let HTK I/O implementation be a single package

1 files changed, 677 insertions, 0 deletions

diff --git a/htk_io/src/KaldiLib/Matrix.h b/htk_io/src/KaldiLib/Matrix.h
new file mode 100644
index 0000000..d33cb0c
--- /dev/null
+++ b/htk_io/src/KaldiLib/Matrix.h
@@ -0,0 +1,677 @@
+#ifndef TNet_Matrix_h
+#define TNet_Matrix_h
+
+#include <stddef.h>
+#include <stdlib.h>
+#include <stdexcept>
+#include <iostream>
+
+#ifdef HAVE_ATLAS
+extern "C"{
+  #include <cblas.h>
+  #include <clapack.h>
+}
+#endif
+
+#include "Common.h"
+#include "MathAux.h"
+#include "Types.h"
+#include "Error.h"
+
+//#define TRACE_MATRIX_OPERATIONS
+#define CHECKSIZE
+
+namespace TNet
+{
+
+
+  //  class matrix_error : public std::logic_error {};
+  //  class matrix_sizes_error : public matrix_error {};
+
+  // declare the class so the header knows about it
+  template<typename _ElemT> class Vector;
+  template<typename _ElemT> class SubVector;
+  template<typename _ElemT> class Matrix;
+  template<typename _ElemT> class SubMatrix;
+
+  // we need to declare the friend << operator here
+  template<typename _ElemT>
+    std::ostream & operator << (std::ostream & rOut, const Matrix<_ElemT> & rM);
+
+  // we need to declare the friend << operator here
+  template<typename _ElemT>
+    std::istream & operator >> (std::istream & rIn, Matrix<_ElemT> & rM);
+
+  // we need to declare this friend function here
+  template<typename _ElemT>
+   _ElemT TraceOfProduct(const Matrix<_ElemT> &A, const Matrix<_ElemT> &B); // tr(A B)
+
+  // we need to declare this friend function here
+  template<typename _ElemT> 
+	 _ElemT TraceOfProductT(const Matrix<_ElemT> &A, const Matrix<_ElemT> &B); // tr(A B^T)==tr(A^T B)
+
+
+  /** **************************************************************************
+   ** **************************************************************************
+   *  @brief Provides a matrix class
+   *
+   *  This class provides a way to work with matrices in TNet.
+   *  It encapsulates basic operations and memory optimizations.
+   *
+   */
+  template<typename _ElemT>
+    class Matrix
+    {
+    public:
+      /// defines a transpose type
+
+      struct HtkHeader
+      {
+        INT_32    mNSamples;              
+        INT_32    mSamplePeriod;
+        INT_16    mSampleSize;
+        UINT_16   mSampleKind;
+      };
+
+
+      /** 
+       * @brief Extension of the HTK header
+       */
+      struct HtkHeaderExt
+      {
+        INT_32 mHeaderSize;
+        INT_32 mVersion;
+        INT_32 mSampSize;
+      };  
+
+
+
+
+      /// defines a type of this
+      typedef Matrix<_ElemT>    ThisType;
+
+      // Constructors
+
+      /// Empty constructor
+      Matrix<_ElemT> ():
+        mpData(NULL), mMCols(0), mMRows(0), mStride(0)
+#ifdef STK_MEMALIGN_MANUAL
+        , mpFreeData(NULL)
+#endif
+      {}
+
+      /// Copy constructor
+      Matrix<_ElemT> (const Matrix<_ElemT> & rM, MatrixTrasposeType trans=NO_TRANS):
+        mpData(NULL) 
+      { if(trans==NO_TRANS){ Init(rM.mMRows, rM.mMCols); Copy(rM); } else { Init(rM.mMCols,rM.mMRows); Copy(rM,TRANS); } }
+
+      /// Copy constructor from another type.
+      template<typename _ElemU>
+      explicit Matrix<_ElemT> (const Matrix<_ElemU> & rM, MatrixTrasposeType trans=NO_TRANS):
+        mpData(NULL) 
+      { if(trans==NO_TRANS){ Init(rM.Rows(), rM.Cols()); Copy(rM); } else { Init(rM.Cols(),rM.Rows()); Copy(rM,TRANS); } }
+
+      /// Basic constructor
+      Matrix(const size_t r, const size_t c, bool clear=true)
+      { mpData=NULL; Init(r, c, clear);  }
+
+
+	  Matrix<_ElemT> &operator = (const Matrix <_ElemT> &other) { Init(other.Rows(), other.Cols()); Copy(other); return *this; } // Needed for inclusion in std::vector
+
+      /// Destructor
+      ~Matrix()
+      { Destroy(); }
+
+
+      /// Initializes matrix (if not done by constructor)
+      ThisType &
+      Init(const size_t r,
+           const size_t c, bool clear=true);
+
+      /**
+       * @brief Dealocates the matrix from memory and resets the dimensions to (0, 0)
+       */
+      void
+      Destroy();
+
+
+      ThisType &
+      Zero();
+
+      ThisType &
+      Unit(); // set to unit.
+
+      /** 
+       * @brief Copies the contents of a matrix
+       * @param rM Source data matrix
+       * @return Returns reference to this
+       */
+      template<typename _ElemU> ThisType &
+        Copy(const Matrix<_ElemU> & rM, MatrixTrasposeType Trans=NO_TRANS);
+
+
+
+      /**
+       * @brief Copies the elements of a vector row-by-row into a matrix
+       * @param rV Source vector
+       * @param nRows Number of rows of returned matrix
+       * @param nCols Number of columns of returned matrix
+       *
+       * Note that rV.Dim() must equal nRows*nCols
+       */
+      ThisType &
+      CopyVectorSplicedRows(const Vector<_ElemT> &rV, const size_t nRows, const size_t nCols);
+
+      /**
+       * @brief Returns @c true if matrix is initialized
+       */
+      bool
+		IsInitialized() const
+      { return mpData != NULL; }
+
+      /// Returns number of rows in the matrix
+      inline size_t
+		Rows() const
+      {
+        return mMRows;
+      }
+
+      /// Returns number of columns in the matrix
+      inline size_t
+      Cols() const
+      {
+        return mMCols;
+      }
+
+      /// Returns number of columns in the matrix memory
+      inline size_t
+		Stride() const
+      {
+        return mStride;
+      }
+
+
+      /**
+       *  @brief Gives access to a specified matrix row without range check
+       *  @return Pointer to the const array
+       */
+      inline const _ElemT*  __attribute__((aligned(16)))
+       pData () const
+      {
+        return mpData;
+      }
+
+
+      /**
+       *  @brief Gives access to a specified matrix row without range check
+       *  @return Pointer to the non-const data array
+       */
+      inline _ElemT* __attribute__((aligned(16)))
+       pData () 
+      {
+        return mpData;
+      }
+
+
+      /**
+       *  @brief pData_workaround is a workaround that allows SubMatrix to get a 
+       *  @return pointer to non-const data even though the Matrix is const... 
+       */
+    protected:
+      inline _ElemT*  __attribute__((aligned(16)))
+       pData_workaround () const
+      {
+        return mpData;
+      }
+    public:
+
+
+      /// Returns size of matrix in memory
+      size_t
+      MSize() const
+      {
+        return mMRows * mStride * sizeof(_ElemT);
+      }
+
+      /// Checks the content of the matrix for nan and inf values
+      void
+      CheckData(const std::string file = "") const
+      {
+        for(size_t row=0; row<Rows(); row++) {
+          for(size_t col=0; col<Cols(); col++) {
+            if(isnan((*this)(row,col)) || isinf((*this)(row,col))) {
+              std::ostringstream os;
+              os << "Invalid value: " << (*this)(row,col)
+                 << " in matrix row: " << row
+                 << " col: " << col
+                 << " file: " << file;
+              Error(os.str());
+            }
+          }
+        }
+      }
+
+      /**
+       *  **********************************************************************
+       *  **********************************************************************
+       *  @defgroup RESHAPE Matrix reshaping rutines
+       *  **********************************************************************
+       *  **********************************************************************
+       * @{
+       */
+
+      /**
+       *  @brief Removes one row from the matrix. The memory is not reallocated.
+       */
+      ThisType &
+      RemoveRow(size_t i);      
+
+      /** @} */
+
+      /**
+       *  **********************************************************************
+       *  **********************************************************************
+       *  @defgroup ACCESS Access functions and operators
+       *  **********************************************************************
+       *  **********************************************************************
+       * @{
+       */
+
+      /**
+       *  @brief Gives access to a specified matrix row without range check
+       *  @return Subvector object representing the row
+       */
+      inline const SubVector<_ElemT>
+      operator []  (size_t i) const
+      {
+        assert(i < mMRows);
+        return SubVector<_ElemT>(mpData + (i * mStride), Cols());
+      }
+
+      inline SubVector<_ElemT>
+      operator []  (size_t i)
+      {
+        assert(i < mMRows);
+        return SubVector<_ElemT>(mpData + (i * mStride), Cols());
+      }
+
+      /**
+       *  @brief Gives access to a specified matrix row without range check
+       *  @return pointer to the first field of the row
+       */
+      inline  _ElemT*
+      pRowData(size_t i) 
+      {
+        assert(i < mMRows);
+        return mpData + i * mStride;
+      }
+
+      /**
+       *  @brief Gives access to a specified matrix row without range check
+       *  @return pointer to the first field of the row (const version)
+       */
+      inline const _ElemT*
+      pRowData(size_t i) const
+      {
+        assert(i < mMRows);
+        return mpData + i * mStride;
+      }
+
+      /**
+       *  @brief Gives access to matrix elements (row, col)
+       *  @return reference to the desired field
+       */
+      inline _ElemT&
+		operator () (size_t r, size_t c)
+      { 
+#ifdef PARANOID
+        assert(r < mMRows && c < mMCols);
+#endif
+		return *(mpData + r * mStride + c); 
+	  }
+
+      /**
+       *  @brief Gives access to matrix elements (row, col)
+       *  @return pointer to the desired field (const version)
+       */
+      inline const _ElemT
+		operator () (size_t r, size_t c) const
+      { 
+#ifdef PARANOID
+        assert(r < mMRows && c < mMCols);
+#endif
+		return *(mpData + r * mStride + c); 
+	  }
+
+      /**
+       * @brief Returns a matrix sub-range
+       * @param ro Row offset
+       * @param r  Rows in range
+       * @param co Column offset
+       * @param c  Coluns in range
+       * See @c SubMatrix class for details
+       */
+      SubMatrix<_ElemT>
+      Range(const size_t    ro, const size_t    r,
+            const size_t    co, const size_t    c)
+      { return SubMatrix<_ElemT>(*this, ro, r, co, c); }
+
+      const SubMatrix<_ElemT>
+      Range(const size_t    ro, const size_t    r,
+            const size_t    co, const size_t    c) const
+      { return SubMatrix<_ElemT>(*this, ro, r, co, c); }
+      /** @} */
+
+
+      /**
+       *  **********************************************************************
+       *  **********************************************************************
+       *  @defgroup MATH ROUTINES
+       *  **********************************************************************
+       *  **********************************************************************
+       *  @{
+       **/
+
+      /**
+       *  @brief Returns sum of all elements
+       */
+      _ElemT&
+      Sum() const;
+
+      ThisType &
+      DotMul(const ThisType& a);
+
+      ThisType &
+      Scale(_ElemT alpha);
+
+      ThisType &
+      ScaleCols(const Vector<_ElemT> &scale); // Equivalent to (*this) = (*this) * diag(scale).
+
+      ThisType &
+      ScaleRows(const Vector<_ElemT> &scale); // Equivalent to (*this) = diag(scale) * (*this);
+
+      /// Sum another matrix rMatrix with this matrix
+      ThisType&
+      Add(const Matrix<_ElemT>& rMatrix);
+
+   
+      /// Sum scaled matrix rMatrix with this matrix
+      ThisType&
+      AddScaled(_ElemT alpha, const Matrix<_ElemT>& rMatrix);
+
+      /// Apply log to all items of the matrix
+      ThisType&
+      ApplyLog();
+
+      /**
+       * @brief Computes the determinant of this matrix
+       * @return Returns the determinant of a matrix
+       * @ingroup MATH
+       *
+       */
+      _ElemT LogAbsDeterminant(_ElemT *DetSign=NULL);
+
+
+      /**
+       *  @brief Performs matrix inplace inversion
+       */
+      ThisType &
+      Invert(_ElemT *LogDet=NULL, _ElemT *DetSign=NULL, bool inverse_needed=true);
+
+      /**
+       *  @brief Performs matrix inplace inversion in double precision, even if this object is not double precision.
+       */
+      ThisType &
+      InvertDouble(_ElemT *LogDet=NULL, _ElemT *DetSign=NULL, bool inverse_needed=true){
+        double LogDet_tmp, DetSign_tmp;
+        Matrix<double> dmat(*this); dmat.Invert(&LogDet_tmp, &DetSign_tmp, inverse_needed); if(inverse_needed) (*this).Copy(dmat); 
+        if(LogDet) *LogDet = LogDet_tmp; if(DetSign) *DetSign = DetSign_tmp;
+        return *this;
+      }
+
+
+      /**
+       *  @brief Inplace matrix transposition. Applicable only to square matrices
+       */
+      ThisType &
+      Transpose()
+      {
+        assert(Rows()==Cols());
+        size_t M=Rows();
+        for(size_t i=0;i<M;i++)
+          for(size_t j=0;j<i;j++){
+           _ElemT &a = (*this)(i,j), &b = (*this)(j,i);
+		   std::swap(a,b);
+        }
+		return *this;
+      }
+
+
+      
+
+
+      bool IsSymmetric(_ElemT cutoff = 1.0e-05) const;
+
+      bool IsDiagonal(_ElemT cutoff = 1.0e-05) const;
+
+      bool IsUnit(_ElemT cutoff = 1.0e-05) const;
+
+      bool IsZero(_ElemT cutoff = 1.0e-05) const;
+
+      _ElemT FrobeniusNorm() const; // sqrt of sum of square elements.
+
+      _ElemT LargestAbsElem() const; // largest absolute value.
+
+	
+      friend _ElemT TNet::TraceOfProduct<_ElemT>(const Matrix<_ElemT> &A, const Matrix<_ElemT> &B); // tr(A B)
+      friend _ElemT TNet::TraceOfProductT<_ElemT>(const Matrix<_ElemT> &A, const Matrix<_ElemT> &B); // tr(A B^T)==tr(A^T B)
+      friend class SubMatrix<_ElemT>; // so it can get around const restrictions on the pointer to mpData.
+
+      /** **********************************************************************
+       *  **********************************************************************
+       *  @defgroup BLAS_ROUTINES BLAS ROUTINES
+       *  @ingroup MATH
+       *  **********************************************************************
+       *  **********************************************************************
+       **/
+
+      ThisType &
+      BlasGer(const _ElemT alpha, const Vector<_ElemT>& rA, const Vector<_ElemT>& rB);
+
+      ThisType &
+	    Axpy(const _ElemT alpha, const Matrix<_ElemT> &rM, MatrixTrasposeType transA=NO_TRANS);
+
+      ThisType &
+      BlasGemm(const _ElemT alpha,
+               const ThisType& rA, MatrixTrasposeType transA,
+               const ThisType& rB, MatrixTrasposeType transB,
+               const _ElemT beta = 0.0);
+
+
+      /** @} */
+
+
+      /** **********************************************************************
+       *  **********************************************************************
+       *  @defgroup IO Input/Output ROUTINES
+       *  **********************************************************************
+       *  **********************************************************************
+       *  @{
+       **/
+
+      friend std::ostream &
+      operator << <> (std::ostream & out, const ThisType & m);
+	  	
+      void PrintOut(char *file);
+      void ReadIn(char *file);
+
+
+      bool
+      LoadHTK(const char* pFileName);
+
+      /** @} */
+
+
+    protected:
+//      inline void swap4b(void *a);
+//      inline void swap2b(void *a);
+
+
+    protected:
+      /// data memory area
+      _ElemT*   mpData;
+
+      /// these atributes store the real matrix size as it is stored in memory
+      /// including memalignment
+      size_t    mMCols;       ///< Number of columns
+      size_t    mMRows;       ///< Number of rows
+      size_t    mStride;      ///< true number of columns for the internal matrix.
+                              ///< This number may differ from M_cols as memory
+                              ///< alignment might be used
+
+#ifdef STK_MEMALIGN_MANUAL
+      /// data to be freed (in case of manual memalignment use, see Common.h)
+      _ElemT*   mpFreeData;
+#endif
+    }; // class Matrix
+
+    template<>  Matrix<float> &  Matrix<float>::Invert(float *LogDet, float *DetSign, bool inverse_needed); // state that we will implement separately for float and double.
+    template<>  Matrix<double> &  Matrix<double>::Invert(double *LogDet, double *DetSign, bool inverse_needed);
+
+
+
+  /** **************************************************************************
+   ** **************************************************************************
+   *  @brief Sub-matrix representation
+   *
+   *  This class provides a way to work with matrix cutouts in STK.
+   *
+   *
+   */
+  template<typename _ElemT>
+    class SubMatrix : public Matrix<_ElemT>
+    {
+    typedef SubMatrix<_ElemT>    ThisType;
+
+    public:
+      /// Constructor
+      SubMatrix(const Matrix<_ElemT>& rT, // Input matrix cannot be const because SubMatrix can change its contents.
+                const size_t    ro,
+                const size_t    r,
+                const size_t    co,
+                const size_t    c);
+
+
+      /// The destructor
+      ~SubMatrix<_ElemT>()
+      {
+#ifndef STK_MEMALIGN_MANUAL
+        Matrix<_ElemT>::mpData = NULL;
+#else
+        Matrix<_ElemT>::mpFreeData = NULL;
+#endif
+      }
+
+      /// Assign operator
+      ThisType& operator=(const ThisType& rSrc)
+      {
+        //std::cout << "[PERFORMing operator= SubMatrix&^2]" << std::flush;
+        this->mpData = rSrc.mpData;
+        this->mMCols = rSrc.mMCols;
+        this->mMRows = rSrc.mMRows;
+        this->mStride = rSrc.mStride;
+        this->mpFreeData = rSrc.mpFreeData;
+        return *this;
+      }
+
+   
+
+      /// Initializes matrix (if not done by constructor)
+      ThisType &
+      Init(const size_t r,
+           const size_t c, bool clear=true)
+      { Error("Submatrix cannot do Init"); return *this; }
+
+      /**
+       * @brief Dealocates the matrix from memory and resets the dimensions to (0, 0)
+       */
+      void
+      Destroy()
+      { Error("Submatrix cannot do Destroy"); }
+
+
+
+    };
+
+
+
+  //Create useful shortcuts
+  typedef Matrix<BaseFloat> BfMatrix;
+  typedef SubMatrix<BaseFloat> BfSubMatrix;
+
+  /**
+   * Function for summing matrices of different types
+   */
+  template<typename _ElemT, typename _ElemU>
+  void Add(Matrix<_ElemT>& rDst,  const Matrix<_ElemU>& rSrc) {
+    assert(rDst.Cols() == rSrc.Cols());
+    assert(rDst.Rows() == rSrc.Rows());
+
+    for(size_t i=0; i<rDst.Rows(); i++) {
+      const _ElemU* p_src = rSrc.pRowData(i);
+      _ElemT* p_dst = rDst.pRowData(i);
+      for(size_t j=0; j<rDst.Cols(); j++) {
+        *p_dst++ += (_ElemT)*p_src++;
+      }
+    }
+  }
+
+  /**
+   * Function for summing matrices of different types
+   */
+  template<typename _ElemT, typename _ElemU>
+  void AddScaled(Matrix<_ElemT>& rDst, const Matrix<_ElemU>& rSrc, _ElemT scale) {
+    assert(rDst.Cols() == rSrc.Cols());
+    assert(rDst.Rows() == rSrc.Rows());
+
+    Vector<_ElemT> tmp(rDst[0]);
+
+    for(size_t i=0; i<rDst.Rows(); i++) {
+      tmp.Copy(rSrc[i]);
+      rDst[i].BlasAxpy(scale, tmp);
+
+      /*
+      const _ElemU* p_src = rSrc.pRowData(i);
+      _ElemT* p_dst = rDst.pRowData(i);
+      for(size_t j=0; j<rDst.Cols(); j++) {
+        *p_dst++ += (_ElemT)(*p_src++) * scale;
+      }
+      */
+    }
+  }
+
+
+
+
+
+} // namespace STK
+
+
+
+//*****************************************************************************
+//*****************************************************************************
+// we need to include the implementation
+#include "Matrix.tcc"
+//*****************************************************************************
+//*****************************************************************************
+
+
+/******************************************************************************
+ ******************************************************************************
+ * The following section contains specialized template definitions
+ * whose implementation is in Matrix.cc
+ */
+
+
+//#ifndef TNet_Matrix_h
+#endif