Skip to content

Commit

Permalink
Silo/Overlink I/O Units and Labels (#1276)
Browse files Browse the repository at this point in the history
  • Loading branch information
@JustinPrivitera
JustinPrivitera committed May 21, 2024
1 parent 0380138 commit 99f5708
Show file tree
Hide file tree
Showing 4 changed files with 464 additions and 56 deletions.
2 changes: 1 addition & 1 deletion src/libs/blueprint/conduit_blueprint_mesh_matset_xforms.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -588,7 +588,7 @@ walk_uni_buffer_by_element_to_multi_buffer_by_element(
// iterate through matset
for (int elem_id = 0; elem_id < num_elems; elem_id ++)
{
for (int many_id = 0; many_id < o2m_idx.size(elem_id); many_id ++)
for (index_t many_id = 0; many_id < o2m_idx.size(elem_id); many_id ++)
{
index_t data_index = o2m_idx.index(elem_id, many_id);

Expand Down
193 changes: 164 additions & 29 deletions src/libs/relay/conduit_relay_io_silo.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -649,17 +649,18 @@ void
copy_point_coords(const int datatype,
void *coords[3],
int ndims,
int *dims,
const int *dims,
const int coord_sys,
std::vector<const char *> &labels,
Node &node)
{
ndims = ndims < 3 ? ndims : 3;
std::vector<const char *> labels = get_coordset_axis_labels(coord_sys);
labels = get_coordset_axis_labels(coord_sys);
CONDUIT_ASSERT(!(coord_sys == DB_CYLINDRICAL && ndims >= 3),
"Blueprint only supports 2D cylindrical coordinates");
for (int i = 0; i < ndims; i ++)
{
if (coords[i] != NULL)
if (coords[i])
{
if (datatype == DB_DOUBLE)
{
Expand All @@ -681,6 +682,27 @@ copy_point_coords(const int datatype,
}
}

//-----------------------------------------------------------------------------
void
set_units_or_labels(char *units_or_labels[3],
const int ndims,
const std::vector<const char *> &labels,
Node &coordset,
const std::string &units_or_labels_string)
{
for (int i = 0; i < ndims; i ++)
{
if (units_or_labels[i])
{
coordset[units_or_labels_string][labels[i]] = units_or_labels[i];
}
else
{
break;
}
}
}

//-----------------------------------------------------------------------------
void
add_sizes_and_offsets(DBzonelist *zones,
Expand Down Expand Up @@ -1110,21 +1132,31 @@ read_ucdmesh_domain(DBucdmesh *ucdmesh_ptr,
<< mesh_name);
}

Node &coordset = mesh_domain["coordsets"][multimesh_name];

mesh_domain["topologies"][multimesh_name]["coordset"] = multimesh_name;
mesh_domain["coordsets"][multimesh_name]["type"] = "explicit";
mesh_domain["topologies"][multimesh_name]["type"] = "unstructured";
coordset["type"] = "explicit";

// explicit coords
int dims[] = {ucdmesh_ptr->nnodes,
ucdmesh_ptr->nnodes,
ucdmesh_ptr->nnodes};
const int dims[] = {ucdmesh_ptr->nnodes,
ucdmesh_ptr->nnodes,
ucdmesh_ptr->nnodes};

const int ndims = ucdmesh_ptr->ndims;

std::vector<const char *> labels;

detail::copy_point_coords(ucdmesh_ptr->datatype,
ucdmesh_ptr->coords,
ucdmesh_ptr->ndims,
ndims,
dims,
ucdmesh_ptr->coord_sys,
mesh_domain["coordsets"][multimesh_name]["values"]);
labels,
coordset["values"]);

detail::set_units_or_labels(ucdmesh_ptr->units, ndims, labels, coordset, "units");
detail::set_units_or_labels(ucdmesh_ptr->labels, ndims, labels, coordset, "labels");
}

//-----------------------------------------------------------------------------
Expand Down Expand Up @@ -1256,12 +1288,18 @@ read_quadmesh_domain(DBquadmesh *quadmesh_ptr,
}
}

std::vector<const char *> labels;

detail::copy_point_coords(quadmesh_ptr->datatype,
quadmesh_ptr->coords,
ndims,
real_dims,
quadmesh_ptr->coord_sys,
labels,
coords_out["values"]);

detail::set_units_or_labels(quadmesh_ptr->units, ndims, labels, coords_out, "units");
detail::set_units_or_labels(quadmesh_ptr->labels, ndims, labels, coords_out, "labels");
}

//-----------------------------------------------------------------------------
Expand All @@ -1271,19 +1309,28 @@ read_pointmesh_domain(DBpointmesh *pointmesh_ptr,
const std::string &multimesh_name,
Node &mesh_domain)
{
Node &coordset = mesh_domain["coordsets"][multimesh_name];

mesh_domain["topologies"][multimesh_name]["type"] = "points";
mesh_domain["topologies"][multimesh_name]["coordset"] = multimesh_name;
mesh_domain["coordsets"][multimesh_name]["type"] = "explicit";
int dims[] = {pointmesh_ptr->nels,
pointmesh_ptr->nels,
pointmesh_ptr->nels};
coordset["type"] = "explicit";
const int dims[] = {pointmesh_ptr->nels,
pointmesh_ptr->nels,
pointmesh_ptr->nels};

const int ndims = pointmesh_ptr->ndims;
std::vector<const char *> labels;

detail::copy_point_coords(pointmesh_ptr->datatype,
pointmesh_ptr->coords,
pointmesh_ptr->ndims,
ndims,
dims,
DB_CARTESIAN,
mesh_domain["coordsets"][multimesh_name]["values"]);
labels,
coordset["values"]);

detail::set_units_or_labels(pointmesh_ptr->units, ndims, labels, coordset, "units");
detail::set_units_or_labels(pointmesh_ptr->labels, ndims, labels, coordset, "labels");
}

//-----------------------------------------------------------------------------
Expand Down Expand Up @@ -1651,6 +1698,15 @@ read_variable_domain_helper(const T *var_ptr,
intermediate_field["volume_dependent"] = volume_dependent;
}

if (var_ptr->units)
{
intermediate_field["units"] = var_ptr->units;
}
if (var_ptr->label)
{
intermediate_field["label"] = var_ptr->label;
}

// TODO investigate the dims, major_order, and stride for vars. Should match the mesh;
// what to do if it is different? Will I need to walk these arrays differently?

Expand Down Expand Up @@ -2067,7 +2123,7 @@ read_matset_domain(DBfile* matset_domain_file_to_use,
else if (opts_matset_style == "multi_buffer_full")
{
conduit::blueprint::mesh::matset::to_multi_buffer_full(intermediate_matset, matset_out);

// we only need to stash the matset for use in converters later if we need
// a different flavor of matset
matset_field_reconstruction["original_matset"].move(intermediate_matset);
Expand Down Expand Up @@ -3647,6 +3703,31 @@ void silo_write_field(DBfile *dbfile,
comp_vals_ptrs,
comp_name_ptrs);

const std::string units = (n_var.has_child("units") ? n_var["units"].as_string() : "");
const std::string label = (n_var.has_child("label") ? n_var["label"].as_string() : "");

// create optlist
detail::SiloObjectWrapperCheckError<DBoptlist, decltype(&DBFreeOptlist)> optlist{
DBMakeOptlist(1),
&DBFreeOptlist,
"Error freeing optlist."};
CONDUIT_ASSERT(optlist.getSiloObject(), "Error creating optlist");

if (!units.empty())
{
CONDUIT_CHECK_SILO_ERROR(DBAddOption(optlist.getSiloObject(),
DBOPT_UNITS,
const_cast<char *>(units.c_str())),
"error adding units option");
}
if (!label.empty())
{
CONDUIT_CHECK_SILO_ERROR(DBAddOption(optlist.getSiloObject(),
DBOPT_LABEL,
const_cast<char *>(label.c_str())),
"error adding label option");
}

const std::string safe_meshname = (write_overlink ? "MESH" : detail::sanitize_silo_varname(topo_name));
int var_type = DB_INVALID_OBJECT;
int silo_error = 0;
Expand Down Expand Up @@ -3680,7 +3761,7 @@ void silo_write_field(DBfile *dbfile,
mixlen, // length of mixed data arrays
silo_vals_type, // Datatype of the variable
centering, // centering (nodal or zonal)
NULL); // optlist
optlist.getSiloObject()); // optlist
}
else
{
Expand All @@ -3702,7 +3783,7 @@ void silo_write_field(DBfile *dbfile,
mixlen, // length of mixed data arrays
silo_vals_type, // Datatype of the variable
centering, // centering (nodal or zonal)
NULL); // optlist
optlist.getSiloObject()); // optlist
}
}
else
Expand All @@ -3718,7 +3799,7 @@ void silo_write_field(DBfile *dbfile,
mixlen, // length of mixed data arrays
silo_vals_type, // Datatype of the variable
centering, // centering (nodal or zonal)
NULL); // optlist
optlist.getSiloObject()); // optlist
}
}
}
Expand Down Expand Up @@ -3774,7 +3855,7 @@ void silo_write_field(DBfile *dbfile,
mixlen, // length of mixed data arrays
silo_vals_type, // Datatype of the variable
centering, // centering (nodal or zonal)
NULL); // optlist
optlist.getSiloObject()); // optlist
}
else
{
Expand All @@ -3797,7 +3878,7 @@ void silo_write_field(DBfile *dbfile,
mixlen, // length of mixed data arrays
silo_vals_type, // Datatype of the variable
centering, // centering (nodal or zonal)
NULL); // optlist
optlist.getSiloObject()); // optlist
}
}
else
Expand All @@ -3814,7 +3895,7 @@ void silo_write_field(DBfile *dbfile,
mixlen, // length of mixed data arrays
silo_vals_type, // Datatype of the variable
centering, // centering (nodal or zonal)
NULL); // optlist
optlist.getSiloObject()); // optlist
}
}
}
Expand All @@ -3835,7 +3916,7 @@ void silo_write_field(DBfile *dbfile,
comp_vals_ptrs.data(), // data values
num_pts, // Number of elements (points)
silo_vals_type, // Datatype of the variable
NULL); // optlist
optlist.getSiloObject()); // optlist
}
else
{
Expand Down Expand Up @@ -4458,7 +4539,7 @@ void silo_write_topo(const Node &mesh_domain,
CONDUIT_ASSERT(mesh_domain.has_path("coordsets"), "mesh missing: coordsets");

// get this topo's coordset name
std::string coordset_name = n_topo["coordset"].as_string();
const std::string coordset_name = n_topo["coordset"].as_string();

n_mesh_info[topo_name]["coordset"].set(coordset_name);

Expand Down Expand Up @@ -4498,7 +4579,7 @@ void silo_write_topo(const Node &mesh_domain,
}

// get coordsys info
std::string coordsys = conduit::blueprint::mesh::utils::coordset::coordsys(n_coords);
const std::string coordsys = conduit::blueprint::mesh::utils::coordset::coordsys(n_coords);
int silo_coordsys_type = detail::get_coordset_silo_type(coordsys);
std::vector<const char *> silo_coordset_axis_labels = detail::get_coordset_axis_labels(silo_coordsys_type);
// create optlist
Expand All @@ -4507,11 +4588,63 @@ void silo_write_topo(const Node &mesh_domain,
&DBFreeOptlist,
"Error freeing state optlist."};
CONDUIT_ASSERT(optlist.getSiloObject(), "Error creating optlist");
CONDUIT_CHECK_SILO_ERROR( DBAddOption(optlist.getSiloObject(),
DBOPT_COORDSYS,
&silo_coordsys_type),
CONDUIT_CHECK_SILO_ERROR(DBAddOption(optlist.getSiloObject(),
DBOPT_COORDSYS,
&silo_coordsys_type),
"error adding coordsys option");

//
// handle units and labels, if they exist
//

std::vector<std::string> units;
std::vector<std::string> labels;
std::vector<const char *> units_str;
std::vector<const char *> labels_str;

if (n_coords.has_child("units"))
{
auto units_itr = n_coords["units"].children();
while (units_itr.has_next())
{
const Node &n_unit = units_itr.next();
units.emplace_back(n_unit.as_string());
}
}
if (n_coords.has_child("labels"))
{
auto labels_itr = n_coords["labels"].children();
while (labels_itr.has_next())
{
const Node &n_label = labels_itr.next();
labels.emplace_back(n_label.as_string());
}
}
for (const std::string &unit_name : units)
{
units_str.emplace_back(unit_name.c_str());
}
for (const std::string &label_name : labels)
{
labels_str.emplace_back(label_name.c_str());
}
for (int i = 0; i < static_cast<int>(units_str.size()); i ++)
{
const int dbopt = (i == 0 ? DBOPT_XUNITS : (i == 1 ? DBOPT_YUNITS : DBOPT_ZUNITS));
CONDUIT_CHECK_SILO_ERROR(DBAddOption(optlist.getSiloObject(),
dbopt,
static_cast<void *>(const_cast<char *>(units_str[i]))),
"error adding units option");
}
for (int i = 0; i < static_cast<int>(labels_str.size()); i ++)
{
const int dbopt = (i == 0 ? DBOPT_XLABEL : (i == 1 ? DBOPT_YLABEL : DBOPT_ZLABEL));
CONDUIT_CHECK_SILO_ERROR(DBAddOption(optlist.getSiloObject(),
dbopt,
static_cast<void *>(const_cast<char *>(labels_str[i]))),
"error adding labels option");
}

int mesh_type = DB_INVALID_OBJECT;

if (topo_type == "unstructured" ||
Expand Down Expand Up @@ -4729,6 +4862,8 @@ void silo_write_matset(DBfile *dbfile,
int ndims = 1;
const std::string mesh_type = n_mesh_info[topo_name]["type"].as_string();
const int num_elems = n_mesh_info[topo_name]["num_elems"].to_value();
CONDUIT_ASSERT(num_elems == silo_matset_compact["matlist"].dtype().number_of_elements(),
"matset " << matset_name << " must have the same number of elements as its associated topology.");
if (mesh_type == "structured" || mesh_type == "rectilinear" || mesh_type == "uniform")
{
ndims = n_mesh_info[topo_name]["ndims"].as_int();
Expand Down Expand Up @@ -5316,7 +5451,7 @@ write_multimats(DBfile *dbfile,
}

detail::SiloObjectWrapperCheckError<DBoptlist, decltype(&DBFreeOptlist)> optlist{
DBMakeOptlist(1),
DBMakeOptlist(4),
&DBFreeOptlist,
"Error freeing optlist."};
CONDUIT_ASSERT(optlist.getSiloObject(), "Error creating options");
Expand Down

0 comments on commit 99f5708

Please sign in to comment.