improve doxygen documentation of PMsrHandler.*

src/classes/PMsrHandler.cpp

@@ -45,13 +45,28 @@
 // Constructor
 //--------------------------------------------------------------------------
 /**
- * <p>Constructor
+ * \brief Constructor that initializes the MSR handler.
  *
- * \param fileName name of a msr-file.
+ * Initializes all internal data structures and extracts the directory path
+ * from the MSR file name. The directory path is used for resolving relative
+ * paths in the MSR file (e.g., for data files).
+ *
+ * Initialization includes:
+ * - Setting default values for all MSR blocks
+ * - Initializing statistics structure (invalid, χ² mode, min=-1, ndf=0)
+ * - Extracting file directory path from file name
+ * - Setting block counter to 0
+ *
+ * \param fileName Path to MSR file (absolute or relative)
+ * \param startupOptions Optional pointer to startup configuration from musrfit_startup.xml
+ * \param fourierOnly If true, only parse Fourier-related blocks (used by musrFT tool)
+ *
+ * \note If fileName contains "/" characters, the directory path is extracted
+ *       and stored in fMsrFileDirectoryPath; otherwise defaults to "./"
  */
 PMsrHandler::PMsrHandler(const Char_t *fileName, PStartupOptions *startupOptions, const Bool_t fourierOnly) :
     fFourierOnly(fourierOnly), fStartupOptions(startupOptions), fFileName(fileName)
-{ 
+{
   // init variables
   fMsrBlockCounter = 0;
 
@@ -83,7 +98,19 @@ PMsrHandler::PMsrHandler(const Char_t *fileName, PStartupOptions *startupOptions
 // Destructor
 //--------------------------------------------------------------------------
 /**
- * <p>Destructor
+ * \brief Destructor that cleans up all data structures.
+ *
+ * Clears all vectors and releases memory:
+ * - Parameter list
+ * - Theory lines
+ * - Functions lines
+ * - Run configurations
+ * - MINUIT commands
+ * - Plot settings
+ * - Statistics data
+ * - Parameter usage flags
+ *
+ * The unique_ptr member (fFuncHandler) is automatically cleaned up.
  */
 PMsrHandler::~PMsrHandler()
 {
@@ -103,11 +130,46 @@ PMsrHandler::~PMsrHandler()
 // ReadMsrFile (public)
 //--------------------------------------------------------------------------
 /**
- * <p>Reads and parses a msr-file.
+ * \brief Reads and parses the MSR file.
  *
- * <p><b>return:</b>
+ * Performs comprehensive parsing of all MSR file blocks in the following order:
- * - PMUSR_SUCCESS if everything is OK
+ * 1. TITLE - File description
- * - line number if an error in the MSR file was encountered which cannot be handled.
+ * 2. FITPARAMETER - Fit parameters with values, errors, and constraints
+ * 3. THEORY - Asymmetry/relaxation function definitions
+ * 4. FUNCTIONS (optional) - User-defined mathematical functions
+ * 5. GLOBAL (optional) - Global fit settings
+ * 6. RUN - Data file specifications and fit ranges
+ * 7. COMMANDS - MINUIT fitting commands
+ * 8. FOURIER (optional) - Fourier transform parameters
+ * 9. PLOT (optional) - Plotting parameters
+ * 10. STATISTIC - Fit results (χ², NDF, convergence)
+ *
+ * After parsing, performs extensive validation:
+ * - Checks for legacy lifetimecorrection syntax
+ * - Validates RUN block integrity (required fields, grouping consistency)
+ * - Verifies parameter name uniqueness
+ * - Checks map index validity
+ * - Validates user-defined functions
+ * - Verifies histogram grouping consistency
+ * - Checks addrun parameter references
+ * - Validates RRF (Rotating Reference Frame) settings
+ * - Checks real FFT requirements
+ * - Validates maximum likelihood settings
+ *
+ * Error Handling:
+ * - Detailed error messages are written to stderr
+ * - Error messages are accumulated in fLastErrorMsg for programmatic access
+ * - Returns line number where error occurred for syntax errors
+ *
+ * \return
+ * - PMUSR_SUCCESS (0) if parsing succeeded
+ * - PMUSR_MSR_FILE_NOT_FOUND if file cannot be opened
+ * - PMUSR_MSR_SYNTAX_ERROR if syntax error encountered
+ * - Positive line number if parsing error occurred at specific line
+ *
+ * \note In Fourier-only mode (fFourierOnly=true), only relevant blocks are parsed
+ *
+ * \see HandleFitParameterEntry, HandleTheoryEntry, HandleRunEntry for block parsing
  */
 Int_t PMsrHandler::ReadMsrFile()
 {
@@ -341,15 +403,42 @@ Int_t PMsrHandler::ReadMsrFile()
 // WriteMsrLogFile (public)
 //--------------------------------------------------------------------------
 /**
- * <p>Writes a mlog-file.
+ * \brief Writes an MSR log file (.mlog) with parsed MSR content.
  *
- * <p><b>return:</b>
+ * Creates a log file with the same base name as the MSR file but with .mlog
- * - PMUSR_SUCCESS everything is OK
+ * extension. The log file contains the parsed and formatted MSR structure,
- * - PMUSR_MSR_LOG_FILE_WRITE_ERROR msr-/mlog-file couldn't be opened
+ * which is useful for:
- * - PMUSR_MSR_SYNTAX_ERROR a syntax error has been encountered
+ * - Debugging MSR file parsing
+ * - Verifying parameter interpretation
+ * - Checking fit range calculations
+ * - Reviewing theory and function definitions
  *
- * \param messages if true some additional messages concerning the statistic block are written.
+ * The log file format mirrors the MSR file structure but with:
- *                 When using musrt0, messages will be set to false.
+ * - Standardized formatting and precision
+ * - Expanded parameter values
+ * - Calculated fit ranges (in bins and microseconds)
+ * - Resolved function definitions
+ * - Complete statistics (if available)
+ *
+ * Processing includes:
+ * - Re-reading original MSR file to preserve comments and structure
+ * - Identifying missing tags (t0, background, data) in RUN blocks
+ * - Formatting numeric values with appropriate precision
+ * - Writing all MSR blocks in canonical format
+ *
+ * \param messages If true, includes additional informational messages about
+ *                 the statistics block. Set to false when called from musrt0
+ *                 to suppress messages.
+ *
+ * \return
+ * - PMUSR_SUCCESS if log file written successfully
+ * - PMUSR_MSR_LOG_FILE_WRITE_ERROR if MSR or log file cannot be opened
+ * - PMUSR_MSR_SYNTAX_ERROR if syntax error encountered during processing
+ *
+ * \note The log file name is constructed by replacing the MSR file extension
+ *       with ".mlog" (e.g., "run1234.msr" → "run1234.mlog")
+ *
+ * \see WriteMsrFile for writing updated MSR files
  */
 Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
 {
@@ -1549,13 +1638,51 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
 // WriteMsrFile (public)
 //--------------------------------------------------------------------------
 /**
- * <p>Writes a msr-file from the internal data structures
+ * \brief Writes an MSR file from internal data structures.
  *
- * <p><b>return:</b>
+ * Creates a complete MSR file with all blocks, typically called after fitting
- * - PMUSR_SUCCESS everything is OK
+ * to save updated parameter values, errors, and fit statistics. The file
- * - PMUSR_MSR_FILE_WRITE_ERROR msr output file couldn't be opened
+ * includes properly formatted blocks in the standard MSR file order.
  *
- * \param filename The name of the output file.
+ * **MSR File Structure Written:**
+ * 1. TITLE block
+ * 2. FITPARAMETER block (with fitted values and errors)
+ * 3. THEORY block
+ * 4. FUNCTIONS block (if functions are defined)
+ * 5. GLOBAL block (if global settings exist)
+ * 6. RUN blocks (one per run)
+ * 7. COMMANDS block
+ * 8. FOURIER block (if Fourier parameters are defined)
+ * 9. PLOT blocks (if plot settings exist)
+ * 10. STATISTIC block (with fit results)
+ *
+ * **Comment Preservation:**
+ * The comment maps allow preserving user comments from specific MSR blocks.
+ * Comments are inserted before the corresponding line based on the map key
+ * (line number). This is useful when updating MSR files while maintaining
+ * documentation.
+ *
+ * **Formatting:**
+ * - Parameters: Right-aligned numbers, left-aligned names and values
+ * - Precision: 6 significant digits for floating-point values
+ * - Boundaries: Properly formatted lower/upper limits
+ * - Separators: Dashed lines between major sections
+ *
+ * \param filename Output MSR file path
+ * \param commentsPAR Optional map of line number → comment for FITPARAMETER block
+ * \param commentsTHE Optional map of line number → comment for THEORY block
+ * \param commentsFUN Optional map of line number → comment for FUNCTIONS block
+ * \param commentsRUN Optional map of line number → comment for RUN blocks
+ *
+ * \return
+ * - PMUSR_SUCCESS if file written successfully
+ * - PMUSR_MSR_FILE_WRITE_ERROR if output file cannot be opened
+ *
+ * \note Comments are removed from the maps after being written
+ * \note The STATISTIC block content depends on fCopyStatisticsBlock flag
+ *
+ * \see WriteMsrLogFile for writing debug/verification log files
+ * \see SetMsrStatisticMin, SetMsrStatisticNdf for updating statistics
  */
 Int_t PMsrHandler::WriteMsrFile(const Char_t *filename, std::map<UInt_t, TString> *commentsPAR, \
                                                         std::map<UInt_t, TString> *commentsTHE, \

src/include/PMsrHandler.h

@@ -45,32 +45,73 @@
 
 //-------------------------------------------------------------
 /**
- * <p>MSR file parser and manager for musrfit framework.
+ * \brief MSR file parser and manager for the musrfit framework.
  *
- * <p>This class handles all MSR (Muon Spin Rotation) file operations including:
+ * PMsrHandler is the central class for managing MSR (Muon Spin Rotation/Relaxation)
- * - Reading and parsing MSR files
+ * files used throughout the musrfit suite. It provides comprehensive functionality for:
- * - Writing MSR files and log files
- * - Validating MSR file content (parameter ranges, theory consistency, etc.)
- * - Managing fit parameters, theory definitions, run configurations
- * - Evaluating user-defined functions
- * - Handling parameter mapping between runs
  *
- * <p>The PMsrHandler performs comprehensive validation during parsing, checking for:
+ * **File Operations:**
- * - Parameter name uniqueness
+ * - Reading and parsing MSR files with full syntax validation
- * - Valid theory-to-parameter mappings
+ * - Writing MSR files with fitted parameters and statistics
- * - Histogram grouping consistency
+ * - Generating log files (.mlog) for debugging
- * - RRF (Rotating Reference Frame) settings
+ * - Preserving user comments during file I/O
- * - Function syntax and parameter usage
  *
- * <p><b>Usage pattern:</b>
+ * **Data Management:**
- * @code
+ * - Fit parameters (values, errors, constraints, names)
- * PMsrHandler handler("myfile.msr");
+ * - Theory definitions (fit functions for asymmetry/relaxation)
+ * - User-defined functions (mathematical expressions)
+ * - Global settings (fit type, data format, etc.)
+ * - Run configurations (data files, histograms, ranges)
+ * - MINUIT commands (fit strategy, precision, etc.)
+ * - Fourier transform parameters
+ * - Plot settings
+ * - Fit statistics (χ², degrees of freedom, convergence)
+ *
+ * **Validation and Integrity Checking:**
+ * - Parameter name uniqueness verification
+ * - Theory-to-parameter mapping validation
+ * - Histogram grouping consistency checks
+ * - RRF (Rotating Reference Frame) configuration validation
+ * - Function syntax and parameter usage verification
+ * - Map index range checking
+ * - Legacy lifetimecorrection detection
+ *
+ * **MSR File Structure:**
+ * An MSR file contains the following blocks (in order):
+ * 1. TITLE - Brief description of the fit
+ * 2. FITPARAMETER - Fit parameters with initial values and constraints
+ * 3. THEORY - Asymmetry/relaxation function definitions
+ * 4. FUNCTIONS (optional) - User-defined mathematical functions
+ * 5. GLOBAL (optional) - Global fit settings
+ * 6. RUN - Data file specifications and fit ranges
+ * 7. COMMANDS - MINUIT fitting commands
+ * 8. FOURIER (optional) - Fourier transform settings
+ * 9. PLOT (optional) - Plotting parameters
+ * 10. STATISTIC - Fit results (χ², NDF, convergence)
+ *
+ * **Usage Example:**
+ * \code
+ * // Reading an MSR file
+ * PMsrHandler handler("run1234.msr");
  * if (handler.ReadMsrFile() == PMUSR_SUCCESS) {
  *   PMsrParamList *params = handler.GetMsrParamList();
- *   // Process parameters, run fits, etc.
+ *
- *   handler.WriteMsrFile("output.msr");
+ *   // Access and modify parameters
+ *   handler.SetMsrParamValue(0, 12.5);
+ *
+ *   // Perform fit (in calling code)
+ *   // ...
+ *
+ *   // Update statistics and write results
+ *   handler.SetMsrStatisticMin(chisq);
+ *   handler.SetMsrStatisticNdf(ndf);
+ *   handler.WriteMsrFile("run1234_fitted.msr");
  * }
- * @endcode
+ * \endcode
+ *
+ * \see PMusr.h for MSR data structure definitions
+ * \see PFunctionHandler for user-defined function evaluation
+ * \see PStartupOptions for configuration settings
  */
 class PMsrHandler
 {
@@ -338,69 +379,99 @@ class PMsrHandler
     virtual Int_t GetNoOfMaps() { return fNoOfMaps; }
 
   private:
-    Bool_t                 fFourierOnly; ///< flag indicating if Fourier transform only is wished. If yes, some part of the msr-file blocks are not needed.
+    Bool_t                 fFourierOnly; ///< Flag indicating Fourier transform only mode (for musrFT)
-    PStartupOptions       *fStartupOptions; ///< contains information about startup options from the musrfit_startup.xml
+    PStartupOptions       *fStartupOptions; ///< Pointer to startup options from musrfit_startup.xml
 
-    TString                fFileName;  ///< file name of the msr-file
+    TString                fFileName;  ///< MSR file name (with path)
-    TString                fMsrFileDirectoryPath; ///< msr-file directory path
+    TString                fMsrFileDirectoryPath; ///< Directory path of the MSR file
-    TString                fTitle;     ///< holds the title string of the msr-file
+    TString                fTitle;     ///< MSR file title string
-    PMsrParamList          fParam;     ///< holds a list of the fit parameters
+    PMsrParamList          fParam;     ///< List of fit parameters with values, errors, constraints
-    PMsrLines              fTheory;    ///< holds the theory definition
+    PMsrLines              fTheory;    ///< Theory block lines defining asymmetry/relaxation functions
-    PMsrLines              fFunctions; ///< holds the user defined functions
+    PMsrLines              fFunctions; ///< User-defined functions block lines
-    PMsrGlobalBlock        fGlobal;    ///< holds the information of the global section
+    PMsrGlobalBlock        fGlobal;    ///< Global block settings (fit type, data format, etc.)
-    PMsrRunList            fRuns;      ///< holds a list of run information
+    PMsrRunList            fRuns;      ///< List of RUN blocks with data file specifications
-    PMsrLines              fCommands;  ///< holds a list of the minuit commands
+    PMsrLines              fCommands;  ///< MINUIT commands block lines
-    PMsrFourierStructure   fFourier;   ///< holds the parameters used for the Fourier transform
+    PMsrFourierStructure   fFourier;   ///< Fourier transform parameters and settings
-    PMsrPlotList           fPlots;     ///< holds a list of the plot input parameters
+    PMsrPlotList           fPlots;     ///< List of PLOT blocks with plotting parameters
-    PMsrStatisticStructure fStatistic; ///< holds the statistic info
+    PMsrStatisticStructure fStatistic; ///< Fit statistics (χ², NDF, convergence status)
 
-    Int_t  fMsrBlockCounter; ///< used to select the proper msr-block
+    Int_t  fMsrBlockCounter; ///< Counter to track current MSR block during parsing
 
-    std::unique_ptr<PFunctionHandler> fFuncHandler; ///< needed to parse functions
+    std::unique_ptr<PFunctionHandler> fFuncHandler; ///< Handler for parsing and evaluating user-defined functions
 
-    PIntVector fParamInUse; ///< array holding the information if a particular parameter is used at all, i.e. if the theory is using it (perhaps via maps or functions)
+    PIntVector fParamInUse; ///< Flags indicating which parameters are actually used in theory/functions
 
-    Bool_t fCopyStatisticsBlock; ///< flag, if true: just copy to old statistics block (musrt0), otherwise write a new one (musrfit)
+    Bool_t fCopyStatisticsBlock; ///< If true, copy old statistics block (musrt0); if false, write new one (musrfit)
 
     Int_t fNoOfMaps;
 
-    std::stringstream fLastErrorMsg;
+    std::stringstream fLastErrorMsg; ///< Stream accumulating error messages during parsing
 
+    /// Parses FITPARAMETER block entries
     virtual Bool_t HandleFitParameterEntry(PMsrLines &line);
+    /// Parses THEORY block entries
     virtual Bool_t HandleTheoryEntry(PMsrLines &line);
+    /// Parses FUNCTIONS block entries
     virtual Bool_t HandleFunctionsEntry(PMsrLines &line);
+    /// Parses GLOBAL block entries
     virtual Bool_t HandleGlobalEntry(PMsrLines &line);
+    /// Parses RUN block entries
     virtual Bool_t HandleRunEntry(PMsrLines &line);
+    /// Parses COMMANDS block entries
     virtual Bool_t HandleCommandsEntry(PMsrLines &line);
+    /// Parses FOURIER block entries
     virtual Bool_t HandleFourierEntry(PMsrLines &line);
+    /// Parses PLOT block entries
     virtual Bool_t HandlePlotEntry(PMsrLines &line);
+    /// Parses STATISTIC block entries
     virtual Bool_t HandleStatisticEntry(PMsrLines &line);
 
+    /// Determines which parameters are used in theory and functions
     virtual void FillParameterInUse(PMsrLines &theory, PMsrLines &funcs, PMsrLines &run);
 
+    /// Initializes Fourier parameter structure with default values
     virtual void InitFourierParameterStructure(PMsrFourierStructure &fourier);
+    /// Removes comments from MSR file line
     virtual void RemoveComment(const TString &str, TString &truncStr);
+    /// Parses Fourier phase value vector
     virtual Bool_t ParseFourierPhaseValueVector(PMsrFourierStructure &fourier, const TString &str, Bool_t &error);
+    /// Parses Fourier phase parameter vector
     virtual Bool_t ParseFourierPhaseParVector(PMsrFourierStructure &fourier, const TString &str, Bool_t &error);
+    /// Parses Fourier phase parameter iteration vector
     virtual Bool_t ParseFourierPhaseParIterVector(PMsrFourierStructure &fourier, const TString &str, Bool_t &error);
 
+    /// Extracts number from string with specific filter pattern
     virtual Bool_t FilterNumber(TString str, const Char_t *filter, Int_t offset, Int_t &no);
 
+    /// Calculates precision needed for formatting a double value
     virtual UInt_t NeededPrecision(Double_t dval, UInt_t precLimit=13);
+    /// Finds position of last significant digit in a double value
     virtual UInt_t LastSignificant(Double_t dval, UInt_t precLimit=6);
 
+    /// Creates detector grouping string from integer vector
     virtual void MakeDetectorGroupingString(TString str, PIntVector &group, TString &result, Bool_t includeDetector = true);
+    /// Formats Fourier phase parameter string for display
     virtual TString BeautifyFourierPhaseParameterString();
 
+    /// Checks for deprecated lifetimecorrection syntax and warns user
     virtual void CheckLegacyLifetimecorrection();
+    /// Validates RUN block structure and consistency
     virtual Bool_t CheckRunBlockIntegrity();
+    /// Checks that all parameter names are unique
     virtual Bool_t CheckUniquenessOfParamNames(UInt_t &parX, UInt_t &parY);
+    /// Validates that all map indices are within parameter range
     virtual Bool_t CheckMaps();
+    /// Validates user-defined functions syntax and parameter usage
     virtual Bool_t CheckFuncs();
+    /// Checks histogram grouping consistency across runs
     virtual Bool_t CheckHistoGrouping();
+    /// Validates addrun parameter references
     virtual Bool_t CheckAddRunParameters();
+    /// Validates RRF (Rotating Reference Frame) settings
     virtual Bool_t CheckRRFSettings();
+    /// Checks if real FFT requirements are met
     virtual Bool_t CheckRealFFT();
+    /// Validates maximum likelihood fit settings
     virtual void CheckMaxLikelihood();
 
     virtual void HandleTheoryArguments(const TString theo, PStringVector &args);