C++ H5Gopen函数代码示例

void CheMPS2::DMRG::loadMPS(const std::string name, TensorT ** MPSlocation, bool * isConverged){

   //The hdf5 file
   hid_t file_id = H5Fopen(name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
      
      //Whether the MPS was converged or not
      hid_t group_id = H5Gopen(file_id, "/Convergence", H5P_DEFAULT);
      
         hid_t dataset_id = H5Dopen(group_id, "Converged_yn", H5P_DEFAULT);
         int toRead;
         H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &toRead);
         isConverged[0] = (toRead==0)?false:true;
         H5Dclose(dataset_id);

      H5Gclose(group_id);
      
      //The MPS
      for (int site=0; site<L; site++){
         
         std::stringstream sstream;
         sstream << "/MPS_" << site;
         hid_t group_id3 = H5Gopen(file_id, sstream.str().c_str(), H5P_DEFAULT);
         
            hid_t dataset_id3     = H5Dopen(group_id3, "Values", H5P_DEFAULT);
            H5Dread(dataset_id3, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, MPSlocation[site]->gStorage());
            H5Dclose(dataset_id3);

         H5Gclose(group_id3);
         
      }
      
      
   H5Fclose(file_id);

}

H5Converter::H5Converter(const std::string& h5_fname, const std::string& out_dir) :
  out_dir_(out_dir)
{
  file_id_ = H5Fopen(h5_fname.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
  root_ = H5Gopen(file_id_, "/", H5P_DEFAULT);
  aux_ = H5Gopen(file_id_, "/aux", H5P_DEFAULT);

  // <aux info>
  // read target ids
  read_dataset(aux_, "ids", targ_ids_);
  std::cerr << "[h5dump] number of targets: " << targ_ids_.size() << 
    std::endl;

  n_targs_ = targ_ids_.size();

  read_dataset(aux_, "lengths", lengths_);
  assert( n_targs_ == lengths_.size() );

  read_dataset(aux_, "eff_lengths", eff_lengths_);
  assert( n_targs_ == eff_lengths_.size() );

  // read bootstrap info
  std::vector<int> n_bs_vec;
  read_dataset(aux_, "num_bootstrap", n_bs_vec);
  n_bs_ = n_bs_vec[0];

  std::cerr << "[h5dump] number of bootstraps: " << n_bs_ << std::endl;
  // </aux info>
  if (n_bs_ > 0) {
    bs_ = H5Gopen(file_id_, "/bootstrap", H5P_DEFAULT);
  }

  std::vector<std::string> tmp;
  read_dataset(aux_, "kallisto_version", tmp);
  kal_version_ = tmp[0];
  tmp.clear();
  std::cerr << "[h5dump] kallisto version: " << kal_version_ << std::endl;

  std::vector<int> idx_version;
  read_dataset(aux_, "index_version", idx_version);
  idx_version_ = static_cast<size_t>(idx_version[0]);
  std::cerr << "[h5dump] index version: " << idx_version_ << std::endl;

  read_dataset(aux_, "start_time", tmp);
  start_time_ = tmp[0];
  tmp.clear();
  std::cerr << "[h5dump] start time: " << start_time_ << std::endl;

  read_dataset(aux_, "call", tmp);
  call_ = tmp[0];
  tmp.clear();
  std::cerr << "[h5dump] shell call: " << call_ << std::endl;

  alpha_buf_.resize( n_targs_, 0.0 );
  assert( n_targs_ == alpha_buf_.size() );

  tpm_buf_.resize( n_targs_, 0.0 );
  assert( n_targs_ == tpm_buf_.size() );
}

/*-------------------------------------------------------------------------
 * Function:	test_misc
 *
 * Purpose:	Test miscellaneous group stuff.
 *
 * Return:	Success:	0
 *
 *		Failure:	number of errors
 *
 * Programmer:	Robb Matzke
 *              Tuesday, November 24, 1998
 *
 * Modifications:
 *              Robb Matzke, 2002-03-28
 *              File is opened by parent instead of here.
 *-------------------------------------------------------------------------
 */
static int
test_misc(hid_t file)
{
    hid_t	g1=-1, g2=-1, g3=-1;
    char	comment[64];

    /* Test current working groups */
    TESTING("miscellaneous group tests");

    /* Create initial groups for testing, then close */
    if ((g1=H5Gcreate(file, "test_1a", 0))<0) goto error;
    if ((g2=H5Gcreate(g1, "sub_1", 0))<0) goto error;
    if ((g3=H5Gcreate(file, "test_1b", 0))<0) goto error;
    if (H5Gset_comment(g3, ".", "hello world")<0) goto error;
    if (H5Gclose(g1)<0) goto error;
    if (H5Gclose(g2)<0) goto error;
    if (H5Gclose(g3)<0) goto error;

    /* Open all groups with absolute names to check for exsistence */
    if ((g1=H5Gopen(file, "/test_1a"))<0) goto error;
    if ((g2=H5Gopen(file, "/test_1a/sub_1"))<0) goto error;
    if ((g3=H5Gopen(file, "/test_1b"))<0) goto error;
    if (H5Gget_comment(g3, "././.", sizeof comment, comment)<0) goto error;
    if (strcmp(comment, "hello world")) {
	H5_FAILED();
	puts("    Read the wrong comment string from the group.");
	printf("    got: \"%s\"\n    ans: \"hello world\"\n", comment);
	goto error;
    }
    if (H5Gclose(g1)<0) goto error;
    if (H5Gclose(g2)<0) goto error;
    if (H5Gclose(g3)<0) goto error;

    /* Check that creating groups with no-op names isn't allowed */
    H5E_BEGIN_TRY {
        g1=H5Gcreate(file, "/", 0);
    } H5E_END_TRY
    if(g1 >= 0) goto error;

    H5E_BEGIN_TRY {
        g1=H5Gcreate(file, "./././", 0);
    } H5E_END_TRY
    if(g1 >= 0) goto error;

    PASSED();
    return 0;

 error:
    H5E_BEGIN_TRY {
	H5Gclose(g1);
	H5Gclose(g2);
	H5Gclose(g3);
    } H5E_END_TRY;
    return 1;
}

static void _extract_all_tasks(FILE *fp, hid_t gid_step, hid_t gid_nodes,
		int nnodes, int stepx)
{

	hid_t	gid_tasks, gid_task = 0, gid_node = -1, gid_level = -1;
	H5G_info_t group_info;
	int	ntasks, itx, len, task_id;
	char	task_name[MAX_GROUP_NAME+1];
	char*   node_name;
	char	buf[MAX_GROUP_NAME+1];
	bool hd = true;

	gid_tasks = get_group(gid_step, GRP_TASKS);
	if (gid_tasks < 0)
		fatal("No tasks in step %d", stepx);
	H5Gget_info(gid_tasks, &group_info);
	ntasks = (int) group_info.nlinks;
	if (ntasks <= 0)
		fatal("No tasks in step %d", stepx);

	for (itx = 0; itx<ntasks; itx++) {
		// Get the name of the group.
		len = H5Lget_name_by_idx(gid_tasks, ".", H5_INDEX_NAME,
		                         H5_ITER_INC, itx, buf, MAX_GROUP_NAME,
		                         H5P_DEFAULT);
		if ((len > 0) && (len < MAX_GROUP_NAME)) {
			gid_task = H5Gopen(gid_tasks, buf, H5P_DEFAULT);
			if (gid_task < 0)
				fatal("Failed to open %s", buf);
		} else
			fatal("Illegal task name %s",buf);
		task_id = get_int_attribute(gid_task, ATTR_TASKID);
		node_name = get_string_attribute(gid_task, ATTR_NODENAME);
		sprintf(task_name,"%s_%d", GRP_TASK, task_id);
		gid_node = H5Gopen(gid_nodes, node_name, H5P_DEFAULT);
		if (gid_node < 0)
			fatal("Failed to open %s for Task_%d",
					node_name, task_id);
		gid_level = get_group(gid_node, GRP_SAMPLES);
		if (gid_level < 0)
			fatal("Failed to open group %s for node=%s task=%d",
					GRP_SAMPLES,node_name, task_id);
		_extract_series(fp, stepx, hd, gid_level, node_name, task_name);

		hd = false;
		xfree(node_name);
		H5Gclose(gid_level);
		H5Gclose(gid_node);
		H5Gclose(gid_task);
	}
	H5Gclose(gid_tasks);
}

static void _merge_node_step_data(hid_t fid_job, char* file_name, int nodeIndex,
				  char* node_name, hid_t jgid_nodes,
				  hid_t jgid_tasks)
{
	hid_t	fid_nodestep, jgid_node, nsgid_root, nsgid_node;
	char	*start_time;
	char	group_name[MAX_GROUP_NAME+1];

	jgid_node = H5Gcreate(jgid_nodes, node_name,
			      H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
	if (jgid_node < 0) {
		error("Failed to create group %s",node_name);
		return;
	}
	put_string_attribute(jgid_node, ATTR_NODENAME, node_name);
	// Process node step file
	// Open the file and the node group.
	fid_nodestep = H5Fopen(file_name, H5F_ACC_RDONLY, H5P_DEFAULT);
	if (fid_nodestep < 0) {
		H5Gclose(jgid_node);
		error("Failed to open %s",file_name);
		return;
	}
	nsgid_root = H5Gopen(fid_nodestep,"/", H5P_DEFAULT);
	sprintf(group_name, "/%s_%s", GRP_NODE, node_name);
	nsgid_node = H5Gopen(nsgid_root, group_name, H5P_DEFAULT);
	if (nsgid_node < 0) {
		H5Gclose(fid_nodestep);
		H5Gclose(jgid_node);
		error("Failed to open node group");
		return;;
	}
	start_time = get_string_attribute(nsgid_node,ATTR_STARTTIME);
	if (start_time == NULL) {
		info("No %s attribute", ATTR_STARTTIME);
	} else {
		put_string_attribute(jgid_node, ATTR_STARTTIME, start_time);
		xfree(start_time);
	}
	_merge_node_totals(jgid_node, nsgid_node);
	_merge_task_totals(jgid_tasks, nsgid_node, node_name);
	_merge_series_data(jgid_tasks, jgid_node, nsgid_node);
	H5Gclose(nsgid_node);
	H5Fclose(fid_nodestep);
	H5Gclose(jgid_node);

	if (!params.keepfiles)
		remove(file_name);

	return;
}

/*-------------------------------------------------------------------------
 * Function:    read_new
 *
 * Purpose:     Test reading a file with "new style" (compact) groups
 *
 * Return:      Success:        0
 *
 *              Failure:        -1
 *
 * Programmer:  Quincey Koziol
 *              Monday, October 24, 2005
 *
 *-------------------------------------------------------------------------
 */
static int
read_new(hid_t fapl)
{
    hid_t		fid = (-1);     /* File ID */
    hid_t		gid = (-1);     /* Group ID */
    char       *srcdir = HDgetenv("srcdir"); /*where the src code is located*/
    char       filename[512]="";  /* test file name */

    TESTING("reading new groups");

    /* Generate correct name for test file by prepending the source path */
    if(srcdir && ((HDstrlen(srcdir) + HDstrlen(FILE_NEW_GROUPS) + 1) < sizeof(filename))) {
        HDstrcpy(filename, srcdir);
        HDstrcat(filename, "/");
    }
    HDstrcat(filename, FILE_NEW_GROUPS);

    /* Open file */
    if((fid = H5Fopen(filename, H5F_ACC_RDONLY, fapl)) < 0) TEST_ERROR;

    /* Attempt to open root group */
    if((gid = H5Gopen(fid, "/")) < 0) TEST_ERROR;

    /* Attempt to open new "empty" group (should fail) */
    H5E_BEGIN_TRY {
        if(H5Gopen(gid, "empty") >= 0) TEST_ERROR;
    } H5E_END_TRY;

    /* Attempt to open new group with link messages (should fail) */
    H5E_BEGIN_TRY {
        if(H5Gopen(gid, "links") >= 0) TEST_ERROR;
    } H5E_END_TRY;

    /* Close root group */
    if(H5Gclose(gid) < 0) TEST_ERROR;

    /* Close first file */
    if(H5Fclose(fid)<0) TEST_ERROR;

    PASSED();
    return 0;

error:
    H5E_BEGIN_TRY {
    	H5Gclose(gid);
    	H5Fclose(fid);
    } H5E_END_TRY;
    return 1;
} /* end read_new() */

fast5_raw_scaling fast5_get_channel_params(fast5_file& fh, const std::string& read_id)
{
    // from scrappie
    fast5_raw_scaling scaling = { NAN, NAN, NAN, NAN };

    std::string scaling_path = fh.is_multi_fast5 ? "/read_" + read_id + "/channel_id"
                                                 :  "/UniqueGlobalKey/channel_id";

    hid_t scaling_group = H5Gopen(fh.hdf5_file, scaling_path.c_str(), H5P_DEFAULT);
    if (scaling_group < 0) {
#ifdef DEBUG_FAST5_IO
        fprintf(stderr, "Failed to open group %s\n", scaling_path.c_str());
#endif
        return scaling;
    }

    scaling.digitisation = fast5_read_float_attribute(scaling_group, "digitisation");
    scaling.offset = fast5_read_float_attribute(scaling_group, "offset");
    scaling.range = fast5_read_float_attribute(scaling_group, "range");
    scaling.sample_rate = fast5_read_float_attribute(scaling_group, "sampling_rate");

    H5Gclose(scaling_group);

    return scaling;
}

/*+++++++++++++++++++++++++
.IDENTifer   PYTABLE_open_group
.PURPOSE     Open/Create a group in an exsisting HDF5-file
.INPUT/OUTPUT
  call as    grpID = PYTABLE_open_group( locID, name, sz_hint ); 

     input:
            hid_t   locID  :   HDF5 object id
	    char    name[]  :   name of the group

.RETURNS     A negative value is returned on failure. 
.COMMENTS    none
-------------------------*/
hid_t PYTABLE_open_group( hid_t locID, const char *name )
{
     hid_t   grpID;
/*
 * check if the group exists, if not create it
 */
     H5E_BEGIN_TRY {
	  if ( (grpID = H5Gopen( locID, name, H5P_DEFAULT )) < 0 ) {
	       grpID = H5Gcreate( locID, name, 
				  H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
	       (void) H5LTset_attribute_string( locID, name, "CLASS", 
					        PY_GROUP_CLASS );
	       (void) H5LTset_attribute_string( locID, name, 
						"PYTABLES_FORMAT_VERSION",
						PY_FORMAT_VERSION );
	       (void) H5LTset_attribute_string( locID, name, "TITLE", 
						name );
	       (void) H5LTset_attribute_string( locID, name, "VERSION", 
						PY_GROUP_VERSION );
	  }
     } H5E_END_TRY;
/*
 * return id of the group
 */
     return grpID;
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void DataContainer::ReadDataContainerStructure(hid_t dcArrayGroupId, DataContainerArrayProxy& proxy, QString h5InternalPath)
{
  QList<QString> dataContainers;
  QH5Utilities::getGroupObjects(dcArrayGroupId, H5Utilities::H5Support_GROUP, dataContainers);
  foreach(QString dataContainerName, dataContainers)
  {
    if(__SHOW_DEBUG_MSG__)
    {
      std::cout << "Data Container:" << dataContainerName.toStdString() << std::endl;
    }
    hid_t containerGid = H5Gopen(dcArrayGroupId, dataContainerName.toLatin1().constData(), H5P_DEFAULT);
    if (containerGid < 0)
    {
      continue;
    }
    HDF5ScopedGroupSentinel sentinel(&containerGid, false);
    DataContainerProxy dcProxy(dataContainerName);
    dcProxy.name = dataContainerName;
    dcProxy.flag = Qt::Checked;

    QString h5Path = h5InternalPath + "/" + dataContainerName;
    // Read the Attribute Matricies for this Data Container
    AttributeMatrix::ReadAttributeMatrixStructure(containerGid, dcProxy, h5Path);

    // Insert the DataContainerProxy proxy into the DataContainerArrayProxy
    proxy.dataContainers.insert(dcProxy.name, dcProxy);
  }
}

extern hid_t get_group(hid_t parent, const char *name)
{
    char buf[MAX_GROUP_NAME];
    hsize_t nobj;
    hid_t gid;
    int i, len;
    H5G_info_t group_info;

    if (parent < 0) {
        debug3("PROFILE: parent is not HDF5 object");
        return -1;
    }
    H5Gget_info(parent, &group_info);
    nobj = group_info.nlinks;
    for (i = 0; (nobj>0) && (i<nobj); i++) {
        // Get the name of the group.
        len = H5Lget_name_by_idx(parent, ".", H5_INDEX_NAME,
                                 H5_ITER_INC, i, buf, MAX_GROUP_NAME,
                                 H5P_DEFAULT);
        if ((len > 0) && (len < MAX_GROUP_NAME)) {
            if (strcmp(buf, name) == 0) {
                gid = H5Gopen(parent, name, H5P_DEFAULT);
                if (gid < 0)
                    error("PROFILE: Failed to open %s",
                          name);
                return gid;
            }
        }
    }

    return -1;
}

void MultiChain::record() {
  //h_config = H5Gopen(h_file,"MultiChain");
  typedef Bead::RealType PosType;
  typedef Bead::Buffer_t Buffer_t;

  Buffer_t chain_buffer,bead_buffer;
  (*(this->begin()))->registerData(bead_buffer);

  chain_buffer.rewind();
  copyToBuffer(chain_buffer);

  HDFAttribIO<Buffer_t> mcout(chain_buffer);
  mcout.overwrite(h_config,"state");

  std::deque<Bead*>::iterator bead_it(this->begin());
  std::deque<Bead*>::iterator bead_end(this->end());
  //create the group and increment counter
  char GrpName[128];
  int ibead=0;
  while(bead_it != bead_end) {
    sprintf(GrpName,"bead%04d",ibead);
    hid_t bead_id = H5Gopen(h_config,GrpName);
    bead_buffer.rewind();
    Bead& bead(**bead_it);
    bead.copyToBuffer(bead_buffer);
    HDFAttribIO<Buffer_t> bout(bead_buffer);
    bout.overwrite(bead_id,"state");
    H5Gclose(bead_id);
    ++bead_it;
    ++ibead;
  }
}

int H5Lexists_safe(hid_t base, char *path)
// -----------------------------------------------------------------------------
// The HDF5 specification only allows H5Lexists to be called on an immediate
// child of the current object. However, you may wish to see whether a whole
// relative path exists, returning false if any of the intermediate links are
// not present. This function does that.
// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5L.html#Link-Exists
// -----------------------------------------------------------------------------
{
  hid_t last = base, next;
  char *pch;
  char pathc[2048];
  strcpy(pathc, path);
  pch = strtok(pathc, "/");
  while (pch != NULL) {
    int exists = H5Lexists(last, pch, H5P_DEFAULT);
    if (!exists) {
      if (last != base) H5Gclose(last);
      return 0;
    }
    else {
      next = H5Gopen(last, pch, H5P_DEFAULT);
      if (last != base) H5Gclose(last);
      last = next;
    }
    pch = strtok(NULL, "/");
  }
  if (last != base) H5Gclose(last);
  return 1;
}

static int
scan_for_max_id( FileHandle* file_ptr, mhdf_Status* status )
{
  hid_t group_id;
  herr_t rval;
  
    /* Check for new format, with max_id as attrib of root group */
#if defined(H5Gopen_vers) && H5Gopen_vers > 1  
  group_id = H5Gopen2( file_ptr->hdf_handle, ROOT_GROUP, H5P_DEFAULT );
#else
  group_id = H5Gopen( file_ptr->hdf_handle, ROOT_GROUP );
#endif
  if (group_id < 0)
  {
    mhdf_setFail( status, "Internal error - invalid file.");
    return 0;
  }
  if (mhdf_read_scalar_attrib( group_id, MAX_ID_ATTRIB,
                               H5T_NATIVE_ULONG, &file_ptr->max_id,
                               status ))
  {
    H5Gclose( group_id );
    return 1;
  }
  
    /* Didn't find it, scan the elements group */
  rval = H5Giterate( group_id, ELEMENT_GROUP_NAME, 0, &max_id_iter, &file_ptr->max_id );
  if (rval)
  {
    H5Gclose( group_id );
    mhdf_setFail( status, "Internal error -- invalid file." );
    return 0;
  }
  
    /* Check node table too */
  rval = get_max_id( group_id, NODE_GROUP_NAME, "coordinates", (unsigned long*)(&file_ptr->max_id) );
  if (rval)
  {
    H5Gclose( group_id );
    mhdf_setFail( status, "Internal error -- invalid file." );
    return 0;
  }
  
    /* Check set table, if it exists */
  rval = mhdf_is_in_group( group_id, SET_GROUP_NAME, status );
  if (rval < 1)
  {
    H5Gclose( group_id );
    return !rval;
  }
  rval = get_max_id( group_id, SET_GROUP_NAME, SET_META_NAME, (unsigned long*)(&file_ptr->max_id) );
  H5Gclose( group_id );
  if (rval)
  {
    mhdf_setFail( status, "Internal error -- invalid file." );
    return 0;
  }

  return 1;
}    

void h5_value_doubles(hid_t file_id, char *group, char *name, double **values,
	int *numValues)
{
  int kk;
  hid_t group_id = H5Gopen(file_id, group, H5P_DEFAULT);
  hid_t data_id = H5Dopen(group_id, name, H5P_DEFAULT);
  hid_t data_space = H5Dget_space(data_id);
  int rank = H5Sget_simple_extent_ndims(data_space);
  hsize_t dims[H5S_MAX_RANK], maxdim[H5S_MAX_RANK];
  H5Sget_simple_extent_dims(data_space, dims, maxdim);
  hid_t data_type = H5Dget_type(data_id);
  H5T_class_t data_class = H5Tget_native_type(data_type, H5T_DIR_DEFAULT);
  size_t data_size = H5Tget_size(data_class);  
  hsize_t elements = 1;
  for (kk=0; kk<rank; kk++)
    elements *= dims[kk];
  void *buf = (void *) MALLOC((size_t)(elements*data_size));
  H5Dread(data_id, data_class, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
  *values = buf;
  *numValues = elements;
  H5Tclose(data_type);
  H5Tclose(data_class);
  H5Sclose(data_space);
  H5Dclose(data_id);
  H5Gclose(group_id); 
}

/* write eigen value and eigen vector for (ibnd, ispin) */
void F77_FUNC_(pwhdf_write_band,PWHDF_WRITE_BAND)(const int* ibnd,
    const int* ispin, const double* e,
   const double* eigv, const int* ngtot)
{
  char spinname[16];
  sprintf(spinname,"band%i/spin%i",(*ibnd)-1,(*ispin)-1);
  hid_t h_spin = H5Gopen(h_twist,spinname);
  hsize_t dim=1;
  hid_t dataspace= H5Screate_simple(1, &dim, NULL);
  hid_t dataset= H5Dcreate(h_spin, "eigenvalue", H5T_NATIVE_DOUBLE, dataspace, H5P_DEFAULT);
  hid_t ret = H5Dwrite(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT,e);
  H5Sclose(dataspace);
  H5Dclose(dataset);

  hsize_t dims[2];
  dims[0] = *ngtot;
  dims[1] = 2;
  dataspace  = H5Screate_simple(2, dims, NULL);
  dataset =  H5Dcreate(h_spin, "eigenvector", H5T_NATIVE_DOUBLE, dataspace, H5P_DEFAULT);
  ret = H5Dwrite(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT,eigv);
  H5Sclose(dataspace);
  H5Dclose(dataset);

  H5Gclose(h_spin);
}