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Blueprint index display_name (#18842) (#19247)
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* Enhance Blueprint reader so it supports renaming fields in the index file.

* Make display_name work with HO materials.

* Added a new test that exercises display_name in a Blueprint index file.

* Refine low-order field as needed if it lives on a refined HO mesh.

* Added GetLastMessage to CLI so we can ask what messages VisIt has issued.

* Added a new test

* Change some logic back since ShapeType can have unintuitive results if the topology is not unstructured.

* Remove a warning that pops up a lot.

* Remove a couple changes.

Co-authored-by: Brad Whitlock <whitlock2@llnl.gov>
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@cyrush @BradWhitlock
cyrush and BradWhitlock committed Jan 30, 2024
1 parent 80ad2cc commit ce1d694
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Showing 19 changed files with 390 additions and 106 deletions.
4 changes: 2 additions & 2 deletions data/axom_klee_test_data.tar.xz
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12 changes: 10 additions & 2 deletions src/avt/Pipeline/Data/avtMaterial.C
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@

#include <climits>
#include <cassert>
#include <cmath>

using std::string;
using std::vector;
Expand Down Expand Up @@ -1951,8 +1952,15 @@ avtMaterial::AssertSelfIsValid() const
assert(mix_zone[midx] < nZones+1); // one-origin
midx = mix_next[midx]-1;
}
float const eps = 1.0e-5;
assert(((1-eps) <= vfsum) && (vfsum <= (1+eps)));
constexpr float eps = 1.0e-5;
float vfsum_err = fabs(1.f - vfsum);
if(vfsum_err >= eps)
{
debug5 << "Zone " << z << " vfsum=" << vfsum
<< ", vfsum_err=" << vfsum_err
<< ", which exceeds eps=" << eps << endl;
assert(vfsum_err <= eps);
}
}
}
}
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2 changes: 1 addition & 1 deletion src/common/misc/FileFunctions.h
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Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,6 @@ FileType MISC_API GetFileType(std::string const &filename, struct dirent const *
VisItStat_t *statbuf = 0);

bool MISC_API ReadTextFile(const std::string &filename, std::string &fileContents);
};
} // end namespace FileFunctions

#endif
203 changes: 162 additions & 41 deletions src/databases/Blueprint/avtBlueprintFileFormat.C
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Original file line number Diff line number Diff line change
Expand Up @@ -82,6 +82,8 @@ using std::string;
using namespace conduit;
using namespace mfem;

const std::string avtBlueprintFileFormat::DISPLAY_NAME("display_name");

// ****************************************************************************
// Method: avtBlueprintFileFormat::FetchMeshAndTopoNames
//
Expand Down Expand Up @@ -499,7 +501,69 @@ avtBlueprintFileFormat::ReadBlueprintMesh(int domain,
}

// ****************************************************************************
// Method: avtBlueprintFileFormat::ReadBlueprintMesh
// Method: avtBlueprintFileFormat::GetBlueprintIndexForField
//
// Purpose:
// Returns a node in the Blueprint index for the field that either has the
// supplied name or has a DISPLAY_NAME that matches the supplied name.
//
// Programmer: Brad Whitlock
// Creation: Tue Jul 18 15:57:00 PDT 2023
//
// Modifications:
//
// ****************************************************************************

const Node *
avtBlueprintFileFormat::GetBlueprintIndexForField(const Node &fields,
const string &abs_varname) const
{
const char *mName = "GetBlueprintIndexForField";
BP_PLUGIN_INFO(mName << ": " << abs_varname);
const Node *retval = nullptr;
string varname = FileFunctions::Basename(abs_varname);

if (fields.has_child(varname))
{
BP_PLUGIN_INFO(mName << ": found " << varname);
retval = fields.fetch_ptr(varname);
}
else
{
// We may have been given a display name for the variable as opposed
// to its real name. See if we can find that.
BP_PLUGIN_INFO(mName << ": checking fields for a display name.");
for(conduit::index_t i = 0; i < fields.number_of_children(); i++)
{
const Node *f = fields.child_ptr(i);
BP_PLUGIN_INFO(mName << ": checking field " << f->name() << ".");
if(f->has_child(DISPLAY_NAME))
{
std::string dn = f->fetch_existing(DISPLAY_NAME).as_string();
if(dn == abs_varname)
{
BP_PLUGIN_INFO(mName << ": " << f->name() << " matched based on "
<< DISPLAY_NAME << " " << dn);
retval = f;
break;
}
}
}

// only throw an error if element_coloring is not in the name
// element_coloring won't be in the index, its automatic.
if(retval == nullptr &&
varname.find("element_coloring") == std::string::npos)
{
BP_PLUGIN_EXCEPTION1(InvalidVariableException,
"field " << varname << " not found in blueprint index");
}
}
return retval;
}

// ****************************************************************************
// Method: avtBlueprintFileFormat::ReadBlueprintField
//
// Purpose:
// Reads a field for the given domain into the `out` conduit Node.
Expand All @@ -521,6 +585,9 @@ avtBlueprintFileFormat::ReadBlueprintMesh(int domain,
// Justin Privitera, Thu Oct 26 12:26:32 PDT 2023
// Fixed warnings.
//
// Brad Whitlock, Tue Jul 18 16:02:13 PDT 2023
// Locate the index node for the variable using GetBlueprintIndexField.
//
// ****************************************************************************

void
Expand Down Expand Up @@ -553,31 +620,22 @@ avtBlueprintFileFormat::ReadBlueprintField(int domain,
BP_PLUGIN_INFO("mesh name: " << mesh_name);
BP_PLUGIN_INFO("topo name: " << topo_name);

string varname = FileFunctions::Basename(abs_varname);

if (!m_root_node["blueprint_index"].has_child(mesh_name))
{
BP_PLUGIN_EXCEPTION1(InvalidVariableException,
"mesh " << mesh_name << " not found in blueprint index");
}

if (!m_root_node["blueprint_index"][mesh_name]["fields"].has_child(varname))
// Look up the index node for the field.
const Node &fields = m_root_node["blueprint_index"][mesh_name]["fields"];
const Node *bp_index_field = GetBlueprintIndexForField(fields, abs_varname);
std::string data_path;
if(bp_index_field != nullptr)
{
// only throw an error if element_coloring is not in the name
// element_coloring won't be in the index, its automatic.
if(varname.find("element_coloring") == std::string::npos)
{
BP_PLUGIN_EXCEPTION1(InvalidVariableException,
"field " << varname << " not found in blueprint index");
}
BP_PLUGIN_INFO(bp_index_field->to_yaml());
data_path = bp_index_field->fetch_existing("path").as_string();
}

const Node &bp_index_field = m_root_node["blueprint_index"][mesh_name]["fields"][varname];
BP_PLUGIN_INFO(bp_index_field.to_yaml());

string topo_tag = bp_index_field["topology"].as_string();
string data_path = bp_index_field["path"].as_string();

try
{
m_tree_cache->FetchBlueprintTree(domain,
Expand Down Expand Up @@ -694,6 +752,9 @@ avtBlueprintFileFormat::DetectHOMaterial(const std::string &mesh_name,
// Justin Privitera, Thu Oct 26 12:26:32 PDT 2023
// Fixed warnings.
//
// Brad Whitlock, Wed Jul 19 13:56:42 PDT 2023
// I added display_name support.
//
// ****************************************************************************

void
Expand Down Expand Up @@ -767,6 +828,11 @@ avtBlueprintFileFormat::ReadBlueprintMatset(int domain,
{
// Make a variable name for the volume fraction field and read it.
std::string matVar = mesh_name + "_" + topo_name + "/" + it->second;
// If there is a display_name, use that to request the data.
const Node &bp_idx_fields = m_root_node["blueprint_index"][mesh_name]["fields"];
const Node *bpi = GetBlueprintIndexForField(bp_idx_fields, it->second);
if(bpi != nullptr && bpi->has_child(DISPLAY_NAME))
matVar = bpi->fetch_existing(DISPLAY_NAME).as_string();
vtkDataArray *da = GetVar(domain, matVar.c_str());

// Save the material field as float into the new out node.
Expand Down Expand Up @@ -1048,9 +1114,19 @@ avtBlueprintFileFormat::AddBlueprintMeshAndFieldMetadata(avtDatabaseMetaData *md
string var_mesh_name = mesh_name + "_" + var_topo_name;
string varname_wmesh = var_mesh_name + "/" + varname;

// Make the variable name that the user sees.
string varname_display(varname_wmesh);
if(n_field.has_child(DISPLAY_NAME))
{
varname_display = n_field[DISPLAY_NAME].as_string();
BP_PLUGIN_INFO("Field \"" << varname
<< "\" is being exposed as \""
<< varname_display << "\".");
}

if (topo_dims[var_topo_name] == 0)
{
BP_PLUGIN_WARNING("Field \"" << varname_wmesh
BP_PLUGIN_WARNING("Field \"" << varname_display
<< "\" defined on unknown topology=\""
<< n_field["topology"].as_string());
continue;
Expand Down Expand Up @@ -1097,7 +1173,6 @@ avtBlueprintFileFormat::AddBlueprintMeshAndFieldMetadata(avtDatabaseMetaData *md
}
else
node_centered = h1 && !l2;

if (!node_centered)
cent = AVT_ZONECENT;
}
Expand All @@ -1106,27 +1181,27 @@ avtBlueprintFileFormat::AddBlueprintMeshAndFieldMetadata(avtDatabaseMetaData *md
// special 1D case
if (ndims == 1)
{
m_curve_names.insert(varname_wmesh);
m_curve_names.insert(varname_display);
avtCurveMetaData *curve = new avtCurveMetaData;
curve->name = varname_wmesh;
curve->name = varname_display;
md->Add(curve);
}
else if (ncomps == 1)
md->Add(new avtScalarMetaData(varname_wmesh, var_mesh_name, cent));
md->Add(new avtScalarMetaData(varname_display, var_mesh_name, cent));
else if (ndims == 2 && ncomps == 2)
md->Add(new avtVectorMetaData(varname_wmesh, var_mesh_name, cent, ncomps));
md->Add(new avtVectorMetaData(varname_display, var_mesh_name, cent, ncomps));
else if (ndims == 2 && ncomps == 3)
md->Add(new avtSymmetricTensorMetaData(varname_wmesh, var_mesh_name, cent, ncomps));
md->Add(new avtSymmetricTensorMetaData(varname_display, var_mesh_name, cent, ncomps));
else if (ndims == 2 && ncomps == 4)
md->Add(new avtTensorMetaData(varname_wmesh, var_mesh_name, cent, ncomps));
md->Add(new avtTensorMetaData(varname_display, var_mesh_name, cent, ncomps));
else if (ndims == 3 && ncomps == 3)
md->Add(new avtVectorMetaData(varname_wmesh, var_mesh_name, cent, ncomps));
md->Add(new avtVectorMetaData(varname_display, var_mesh_name, cent, ncomps));
else if (ndims == 3 && ncomps == 6)
md->Add(new avtSymmetricTensorMetaData(varname_wmesh, var_mesh_name, cent, ncomps));
md->Add(new avtSymmetricTensorMetaData(varname_display, var_mesh_name, cent, ncomps));
else if (ndims == 3 && ncomps == 9)
md->Add(new avtTensorMetaData(varname_wmesh, var_mesh_name, cent, ncomps));
md->Add(new avtTensorMetaData(varname_display, var_mesh_name, cent, ncomps));
else
md->Add(new avtArrayMetaData(varname_wmesh, var_mesh_name, cent, ncomps));
md->Add(new avtArrayMetaData(varname_display, var_mesh_name, cent, ncomps));
}
}
}
Expand Down Expand Up @@ -1155,8 +1230,10 @@ avtBlueprintFileFormat::AddBlueprintMaterialsMetadata(avtDatabaseMetaData *md,
const Node &n_mesh_info)
{
if (!n_mesh_info.has_child("matsets"))
{
BP_PLUGIN_INFO("Input data file has no matsets.");
return;

}
BP_PLUGIN_INFO("adding materials for " << mesh_name);

NodeConstIterator msets_itr = n_mesh_info["matsets"].children();
Expand Down Expand Up @@ -2070,15 +2147,20 @@ avtBlueprintFileFormat::GetMesh(int domain, const char *abs_meshname)
// `m_new_refine` is passed to `RefineGridFunctionToVTK` so it can choose
// the appropriate MFEM LOR scheme.
//
// Justin Privitera, Wed Aug 24 11:08:51 PDT 2022
// Encased in try-catch block.
// Justin Privitera, Wed Aug 24 11:08:51 PDT 2022
// Encased in try-catch block.
//
// Justin Privitera, Tue Aug 23 14:40:24 PDT 2022
// Removed `CONDUIT_HAVE_PARTITION_FLATTEN` check.
//
// Justin Privitera, Thu Oct 26 12:26:32 PDT 2023
// Fixed warnings.
//
// Justin Privitera, Thu Oct 26 12:26:32 PDT 2023
// Fixed warnings.
//
// Brad Whitlock, Tue Dec 19 14:45:13 PST 2023
// Add MFEM refinement for certain fields that are low-order but live on a
// mesh that has been refined. This prevents the field from having too few
// values for the refined mesh.
//
// ****************************************************************************

vtkDataArray *
Expand Down Expand Up @@ -2143,6 +2225,7 @@ avtBlueprintFileFormat::GetVar(int domain, const char *abs_varname)
Node *field_ptr = &n_field;

ReadBlueprintField(domain,abs_varname_str,*field_ptr);

// check for empty field case
if(field_ptr->dtype().is_empty())
{
Expand Down Expand Up @@ -2199,11 +2282,14 @@ avtBlueprintFileFormat::GetVar(int domain, const char *abs_varname)
BP_PLUGIN_INFO("topo name: " << topo_name);

const Node &n_topo = n_mesh["topologies/" + topo_name];

int tdims = -1;
if (n_topo.has_path("elements/shape"))
{
if (n_topo["elements/shape"].as_string() == "polyhedral" ||
n_topo["elements/shape"].as_string() == "polygonal")
// Get the shape's topological dimension.
conduit::blueprint::mesh::utils::ShapeType shape(n_topo);
tdims = shape.dim;

if (shape.is_polygonal() || shape.is_polyhedral())
{
string field_name, coords_name;
// get name of coordset from topology
Expand All @@ -2230,9 +2316,44 @@ avtBlueprintFileFormat::GetVar(int domain, const char *abs_varname)
}
}

// low-order case, use vtk
res = avtConduitBlueprintDataAdaptor::BlueprintToVTK::FieldToVTK(n_topo,
*field_ptr);
// Check whether the data need to be refined anyway.
const bool meshIsHO = n_mesh.has_path("topologies/" + topo_name + "/grid_function");
if(meshIsHO && (tdims >= 2) && ((m_selected_lod+1) > 1))
{
// The field data are low-order but need to be refined anyway since
// the mesh got refined.

// Wrap as HO-compatible field.
conduit::Node fieldHO;
fieldHO["topology"] = topo_name;
if(field_ptr->fetch_existing("association").as_string() == "element")
fieldHO["basis"] = (tdims == 2) ? "L2_T2_2D_P0" : "L2_T2_3D_P0";
else
fieldHO["basis"] = (tdims == 2) ? "H1_2D_P1" : "H1_3D_P1";
fieldHO["values"].set_external(field_ptr->fetch_existing("values"));

// create an mfem mesh
mfem::Mesh *mesh = avtConduitBlueprintDataAdaptor::BlueprintToMFEM::MeshToMFEM(n_mesh);

// create the grid fuction
mfem::GridFunction *gf = avtConduitBlueprintDataAdaptor::BlueprintToMFEM::FieldToMFEM(mesh,
fieldHO);
// refine the grid function into a vtk data array
res = avtMFEMDataAdaptor::RefineGridFunctionToVTK(mesh,
gf,
m_selected_lod+1,
m_new_refine);

// cleanup mfem data
delete gf;
delete mesh;
}
else
{
// low-order case, use vtk
res = avtConduitBlueprintDataAdaptor::BlueprintToVTK::FieldToVTK(n_topo,
*field_ptr);
}
}
// if we have a basis, this field is actually an mfem grid function
else if(field_ptr->has_child("basis"))
Expand Down
3 changes: 3 additions & 0 deletions src/databases/Blueprint/avtBlueprintFileFormat.h
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Original file line number Diff line number Diff line change
Expand Up @@ -104,6 +104,7 @@ class avtBlueprintFileFormat : public avtSTMDFileFormat
{ return false; }

private:
static const std::string DISPLAY_NAME;

void AddBlueprintMeshAndFieldMetadata(avtDatabaseMetaData *md,
std::string const &mesh_name,
Expand Down Expand Up @@ -145,6 +146,8 @@ class avtBlueprintFileFormat : public avtSTMDFileFormat

avtMaterial *GetMaterial(int domain, const char *mat_name);

const conduit::Node *GetBlueprintIndexForField(const conduit::Node &fields,
const std::string &abs_varname) const;

conduit::Node m_root_node;

Expand Down

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