mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 15:21:11 +00:00
Possibility to dump/retrieve tree on disk. Dump voids particle positions correctly
This commit is contained in:
Guilhem Lavaux
parent
3088bb5733
commit
8bf13dfb8b
4 changed files with 168 additions and 28 deletions
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@ -1,5 +1,5 @@
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/*
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File autogenerated by gengetopt version 2.22
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File autogenerated by gengetopt version 2.22.2
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generated with the following command:
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gengetopt -i buildObservedVoids.ggo -f buildObservedVoids_conf -a buildObservedVoids_info -F buildObservedVoids_conf -C
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@ -17,6 +17,10 @@
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#include <stdlib.h>
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#include <string.h>
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#ifndef FIX_UNUSED
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#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
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#endif
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#include "getopt.h"
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#include "buildObservedVoids_conf.h"
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@ -40,8 +44,11 @@ const char *buildObservedVoids_info_help[] = {
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" -g, --gridOutput=STRING 3d grid output of voids \n (default=`all_voids.nc')",
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" -q, --quiet Quiet output (default=off)",
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" --dumpVoids=STRING Dump the particles in void in a file",
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" --dumpIds Dump particle ids (default=off)",
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" --ramsesBase=STRING Base directory for ramses",
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" --ramsesId=INT Ramses snapshot id",
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" --dumpTree Dump the void tree (default=off)",
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" --getTree Restore tree from file (default=off)",
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0
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};
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@ -106,13 +113,17 @@ void clear_given (struct buildObservedVoids_info *args_info)
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args_info->gridOutput_given = 0 ;
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args_info->quiet_given = 0 ;
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args_info->dumpVoids_given = 0 ;
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args_info->dumpIds_given = 0 ;
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args_info->ramsesBase_given = 0 ;
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args_info->ramsesId_given = 0 ;
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args_info->dumpTree_given = 0 ;
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args_info->getTree_given = 0 ;
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}
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static
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void clear_args (struct buildObservedVoids_info *args_info)
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{
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FIX_UNUSED (args_info);
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args_info->desc_arg = NULL;
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args_info->desc_orig = NULL;
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args_info->partzone_arg = NULL;
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@ -132,9 +143,12 @@ void clear_args (struct buildObservedVoids_info *args_info)
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args_info->quiet_flag = 0;
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args_info->dumpVoids_arg = NULL;
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args_info->dumpVoids_orig = NULL;
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args_info->dumpIds_flag = 0;
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args_info->ramsesBase_arg = NULL;
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args_info->ramsesBase_orig = NULL;
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args_info->ramsesId_orig = NULL;
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args_info->dumpTree_flag = 0;
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args_info->getTree_flag = 0;
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}
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@ -155,15 +169,20 @@ void init_args_info(struct buildObservedVoids_info *args_info)
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args_info->gridOutput_help = buildObservedVoids_info_help[9] ;
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args_info->quiet_help = buildObservedVoids_info_help[10] ;
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args_info->dumpVoids_help = buildObservedVoids_info_help[11] ;
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args_info->ramsesBase_help = buildObservedVoids_info_help[12] ;
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args_info->ramsesId_help = buildObservedVoids_info_help[13] ;
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args_info->dumpIds_help = buildObservedVoids_info_help[12] ;
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args_info->ramsesBase_help = buildObservedVoids_info_help[13] ;
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args_info->ramsesId_help = buildObservedVoids_info_help[14] ;
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args_info->dumpTree_help = buildObservedVoids_info_help[15] ;
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args_info->getTree_help = buildObservedVoids_info_help[16] ;
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}
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void
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buildObservedVoids_conf_print_version (void)
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{
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printf ("%s %s\n", BUILDOBSERVEDVOIDS_CONF_PACKAGE, BUILDOBSERVEDVOIDS_CONF_VERSION);
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printf ("%s %s\n",
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(strlen(BUILDOBSERVEDVOIDS_CONF_PACKAGE_NAME) ? BUILDOBSERVEDVOIDS_CONF_PACKAGE_NAME : BUILDOBSERVEDVOIDS_CONF_PACKAGE),
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BUILDOBSERVEDVOIDS_CONF_VERSION);
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}
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static void print_help_common(void) {
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@ -178,7 +197,7 @@ static void print_help_common(void) {
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printf("\n");
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if (strlen(buildObservedVoids_info_description) > 0)
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printf("%s\n", buildObservedVoids_info_description);
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printf("%s\n\n", buildObservedVoids_info_description);
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}
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void
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@ -262,8 +281,9 @@ buildObservedVoids_conf_release (struct buildObservedVoids_info *args_info)
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static void
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write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
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write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
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{
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FIX_UNUSED (values);
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if (arg) {
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fprintf(outfile, "%s=\"%s\"\n", opt, arg);
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} else {
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@ -307,10 +327,16 @@ buildObservedVoids_conf_dump(FILE *outfile, struct buildObservedVoids_info *args
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write_into_file(outfile, "quiet", 0, 0 );
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if (args_info->dumpVoids_given)
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write_into_file(outfile, "dumpVoids", args_info->dumpVoids_orig, 0);
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if (args_info->dumpIds_given)
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write_into_file(outfile, "dumpIds", 0, 0 );
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if (args_info->ramsesBase_given)
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write_into_file(outfile, "ramsesBase", args_info->ramsesBase_orig, 0);
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if (args_info->ramsesId_given)
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write_into_file(outfile, "ramsesId", args_info->ramsesId_orig, 0);
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if (args_info->dumpTree_given)
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write_into_file(outfile, "dumpTree", 0, 0 );
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if (args_info->getTree_given)
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write_into_file(outfile, "getTree", 0, 0 );
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i = EXIT_SUCCESS;
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@ -347,7 +373,7 @@ buildObservedVoids_conf_free (struct buildObservedVoids_info *args_info)
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char *
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gengetopt_strdup (const char *s)
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{
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char *result = NULL;
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char *result = 0;
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if (!s)
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return result;
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@ -369,7 +395,7 @@ buildObservedVoids_conf_ext (int argc, char * const *argv, struct buildObservedV
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struct buildObservedVoids_conf_params *params)
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{
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int result;
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result = buildObservedVoids_conf_internal (argc, argv, args_info, params, NULL);
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result = buildObservedVoids_conf_internal (argc, argv, args_info, params, 0);
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if (result == EXIT_FAILURE)
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{
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@ -392,7 +418,7 @@ buildObservedVoids_conf2 (int argc, char * const *argv, struct buildObservedVoid
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params.check_ambiguity = 0;
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params.print_errors = 1;
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result = buildObservedVoids_conf_internal (argc, argv, args_info, ¶ms, NULL);
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result = buildObservedVoids_conf_internal (argc, argv, args_info, ¶ms, 0);
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if (result == EXIT_FAILURE)
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{
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@ -408,7 +434,7 @@ buildObservedVoids_conf_required (struct buildObservedVoids_info *args_info, con
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{
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int result = EXIT_SUCCESS;
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if (buildObservedVoids_conf_required2(args_info, prog_name, NULL) > 0)
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if (buildObservedVoids_conf_required2(args_info, prog_name, 0) > 0)
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result = EXIT_FAILURE;
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if (result == EXIT_FAILURE)
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@ -423,6 +449,7 @@ buildObservedVoids_conf_required (struct buildObservedVoids_info *args_info, con
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int
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buildObservedVoids_conf_required2 (struct buildObservedVoids_info *args_info, const char *prog_name, const char *additional_error)
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{
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FIX_UNUSED (additional_error);
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int error = 0;
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/* checks for required options */
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@ -474,13 +501,15 @@ static char *package_name = 0;
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static
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int update_arg(void *field, char **orig_field,
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unsigned int *field_given, unsigned int *prev_given,
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char *value, char *possible_values[], const char *default_value,
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char *value, const char *possible_values[],
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const char *default_value,
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buildObservedVoids_conf_arg_type arg_type,
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int check_ambiguity, int override,
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int no_free, int multiple_option,
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const char *long_opt, char short_opt,
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const char *additional_error)
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{
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FIX_UNUSED (field);
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char *stop_char = 0;
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const char *val = value;
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int found;
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@ -502,6 +531,7 @@ int update_arg(void *field, char **orig_field,
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return 1; /* failure */
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}
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FIX_UNUSED (default_value);
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if (field_given && *field_given && ! override)
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return 0;
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@ -569,7 +599,8 @@ int update_arg(void *field, char **orig_field,
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int
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buildObservedVoids_conf_internal (int argc, char * const *argv, struct buildObservedVoids_info *args_info,
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buildObservedVoids_conf_internal (
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int argc, char * const *argv, struct buildObservedVoids_info *args_info,
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struct buildObservedVoids_conf_params *params, const char *additional_error)
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{
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int c; /* Character of the parsed option. */
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@ -616,9 +647,12 @@ buildObservedVoids_conf_internal (int argc, char * const *argv, struct buildObse
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{ "gridOutput", 1, NULL, 'g' },
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{ "quiet", 0, NULL, 'q' },
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{ "dumpVoids", 1, NULL, 0 },
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{ "dumpIds", 0, NULL, 0 },
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{ "ramsesBase", 1, NULL, 0 },
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{ "ramsesId", 1, NULL, 0 },
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{ NULL, 0, NULL, 0 }
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{ "dumpTree", 0, NULL, 0 },
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{ "getTree", 0, NULL, 0 },
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{ 0, 0, 0, 0 }
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};
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c = getopt_long (argc, argv, "hVd:p:v:m:f:o:g:q", long_options, &option_index);
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@ -760,6 +794,18 @@ buildObservedVoids_conf_internal (int argc, char * const *argv, struct buildObse
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additional_error))
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goto failure;
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}
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/* Dump particle ids. */
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else if (strcmp (long_options[option_index].name, "dumpIds") == 0)
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{
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if (update_arg((void *)&(args_info->dumpIds_flag), 0, &(args_info->dumpIds_given),
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&(local_args_info.dumpIds_given), optarg, 0, 0, ARG_FLAG,
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check_ambiguity, override, 1, 0, "dumpIds", '-',
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additional_error))
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goto failure;
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}
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/* Base directory for ramses. */
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else if (strcmp (long_options[option_index].name, "ramsesBase") == 0)
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@ -788,6 +834,30 @@ buildObservedVoids_conf_internal (int argc, char * const *argv, struct buildObse
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additional_error))
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goto failure;
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}
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/* Dump the void tree. */
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else if (strcmp (long_options[option_index].name, "dumpTree") == 0)
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{
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if (update_arg((void *)&(args_info->dumpTree_flag), 0, &(args_info->dumpTree_given),
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&(local_args_info.dumpTree_given), optarg, 0, 0, ARG_FLAG,
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check_ambiguity, override, 1, 0, "dumpTree", '-',
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additional_error))
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goto failure;
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}
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/* Restore tree from file. */
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else if (strcmp (long_options[option_index].name, "getTree") == 0)
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{
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if (update_arg((void *)&(args_info->getTree_flag), 0, &(args_info->getTree_given),
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&(local_args_info.getTree_given), optarg, 0, 0, ARG_FLAG,
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check_ambiguity, override, 1, 0, "getTree", '-',
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additional_error))
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goto failure;
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}
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break;
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@ -830,7 +900,7 @@ failure:
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/* 3 is for "--" and "=" */
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static int
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_buildObservedVoids_conf_configfile (char * const filename, int *my_argc)
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_buildObservedVoids_conf_configfile (const char *filename, int *my_argc)
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{
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FILE* file;
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char my_argv[CONFIG_FILE_LINE_BUFFER_SIZE+1];
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@ -842,14 +912,14 @@ _buildObservedVoids_conf_configfile (char * const filename, int *my_argc)
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size_t len, next_token;
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char delimiter;
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if ((file = fopen(filename, "r")) == NULL)
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if ((file = fopen(filename, "r")) == 0)
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{
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fprintf (stderr, "%s: Error opening configuration file '%s'\n",
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BUILDOBSERVEDVOIDS_CONF_PACKAGE, filename);
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return EXIT_FAILURE;
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}
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while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != NULL)
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while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != 0)
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{
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++line_num;
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my_argv[0] = '\0';
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@ -876,7 +946,7 @@ _buildObservedVoids_conf_configfile (char * const filename, int *my_argc)
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if (fopt[next_token] == '\0') /* the line is over */
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{
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farg = NULL;
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farg = 0;
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equal = 0;
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goto noarg;
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}
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@ -967,7 +1037,8 @@ _buildObservedVoids_conf_configfile (char * const filename, int *my_argc)
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}
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int
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buildObservedVoids_conf_configfile (char * const filename,
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buildObservedVoids_conf_configfile (
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const char *filename,
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struct buildObservedVoids_info *args_info,
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int override, int initialize, int check_required)
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{
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@ -983,7 +1054,7 @@ buildObservedVoids_conf_configfile (char * const filename,
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}
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int
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buildObservedVoids_conf_config_file (char * const filename,
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buildObservedVoids_conf_config_file (const char *filename,
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struct buildObservedVoids_info *args_info,
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struct buildObservedVoids_conf_params *params)
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{
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|
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@ -1,6 +1,6 @@
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/** @file buildObservedVoids_conf.h
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* @brief The header file for the command line option parser
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* generated by GNU Gengetopt version 2.22
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* generated by GNU Gengetopt version 2.22.2
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* http://www.gnu.org/software/gengetopt.
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* DO NOT modify this file, since it can be overwritten
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* @author GNU Gengetopt by Lorenzo Bettini */
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@ -20,10 +20,15 @@ extern "C" {
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#endif /* __cplusplus */
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#ifndef BUILDOBSERVEDVOIDS_CONF_PACKAGE
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/** @brief the program name */
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/** @brief the program name (used for printing errors) */
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#define BUILDOBSERVEDVOIDS_CONF_PACKAGE "buildObservedVoids"
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#endif
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#ifndef BUILDOBSERVEDVOIDS_CONF_PACKAGE_NAME
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/** @brief the complete program name (used for help and version) */
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#define BUILDOBSERVEDVOIDS_CONF_PACKAGE_NAME "buildObservedVoids"
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#endif
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#ifndef BUILDOBSERVEDVOIDS_CONF_VERSION
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/** @brief the program version */
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#define BUILDOBSERVEDVOIDS_CONF_VERSION "0"
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@ -63,12 +68,18 @@ struct buildObservedVoids_info
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char * dumpVoids_arg; /**< @brief Dump the particles in void in a file. */
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char * dumpVoids_orig; /**< @brief Dump the particles in void in a file original value given at command line. */
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const char *dumpVoids_help; /**< @brief Dump the particles in void in a file help description. */
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int dumpIds_flag; /**< @brief Dump particle ids (default=off). */
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const char *dumpIds_help; /**< @brief Dump particle ids help description. */
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char * ramsesBase_arg; /**< @brief Base directory for ramses. */
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char * ramsesBase_orig; /**< @brief Base directory for ramses original value given at command line. */
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const char *ramsesBase_help; /**< @brief Base directory for ramses help description. */
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int ramsesId_arg; /**< @brief Ramses snapshot id. */
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char * ramsesId_orig; /**< @brief Ramses snapshot id original value given at command line. */
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const char *ramsesId_help; /**< @brief Ramses snapshot id help description. */
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int dumpTree_flag; /**< @brief Dump the void tree (default=off). */
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const char *dumpTree_help; /**< @brief Dump the void tree help description. */
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int getTree_flag; /**< @brief Restore tree from file (default=off). */
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const char *getTree_help; /**< @brief Restore tree from file help description. */
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unsigned int help_given ; /**< @brief Whether help was given. */
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unsigned int version_given ; /**< @brief Whether version was given. */
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@ -82,8 +93,11 @@ struct buildObservedVoids_info
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unsigned int gridOutput_given ; /**< @brief Whether gridOutput was given. */
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unsigned int quiet_given ; /**< @brief Whether quiet was given. */
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unsigned int dumpVoids_given ; /**< @brief Whether dumpVoids was given. */
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unsigned int dumpIds_given ; /**< @brief Whether dumpIds was given. */
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unsigned int ramsesBase_given ; /**< @brief Whether ramsesBase was given. */
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unsigned int ramsesId_given ; /**< @brief Whether ramsesId was given. */
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unsigned int dumpTree_given ; /**< @brief Whether dumpTree was given. */
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unsigned int getTree_given ; /**< @brief Whether getTree was given. */
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} ;
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@ -206,7 +220,7 @@ void buildObservedVoids_conf_free (struct buildObservedVoids_info *args_info);
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* @return 0 if everything went fine, NON 0 if an error took place
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* @deprecated use buildObservedVoids_conf_config_file() instead
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*/
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int buildObservedVoids_conf_configfile (char * const filename,
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int buildObservedVoids_conf_configfile (const char *filename,
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struct buildObservedVoids_info *args_info,
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int override, int initialize, int check_required);
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|
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@ -217,7 +231,7 @@ int buildObservedVoids_conf_configfile (char * const filename,
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* @param params additional parameters for the parser
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* @return 0 if everything went fine, NON 0 if an error took place
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*/
|
||||
int buildObservedVoids_conf_config_file (char * const filename,
|
||||
int buildObservedVoids_conf_config_file (const char *filename,
|
||||
struct buildObservedVoids_info *args_info,
|
||||
struct buildObservedVoids_conf_params *params);
|
||||
|
||||
|
|
|
|||
|
|
@ -2,5 +2,5 @@ CC= gcc
|
|||
CXX= g++
|
||||
CPPFLAGS=
|
||||
LDFLAGS= -L/usr/local/lib -lCosmoTool -lgsl -lgslcblas
|
||||
CXXFLAGS= $(CPPFLAGS) -ggdb -O3 -ffast-math
|
||||
CFLAGS= $(CPPFLAGS) -ggdb -O3 -ffast-math
|
||||
CXXFLAGS= $(CPPFLAGS) -ggdb -O0 -ftree-vectorize -ftree-vectorizer-verbose=2 -ffast-math
|
||||
CFLAGS= $(CPPFLAGS) -ggdb -O0 -ftree-vectorize -ftree-vectorizer-verbose=2 -ffast-math
|
||||
|
|
|
|||
|
|
@ -15,16 +15,39 @@ struct VoidNode
|
|||
std::list<VoidNode *> children;
|
||||
};
|
||||
|
||||
struct VoidNodeOnDisk
|
||||
{
|
||||
int vid;
|
||||
int parent;
|
||||
};
|
||||
|
||||
class VoidTree
|
||||
{
|
||||
protected:
|
||||
uint32_t totalNumNodes;
|
||||
uint32_t totalNumNodes, activeNodes;
|
||||
VoidNode *nodes;
|
||||
VoidNode *rootNode;
|
||||
ZobovRep& zobov;
|
||||
public:
|
||||
typedef std::list<VoidNode *> VoidList;
|
||||
|
||||
void dumpTree(std::ostream& o)
|
||||
{
|
||||
VoidNodeOnDisk data;
|
||||
|
||||
o.write((char*)&activeNodes, sizeof(uint32_t));
|
||||
for (uint32_t i = 0; i < activeNodes; i++)
|
||||
{
|
||||
data.vid = nodes[i].vid;
|
||||
if (nodes[i].parent == 0)
|
||||
data.parent = -1;
|
||||
else
|
||||
data.parent = nodes[i].parent - nodes;
|
||||
o.write((char *)&data, sizeof(VoidNodeOnDisk));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
int lookupParent(int voidId, const std::vector<std::list<int> >& voids_for_zones)
|
||||
{
|
||||
int lastSize = 0x7fffffff;
|
||||
|
|
@ -33,7 +56,7 @@ public:
|
|||
const std::list<int>& candidateList = voids_for_zones[ref_void.zId.front()];
|
||||
std::list<int>::const_iterator iter_candidate = candidateList.begin();
|
||||
|
||||
//std::cout << "candidate list size is " << candidateList.size() << std::endl;
|
||||
// std::cout << "candidate list size is " << candidateList.size() << std::endl;
|
||||
|
||||
while (iter_candidate != candidateList.end())
|
||||
{
|
||||
|
|
@ -91,6 +114,38 @@ public:
|
|||
std::cout << "Failure to lookup parent (2)" << std::endl;
|
||||
return -1;
|
||||
}
|
||||
|
||||
VoidTree(ZobovRep& rep, std::istream& disk)
|
||||
: zobov(rep)
|
||||
{
|
||||
totalNumNodes = rep.allVoids.size();
|
||||
|
||||
disk.read((char *)&activeNodes, sizeof(uint32_t));
|
||||
nodes = new VoidNode[activeNodes];
|
||||
rootNode = 0;
|
||||
for (uint32_t i = 0; i < activeNodes; i++)
|
||||
{
|
||||
VoidNodeOnDisk data;
|
||||
|
||||
disk.read((char *)&data, sizeof(data));
|
||||
nodes[i].vid = data.vid;
|
||||
if (data.parent < 0)
|
||||
{
|
||||
if (rootNode != 0)
|
||||
{
|
||||
std::cerr << "Multiple root to the tree !!!" << std::endl;
|
||||
abort();
|
||||
}
|
||||
nodes[i].parent = 0;
|
||||
rootNode = &nodes[i];
|
||||
}
|
||||
else
|
||||
{
|
||||
nodes[i].parent = nodes + data.parent;
|
||||
nodes[i].parent->children.push_back(&nodes[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
VoidTree(ZobovRep& rep)
|
||||
: zobov(rep)
|
||||
|
|
@ -113,7 +168,6 @@ public:
|
|||
{
|
||||
nodes[i].vid = i;
|
||||
nodes[i].parent = 0;
|
||||
nodes[i].children.clear();
|
||||
}
|
||||
|
||||
std::cout << "Linking voids together..." << std::endl;
|
||||
|
|
@ -149,6 +203,7 @@ public:
|
|||
}
|
||||
rootNode = &nodes[i];
|
||||
}
|
||||
activeNodes = inserted;
|
||||
}
|
||||
|
||||
~VoidTree()
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue