[mlpack-git] master: Adds inplace transpose method and some tests. This method used in Load() now. (7881c3e)

[gitdub at big.cc.gt.atl.ga.us]

Repository : https://github.com/mlpack/mlpack

On branch  : master
Link       : https://github.com/mlpack/mlpack/compare/904762495c039e345beba14c1142fd719b3bd50e...f94823c800ad6f7266995c700b1b630d5ffdcf40

>---------------------------------------------------------------

commit 7881c3e3e69b74b902e370a9ccd8348ffb9ff3c5
Author: Vladimir Glazachev <glazachev.vladimir at gmail.com>
Date:   Sun Feb 22 04:51:43 2015 +0400

    Adds inplace transpose method and some tests. This method used in Load() now.


>---------------------------------------------------------------

7881c3e3e69b74b902e370a9ccd8348ffb9ff3c5
 src/mlpack/core/arma_extend/CMakeLists.txt         |  1 +
 src/mlpack/core/arma_extend/arma_extend.hpp        |  3 ++
 .../core/arma_extend/fn_inplace_transpose.hpp      | 21 +++++++++
 src/mlpack/core/data/load_impl.hpp                 |  4 +-
 src/mlpack/tests/arma_extend_test.cpp              | 52 ++++++++++++++++++++++
 5 files changed, 80 insertions(+), 1 deletion(-)

diff --git a/src/mlpack/core/arma_extend/CMakeLists.txt b/src/mlpack/core/arma_extend/CMakeLists.txt
index 43f6ee1..36b8593 100644
--- a/src/mlpack/core/arma_extend/CMakeLists.txt
+++ b/src/mlpack/core/arma_extend/CMakeLists.txt
@@ -3,6 +3,7 @@
 set(SOURCES
   arma_extend.hpp
   fn_ccov.hpp
+  fn_inplace_transpose.hpp
   glue_ccov_meat.hpp
   glue_ccov_proto.hpp
   hdf5_misc.hpp
diff --git a/src/mlpack/core/arma_extend/arma_extend.hpp b/src/mlpack/core/arma_extend/arma_extend.hpp
index ec50735..c3c2d98 100644
--- a/src/mlpack/core/arma_extend/arma_extend.hpp
+++ b/src/mlpack/core/arma_extend/arma_extend.hpp
@@ -47,6 +47,9 @@ namespace arma {
 
   // unary minus for sparse matrices
   #include "operator_minus.hpp"
+
+  // inplace_transpose()
+  #include "fn_inplace_transpose.hpp"
 };
 
 #endif
diff --git a/src/mlpack/core/arma_extend/fn_inplace_transpose.hpp b/src/mlpack/core/arma_extend/fn_inplace_transpose.hpp
new file mode 100644
index 0000000..83e8bec
--- /dev/null
+++ b/src/mlpack/core/arma_extend/fn_inplace_transpose.hpp
@@ -0,0 +1,21 @@
+
+/**
+ * This method automatically selects the transpose method,
+ * depending on available memory.
+ */
+template<typename eT>
+bool
+inline
+inplace_transpose(Mat<eT>& X)
+  {
+    try
+    {
+      X = trans(X);
+      return false;
+    }
+    catch (std::bad_alloc& exception)
+    {
+      inplace_trans(X, "lowmem");
+      return true;
+    }
+  }
diff --git a/src/mlpack/core/data/load_impl.hpp b/src/mlpack/core/data/load_impl.hpp
index c1fe470..fee0e65 100644
--- a/src/mlpack/core/data/load_impl.hpp
+++ b/src/mlpack/core/data/load_impl.hpp
@@ -220,7 +220,9 @@ bool Load(const std::string& filename,
 
   // Now transpose the matrix, if necessary.
   if (transpose)
-    matrix = trans(matrix);
+  {
+    arma::inplace_transpose(matrix);
+  }
 
   Timer::Stop("loading_data");
 
diff --git a/src/mlpack/tests/arma_extend_test.cpp b/src/mlpack/tests/arma_extend_test.cpp
index 13c7246..10d5af6 100644
--- a/src/mlpack/tests/arma_extend_test.cpp
+++ b/src/mlpack/tests/arma_extend_test.cpp
@@ -49,6 +49,58 @@ BOOST_AUTO_TEST_CASE(InplaceReshapeMatrixTest)
 }
 
 /**
+ * Make sure we can still transpose correct.
+ */
+BOOST_AUTO_TEST_CASE(InplaceTransposeTest)
+{
+  mat X;
+  X.randu(2, 4);
+
+  mat Y = X;
+
+  BOOST_REQUIRE(arma::inplace_transpose(X) == false);
+  BOOST_REQUIRE_EQUAL(X.n_rows, 4);
+  BOOST_REQUIRE_EQUAL(X.n_cols, 2);
+
+  for (size_t i = 0; i < X.n_rows; ++i)
+    for (size_t j = 0; j < X.n_cols; ++j)
+      BOOST_REQUIRE_CLOSE(X.at(i, j), Y.at(j, i), 1e-5);
+}
+
+/**
+ * Try to transpose using low-mem method.
+ */
+BOOST_AUTO_TEST_CASE(InplaceTransposeLowMemTest)
+{
+  mat X;
+
+  int width = 1000;
+  int height = 50000;
+
+  size_t n_iters = 50;
+
+  for (size_t i = 0; i < n_iters; ++i)
+  {
+    try
+    {
+      X.zeros(height, width);
+      if (inplace_transpose(X))
+      {
+        break;
+      }
+    }
+    catch (std::bad_alloc& exception)
+    {
+      BOOST_FAIL("bad_alloc exception.");
+    }
+    height *= 2;
+  }
+
+  BOOST_REQUIRE_EQUAL(X.n_rows, width);
+  BOOST_REQUIRE_EQUAL(X.n_cols, height);
+}
+
+/**
  * Test const_row_col_iterator for basic functionality.
  */
 BOOST_AUTO_TEST_CASE(ConstRowColIteratorTest)