Merge pull request #769 from benjaminlarson/benConvertFieldIndices

Closes #747. Test network to come from me

Author: dcwhite

src/Core/Algorithms/Factory/HardCodedAlgorithmFactory.cc

@@ -56,6 +56,7 @@
 #include <Core/Algorithms/Legacy/Fields/TransformMesh/ScaleFieldMeshAndData.h>
 #include <Core/Algorithms/Legacy/Fields/TransformMesh/ProjectPointsOntoMesh.h>
 #include <Core/Algorithms/Legacy/Fields/FieldData/SwapFieldDataWithMatrixEntriesAlgo.h> 
+#include <Core/Algorithms/Legacy/Fields/FieldData/ConvertIndicesToFieldDataAlgo.h> 
 #include <Core/Algorithms/Legacy/Fields/Mapping/BuildMappingMatrixAlgo.h>
 #include <Core/Algorithms/Math/AddKnownsToLinearSystem.h>
 #include <Core/Algorithms/Math/LinearSystem/SolveLinearSystemAlgo.h>
@@ -165,6 +166,7 @@ void HardCodedAlgorithmFactory::addToMakerMap()
 	  ADD_MODULE_ALGORITHM(FlipSurfaceNormals,FlipSurfaceNormalsAlgo)
 	  ADD_MODULE_ALGORITHM(BuildNoiseColumnMatrix,BuildNoiseColumnMatrixAlgorithm)
       ADD_MODULE_ALGORITHM(BuildMappingMatrix, BuildMappingMatrixAlgo)
+	  ADD_MODULE_ALGORITHM(ConvertIndicesToFieldData, ConvertIndicesToFieldDataAlgo)
     ;
   }
 }

src/Core/Algorithms/Legacy/Fields/CMakeLists.txt

@@ -35,7 +35,7 @@ SET(Core_Algorithms_Legacy_Fields_HEADERS
   FieldData/BuildMatrixOfSurfaceNormalsAlgo.h
   #Mapping/ApplyMappingMatrix.h
   #FieldData/CalculateFieldDataMetric.h
-  #FieldData/ConvertIndicesToFieldData.h
+  FieldData/ConvertIndicesToFieldDataAlgo.h
   FieldData/CalculateGradientsAlgo.h
   FieldData/CalculateVectorMagnitudesAlgo.h
   #FieldData/ConvertMappingMatrixToFieldData.h
@@ -116,7 +116,7 @@ SET(Core_Algorithms_Legacy_Fields_SRCS
 #FieldData/ConvertFieldDataType.cc
   FieldData/ConvertFieldBasisType.cc
   FieldData/SwapFieldDataWithMatrixEntriesAlgo.cc
-  #FieldData/ConvertIndicesToFieldData.cc
+  FieldData/ConvertIndicesToFieldDataAlgo.cc
   #FieldData/GetFieldData.cc
   #FieldData/ConvertMappingMatrixToFieldData.cc
   FieldData/SetFieldData.cc

src/Core/Algorithms/Legacy/Fields/FieldData/ConvertIndicesToFieldDataAlgo.cc

@@ -0,0 +1,238 @@
+/*
+   For more information, please see: http://software.sci.utah.edu
+
+   The MIT License
+
+   Copyright (c) 2009 Scientific Computing and Imaging Institute,
+   University of Utah.
+
+
+   Permission is hereby granted, free of charge, to any person obtaining a
+   copy of this software and associated documentation files (the "Software"),
+   to deal in the Software without restriction, including without limitation
+   the rights to use, copy, modify, merge, publish, distribute, sublicense,
+   and/or sell copies of the Software, and to permit persons to whom the
+   Software is furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included
+   in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+   OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+   THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+   FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+   DEALINGS IN THE SOFTWARE.
+   */
+
+#include <Core/Algorithms/Legacy/Fields/FieldData/ConvertIndicesToFieldDataAlgo.h>
+#include <Core/Datatypes/Legacy/Field/Field.h>
+#include <Core/Datatypes/Legacy/Field/VField.h>
+#include <Core/Datatypes/Matrix.h>
+#include <Core/Datatypes/MatrixTypeConversions.h>
+#include <Core/Datatypes/SparseRowMatrix.h>
+#include <Core/Datatypes/DatatypeFwd.h> 
+#include <Core/Datatypes/Legacy/Field/FieldInformation.h>
+#include <Core/Datatypes/DenseMatrix.h>
+
+#include <Core/Algorithms/Base/AlgorithmVariableNames.h>
+#include <Core/Algorithms/Base/AlgorithmPreconditions.h>
+
+using namespace SCIRun::Core::Algorithms;
+using namespace SCIRun::Core::Geometry; 
+using namespace SCIRun::Core::Algorithms::Fields;
+using namespace SCIRun::Core::Algorithms::Fields::Parameters;
+using namespace SCIRun::Core::Datatypes;
+using namespace SCIRun;
+
+ALGORITHM_PARAMETER_DEF(Fields, OutputFieldDataType); 
+
+ConvertIndicesToFieldDataAlgo::ConvertIndicesToFieldDataAlgo()
+{
+  add_option(Parameters::OutputFieldDataType, "double","double|float|char|unsigned char|short|unsigned short|int|unsigned int");
+}
+
+bool
+ConvertIndicesToFieldDataAlgo::runImpl(FieldHandle input_field, DenseMatrixHandle input_matrix, FieldHandle& output_field) const
+{
+  ScopedAlgorithmStatusReporter r(this, "ConvertIndicesToFieldData");
+
+  if (!input_field)
+  {
+    error("No input field");
+    return (false);
+  }
+
+  FieldInformation fi(input_field);
+  output_field = CreateField(fi);
+	FieldInformation fo(output_field); 
+
+	if (fi.is_nonlinear())
+	{
+		error("This function has not yet been defined for non-linear elements");
+		return (false);
+	}
+
+	if (fi.is_nodata())
+	{
+		error("This function has not yet been defined for fields with no data");
+		return (false);
+	}
+
+	if (fi.is_vector() || fi.is_tensor())
+	{
+		error("This function has not yet been defined for fields with vectors or tensors as indices");
+		return (false);
+	}
+
+ 	size_type nrows = input_matrix->nrows();
+	size_type ncols = input_matrix->ncols();
+
+	std::string algotype;
+
+	if (ncols == 1)
+	{
+		algotype = "Scalar";
+	}
+	else if (ncols == 3)
+	{
+		algotype = "Vector";
+	}
+	else if (ncols == 6 || ncols == 9)
+	{
+		algotype = "Tensor";
+	}
+	else
+	{
+		if (nrows == 1)
+		{
+			algotype = "Scalar";
+		}
+		else if (nrows == 3)
+		{
+			algotype = "Vector";
+		}
+		else if (nrows == 6 || nrows == 9)
+		{
+			algotype = "Tensor";
+		}
+		else
+		{
+			error("Data does not have dimension of 1, 3, 6, or 9");
+			return (false);
+		}
+	}
+
+	if (algotype == "Scalar")
+	{
+		std::string datatype;
+		get_option(Parameters::OutputFieldDataType);
+		fo.set_data_type(get_option(Parameters::OutputFieldDataType));
+	}
+	if (algotype == "Vector") fo.make_vector();
+	if (algotype == "Tensor") fo.make_tensor();
+
+	//--------------------------------
+	// VIRTUAL INTERFACE
+
+	output_field = CreateField(fo, input_field->mesh());
+	VField* vinput = input_field->vfield();
+	VField* voutput = output_field->vfield();
+	voutput->resize_fdata();
+
+	if (algotype == "Scalar")
+	{
+		int max_index = input_matrix->nrows() * input_matrix->ncols();
+		const double *dataptr = input_matrix->data();
+		VMesh::size_type sz = vinput->num_values();
+		for (VMesh::index_type r = 0; r<sz; r++)
+		{
+			int idx;
+			vinput->get_value(idx, r);
+			if ((idx < 0) || (idx >= max_index))
+			{
+				error("Index exceeds matrix dimensions");
+				return (false);
+			}
+			voutput->set_value(dataptr[idx], r);
+		}
+		return (true);
+	}
+	else if (algotype == "Vector")
+	{
+		if (input_matrix->ncols() != 3)
+		{
+			input_matrix.reset(new DenseMatrix(input_matrix->transpose())); 
+		}
+
+		const double *dataptr = input_matrix->data();
+		int max_index = input_matrix->nrows();
+
+		VMesh::size_type sz = vinput->num_values();
+		for (VMesh::index_type r = 0; r<sz; r++)
+		{
+			int idx;
+			vinput->get_value(idx, r);
+			if ((idx < 0) || (idx >= max_index))
+			{
+				error("Index exceeds matrix dimensions");
+				return (false);
+			}
+			voutput->set_value(Vector(dataptr[3 * idx], dataptr[3 * idx + 1], dataptr[3 * idx + 2]), r);
+		}
+		return (true);
+	}
+	else if (algotype == "Tensor")
+	{
+		if ((input_matrix->ncols() != 6) && (input_matrix->ncols() != 9))
+		{
+			input_matrix.reset(new DenseMatrix(input_matrix->transpose())); 
+		}
+		
+		int max_index = input_matrix->nrows(); 
+		const double *dataptr = input_matrix->data(); 
+		int ncols = input_matrix->ncols(); 
+
+		VMesh::size_type sz = vinput->num_values();
+		for (VMesh::index_type r = 0; r<sz; r++)
+		{
+			int idx;
+			vinput->get_value(idx, r);
+			if ((idx < 0) || (idx >= max_index))
+			{
+				error("Index exceeds matrix dimensions");
+				return (false);
+			}
+			if (ncols == 6)
+			{
+				voutput->set_value(Tensor(dataptr[3 * idx], dataptr[3 * idx + 1], dataptr[3 * idx + 2], dataptr[3 * idx + 3], dataptr[3 * idx + 4], dataptr[3 * idx + 5]), r);
+			}
+			else
+			{
+				voutput->set_value(Tensor(dataptr[3 * idx], dataptr[3 * idx + 1], dataptr[3 * idx + 2], dataptr[3 * idx + 4], dataptr[3 * idx + 5], dataptr[3 * idx + 8]), r);
+			}
+		}
+		AlgorithmOutput output;
+		output[Variables::OutputField] = output_field;
+		return (true);
+	}
+
+	// keep the compiler happy:
+	// it seems reasonable to return false if none of the cases apply (AK)
+	return (false);
+}
+
+AlgorithmOutput ConvertIndicesToFieldDataAlgo::run_generic(const AlgorithmInput& input) const
+{
+  auto field = input.get<Field>(Variables::InputField);
+  auto inputmatrix = input.get<DenseMatrix>(Variables::InputMatrix);
+
+  FieldHandle output_field;
+  if (!runImpl(field, inputmatrix, output_field))
+    THROW_ALGORITHM_PROCESSING_ERROR("False returned on legacy run call.");
+
+  AlgorithmOutput output;
+  output[Variables::OutputField] = output_field;
+  return output;
+}

src/Core/Algorithms/Legacy/Fields/FieldData/ConvertIndicesToFieldDataAlgo.h

@@ -0,0 +1,60 @@
+/*
+   For more information, please see: http://software.sci.utah.edu
+
+   The MIT License
+
+   Copyright (c) 2009 Scientific Computing and Imaging Institute,
+   University of Utah.
+
+
+   Permission is hereby granted, free of charge, to any person obtaining a
+   copy of this software and associated documentation files (the "Software"),
+   to deal in the Software without restriction, including without limitation
+   the rights to use, copy, modify, merge, publish, distribute, sublicense,
+   and/or sell copies of the Software, and to permit persons to whom the
+   Software is furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included
+   in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+   OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+   THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+   FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+   DEALINGS IN THE SOFTWARE.
+   */
+
+
+#ifndef CORE_ALGORITHMS_FIELDS_FIELDDATA_CONVERTINDICESTOFIELDDATAALGO_H
+#define CORE_ALGORITHMS_FIELDS_FIELDDATA_CONVERTINDICESTOFIELDDATAALGO_H 1
+
+#include <Core/Algorithms/Base/AlgorithmBase.h>
+#include <Core/Algorithms/Legacy/Fields/share.h>
+
+namespace SCIRun {
+  namespace Core {
+    namespace Algorithms {
+      namespace Fields {
+
+        ALGORITHM_PARAMETER_DECL(OutputFieldDataType);
+
+				class SCISHARE	ConvertIndicesToFieldDataAlgo : public AlgorithmBase
+        {
+        public:
+					ConvertIndicesToFieldDataAlgo();
+
+          bool runImpl(FieldHandle input_field, Datatypes::DenseMatrixHandle input_matrix, FieldHandle& output_field)const;
+
+         // bool runImpl(FieldHandle input, Datatypes::MatrixHandle input_matrix, FieldHandle& output) const;
+
+          virtual AlgorithmOutput run_generic(const AlgorithmInput& input) const override;
+        };
+      }
+    }
+  }
+}
+
+#endif
+

src/Interface/Modules/Factory/ModuleDialogFactory.cc

@@ -80,6 +80,7 @@
 #include <Interface/Modules/Fields/ConvertFieldBasisDialog.h>
 #include <Interface/Modules/Fields/SwapFieldDataWithMatrixEntriesDialog.h>
 #include <Interface/Modules/Fields/ConvertFieldBasisDialog.h>
+#include <Interface/Modules/Fields/ConvertIndicesToFieldDataDialog.h>
 #include <Interface/Modules/Forward/BuildBEMatrixDialog.h>
 #include <Interface/Modules/Inverse/SolveInverseProblemWithTikhonovDialog.h>
 #include <Interface/Modules/FiniteElements/ApplyFEMCurrentSourceDialog.h>
@@ -172,7 +173,8 @@ void ModuleDialogFactory::addDialogsToMakerMap1()
 	  ADD_MODULE_DIALOG(BuildNoiseColumnMatrix,BuildNoiseColumnMatrixDialog)
 		ADD_MODULE_DIALOG(SwapFieldDataWithMatrixEntries, SwapFieldDataWithMatrixEntriesDialog)
 		ADD_MODULE_DIALOG(BuildMappingMatrix, BuildMappingMatrixDialog)
-	  ADD_MODULE_DIALOG(EditMeshBoundingBox, EditMeshBoundingBoxDialog)
+		ADD_MODULE_DIALOG(EditMeshBoundingBox, EditMeshBoundingBoxDialog)
+		ADD_MODULE_DIALOG(ConvertIndicesToFieldData, ConvertIndicesToFieldDataDialog)
     ADD_MODULE_DIALOG(SolveInverseProblemWithTikhonov, SolveInverseProblemWithTikhonovDialog)
   ;
 }

src/Interface/Modules/Fields/CMakeLists.txt

@@ -50,6 +50,7 @@ SET(Interface_Modules_Fields_FORMS
   calculatedistancetofield.ui #TODO: fix case
   calculatedistancetofieldboundary.ui #TODO: fix case
   MapFieldDataOntoElems.ui
+  ConvertIndicesToFieldData.ui
   MapFieldDataOntoNodes.ui
   ClipFieldByFunction.ui
   RefineMesh.ui
@@ -87,6 +88,7 @@ SET(Interface_Modules_Fields_HEADERS
   share.h
   SwapFieldDataWithMatrixEntriesDialog.h
   EditMeshBoundingBoxDialog.h
+  ConvertIndicesToFieldDataDialog.h
 )
 
 SET(Interface_Modules_Fields_SOURCES
@@ -117,6 +119,7 @@ SET(Interface_Modules_Fields_SOURCES
   SwapFieldDataWithMatrixEntriesDialog.cc
   RefineMeshDialog.cc
   EditMeshBoundingBoxDialog.cc
+  ConvertIndicesToFieldDataDialog.cc
 )
 
 IF(WITH_TETGEN)