Merge pull request #1424 from VinzenzBildstein/main

Some improvements to TNucleus and to the doxygen documentation

.gitignore

@@ -31,6 +31,4 @@ grsi_logon.C
 *.pcm
 *Data
 .grsirc
-documentation
 wiki
-doxygen

doxygen/DoxygenLayout.xml

@@ -47,9 +47,6 @@
   <class>
     <briefdescription visible="yes"/>
     <detaileddescription title=""/>
-    <includes visible="$SHOW_HEADERFILE"/>
-    <inheritancegraph visible="$CLASS_GRAPH"/>
-    <collaborationgraph visible="yes"/>
     <memberdecl>
       <nestedclasses visible="yes" title=""/>
       <publictypes title=""/>
@@ -84,6 +81,8 @@
       <related title="" subtitle=""/>
       <membergroups visible="yes"/>
     </memberdecl>
+    <inheritancegraph visible="$CLASS_GRAPH"/>
+    <collaborationgraph visible="yes"/>
     <memberdef>
       <inlineclasses title=""/>
       <typedefs title=""/>

include/GCanvas.h

@@ -138,10 +138,12 @@ class GMarker : public TObject {
 ///   histograms on a new canvas, or (for 2D histograms) create new GH2D from
 ///   histogram and draw it on a new canvas (using "colz").
 /// - control click: doesn't do anything right now, code for TCutG is commented out.
+///
 /// For TLevelSchemes we also have:
 /// - mouse wheel to change zoom level
 /// - mouse drag to zoom in
 /// - u unzooms.
+///
 /// Also adds keyboard controls for 1D histograms:
 /// - left/right arrow moves the range left/right by 50%.
 /// - up/down arrow on GH1D histograms selects the next/previous histogram and draws it.
@@ -170,6 +172,7 @@ class GMarker : public TObject {
 /// - R	Bring up the dialogue box used to set the desired y-axis range.
 /// - s	Show peak values.
 /// - S	Remove peak values. 
+///
 /// And for 2D histograms these keyboard controls are added:
 /// - left/right arrow moves the range left/right by 50%.
 /// - up/down arrow moves the range up/down by 50%.

include/TNucleus.h

@@ -38,7 +38,10 @@ class TNucleus : public TNamed {
 
 	~TNucleus() override;
 
-	static std::string SortName(const char* name);
+	static void ParseName(const char* input, std::string& symbol, int& number, std::string& element) { std::string tmp(input); return ParseName(tmp, symbol, number, element); }
+	static void ParseName(std::string input, std::string& symbol, int& number, std::string& element);
+	static std::string SortName(const char* input) { std::string tmp(input); return SortName(tmp); }
+	static std::string SortName(std::string input);
 	void SetZ(int);              ///< Sets the Z (# of protons) of the nucleus
 	void SetN(int);              ///< Sets the N (# of neutrons) of the nucleus
 	void SetMassExcess(double);  ///< Sets the mass excess of the nucleus (in MeV)

include/TUserSettings.h

@@ -49,6 +49,15 @@
 /// where userSettings is of type TUserSettings* and filename is 
 /// either a std::string or char*.
 ///
+/// The settings file is expected to have the format
+/// parameter name: value
+/// where parameter name is a string w/o whitespace and value is the value of the parameter
+/// the type of the value (bool, int, double, std::string, or vectors of these types) will be determined automatically.
+/// Vectors are comma separated values of one type.
+/// The default type is std::string.
+/// Any lines starting with '#' or '//' or without a colon will be ignored.
+/// See "examples/AngularCorrelationSettings.par" for an example of a settings file.
+///
 /////////////////////////////////////////////////////////////
 
 class TUserSettings : public TNamed {

libraries/TAnalysis/TNucleus/TNucleus.cxx

@@ -25,58 +25,20 @@ std::string& TNucleus::massfile()
 TNucleus::TNucleus(const char* name)
 {
 	// Creates a nucleus based on symbol (ex. 26Na OR Na26) and sets all parameters from mass.dat
-	std::string Name = name;
-	int           Number = 0;
+	int           number = 0;
 	std::string   symbol;
 	std::string   element;
-	int           first_digit, first_letter;
 	int           z, n;
 	std::string   sym_name;
 	double        mass;
 	bool          found = false;
 	std::string   line;
 	std::ifstream infile;
-	std::string   MassFile;
-	Name.erase(std::remove_if(Name.begin(), Name.end(), (int (*)(int))std::isspace), Name.end());
-
-	if(Name.length() < 2) {
-		switch(Name[0]) {
-			case 'p':
-				Name.clear();
-				Name.assign("h1");
-				break;
-			case 'd':
-				Name.clear();
-				Name.assign("h2");
-				break;
-			case 't':
-				Name.clear();
-				Name.assign("h3");
-				break;
-			case 'a':
-				Name.clear();
-				Name.assign("he4");
-				break;
-			default:
-				std::cout<<"error, type numbersymbol, or symbolnumber, i.e. 30Mg oder Mg30"<<std::endl;
-				return;
-		};
-	}
+	std::string   massFile;
+	ParseName(name, symbol, number, element);
 	try {
-		first_digit  = Name.find_first_of("0123456789 \t\n\r");
-		first_letter = Name.find_first_not_of("0123456789 \t\n\r");
-
-		if(first_digit > first_letter) {
-			Number = atoi(Name.substr(first_digit).c_str());
-			symbol.append(Name.substr(first_letter, first_digit - first_letter));
-		} else {
-			Number = atoi(Name.substr(first_digit, first_letter - first_digit).c_str());
-			symbol.append(Name.substr(first_letter));
-		}
-		element.append(std::to_string(static_cast<long long>(Number)));
-		element.append(symbol);
-		MassFile = massfile();
-		infile.open(MassFile.c_str());
+		massFile = massfile();
+		infile.open(massFile.c_str());
 		while(!getline(infile, line).fail()) {
 			if(line.length() < 1) {
 				continue;
@@ -96,7 +58,7 @@ TNucleus::TNucleus(const char* name)
 		return;
 	}
 	if(!found) {
-		std::cout<<"Warning: Element "<<element<<" not found in the mass table "<<MassFile<<"."<<std::endl
+		std::cout<<"Warning: Element "<<element<<" not found in the mass table "<<massFile<<"."<<std::endl
 		         <<"Nucleus not set!"<<std::endl;
 		return;
 	}
@@ -177,51 +139,64 @@ TNucleus::~TNucleus()
 	fTransitionListByEnergy.Delete();
 }
 
-std::string TNucleus::SortName(const char* name)
+void TNucleus::ParseName(std::string name, std::string& symbol, int& number, std::string& element)
 {
-	// Names a nucleus based on symbol (ex. 26Na OR Na26). This is to get a nice naming convention.
-	std::string Name = name;
-	int         Number = 0;
-	std::string symbol;
-	std::string element;
-	Name.erase(std::remove_if(Name.begin(), Name.end(), (int (*)(int))std::isspace), Name.end());
-
-	if(Name.length() < 2) {
-		switch(Name[0]) {
+	/// Strips any non-alphanumeric character from input, parses rest as number and symbol.
+	/// E.g. turns "na26" into "Na" and 26 or "  152  EU... " into "Eu" and 152.
+	/// Only uses the first number and first letter, so "na26   eu152" would be turned into "Na" and 26,
+	/// but "na26  152eu" would be turned into "Na" and 26152, and "26na  152eu" would be turned into "Na152eu" and 26.
+	/// Special inputs are "p" for "H" and 1, "d" for "H" and 2, "t" for "H" and 3, and "a" for "He" and 4.
+	/// element simply is the combined string of number and element.
+
+	// remove any characters that aren't alphanumeric
+	name.erase(std::remove_if(name.begin(), name.end(), [](char c) { return !std::isalnum(c); }), name.end());
+
+	// special single letter cases
+	if(name.length() == 1) {
+		switch(name[0]) {
 			case 'p':
-				Name.clear();
-				Name.assign("h1");
-				break;
+				symbol.assign("H");
+				return ;
 			case 'd':
-				Name.clear();
-				Name.assign("h2");
-				break;
+				symbol.assign("H");
+				return;
 			case 't':
-				Name.clear();
-				Name.assign("h3");
-				break;
+				symbol.assign("H");
+				return;
 			case 'a':
-				Name.clear();
-				Name.assign("he4");
-				break;
+				symbol.assign("He");
+				return;
 			default:
-				std::cout<<"error, type numbersymbol, or symbolnumber, i.e. 30Mg oder Mg30"<<std::endl;
-				return "";
+				std::cout<<"error, type numbersymbol, or symbolnumber, i.e. 30Mg oder Mg30, not "<<name<<std::endl;
+				return;
 		};
 	}
-	int first_digit  = Name.find_first_of("0123456789 \t\n\r");
-	int first_letter = Name.find_first_not_of("0123456789 \t\n\r");
-	if(first_digit > first_letter) {
-		Number = atoi(Name.substr(first_digit).c_str());
-		symbol.append(Name.substr(first_letter, first_digit - first_letter));
+
+	int firstDigit  = name.find_first_of("0123456789");
+	int firstLetter = name.find_first_not_of("0123456789");
+	if(firstDigit > firstLetter) {
+		number = atoi(name.substr(firstDigit).c_str());
+		symbol.append(name.substr(firstLetter, firstDigit - firstLetter));
 	} else {
-		Number = atoi(Name.substr(first_digit, first_letter - first_digit).c_str());
-		symbol.append(Name.substr(first_letter));
+		number = atoi(name.substr(firstDigit, firstLetter - firstDigit).c_str());
+		symbol.append(name.substr(firstLetter));
 	}
+	// make certain the symbol starts with upper case and rest is lower case by first transforming everything to lower case and then the first character to upper case.
 	std::transform(symbol.begin(), symbol.end(), symbol.begin(), ::tolower);
 	symbol[0] = toupper(symbol[0]);
-	element.append(std::to_string(static_cast<long long>(Number)));
+	element.append(std::to_string(static_cast<long long>(number)));
 	element.append(symbol);
+}
+
+std::string TNucleus::SortName(std::string input)
+{
+	/// Strips any non-alphanumeric character from input, parses rest as number and symbol.
+	/// E.g. turns "na26" into "26Na" or "  152  EU... " into "152Eu".
+	/// Special inputs are "p" for "1H", "d" for "2H", "t" for "2H", and "a" for "4He".
+	int         number = 0;
+	std::string symbol;
+	std::string element;
+	ParseName(input, symbol, number, element);
 
 	return element;
 }