xmlwriter.c

来自「General Hidden Markov Model Library 一个通用」· C语言 代码 · 共 1,065 行 · 第 1/3 页

/* 	goto STOP; */
/*       } */
    }
  }

  /* writing class label */
  if (f->model.d[moNo]->model_type & GHMM_kLabeledStates) {
    cLabel = f->model.d[moNo]->label[sNo];
    rc = xmlTextWriterWriteFormatElement(writer, BAD_CAST "class", "%d", cLabel);
    if (rc<0) {
      GHMM_LOG(LERROR, "failed to write class label");
      goto STOP;
    }
  }
  
  /* duration (not implemented yet, maybe never */
#if 0
  if (f->model.d[moNo]->model_type & GHMM_kDurations) {
    if (f->model.d[moNo]->duration[sNo] > 0) {
      rc = xmlTextWriterWriteElement(writer, BAD_CAST "duration",
				     BAD_CAST f->model.d[moNo]->duration[sNo]);
      if (rc<0) {
	GHMM_LOG(LERROR, "Error at xmlTextWriterWriteElement (duration)");
	goto STOP;
      }
    }
  }
#endif

  /* writing positions */
  if ((f->model.d[moNo]->s[sNo].xPosition > 0)
      && (f->model.d[moNo]->s[sNo].xPosition > 0)) {
    if (xmlTextWriterStartElement(writer, BAD_CAST "position") < 0) {
      GHMM_LOG(LERROR, "failed to start position element (position)"); goto STOP;}
    if (0 > xmlTextWriterWriteFormatAttribute(writer, BAD_CAST "x", "%d",
					  f->model.d[moNo]->s[sNo].xPosition)) {
      GHMM_LOG(LERROR, "failed to write x position"); goto STOP;}
    if (0 > xmlTextWriterWriteFormatAttribute(writer, BAD_CAST "y", "%d",
					  f->model.d[moNo]->s[sNo].yPosition)) {
      GHMM_LOG(LERROR, "failed to write y position"); goto STOP;}
    if (xmlTextWriterEndElement(writer) < 0) {
      GHMM_LOG(LERROR, "Error at xmlTextWriterEndElement (position)"); goto STOP;}
  }


  /* writing tied states */
  if (f->model.d[moNo]->model_type & GHMM_kTiedEmissions) {
    tied = f->model.d[moNo]->tied_to[sNo];
    if (tied != GHMM_kUntied) {
      rc = xmlTextWriterWriteFormatElement(writer, BAD_CAST "tiedTo", "%d", tied);
      if (rc<0) {
	GHMM_LOG(LERROR, "failed to write tiedTo element");
	goto STOP;
      }
    }
  }

  return 0;
STOP:
  return -1;
#undef CUR_PROC
}

/* ========================================================================= */
static int writeDiscreteSwitchingStateContents(xmlTextWriterPtr writer,
					       ghmm_xmlfile* f, int moNo,
					       int sNo) {
#define CUR_PROC "writeDiscreteSwitchingStateContents"

  int bgId, cLabel, rc, order, tied;
  char * tmp=NULL;

  /* writing discrete distribution */
  if (0 > xmlTextWriterStartElement(writer, BAD_CAST "discrete")) {
    GHMM_LOG(LERROR, "Error at xmlTextWriterStartElement (discrete)");
    goto STOP;
  }

  if (0 > xmlTextWriterWriteAttribute(writer, BAD_CAST "id", BAD_CAST "0")) {
    GHMM_LOG(LERROR, "failed to write alphabet id");
    goto STOP;
  }

  if (f->model.ds[moNo]->s[sNo].fix)
    if (0 > xmlTextWriterWriteAttribute(writer, BAD_CAST "fixed", BAD_CAST "1")) {
      GHMM_LOG(LERROR, "failed to write fixed attriute");
      goto STOP;
    }

  if ((f->model.ds[moNo]->model_type & GHMM_kHigherOrderEmissions)
      && f->model.ds[moNo]->order[sNo]) {
    order = f->model.ds[moNo]->order[sNo];
    if (0 > xmlTextWriterWriteFormatAttribute(writer, BAD_CAST "order", "%d", order)) {
      GHMM_LOG(LERROR, "failed to write order attribute for discrete distribution");
      goto STOP;
    }
  } else
    order = 0;

  tmp = doubleArrayToCSV(f->model.ds[moNo]->s[sNo].b, pow(f->model.ds[moNo]->M, order+1));
  if (tmp) {
    if (0 > xmlTextWriterWriteRaw(writer, BAD_CAST tmp)) {
      GHMM_LOG(LERROR, "Error at xmlTextWriterWriteRaw while writing"
	       "discrete distribution CSV");
      m_free(tmp);
      goto STOP;
    }
    m_free(tmp);
  } else {
    GHMM_LOG(LERROR, "converting array to CSV failed for discrete distribution");
    goto STOP;
  }
  
  /* end discrete distribution */
  if (0 > xmlTextWriterEndElement(writer)) {
    GHMM_LOG(LERROR, "Error at xmlTextWriterEndElement (discrete)");
    goto STOP;
  }

  /* writing backgroung key */
  if (f->model.ds[moNo]->model_type & GHMM_kBackgroundDistributions) {
    bgId = f->model.ds[moNo]->background_id[sNo];
    if (bgId != GHMM_kNoBackgroundDistribution) {
      if (f->model.ds[moNo]->bp->name[bgId]) {
	rc = xmlTextWriterWriteElement(writer, BAD_CAST "backgroundKey",
				       BAD_CAST f->model.ds[moNo]->bp->name[bgId]);
	if (rc<0) {
	  GHMM_LOG(LERROR, "Error at xmlTextWriterWriteElement (backgroundKey)");
	  goto STOP;
	}
      } else {
	GHMM_LOG(LERROR, "background name is NULL pointer, invalid model");
	goto STOP;
      }
    }
  }

  /* writing class label */
  if (f->model.ds[moNo]->model_type & GHMM_kLabeledStates) {
    cLabel = f->model.ds[moNo]->label[sNo];
    rc = xmlTextWriterWriteFormatElement(writer, BAD_CAST "class", "%d", cLabel);
    if (rc<0) {
      GHMM_LOG(LERROR, "failed to write class label");
      goto STOP;
    }
  }
  
  /* duration (not implemented yet, maybe never */
#if 0
  if (f->model.ds[moNo]->model_type & GHMM_kDurations) {
    if (f->model.ds[moNo]->duration[sNo] > 0) {
      rc = xmlTextWriterWriteElement(writer, BAD_CAST "duration",
				     BAD_CAST f->model.ds[moNo]->duration[sNo]);
      if (rc<0) {
	GHMM_LOG(LERROR, "Error at xmlTextWriterWriteElement (duration)");
	goto STOP;
      }
    }
  }
#endif

  /* writing positions */
  if ((f->model.ds[moNo]->s[sNo].xPosition > 0)
      && (f->model.ds[moNo]->s[sNo].xPosition > 0)) {
    if (xmlTextWriterStartElement(writer, BAD_CAST "position") < 0) {
      GHMM_LOG(LERROR, "failed to start position element (position)"); goto STOP;}
    if (0 > xmlTextWriterWriteFormatAttribute(writer, BAD_CAST "x", "%d",
					  f->model.ds[moNo]->s[sNo].xPosition)) {
      GHMM_LOG(LERROR, "failed to write x position"); goto STOP;}
    if (0 > xmlTextWriterWriteFormatAttribute(writer, BAD_CAST "y", "%d",
					  f->model.ds[moNo]->s[sNo].yPosition)) {
      GHMM_LOG(LERROR, "failed to write y position"); goto STOP;}
    if (xmlTextWriterEndElement(writer) < 0) {
      GHMM_LOG(LERROR, "Error at xmlTextWriterEndElement (position)"); goto STOP;}
  }


  /* writing tied states */
  if (f->model.ds[moNo]->model_type & GHMM_kTiedEmissions) {
    tied = f->model.ds[moNo]->tied_to[sNo];
    if (tied != GHMM_kUntied) {
      rc = xmlTextWriterWriteFormatElement(writer, BAD_CAST "tiedTo", "%d", tied);
      if (rc<0) {
	GHMM_LOG(LERROR, "failed to write tiedTo element");
	goto STOP;
      }
    }
  }

  return 0;
STOP:
  return -1;
#undef CUR_PROC
}

/* ========================================================================= */
static int writeContinuousStateContents(xmlTextWriterPtr writer, ghmm_xmlfile* f,
				      int moNo, int sNo) {
#define CUR_PROC "writeContinuousStateContents"

  int i;
  int allFixed = 0;
  char * estr; /* needed for WRITE_DOUBLE_ATTRIBUTE macro */

  /* writing continuous distribution */
  if (0 > xmlTextWriterStartElement(writer, BAD_CAST "mixture")) {
    GHMM_LOG(LERROR, "Error at xmlTextWriterStartElement (mixture)");
    goto STOP;
  }

  if (f->model.c[moNo]->s[sNo].fix)
    allFixed = 1;

  for(i=0; i < f->model.c[moNo]->s[sNo].M; i++){
    switch (f->model.c[moNo]->s[sNo].density[i]) {
      case normal:
        if (0 > xmlTextWriterStartElement(writer, BAD_CAST "normal")) {
          GHMM_LOG(LERROR, "Error at xmlTextWriterStartElement (normal)");
          goto STOP;
        }
	WRITE_DOUBLE_ATTRIBUTE(writer, "mean", f->model.c[moNo]->s[sNo].mue[i]);
	WRITE_DOUBLE_ATTRIBUTE(writer, "variance", f->model.c[moNo]->s[sNo].u[i]);
        break;       
      case normal_left:
        if (0 > xmlTextWriterStartElement(writer, BAD_CAST "normalTruncatedLeft")) {
          GHMM_LOG(LERROR, "Error at xmlTextWriterStartElement (normalTruncatedLeft)");
          goto STOP;
        }
	WRITE_DOUBLE_ATTRIBUTE(writer, "mean", f->model.c[moNo]->s[sNo].mue[i]);
	WRITE_DOUBLE_ATTRIBUTE(writer, "variance", f->model.c[moNo]->s[sNo].u[i]);
        WRITE_DOUBLE_ATTRIBUTE(writer, "min", f->model.c[moNo]->s[sNo].a[i]);
        break;
      case normal_right:     
        if (0 > xmlTextWriterStartElement(writer, BAD_CAST "normalTruncatedRight")) {
          GHMM_LOG(LERROR, "Error at xmlTextWriterStartElement (normalTruncatedRight)");
          goto STOP;
        }
	WRITE_DOUBLE_ATTRIBUTE(writer, "mean", f->model.c[moNo]->s[sNo].mue[i]);
	WRITE_DOUBLE_ATTRIBUTE(writer, "variance", f->model.c[moNo]->s[sNo].u[i]);
        WRITE_DOUBLE_ATTRIBUTE(writer, "max", f->model.c[moNo]->s[sNo].a[i]);
        break;
      case uniform:
        if (0 > xmlTextWriterStartElement(writer, BAD_CAST "uniform")) {
          GHMM_LOG(LERROR, "Error at xmlTextWriterStartElement (uniform)");
          goto STOP;
        }
        WRITE_DOUBLE_ATTRIBUTE(writer, "min", f->model.c[moNo]->s[sNo].u[i]);
        WRITE_DOUBLE_ATTRIBUTE(writer, "max", f->model.c[moNo]->s[sNo].mue[i]);
        break;
      default:
        GHMM_LOG_PRINTF(LERROR, LOC, "invalid density %d at position %d", f->model.c[moNo]->s[sNo].density[i], i);
	goto STOP;
    }
  
    /*optional values */ 
    if (allFixed || f->model.c[moNo]->s[sNo].mixture_fix[i]){
      if (0 > xmlTextWriterWriteAttribute(writer, BAD_CAST "fixed", BAD_CAST "1")) {
	GHMM_LOG(LERROR, "failed to set fixed attribute"); 
	goto STOP;
      }
    }
    if (f->model.c[moNo]->s[sNo].M > 1){
      WRITE_DOUBLE_ATTRIBUTE(writer, "prior", f->model.c[moNo]->s[sNo].c[i]);
    }
    if (0 > xmlTextWriterEndElement(writer)) {
      GHMM_LOG(LERROR, "Error at xmlTextWriterEndElement (all densities)");
      goto STOP;
    }
  }

  /* end mixture tag */
  if (0 > xmlTextWriterEndElement(writer)) {
    GHMM_LOG(LERROR, "Error at xmlTextWriterEndElement (mixture)");
    goto STOP;
  }
  
  /* writing positions */
  if ((f->model.c[moNo]->s[sNo].xPosition > 0)
      && (f->model.c[moNo]->s[sNo].yPosition > 0)) {
    if (xmlTextWriterStartElement(writer, BAD_CAST "position") < 0) {
      GHMM_LOG(LERROR, "failed to start position element (position)"); goto STOP;}
    if (0 > xmlTextWriterWriteFormatAttribute(writer, BAD_CAST "x", "%d",
					  f->model.c[moNo]->s[sNo].xPosition)) {
      GHMM_LOG(LERROR, "failed to write x position"); goto STOP;    }
    if (0 > xmlTextWriterWriteFormatAttribute(writer, BAD_CAST "y", "%d",
					  f->model.c[moNo]->s[sNo].yPosition)) {
      GHMM_LOG(LERROR, "failed to write y position"); goto STOP;}
    if (xmlTextWriterEndElement(writer) < 0) {
      GHMM_LOG(LERROR, "Error at xmlTextWriterEndElement (position)"); goto STOP;}
  }

  return 0;
STOP:
  return -1;
#undef CUR_PROC
}


/* ========================================================================= */
static int writeState(xmlTextWriterPtr writer, ghmm_xmlfile* f, int moNo, int sNo) {
#define CUR_PROC "writeState"

  int rc;
  double w_pi;
  unsigned char * w_desc=NULL;
  char * estr; /* needed for WRITE_DOUBLE_ATTRIBUTE macro */

  /* start state */
  if (0 > xmlTextWriterStartElement(writer, BAD_CAST "state")) {
    GHMM_LOG(LERROR, "Error at xmlTextWriterStartElement (state)");
    goto STOP;
  }

  /* write id attribute */
  if (0 > xmlTextWriterWriteFormatAttribute(writer, BAD_CAST "id", "%d", sNo))
    GHMM_LOG(LERROR, "failed to write statte id attribute");

  /* read state attribute from different model types */
  switch (f->modelType & PTR_TYPE_MASK) {
  case GHMM_kDiscreteHMM:
    w_pi = f->model.d[moNo]->s[sNo].pi;
    w_desc = f->model.d[moNo]->s[sNo].desc;
    break;
  case (GHMM_kDiscreteHMM+GHMM_kTransitionClasses):
    w_pi = f->model.ds[moNo]->s[sNo].pi;
    w_desc = f->model.ds[moNo]->s[sNo].desc;
    break;
  case (GHMM_kDiscreteHMM+GHMM_kPairHMM):
  case (GHMM_kDiscreteHMM+GHMM_kPairHMM+GHMM_kTransitionClasses):
    /*
    w_pi = f->model.d[moNo]->s[sNo].pi;
    w_desc = f->model.d[moNo]->s[sNo];
    */
    break;
  case GHMM_kContinuousHMM:
  case (GHMM_kContinuousHMM+GHMM_kTransitionClasses):
    w_pi = f->model.c[moNo]->s[sNo].pi;
    w_desc = f->model.c[moNo]->s[sNo].desc;
    break;
  default:
    GHMM_LOG(LCRITIC, "invalid modelType");}

  /* write initial probability as attribute */
  WRITE_DOUBLE_ATTRIBUTE(writer, "initial", w_pi);

  /* write state description */
  if (w_desc) {
    if (xmlTextWriterWriteAttribute(writer, BAD_CAST "desc", BAD_CAST replaceXMLEntity(w_desc)))
      GHMM_LOG(LERROR, "writing state description failed");
  }

  /* write state contents for different model types */
  switch (f->modelType & PTR_TYPE_MASK) {
  case GHMM_kDiscreteHMM:
    rc = writeDiscreteStateContents(writer, f, moNo, sNo);