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Document the hmm_generate executable

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This commit is contained in:
Ryan Curtin
2010-05-25 21:09:34 +00:00
parent 58faa6bfb6
commit 8a5204a70d
1 changed files with 47 additions and 54 deletions
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fastlib/trunk/mlpack/hmm/generate.cc
+47 -54
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@@ -9,12 +9,13 @@
* See the usage() function for complete option list
*/
#include "fastlib/fastlib.h"
#include <fastlib/fastlib.h>
#include "support.h"
#include "discreteHMM.h"
#include "gaussianHMM.h"
#include "mixgaussHMM.h"
#include "mixtureDST.h"
#include "hmm_documentation.h"
using namespace hmm_support;
@@ -24,30 +25,47 @@ success_t generate_mixture();
void usage();
const fx_entry_doc hmm_generate_main_entries[] = {
{"input_model", FX_REQUIRED, FX_STR, NULL,
"A .hmm file containing an HMM profile.\n"},
{"output_observation_file", FX_PARAM, FX_STR, NULL,
"Output file for the generated observed variable sequences.\n"
" (default observed.<type>.seq)\n"},
{"output_state_file", FX_PARAM, FX_STR, NULL,
"Output file for the generated hidden state sequences.\n"
" (default state.<type>.seq)\n"},
{"type", FX_REQUIRED, FX_STR, NULL,
" HMM type : discrete | gaussian | mixture.\n"},
{"profile", FX_REQUIRED, FX_STR, NULL,
" A file containing HMM profile.\n"},
"HMM type: discrete | gaussian | mixture\n"},
{"length", FX_PARAM, FX_INT, NULL,
" Sequence length, default = 10.\n"},
"Sequence length (default 10)\n"},
{"lenmax", FX_PARAM, FX_INT, NULL,
" Maximum sequence length, default = length\n"},
"Maximum sequence length (default <length>)\n"},
{"numseq", FX_PARAM, FX_INT, NULL,
" Number of sequance, default = 10.\n"},
{"seqfile", FX_PARAM, FX_STR, NULL,
" Output file for the generated sequences.\n"},
{"statefile", FX_PARAM, FX_STR, NULL,
" Output file for the generated state sequences.\n"},
"Number of sequences to generate (default 10).\n"},
FX_ENTRY_DOC_DONE
};
const fx_submodule_doc hmm_generate_main_submodules[] = {
{"formats", &hmm_format_doc,
"Documentation for file formats used by this program and other MLPACK HMM tools\n"},
FX_SUBMODULE_DOC_DONE
};
const fx_module_doc hmm_generate_main_doc = {
hmm_generate_main_entries, hmm_generate_main_submodules,
"This is a program generating sequences from HMM models.\n"
"The hmm_generate utility is used to generate a random sequence from an input\n"
"HMM profile, which is given as a parameter. Then, random sequences are\n"
"generated and stored in two files; one file (specified by\n"
"--output_observation_file) stores the observed variable sequences, and the\n"
"other (specified by --output_state_file) stores the hidden state sequences.\n"
"\n"
"The maximum sequence length parameter (lenmax) can be used to generate a\n"
"series of sequences of varying length. For instance, if numseq is 3, length\n"
"is 10, and lenmax is 12, the first sequence will be 10 states long; the second\n"
"will be 11 states long; the last will be 12 states long. However, lenmax must\n"
"always be greater than length.\n"
"\n"
"For more information on the formats used by this utility, see the help in\n"
"the formats submodule (--help=formats).\n"
};
int main(int argc, char* argv[]) {
@@ -62,45 +80,28 @@ int main(int argc, char* argv[]) {
else if (strcmp(type, "mixture")==0)
s = generate_mixture();
else {
printf("Unrecognized type: must be: discrete | gaussian | mixture !!!\n");
FATAL("Unrecognized type; must be 'discrete', 'gaussian', or 'mixture'.\n");
return SUCCESS_PASS;
}
}
else {
printf("Unrecognized type: must be: discrete | gaussian | mixture !!!\n");
FATAL("Unrecognized type; must be 'discrete', 'gaussian', or 'mixture'.\n");
s = SUCCESS_FAIL;
}
if (!PASSED(s)) usage();
fx_done(NULL);
}
void usage() {
printf("\nUsage:\n");
printf(" generate --type=={discrete|gaussian|mixture} OPTIONS\n");
printf("[OPTIONS]\n");
printf(" --profile=file : file contains HMM profile\n");
printf(" --length=NUM : sequence length\n");
printf(" --lenmax=NUM : maximum sequence length, default = length\n");
printf(" --numseq=NUM : number of sequence\n");
printf(" --seqfile=file : output file for generated sequences\n");
printf(" --statefile=file : output file for generated state sequences\n");
}
success_t generate_mixture() {
if (!fx_param_exists(NULL, "profile")) {
printf("--profile must be defined.\n");
return SUCCESS_FAIL;
}
const char* profile = fx_param_str_req(NULL, "profile");
const char* profile = fx_param_str_req(NULL, "input_model");
const int seqlen = fx_param_int(NULL, "length", 10);
const int seqlmax = fx_param_int(NULL, "lenmax", seqlen);
const int numseq = fx_param_int(NULL, "numseq", 10);
const char* seqout = fx_param_str(NULL, "seqfile", "seq.mix.out");
const char* stateout = fx_param_str(NULL, "statefile", "state.mix.out");
const char* seqout = fx_param_str(NULL, "output_observation_file", "observed.mix.seq");
const char* stateout = fx_param_str(NULL, "output_state_file", "state.mix.seq");
DEBUG_ASSERT_MSG(seqlen <= seqlmax, "LENMAX must bigger than LENGTH");
DEBUG_ASSERT_MSG(numseq > 0, "NUMSEQ must be positive");
DEBUG_ASSERT_MSG(seqlen <= seqlmax, "lenmax must bigger than length");
DEBUG_ASSERT_MSG(numseq > 0, "numseq must be positive");
double step = (double) (seqlmax-seqlen) / numseq;
@@ -137,19 +138,15 @@ success_t generate_mixture() {
}
success_t generate_gaussian() {
if (!fx_param_exists(NULL, "profile")) {
printf("--profile must be defined.\n");
return SUCCESS_FAIL;
}
const char* profile = fx_param_str_req(NULL, "profile");
const char* profile = fx_param_str_req(NULL, "input_model");
const int seqlen = fx_param_int(NULL, "length", 10);
const int seqlmax = fx_param_int(NULL, "lenmax", seqlen);
const int numseq = fx_param_int(NULL, "numseq", 10);
const char* seqout = fx_param_str(NULL, "seqfile", "seq.gauss.out");
const char* stateout = fx_param_str(NULL, "statefile", "state.gauss.out");
const char* seqout = fx_param_str(NULL, "output_observation_file", "observed.gauss.seq");
const char* stateout = fx_param_str(NULL, "output_state_file", "state.gauss.seq");
DEBUG_ASSERT_MSG(seqlen <= seqlmax, "LENMAX must bigger than LENGTH");
DEBUG_ASSERT_MSG(numseq > 0, "NUMSEQ must be positive");
DEBUG_ASSERT_MSG(seqlen <= seqlmax, "lenmax must bigger than length");
DEBUG_ASSERT_MSG(numseq > 0, "numseq must be positive");
double step = (double) (seqlmax-seqlen) / numseq;
@@ -184,19 +181,15 @@ success_t generate_gaussian() {
}
success_t generate_discrete() {
if (!fx_param_exists(NULL, "profile")) {
printf("--profile must be defined.\n");
return SUCCESS_FAIL;
}
const char* profile = fx_param_str_req(NULL, "profile");
const char* profile = fx_param_str_req(NULL, "input_model");
const int seqlen = fx_param_int(NULL, "length", 10);
const int seqlmax = fx_param_int(NULL, "lenmax", seqlen);
const int numseq = fx_param_int(NULL, "numseq", 10);
const char* seqout = fx_param_str(NULL, "seqfile", "seq.out");
const char* stateout = fx_param_str(NULL, "statefile", "state.out");
const char* seqout = fx_param_str(NULL, "output_observation_file", "observed.dis.out");
const char* stateout = fx_param_str(NULL, "output_state_file", "state.dis.out");
DEBUG_ASSERT_MSG(seqlen <= seqlmax, "LENMAX must bigger than LENGTH");
DEBUG_ASSERT_MSG(numseq > 0, "NUMSEQ must be positive");
DEBUG_ASSERT_MSG(seqlen <= seqlmax, "lenmax must bigger than length");
DEBUG_ASSERT_MSG(numseq > 0, "numseq must be positive");
double step = (double) (seqlmax-seqlen) / numseq;