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HMM codes

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tqlong
2008-01-18 16:20:44 +00:00
parent 710716fb24
commit 2839a8b920
1 changed files with 119 additions and 18 deletions
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fastlib/u/tqlong/hmm/hmm.cc
+119 -18
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@@ -9,23 +9,64 @@ success_t generate_mode();
success_t loglik_mode();
success_t viterbi_mode();
success_t train_mode();
void usage();
int main(int argc, char* argv[]) {
fx_init(argc, argv);
const char* mode = fx_param_str_req(NULL, "mode");
if (strcmp(mode, "generate") == 0)
generate_mode();
else if (strcmp(mode, "loglik") == 0)
loglik_mode();
else if (strcmp(mode, "viterbi") == 0)
viterbi_mode();
else if (strcmp(mode, "train") == 0)
train_mode();
else
printf("Unrecognized mode: must be: generate | loglik | viterbi | train !!!\n");
success_t s = SUCCESS_PASS;
const char* mode = fx_param_str(NULL, "mode","");
if (fx_param_exists(NULL,"type"))
if (strcmp(mode, "generate") == 0)
s = generate_mode();
else if (strcmp(mode, "loglik") == 0)
s = loglik_mode();
else if (strcmp(mode, "viterbi") == 0)
s = viterbi_mode();
else if (strcmp(mode, "train") == 0)
s = train_mode();
else {
printf("Unrecognized mode: must be: generate | loglik | viterbi | train !!!\n");
s = SUCCESS_FAIL;
}
else {
printf("Unrecognized type: must be: discrete | gaussian | mixture !!!\n");
s = SUCCESS_FAIL;
}
if (!PASSED(s)) usage();
fx_done();
}
void usage() {
printf("\nUsage:\n");
printf(" hmm --mode={generate|loglik|viterbi|train} --type=={discrete|gaussian|mixture} options\n");
printf("MODES\n");
printf("[generate]\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");
printf("[loglik]\n");
printf(" --profile=file : file contains HMM profile\n");
printf(" --seqfile=file : file contains input sequences\n");
printf(" --logfile=file : output file for log-likelihood of the sequences\n");
printf("[viterbi]\n");
printf(" --profile=file : file contains HMM profile\n");
printf(" --seqfile=file : file contains input sequences\n");
printf(" --statefile=file : output file for state sequences\n");
printf("[train]\n");
printf(" --algorithm={baumwelch|viterbi} : algorithm used for training, default Baum-Welch\n");
printf(" --seqfile=file : file contains input sequences\n");
printf(" --guess=file : file contains guess HMM profile\n");
printf(" --numstate=NUM : if no guess profile is specified, at least specify the number of state\n");
printf(" --profile=file : output file for estimated HMM profile\n");
}
success_t train_baumwelch();
success_t train_viterbi();
@@ -37,7 +78,7 @@ success_t train_mode() {
return train_viterbi();
else {
printf("Unrecognized algorithm: must be baumwelch or viterbi !!!\n");
return SUCCESS_PASS;
return SUCCESS_FAIL;
}
}
@@ -55,11 +96,15 @@ success_t viterbi_mode() {
return viterbi_mixture();
else {
printf("Unrecognized type: must be: discrete | gaussian | mixture !!!\n");
return SUCCESS_PASS;
return SUCCESS_FAIL;
}
}
success_t viterbi_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* seqin = fx_param_str(NULL, "seqfile", "seq.mix.out");
const char* stateout = fx_param_str(NULL, "statefile", "state.viterbi.mix.out");
@@ -95,6 +140,10 @@ success_t viterbi_mixture() {
}
success_t viterbi_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* seqin = fx_param_str(NULL, "seqfile", "seq.gauss.out");
const char* stateout = fx_param_str(NULL, "statefile", "state.viterbi.gauss.out");
@@ -141,6 +190,10 @@ success_t viterbi_gaussian() {
}
success_t viterbi_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* seqin = fx_param_str(NULL, "seqfile", "seq.out");
const char* stateout = fx_param_str(NULL, "statefile", "state_viterbi.out");
@@ -186,11 +239,15 @@ success_t loglik_mode() {
return loglik_mixture();
else {
printf("Unrecognized type: must be: discrete | gaussian | mixture !!!\n");
return SUCCESS_PASS;
return SUCCESS_FAIL;
}
}
success_t loglik_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* seqin = fx_param_str(NULL, "seqfile", "seq.mix.out");
const char* logout = fx_param_str(NULL, "logfile", "log.mix.out");
@@ -227,6 +284,10 @@ success_t loglik_mixture() {
}
success_t loglik_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* seqin = fx_param_str(NULL, "seqfile", "seq.gauss.out");
const char* logout = fx_param_str(NULL, "logfile", "log.gauss.out");
@@ -275,6 +336,10 @@ success_t loglik_gaussian() {
}
success_t loglik_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* seqin = fx_param_str(NULL, "seqfile", "seq.out");
const char* logout = fx_param_str(NULL, "logfile", "log.out");
@@ -328,6 +393,10 @@ success_t generate_mode() {
}
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 int seqlen = fx_param_int(NULL, "length", 10);
const int seqlmax = fx_param_int(NULL, "lenmax", seqlen);
@@ -373,6 +442,10 @@ 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 int seqlen = fx_param_int(NULL, "length", 10);
const int seqlmax = fx_param_int(NULL, "lenmax", seqlen);
@@ -418,6 +491,10 @@ 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 int seqlen = fx_param_int(NULL, "length", 10);
const int seqlmax = fx_param_int(NULL, "lenmax", seqlen);
@@ -463,6 +540,10 @@ success_t generate_discrete() {
}
success_t train_baumwelch_mixture() {
if (!fx_param_exists(NULL, "seqfile")) {
printf("--seqfile must be defined.\n");
return SUCCESS_FAIL;
}
Matrix gTR;
ArrayList<MixtureGauss> gMIX;
ArrayList<Matrix> seqs;
@@ -499,6 +580,10 @@ success_t train_baumwelch_mixture() {
}
success_t train_baumwelch_gaussian() {
if (!fx_param_exists(NULL, "seqfile")) {
printf("--seqfile must be defined.\n");
return SUCCESS_FAIL;
}
Matrix gTR;
ArrayList<Vector> gME;
ArrayList<Matrix> gCO;
@@ -531,7 +616,11 @@ success_t train_baumwelch_gaussian() {
}
success_t train_baumwelch_discrete() {
//ArrayList<Matrix> matlst;
if (!fx_param_exists(NULL, "seqfile")) {
printf("--seqfile must be defined.\n");
return SUCCESS_FAIL;
}
Matrix gTR, gEM;
ArrayList<Vector> seqs;
@@ -583,6 +672,10 @@ success_t train_baumwelch_discrete() {
}
success_t train_viterbi_mixture() {
if (!fx_param_exists(NULL, "seqfile")) {
printf("--seqfile must be defined.\n");
return SUCCESS_FAIL;
}
Matrix gTR;
ArrayList<MixtureGauss> gMIX;
ArrayList<Matrix> seqs;
@@ -619,6 +712,10 @@ success_t train_viterbi_mixture() {
}
success_t train_viterbi_gaussian() {
if (!fx_param_exists(NULL, "seqfile")) {
printf("--seqfile must be defined.\n");
return SUCCESS_FAIL;
}
Matrix gTR;
ArrayList<Vector> gME;
ArrayList<Matrix> gCO;
@@ -651,7 +748,11 @@ success_t train_viterbi_gaussian() {
}
success_t train_viterbi_discrete() {
//ArrayList<Matrix> matlst;
if (!fx_param_exists(NULL, "seqfile")) {
printf("--seqfile must be defined.\n");
return SUCCESS_FAIL;
}
Matrix gTR, gEM;
ArrayList<Vector> seqs;
@@ -712,7 +813,7 @@ success_t train_baumwelch() {
return train_baumwelch_mixture();
else {
printf("Unrecognized type: must be: discrete | gaussian | mixture !!!\n");
return SUCCESS_PASS;
return SUCCESS_FAIL;
}
}
@@ -726,6 +827,6 @@ success_t train_viterbi() {
return train_viterbi_mixture();
else {
printf("Unrecognized type: must be: discrete | gaussian | mixture !!!\n");
return SUCCESS_PASS;
return SUCCESS_FAIL;
}
}