#===============================================
# MultiSpectraFit
#===============================================
package MultiSpectraFit;
use TkFittingCommon2;
@ISA = qw(TkFittingCommon2);

#公開したいサブルーチン
#@EXPORT = qw(DelSpace Reduce01 MakePath RegExpQuote);

use strict;

use Utils;
use IniFile;
use CSV;

use MyTk::GraphFrameArray;
use MyTk::MyDragDrop;
use GraphData;

use Sci::Science;
use Sci::PES;
use Sci::Ellipsometry;
use Sci::Optimize;

#============================================================
#　変数等取得関数
#============================================================
	my $ProgramName = "MultiSpectraFit/2013";

#============================================================
#　コンストラクタ、デストラクタ
#============================================================
#呼び出されることはない
sub new
{
	my ($class, $app, @a) = @_;
#	my ($module, $app, $canvas) = @_;

	my $self = TkFittingCommon2->new($app, @a);
	my $this = bless $self, $class;
#	my $this = {};
#	bless $this;
	$this->SetApplication($app) if($app);
#	$this->SetCanvas($canvas) if($canvas);

	return $this;
}

sub DESTROY
{
	my $this = shift;
	$this->SUPER::DESTROY(@_);
}

#============================================================
#　継承クラスで定義しなおす関数
#============================================================
sub CreateLeftFrame
{
	my ($this, $ConfigSide, @args) = @_;
#	return $this->SUPER::CreateLeftFrame();
	return undef;
}

sub CreateSelectFilePane
{
	my ($this) = @_;
#	return $this->SUPER::CreateSelectFilePane();
	return undef;
}

sub CreateFileContentPane
{
	return undef;
}

sub CreateWidgets
{
	my ($this, $DoSuperOnly) = @_;
	$DoSuperOnly = 0 if(!defined $DoSuperOnly);
	my $mw     = $this->mw();

	$this->{ini}  = new IniFile(undef, 0, 0);
	$this->{dini} = new IniFile(undef, 0, 0);
	$this->{ini}->{nSpectra} = 2;
	$this->InitializeParameters($this->{ini}, $this->{dini});

	$this->SUPER::CreateWidgets();
	return if($DoSuperOnly);

	$mw->SetTitle("$ProgramName / TkPlot");
	$this->App()->SetProgram("$ProgramName / TkPlot");

#===================================================
# ペインを作製
#===================================================
	my $EntryWidth = $this->{EntryWidth} = 12;

	$mw->{NoteBook} = $this->MakeNotebookPanes($mw, $EntryWidth,
			$this->{ini}->pVariable("nFilmLayers", 1),
			$this->{ini}->pVariable("nLorentz",    3),
			$this->{ini}->pVariable("nDrude",      0),
			$this->{ini}->pVariable("nStepBG",     2),
			$this->{ini}->pVariable("nGL",         6),
			[qw(Main Vars ViewRange LSQ Setup GraphFrame)],
#			[qw(Main ViewRange LSQ GaussLorentz Setup GraphFrame)],
			[qw()],
#			[qw(nPESStepBG nGaussLorentz)],
		);
	$mw->{NoteBook}->pack(-fill => 'both', -expand => 'yes');

	$this->UpdateParameters();

#ツールバーのOpenボタンをファイル読み込みにバインドする
	my $Samplefmask = '*.csv;*.spe;*.jel;*.asp;*.smo;*isa;*.ref;*.pal;*.bef;*.aft';
	$mw->{OpenButton}->configure(
			-command  => sub { 
					$this->{SampleCSV} = $this->ChooseFile("open", $Samplefmask, "ChooseSampleFile", 
														"SampleCSV", $this->{SampleFileFrame});
				},
		) if($mw->{OpenButton});

	my $DragDrop = new MyDragDrop();
	$DragDrop->ConfigureDrop(
				$this->mw(),
				[
					"\\.prm\$",  $this->{ParamFileEntry}, 
					sub { $this->ReadParameterFile($_[0]); },
				],
				[
					".*",     $this->{Sample1CSVFileEntry},   
					sub { 
						$this->{Sample1CSVFileEntry}->SetText($_[0]);
						$this->ReadSampleDataFile($_[0], 1, 1); 
					},
				],
			);

	my $IniFile = $this->App()->IniFile();
	$this->SetGeometry($IniFile->GetString("Window", "geometry", ''));

#	$this->OnDestroy( sub { $this->Close(); } );
#	$this->{FileNameEntry}->bind('<Destroy>' => sub { $this->Close(); } );
	$this->bind('<Configure>' => sub {
				$this->App()->IniFile()->WriteString("Window", "geometry", $this->geometry());
			} );
}

sub BuildMainPane
{
	my ($this, $MainPaneFrame, $EntryWidth) = @_;

	my $Frame = $MainPaneFrame->MyFrame()->pack(-anchor => 'nw', -fill => 'x');
	my $savefmask = '*.prm';
	$this->{ParameterFileFrame} = $this->MakeChooseFileEntry(
				$Frame, 'Param', 'Param:', $this->{ini}->pVariable("ParameterFile", ""), 
				'&Choose', sub {
					$this->ChooseFile("save", $savefmask, "ChooseParameterFile", @_); 
				},
			1,         sub { $this->SaveParameterFile("SaveParam", '', @_); },
			1,         sub { $this->EditFile('EditParam', @_); },
			[]
			);
	$this->{ParameterFileFrame}->pack(-anchor => 'nw', -fill => 'x');

	$Frame = $MainPaneFrame->MyFrame()->pack(-anchor => 'nw', -fill => 'x');
	my $Samplefmask = '*.*'; #'*.csv;*.spe;*.jel;*.asp;*.smo;*isa;*.ref;*.pal;*.bef;*.aft';
	$this->{SampleFileFrame} = $this->MakeChooseFileEntry(
			$Frame, 'SampleCSV', 'Sample:', $this->{ini}->pVariable("SampleCSVFile", ""), 
			'&Choose', sub {
					$this->{SampleCSV} = $this->ChooseFile("open", $Samplefmask, "ChooseSampleFile", @_);
					$this->AssignGraphData();
					$this->Draw();
				},
			0,         sub {},
			1,         sub { $this->EditFile('EditSampleCSV', @_); },
			['X1', 'Y1']
			);
	$this->{SampleFileFrame}->pack(-anchor => 'nw', -fill => 'x');
	$this->{SampleFileFrame}->{pXDataLabel} = ['.*E.*', '.*eV.*'];
	$this->{SampleFileFrame}->{pYDataLabel} = ['.*signal.*', 'i.*', '.*'];

	for(my $i = 0 ; $i < $this->{ini}->{nSpectra} ; $i++) {
		my $i1 = $i;
		$Frame = $MainPaneFrame->MyFrame()->pack(-anchor => 'nw', -fill => 'x');
		$this->{"Spectrum${i}FileFrame"} = $this->MakeChooseFileEntry(
				$Frame, "Spectrum$i", "Spectrum$i:", $this->{ini}->pVariable("SpectrumCSVFile${i}", ""), 
				'&Choose', sub {
						$this->{"SpectrumCSV${i1}"} = $this->ChooseFile("open", $Samplefmask, "ChooseSpectrumFile$i1", @_);
						$this->AssignGraphData();
						$this->Draw();
					},
				0,         sub {},
				1,         sub { $this->EditFile("EditSpectrumCSV$i", @_); },
				['X1', 'Y1']
				);
		$this->{"Spectrum${i}FileFrame"}->pack(-anchor => 'nw', -fill => 'x');
		$this->{"Spectrum${i}FileFrame"}->{pXDataLabel} = ['.*E.*', '.*eV.*'];
		$this->{"Spectrum${i}FileFrame"}->{pYDataLabel} = ['.*signal.*', 'i.*', '.*'];
	}

	$Frame = $MainPaneFrame->MyFrame()->pack(-anchor => 'nw', -fill => 'x');
	$this->mw()->{LSQFrame2} = $this->MakeLSQPanes(
			$Frame, $EntryWidth,
			'Fitting',
			[qw(FittingRange)],
			[],
			[],
			['FitXMin', 'Emin:', 'FitXMax', 'Emax:', 'nSkipData', 'nSkip:'],
			['EPS', 'EPS:', 'nMaxIter', 'MaxIter:', 'nSaveSpectraInterval', 'SaveIntvl:'], 
			);
	$this->mw()->{LSQFrame2}->pack(-anchor => 'nw', -expand => 'yes', -fill => 'x');

	$Frame = $MainPaneFrame->MyLabFrame(
			-label     => 'Constant BG',
			-labelside => 'acrosstop',
			)->pack(-anchor => 'nw');
	$this->MakeCheckEntry($Frame, "BG", "BG:", $this->{dini}->pVariable('BGcheck', 0),
			$this->{ini}->pVariable('BG', 0.0), "%g", $EntryWidth, "", 0, 0);

	$Frame = $MainPaneFrame->MyLabFrame(
			-label     => 'Spectra parameters',
			-labelside => 'acrosstop',
			)->pack(-anchor => 'nw');
	$EntryWidth = 12;
	for(my $i = 0 ; $i < $this->{ini}->{nSpectra} ; $i++) {
		$this->MakeCheckEntry($Frame, "k$i", "Spectrum$i k:", $this->{dini}->pVariable("k${i}check", 1),
				$this->{ini}->pVariable("k$i", 1.0),  "%g", $EntryWidth, "", 2*$i, 0);
		$this->MakeCheckEntry($Frame, "dE$i", "dE:", $this->{dini}->pVariable("dE${i}check", 1),
				$this->{ini}->pVariable("dE$i", 0.0), "%g", $EntryWidth, "", 2*$i, 1);
	}

	$this->BuildFooter($MainPaneFrame, $EntryWidth);
	$this->UpdateParameters();
}


sub BuildVarsPane
{
	my ($this, $MainPaneFrame, $EntryWidth) = @_;

	my $Frame = $MainPaneFrame->MyLabFrame(
			-label     => 'Constant BG',
			-labelside => 'acrosstop',
			)->pack(-anchor => 'nw');
	my $row = 1;
	$this->MakeParameterConditionHeading($Frame, 0, 0);
	my @array = qw(BG);
	foreach my $key (@array) {
		$this->MakeParameterConditionColumn($Frame, "$key", "$key:", "%12.6g", 
			$this->{dini}->pVariable("$key", 0.0),        $this->{dini}->pVariable("${key}check", 0),
			$this->{dini}->pVariable("${key}scale", 0.1), $this->{dini}->pVariable("${key}min", ''), $this->{dini}->pVariable("${key}max", ''), 
			$EntryWidth, $row++);
	}

	$Frame = $MainPaneFrame->MyLabFrame(
			-label     => 'Spectra parameters',
			-labelside => 'acrosstop',
			)->pack(-anchor => 'nw');
	$row = 1;
	$this->MakeParameterConditionHeading($Frame, 0, 0);
	@array = qw(k dE);
	for(my $i = 0 ; $i < $this->{ini}->{nSpectra} ; $i++) {
		foreach my $key0 (@array) {
			my $key = "$key0$i";
			$this->MakeParameterConditionColumn($Frame, "$key", "$key:", "%12.6g", 
				$this->{dini}->pVariable("$key", 0.0),        $this->{dini}->pVariable("${key}check", 0),
				$this->{dini}->pVariable("${key}scale", 0.1), $this->{dini}->pVariable("${key}min", ''), $this->{dini}->pVariable("${key}max", ''), 
				$EntryWidth, $row++);
		}
	}

	$this->BuildFooter($MainPaneFrame, $EntryWidth);
	$this->UpdateParameters();
}

sub BuildLSQPane
{
	my ($this, $MainPaneFrame, $EntryWidth) = @_;

	my $Frame = $MainPaneFrame->MyFrame()->pack(-anchor => 'nw', -fill => 'x');
	$this->mw()->{LSQFrame} = $this->MakeLSQPanes(
				$Frame, $EntryWidth,
				'Fitting',
				[qw(LSQMethod FittingRange FittingConditions)],
#				[qw(LSQMethod FitTo FittingRange FittingConditions)],
				['Amoeba::Simplex', 'PDL::Simplex', 'ModifiedNewton'],
				['PES'],
				['FitXMin', 'Emin:', 'FitXMax', 'Emax:', 'nSkipData', 'nSkip:'],
				['EPS', 'EPS:', 'nMaxIter', 'MaxIter:', 'nSaveSpectraInterval', 'SaveIntvl:'], 
			);
	$this->mw()->{LSQFrame}->pack(-anchor => 'nw', -expand => 'yes', -fill => 'x');
#	$this->mw()->{LSQFrame}->{FitToListBox}->SetText('alpha');

	$this->BuildFooter($MainPaneFrame, $EntryWidth);
}

sub BuildViewRangePane
{
	my ($this, $MainFrame, $EntryWidth) = @_;

	$this->SUPER::BuildViewRangePane($MainFrame, $EntryWidth,
				[
					['x'], ['x']
				],
				[
					['x'], ['x']
				]
			);
	if($this->mw()->{NoteBook}->{ViewRangePaneFrame}->{GraphFrame1ViewY0Button}) {
		$this->mw()->{NoteBook}->{ViewRangePaneFrame}->{GraphFrame1ViewY0Button}->Select();
		$this->mw()->{NoteBook}->{ViewRangePaneFrame}->{GraphFrame1ViewY0Entry}->SetText(0.0);
	}

	$this->BuildFooter($MainFrame, $EntryWidth);
}

sub BuildFooter
{
	my ($this, $MainFrame, $EntryWidth) = @_;

	my $Frame1 = $MainFrame->MyFrame()->pack(-anchor => 'nw', -fill => 'x');
#	my $ButtonFrame = $this->MakeFittingButtons($Frame1, ("RePlot", "RestoreScale", "Re&calc", "&Fit", "Flip X", "&Save"));
	my $ButtonFrame = $this->MakeFittingButtons($Frame1, ("Re&calc", "&Fit", "&Save"));
	$ButtonFrame->pack(-anchor => 'nw', -expand => 'yes', -fill => 'x');

#	$this->{RestoreScaleButton}->configure(
#		-command => sub { $this->RestoreScale(); },
#		);
}

#sub RestoreScale
#{
#	my ($this, $ResetViewRange, $CreateGraphFrame, $AssignGraphData, $Draw) = @_;
#	$ResetViewRange = 1 if(!defined $ResetViewRange);
#	$this->RePlot($ResetViewRange, $CreateGraphFrame, $AssignGraphData, $Draw, $this->{ini}->{FlipX});
#}

#sub RestoreViewScale
#{
#	my ($this, $ResetViewRange, $CreateGraphFrame, $AssignGraphData, $Draw) = @_;
#	$this->RestoreScale();
#}

sub RePlot
{
	my ($this, $ResetViewRange, $CreateGraphFrame, $AssignGraphData, $Draw) = @_;
	$this->Recalc();
}

sub ChooseFile
{
#action = 'open'; #'save'
#fmask = '*.csv;*.spe;*.jel;*.asp;*.smo;*isa;*.ref;*.pal;*.bef;*.aft;*.prm';
	my ($this, $action, $fmask, $Option, $name, $Frame) = @_;
#print "TkFittingCommon2::ChooseFile: a=$action, f=$fmask, n=$name, F=$Frame, o=$Option\n";
	my $App = $this->App();
	my $canvas = $this->Canvas();
	my $mw = $this->mw();
	my $Entry = $Frame->{PathEntry};

	my $filepath = $this->ChooseAFile($name, $action, $fmask, '', "Choose file", $Entry, $Option);
	return undef if(!defined $filepath or $filepath eq '');

	my $ret;
	if($Option eq 'ChooseParameterFile') {
		$ret = $this->ReadParameterFile($filepath, 1, $Frame);
	}
	elsif($Option =~ /ChooseSample.*File/i) {
		$ret = $this->ReadSampleDataFile($filepath, 1, $Frame);
	}
	elsif($Option =~ /ChooseSpectrumFile(\d*)/i) {
		my $idx = $1;
#print "Option=$Option  idx=$idx\n";
		$ret = $this->ReadSpectrumDataFile($filepath, $idx, 1, $Frame);
	}
	elsif($Option =~ /ChooseSubstrateFile/i) {
		$ret = $this->ReadSubstrateDataFile($filepath, 1, $Frame);
	}
	return undef unless($ret);
	$this->CreateGraphFrame() if(!$this->GetGraphFrameArray());

	return $ret;
}

#===================================================
# データ処理
#===================================================
sub BuildOptimize
{
	my ($this, $IsPrint) = @_;
	$IsPrint = 1 if(!defined $IsPrint);

	my $ini    = $this->{ini};
	my $dini   = $this->{dini};

	my $optimize = $this->{Optimize} = new Optimize;;
	$optimize->AddParameters(
			"BG",  \$ini->{BG},
			$dini->{BGcheck}, $dini->{BGscale}, $dini->{BGmin}, $dini->{BGmax},
			sub {
				$ini->{BG} = $_[0];
			},
		);

	for(my $i = 0 ; $i < $this->{ini}->{nSpectra} ; $i++) {
		my $ii = $i;
		$optimize->AddParameters(
			"k$ii",  \$ini->{"k$ii"},
			$dini->{"k${ii}check"}, $dini->{"k${ii}scale"}, $dini->{"k${ii}min"}, $dini->{"k${ii}max"},
			sub {
				$ini->{"k$ii"} = $_[0];
			},

			"dE$ii",  \$ini->{"dE$ii"},
			$dini->{"dE${ii}check"}, $dini->{"dE${ii}scale"}, $dini->{"dE${ii}min"}, $dini->{"dE${ii}max"},
			sub {
				$ini->{"dE$ii"} = $_[0];
			},
		);
	}
}

sub Recalc
{
	my ($this) = @_;
	return if(!defined $this->{DataFile});

	my $ini = $this->{ini};

	my $X1Label   = $this->{SampleFileFrame}->{X1ListBox}->GetText();
	my $Y1Label   = $this->{SampleFileFrame}->{Y1ListBox}->GetText();
	my $XMin      = $ini->{FitXMin};
	my $XMax      = $ini->{FitXMax};
	my $nSkipData = $ini->{nSkipData};
	my $pXS        = $this->{DataFile}->GetData($X1Label) if($X1Label);
	my $pYS       = $this->{DataFile}->GetData($Y1Label) if($Y1Label);

	my (@pSpectrumData);
	my $nCurves = 0;
	for(my $i = 0 ; $i < $this->{ini}->{nSpectra} ; $i++) {
		my ($DataKey, $FrameKey) = ("SpectrumFile$i", "Spectrum${i}FileFrame");
#print "Recalc: $i: $DataKey\n";

		my $pData    = $this->{$DataKey};
		next if(!defined $pData);
		my $nData    = $pData->nData();
		next if($nData <= 0);

		my $Frame     = $this->{$FrameKey};
		$X1Label      = $Frame->{X1ListBox}->GetText();
		$Y1Label      = $Frame->{Y1ListBox}->GetText();
		$X1Label      = 'X'  if(!$X1Label);
		$Y1Label      = 'Y1' if(!$Y1Label);
		$pData->GetData($Frame->{X1ListBox}->GetText());
		$pData->GetData($Frame->{Y1ListBox}->GetText());

		$pSpectrumData[$nCurves] = $pData;
		$nCurves++;
	}

	my (@X, @Y);
	my $c = 0;
	for(my $i = 0 ; $i < @$pXS ; $i++) {
		my $x = $pXS->[$i];
		next if($x < $XMin or $XMax < $x);
		next if($nSkipData > 0 and $i % $nSkipData != 0);
		$X[$c] = $x;
		$Y[$c] = $pYS->[$i];
		$c++;
	}

	my ($pYTotal, $ppCalY) = $this->CalTotalSpectrum(\@X, \@pSpectrumData, $this->{ini});
	$this->{pObsX}  = \@X;
	$this->{pObsY}  = \@Y;
	$this->{pCalX}  = \@X;
	$this->{pCalY}  = $pYTotal;
	$this->{ppCalY} = $ppCalY;

	$this->SUPER::RePlot();
}

sub Fit
{
	my ($this) = @_;
	return if(!defined $this->{DataFile});

	my $ini    = $this->{ini};
	$this->UpdateParameters();
	$this->BuildOptimize();

	my $Method = $this->mw()->{LSQFrame}->{LSQMethodListBox}->GetText(); #$this->{LSQMethodListBox}->GetText();
	my $optimize = $this->{Optimize};
print "Method: $Method\n";
print "nMaxIter: $ini->{nMaxIter}\n";

	my $X1Label   = $this->{SampleFileFrame}->{X1ListBox}->GetText();
	my $Y1Label   = $this->{SampleFileFrame}->{Y1ListBox}->GetText();
	my $XMin      = $ini->{FitXMin};
	my $XMax      = $ini->{FitXMax};
	my $nSkipData = $ini->{nSkipData};
	my $pXS       = $this->{DataFile}->GetData($X1Label) if($X1Label);
	my $pYS       = $this->{DataFile}->GetData($Y1Label) if($Y1Label);

	my (@pSpectrumData);
	my $nCurves = 0;
	for(my $i = 0 ; $i < $this->{ini}->{nSpectra} ; $i++) {
		my ($DataKey, $FrameKey) = ("SpectrumFile$i", "Spectrum${i}FileFrame");
#print "Recalc: $i: $DataKey\n";

		my $pData    = $this->{$DataKey};
		next if(!defined $pData);
		my $nData    = $pData->nData();
		next if($nData <= 0);

		my $Frame     = $this->{$FrameKey};
		$X1Label      = $Frame->{X1ListBox}->GetText();
		$Y1Label      = $Frame->{Y1ListBox}->GetText();
		$X1Label      = 'X'  if(!$X1Label);
		$Y1Label      = 'Y1' if(!$Y1Label);
		$pData->GetData($Frame->{X1ListBox}->GetText());
		$pData->GetData($Frame->{Y1ListBox}->GetText());

		$pSpectrumData[$nCurves] = $pData;
		$nCurves++;
	}

	my (@X, @Y);
	my $c = 0;
	for(my $i = 0 ; $i < @$pXS ; $i++) {
		my $x = $pXS->[$i];
		next if($x < $XMin or $XMax < $x);
		next if($nSkipData > 0 and $i % $nSkipData != 0);
		$X[$c] = $x;
		$Y[$c] = $pYS->[$i];
		$c++;
	}

#=========================================================
# 最適化の実行
#=========================================================
	$optimize->SetnS2Calculation(0);
	my ($OptVars, $MinVal) = $optimize->Optimize(
				$Method, undef, undef, undef,
				$ini->{EPS}, $ini->{nMaxIter}, $ini->{iPrintLevel},
				sub { $this->CalS2(\@X, \@Y, \@pSpectrumData, @_); },
				undef,
				sub { Optimize::BuildDifferentialMatrixes(@_); },
				);
	print "\nOptimized at:\n";

	$optimize->RecoverParameters($OptVars);
	$optimize->PrintParameters(1, $OptVars, $MinVal, 1);

	$this->SetS2($MinVal);

	$this->UpdateParameters();
	$this->Recalc();
}

sub CalTotalSpectrum
{
	my ($this, $pX, $ppSpectrumData, $ini) = @_;

	my $BG = $ini->{BG};
	my (@k, @dE);
	my @pCalY;
	my @YTotal;
	for(my $j = 0 ; $j < @$pX ; $j++) {
		$YTotal[$j] = $BG;
#		$YTotal[$j] = 0.0;
	}

	for(my $i = 0 ; $i < $ini->{nSpectra} ; $i++) {
		my $k     = $ini->{"k$i"};
		my $dE    = $ini->{"dE$i"};
		my $pData = $ppSpectrumData->[$i];
		next if(!defined $pData);

		my @YCal;
		for(my $j = 0 ; $j < @$pX ; $j++) {
			my $x        = $pX->[$j];
			my $y        = $k * $pData->YVal($x + $dE);
			$YCal[$j]    = $y;
			$YTotal[$j] += $y;
		}
		$pCalY[$i] = \@YCal;
	}
	return (\@YTotal, \@pCalY);
}

sub CalS2
{
	my ($this, $pX, $pY, $ppSpectrumData, $pVars, $iPrintLevel) = @_;
#print "pVars=", join(',', @$pVars), "\n";

	my $optimize = $this->{Optimize};
	my $ini      = $this->{ini};
	$optimize->RecoverParameters($pVars);

	my %p;
	my $idx = 0;
	$p{nSpectra} = $ini->{nSpectra};
	$p{BG} = $pVars->[$idx++];
	for(my $i = 0 ; $i < $this->{ini}->{nSpectra} ; $i++) {
		$p{"k$i"}  = $pVars->[$idx++];
		$p{"dE$i"} = $pVars->[$idx++];
	}
	my ($pYTotal, $ppCalY) = $this->CalTotalSpectrum($pX, $ppSpectrumData, \%p);

	my $S2 = 0.0;
	my $I2 = 0.0;
	my $c = 0;
	for(my $i = 0 ; $i < @$pX ; $i++) {
		my $x = $pX->[$i];
		my $d = $pYTotal->[$i] - $pY->[$i];
		$S2 += $d * $d;
		$I2 += $pY->[$i] * $pY->[$i];
		$c++;
	}
#	$S2 = sqrt($S2 / $c) if($c > 0);
	$S2 = sqrt($S2 / $I2);

	$optimize->IncrementnS2();
	my $nS2         = $optimize->nS2Calculation();
	my $nS2Interval = $ini->{nSaveSpectraInterval};
	print "S2[$nS2] = $S2 / ";
	$S2 += $optimize->CalPenalty(1.0e10, $pVars, 1);
	print "$S2\n";
	$optimize->PrintParameters(1, $pVars, $S2, 0);

	if($nS2Interval > 0 and $nS2 % $nS2Interval == 0) {
		$this->SetS2($S2);
		$this->Recalc();
		$this->RePlot();
	}
	$this->UpdateParameters();
	$this->mw()->update();

	return $S2;
}

sub Save
{
	my ($this) = @_;

	$this->Recalc() if(!defined $this->{pCalX});

	my $path = $this->{ini}->{ParameterFile};
	$path =  $this->{ini}->{SampleCSVFile} if(!$path);
	my ($drive, $directory, $filename, $ext1, $lastdir, $filebody) = Deps::SplitFilePath($path);
	my $dir = Deps::ExtractDirectory($path);
	$path = Deps::MakePath($dir, "MultiFit-$filebody.csv", 0);
$this->print("\nSave decomposed spectra to [$path].\n");

	my $out = new JFile($path, "w");
	if(!$out) {
		$this->print("Error: Can not write to [$path].\n");
		return;
	}
#	$out->print("E,PES(obs),PES(cal)");
#	$out->print(",BG(cal)\n");
#
#	my $pE       = $this->{pCalX};
#	my $pObs     = $this->{pObsY};
#	my $pPES     = $this->{pCalY};
#	my $pBG      = $this->{pCalBG};
#	for(my $i = 0 ; $i < @$pE ; $i++) {
#		$out->print("$pE->[$i],$pObs->[$i],$pPES->[$i]");
#		$out->print(",$pBG->[$i]\n");
#	}

	$out->print("E,PES(sample),PES(fitted)");
	for(my $i = 0 ; $i < $this->{ini}->{nSpectra} ; $i++) {
		$out->print(",PES(Spectrum$i)");
	}
	$out->print("\n");

	my $pCalX = $this->{pCalX};
	my $pObs  = $this->{pObsY};
	my $pCalY = $this->{pCalY};
	for(my $i = 0 ; $i < @$pCalX ; $i++) {
		$out->print("$pCalX->[$i],$pObs->[$i],$pCalY->[$i]");
		for(my $is = 0 ; $is < $this->{ini}->{nSpectra} ; $is++) {
			my $pCalX = $this->{pCalX};
			my $pCalY = $this->{ppCalY}->[$is];
			if(defined $pCalY->[$i]) {
				$out->print(",$pCalY->[$i]");
			}
			else {
				$out->print(",");
			}
		}
		$out->print("\n");
	}
	$out->Close();
}

sub SaveParameterFile
{
	my ($this, $Option, $filepath, $name, $Frame) = @_;
	$filepath = $Frame->{PathEntry}->GetText() if($filepath eq '');

	$this->{ini}->{SampleX1}       = $this->{SampleFileFrame}->{X1ListBox}->GetText();
	$this->{ini}->{SampleY1}       = $this->{SampleFileFrame}->{Y1ListBox}->GetText();
#	$this->{ini}->{AppFunction}    = $this->{ChooseAppFunctionListBox}->GetText();
#	$this->{ini}->{ConductionType} = $this->{ChooseConductionTypeListBox}->GetText();
	$this->{ini}->{YAxisPlotType}  = $this->mw()->{NoteBook}->{ViewRangePaneFrame}->{GraphFrame1YAxisListBox}->GetText();

	if(!defined $filepath or $filepath eq '') {
		$filepath = $this->{ini}->{SampleCSVFile};
#		$filepath = $this->{ini}->{SubstrateCSVFile} if(!defined $filepath or $filepath eq '');
		$filepath = 'save.prm' if(!defined $filepath or $filepath eq '');
		$filepath =~ s/\.csv$/\.prm/i;
		$filepath = Deps::ExtractFileName($filepath);

		$filepath = $this->ChooseSaveFile($filepath, '*.prm');
		if($filepath) {
			my $ext = Deps::ExtractExtention($filepath);
			if(!defined $ext or $ext eq '') {
				$filepath = Deps::ReplaceExtension($filepath, ".prm");
			}
			$this->{ini}->{ParameterFile} = $filepath;
		}
		else {
			return;
		}
	}
	$this->{ini}->SetIniFile($filepath, undef, 1);
	$this->App()->print("\nSaveParameterFile:\n");
	$this->ComposeParameters($this->{dini}, $this->{ini});
	$this->{ini}->WriteAll();
	$this->DecomposeParameters($this->{ini}, $this->{dini});
}

sub ReadParameterFile
{
	my ($this, $filepath) = @_;
	my $ini  = $this->{ini};
	my $dini = $this->{dini};

	$this->Initialize(1, 1);
	$this->App()->print("\nRead paramter from [$filepath].\n");

	$this->{ini}->ReadAll($filepath);
	$this->DecomposeParameters($ini, $dini);
	$this->RefreshMainPane($this->{EntryWidth});

	my $DataFrame = $this->{SampleFileFrame};
	$this->{ini}->{SampleX1} = $this->{ini}->{X}  if(!defined $this->{ini}->{SampleX1});
	$this->{ini}->{SampleY1} = $this->{ini}->{Y1} if(!defined $this->{ini}->{SampleY1});
	$DataFrame->{X1ListBox}->SetText($this->{ini}->{SampleX1}) if($this->{ini}->{SampleX1});
	$DataFrame->{Y1ListBox}->SetText($this->{ini}->{SampleY1}) if($this->{ini}->{SampleY1});

#	$this->{ChooseAppFunctionListBox}->SetText($this->{ini}->{AppFunction});
#	$this->{ChooseConductionTypeListBox}->SetText($this->{ini}->{ConductionType});

	if($this->{ini}->{SampleCSVFile}) {
		my $path = $this->{ini}->{SampleCSVFile};
		next if($path eq '');
		$path = $this->GetValidDataPath($path, $filepath, $this->{ini}->{ParameterFile});
		my $ret = $this->ReadSampleDataFile($path, 1, 0, 0);
		return undef unless($ret);
		$this->{ini}->{SampleCSVFile} = $path;
		$this->{ini}->{ParameterFile} = $filepath;
	}
	for(my $i = 0 ; $i < $this->{ini}->{nSpectra} ; $i++) {
		my $FileKey = "SpectrumCSVFile$i";
		my $path = $this->{ini}->{$FileKey};
		next if($path eq '');
		$path = $this->GetValidDataPath($path, $filepath, $this->{ini}->{ParameterFile});
		my $ret = $this->ReadSpectrumDataFile($path, $i, 1, 0, 0);
		return undef unless($ret);
		$this->{ini}->{$FileKey}      = $path;
		$this->{ini}->{ParameterFile} = $filepath;
	}

#	$this->RePlot(0, 1, 0, 0);

	$this->RefreshViewRangePane($this->{EntryWidth});

	my $YAxisListBox = $this->{ini}->{YAxisPlotType}; #$this->mw()->{NoteBook}->{ViewRangePaneFrame}->{GraphFrame1YAxisListBox};
	if($YAxisListBox) {
		$this->mw()->{NoteBook}->{ViewRangePaneFrame}->{GraphFrame1YAxisListBox}->SetText($this->{ini}->{YAxisPlotType}) if($this->{ini}->{YAxisPlotType});
	}

	$this->CreateGraphFrame() if(!$this->GetGraphFrameArray());
	$this->AssignGraphData();
	$this->Draw();
#	$this->RePlot(1, 0, 1, 1);

	return 1;
}

sub ReadSampleDataFile
{
	my ($this, $filepath, $IsPrint, $UpdateRange, $IsPlot, $Frame) = @_;
	return undef if($filepath eq '');
	$UpdateRange = 1 if(!defined $UpdateRange);
	$IsPlot = 1 if(!defined $IsPlot);

	my $App = $this->App();
	$Frame = $this->{SampleFileFrame} if(!defined $Frame);
	my $pXDataLabel = $Frame->{pXDataLabel};
	my $pYDataLabel = $Frame->{pYDataLabel};
#print "type=$type\n";

	$this->Initialize(0, 1);
	my $pData = $this->{DataFile} = new Ellipsometry;

	$this->{Path} = $filepath;
	my ($nData, $pLabelArray, @pDataArray) = $pData->Read($filepath);
	if(!defined $nData) {
		$App->print("Error: Can not read [$filepath].\n");
		return $this->{Path} = undef;
	}
	
	if(!Utils::IsConstantStepArray($pDataArray[0], 0.01)) {
		$App->print("Error: The data step for X is not constant.\n");
		return $this->{Path} = undef;
	}

	my $nDataArray = $this->{DataFile}->nDataArray();
	$Frame->{X1ListBox}->DeleteAllItem() if(defined $Frame->{X1ListBox});
	$Frame->{Y1ListBox}->DeleteAllItem() if(defined $Frame->{Y1ListBox});
	for(my $i = 0 ; $i < $nDataArray ; $i++) {
		$Frame->{X1ListBox}->AddItem($pLabelArray->[$i]) if(defined $Frame->{X1ListBox});
		$Frame->{Y1ListBox}->AddItem($pLabelArray->[$i]) if(defined $Frame->{Y1ListBox});
	}
	$Frame->{X1ListBox}->SetCurSel(@$pXDataLabel) if(defined $Frame->{X1ListBox});
	$Frame->{Y1ListBox}->SetCurSel(@$pYDataLabel) if(defined $Frame->{Y1ListBox});
	my $pX = $pData->GetXData(@$pXDataLabel);
	$pData->GetYData(@$pYDataLabel);
	if($pX->[1] < $pX->[0]) {
		$this->{DataFile}->ReverseData();
	}

	$pData->CalMinMax();
	($this->{ini}->{FitEmin}, $this->{ini}->{FitEmax}) = $pData->GetXMinMax() 
		if(!defined $this->{ini}->{FitEmin} or $this->{ini}->{FitEmin} eq '');

	if($UpdateRange or !defined $this->{ini}->{FitXMin}) {
		($this->{ini}->{FitXMin}, $this->{ini}->{FitXMax}) = Utils::CalMinMax($pDataArray[0]);
	}

	if($IsPlot) {
		$this->RePlot($UpdateRange);
	}
	else {
		$this->CreateGraphFrame() if(!$this->GetGraphFrameArray());
		$this->AssignGraphData();
	}

	return $filepath;
}

sub ReadSpectrumDataFile
{
	my ($this, $filepath, $idx, $IsPrint, $UpdateRange, $IsPlot, $Frame) = @_;
	$UpdateRange = 1 if(!defined $UpdateRange);
	$IsPlot = 1 if(!defined $IsPlot);

	my $App = $this->App();
	$Frame = $this->{"Spectrum${idx}FileFrame"} if(!defined $Frame);
	my $pXDataLabel = $Frame->{pXDataLabel};
	my $pYDataLabel = $Frame->{pYDataLabel};

	my $pData = $this->{"SpectrumFile$idx"} = new Ellipsometry;
#print "Read [$filepath] as Spectrum data #$idx\n";

	$this->{"SpectrumFilePath$idx"} = $filepath;
	my ($nData, $pLabelArray, @pDataArray) = $pData->Read($filepath);
	if(!defined $nData) {
		$App->print("Error: Can not read [$filepath].\n");
		return $this->{"SpectrumFilePath$idx"} = undef;
	}
	
	if(!Utils::IsConstantStepArray($pDataArray[0], 0.01)) {
		$App->print("Error: The data step for X is not constant.\n");
		return $this->{"SpectrumFilePath$idx"} = undef;
	}

	my $nDataArray = $this->{"SpectrumFile$idx"}->nDataArray();

	$Frame->{X1ListBox}->DeleteAllItem() if(defined $Frame->{X1ListBox});
	$Frame->{Y1ListBox}->DeleteAllItem() if(defined $Frame->{Y1ListBox});
	for(my $i = 0 ; $i < $nDataArray ; $i++) {
		$Frame->{X1ListBox}->AddItem($pLabelArray->[$i]) if(defined $Frame->{X1ListBox});
		$Frame->{Y1ListBox}->AddItem($pLabelArray->[$i]) if(defined $Frame->{Y1ListBox});
	}
	$Frame->{X1ListBox}->SetCurSel(@$pXDataLabel) if(defined $Frame->{X1ListBox});
	$Frame->{Y1ListBox}->SetCurSel(@$pYDataLabel) if(defined $Frame->{Y1ListBox});
	my $pX = $pData->GetXData(@$pXDataLabel);
	$pData->GetYData(@$pYDataLabel);
	if($pX->[1] < $pX->[0]) {
		$this->{"SpectrumFile$idx"}->ReverseData();
	}

	$pData->CalMinMax();

	$this->CreateGraphFrame() if(!$this->GetGraphFrameArray());
#	$this->AssignGraphData();
#	$this->RePlot($UpdateRange);

	return $filepath;
}

sub CreateGraphFrame
{
	my ($this, $canvas, $TargetData, $DoUpdate) = @_;
	return if(!$DoUpdate and $this->GetGraphFrameArray());

	$canvas = $this->Canvas();
	my $App = $this->App();
	my $font = $App->{GraphFrameFont};
	my @font = split(/,/, $font) if($font);
	my $w = $canvas->width();
	my $h = $canvas->height();

	my $RefreshGraphScaleFrame = (defined $this->{GraphFrameArray})? 0 : 1;

	my $GraphFrameArray = $this->{GraphFrameArray} = new GraphFrameArray($this->mw());
	$GraphFrameArray->SetCanvasSize($w, $h);

	$GraphFrameArray->AddGraphFrame();
	my $GraphFrame0  = $GraphFrameArray->GetGraphFrame(0);
	my $FramePosStr0 = $App->{GraphFrame0Position};
	$GraphFrame0->SetPositionByStr($FramePosStr0);

	my $XScale0 = $GraphFrame0->GetXScale(0);
	my $YScale0 = $GraphFrame0->GetYScale(0);
	$XScale0->SetScaleStringVisible(1);
	$XScale0->SetCaptionVisible(1);

	$GraphFrame0->SetViewRange(0, 0, 1, 1);

	if($RefreshGraphScaleFrame) {
		my $EntryWidth = $this->{EntryWidth};
		$this->RefreshViewRangePane($EntryWidth);
	}
}

sub AssignGraphData
{
	my ($this, $ResetViewRange) = @_;
	$ResetViewRange = 1 if(!defined $ResetViewRange);
	my $ini = $this->{ini};
#	return if(!defined $ini->{SampleCSVFile});
	return if(!defined $this->mw()->{NoteBook}->{ViewRangePaneFrame}->{GraphFrame1YAxisListBox});

	my $GraphFrameArray = $this->GetGraphFrameArray();
	my $GraphFrame0  = $GraphFrameArray->GetGraphFrame(0);
	$GraphFrame0->ClearAllData();

	my ($X1Label, $Y1Label);
	my @colors = ("black", "blue", "red", "green", "cyan", "purple", "yellow", "darkgray");
	for(my $i = -1 ; $i < $this->{ini}->{nSpectra} ; $i++) {
		my ($DataKey, $FrameKey);
		if($i == -1) {
			$DataKey  = "DataFile";
			$FrameKey = "SampleFileFrame";
		}
		else {
			$DataKey  = "SpectrumFile$i";
			$FrameKey = "Spectrum${i}FileFrame";
		}

		my $pData    = $this->{$DataKey};
		next if(!defined $pData);
		my $nData    = $pData->nData();
		next if($nData <= 0);

		my $Frame    = $this->{$FrameKey};
		$X1Label  = $Frame->{X1ListBox}->GetText();
		$Y1Label  = $Frame->{Y1ListBox}->GetText();
		$X1Label     = 'X'  if(!$X1Label);
		$Y1Label     = 'Y1' if(!$Y1Label);
		my $pX       = $pData->GetData($Frame->{X1ListBox}->GetText());
		my $pY1      = $pData->GetData($Frame->{Y1ListBox}->GetText());
		$GraphFrame0->SetXCaption($X1Label);
		$GraphFrame0->SetYCaption($Y1Label);
		my $color    = $colors[($i+1) % @colors];
		my $label    = ($i == -1)? "Sample data" : "Spectrum$i";
		my $fname    = ($i == -1)? $ini->{"SampleCSVFile"} : $ini->{"SpectrumCSVFile$i"};
		if($pX) {
			$GraphFrame0->AddGraphData($pX, $pY1,
					2, $color, "", 6, $color, 0, $color, "XAutoSkip", "Energy", "$fname - $label") if($pY1);
		}
	}

	my $pCalX = $this->{pCalX};
	my $pCalY = $this->{pCalY};
	if($pCalX) {
		$GraphFrame0->AddGraphData($pCalX, $pCalY,
				0, "", "circle", 3, "", 1, "red", "XAutoSkip", "Energy", "Calc (total)") if($pCalY);
	}
	for(my $i = 0 ; $i < $this->{ini}->{nSpectra} ; $i++) {
		my $pCalX = $this->{pCalX};
		my $pCalY = $this->{ppCalY}->[$i];
		next if(!defined $pCalY);

		$GraphFrame0->AddGraphData($pCalX, $pCalY,
				0, "", "cross", 3, "", 1, "green", "XAutoSkip", "Energy", "Calc ($i)") if($pCalY);
	}

	$GraphFrame0->SetXScalePlotType('x');
	$GraphFrame0->SetYScalePlotType('x');
	$this->SetViewRange($ResetViewRange);#, $FlipX);
}

sub Initialize
{
	my ($this, $InitializeParameterFile, $InitializeData) = @_;

	$this->{DataFile} = new Ellipsometry;

	if($InitializeParameterFile) {
		$this->{ini}->{SampleCSVFile} = '';
#		$this->{ini}->{FlipX}         = 0;
		$this->{ini}->{FitXMin}       = '';
		$this->{ini}->{FitXMax}       = '';
	}
	if($InitializeData) {
		$this->{pCalX}  = undef;
		$this->{pCalY}  = undef;
		$this->{pCalBG} = undef;
	}
}

sub InitializeParameters
{
	my ($this, $ini, $dini) = @_;

	$this->AddParameters($ini, $dini, "BG",   0.0, 1, 1000.0, 0.0, '');
	for(my $i = 0 ; $i < $this->{ini}->{nSpectra} ; $i++) {
		$this->AddParameters($ini, $dini, "k$i",  1.0, 1, 0.1, 0.0, '');
		$this->AddParameters($ini, $dini, "dE$i", 0.0, 1, 0.1,  '', '');
	}
}

1;