Merge pull request #1600 from LLNL/feature/kweiss/improve-shaping-logging

Improves some logging calls during shaping

Author: kennyweiss

src/axom/bump/docs/sphinx/bump_utilities.rst

@@ -119,7 +119,7 @@ new explicit coordset where each point corresponds to a single index from the no
 stored in SliceData. This class can be used to select a subset of a coordset, reorder nodes
 in a coordset, or repeat nodes in a coordset.
 
-.. literalinclude:: ../../utilities/ExtractZones.hpp
+.. literalinclude:: ../../ExtractZones.hpp
    :start-after: _bump_utilities_coordsetslicer_begin
    :end-before: _bump_utilities_coordsetslicer_end
    :language: C++
@@ -132,7 +132,7 @@ The ``axom::bump::ExtractZones`` class takes a list of selected zone ids and ext
 a new mesh from a source mesh that includes only the selected zones. There is a derived class
 ``ExtractZonesAndMatset`` that also extracts a matset, if present.
 
-.. literalinclude:: ../../utilities/ExtractZones.hpp
+.. literalinclude:: ../../ExtractZones.hpp
    :start-after: _bump_utilities_extractzones_begin
    :end-before: _bump_utilities_extractzones_end
    :language: C++
@@ -206,7 +206,7 @@ The ``axom::bump::MakeUnstructured`` class takes a structured topology
 and creates a new unstructured topology. This class does not need views to wrap the input
 structured topology.
 
-.. literalinclude:: ../../tests/bump_blueprint_utilities.cpp
+.. literalinclude:: ../../tests/bump_mesh_operations.cpp
    :start-after: _bump_utilities_makeunstructured_begin
    :end-before: _bump_utilities_makeunstructured_end
    :language: C++
@@ -243,7 +243,7 @@ The ``axom::bump::MatsetSlicer`` class is similar to the ``FieldSlicer``
 class except it slices matsets instead of fields. The same ``SliceData`` can be passed to
 MatsetSlicer to pull out and assemble a new matset data for a specific list of zones.
 
-.. literalinclude:: ../../utilities/ExtractZones.hpp
+.. literalinclude:: ../../ExtractZones.hpp
    :start-after: _bump_utilities_matsetslicer_begin
    :end-before: _bump_utilities_matsetslicer_end
    :language: C++
@@ -339,7 +339,7 @@ also expose polyhedra as a special ``PolyhedralFaces`` representation that repre
 polyhedron as a collection of ``axom::primal::Plane`` objects. This mode is selected by
 instantiating ``PrimalAdaptor`` with the ``makeFaces`` template parameter set to true.
 
-.. literalinclude:: ../../utilities/MakeZoneVolumes.hpp
+.. literalinclude:: ../../MakeZoneVolumes.hpp
    :start-after: _bump_utilities_makezonevolumes_begin
    :end-before: _bump_utilities_makezonevolumes_end
    :language: C++
@@ -353,7 +353,7 @@ The ``axom::bump::RecenterField`` class uses an O2M relation to average
 field data from multiple values to an averaged value. In Axom, this is used to convert a field
 associated with the elements to a new field associated with the nodes.
 
-.. literalinclude:: ../../tests/bump_blueprint_utilities.cpp
+.. literalinclude:: ../../tests/bump_mesh_operations.cpp
    :start-after: _bump_utilities_recenterfield_begin
    :end-before: _bump_utilities_recenterfield_end
    :language: C++
@@ -389,7 +389,7 @@ intersected with the zones in the target mesh and their overlaps are determined
 used to build a new matset on the target mesh. Each zone in the target mesh may recieve
 contributions from multiple zones and materials in the source mesh.
 
-.. literalinclude:: ../../tests/mir_topology_mapper.cpp
+.. literalinclude:: ../../tests/bump_topology_mapper.cpp
    :start-after: _bump_utilities_topologymapper_begin
    :end-before: _bump_utilities_topologymapper_end
    :language: C++
@@ -404,7 +404,7 @@ sorted list of unique outputs, along with a list of offsets into the original va
 one representative value in the original list for each unique value. This class is used to help
 merge points.
 
-.. literalinclude:: ../../tests/mir_clipfield.cpp
+.. literalinclude:: ../../tests/bump_clipfield.cpp
    :start-after: _bump_utilities_unique_begin
    :end-before: _bump_utilities_unique_end
    :language: C++

src/axom/bump/docs/sphinx/index.rst

@@ -3,7 +3,6 @@
 .. ##
 .. ## SPDX-License-Identifier: (BSD-3-Clause)
 
-=======================
 BUMP User Documentation
 =======================
 
@@ -18,7 +17,6 @@ API Documentation
 
 Doxygen generated API documentation can be found here: `API documentation <../../../../doxygen/html/coretop.html>`_
 
-
 .. toctree::
    :caption: Contents
    :maxdepth: 1

src/axom/quest/DiscreteShape.cpp

@@ -54,12 +54,12 @@ class AffineMatrixVisitor : public klee::GeometryOperatorVisitor
 
   void visit(const klee::CompositeOperator&) override
   {
-    SLIC_WARNING("CompositeOperator not supported for Shaper query");
+    SLIC_WARNING_ROOT("CompositeOperator not supported for Shaper query");
     m_isValid = false;
   }
   void visit(const klee::SliceOperator&) override
   {
-    SLIC_WARNING("SliceOperator not yet supported for Shaper query");
+    SLIC_WARNING_ROOT("SliceOperator not yet supported for Shaper query");
     m_isValid = false;
   }
 
@@ -145,9 +145,9 @@ std::shared_ptr<mint::Mesh> DiscreteShape::createMeshRepresentation()
   if(!m_shape.getGeometry().hasGeometry())
   {
     // If shape has no geometry, there's nothing to discretize.
-    SLIC_DEBUG(axom::fmt::format("Current shape '{}' of material '{}' has no geometry",
-                                 m_shape.getName(),
-                                 m_shape.getMaterial()));
+    SLIC_DEBUG_ROOT(axom::fmt::format("Current shape '{}' of material '{}' has no geometry",
+                                      m_shape.getName(),
+                                      m_shape.getMaterial()));
     return m_meshRep;
   }
 
@@ -163,8 +163,8 @@ std::shared_ptr<mint::Mesh> DiscreteShape::createMeshRepresentation()
 
   if(utilities::string::endsWith(shapePath, ".stl"))
   {
-    SLIC_ASSERT_MSG(file_format == "stl",
-                    axom::fmt::format(" '{}' format requires .stl file type", file_format));
+    SLIC_ERROR_ROOT_IF(file_format != "stl",
+                       axom::fmt::format(" '{}' format requires .stl file type", file_format));
 
     axom::mint::Mesh* meshRep = nullptr;
 #ifdef AXOM_USE_MPI
@@ -178,8 +178,8 @@ std::shared_ptr<mint::Mesh> DiscreteShape::createMeshRepresentation()
   }
   else if(utilities::string::endsWith(shapePath, ".proe"))
   {
-    SLIC_ASSERT_MSG(file_format == "proe",
-                    axom::fmt::format(" '{}' format requires .proe file type", file_format));
+    SLIC_ERROR_ROOT_IF(file_format != "proe",
+                       axom::fmt::format(" '{}' format requires .proe file type", file_format));
 
     axom::mint::Mesh* meshRep = nullptr;
 #ifdef AXOM_USE_MPI
@@ -192,8 +192,8 @@ std::shared_ptr<mint::Mesh> DiscreteShape::createMeshRepresentation()
 #ifdef AXOM_USE_C2C
   else if(utilities::string::endsWith(shapePath, ".contour"))
   {
-    SLIC_ASSERT_MSG(file_format == "c2c",
-                    axom::fmt::format(" '{}' format requires .contour file type", file_format));
+    SLIC_ERROR_ROOT_IF(file_format != "c2c",
+                       axom::fmt::format(" '{}' format requires .contour file type", file_format));
 
     // Get the transforms that are being applied to the mesh. Get them
     // as a single concatenated matrix.
@@ -230,7 +230,7 @@ std::shared_ptr<mint::Mesh> DiscreteShape::createMeshRepresentation()
 #endif
   else
   {
-    SLIC_ERROR(
+    SLIC_ERROR_ROOT(
       axom::fmt::format("Unsupported filetype for this Axom configuration. "
                         "Provided file was '{}', with format '{}'",
                         shapePath,
@@ -716,7 +716,7 @@ numerics::Matrix<double> DiscreteShape::sorAxisRotMatrix(const Vector3D& dir)
 void DiscreteShape::setSamplesPerKnotSpan(int nSamples)
 {
   using axom::utilities::clampLower;
-  SLIC_WARNING_IF(
+  SLIC_WARNING_ROOT_IF(
     nSamples < 1,
     axom::fmt::format("Samples per knot span must be at least 1. Provided value was {}", nSamples));
 
@@ -725,25 +725,26 @@ void DiscreteShape::setSamplesPerKnotSpan(int nSamples)
 
 void DiscreteShape::setVertexWeldThreshold(double threshold)
 {
-  SLIC_WARNING_IF(
+  SLIC_WARNING_ROOT_IF(
     threshold <= 0.,
-    axom::fmt::format("Vertex weld threshold should be positive Provided value was {}", threshold));
+    axom::fmt::format("Vertex weld threshold should be positive. Provided value was {}", threshold));
 
   m_vertexWeldThreshold = threshold;
 }
 
 void DiscreteShape::setPercentError(double percent)
 {
   using axom::utilities::clampVal;
-  SLIC_WARNING_IF(percent <= MINIMUM_PERCENT_ERROR,
-                  axom::fmt::format("Percent error must be greater than {}. Provided value "
-                                    "was {}. Dynamic refinement will not be used.",
-                                    MINIMUM_PERCENT_ERROR,
-                                    percent));
-  SLIC_WARNING_IF(percent > MAXIMUM_PERCENT_ERROR,
-                  axom::fmt::format("Percent error must be less than {}. Provided value was {}",
-                                    MAXIMUM_PERCENT_ERROR,
-                                    percent));
+  SLIC_WARNING_ROOT_IF(percent <= MINIMUM_PERCENT_ERROR,
+                       axom::fmt::format("Percent error must be greater than {}. Provided value "
+                                         "was {}. Dynamic refinement will not be used.",
+                                         MINIMUM_PERCENT_ERROR,
+                                         percent));
+  SLIC_WARNING_ROOT_IF(
+    percent > MAXIMUM_PERCENT_ERROR,
+    axom::fmt::format("Percent error must be less than {}. Provided value was {}",
+                      MAXIMUM_PERCENT_ERROR,
+                      percent));
   if(percent <= MINIMUM_PERCENT_ERROR)
   {
     m_refinementType = DiscreteShape::RefinementUniformSegments;
@@ -753,8 +754,8 @@ void DiscreteShape::setPercentError(double percent)
 
 void DiscreteShape::setPrefixPath(const std::string& prefixPath)
 {
-  SLIC_ERROR_IF(!prefixPath.empty() && !axom::utilities::filesystem::pathExists(prefixPath),
-                "Path '" + prefixPath + "' does not exist.");
+  SLIC_ERROR_ROOT_IF(!prefixPath.empty() && !axom::utilities::filesystem::pathExists(prefixPath),
+                     axom::fmt::format("Path '{}' does not exist.", prefixPath));
   m_prefixPath = prefixPath;
 }
 
@@ -765,16 +766,16 @@ void DiscreteShape::setParentGroup(axom::sidre::Group* parentGroup)
     // Use object address to create a unique name for sidre group under parent.
     std::string myGroupName;
     int i = 0;
-    while(myGroupName.empty())
+    do
     {
-      std::ostringstream os;
-      os << "DiscreteShapeTemp-" << i;
-      if(!parentGroup->hasGroup(os.str()))
+      const std::string str = axom::fmt::format("DiscreteShapeTemp-{}", i);
+      if(!parentGroup->hasGroup(str))
       {
-        myGroupName = os.str();
+        myGroupName = str;
       }
       ++i;
-    }
+    } while(myGroupName.empty());
+
     m_sidreGroup = parentGroup->createGroup(myGroupName);
   }
 }

src/axom/quest/Shaper.cpp

@@ -175,7 +175,7 @@ void Shaper::setFilePath(const std::string& filePath)
 void Shaper::setSamplesPerKnotSpan(int nSamples)
 {
   using axom::utilities::clampLower;
-  SLIC_WARNING_IF(
+  SLIC_WARNING_ROOT_IF(
     nSamples < 1,
     axom::fmt::format("Samples per knot span must be at least 1. Provided value was {}", nSamples));
 
@@ -184,7 +184,7 @@ void Shaper::setSamplesPerKnotSpan(int nSamples)
 
 void Shaper::setVertexWeldThreshold(double threshold)
 {
-  SLIC_WARNING_IF(
+  SLIC_WARNING_ROOT_IF(
     threshold <= 0.,
     axom::fmt::format("Vertex weld threshold should be positive Provided value was {}", threshold));
 
@@ -194,15 +194,16 @@ void Shaper::setVertexWeldThreshold(double threshold)
 void Shaper::setPercentError(double percent)
 {
   using axom::utilities::clampVal;
-  SLIC_WARNING_IF(percent <= MINIMUM_PERCENT_ERROR,
-                  axom::fmt::format("Percent error must be greater than {}. Provided value "
-                                    "was {}. Dynamic refinement will not be used.",
-                                    MINIMUM_PERCENT_ERROR,
-                                    percent));
-  SLIC_WARNING_IF(percent > MAXIMUM_PERCENT_ERROR,
-                  axom::fmt::format("Percent error must be less than {}. Provided value was {}",
-                                    MAXIMUM_PERCENT_ERROR,
-                                    percent));
+  SLIC_WARNING_ROOT_IF(percent <= MINIMUM_PERCENT_ERROR,
+                       axom::fmt::format("Percent error must be greater than {}. Provided value "
+                                         "was {}. Dynamic refinement will not be used.",
+                                         MINIMUM_PERCENT_ERROR,
+                                         percent));
+  SLIC_WARNING_ROOT_IF(
+    percent > MAXIMUM_PERCENT_ERROR,
+    axom::fmt::format("Percent error must be less than {}. Provided value was {}",
+                      MAXIMUM_PERCENT_ERROR,
+                      percent));
   if(percent <= MINIMUM_PERCENT_ERROR)
   {
     m_refinementType = DiscreteShape::RefinementUniformSegments;
@@ -237,8 +238,9 @@ void Shaper::loadShapeInternal(const klee::Shape& shape, double percentError, do
   SLIC_INFO_ROOT(
     axom::fmt::format("{:-^80}", axom::fmt::format(" Loading shape '{}' ", shape.getName())));
 
-  SLIC_ASSERT_MSG(this->isValidFormat(this->shapeFormat(shape)),
-                  axom::fmt::format("Shape has unsupported format: '{}", this->shapeFormat(shape)));
+  SLIC_ERROR_ROOT_IF(
+    !this->isValidFormat(this->shapeFormat(shape)),
+    axom::fmt::format("Shape has unsupported format: '{}", this->shapeFormat(shape)));
 
   // Code for discretizing shapes has been factored into DiscreteShape class.
   DiscreteShape discreteShape(shape, m_dataStore.getRoot(), m_prefixPath);

src/axom/quest/examples/shaping_driver.cpp

@@ -105,7 +105,7 @@ struct Input
       auto res = axom::NumericArray<int, 2>(boxResolution.data());
       auto bbox = BBox2D(Pt2D(boxMins.data()), Pt2D(boxMaxs.data()));
 
-      SLIC_INFO(
+      SLIC_INFO_ROOT(
         axom::fmt::format("Creating inline box mesh of resolution {} and bounding box {}", res, bbox));
 
       mesh = quest::util::make_cartesian_mfem_mesh_2D(bbox, res, outputOrder);
@@ -118,14 +118,14 @@ struct Input
       auto res = axom::NumericArray<int, 3>(boxResolution.data());
       auto bbox = BBox3D(Pt3D(boxMins.data()), Pt3D(boxMaxs.data()));
 
-      SLIC_INFO(
+      SLIC_INFO_ROOT(
         axom::fmt::format("Creating inline box mesh of resolution {} and bounding box {}", res, bbox));
 
       mesh = quest::util::make_cartesian_mfem_mesh_3D(bbox, res, outputOrder);
     }
     break;
     default:
-      SLIC_ERROR("Only 2D and 3D meshes are currently supported.");
+      SLIC_ERROR_ROOT("Only 2D and 3D meshes are currently supported.");
       break;
     }
 
@@ -456,7 +456,6 @@ int main(int argc, char** argv)
 
 #ifdef AXOM_USE_MPI
     MPI_Bcast(&retval, 1, MPI_INT, 0, MPI_COMM_WORLD);
-    MPI_Finalize();
 #endif
     exit(retval);
   }

src/axom/sina/docs/sphinx/hdf5_vs_json.rst

@@ -3,11 +3,11 @@
 .. ##
 .. ## SPDX-License-Identifier: (BSD-3-Clause)
 
-.. _curvesets-label:
+.. _output-format-label:
 
-=========
+=============
 HDF5 and JSON
-=========
+=============
 
 Sina's C++ and Python Code supports loading both JSON and HDF5 files as Documents,
 and saving Documents to either file type.
@@ -21,7 +21,7 @@ Why You Should Use JSON
 ------------------------------
 
 * JSON is more universally parsable
-* JSON code is human readable allowing you more, easier flexibility with searching for relevent data.  This is most applicable with smaller files since large amounts of data or curve sets quickly become more efficient to navigate digitally
+* JSON code is human readable allowing you more, easier flexibility with searching for relevant data.  This is most applicable with smaller files since large amounts of data or curve sets quickly become more efficient to navigate digitally
 * JSON outperforms HDF5 in speed and size efficiency when dealing with non-curve set data and outperforms at smaller curve set sizes (just before :math:`10^2` Curve Sets for Size and around :math:`10^3.25` for Speed)
 
 ------------------------------