├── Makefile ├── README ├── aaron_utils.hpp ├── cmdline.c ├── cmdline.h ├── gpl.txt ├── onmi.cpp └── onmi_opts.ggo /Makefile: -------------------------------------------------------------------------------- 1 | .PHONY: gitstatus.txt help clean 2 | BITS= 3 | #BITS=-m32 4 | #BITS=-m64 5 | 6 | all: onmi 7 | 8 | help: 9 | echo check the makefile 10 | 11 | clean: 12 | -rm tags *.o onmi 13 | 14 | tags: 15 | ctags *.[ch]pp 16 | 17 | 18 | #-Wclobbered -Wempty-body \ -Wignored-qualifiers -Woverride-init \ -Wtype-limits -Wunused-but-set-parameter 19 | # I'm including most of the -Wextra flags, but I want rid of the enum-in-conditional warning from boost 20 | CXXFLAGS:= \ 21 | -Wmissing-field-initializers \ 22 | -Wsign-compare \ 23 | -Wuninitialized \ 24 | -Wunused-parameter \ 25 | -Wunused \ 26 | -Wall -Wformat #-Werror 27 | CXXFLAGS += -Wextra 28 | 29 | 30 | #CXXFLAGS= ${BITS} -g 31 | LDFLAGS+= -lrt -lm 32 | CC=g++ 33 | #CXXFLAGS= ${BITS} -O3 -p -pg ${CXXFLAGS} # -DNDEBUG 34 | CXXFLAGS:= ${BITS} -O3 ${CXXFLAGS} # -DNDEBUG 35 | CXXFLAGS += -std=c++11 36 | #CXXFLAGS= -O2 37 | 38 | onmi: onmi.o cmdline.o 39 | 40 | cmdline.c.FORCE: 41 | # remake cmdline.c . But it's OK unless you change the .ggo file. You'll need gengetopt(1) to be able to run this. 42 | gengetopt --unamed-opts < onmi_opts.ggo 43 | -------------------------------------------------------------------------------- /README: -------------------------------------------------------------------------------- 1 | An implementation of a Normalized Mutual Information (NMI) measure for sets of overlapping clusters. 2 | 3 | Fully described in: 4 | "Normalized Mutual Information to evaluate overlapping community finding algorithms" 5 | by Aaron F. McDaid, Derek Greene, Neil Hurley 6 | http://arxiv.org/abs/1110.2515 7 | 8 | Our method is based on the method described in Appendix B at the end of: 9 | "Detecting the overlapping and hierarchical community structure in complex networks" 10 | by Andrea Lancichinetti, Santo Fortunato and János Kertész 11 | http://iopscience.iop.org/1367-2630/11/3/033015/ 12 | 13 | 14 | == Usage == 15 | 16 | make onmi 17 | onmi FILE1 FILE2 18 | 19 | The filesnames record the sets of communities. A typical use case is to have 20 | the "true" communities in one file and and those found by your algorithm 21 | in the other file. One line per community. The nodes are 22 | separated by whitespace, and any non-whitespace characters may be used in the 23 | node names. 24 | 25 | 26 | == Contact == 27 | 28 | Send any comments or queries or requests to aaronmcdaid@gmail.com 29 | 30 | 31 | == Citation for Bibtex == 32 | 33 | @article{McDaidNMI, 34 | abstract = {Given the increasing popularity of algorithms for overlapping clustering, in 35 | particular in social network analysis, quantitative measures are needed to 36 | measure the accuracy of a method. Given a set of true clusters, and the set of 37 | clusters found by an algorithm, these sets of clusters must be compared to see 38 | how similar or different the sets are. A normalized measure is desirable in 39 | many contexts, for example assigning a value of 0 where the two sets are 40 | totally dissimilar, and 1 where they are identical. A measure based on 41 | normalized mutual information, [1], has recently become popular. We demonstrate 42 | unintuitive behaviour of this measure, and show how this can be corrected by 43 | using a more conventional normalization. We compare the results to that of 44 | other measures, such as the Omega index [2].}, 45 | archivePrefix = {arXiv}, 46 | author = {McDaid, Aaron F. and Greene, Derek and Hurley, Neil}, 47 | citeulike-article-id = {9896732}, 48 | citeulike-linkout-0 = {http://arxiv.org/abs/1110.2515}, 49 | citeulike-linkout-1 = {http://arxiv.org/pdf/1110.2515}, 50 | day = {11}, 51 | eprint = {1110.2515}, 52 | month = oct, 53 | posted-at = {2011-10-13 02:42:56}, 54 | priority = {0}, 55 | title = {Normalized Mutual Information to evaluate overlapping community finding algorithms}, 56 | url = {http://arxiv.org/abs/1110.2515}, 57 | year = {2011} 58 | } 59 | -------------------------------------------------------------------------------- /aaron_utils.hpp: -------------------------------------------------------------------------------- 1 | #ifndef _AARON_UTILS_H 2 | #define _AARON_UTILS_H 3 | 4 | #include 5 | 6 | #define PP(x) do{ std::cout << #x << ":" << x << std::endl ;}while(0) 7 | #define PP2(x,y) do{ std::cout << #x << ',' << #y << ":\t" << x << " , " << y << std::endl ;}while(0) 8 | #define PP3(x,y,z) do{ std::cout << #x << ',' << #y << ',' << #z << ":\t" << x << " , " << y << " , " << z << std::endl ;}while(0) 9 | #define PP4(x,y,z,w) do{ std::cout << #x << ',' << #y << ',' << #z << ',' << #w << ":\t" << x << " , " << y << " , " << z << " , " << w << std::endl ;}while(0) 10 | 11 | #define PP1_v(...) do { if(global_verbose_flag) PP(__VA_ARGS__); } while(0) 12 | #define PP2_v(...) do { if(global_verbose_flag) PP2(__VA_ARGS__); } while(0) 13 | 14 | #define unless(x) if(!(x)) 15 | 16 | #define DYINGWORDS(x) for (int klsdjfslkfj = (x) ? 0 : 1; klsdjfslkfj!=0; klsdjfslkfj--, ({ assert (x); }) ) 17 | 18 | #define VERYCLOSE(a,b) (1e-10 > fabs((a)-(b))) 19 | 20 | #endif 21 | -------------------------------------------------------------------------------- /cmdline.c: -------------------------------------------------------------------------------- 1 | /* 2 | File autogenerated by gengetopt version 2.22.5 3 | generated with the following command: 4 | gengetopt --unamed-opts 5 | 6 | The developers of gengetopt consider the fixed text that goes in all 7 | gengetopt output files to be in the public domain: 8 | we make no copyright claims on it. 9 | */ 10 | 11 | /* If we use autoconf. */ 12 | #ifdef HAVE_CONFIG_H 13 | #include "config.h" 14 | #endif 15 | 16 | #include 17 | #include 18 | #include 19 | 20 | #ifndef FIX_UNUSED 21 | #define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */ 22 | #endif 23 | 24 | #include 25 | 26 | #include "cmdline.h" 27 | 28 | const char *gengetopt_args_info_purpose = "Compare sets of sets using various measures"; 29 | 30 | const char *gengetopt_args_info_usage = "Usage: oNMI [OPTIONS]... filename filename"; 31 | 32 | const char *gengetopt_args_info_description = ""; 33 | 34 | const char *gengetopt_args_info_help[] = { 35 | " -h, --help Print help and exit", 36 | " -V, --version Print version and exit", 37 | " -v, --verbose detailed debugging (default=off)", 38 | " -o, --omega print the Omega measure (can be slow) (default=off)", 39 | 0 40 | }; 41 | 42 | typedef enum {ARG_NO 43 | , ARG_FLAG 44 | } cmdline_parser_arg_type; 45 | 46 | static 47 | void clear_given (struct gengetopt_args_info *args_info); 48 | static 49 | void clear_args (struct gengetopt_args_info *args_info); 50 | 51 | static int 52 | cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info, 53 | struct cmdline_parser_params *params, const char *additional_error); 54 | 55 | 56 | static char * 57 | gengetopt_strdup (const char *s); 58 | 59 | static 60 | void clear_given (struct gengetopt_args_info *args_info) 61 | { 62 | args_info->help_given = 0 ; 63 | args_info->version_given = 0 ; 64 | args_info->verbose_given = 0 ; 65 | args_info->omega_given = 0 ; 66 | } 67 | 68 | static 69 | void clear_args (struct gengetopt_args_info *args_info) 70 | { 71 | FIX_UNUSED (args_info); 72 | args_info->verbose_flag = 0; 73 | args_info->omega_flag = 0; 74 | 75 | } 76 | 77 | static 78 | void init_args_info(struct gengetopt_args_info *args_info) 79 | { 80 | 81 | 82 | args_info->help_help = gengetopt_args_info_help[0] ; 83 | args_info->version_help = gengetopt_args_info_help[1] ; 84 | args_info->verbose_help = gengetopt_args_info_help[2] ; 85 | args_info->omega_help = gengetopt_args_info_help[3] ; 86 | 87 | } 88 | 89 | void 90 | cmdline_parser_print_version (void) 91 | { 92 | printf ("%s %s\n", 93 | (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE), 94 | CMDLINE_PARSER_VERSION); 95 | } 96 | 97 | static void print_help_common(void) { 98 | cmdline_parser_print_version (); 99 | 100 | if (strlen(gengetopt_args_info_purpose) > 0) 101 | printf("\n%s\n", gengetopt_args_info_purpose); 102 | 103 | if (strlen(gengetopt_args_info_usage) > 0) 104 | printf("\n%s\n", gengetopt_args_info_usage); 105 | 106 | printf("\n"); 107 | 108 | if (strlen(gengetopt_args_info_description) > 0) 109 | printf("%s\n\n", gengetopt_args_info_description); 110 | } 111 | 112 | void 113 | cmdline_parser_print_help (void) 114 | { 115 | int i = 0; 116 | print_help_common(); 117 | while (gengetopt_args_info_help[i]) 118 | printf("%s\n", gengetopt_args_info_help[i++]); 119 | } 120 | 121 | void 122 | cmdline_parser_init (struct gengetopt_args_info *args_info) 123 | { 124 | clear_given (args_info); 125 | clear_args (args_info); 126 | init_args_info (args_info); 127 | 128 | args_info->inputs = 0; 129 | args_info->inputs_num = 0; 130 | } 131 | 132 | void 133 | cmdline_parser_params_init(struct cmdline_parser_params *params) 134 | { 135 | if (params) 136 | { 137 | params->override = 0; 138 | params->initialize = 1; 139 | params->check_required = 1; 140 | params->check_ambiguity = 0; 141 | params->print_errors = 1; 142 | } 143 | } 144 | 145 | struct cmdline_parser_params * 146 | cmdline_parser_params_create(void) 147 | { 148 | struct cmdline_parser_params *params = 149 | (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params)); 150 | cmdline_parser_params_init(params); 151 | return params; 152 | } 153 | 154 | 155 | 156 | static void 157 | cmdline_parser_release (struct gengetopt_args_info *args_info) 158 | { 159 | unsigned int i; 160 | 161 | 162 | for (i = 0; i < args_info->inputs_num; ++i) 163 | free (args_info->inputs [i]); 164 | 165 | if (args_info->inputs_num) 166 | free (args_info->inputs); 167 | 168 | clear_given (args_info); 169 | } 170 | 171 | 172 | static void 173 | write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[]) 174 | { 175 | FIX_UNUSED (values); 176 | if (arg) { 177 | fprintf(outfile, "%s=\"%s\"\n", opt, arg); 178 | } else { 179 | fprintf(outfile, "%s\n", opt); 180 | } 181 | } 182 | 183 | 184 | int 185 | cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info) 186 | { 187 | int i = 0; 188 | 189 | if (!outfile) 190 | { 191 | fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE); 192 | return EXIT_FAILURE; 193 | } 194 | 195 | if (args_info->help_given) 196 | write_into_file(outfile, "help", 0, 0 ); 197 | if (args_info->version_given) 198 | write_into_file(outfile, "version", 0, 0 ); 199 | if (args_info->verbose_given) 200 | write_into_file(outfile, "verbose", 0, 0 ); 201 | if (args_info->omega_given) 202 | write_into_file(outfile, "omega", 0, 0 ); 203 | 204 | 205 | i = EXIT_SUCCESS; 206 | return i; 207 | } 208 | 209 | int 210 | cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info) 211 | { 212 | FILE *outfile; 213 | int i = 0; 214 | 215 | outfile = fopen(filename, "w"); 216 | 217 | if (!outfile) 218 | { 219 | fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename); 220 | return EXIT_FAILURE; 221 | } 222 | 223 | i = cmdline_parser_dump(outfile, args_info); 224 | fclose (outfile); 225 | 226 | return i; 227 | } 228 | 229 | void 230 | cmdline_parser_free (struct gengetopt_args_info *args_info) 231 | { 232 | cmdline_parser_release (args_info); 233 | } 234 | 235 | /** @brief replacement of strdup, which is not standard */ 236 | char * 237 | gengetopt_strdup (const char *s) 238 | { 239 | char *result = 0; 240 | if (!s) 241 | return result; 242 | 243 | result = (char*)malloc(strlen(s) + 1); 244 | if (result == (char*)0) 245 | return (char*)0; 246 | strcpy(result, s); 247 | return result; 248 | } 249 | 250 | int 251 | cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info) 252 | { 253 | return cmdline_parser2 (argc, argv, args_info, 0, 1, 1); 254 | } 255 | 256 | int 257 | cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info, 258 | struct cmdline_parser_params *params) 259 | { 260 | int result; 261 | result = cmdline_parser_internal (argc, argv, args_info, params, 0); 262 | 263 | if (result == EXIT_FAILURE) 264 | { 265 | cmdline_parser_free (args_info); 266 | exit (EXIT_FAILURE); 267 | } 268 | 269 | return result; 270 | } 271 | 272 | int 273 | cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required) 274 | { 275 | int result; 276 | struct cmdline_parser_params params; 277 | 278 | params.override = override; 279 | params.initialize = initialize; 280 | params.check_required = check_required; 281 | params.check_ambiguity = 0; 282 | params.print_errors = 1; 283 | 284 | result = cmdline_parser_internal (argc, argv, args_info, ¶ms, 0); 285 | 286 | if (result == EXIT_FAILURE) 287 | { 288 | cmdline_parser_free (args_info); 289 | exit (EXIT_FAILURE); 290 | } 291 | 292 | return result; 293 | } 294 | 295 | int 296 | cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name) 297 | { 298 | FIX_UNUSED (args_info); 299 | FIX_UNUSED (prog_name); 300 | return EXIT_SUCCESS; 301 | } 302 | 303 | 304 | static char *package_name = 0; 305 | 306 | /** 307 | * @brief updates an option 308 | * @param field the generic pointer to the field to update 309 | * @param orig_field the pointer to the orig field 310 | * @param field_given the pointer to the number of occurrence of this option 311 | * @param prev_given the pointer to the number of occurrence already seen 312 | * @param value the argument for this option (if null no arg was specified) 313 | * @param possible_values the possible values for this option (if specified) 314 | * @param default_value the default value (in case the option only accepts fixed values) 315 | * @param arg_type the type of this option 316 | * @param check_ambiguity @see cmdline_parser_params.check_ambiguity 317 | * @param override @see cmdline_parser_params.override 318 | * @param no_free whether to free a possible previous value 319 | * @param multiple_option whether this is a multiple option 320 | * @param long_opt the corresponding long option 321 | * @param short_opt the corresponding short option (or '-' if none) 322 | * @param additional_error possible further error specification 323 | */ 324 | static 325 | int update_arg(void *field, char **orig_field, 326 | unsigned int *field_given, unsigned int *prev_given, 327 | char *value, const char *possible_values[], 328 | const char *default_value, 329 | cmdline_parser_arg_type arg_type, 330 | int check_ambiguity, int override, 331 | int no_free, int multiple_option, 332 | const char *long_opt, char short_opt, 333 | const char *additional_error) 334 | { 335 | char *stop_char = 0; 336 | const char *val = value; 337 | int found; 338 | FIX_UNUSED (field); 339 | 340 | stop_char = 0; 341 | found = 0; 342 | 343 | if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given))) 344 | { 345 | if (short_opt != '-') 346 | fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n", 347 | package_name, long_opt, short_opt, 348 | (additional_error ? additional_error : "")); 349 | else 350 | fprintf (stderr, "%s: `--%s' option given more than once%s\n", 351 | package_name, long_opt, 352 | (additional_error ? additional_error : "")); 353 | return 1; /* failure */ 354 | } 355 | 356 | FIX_UNUSED (default_value); 357 | 358 | if (field_given && *field_given && ! override) 359 | return 0; 360 | if (prev_given) 361 | (*prev_given)++; 362 | if (field_given) 363 | (*field_given)++; 364 | if (possible_values) 365 | val = possible_values[found]; 366 | 367 | switch(arg_type) { 368 | case ARG_FLAG: 369 | *((int *)field) = !*((int *)field); 370 | break; 371 | default: 372 | break; 373 | }; 374 | 375 | 376 | /* store the original value */ 377 | switch(arg_type) { 378 | case ARG_NO: 379 | case ARG_FLAG: 380 | break; 381 | default: 382 | if (value && orig_field) { 383 | if (no_free) { 384 | *orig_field = value; 385 | } else { 386 | if (*orig_field) 387 | free (*orig_field); /* free previous string */ 388 | *orig_field = gengetopt_strdup (value); 389 | } 390 | } 391 | }; 392 | 393 | return 0; /* OK */ 394 | } 395 | 396 | 397 | int 398 | cmdline_parser_internal ( 399 | int argc, char **argv, struct gengetopt_args_info *args_info, 400 | struct cmdline_parser_params *params, const char *additional_error) 401 | { 402 | int c; /* Character of the parsed option. */ 403 | 404 | int error = 0; 405 | struct gengetopt_args_info local_args_info; 406 | 407 | int override; 408 | int initialize; 409 | int check_required; 410 | int check_ambiguity; 411 | 412 | package_name = argv[0]; 413 | 414 | override = params->override; 415 | initialize = params->initialize; 416 | check_required = params->check_required; 417 | check_ambiguity = params->check_ambiguity; 418 | 419 | if (initialize) 420 | cmdline_parser_init (args_info); 421 | 422 | cmdline_parser_init (&local_args_info); 423 | 424 | optarg = 0; 425 | optind = 0; 426 | opterr = params->print_errors; 427 | optopt = '?'; 428 | 429 | while (1) 430 | { 431 | int option_index = 0; 432 | 433 | static struct option long_options[] = { 434 | { "help", 0, NULL, 'h' }, 435 | { "version", 0, NULL, 'V' }, 436 | { "verbose", 0, NULL, 'v' }, 437 | { "omega", 0, NULL, 'o' }, 438 | { 0, 0, 0, 0 } 439 | }; 440 | 441 | c = getopt_long (argc, argv, "hVvo", long_options, &option_index); 442 | 443 | if (c == -1) break; /* Exit from `while (1)' loop. */ 444 | 445 | switch (c) 446 | { 447 | case 'h': /* Print help and exit. */ 448 | cmdline_parser_print_help (); 449 | cmdline_parser_free (&local_args_info); 450 | exit (EXIT_SUCCESS); 451 | 452 | case 'V': /* Print version and exit. */ 453 | cmdline_parser_print_version (); 454 | cmdline_parser_free (&local_args_info); 455 | exit (EXIT_SUCCESS); 456 | 457 | case 'v': /* detailed debugging. */ 458 | 459 | 460 | if (update_arg((void *)&(args_info->verbose_flag), 0, &(args_info->verbose_given), 461 | &(local_args_info.verbose_given), optarg, 0, 0, ARG_FLAG, 462 | check_ambiguity, override, 1, 0, "verbose", 'v', 463 | additional_error)) 464 | goto failure; 465 | 466 | break; 467 | case 'o': /* print the Omega measure (can be slow). */ 468 | 469 | 470 | if (update_arg((void *)&(args_info->omega_flag), 0, &(args_info->omega_given), 471 | &(local_args_info.omega_given), optarg, 0, 0, ARG_FLAG, 472 | check_ambiguity, override, 1, 0, "omega", 'o', 473 | additional_error)) 474 | goto failure; 475 | 476 | break; 477 | 478 | case 0: /* Long option with no short option */ 479 | case '?': /* Invalid option. */ 480 | /* `getopt_long' already printed an error message. */ 481 | goto failure; 482 | 483 | default: /* bug: option not considered. */ 484 | fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : "")); 485 | abort (); 486 | } /* switch */ 487 | } /* while */ 488 | 489 | 490 | 491 | 492 | cmdline_parser_release (&local_args_info); 493 | 494 | if ( error ) 495 | return (EXIT_FAILURE); 496 | 497 | if (optind < argc) 498 | { 499 | int i = 0 ; 500 | int found_prog_name = 0; 501 | /* whether program name, i.e., argv[0], is in the remaining args 502 | (this may happen with some implementations of getopt, 503 | but surely not with the one included by gengetopt) */ 504 | 505 | i = optind; 506 | while (i < argc) 507 | if (argv[i++] == argv[0]) { 508 | found_prog_name = 1; 509 | break; 510 | } 511 | i = 0; 512 | 513 | args_info->inputs_num = argc - optind - found_prog_name; 514 | args_info->inputs = 515 | (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ; 516 | while (optind < argc) 517 | if (argv[optind++] != argv[0]) 518 | args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ; 519 | } 520 | 521 | return 0; 522 | 523 | failure: 524 | 525 | cmdline_parser_release (&local_args_info); 526 | return (EXIT_FAILURE); 527 | } 528 | -------------------------------------------------------------------------------- /cmdline.h: -------------------------------------------------------------------------------- 1 | /** @file cmdline.h 2 | * @brief The header file for the command line option parser 3 | * generated by GNU Gengetopt version 2.22.5 4 | * http://www.gnu.org/software/gengetopt. 5 | * DO NOT modify this file, since it can be overwritten 6 | * @author GNU Gengetopt by Lorenzo Bettini */ 7 | 8 | #ifndef CMDLINE_H 9 | #define CMDLINE_H 10 | 11 | /* If we use autoconf. */ 12 | #ifdef HAVE_CONFIG_H 13 | #include "config.h" 14 | #endif 15 | 16 | #include /* for FILE */ 17 | 18 | #ifdef __cplusplus 19 | extern "C" { 20 | #endif /* __cplusplus */ 21 | 22 | #ifndef CMDLINE_PARSER_PACKAGE 23 | /** @brief the program name (used for printing errors) */ 24 | #define CMDLINE_PARSER_PACKAGE "oNMI" 25 | #endif 26 | 27 | #ifndef CMDLINE_PARSER_PACKAGE_NAME 28 | /** @brief the complete program name (used for help and version) */ 29 | #define CMDLINE_PARSER_PACKAGE_NAME "oNMI" 30 | #endif 31 | 32 | #ifndef CMDLINE_PARSER_VERSION 33 | /** @brief the program version */ 34 | #define CMDLINE_PARSER_VERSION "0.1" 35 | #endif 36 | 37 | /** @brief Where the command line options are stored */ 38 | struct gengetopt_args_info 39 | { 40 | const char *help_help; /**< @brief Print help and exit help description. */ 41 | const char *version_help; /**< @brief Print version and exit help description. */ 42 | int verbose_flag; /**< @brief detailed debugging (default=off). */ 43 | const char *verbose_help; /**< @brief detailed debugging help description. */ 44 | int omega_flag; /**< @brief print the Omega measure (can be slow) (default=off). */ 45 | const char *omega_help; /**< @brief print the Omega measure (can be slow) help description. */ 46 | 47 | unsigned int help_given ; /**< @brief Whether help was given. */ 48 | unsigned int version_given ; /**< @brief Whether version was given. */ 49 | unsigned int verbose_given ; /**< @brief Whether verbose was given. */ 50 | unsigned int omega_given ; /**< @brief Whether omega was given. */ 51 | 52 | char **inputs ; /**< @brief unamed options (options without names) */ 53 | unsigned inputs_num ; /**< @brief unamed options number */ 54 | } ; 55 | 56 | /** @brief The additional parameters to pass to parser functions */ 57 | struct cmdline_parser_params 58 | { 59 | int override; /**< @brief whether to override possibly already present options (default 0) */ 60 | int initialize; /**< @brief whether to initialize the option structure gengetopt_args_info (default 1) */ 61 | int check_required; /**< @brief whether to check that all required options were provided (default 1) */ 62 | int check_ambiguity; /**< @brief whether to check for options already specified in the option structure gengetopt_args_info (default 0) */ 63 | int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */ 64 | } ; 65 | 66 | /** @brief the purpose string of the program */ 67 | extern const char *gengetopt_args_info_purpose; 68 | /** @brief the usage string of the program */ 69 | extern const char *gengetopt_args_info_usage; 70 | /** @brief all the lines making the help output */ 71 | extern const char *gengetopt_args_info_help[]; 72 | 73 | /** 74 | * The command line parser 75 | * @param argc the number of command line options 76 | * @param argv the command line options 77 | * @param args_info the structure where option information will be stored 78 | * @return 0 if everything went fine, NON 0 if an error took place 79 | */ 80 | int cmdline_parser (int argc, char **argv, 81 | struct gengetopt_args_info *args_info); 82 | 83 | /** 84 | * The command line parser (version with additional parameters - deprecated) 85 | * @param argc the number of command line options 86 | * @param argv the command line options 87 | * @param args_info the structure where option information will be stored 88 | * @param override whether to override possibly already present options 89 | * @param initialize whether to initialize the option structure my_args_info 90 | * @param check_required whether to check that all required options were provided 91 | * @return 0 if everything went fine, NON 0 if an error took place 92 | * @deprecated use cmdline_parser_ext() instead 93 | */ 94 | int cmdline_parser2 (int argc, char **argv, 95 | struct gengetopt_args_info *args_info, 96 | int override, int initialize, int check_required); 97 | 98 | /** 99 | * The command line parser (version with additional parameters) 100 | * @param argc the number of command line options 101 | * @param argv the command line options 102 | * @param args_info the structure where option information will be stored 103 | * @param params additional parameters for the parser 104 | * @return 0 if everything went fine, NON 0 if an error took place 105 | */ 106 | int cmdline_parser_ext (int argc, char **argv, 107 | struct gengetopt_args_info *args_info, 108 | struct cmdline_parser_params *params); 109 | 110 | /** 111 | * Save the contents of the option struct into an already open FILE stream. 112 | * @param outfile the stream where to dump options 113 | * @param args_info the option struct to dump 114 | * @return 0 if everything went fine, NON 0 if an error took place 115 | */ 116 | int cmdline_parser_dump(FILE *outfile, 117 | struct gengetopt_args_info *args_info); 118 | 119 | /** 120 | * Save the contents of the option struct into a (text) file. 121 | * This file can be read by the config file parser (if generated by gengetopt) 122 | * @param filename the file where to save 123 | * @param args_info the option struct to save 124 | * @return 0 if everything went fine, NON 0 if an error took place 125 | */ 126 | int cmdline_parser_file_save(const char *filename, 127 | struct gengetopt_args_info *args_info); 128 | 129 | /** 130 | * Print the help 131 | */ 132 | void cmdline_parser_print_help(void); 133 | /** 134 | * Print the version 135 | */ 136 | void cmdline_parser_print_version(void); 137 | 138 | /** 139 | * Initializes all the fields a cmdline_parser_params structure 140 | * to their default values 141 | * @param params the structure to initialize 142 | */ 143 | void cmdline_parser_params_init(struct cmdline_parser_params *params); 144 | 145 | /** 146 | * Allocates dynamically a cmdline_parser_params structure and initializes 147 | * all its fields to their default values 148 | * @return the created and initialized cmdline_parser_params structure 149 | */ 150 | struct cmdline_parser_params *cmdline_parser_params_create(void); 151 | 152 | /** 153 | * Initializes the passed gengetopt_args_info structure's fields 154 | * (also set default values for options that have a default) 155 | * @param args_info the structure to initialize 156 | */ 157 | void cmdline_parser_init (struct gengetopt_args_info *args_info); 158 | /** 159 | * Deallocates the string fields of the gengetopt_args_info structure 160 | * (but does not deallocate the structure itself) 161 | * @param args_info the structure to deallocate 162 | */ 163 | void cmdline_parser_free (struct gengetopt_args_info *args_info); 164 | 165 | /** 166 | * Checks that all the required options were specified 167 | * @param args_info the structure to check 168 | * @param prog_name the name of the program that will be used to print 169 | * possible errors 170 | * @return 171 | */ 172 | int cmdline_parser_required (struct gengetopt_args_info *args_info, 173 | const char *prog_name); 174 | 175 | 176 | #ifdef __cplusplus 177 | } 178 | #endif /* __cplusplus */ 179 | #endif /* CMDLINE_H */ 180 | -------------------------------------------------------------------------------- /gpl.txt: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /onmi.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright: Aaron F. McDaid 2011 aaronmcdaid@gmail.com 3 | * See our paper on arXiv: "Normalized Mutual Information to evaluate overlapping 4 | * community finding algorithms" by Aaron F. McDaid, Derek Greene, Neil Hurley. 5 | * 6 | * This program is free software: you can redistribute it and/or modify 7 | * it under the terms of the GNU General Public License as published by 8 | * the Free Software Foundation, either version 3 of the License, or 9 | * (at your option) any later version. 10 | * 11 | * This program is distributed in the hope that it will be useful, 12 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 13 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14 | * GNU General Public License for more details. 15 | * 16 | * You should have received a copy of the GNU General Public License 17 | * along with this program. If not, see . 18 | */ 19 | #include 20 | #include 21 | #include 22 | #include 23 | #include 24 | #include 25 | 26 | #include 27 | #include 28 | #include 29 | #include 30 | #include 31 | #include 32 | 33 | #include "aaron_utils.hpp" 34 | 35 | #include "cmdline.h" 36 | 37 | 38 | using namespace std; 39 | 40 | /* 41 | * Examples of args 42 | * -z 43 | * -f 1,2,3 44 | * -a (optional arg) 45 | */ 46 | 47 | //exceptions 48 | struct MissingFile {}; 49 | struct EmptyFile {}; 50 | 51 | void oNMI(const char * file1, const char * file2, const bool do_omega_also); 52 | 53 | static int global_verbose_flag = 0; 54 | 55 | int main(int argc, char ** argv) { 56 | // std::locale system_locale(""); 57 | // std::cout.imbue(system_locale); // to get comma-separated integers. 58 | gengetopt_args_info args_info; 59 | if (cmdline_parser (argc, argv, &args_info) != 0) 60 | exit(1) ; 61 | if(args_info.inputs_num != 2) { 62 | cmdline_parser_print_help(); 63 | exit(1); 64 | } 65 | if(args_info.verbose_flag) { 66 | global_verbose_flag = 1; 67 | } 68 | const char *file1 = args_info.inputs[0]; 69 | const char *file2 = args_info.inputs[1]; 70 | oNMI(file1, file2, args_info.omega_flag); 71 | } 72 | 73 | typedef std::string Node; 74 | typedef std::vector< std::set< Node > > Grouping; 75 | struct NodeToGroup : public 76 | unordered_map< Node, set > 77 | { 78 | int sharedGroups(const Node n_, const Node m_) const { 79 | // PP2(n_,m_); 80 | static const set emptySet; 81 | 82 | const set * nGrps; 83 | if(this->count(n_)==1) 84 | nGrps = &(this->find(n_)->second); 85 | else 86 | nGrps = &emptySet; 87 | // PP(nGrps->size()); 88 | 89 | const set * mGrps; 90 | if(this->count(m_)==1) 91 | mGrps = &(this->find(m_)->second); 92 | else 93 | mGrps = &emptySet; 94 | // PP(mGrps->size()); 95 | 96 | vector intersection; 97 | set_intersection( 98 | nGrps->begin(), nGrps->end(), 99 | mGrps->begin(), mGrps->end(), 100 | back_inserter(intersection) 101 | ); 102 | const int inter = intersection.size(); 103 | // PP(inter); 104 | 105 | assert(inter <= (int)nGrps->size()); 106 | assert(inter <= (int)mGrps->size()); 107 | 108 | return inter; 109 | } 110 | }; 111 | struct OverlapMatrix { 112 | std::map< pair , int> om; // the pair is an ordered pair. 113 | int N; 114 | }; 115 | 116 | Grouping fileToSet(const char * file) { 117 | Grouping ss; 118 | std::ifstream f(file); 119 | unless(f.is_open()) 120 | throw MissingFile(); 121 | for(std::string line; getline(f, line); ) { 122 | Grouping::value_type s; 123 | istringstream fields(line); 124 | //forEach(const std::string &field, amd::rangeOverStream(fields, "\t ")) { 125 | for(std::string field; fields >> field; ) { 126 | if(field.length() == 0) { 127 | cerr << "Warning: two consecutive tabs, or tab at the start of a line. Ignoring empty fields like this" << endl; 128 | } else { 129 | s.insert(field); 130 | } 131 | } 132 | if(s.size()==0) { 133 | cerr << "Warning: ignoring empty sets in file: " << file << endl; 134 | } else { 135 | ss.push_back(s); 136 | } 137 | } 138 | return ss; 139 | } 140 | NodeToGroup nodeToGroup(const Grouping &g) { 141 | NodeToGroup n2g; 142 | for(int grpId = 0; grpId < (int)g.size(); grpId++) { 143 | const Grouping::value_type &grp = g.at(grpId); 144 | for(const Node &n : grp) { 145 | n2g[n].insert(grpId); 146 | } 147 | } 148 | return n2g; 149 | } 150 | 151 | 152 | const OverlapMatrix overlapMatrix(const NodeToGroup &ng1, const NodeToGroup &ng2) { 153 | OverlapMatrix om; 154 | unordered_set< Node > nodes; 155 | for(const NodeToGroup::value_type &n : ng2) { 156 | nodes.insert(n.first); 157 | } 158 | for(const NodeToGroup::value_type &n: ng1) { 159 | nodes.insert(n.first); 160 | } 161 | for(auto const &n: nodes) { 162 | if(ng1.count(n)) for(const int g1: ng1.find(n)->second) { 163 | if(ng2.count(n)) for(const int g2: ng2.find(n)->second) { 164 | om.om[make_pair(g1,g2)] ++; 165 | } 166 | } 167 | } 168 | om.N=nodes.size(); 169 | return om; 170 | } 171 | 172 | double H(const int x, const int N) { 173 | if(x==0) 174 | return 0.0; 175 | const double Px = double(x) / double(N); 176 | assert(x>0 && Px > 0.0); 177 | return -x * log2(Px); 178 | } 179 | double h (const double p) { 180 | if(p==0) 181 | return 0; 182 | assert(p>0); 183 | return -p*log2(p); 184 | } 185 | double H_X_given_Y (const int y, const int x, const int o, const int N) { 186 | // the NON-NORMALIZED mutual information 187 | // given sets of size 'l' and 'r', where there are 'o' nodes in common, what's their similarity score? 188 | assert(o>0 && y>=o && x>=o && y <= N && x <= N); 189 | const double H_Y = H(y,N) + H(N-y,N); 190 | const double H_X = H(x,N) + H(N-x,N); // just used in the assertion 191 | 192 | const double Px0y0 = (N-x-y+o) /double(N); // TODO delete these, and following, lines 193 | const double Px1y0 = (x-o) /double(N); 194 | const double Px0y1 = (y-o) /double(N); 195 | const double Px1y1 = o /double(N); 196 | DYINGWORDS(VERYCLOSE(Px0y0 + Px0y1 + Px1y0 + Px1y1, 1.0)) { 197 | PP(Px0y0); 198 | PP(Px1y0); 199 | PP(Px0y1); 200 | PP(Px1y1); 201 | PP(Px0y0 + Px0y1 + Px1y0 + Px1y1 - 1.0); 202 | } 203 | // PP(h(Px0y0)); 204 | // PP(h(Px1y1)); 205 | // PP(h(Px0y1)); 206 | // PP(h(Px1y0)); 207 | // PP( h(Px0y0)+h(Px1y1) -h(Px0y1)-h(Px0y1) ); 208 | if( h(Px0y0)+h(Px1y1) <= h(Px0y1)+h(Px1y0) ) 209 | return H_X; 210 | const double H_XY = 211 | H(N-x-y+o, N) 212 | + H(x-o, N) 213 | + H(y-o, N) 214 | + H(o, N) 215 | ; 216 | if(H_X < H_XY - H_Y) { // this shouldn't really happen, except by a roundoff error 217 | DYINGWORDS( VERYCLOSE(H_X , H_XY - H_Y)) { 218 | PP(H_X); 219 | PP(H_XY - H_Y); 220 | PP(H_X - (H_XY - H_Y)); 221 | } 222 | return H_X; 223 | } else 224 | return H_XY - H_Y; 225 | } 226 | 227 | double HX_given_BestY (const OverlapMatrix &om, const Grouping &g1, const Grouping &g2, const int realxId) { 228 | // realxId is a community in g2. 229 | // X is g2, Y is g1 230 | // we're looking for the bits to encode X_realxId given all of Y 231 | const int sizeOfXComm = g2.at(realxId).size(); 232 | double bestSoFar = H(sizeOfXComm,om.N) + H(om.N-sizeOfXComm,om.N); 233 | std::map< pair ,int >::const_iterator i = om.om.lower_bound(make_pair(realxId , std::numeric_limits::min())); 234 | std::map< pair ,int >::const_iterator endOfRange = om.om.lower_bound(make_pair(realxId+1, std::numeric_limits::min())); 235 | for(; i != endOfRange; ++ i) 236 | { 237 | int xId = i->first.first; 238 | int yId = i->first.second; 239 | assert(realxId == xId); 240 | const int overlap = i->second; 241 | const double H_XgivenY = H_X_given_Y(g1.at(yId).size(),g2.at(xId).size(), overlap, om.N); 242 | if(bestSoFar > H_XgivenY) 243 | bestSoFar = H_XgivenY; 244 | // cout << '\t'; PPt(g1.at(fromId).size()); 245 | // PPt(g2.at(xId).size()); 246 | // PPt(overlap); 247 | // PP(H_XgivenY); 248 | } 249 | return bestSoFar; 250 | } 251 | 252 | template 253 | double VI_oneSide (const OverlapMatrix &om, const Grouping &g1, const Grouping &g2) { 254 | // this doesn't return the (N)MI. It's the non-mutual information, optionally normalized too soon 255 | const int N = om.N; 256 | double total = 0.0; 257 | for(int toId = 0; toId < (int)g2.size(); toId++) { 258 | const double unnorm = HX_given_BestY(om, g1, g2, toId); 259 | if(normalizeTooSoon) { 260 | const int x = g2.at(toId).size(); 261 | const double H_X = H(x,N) + H(N-x,N); 262 | const double norm = unnorm / H_X; // might be NaN 263 | if(H_X == 0.0) { // the communities take up the whole set of nodes, and hence won't need any bits to be encoded. No need to add anything to 'total' 264 | assert(unnorm == 0.0); 265 | 266 | // in this case norm is 0/0, but we'll just define this as 1 // This is the bugfix/ambiguityfix to make it the same as the LFK software 267 | total += 1.0; 268 | } else { 269 | unless(norm <= 1.01) { 270 | PP(x); 271 | PP(N); 272 | PP(H_X); 273 | PP(unnorm); 274 | PP(unnorm / H_X); 275 | PP(unnorm - H_X); 276 | } 277 | assert(norm <= 1.01); 278 | assert(norm >= -0.01); 279 | total += norm; 280 | } 281 | } else { 282 | total += unnorm; 283 | } 284 | } 285 | if(normalizeTooSoon) { 286 | return total / g2.size(); // why is this total zero? When it should be one in some cases. 287 | } else 288 | return total; 289 | } 290 | double LFKNMI(const OverlapMatrix &om, const OverlapMatrix &omFlipped, const Grouping &g1, const Grouping &g2) { 291 | return 1.0 - 0.5 * 292 | ( VI_oneSide(omFlipped, g1, g2) 293 | + VI_oneSide(om , g2, g1) ); 294 | } 295 | struct Max { 296 | double operator() (const double H_Xs, const double H_Ys) const { 297 | return H_Xs > H_Ys ? H_Xs : H_Ys; 298 | } 299 | }; 300 | struct Sum { 301 | double operator() (const double H_Xs, const double H_Ys) const { 302 | return 0.5 * (H_Xs + H_Ys); 303 | } 304 | }; 305 | struct Min { 306 | double operator() (const double H_Xs, const double H_Ys) const { 307 | return H_Xs > H_Ys ? H_Ys : H_Xs; 308 | } 309 | }; 310 | template 311 | double aaronNMI(const OverlapMatrix &om, const OverlapMatrix &omFlipped, const Grouping &g1, const Grouping &g2) { 312 | double H_Xs = 0.0; 313 | for(int toId = 0; toId < (int)g2.size(); toId++) { 314 | const int x = g2.at(toId).size(); 315 | H_Xs += H(x, om.N)+H(om.N-x, om.N); 316 | } 317 | double H_Ys = 0.0; 318 | for(int fromId = 0; fromId < (int)g1.size(); fromId++) { 319 | const int x = g1.at(fromId).size(); 320 | H_Ys += H(x, om.N)+H(om.N-x, om.N); 321 | } 322 | return 323 | 0.5*( H_Xs+H_Ys - VI_oneSide(omFlipped, g1, g2) - VI_oneSide(om, g2, g1) ) 324 | / Combiner()(H_Xs, H_Ys) 325 | ; 326 | } 327 | 328 | typedef long long int lli; 329 | 330 | pair omega(const NodeToGroup &ng1, const NodeToGroup &ng2) { 331 | // To understand this implement this implementation, look at the formulation 332 | // on page 6 of this: http://www.aclweb.org/anthology/W12-2602 333 | // That defines: 334 | // 335 | // Obs(s1,s2) - Exp(s1,s2) 336 | // Omega(s1,s2) = ----------------------- 337 | // 1 - Exp(s1,s2) 338 | // 339 | // The only 'trick' I have used is to multiply above and below the line by N^2 340 | // 341 | // Finally, note that the Omega index can be negative. 342 | // Obs and Exp are each guaranteed to be between 0 and 1 (inclusive). 343 | // Therefore, the maximum Omega index is 1.0. 344 | // I think the minimum is -1.0, although not certain that can be attained. 345 | 346 | // First step is to identify all the distinct nodes 347 | set nodes; 348 | for(NodeToGroup::const_iterator i = ng1.begin(); i!=ng1.end(); i++) { nodes.insert(i->first); } 349 | for(NodeToGroup::const_iterator i = ng2.begin(); i!=ng2.end(); i++) { nodes.insert(i->first); } 350 | 351 | vector nodesv; 352 | for(set::const_iterator i=nodes.begin(); i!=nodes.end(); i++) { nodesv.push_back(*i); } 353 | const int N=nodesv.size(); 354 | 355 | // Now to start populating the relevant statistics 356 | map A; // number of pairs of nodes sharing this number of clusters, where both covers agree on this number 357 | map N_bottom; // necessary for computing the expected number. For one cover, the distribution of the shared-cluster-count. 358 | map N_side; // necessary for computing the expected number. For the other cover, the distribution of the shared-cluster-count. 359 | 360 | int minJK = 0; 361 | lli sumOfSquares = 0; 362 | for(int n=0; n &Nj: N_bottom) { 392 | bigN += Nj.second; 393 | } 394 | { // verification 395 | /* 396 | forEach(const typeof(pair) &Aj, amd::mk_range(A)) { 397 | PP2(Aj.first, Aj.second); 398 | } 399 | forEach(const typeof(pair< pair,int>) &Bij, amd::mk_range(B)) { 400 | PP3(Bij.first.first, Bij.first.second, Bij.second); 401 | } 402 | forEach(const typeof(pair) &Nj, amd::mk_range(N_bottom)) { 403 | // PP2(Nj.first, Nj.second); 404 | } 405 | */ 406 | int verifyNumPairs3 = 0; 407 | for(const pair &Nj: N_side ) { 408 | // PP2(Nj.first, Nj.second); 409 | verifyNumPairs3 += Nj.second; 410 | } 411 | assert(bigN == N*(N-1)/2); 412 | assert(verifyNumPairs3 == N*(N-1)/2); 413 | } 414 | 415 | double L2norm = sqrt(sumOfSquares); 416 | 417 | lli numerator = 0; 418 | for(int j=0; j<=minJK; j++) { 419 | numerator += bigN * A[j]; 420 | numerator -= N_bottom[j] * N_side[j]; 421 | } 422 | lli denominator = 0; 423 | denominator += bigN * bigN; 424 | for(int j=0; j<=minJK; j++) { 425 | denominator -= N_bottom[j] * N_side[j]; 426 | assert(denominator >= 0); 427 | } 428 | PP1_v(numerator); 429 | PP1_v(denominator); 430 | double O = double(numerator) / double(denominator); 431 | return make_pair(O,L2norm); 432 | } 433 | 434 | void oNMI(const char * file1, const char * file2, const bool do_omega_also) { 435 | Grouping g1 = fileToSet(file1); 436 | Grouping g2 = fileToSet(file2); 437 | PP1_v(g1.size()); 438 | PP1_v(g2.size()); 439 | unless(g1.size() > 0) throw EmptyFile(); 440 | unless(g2.size() > 0) throw EmptyFile(); 441 | NodeToGroup n2g1 = nodeToGroup(g1); 442 | NodeToGroup n2g2 = nodeToGroup(g2); 443 | PP1_v(n2g1.size()); 444 | PP1_v(n2g2.size()); 445 | const OverlapMatrix om = overlapMatrix(n2g1, n2g2); 446 | 447 | OverlapMatrix omFlipped; 448 | omFlipped.N = om.N; 449 | for(pair< pair ,int> p: om.om) { 450 | swap(p.first.first, p.first.second); 451 | bool wasInserted = omFlipped.om.insert(p).second; 452 | assert(wasInserted); 453 | } 454 | assert(omFlipped.om.size() == om.om.size()); 455 | 456 | if(global_verbose_flag) { 457 | cout << " \'" << file2 << "\' given \'" << file1 << "\"" << endl; 458 | for(int toId = 0; toId < (int)g2.size(); toId++) { 459 | PP(HX_given_BestY(omFlipped, g1, g2, toId)); 460 | } 461 | cout << " \'" << file1 << "\' given \'" << file2 << "\"" << endl; 462 | for(int fromId = 0; fromId < (int)g1.size(); fromId++) { 463 | PP(HX_given_BestY(om , g2, g1, fromId)); 464 | } 465 | cout << "Here:" << endl; 466 | } 467 | const double LFKnmi_ = LFKNMI(om, omFlipped, g1, g2); 468 | if(do_omega_also) { 469 | pair OmegaAndL2Norm = omega(n2g1, n2g2); 470 | const double Omega = OmegaAndL2Norm.first; 471 | const double L2norm = OmegaAndL2Norm.second; 472 | cout << "Datum:\t"; PP(Omega); 473 | cout << "Datum:\t"; PP(L2norm); 474 | } 475 | cout << "NMI:\t"; cout << aaronNMI(om, omFlipped, g1, g2) << endl; 476 | cout << "Other measures:" << endl; 477 | cout << " lfkNMI:\t"; cout << LFKnmi_ << endl; 478 | cout << " NMI:\t"; cout << aaronNMI(om, omFlipped, g1, g2) << endl; 479 | // PP(aaronNMI(om, g1, g2)); This is awful :-) 480 | } 481 | -------------------------------------------------------------------------------- /onmi_opts.ggo: -------------------------------------------------------------------------------- 1 | package "oNMI" 2 | version "0.1" 3 | purpose "Compare sets of sets using various measures" 4 | usage "oNMI [OPTIONS]... filename filename" 5 | option "verbose" v "detailed debugging" flag off 6 | option "omega" o "print the Omega measure (can be slow)" flag off 7 | --------------------------------------------------------------------------------