ENH: Finish adding sample N-Way array filters and tests.

Filtering/vtkArrayData.h

@@ -31,6 +31,10 @@ class vtkInformationVector;
 
 // .NAME vtkArrayData - Pipeline data object that acts as a container
 // for a single vtkArray
+
+// .SECTION Thanks
+// Developed by Timothy M. Shead (tshead@sandia.gov) at Sandia National Laboratories.
+
 class VTK_FILTERING_EXPORT vtkArrayData : public vtkDataObject
 {
 public:

Filtering/vtkArrayDataAlgorithm.h

@@ -39,6 +39,9 @@
 // signature. For even older filters that don't implement ExecuteData the
 // default implementation calls the even older Execute() signature.
 
+// .SECTION Thanks
+// Developed by Timothy M. Shead (tshead@sandia.gov) at Sandia National Laboratories.
+
 #ifndef __vtkArrayDataAlgorithm_h
 #define __vtkArrayDataAlgorithm_h
 

Filtering/vtkFactoredArrayData.h

@@ -31,6 +31,9 @@ class vtkArray;
 // collection of vtkArray instances.  Used to store the "factored"
 // representation of a larger array.
 
+// .SECTION Thanks
+// Developed by Timothy M. Shead (tshead@sandia.gov) at Sandia National Laboratories.
+
 class VTK_FILTERING_EXPORT vtkFactoredArrayData : public vtkDataObject
 {
 public:

Filtering/vtkFactoredArrayDataAlgorithm.h

@@ -39,6 +39,9 @@
 // signature. For even older filters that don't implement ExecuteData the
 // default implementation calls the even older Execute() signature.
 
+// .SECTION Thanks
+// Developed by Timothy M. Shead (tshead@sandia.gov) at Sandia National Laboratories.
+
 #ifndef __vtkFactoredArrayDataAlgorithm_h
 #define __vtkFactoredArrayDataAlgorithm_h
 

Infovis/CMakeLists.txt

@@ -75,6 +75,7 @@ vtkXMLTreeReader.cxx
 
 # Add these classes only if using Boost
 IF(VTK_USE_BOOST)
+
   SET(Kit_SRCS
     ${Kit_SRCS}
     vtkBoostBiconnectedComponents.cxx
@@ -86,8 +87,36 @@ IF(VTK_USE_BOOST)
     vtkBoostPrimMinimumSpanningTree.cxx
     vtkBoostSplitTableField.cxx
   )
+
 ENDIF(VTK_USE_BOOST)
 
+IF(VTK_USE_N_WAY_ARRAYS)
+
+  SET(Kit_SRCS
+    ${Kit_SRCS}
+    vtkAdjacencyMatrixToEdgeTable.cxx
+    vtkArrayToTable.cxx
+    vtkCosineSimilarity.cxx
+    vtkDiagonalMatrixSource.cxx
+    vtkExtractFactoredArray.cxx
+    vtkMatricizeArray.cxx
+    vtkMatrixColumnNorm.cxx
+    vtkNormalizeMatrixVectors.cxx
+    vtkTableToSparseArray.cxx
+    vtkTransposeMatrix.cxx
+    )
+
+  IF(VTK_USE_BOOST)
+
+    SET(Kit_SRCS
+      ${Kit_SRCS}
+      vtkBoostLogWeighting.cxx
+      vtkBoostRandomSparseArraySource.cxx
+    )
+
+  ENDIF(VTK_USE_BOOST)
+ENDIF(VTK_USE_N_WAY_ARRAYS)
+
 # Add these classes only if vtkTypeUInt64Array exists
 SET(VTK_HAS_UINT64_ARRAY 0)
 IF(VTK_SIZEOF_LONG_LONG MATCHES "^8$")

Infovis/Testing/Cxx/ArrayAPIDenseCoordinates.cxx

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    ArrayAPIDenseCoordinates.cxx
+  
+-------------------------------------------------------------------------
+  Copyright 2008 Sandia Corporation.
+  Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+  the U.S. Government retains certain rights in this software.
+-------------------------------------------------------------------------
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+
+#include <vtkArrayData.h>
+#include <vtkArrayPrint.h>
+#include <vtkDenseArray.h>
+#include <vtkDiagonalMatrixSource.h>
+#include <vtkSmartPointer.h>
+#include <vtkSparseArray.h>
+
+#include <vtksys/ios/iostream>
+#include <vtksys/stl/stdexcept>
+
+#define test_expression(expression) \
+{ \
+  if(!(expression)) \
+    throw vtkstd::runtime_error("Expression failed: " #expression); \
+}
+
+int ArrayAPIDenseCoordinates(int argc, char* argv[])
+{
+  try
+    {
+    vtkSmartPointer<vtkDiagonalMatrixSource> source = vtkSmartPointer<vtkDiagonalMatrixSource>::New();
+    source->SetExtents(3);
+    source->SetArrayType(vtkDiagonalMatrixSource::DENSE);
+    source->SetDiagonal(1.0);
+    source->SetSuperDiagonal(0.5);
+    source->SetSubDiagonal(-0.5);
+    source->Update();
+
+    vtkDenseArray<double>* const array = vtkDenseArray<double>::SafeDownCast(source->GetOutput()->GetArray());
+
+    cout << "dense diagonal matrix:\n";
+    vtkPrintMatrixFormat(cout, array);
+
+    cout << "dense diagonal coordinates:\n";
+    vtkPrintCoordinateFormat(cout, array);
+
+    test_expression(array);
+    test_expression(array->GetValue(vtkArrayCoordinates(0, 0)) == 1.0);
+    test_expression(array->GetValue(vtkArrayCoordinates(1, 0)) == -0.5);
+    test_expression(array->GetValue(vtkArrayCoordinates(2, 0)) == 0.0);
+    test_expression(array->GetValue(vtkArrayCoordinates(0, 1)) == 0.5);
+    test_expression(array->GetValue(vtkArrayCoordinates(1, 1)) == 1.0);
+    test_expression(array->GetValue(vtkArrayCoordinates(2, 1)) == -0.5);
+    test_expression(array->GetValue(vtkArrayCoordinates(0, 2)) == 0.0);
+    test_expression(array->GetValue(vtkArrayCoordinates(1, 2)) == 0.5);
+    test_expression(array->GetValue(vtkArrayCoordinates(2, 2)) == 1.0);
+
+    for(vtkIdType n = 0; n != array->GetNonNullSize(); ++n)
+      {
+      vtkArrayCoordinates coordinates;
+      array->GetCoordinatesN(n, coordinates);
+
+      if(coordinates[0] == 0 && coordinates[1] == 0)
+        {
+        test_expression(array->GetValueN(n) == 1.0);
+        }
+      else if(coordinates[0] == 0 && coordinates[1] == 1)
+        {
+        test_expression(array->GetValueN(n) == 0.5);
+        }
+      else if(coordinates[0] == 1 && coordinates[1] == 0)
+        {
+        test_expression(array->GetValueN(n) == -0.5);
+        }
+      }
+
+    return 0;
+    }
+  catch(vtkstd::exception& e)
+    {
+    cerr << e.what() << endl;
+    return 1;
+    }
+}
+

Infovis/Testing/Cxx/ArrayCosineSimilarity.cxx

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    ArrayCosineSimilarity.cxx
+  
+-------------------------------------------------------------------------
+  Copyright 2008 Sandia Corporation.
+  Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+  the U.S. Government retains certain rights in this software.
+-------------------------------------------------------------------------
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+
+#include <vtkArrayData.h>
+#include <vtkArrayPrint.h>
+#include <vtkCosineSimilarity.h>
+#include <vtkDenseArray.h>
+#include <vtkSmartPointer.h>
+#include <vtkTable.h>
+#include <vtkVariant.h>
+
+#include <vtksys/ios/iostream>
+#include <vtksys/stl/stdexcept>
+
+#define test_expression(expression) \
+{ \
+  if(!(expression)) \
+    throw vtkstd::runtime_error("Expression failed: " #expression); \
+}
+
+static const bool close_enough(const double lhs, const double rhs)
+{
+  return fabs(lhs - rhs) < 1.0e-12;
+}
+
+int ArrayCosineSimilarity(int argc, char* argv[])
+{
+  cout << setprecision(17);
+  
+  try
+    {
+    vtkSmartPointer<vtkDenseArray<double> > source = vtkSmartPointer<vtkDenseArray<double> >::New();
+    source->Resize(vtkArrayExtents(2, 4));
+    source->SetValue(vtkArrayCoordinates(0, 0), 1);
+    source->SetValue(vtkArrayCoordinates(1, 0), 0);
+    source->SetValue(vtkArrayCoordinates(0, 1), 1);
+    source->SetValue(vtkArrayCoordinates(1, 1), 1);
+    source->SetValue(vtkArrayCoordinates(0, 2), 0);
+    source->SetValue(vtkArrayCoordinates(1, 2), 1);
+    source->SetValue(vtkArrayCoordinates(0, 3), -1);
+    source->SetValue(vtkArrayCoordinates(1, 3), 1);
+
+    cout << "source matrix:\n";
+    vtkPrintMatrixFormat(cout, source.GetPointer());
+    
+    vtkSmartPointer<vtkArrayData> source_data = vtkSmartPointer<vtkArrayData>::New();
+    source_data->SetArray(source);
+     
+    vtkSmartPointer<vtkCosineSimilarity> similarity = vtkSmartPointer<vtkCosineSimilarity>::New();
+    similarity->AddInputConnection(source_data->GetProducerPort());
+    similarity->SetVectorDimension(1);
+    similarity->Update();
+
+    vtkTable* const table = similarity->GetOutput();
+    test_expression(table->GetNumberOfColumns() == 3);
+
+    cout << "similarity table:\n";
+    for(vtkIdType row = 0; row < table->GetNumberOfRows(); ++row)
+      {
+      cout
+        << table->GetValue(row, 0).ToInt()
+        << " -> "
+        << table->GetValue(row, 1).ToInt()
+        << ": "
+        << table->GetValue(row, 2).ToDouble()
+        << "\n";
+      }
+    return 0;
+    }
+  catch(vtkstd::exception& e)
+    {
+    cerr << e.what() << endl;
+    return 1;
+    }
+}
+

Infovis/Testing/Cxx/ArrayDiagonalMatrixSource.cxx

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    ArrayDiagonalMatrixSource.cxx
+  
+-------------------------------------------------------------------------
+  Copyright 2008 Sandia Corporation.
+  Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+  the U.S. Government retains certain rights in this software.
+-------------------------------------------------------------------------
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+
+#include <vtkArrayData.h>
+#include <vtkArrayPrint.h>
+#include <vtkDenseArray.h>
+#include <vtkDiagonalMatrixSource.h>
+#include <vtkSmartPointer.h>
+#include <vtkSparseArray.h>
+
+#include <vtksys/ios/iostream>
+#include <vtksys/stl/stdexcept>
+
+#define test_expression(expression) \
+{ \
+  if(!(expression)) \
+    throw vtkstd::runtime_error("Expression failed: " #expression); \
+}
+
+int ArrayDiagonalMatrixSource(int argc, char* argv[])
+{
+  try
+    {
+    vtkSmartPointer<vtkDiagonalMatrixSource> source = vtkSmartPointer<vtkDiagonalMatrixSource>::New();
+    source->SetExtents(3);
+    source->SetArrayType(vtkDiagonalMatrixSource::SPARSE);
+    source->SetDiagonal(1.0);
+    source->SetSuperDiagonal(0.5);
+    source->SetSubDiagonal(-0.5);
+    source->Update();
+
+    vtkSparseArray<double>* const sparse_array = vtkSparseArray<double>::SafeDownCast(source->GetOutput()->GetArray());
+    
+    cout << "sparse diagonal matrix:\n";
+    vtkPrintMatrixFormat(cout, sparse_array);
+
+    test_expression(sparse_array);
+    test_expression(sparse_array->GetValue(vtkArrayCoordinates(0, 0)) == 1.0);
+    test_expression(sparse_array->GetValue(vtkArrayCoordinates(1, 0)) == -0.5);
+    test_expression(sparse_array->GetValue(vtkArrayCoordinates(2, 0)) == 0.0);
+    test_expression(sparse_array->GetValue(vtkArrayCoordinates(0, 1)) == 0.5);
+    test_expression(sparse_array->GetValue(vtkArrayCoordinates(1, 1)) == 1.0);
+    test_expression(sparse_array->GetValue(vtkArrayCoordinates(2, 1)) == -0.5);
+    test_expression(sparse_array->GetValue(vtkArrayCoordinates(0, 2)) == 0.0);
+    test_expression(sparse_array->GetValue(vtkArrayCoordinates(1, 2)) == 0.5);
+    test_expression(sparse_array->GetValue(vtkArrayCoordinates(2, 2)) == 1.0);
+
+    source->SetArrayType(vtkDiagonalMatrixSource::DENSE);
+    source->Update();
+
+    vtkDenseArray<double>* const dense_array = vtkDenseArray<double>::SafeDownCast(source->GetOutput()->GetArray());
+
+    cout << "dense diagonal matrix:\n";
+    vtkPrintMatrixFormat(cout, dense_array);
+
+    test_expression(dense_array);
+    test_expression(dense_array->GetValue(vtkArrayCoordinates(0, 0)) == 1.0);
+    test_expression(dense_array->GetValue(vtkArrayCoordinates(1, 0)) == -0.5);
+    test_expression(dense_array->GetValue(vtkArrayCoordinates(2, 0)) == 0.0);
+    test_expression(dense_array->GetValue(vtkArrayCoordinates(0, 1)) == 0.5);
+    test_expression(dense_array->GetValue(vtkArrayCoordinates(1, 1)) == 1.0);
+    test_expression(dense_array->GetValue(vtkArrayCoordinates(2, 1)) == -0.5);
+    test_expression(dense_array->GetValue(vtkArrayCoordinates(0, 2)) == 0.0);
+    test_expression(dense_array->GetValue(vtkArrayCoordinates(1, 2)) == 0.5);
+    test_expression(dense_array->GetValue(vtkArrayCoordinates(2, 2)) == 1.0);
+
+    return 0;
+    }
+  catch(vtkstd::exception& e)
+    {
+    cerr << e.what() << endl;
+    return 1;
+    }
+}
+

Infovis/Testing/Cxx/ArrayExtractFactoredArray.cxx

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    ArrayExtractFactoredArray.cxx
+  
+-------------------------------------------------------------------------
+  Copyright 2008 Sandia Corporation.
+  Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+  the U.S. Government retains certain rights in this software.
+-------------------------------------------------------------------------
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+
+#include <vtkArrayData.h>
+#include <vtkArrayPrint.h>
+#include <vtkExtractFactoredArray.h>
+#include <vtkFactoredArrayData.h>
+#include <vtkSmartPointer.h>
+#include <vtkSparseArray.h>
+
+#include <vtksys/ios/iostream>
+#include <vtksys/stl/stdexcept>
+
+#define test_expression(expression) \
+{ \
+  if(!(expression)) \
+    throw vtkstd::runtime_error("Expression failed: " #expression); \
+}
+
+int ArrayExtractFactoredArray(int argc, char* argv[])
+{
+  try
+    {
+    vtkSmartPointer<vtkSparseArray<double> > a = vtkSmartPointer<vtkSparseArray<double> >::New();
+    vtkSmartPointer<vtkSparseArray<double> > b = vtkSmartPointer<vtkSparseArray<double> >::New();
+
+    vtkSmartPointer<vtkFactoredArrayData> factored = vtkSmartPointer<vtkFactoredArrayData>::New();
+    factored->AddArray(a);
+    factored->AddArray(b);
+
+    vtkSmartPointer<vtkExtractFactoredArray> extract = vtkSmartPointer<vtkExtractFactoredArray>::New();
+    extract->AddInputConnection(factored->GetProducerPort());
+
+    extract->SetIndex(0);
+    extract->Update();
+    test_expression(extract->GetOutput()->GetArray() == a.GetPointer());
+
+    extract->SetIndex(1);
+    extract->Update();
+    test_expression(extract->GetOutput()->GetArray() == b.GetPointer());
+
+    return 0;
+    }
+  catch(vtkstd::exception& e)
+    {
+    cout << e.what() << endl;
+    return 1;
+    }
+}
+

Infovis/Testing/Cxx/ArrayMatricizeArray.cxx

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    ArrayMatricizeArray.cxx
+  
+-------------------------------------------------------------------------
+  Copyright 2008 Sandia Corporation.
+  Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+  the U.S. Government retains certain rights in this software.
+-------------------------------------------------------------------------
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+
+#include <vtkArrayData.h>
+#include <vtkArrayPrint.h>
+#include <vtkMatricizeArray.h>
+#include <vtkSmartPointer.h>
+#include <vtkSparseArray.h>
+
+#include <vtksys/ios/iostream>
+#include <vtksys/stl/stdexcept>
+
+#define test_expression(expression) \
+{ \
+  if(!(expression)) \
+    throw vtkstd::runtime_error("Expression failed: " #expression); \
+}
+
+int ArrayMatricizeArray(int argc, char* argv[])
+{
+  try
+    {
+    // Create an array ...
+    vtkSmartPointer<vtkSparseArray<double> > array = vtkSmartPointer<vtkSparseArray<double> >::New();
+    array->Resize(vtkArrayExtents(2, 2, 2));
+
+    double value = 0;
+    const vtkArrayExtents extents = array->GetExtents();
+    for(int i = 0; i != extents[0]; ++i)
+      {
+      for(int j = 0; j != extents[1]; ++j)
+        {
+        for(int k = 0; k != extents[2]; ++k)
+          {
+          array->AddValue(vtkArrayCoordinates(i, j, k), value++);
+          }
+        }
+      }
+
+    cout << "array source:\n";
+    vtkPrintCoordinateFormat(cout, array.GetPointer());
+
+    // Create an array data object to hold it ...
+    vtkSmartPointer<vtkArrayData> array_data = vtkSmartPointer<vtkArrayData>::New();
+    array_data->SetArray(array);
+
+    // Matricize it ...
+    vtkSmartPointer<vtkMatricizeArray> matricize = vtkSmartPointer<vtkMatricizeArray>::New();
+    matricize->SetInput(array_data);
+    matricize->SetSliceDimension(0);
+    matricize->Update();
+
+    vtkSparseArray<double>* const matricized_array = vtkSparseArray<double>::SafeDownCast(matricize->GetOutput()->GetArray());
+    test_expression(matricized_array);
+
+    cout << "matricize output:\n";
+    vtkPrintCoordinateFormat(cout, matricized_array);
+
+    test_expression(matricized_array->GetValue(vtkArrayCoordinates(0, 0)) == 0);
+    test_expression(matricized_array->GetValue(vtkArrayCoordinates(0, 1)) == 1);
+    test_expression(matricized_array->GetValue(vtkArrayCoordinates(0, 2)) == 2);
+    test_expression(matricized_array->GetValue(vtkArrayCoordinates(0, 3)) == 3);
+    test_expression(matricized_array->GetValue(vtkArrayCoordinates(1, 0)) == 4);
+    test_expression(matricized_array->GetValue(vtkArrayCoordinates(1, 1)) == 5);
+    test_expression(matricized_array->GetValue(vtkArrayCoordinates(1, 2)) == 6);
+    test_expression(matricized_array->GetValue(vtkArrayCoordinates(1, 3)) == 7);
+
+    return 0;
+    }
+  catch(vtkstd::exception& e)
+    {
+    cout << e.what() << endl;
+    return 1;
+    }
+}
+

Infovis/Testing/Cxx/ArrayMatrixColumnNorm.cxx

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    ArrayMatrixColumnNorm.cxx
+  
+-------------------------------------------------------------------------
+  Copyright 2008 Sandia Corporation.
+  Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+  the U.S. Government retains certain rights in this software.
+-------------------------------------------------------------------------
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+
+#include <vtkArrayData.h>
+#include <vtkArrayPrint.h>
+#include <vtkMatrixColumnNorm.h>
+#include <vtkDenseArray.h>
+#include <vtkDiagonalMatrixSource.h>
+#include <vtkSmartPointer.h>
+#include <vtkSparseArray.h>
+
+#include <vtksys/ios/iostream>
+#include <vtksys/stl/stdexcept>
+
+#define test_expression(expression) \
+{ \
+  if(!(expression)) \
+    throw vtkstd::runtime_error("Expression failed: " #expression); \
+}
+
+static const bool close_enough(const double lhs, const double rhs)
+{
+  return fabs(lhs - rhs) < 1.0e-12;
+}
+
+int ArrayMatrixColumnNorm(int argc, char* argv[])
+{
+  cout << setprecision(17);
+  
+  try
+    {
+    vtkSmartPointer<vtkDiagonalMatrixSource> source = vtkSmartPointer<vtkDiagonalMatrixSource>::New();
+    source->SetExtents(3);
+    source->SetArrayType(vtkDiagonalMatrixSource::SPARSE);