB_CHANNELS = channelName.length;
	}
	for(i=0;i<_NB_CHANNELS;i++){
		if(_EXPORT_RGB_CHANNEL[i]){
			tmp = tmp+"1";
			channelSelected = true;
		}else{
			tmp = tmp+"0";
		}
	}
	if(channelSelected)	options = options+ " --channelRGB="+tmp;
	
	//Fusion Parameters
	if (_FUSION_COMPUTE_OVERLAP) options = options + " --computeOverlap";
	options = options + " --fusion-method=" + _FUSION_METHOD; 
	options = options + " --regression-threshold=" + _FUSION_REGRESSION_THRESHOLD;
	options = options + " --displacement-threshold=" + _FUSION_DISPLACEMENT_THRESHOLD;
	options = options + " --abs-displacement-threshold=" + _FUSION_ABS_DISPLACEMENT_THRESHOLD;

	//Image Correction
	if (_CORRECT_INDEX_FLAT_FIELD) options = options + " --index-flatfield";
	if (_CORRECT_NORMALIZE) options = options + " --normalize";
	
	options = options + " --pseudoflatfield=" + _CORRECT_PSEUDO_FLAT_FIELD_RADIUS;
	options = options + " --rollingball=" + _CORRECT_ROLLING_BALL_RADIUS;
	
	options = options + " --subtract-background-radius=" + _CORRECT_FIND_AND_SUB_BACK_RADIUS;
	options = options + " --subtract-background-offset=" + _CORRECT_FIND_AND_SUB_BACK_OFFSET;
	options = options + " --subtract-background-iterations=" + _CORRECT_FIND_AND_SUB_BACK_ITERATIONS;
	options = options + " --subtract-background-skip=" + _CORRECT_FIND_AND_SUB_BACK_SKIP;

	//Export Colors
	colors = String.join(_COLORS_SELECTED);
	colors = replace(colors, " ", "");
	options = options + " --colours=" + colors;
	minMaxList = "";
	for(i=0; i<_NB_CHANNELS; i++){
		minMax = getMinMax(i + 1);
		minMaxList = minMaxList + minMax[0] + "," + minMax[1];
		if (i < _NB_CHANNELS - 1) {
			minMaxList = minMaxList + ",";
		}
	}
	options = options + " --min-max-display=" + minMaxList;
	if(_CUSTOM_OUTPUT_FOLDER != ""){
		options = options + " --customOutput=" + _CUSTOM_OUTPUT_FOLDER;
	}
	options = options + " " + _OPERA_INDEX_FILE;
	return options;
}

function setOptions(){
	channelNames = getChannelsFromIndex();
	_NB_CHANNELS = channelNames.length;
	Dialog.create("Options");
	addStitchingBaseDialog(channelNames);
	addFusionDialog();
	addExportOptionsDialog(channelNames);
	addExportColoursDialog(channelNames);
	addExportBoundsDialog(channelNames);
	Dialog.addDirectory("Custom Output Folder",_CUSTOM_OUTPUT_FOLDER);

	Dialog.show();

	getStitchingBaseDialog(channelNames);
	getFusionDialog();
	getExportOptionsDialog();
	getExportColoursDialog();
	getExportBoundsDialog();
	_CUSTOM_OUTPUT_FOLDER = Dialog.getString();
}

macro "Open Correction Options" {
	setCorrectionOptions();
}

function setCorrectionOptions(){
	Dialog.create("Image Correction Options");
	
	addCorrectionDialog();
	Dialog.show();
	getCorrectionDialog();
}

function addStitchingBaseDialog(channelNames) {
	// What is the form of images
	Dialog.addMessage("Montage", 14);
	Dialog.addRadioButtonGroup("", _ASSEMBLING_BASE, 1, 2, _ASSEMBLING_BASE[0]);
	Dialog.addNumber("Padding", _PADDING);

	//Requires channelNames Array
	// _STITCHING_BASE = newArray("Z-Slice","Max Intensity Projection");
	Dialog.addMessage("Base for stitching", 14);
	sopState = _STITCHING_BASE[0];
	if(_STITCH_ON_PROJECTION){	sopState = _STITCHING_BASE[1];}
	Dialog.addRadioButtonGroup("", _STITCHING_BASE, 1, 2, sopState);
	
	Dialog.addNumber("z-slice for stitching (0 for middle slice)", _ZSLICE);

	Dialog.addChoice("Channel for Stitching",channelNames,channelNames[_CHANNEL-1]);
}

function getStitchingBaseDialog(channelNames){
	_MONTAGE = (Dialog.getRadioButton() == _ASSEMBLING_BASE[1]);
	_PADDING    = Dialog.getNumber();

	stitchingBase = Dialog.getRadioButton();
	_STITCH_ON_PROJECTION = (stitchingBase == _STITCHING_BASE[1]);

	// if(stitchingBase == _STITCHING_BASE[1]){
	// 	_STITCH_ON_PROJECTION = true;
	// }else{
	// 	_STITCH_ON_PROJECTION = false;
	// }
	
	_ZSLICE = Dialog.getNumber();
	
	chan = Dialog.getChoice();
	for(i = 0; i < _NB_CHANNELS; i++){
		if(channelNames[i]==chan){
			_CHANNEL = i+1;
			break;
		}
	}
}

function addExportOptionsDialog(channelNames){
	Dialog.addMessage("Export Options",14);

	Dialog.addCheckbox("Export Z-Stack of Fields", _EXPORT_Z_STACK_FIELDS);
	Dialog.addToSameRow();
	Dialog.addCheckbox("+ Composite ", _EXPORT_Z_STACK_FIELDS_COMPOSITE);
	
	Dialog.addCheckbox("Export Projections of Fields", _EXPORT_PROJECTION_FIELDS);
	Dialog.addToSameRow();
	Dialog.addCheckbox("+ Composite ", _EXPORT_PROJECTION_FIELDS_COMPOSITE);
	
	Dialog.addCheckbox("Export Z-Stack of Mosaics", _EXPORT_Z_STACK_MOSAIC);
	Dialog.addToSameRow();
	Dialog.addCheckbox("+ Composite ", _EXPORT_Z_STACK_MOSAIC_COMPOSITE);
	
	Dialog.addCheckbox("Export Projection of Mosaics", _EXPORT_PROJECTION_MOSAIC);
	Dialog.addToSameRow();
	Dialog.addCheckbox("+ Composite ", _EXPORT_PROJECTION_MOSAIC_COMPOSITE);

	Dialog.addCheckbox("RGB of Projection of Mosaic", _EXPORT_PROJECTION_MOSAIC_RGB);

	Dialog.addMessage("invert and export individual channel:");
	for(i=0;i<_NB_CHANNELS;i++){
		if(i%_CHANNEL_PER_ROW_IN_DIALOG !=0){
			Dialog.addToSameRow();
		}
		Dialog.addCheckbox(channelNames[i],_EXPORT_RGB_CHANNEL[i]);
	}
}

function getExportOptionsDialog(){
	_EXPORT_Z_STACK_FIELDS = Dialog.getCheckbox();
	_EXPORT_Z_STACK_FIELDS_COMPOSITE = Dialog.getCheckbox();
	_EXPORT_PROJECTION_FIELDS = Dialog.getCheckbox();
	_EXPORT_PROJECTION_FIELDS_COMPOSITE = Dialog.getCheckbox();
	_EXPORT_Z_STACK_MOSAIC = Dialog.getCheckbox();
	_EXPORT_Z_STACK_MOSAIC_COMPOSITE = Dialog.getCheckbox();
	_EXPORT_PROJECTION_MOSAIC = Dialog.getCheckbox();
	_EXPORT_PROJECTION_MOSAIC_COMPOSITE = Dialog.getCheckbox();
	_EXPORT_PROJECTION_MOSAIC_RGB = Dialog.getCheckbox();

	for(i=0;i<_NB_CHANNELS;i++){
		_EXPORT_RGB_CHANNEL[i]=Dialog.getCheckbox();
	}
}


function addFusionDialog(){
	Dialog.addMessage("Fusion parameters:",14);
	
	Dialog.addCheckbox("Compute Overlap", _FUSION_COMPUTE_OVERLAP);
	Dialog.addChoice("method: ", _FUSION_METHODS, _FUSION_METHOD);
	//Dialog.addMessage("Threshold:");
	Dialog.addNumber("regression threshold: ", _FUSION_REGRESSION_THRESHOLD);
	Dialog.addNumber("max/avg displacement threshold: ", _FUSION_DISPLACEMENT_THRESHOLD);
	Dialog.addNumber("absolute displacement threshold: ", _FUSION_ABS_DISPLACEMENT_THRESHOLD);
}

function getFusionDialog(){
	_FUSION_COMPUTE_OVERLAP = Dialog.getCheckbox();
	_FUSION_METHOD = Dialog.getChoice();
	_FUSION_REGRESSION_THRESHOLD = Dialog.getNumber();
	_FUSION_DISPLACEMENT_THRESHOLD = Dialog.getNumber();
	_FUSION_ABS_DISPLACEMENT_THRESHOLD = Dialog.getNumber();
}


function addCorrectionDialog(){
	Dialog.addMessage("Image correction/normalization:",14);

	Dialog.addCheckbox("! Experimental ! Flatfield correction from index-file ", _CORRECT_INDEX_FLAT_FIELD);	
	Dialog.addToSameRow();
	Dialog.addCheckbox("normalize", _CORRECT_NORMALIZE);
	Dialog.addNumber("pseudo flat field radius (0 = off): ", _CORRECT_PSEUDO_FLAT_FIELD_RADIUS);
	Dialog.addToSameRow();
	Dialog.addNumber("rolling ball radius (0 = off): ", _CORRECT_ROLLING_BALL_RADIUS);
	Dialog.addNumber("find background radius (0 = off): ", _CORRECT_FIND_AND_SUB_BACK_RADIUS);
	Dialog.addToSameRow();
	Dialog.addNumber("find background offset: ", _CORRECT_FIND_AND_SUB_BACK_OFFSET);
	Dialog.addNumber("find background iterations: ", _CORRECT_FIND_AND_SUB_BACK_ITERATIONS);
	Dialog.addToSameRow();
	Dialog.addNumber("find background skip limit: ", _CORRECT_FIND_AND_SUB_BACK_SKIP);
}

function getCorrectionDialog(){
	_CORRECT_INDEX_FLAT_FIELD = Dialog.getCheckbox();
	_CORRECT_NORMALIZE = Dialog.getCheckbox();
	_CORRECT_PSEUDO_FLAT_FIELD_RADIUS = Dialog.getNumber();
	_CORRECT_ROLLING_BALL_RADIUS = Dialog.getNumber();
	_CORRECT_FIND_AND_SUB_BACK_RADIUS = Dialog.getNumber();
	_CORRECT_FIND_AND_SUB_BACK_OFFSET = Dialog.getNumber();
	_CORRECT_FIND_AND_SUB_BACK_ITERATIONS = Dialog.getNumber();
	_CORRECT_FIND_AND_SUB_BACK_SKIP = Dialog.getNumber();
}


function addExportColoursDialog(channelNames){
	Dialog.addMessage("Export Colours:", 14);

	for(i=0;i<_NB_CHANNELS;i++){
		if(i%_CHANNEL_PER_ROW_IN_DIALOG != 0){
			Dialog.addToSameRow();
		}
		Dialog.addChoice(channelNames[i], _COLORS, _COLORS_SELECTED[i]);
	}
}

function getExportColoursDialog(){
	for(i=0; i<_NB_CHANNELS; i++){
		_COLORS_SELECTED[i]=Dialog.getChoice();
	}
}


function addExportBoundsDialog(channelNames){
	Dialog.addMessage("Export Bounds:",14);

	for(i=0;i<_NB_CHANNELS;i++){
		minMax=getMinMax(i+1);
		Dialog.addNumber(channelNames[i]+":  Min",minMax[0]);
		Dialog.addToSameRow();
		Dialog.addNumber("Max",minMax[1]);
	}
}

function getExportBoundsDialog(){
	for(i=1;i<=_NB_CHANNELS;i++){
		min=Dialog.getNumber();
		max=Dialog.getNumber();
		saveMinMax(i, min, max);
	}
}


function setChannelBounds(){
	channelName = getChannelsFromIndex();
	_NB_CHANNELS = channelName.length;
	Dialog.create("Channel Bounds");
	for(i=1;i<=_NB_CHANNELS;i++){
		minMax=getMinMax(i);
		Dialog.addNumber("Min", minMax[0]);
		Dialog.addToSameRow();
		Dialog.addNumber("Max", minMax[1]);
	}

	Dialog.show();
	for(i=1;i<=_NB_CHANNELS;i++){
		min=Dialog.getNumber();
		max=Dialog.getNumber();
		saveMinMax(i, min, max);
	}
}

function saveMinMax(channel,min,max){
	setParameterDefault("channel"+channel+"Min",min);	
	setParameterDefault("channel"+channel+"Max",max);	
}

function getMinMax(channel){
	min = getParameterDefault("channel"+channel+"Min",0);
	max = getParameterDefault("channel"+channel+"Max",65534);
	return newArray(min, max);
}

function loadWellNames(){
	_OPERA_INDEX_FILE = getIndexFile();
	baseDir = File.getDirectory(_OPERA_INDEX_FILE);

	wells = getWells();
	
	if (_WELLS_NAMES.length != wells.length){
		_WELLS_NAMES = newArray(wells.length);
	}
	
	if(File.exists(baseDir + _WELLS_NAMES_FILE)){
		str = File.openAsString(baseDir + _WELLS_NAMES_FILE);
		lines=split(str,"\n");
		nbLinesInWellNames = lines.length;
		
		for(currentWellID=0; currentWellID<wells.length; currentWellID++){
			_WELLS_NAMES[currentWellID]="";
			
			for(lineID=0; lineID<nbLinesInWellNames; lineID++){
				line = split(lines[lineID],":");
				if(line.length>1){
					if(line[0] == wells[currentWellID]){
						_WELLS_NAMES[currentWellID]=line[1];
					}
				}
			}
		}
	}else{
		path = baseDir + _WELLS_NAMES_FILE;
		for(i=0;i<wells.length;i++){
			well = wells[i];
			File.append(""+well+":", path);
			_WELLS_NAMES[i]="";
		}
	}
}

function renameWells() {
	_OPERA_INDEX_FILE = getIndexFile();
	baseDir =File.getDirectory(_OPERA_INDEX_FILE);
	
	wells = getWells();

	loadWellNames();

	Dialog.create("Rename Wells");
	lastRow = "00";
	for(i=0;i<wells.length;i++){
		well = wells[i];
		row = substring(well, 0, 2);  
		if (row==lastRow) {
			Dialog.addToSameRow();
		}
		lastRow = row;
		Dialog.addString(well, _WELLS_NAMES[i],8);
	}

	Dialog.show();

	path = baseDir + _WELLS_NAMES_FILE;
	File.delete(baseDir + _WELLS_NAMES_FILE);
	for(i=0;i<wells.length;i++){
		well = wells[i];
		_WELLS_NAMES[i] = Dialog.getString();
		File.append(""+well+":"+_WELLS_NAMES[i]+"", path);
	}
}

function selectWells() {
	_OPERA_INDEX_FILE = getIndexFile();
	wells = getWells();
	if (_SELECTED_WELLS.length != _WELLS.length) _SELECTED_WELLS = newArray(_WELLS.length);
	
	Dialog.create("Select Wells");
	lastRow = "00";
	for (i = 0; i < wells.length; i++) {
		well = wells[i];
		row = substring(well, 0, 2);  
		if (row==lastRow) {
			Dialog.addToSameRow();
		}
		lastRow = row;
		Dialog.addCheckbox(well, _SELECTED_WELLS[i]);
	}
	Dialog.addCheckbox("export all", _EXPORT_ALL);
	
	Dialog.show();
	
	for (i = 0; i < wells.length; i++) {
		_SELECTED_WELLS[i] = Dialog.getCheckbox();
	}
	_EXPORT_ALL = Dialog.getCheckbox();

	
}

function setIndexFile() {
	_WELLS_DEFINED = false;
	_CHANNELS_DEFINED = false;
	newFile  = getDir("Please select the folder containing the index file (Index.idx.xml)!");
	newFile = replace(newFile, "\\", "/");
	newFile = newFile + "Index.idx.xml";
	if (File.exists(newFile)) {
		setParameterDefault("indexFile",newFile);
	}else{
        print("Index File not found !");
        setIndexFile();
	}
}

function getIndexFile() {
	res = _OPERA_INDEX_FILE;
	if (!File.exists(res)) res = getParameterDefault("indexFile","-");
    if (!File.exists(res)){
        setIndexFile();
        res = getParameterDefault("indexFile","-");
    }
	wsIndex = indexOf(res, " "); 
	if (wsIndex>-1){
		print("Path to index file contains a whitespace !");
		print("\""+substring(res, 0, wsIndex+1)+"[  ]"+substring(res, wsIndex)+"\"");
		print("Please remove the whitespace !");
	}
	return res;
}

function getParameterDefault(parameter,default) {
	return call("ij.Prefs.get", "operaExportTools."+parameter, default);
}

function setParameterDefault(parameter,value) {
	call("ij.Prefs.set", "operaExportTools."+parameter, value); 
}

function getWells() {
	if(_WELLS_DEFINED){
		return _WELLS;
	}
	content = File.openAsRawString(_OPERA_INDEX_FILE, _BYTES_TO_READ);
	lines = split(content, "\n");
	wells = newArray(0);
	started = false;
	finished = false;
	for (i = 0; i < lines.length && !finished; i++) {
		line = String.trim(lines[i]);
		if (startsWith(line, "<Well id=")) {
			started = true;
			line = replace(line, '<Well id="', "");
			line = replace(line, '" />', "");
			wells = Array.concat(wells, line);
		} else {
			if (started) finished = true;
		}
	}
	_WELLS_DEFINED = true;
	_WELLS = wells;
	return wells;
}

function getChannelsFromIndex(){
	if(_CHANNELS_DEFINED){
		return _CHANNELS_NAMES;
	}
	lineStart = "<FlatfieldProfile>";
	startMarker = "ChannelName: ";
	endMarker = ",";
	channels = newArray();
	channels = getDataFromIndex(lineStart,startMarker,endMarker);
	_CHANNELS_DEFINED = true;
	_CHANNELS_NAMES = channels;
	return channels;
}

function getDataFromIndex(lineStart,startMarker,endMarker){
	indexFile = getIndexFile();
	content = File.openAsRawString(indexFile, _BYTES_TO_READ);
	lines = split(content, "\n");
	outData = newArray();
	
	for (i = 0; i < lines.length; i++) {
		line = String.trim(lines[i]);
		if (startsWith(line, lineStart)) {
			startIndex = indexOf(line,startMarker)+startMarker.length;
			subString = substring(line, startIndex);
			subString = substring(subString, 0, indexOf(subString,endMarker));
			outData = Array.concat(outData,subString);
		}
	}
	return outData;
}

function EXP_getDataFromIndex(lineStart,startMarker,endMarker,skipFirst){
	indexFile = getIndexFile();
	content = File.openAsRawString(indexFile, _BYTES_TO_READ);
	lines = split(content, "\n");
	outData = newArray();
	
	for (i = 0; i < lines.length; i++) {
		line = String.trim(lines[i]);
		if (startsWith(line, lineStart)) {
			startIndex = indexOf(line,startMarker)+startMarker.length;
			subString = substring(line, startIndex);
			if(skipFirst){
				secondStartIndex = indexOf(subString,startMarker)+startMarker.length;
				subString = substring(subString, secondStartIndex);
			}
			subString = substring(subString, 0, indexOf(subString,endMarker));
			outData = Array.concat(outData,subString);
		}
	}
	return outData;
}

macro "Get Flatfield Coefficients"{
	channelNumber = getNumber("Channel", 1);
	coeffsBG = getFlatfieldBGCoefficients(channelNumber);
	Array.print(coeffsBG);
	coeffsFG = getFlatfieldFGCoefficients(channelNumber);
	Array.print(coeffsFG);
	
}

function getFlatfieldCoefficients(channelNumber){
	indexFile = getIndexFile();
	content = File.openAsRawString(indexFile, _BYTES_TO_READ);
	lines = split(content, "\n");
	found=false;
	nrCols = 0;
	nrRows = 0;
	channels = newArray();
	
	lineStart ="<FlatfieldProfile>";
	startMarker = "Coefficients: ";
	endMarker = ", Dims: ";

	test = newArray();
	test = getDataFromIndex(lineStart,startMarker,endMarker);
	coeffDirty = split(test[channelNumber-1]);
	coeffClean = newArray(coeffDirty.length);
	for(i=0;i<coeffDirty.length;i++){
		coeffClean[i] = String.trim( replace(replace(replace(coeffDirty[i], "[", "") ,"]","") ,",","") );
	}
	return coeffClean;
}

function getFlatfieldBGCoefficients(channelNumber){
	indexFile = getIndexFile();
	content = File.openAsRawString(indexFile, _BYTES_TO_READ);
	lines = split(content, "\n");
	found=false;
	nrCols = 0;
	nrRows = 0;
	channels = newArray();
	
	lineStart ="<FlatfieldProfile>";
	startMarker = "Coefficients: ";
	endMarker = ", Dims: ";

	test = newArray();
	test = getDataFromIndex(lineStart,startMarker,endMarker);
	coeffDirty = split(test[channelNumber-1]);
	coeffClean = newArray(coeffDirty.length);
	for(i=0;i<coeffDirty.length;i++){
		coeffClean[i] = String.trim( replace(replace(replace(coeffDirty[i], "[", "") ,"]","") ,",","") );
	}
	return coeffClean;
}

function getFlatfieldFGCoefficients(channelNumber){
	indexFile = getIndexFile();
	content = File.openAsRawString(indexFile, _BYTES_TO_READ);
	lines = split(content, "\n");
	found=false;
	nrCols = 0;
	nrRows = 0;
	channels = newArray();
	
	lineStart ="<FlatfieldProfile>";
	startMarker = "Coefficients: ";
	endMarker = ", Dims: ";

	test = newArray();
	test = EXP_getDataFromIndex(lineStart,startMarker,endMarker,true);
	coeffDirty = split(test[channelNumber-1]);
	coeffClean = newArray(coeffDirty.length);
	for(i=0;i<coeffDirty.length;i++){
		coeffClean[i] = String.trim( replace(replace(replace(coeffDirty[i], "[", "") ,"]","") ,",","") );
	}
	return coeffClean;
}

macro "Create BG/FG Images"{
	imageSize = newArray(1080,1080);
	nbChannels = 3;
	channelMeans = getDataFromIndex("<FlatfieldProfile>",", Mean: ",", ");
	for(chan=1;chan<=nbChannels;chan++){
		coeffsBG = getFlatfieldBGCoefficients(chan);
		coeffsFG = getFlatfieldFGCoefficients(chan);
		//Array.print(coeffsBG);
		//Array.print(coeffsFG);
		chanMean = channelMeans[chan-1];
		originalBackgroundID = createBackgroundImage("background-"+chan,coeffsBG,imageSize,chanMean);
		originalForegroundID = createBackgroundImage("foreground-"+chan,coeffsFG,imageSize,chanMean);
	}
}

function createBackgroundImage(title,coeffs,size,factor){
	newImage(title, "32-bit", size[0], size[1], 1);
	imageID = getImageID();
 	w = getWidth(); 
 	h = getHeight();
 	Table.create("Background values");
 	i=0;
	for (y=0; y<h; y++) {
		for (x=0; x<w; x++){
			pixelOut = getValueOfPixelAfterPolynom(coeffs,x,y,size[0], size[1]);
			//setPixel(x, y, pixelOut);
			Table.set("pixelIntensity",i,pixelOut);
			i=i+1;
		}
	}
	
	bgPixels = Table.getColumn("pixelIntensity");
	Array.getStatistics(bgPixels, minB, maxB, meanB, stdDevB);
	
	tableItt=0;
	for (y=0; y<h; y++) {
		for (x=0; x<w; x++){
			pixel = Table.get("pixelIntensity",tableItt);
			pixel = parseFloat(pixel);
			pixelNorm = (pixel-minB)/(maxB-minB);
			
			a = 0;
			b= factor; 
		
			pixelOut = a + (pixelNorm * b);
			
			setPixel(x, y, pixelOut);
			Table.set("pixelIntensity",tableItt,pixelOut);
			tableItt=tableItt+1;
		}
	}
	return imageID;
}

function prepareFlatfieldFolder(){
	_OPERA_INDEX_FILE = getIndexFile();
	
	channels = getChannelsFromIndex();
	nbChannels = channels.length;
	
	directory = File.getDirectory(_OPERA_INDEX_FILE);
	outDirectory = directory + "/flatfield/";
	
	if(!File.exists(outDirectory)){
		File.makeDirectory(outDirectory);
	}

	filelist = getFileList(directory);
	imageSize = newArray(2);
	for (i = 0; i < lengthOf(filelist); i++) {
		if (endsWith(filelist[i], ".tiff")){
			open(directory+filelist[i]);
			imageSize[0]=getWidth();
			imageSize[1]=getHeight();
			close();
			break;
		}
	}
	channelMeans = getDataFromIndex("<FlatfieldProfile>",", Mean: ",", ");
	for(chan=1;chan<=nbChannels;chan++){
		coeffs = getFlatfieldCoefficients(chan);
		chanMean = channelMeans[chan-1];
		//print("Creating flatfield image for channel "+chan+", using mean = "+chanMean);
		//Array.print(Array.concat("Coefficients:",coeffs));
		originalBackgroundID = createBackgroundImage("background",coeffs,imageSize,chanMean);
		saveAs(outDirectory+chan+".tiff");
		close();
	}	
}

function getValueOfPixelAfterPolynom(coeffs,x,y,scaleX,scaleY){
	polX = (x/(0.5*scaleX))-1;
	polY = (y/(0.5*scaleY))-1;
	pixelValue = getValueOfPolynom(coeffs,x,y);
	//print(pixelValue);
	return pixelValue;
}

function getValueOfPolynom(coeffs,x,y){
	outPixelValue0= 0 + coeffs[0]; 
	outPixelValue1= 0 + coeffs[1]	* polX 				 	+ coeffs[2] * polY;
	outPixelValue2= 0 + coeffs[3]	* polX*polX 			+ coeffs[4] * polX*polY 			+ coeffs[5] * polY*polY;
	outPixelValue3= 0 + coeffs[6]	* polX*polX*polX 		+ coeffs[7] * polX*polX*polY 		+ coeffs[8] * polX*polY*polY 		+ coeffs[9] * polY*polY*polY;
	outPixelValue4= 0 + coeffs[10]	* polX*polX*polX*polX 	+ coeffs[11]* polX*polX*polX*polY	+ coeffs[12]* polX*polX*polY*polY 	+ coeffs[13]* polX*polY*polY*polY + coeffs[14] * polY*polY*polY*polY;
	outPixelValue = outPixelValue0+outPixelValue1+outPixelValue2+outPixelValue3+outPixelValue4;
	return outPixelValue;
}