Center Matrix Test is working!

Author: allywarner

src/Core/Algorithms/Math/ComputePCA.cc

@@ -39,6 +39,7 @@ void ComputePCAAlgo::run(MatrixHandle input, DenseMatrixHandle& LeftPrinMat, Den
 {
     if (matrix_is::dense(input))
     {
+        
         auto denseInput = matrix_cast::as_dense(input);
 
         auto rows = denseInput->rows();
@@ -61,6 +62,18 @@ void ComputePCAAlgo::run(MatrixHandle input, DenseMatrixHandle& LeftPrinMat, Den
     }
 }
 
+DenseMatrix ComputePCAAlgo::centerData(DenseMatrixHandle input_matrix)
+{
+    auto denseInput = matrix_cast::as_dense(input_matrix);
+    
+    auto rows = denseInput->rows();
+    
+    auto centerMatrix = Eigen::MatrixXd::Identity(rows,rows) - (1.0/rows)*Eigen::MatrixXd::Constant(rows,rows,1);
+    
+    auto denseInputCentered = centerMatrix * *denseInput;
+        
+    return denseInputCentered.eval();
+}
 
 AlgorithmOutput ComputePCAAlgo::run_generic(const AlgorithmInput& input) const
 {

src/Core/Algorithms/Math/ComputePCA.h

@@ -43,6 +43,7 @@ namespace SCIRun {
                     static AlgorithmOutputName RightPrincipalMatrix;
                     void run(Datatypes::MatrixHandle input_matrix, Datatypes::DenseMatrixHandle& LeftPrinMat, Datatypes::DenseMatrixHandle& PrinVals, Datatypes::DenseMatrixHandle& RightPrinMat) const;
                     virtual AlgorithmOutput run_generic(const AlgorithmInput& input) const;
+                    static Datatypes::DenseMatrix centerData(Datatypes::DenseMatrixHandle input_matrix);
                 };
 
             }}}}

src/Core/Algorithms/Math/Tests/CMakeLists.txt

@@ -39,6 +39,7 @@ SET(Algorithms_Math_Tests_SRCS
   ConvertMatrixTypeTests.cc
   SelectSubMatrixTests.cc
   GetMatrixSliceAlgoTests.cc
+  ComputePCAtest.cc
 )
 
 #SET(Engine_Network_Tests_HEADERS

src/Core/Algorithms/Math/Tests/ComputePCAtest.cc

@@ -0,0 +1,124 @@
+/*
+ For more information, please see: http://software.sci.utah.edu
+ 
+ The MIT License
+ 
+ Copyright (c) 2015 Scientific Computing and Imaging Institute,
+ University of Utah.
+ 
+ License for the specific language governing rights and limitations under
+ 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 <gtest/gtest.h>
+
+#include <Core/Datatypes/DenseMatrix.h>
+#include <Core/Datatypes/MatrixComparison.h>
+#include <Testing/Utils/MatrixTestUtilities.h>
+#include <Core/Algorithms/Math/ComputePCA.h>
+
+using namespace SCIRun::Core::Datatypes;
+using namespace SCIRun::Core::Algorithms::Math;
+using namespace SCIRun::TestUtils;
+
+
+namespace
+{
+    //Matrix for input
+    DenseMatrixHandle inputMatrix()
+    {
+        int column1 [12] = {5,4,7,8,10,10,4,6,8,7,9,6};
+        int column2 [12] = {7,6,9,8,5,7,9,3,4,5,5,9};
+        
+        DenseMatrixHandle inputM(boost::make_shared<DenseMatrix>(12,2));
+        for (int i = 0; i < inputM->rows(); i++){
+            (*inputM)(i,0) = column1[i];
+            (*inputM)(i,1) = column2[i];
+        }
+        return inputM;
+    }
+    
+    //A after it is centered
+    DenseMatrixHandle centeredInputMatrix()
+    {
+    
+        double centeredColumn1 [12] = {-2.0,-3.0,-0.0,1.0,3.0,3.0,-3.0,-1.0,1.0,-0.0,2.0,-1.0};
+        double centeredColumn2 [12] = {0.583333,-0.416667,2.583333,1.583333,-1.416667,0.583333,2.583333,-3.416667,-2.416667,-1.416667,-1.416667,2.583333};
+        
+        DenseMatrixHandle centeredM(boost::make_shared<DenseMatrix>(12,2));
+        for (int i = 0; i < centeredM->rows(); i++){
+            (*centeredM)(i,0) = centeredColumn1[i];
+            (*centeredM)(i,1) = centeredColumn2[i];
+        }
+        return centeredM;
+                                
+    }
+                            
+    //Outputs: U,S,V
+    DenseMatrixHandle outputU()
+    {}
+    DenseMatrixHandle outputS()
+    {}
+    DenseMatrixHandle outputV()
+    {}
+    
+}
+
+
+
+TEST(ComputePCAtest, CenterData)
+{
+    ComputePCAAlgo algo;
+    
+    DenseMatrixHandle m1(inputMatrix());
+    
+    auto centered = ComputePCAAlgo::centerData(m1);
+    
+    auto expected = *centeredInputMatrix();
+    
+    for (int i = 0; i < centered.rows(); ++i) {
+        for (int j = 0; j < centered.cols(); ++j)
+            EXPECT_NEAR(expected(i,j), centered(i,j), 1e-5);
+    }
+}
+
+//TEST(ComputePCAtest, output1)
+//{
+//    ComputePCAAlgorithm algo;
+//    
+//    DenseMatrixHandle m1(testMatrix());
+//    ComputePCAAlgorithm::Outputs result = algo.run(ComputePCAAlgorithm::Inputs(m1),ComputePCAAlgorithm);
+//    
+//}
+//
+//TEST(ComputePCAtest, output2)
+//{
+//    ComputePCAAlgorithm algo;
+//    
+//    DenseMatrixHandle m1(testMatrix());
+//    
+//}
+//
+//TEST(ComputePCAtest, output3)
+//{
+//    ComputePCAAlgorithm algo;
+//    
+//    DenseMatrixHandle m1(testMatrix());
+//    
+//}