updated

mytools/Makefile

@@ -1,11 +1,11 @@
-PROGS= showZobov
+PROGS= showZobov buildObservedVoids
 
 CXX=g++
 CC=gcc
 
 include config.mk
 
-SOURCES= showZobov.cpp loadZobov.cpp zobovConf.c 
+SOURCES= showZobov.cpp loadZobov.cpp zobovConf.c buildObservedVoids.cpp 
 
 LIBS= $(LDFLAGS) 
 
@@ -15,6 +15,8 @@ showZobov: showZobov.o loadZobov.o zobovConf.o
 
 testZobov: testZobov.o loadZobov.o
 
+buildObservedVoids: buildObservedVoids.o loadZobov.o buildObservedVoids_conf.o
+
 depend: $(SOURCES)
 	@echo "[DEPENDS] $^"
 	@$(CC) $(CPPFLAGS) -M -MM $^ > .mydepends
@@ -36,7 +38,11 @@ clean:
 
 zobovConf.c zobovConf.h: showZobov.ggo Makefile
 	@echo "[OPT] $@"
-	gengetopt  -i $<  -f zobovConf  -a zobovConf_info  -F zobovConf -C
+	@gengetopt  -i $<  -f zobovConf  -a zobovConf_info  -F zobovConf -C
+
+buildObservedVoids_conf.c buildObservedVoids_conf.h: buildObservedVoids.ggo Makefile
+	@echo "[OPT] $@"
+	@gengetopt -i $< -f buildObservedVoids_conf -a buildObservedVoids_info -F buildObservedVoids_conf -C
 
 %.o: %.c
 	@echo "[C] $< ..."

mytools/buildObservedVoids_conf.h

@@ -0,0 +1,239 @@
+/** @file buildObservedVoids_conf.h
+ *  @brief The header file for the command line option parser
+ *  generated by GNU Gengetopt version 2.22.2
+ *  http://www.gnu.org/software/gengetopt.
+ *  DO NOT modify this file, since it can be overwritten
+ *  @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef BUILDOBSERVEDVOIDS_CONF_H
+#define BUILDOBSERVEDVOIDS_CONF_H
+
+/* If we use autoconf.  */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h> /* for FILE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef BUILDOBSERVEDVOIDS_CONF_PACKAGE
+/** @brief the program name (used for printing errors) */
+#define BUILDOBSERVEDVOIDS_CONF_PACKAGE "buildObservedVoids"
+#endif
+
+#ifndef BUILDOBSERVEDVOIDS_CONF_PACKAGE_NAME
+/** @brief the complete program name (used for help and version) */
+#define BUILDOBSERVEDVOIDS_CONF_PACKAGE_NAME "buildObservedVoids"
+#endif
+
+#ifndef BUILDOBSERVEDVOIDS_CONF_VERSION
+/** @brief the program version */
+#define BUILDOBSERVEDVOIDS_CONF_VERSION "0"
+#endif
+
+/** @brief Where the command line options are stored */
+struct buildObservedVoids_info
+{
+  const char *help_help; /**< @brief Print help and exit help description.  */
+  const char *version_help; /**< @brief Print version and exit help description.  */
+  char * desc_arg;	/**< @brief The description file name for the voids (jozov generated).  */
+  char * desc_orig;	/**< @brief The description file name for the voids (jozov generated) original value given at command line.  */
+  const char *desc_help; /**< @brief The description file name for the voids (jozov generated) help description.  */
+  char * adj_arg;	/**< @brief Adjacent file name (jozov generated).  */
+  char * adj_orig;	/**< @brief Adjacent file name (jozov generated) original value given at command line.  */
+  const char *adj_help; /**< @brief Adjacent file name (jozov generated) help description.  */
+  char * void_arg;	/**< @brief Void/zone bind filename (jozov generated).  */
+  char * void_orig;	/**< @brief Void/zone bind filename (jozov generated) original value given at command line.  */
+  const char *void_help; /**< @brief Void/zone bind filename (jozov generated) help description.  */
+  double minProba_arg;	/**< @brief Minimal probability to accept (default='0.0').  */
+  char * minProba_orig;	/**< @brief Minimal probability to accept original value given at command line.  */
+  const char *minProba_help; /**< @brief Minimal probability to accept help description.  */
+  double densityThreshold_arg;	/**< @brief Density threshold to consider a stable void (default='-0.8').  */
+  char * densityThreshold_orig;	/**< @brief Density threshold to consider a stable void original value given at command line.  */
+  const char *densityThreshold_help; /**< @brief Density threshold to consider a stable void help description.  */
+  char * ramsesDir_arg;	/**< @brief Ramses base output directory.  */
+  char * ramsesDir_orig;	/**< @brief Ramses base output directory original value given at command line.  */
+  const char *ramsesDir_help; /**< @brief Ramses base output directory help description.  */
+  int ramsesId_arg;	/**< @brief Ramses output id.  */
+  char * ramsesId_orig;	/**< @brief Ramses output id original value given at command line.  */
+  const char *ramsesId_help; /**< @brief Ramses output id help description.  */
+  char * configFile_arg;	/**< @brief Configuration file.  */
+  char * configFile_orig;	/**< @brief Configuration file original value given at command line.  */
+  const char *configFile_help; /**< @brief Configuration file help description.  */
+  char * output_arg;	/**< @brief Output file (default='void_info.txt').  */
+  char * output_orig;	/**< @brief Output file original value given at command line.  */
+  const char *output_help; /**< @brief Output file help description.  */
+  char * gridOutput_arg;	/**< @brief 3d grid output of voids (default='all_voids.nc').  */
+  char * gridOutput_orig;	/**< @brief 3d grid output of voids original value given at command line.  */
+  const char *gridOutput_help; /**< @brief 3d grid output of voids help description.  */
+  int quiet_flag;	/**< @brief Quiet output (default=off).  */
+  const char *quiet_help; /**< @brief Quiet output help description.  */
+  
+  unsigned int help_given ;	/**< @brief Whether help was given.  */
+  unsigned int version_given ;	/**< @brief Whether version was given.  */
+  unsigned int desc_given ;	/**< @brief Whether desc was given.  */
+  unsigned int adj_given ;	/**< @brief Whether adj was given.  */
+  unsigned int void_given ;	/**< @brief Whether void was given.  */
+  unsigned int minProba_given ;	/**< @brief Whether minProba was given.  */
+  unsigned int densityThreshold_given ;	/**< @brief Whether densityThreshold was given.  */
+  unsigned int ramsesDir_given ;	/**< @brief Whether ramsesDir was given.  */
+  unsigned int ramsesId_given ;	/**< @brief Whether ramsesId was given.  */
+  unsigned int configFile_given ;	/**< @brief Whether configFile was given.  */
+  unsigned int output_given ;	/**< @brief Whether output was given.  */
+  unsigned int gridOutput_given ;	/**< @brief Whether gridOutput was given.  */
+  unsigned int quiet_given ;	/**< @brief Whether quiet was given.  */
+
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct buildObservedVoids_conf_params
+{
+  int override; /**< @brief whether to override possibly already present options (default 0) */
+  int initialize; /**< @brief whether to initialize the option structure buildObservedVoids_info (default 1) */
+  int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+  int check_ambiguity; /**< @brief whether to check for options already specified in the option structure buildObservedVoids_info (default 0) */
+  int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
+
+/** @brief the purpose string of the program */
+extern const char *buildObservedVoids_info_purpose;
+/** @brief the usage string of the program */
+extern const char *buildObservedVoids_info_usage;
+/** @brief all the lines making the help output */
+extern const char *buildObservedVoids_info_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int buildObservedVoids_conf (int argc, char * const *argv,
+  struct buildObservedVoids_info *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use buildObservedVoids_conf_ext() instead
+ */
+int buildObservedVoids_conf2 (int argc, char * const *argv,
+  struct buildObservedVoids_info *args_info,
+  int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int buildObservedVoids_conf_ext (int argc, char * const *argv,
+  struct buildObservedVoids_info *args_info,
+  struct buildObservedVoids_conf_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int buildObservedVoids_conf_dump(FILE *outfile,
+  struct buildObservedVoids_info *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int buildObservedVoids_conf_file_save(const char *filename,
+  struct buildObservedVoids_info *args_info);
+
+/**
+ * Print the help
+ */
+void buildObservedVoids_conf_print_help(void);
+/**
+ * Print the version
+ */
+void buildObservedVoids_conf_print_version(void);
+
+/**
+ * Initializes all the fields a buildObservedVoids_conf_params structure 
+ * to their default values
+ * @param params the structure to initialize
+ */
+void buildObservedVoids_conf_params_init(struct buildObservedVoids_conf_params *params);
+
+/**
+ * Allocates dynamically a buildObservedVoids_conf_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized buildObservedVoids_conf_params structure
+ */
+struct buildObservedVoids_conf_params *buildObservedVoids_conf_params_create(void);
+
+/**
+ * Initializes the passed buildObservedVoids_info structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void buildObservedVoids_conf_init (struct buildObservedVoids_info *args_info);
+/**
+ * Deallocates the string fields of the buildObservedVoids_info structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void buildObservedVoids_conf_free (struct buildObservedVoids_info *args_info);
+
+/**
+ * The config file parser (deprecated version)
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use buildObservedVoids_conf_config_file() instead
+ */
+int buildObservedVoids_conf_configfile (const char *filename,
+  struct buildObservedVoids_info *args_info,
+  int override, int initialize, int check_required);
+
+/**
+ * The config file parser
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int buildObservedVoids_conf_config_file (const char *filename,
+  struct buildObservedVoids_info *args_info,
+  struct buildObservedVoids_conf_params *params);
+
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ *   possible errors
+ * @return
+ */
+int buildObservedVoids_conf_required (struct buildObservedVoids_info *args_info,
+  const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* BUILDOBSERVEDVOIDS_CONF_H */

mytools/config.mk

@@ -1,6 +1,6 @@
 CC= gcc
 CXX= g++
-CPPFLAGS=  -I$(HOME)/Science/Software/CosmoToolbox/install/include
-LDFLAGS= -L$(HOME)/Science/Software/CosmoToolbox/install/lib -lCosmoTool
-CXXFLAGS= $(CPPFLAGS) -ggdb -O0 -ffast-math
-CFLAGS= $(CPPFLAGS) -ggdb -O0 -ffast-math
+CPPFLAGS=  
+LDFLAGS=  -lCosmoTool
+CXXFLAGS= $(CPPFLAGS) -ggdb -O3 -ffast-math
+CFLAGS= $(CPPFLAGS) -ggdb -O3 -ffast-math

mytools/voidTree.hpp

@@ -0,0 +1,156 @@
+#ifndef _VOID_TREE_HPP
+#define _VOID_TREE_HPP
+
+#include <iostream>
+#include <stdint.h>
+#include "loadZobov.hpp"
+#include <list>
+#include <set>
+#include <vector>
+
+struct VoidNode
+{
+  int vid;
+  VoidNode *parent;
+  std::list<VoidNode *> children;
+};
+
+class VoidTree
+{
+protected:
+  uint32_t totalNumNodes;
+  VoidNode *nodes;
+  VoidNode *rootNode;  
+  ZobovRep& zobov;
+public:
+  typedef std::list<VoidNode *> VoidList;
+
+  int lookupParent(int voidId)
+  {
+    std::set<ZobovZone *> sref;
+    sref.insert(zobov.allVoids[voidId].zId.begin(), zobov.allVoids[voidId].zId.end());
+    
+    
+    std::vector<ZobovZone *> sout(sref.size());  
+    int lastSize = 0x7fffffff;
+    int goodParent = voidId;
+
+    // Voids are sorted according to volume
+    for (int i = voidId-1; i >= 0; i--) 
+      {
+	std::set<ZobovZone *> s1;
+	
+	int counter = 0;
+	s1.insert(zobov.allVoids[i].zId.begin(), zobov.allVoids[i].zId.end());
+	for (std::set<ZobovZone *>::iterator iter = s1.begin(), iter2 = sref.begin();
+	     iter != s1.end() && iter2 != sref.end();
+	     ++iter)
+	  {
+	    if (*iter == *iter2)
+	      {
+		counter++;
+		++iter2;
+	      }
+	    else while (*iter > *iter2 && iter2 != sref.end())
+		   ++iter2;
+	  }
+	
+	if (counter == sref.size() && s1.size() < lastSize)
+	  {
+	    return i;
+	  }
+      }
+    return -1;
+  }
+  
+  VoidTree(ZobovRep& rep)
+    : zobov(rep)
+  {
+    totalNumNodes = rep.allVoids.size();
+    
+    nodes = new VoidNode[totalNumNodes];
+
+    for (int i = 0; i < rep.allVoids.size(); i++)
+      {
+	nodes[i].vid = i;
+	nodes[i].parent = 0;
+	nodes[i].children.clear();
+      }
+
+    std::cout << "Linking voids together..." << std::endl;
+    double volMin = 4*M_PI/3*pow(4.*512/500.,3);
+    int inserted = 0;
+    for (int i = rep.allVoids.size()-1; i>=0;i--)
+      {
+        if (rep.allVoids[i].volume < volMin) continue;
+
+	int p = lookupParent(i);
+
+	std::cout << i << std::endl;
+	
+	if (p < 0)
+	  {
+	    if (i != 0)
+	      std::cerr << "Warning ! Voids without parent and it is not the root !" << std::endl;
+	    continue;
+	  }
+
+	nodes[p].children.push_back(&nodes[i]);
+	nodes[i].parent = &nodes[p];
+	inserted++;
+      }
+
+    rootNode = 0;
+    for (int i = inserted; i < totalNumNodes; i++)
+      if (nodes[i].parent == 0)
+	{
+	  if (rootNode != 0)
+	    {
+	      std::cerr << "Multiple root to the tree !!!" << std::endl;
+	      abort();
+	    }
+	  rootNode = &nodes[i];
+	}
+  }
+
+  ~VoidTree()
+  {
+    delete[] nodes;
+  }
+
+  int getParent(int vid) const
+  {
+    assert(nodes[vid].parent != 0);
+    return nodes[vid].parent->vid;
+  }
+  
+  const VoidList& getChildren(int vid) const
+  {
+    return nodes[vid].children;
+  }
+
+
+  template<typename T>
+  void walkNode(VoidNode *node, T& traverse)
+  {
+    VoidList::iterator i;
+    
+    if (!traverse(node))
+      return;
+
+    while (i != node->children.end())
+      {
+	walkNode(*i, traverse);
+	++i;
+      }
+  }
+
+  template<typename T>
+  void walk(T& traverse)
+  {
+    walkNode(rootNode, traverse);
+  }
+  
+};
+
+#endif

mytools/zobovConf.c

@@ -1,5 +1,5 @@
 /*
-  File autogenerated by gengetopt version 2.22
+  File autogenerated by gengetopt version 2.22.2
   generated with the following command:
   gengetopt -i showZobov.ggo -f zobovConf -a zobovConf_info -F zobovConf -C 
 
@@ -17,6 +17,10 @@
 #include <stdlib.h>
 #include <string.h>
 
+#ifndef FIX_UNUSED
+#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
+#endif
+
 #include "getopt.h"
 
 #include "zobovConf.h"
@@ -119,6 +123,7 @@ void clear_given (struct zobovConf_info *args_info)
 static
 void clear_args (struct zobovConf_info *args_info)
 {
+  FIX_UNUSED (args_info);
   args_info->desc_arg = NULL;
   args_info->desc_orig = NULL;
   args_info->adj_arg = NULL;
@@ -173,7 +178,9 @@ void init_args_info(struct zobovConf_info *args_info)
 void
 zobovConf_print_version (void)
 {
-  printf ("%s %s\n", ZOBOVCONF_PACKAGE, ZOBOVCONF_VERSION);
+  printf ("%s %s\n",
+     (strlen(ZOBOVCONF_PACKAGE_NAME) ? ZOBOVCONF_PACKAGE_NAME : ZOBOVCONF_PACKAGE),
+     ZOBOVCONF_VERSION);
 }
 
 static void print_help_common(void) {
@@ -188,7 +195,7 @@ static void print_help_common(void) {
   printf("\n");
 
   if (strlen(zobovConf_info_description) > 0)
-    printf("%s\n", zobovConf_info_description);
+    printf("%s\n\n", zobovConf_info_description);
 }
 
 void
@@ -270,8 +277,9 @@ zobovConf_release (struct zobovConf_info *args_info)
 
 
 static void
-write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
 {
+  FIX_UNUSED (values);
   if (arg) {
     fprintf(outfile, "%s=\"%s\"\n", opt, arg);
   } else {
@@ -361,7 +369,7 @@ zobovConf_free (struct zobovConf_info *args_info)
 char *
 gengetopt_strdup (const char *s)
 {
-  char *result = NULL;
+  char *result = 0;
   if (!s)
     return result;
 
@@ -383,7 +391,7 @@ zobovConf_ext (int argc, char * const *argv, struct zobovConf_info *args_info,
                    struct zobovConf_params *params)
 {
   int result;
-  result = zobovConf_internal (argc, argv, args_info, params, NULL);
+  result = zobovConf_internal (argc, argv, args_info, params, 0);
 
   if (result == EXIT_FAILURE)
     {
@@ -406,7 +414,7 @@ zobovConf2 (int argc, char * const *argv, struct zobovConf_info *args_info, int
   params.check_ambiguity = 0;
   params.print_errors = 1;
 
-  result = zobovConf_internal (argc, argv, args_info, &params, NULL);
+  result = zobovConf_internal (argc, argv, args_info, &params, 0);
 
   if (result == EXIT_FAILURE)
     {
@@ -422,7 +430,7 @@ zobovConf_required (struct zobovConf_info *args_info, const char *prog_name)
 {
   int result = EXIT_SUCCESS;
 
-  if (zobovConf_required2(args_info, prog_name, NULL) > 0)
+  if (zobovConf_required2(args_info, prog_name, 0) > 0)
     result = EXIT_FAILURE;
 
   if (result == EXIT_FAILURE)
@@ -437,6 +445,7 @@ zobovConf_required (struct zobovConf_info *args_info, const char *prog_name)
 int
 zobovConf_required2 (struct zobovConf_info *args_info, const char *prog_name, const char *additional_error)
 {
+  FIX_UNUSED (additional_error);
   int error = 0;
 
   /* checks for required options */
@@ -500,13 +509,15 @@ static char *package_name = 0;
 static
 int update_arg(void *field, char **orig_field,
                unsigned int *field_given, unsigned int *prev_given, 
-               char *value, char *possible_values[], const char *default_value,
+               char *value, const char *possible_values[],
+               const char *default_value,
                zobovConf_arg_type arg_type,
                int check_ambiguity, int override,
                int no_free, int multiple_option,
                const char *long_opt, char short_opt,
                const char *additional_error)
 {
+  FIX_UNUSED (field);
   char *stop_char = 0;
   const char *val = value;
   int found;
@@ -528,6 +539,7 @@ int update_arg(void *field, char **orig_field,
       return 1; /* failure */
     }
 
+  FIX_UNUSED (default_value);
     
   if (field_given && *field_given && ! override)
     return 0;
@@ -595,7 +607,8 @@ int update_arg(void *field, char **orig_field,
 
 
 int
-zobovConf_internal (int argc, char * const *argv, struct zobovConf_info *args_info,
+zobovConf_internal (
+  int argc, char * const *argv, struct zobovConf_info *args_info,
                         struct zobovConf_params *params, const char *additional_error)
 {
   int c;	/* Character of the parsed option.  */
@@ -647,7 +660,7 @@ zobovConf_internal (int argc, char * const *argv, struct zobovConf_info *args_in
         { "galax",	0, NULL, 0 },
         { "output",	1, NULL, 'o' },
         { "interactive",	0, NULL, 0 },
-        { NULL,	0, NULL, 0 }
+        { 0,  0, 0, 0 }
       };
 
       c = getopt_long (argc, argv, "hVd:a:v:i:slm:b:r:f:qp:o:", long_options, &option_index);
@@ -883,7 +896,7 @@ failure:
 /* 3 is for "--" and "=" */
 
 static int
-_zobovConf_configfile (char * const filename, int *my_argc)
+_zobovConf_configfile (const char *filename, int *my_argc)
 {
   FILE* file;
   char my_argv[CONFIG_FILE_LINE_BUFFER_SIZE+1];
@@ -895,14 +908,14 @@ _zobovConf_configfile (char * const filename, int *my_argc)
   size_t len, next_token;
   char delimiter;
 
-  if ((file = fopen(filename, "r")) == NULL)
+  if ((file = fopen(filename, "r")) == 0)
     {
       fprintf (stderr, "%s: Error opening configuration file '%s'\n",
                ZOBOVCONF_PACKAGE, filename);
       return EXIT_FAILURE;
     }
 
-  while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != NULL)
+  while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != 0)
     {
       ++line_num;
       my_argv[0] = '\0';
@@ -929,7 +942,7 @@ _zobovConf_configfile (char * const filename, int *my_argc)
 
       if (fopt[next_token] == '\0') /* the line is over */
         {
-          farg  = NULL;
+          farg  = 0;
           equal = 0;
           goto noarg;
         }
@@ -1020,7 +1033,8 @@ _zobovConf_configfile (char * const filename, int *my_argc)
 }
 
 int
-zobovConf_configfile (char * const filename,
+zobovConf_configfile (
+  const char *filename,
                            struct zobovConf_info *args_info,
                            int override, int initialize, int check_required)
 {
@@ -1036,7 +1050,7 @@ zobovConf_configfile (char * const filename,
 }
 
 int
-zobovConf_config_file (char * const filename,
+zobovConf_config_file (const char *filename,
                            struct zobovConf_info *args_info,
                            struct zobovConf_params *params)
 {

mytools/zobovConf.h

@@ -1,6 +1,6 @@
 /** @file zobovConf.h
  *  @brief The header file for the command line option parser
- *  generated by GNU Gengetopt version 2.22
+ *  generated by GNU Gengetopt version 2.22.2
  *  http://www.gnu.org/software/gengetopt.
  *  DO NOT modify this file, since it can be overwritten
  *  @author GNU Gengetopt by Lorenzo Bettini */
@@ -20,10 +20,15 @@ extern "C" {
 #endif /* __cplusplus */
 
 #ifndef ZOBOVCONF_PACKAGE
-/** @brief the program name */
+/** @brief the program name (used for printing errors) */
 #define ZOBOVCONF_PACKAGE "showZobov"
 #endif
 
+#ifndef ZOBOVCONF_PACKAGE_NAME
+/** @brief the complete program name (used for help and version) */
+#define ZOBOVCONF_PACKAGE_NAME "showZobov"
+#endif
+
 #ifndef ZOBOVCONF_VERSION
 /** @brief the program version */
 #define ZOBOVCONF_VERSION "0"
@@ -214,7 +219,7 @@ void zobovConf_free (struct zobovConf_info *args_info);
  * @return 0 if everything went fine, NON 0 if an error took place
  * @deprecated use zobovConf_config_file() instead
  */
-int zobovConf_configfile (char * const filename,
+int zobovConf_configfile (const char *filename,
   struct zobovConf_info *args_info,
   int override, int initialize, int check_required);
 
@@ -225,7 +230,7 @@ int zobovConf_configfile (char * const filename,
  * @param params additional parameters for the parser
  * @return 0 if everything went fine, NON 0 if an error took place
  */
-int zobovConf_config_file (char * const filename,
+int zobovConf_config_file (const char *filename,
   struct zobovConf_info *args_info,
   struct zobovConf_params *params);