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Silo/Overlink I/O Units and Labels #1276

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merged 10 commits into from
May 21, 2024
Merged

Silo/Overlink I/O Units and Labels #1276

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4e1e2a1
meshes are done
JustinPrivitera Apr 24, 2024
1f16e79
added another test
JustinPrivitera Apr 24, 2024
23c64f3
I need git to save me
JustinPrivitera Apr 24, 2024
9113d51
fields is done but no tests
JustinPrivitera Apr 24, 2024
e369c3f
round trip test for field units and label
JustinPrivitera Apr 29, 2024
78d8421
scary
JustinPrivitera Apr 30, 2024
ee9133d
merge
JustinPrivitera Apr 30, 2024
1a1a6b5
merge better
JustinPrivitera Apr 30, 2024
bce30b1
sorry
JustinPrivitera Apr 30, 2024
1567117
fix todo
JustinPrivitera Apr 30, 2024
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2 changes: 1 addition & 1 deletion src/libs/blueprint/conduit_blueprint_mesh_matset_xforms.cpp
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Open in desktop
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
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Open in desktop
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
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