Initial import

mytools/Makefile

@@ -0,0 +1,47 @@
+PROGS= showZobov
+
+CXX=g++
+CC=gcc
+
+include config.mk
+
+SOURCES= showZobov.cpp loadZobov.cpp zobovConf.c 
+
+LIBS= $(LDFLAGS) 
+
+all: $(PROGS)
+
+showZobov: showZobov.o loadZobov.o zobovConf.o
+
+depend: $(SOURCES)
+	@echo "[DEPENDS] $^"
+	@$(CC) $(CPPFLAGS) -M -MM $^ > .mydepends
+
+distclean: clean
+	@rm -f .mydepends
+
+clean: 
+	@rm -f *.o
+	@rm -f $(PROGS)
+
+.mydepends: $(SOURCES) 
+	@touch .mydepends
+	@make depend
+
+%.prog:
+	@echo "[L] $@"
+	@$(CXX) -o $@ $^ $(LIBS)
+
+zobovConf.c zobovConf.h: showZobov.ggo Makefile
+	@echo "[OPT] $@"
+	gengetopt  -i $<  -f zobovConf  -a zobovConf_info  -F zobovConf -C
+
+%.o: %.c
+	@echo "[C] $< ..."
+	@$(CC) -c -o  $@ $< $(CFLAGS)
+
+%.o: %.cpp
+	@echo "[C++] $< ..."
+	@$(CXX) -c -o $@ $< $(CXXFLAGS)
+
+include .mydepends

mytools/config.mk

@@ -0,0 +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

mytools/loadZobov.cpp

@@ -0,0 +1,136 @@
+#include <string>
+#include <fstream>
+#include <iostream>
+#include <vector>
+#include <cstdlib>
+#include <sstream>
+#include "loadZobov.hpp"
+
+using namespace std;
+
+bool loadZobov(const char *descName, const char *adjName, const char *volName, ZobovRep& z)
+{
+  ifstream descFile(descName);
+  ifstream adjFile(adjName);
+  ifstream volFile(volName);
+  int32_t numParticles, numZones, numPinZone;
+  int32_t totalParticles;
+  int32_t numVoids;
+
+  adjFile.read((char *)&numParticles, sizeof(numParticles));
+  adjFile.read((char *)&numZones, sizeof(numZones));
+  if (!adjFile)
+    return false;
+
+  cout << "Number of particles = " << numParticles << endl;
+  cout << "Number of zones = " << numZones << endl;
+
+  totalParticles = 0;
+  z.allZones.resize(numZones);
+  for (int zone = 0; zone < numZones; zone++)
+    {
+      adjFile.read((char *)&numPinZone, sizeof(numPinZone));
+      if (!adjFile)
+	{
+	  cout << "Problem on the zone " << zone << " / " << numZones << endl;
+	  return false;
+	}
+      
+      z.allZones[zone].pId.resize(numPinZone);
+      adjFile.read((char *)&z.allZones[zone].pId[0], sizeof(int)*numPinZone);
+
+      totalParticles += numPinZone;      
+    }
+  cout << "Zoned " << totalParticles << endl;
+
+  if (totalParticles != numParticles)
+    {
+      cerr << "The numbers of particles are inconsistent ! (" << totalParticles << " vs " << numParticles << ")"<< endl;
+      abort();
+    }
+
+  volFile.read((char *)&numVoids, sizeof(numVoids));
+  if (!volFile)
+    return false;
+
+  cout << "Number of voids = " << numVoids << endl;
+
+  z.allVoids.resize(numVoids);
+  for (int v = 0; v < numVoids; v++)
+    {
+      int32_t numZinV;
+
+      volFile.read((char *)&numZinV, sizeof(numZinV));
+      if (!volFile)
+	return false;
+
+      z.allVoids[v].zId.resize(numZinV);
+
+      int *zId = new int[numZinV];      
+
+      volFile.read((char *)zId, sizeof(int)*numZinV);
+      for (int k = 0; k < numZinV; k++)
+	z.allVoids[v].zId[k] = &z.allZones[zId[k]];
+
+      delete[] zId;
+    }
+
+  cout << "Loading description" << endl;
+
+  string line;
+  getline(descFile, line);
+  getline(descFile, line);
+  getline(descFile, line);
+  while (!descFile.eof())
+    {
+      istringstream lineStream(line.c_str());
+      int orderId, volId, coreParticle, numParticlesInZone, numZonesInVoid, numInVoid;
+      float coreDensity, volumeZone, volumeVoid, densityContrast;
+      float probability;
+
+      lineStream
+	>> orderId
+	   >> volId
+	   >> coreParticle
+	   >> coreDensity
+	   >> volumeZone
+	   >> numParticlesInZone
+	   >> numZonesInVoid
+	   >> volumeVoid
+	   >> numInVoid
+	   >> densityContrast
+	   >> probability;
+      if (!lineStream)
+	{
+	  cerr << "Error in text stream" << endl;
+	  abort();
+	}
+      
+      z.allVoids[volId].proba = probability;
+      z.allVoids[volId].volume = volumeVoid;
+      z.allVoids[volId].numParticles = numInVoid;
+      z.allVoids[volId].coreParticle = coreParticle;
+      
+      // Sanity check
+      int actualNumber = 0;
+      for (int j = 0; j < z.allVoids[volId].zId.size(); j++)
+	actualNumber += z.allVoids[volId].zId[j]->pId.size();
+      
+      if (actualNumber != numInVoid)
+	{
+	  cerr << "Sanity check failed."
+	       << " The number of particles in the description (" 
+	       << numInVoid
+	       << ") is different from the one in the file ("
+	       << actualNumber << ")" << endl;
+	}
+      getline(descFile, line);
+    }
+
+  cout << "Done loading" << endl;
+
+
+  
+
+  return true;
+}

mytools/loadZobov.hpp

@@ -0,0 +1,28 @@
+#ifndef __LOAD_ZOBOV_HPP
+#define __LOAD_ZOBOV_HPP
+
+#include <vector>
+
+struct ZobovZone
+{
+  std::vector<int> pId;
+};
+
+struct ZobovVoid
+{
+  std::vector<ZobovZone *> zId;
+  float proba;
+  int numParticles, coreParticle;
+  float volume;
+};
+
+struct ZobovRep
+{
+  std::vector<ZobovZone> allZones;
+  std::vector<ZobovVoid> allVoids;
+};
+
+bool loadZobov(const char *descName,
+	       const char *adjName, const char *volName, ZobovRep& z);
+
+#endif

mytools/zobovConf.h

@@ -0,0 +1,243 @@
+/** @file zobovConf.h
+ *  @brief The header file for the command line option parser
+ *  generated by GNU Gengetopt version 2.22
+ *  http://www.gnu.org/software/gengetopt.
+ *  DO NOT modify this file, since it can be overwritten
+ *  @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef ZOBOVCONF_H
+#define ZOBOVCONF_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 ZOBOVCONF_PACKAGE
+/** @brief the program name */
+#define ZOBOVCONF_PACKAGE "showZobov"
+#endif
+
+#ifndef ZOBOVCONF_VERSION
+/** @brief the program version */
+#define ZOBOVCONF_VERSION "0"
+#endif
+
+/** @brief Where the command line options are stored */
+struct zobovConf_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.  */
+  char * desc_orig;	/**< @brief The description file name for the voids original value given at command line.  */
+  const char *desc_help; /**< @brief The description file name for the voids help description.  */
+  char * adj_arg;	/**< @brief Adjacent file name.  */
+  char * adj_orig;	/**< @brief Adjacent file name original value given at command line.  */
+  const char *adj_help; /**< @brief Adjacent file name help description.  */
+  char * void_arg;	/**< @brief Void/zone bind filename.  */
+  char * void_orig;	/**< @brief Void/zone bind filename original value given at command line.  */
+  const char *void_help; /**< @brief Void/zone bind filename help description.  */
+  int id_arg;	/**< @brief Void id to extract.  */
+  char * id_orig;	/**< @brief Void id to extract original value given at command line.  */
+  const char *id_help; /**< @brief Void id to extract help description.  */
+  int sProba_flag;	/**< @brief Sort against probability (default=off).  */
+  const char *sProba_help; /**< @brief Sort against probability help description.  */
+  int sVol_flag;	/**< @brief Sort against volume (default=on).  */
+  const char *sVol_help; /**< @brief Sort against volume help description.  */
+  double mProba_arg;	/**< @brief Minimal probability to accept (default='0.0').  */
+  char * mProba_orig;	/**< @brief Minimal probability to accept original value given at command line.  */
+  const char *mProba_help; /**< @brief Minimal probability to accept 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.  */
+  int quiet_flag;	/**< @brief Quiet mode (default=off).  */
+  const char *quiet_help; /**< @brief Quiet mode help description.  */
+  char * move_arg;	/**< @brief Move the center by (x,y,z) (default='(0,0,0)').  */
+  char * move_orig;	/**< @brief Move the center by (x,y,z) original value given at command line.  */
+  const char *move_help; /**< @brief Move the center by (x,y,z) help description.  */
+  int galax_flag;	/**< @brief Output is galax particles (default=off).  */
+  const char *galax_help; /**< @brief Output is galax particles help description.  */
+  char * output_arg;	/**< @brief Output file (default='voidDesc').  */
+  char * output_orig;	/**< @brief Output file original value given at command line.  */
+  const char *output_help; /**< @brief Output file 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 id_given ;	/**< @brief Whether id was given.  */
+  unsigned int sProba_given ;	/**< @brief Whether sProba was given.  */
+  unsigned int sVol_given ;	/**< @brief Whether sVol was given.  */
+  unsigned int mProba_given ;	/**< @brief Whether mProba 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 quiet_given ;	/**< @brief Whether quiet was given.  */
+  unsigned int move_given ;	/**< @brief Whether move was given.  */
+  unsigned int galax_given ;	/**< @brief Whether galax was given.  */
+  unsigned int output_given ;	/**< @brief Whether output was given.  */
+
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct zobovConf_params
+{
+  int override; /**< @brief whether to override possibly already present options (default 0) */
+  int initialize; /**< @brief whether to initialize the option structure zobovConf_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 zobovConf_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 *zobovConf_info_purpose;
+/** @brief the usage string of the program */
+extern const char *zobovConf_info_usage;
+/** @brief all the lines making the help output */
+extern const char *zobovConf_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 zobovConf (int argc, char * const *argv,
+  struct zobovConf_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 zobovConf_ext() instead
+ */
+int zobovConf2 (int argc, char * const *argv,
+  struct zobovConf_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 zobovConf_ext (int argc, char * const *argv,
+  struct zobovConf_info *args_info,
+  struct zobovConf_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 zobovConf_dump(FILE *outfile,
+  struct zobovConf_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 zobovConf_file_save(const char *filename,
+  struct zobovConf_info *args_info);
+
+/**
+ * Print the help
+ */
+void zobovConf_print_help(void);
+/**
+ * Print the version
+ */
+void zobovConf_print_version(void);
+
+/**
+ * Initializes all the fields a zobovConf_params structure 
+ * to their default values
+ * @param params the structure to initialize
+ */
+void zobovConf_params_init(struct zobovConf_params *params);
+
+/**
+ * Allocates dynamically a zobovConf_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized zobovConf_params structure
+ */
+struct zobovConf_params *zobovConf_params_create(void);
+
+/**
+ * Initializes the passed zobovConf_info structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void zobovConf_init (struct zobovConf_info *args_info);
+/**
+ * Deallocates the string fields of the zobovConf_info structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void zobovConf_free (struct zobovConf_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 zobovConf_config_file() instead
+ */
+int zobovConf_configfile (char * const filename,
+  struct zobovConf_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 zobovConf_config_file (char * const filename,
+  struct zobovConf_info *args_info,
+  struct zobovConf_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 zobovConf_required (struct zobovConf_info *args_info,
+  const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* ZOBOVCONF_H */