From 38d55a3ebed879ab7264da77812d33a0c36a64b5 Mon Sep 17 00:00:00 2001
From: Zaher Salman <zaher.salman@psi.ch>
Date: Thu, 3 Sep 2015 10:13:40 +0200
Subject: [PATCH] The chemical formula from the GUI will be added to the
 _Seq_Results.dat file header and used by the root macro when plotting the
 fractions.

---
 trimsp/src/TrimSPGUI4/TrimSPGUI4.pm    | 21 ++++++++++++++--
 trimsp/src/TrimSPGUI4/Ui_TrimSPGUI4.pm |  2 +-
 trimsp/src/plotFrc.C                   | 34 +++++++++++++++++---------
 3 files changed, 42 insertions(+), 15 deletions(-)

diff --git a/trimsp/src/TrimSPGUI4/TrimSPGUI4.pm b/trimsp/src/TrimSPGUI4/TrimSPGUI4.pm
index 8fa2599..7771292 100644
--- a/trimsp/src/TrimSPGUI4/TrimSPGUI4.pm
+++ b/trimsp/src/TrimSPGUI4/TrimSPGUI4.pm
@@ -617,11 +617,28 @@ sub StartSequenceOne
 	$Progress=90;
 	this->{ui}->progress->setValue($Progress);
 	this->{ui}->progress->update();
-	sleep(10);
+#	sleep(10);
     }
 
+# An easy way to keep track of chemical formula is to replace impL_i by the corresponding chemical formula of layer i
+    open (INF,q{<}, "fort.33" );
+    my @lines = <INF>;
+    close(INF);
+    my $all_lines = join("",@lines);
+    for (my $i=1;$i<=$All{"numLayer"};$i++){
+	my $LComp = "L".$i."Comp";
+	my $chem_formula = $All{"$LComp"};
+	my $place_holder = "impL".$i;
+	$all_lines =~ s/$place_holder/$chem_formula/g;
+    }
+
+    my $seq_file = $All{"fileNamePrefix"}."_Seq_Results.dat";
+    open (SEQF,q{>}, "$seq_file" );
+    print SEQF $all_lines;
+    close(SEQF);
+
 # Move the fort.33 file into the subdirectory and change its name
-    $cmd="rm -f eingabe1.inp; mv -f fort.33 ".$All{"fileNamePrefix"}."_Seq_Results.dat";
+    $cmd="rm -f eingabe1.inp; rm -f fort.33";
     system($cmd);
     $Progress=100;
     this->{ui}->progress->setValue($Progress);
diff --git a/trimsp/src/TrimSPGUI4/Ui_TrimSPGUI4.pm b/trimsp/src/TrimSPGUI4/Ui_TrimSPGUI4.pm
index cfc926a..ab2ce28 100644
--- a/trimsp/src/TrimSPGUI4/Ui_TrimSPGUI4.pm
+++ b/trimsp/src/TrimSPGUI4/Ui_TrimSPGUI4.pm
@@ -1531,4 +1531,4 @@ sub retranslate_ui {
     retranslateUi( $trimSPGUI4 );
 }
 
-1;
\ No newline at end of file
+1;
diff --git a/trimsp/src/plotFrc.C b/trimsp/src/plotFrc.C
index 1bf9039..b26a25e 100644
--- a/trimsp/src/plotFrc.C
+++ b/trimsp/src/plotFrc.C
@@ -13,7 +13,7 @@
 void plotFrc(char *FileName)
 {
   TObjString *ostr;
-  TString str,xlab,ylab;
+  TString str,xlab;
 
   TString  line, label, treeLabel;
   TString  rootFileName;
@@ -43,8 +43,6 @@ void plotFrc(char *FileName)
       nPars=ntokens;
       ostr = dynamic_cast<TObjString*>(labels->At(0));
       xlab = ostr->GetString();
-      ylab = ostr->GetString();
-
     } else {
       token = line.Tokenize(" ");
       ntokens = token->GetEntries();
@@ -148,14 +146,14 @@ void plotFrc(char *FileName)
 
   if (Flag[0]==1){
     TGraph *gr1 = new TGraph(i,x,yl1);
-    gr1->GetXaxis()->SetTitle(xlab);
-    gr1->GetYaxis()->SetTitle("Implanted Fraction");
     //  gr1->Draw("APC");
     gr1->SetMarkerStyle(20);
     gr1->SetMarkerColor(TColor::kRed);
     gr1->SetLineColor(TColor::kRed);
     // Preferably get the chemical formula from header
-    legend->AddEntry(gr1,"Layer 1");
+    ostr = dynamic_cast<TObjString*>(labels->At(10));
+    xlab = ostr->GetString();
+    legend->AddEntry(gr1,xlab);
     mg->Add(gr1);
   }
   
@@ -166,7 +164,9 @@ void plotFrc(char *FileName)
     gr2->SetLineColor(TColor::kGreen);
     //  gr2->Draw("PC");
     // Preferably get the chemical formula from header
-    legend->AddEntry(gr2,"Layer 2");
+    ostr = dynamic_cast<TObjString*>(labels->At(11));
+    xlab = ostr->GetString();
+    legend->AddEntry(gr2,xlab);
     mg->Add(gr2);
   }
   
@@ -177,7 +177,9 @@ void plotFrc(char *FileName)
     gr3->SetLineColor(TColor::kBlue);
     //  gr3->Draw("PC");
     // Preferably get the chemical formula from header
-    legend->AddEntry(gr3,"Layer 3");
+    ostr = dynamic_cast<TObjString*>(labels->At(12));
+    xlab = ostr->GetString();
+    legend->AddEntry(gr3,xlab);
     mg->Add(gr3);
   }
   
@@ -188,7 +190,9 @@ void plotFrc(char *FileName)
     gr4->SetLineColor(TColor::kMagenta);
     //  gr4->Draw("PC");
     // Preferably get the chemical formula from header
-    legend->AddEntry(gr4,"Layer 4");
+    ostr = dynamic_cast<TObjString*>(labels->At(13));
+    xlab = ostr->GetString();
+    legend->AddEntry(gr4,xlab);
     mg->Add(gr4);
   }
   
@@ -199,7 +203,9 @@ void plotFrc(char *FileName)
     gr5->SetLineColor(TColor::kOrange);
     //  gr5->Draw("PC");
     // Preferably get the chemical formula from header
-    legend->AddEntry(gr5,"Layer 5");
+    ostr = dynamic_cast<TObjString*>(labels->At(14));
+    xlab = ostr->GetString();
+    legend->AddEntry(gr5,xlab);
     mg->Add(gr5);
   }
   
@@ -210,7 +216,9 @@ void plotFrc(char *FileName)
     gr6->SetLineColor(TColor::kViolet);
     //  gr6->Draw("PC");
     // Preferably get the chemical formula from header
-    legend->AddEntry(gr6,"Layer 6");
+    ostr = dynamic_cast<TObjString*>(labels->At(15));
+    xlab = ostr->GetString();
+    legend->AddEntry(gr6,xlab);
     mg->Add(gr6);
   }
   
@@ -221,7 +229,9 @@ void plotFrc(char *FileName)
     gr7->SetLineColor(TColor::kAzure+7);
     //  gr7->Draw("PC");
     // Preferably get the chemical formula from header
-    legend->AddEntry(gr7,"Layer 7");
+    ostr = dynamic_cast<TObjString*>(labels->At(16));
+    xlab = ostr->GetString();
+    legend->AddEntry(gr7,xlab);
     mg->Add(gr7);
   }