# HG changeset patch
# User idamnjanovic
# Date 1300285017 0
# Node ID c3eca463202dd7ca8cf7bd461c65539913962d81
# Parent  5f1f436057ca375ff53ecc7ebe79d6e5b1ad80f4


diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/add_dc.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/add_dc.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,33 @@
+function x = add_dc(y,dc,columns)
+%ADD_DC Add DC channel to signals.
+%   X = ADD_DC(Y,DC) adds the specified DC value to the (possibly
+%   multi-dimensional) signal Y, returning the result as X. DC should be a
+%   scalar value.
+%
+%   X = ADD_DC(Y,DC,'columns') where Y is a 2D matrix and DC is an array of
+%   length size(Y,2), treats the columns of Y as individual 1D signals, 
+%   adding to each one the corresponding DC value from the DC array. X is
+%   the same size as Y and contains the resulting signals.
+%
+%   See also REMOVE_DC.
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  April 2009
+
+
+if (nargin==3 && strcmpi(columns,'columns')), columns = 1;
+else columns = 0;
+end
+
+if (columns)
+  x = addtocols(y,dc);
+else
+  x = y + dc;
+end
+
+
+
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/addtocols.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/addtocols.c	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,85 @@
+/**************************************************************************
+ *
+ * File name: addtocols.c
+ *
+ * Ron Rubinstein
+ * Computer Science Department
+ * Technion, Haifa 32000 Israel
+ * ronrubin@cs
+ *
+ * Last Updated: 19.4.2009
+ *
+ *************************************************************************/
+
+
+#include "mex.h"
+
+
+/* Input Arguments */
+
+#define	X_IN	prhs[0]
+#define V_IN  prhs[1]
+
+
+/* Output Arguments */
+
+#define	Y_OUT	plhs[0]
+
+
+void mexFunction(int nlhs, mxArray *plhs[], 
+		             int nrhs, const mxArray*prhs[])
+     
+{ 
+    double *x, *y, *v, *xend;  
+    mwSize m,n,m1,n1;
+    mwIndex counter; 
+    
+    
+    /* Check for proper number of arguments */
+    
+    if (nrhs != 2) {
+      mexErrMsgTxt("Two input arguments required."); 
+    } else if (nlhs > 1) {
+      mexErrMsgTxt("Too many output arguments."); 
+    } 
+    
+    
+    /* Check the the input dimensions */ 
+    
+    m = mxGetM(X_IN);
+    n = mxGetN(X_IN);
+    if (!mxIsDouble(X_IN) || mxIsComplex(X_IN) || mxGetNumberOfDimensions(X_IN)>2) {
+      mexErrMsgTxt("ADDTOCOLS requires that X be a double matrix.");
+    }
+    m1 = mxGetM(V_IN);
+    n1 = mxGetN(V_IN);
+    if (!mxIsDouble(V_IN) || mxIsComplex(V_IN) || (m1!=1 && n1!=1)) {
+      mexErrMsgTxt("ADDTOCOLS requires that V be a double vector.");
+    }
+    if ((m1==1 && n1!=n) || (n1==1 && m1!=n)) {
+      mexErrMsgTxt("Error in ADDTOCOLS: dimensions of V and X must agree.");
+    }
+    
+    
+    /* Create a matrix for the return argument */ 
+    Y_OUT = mxCreateDoubleMatrix(m, n, mxREAL);
+         
+    
+    /* Assign pointers to the various parameters */ 
+    x = mxGetPr(X_IN); 
+    v = mxGetPr(V_IN);
+    y = mxGetPr(Y_OUT);
+            
+    
+    /* Do the actual computation */
+    
+    xend = x+(m*n);
+    counter = 0;
+    while (x<xend) {
+      (*y) = (*x) + (*v);
+      y++; x++; counter++;
+      if (counter==m) {v++; counter=0;}
+    }
+    
+    return;
+}
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/addtocols.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/addtocols.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,13 @@
+%ADDTOCOLS Add values to the columns of a matrix.
+%  Y=ADDTOCOLS(X,V) adds to each column of the MxN matrix X the
+%  corresponding value from the N-element vector V.
+%
+%  See also NORMCOLS.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  June 2005
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/col2imstep.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/col2imstep.c	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,146 @@
+/**************************************************************************
+ *
+ * File name: col2imstep.c
+ *
+ * Ron Rubinstein
+ * Computer Science Department
+ * Technion, Haifa 32000 Israel
+ * ronrubin@cs
+ *
+ * Last Updated: 31.8.2009
+ *
+ *************************************************************************/
+
+
+#include "mex.h"
+
+
+/* Input Arguments */
+
+#define	B_IN	 prhs[0]
+#define N_IN   prhs[1]
+#define SZ_IN  prhs[2]
+#define S_IN   prhs[3]
+
+
+/* Output Arguments */
+
+#define	X_OUT	plhs[0]
+
+
+void mexFunction(int nlhs, mxArray *plhs[], 
+		             int nrhs, const mxArray*prhs[])
+     
+{ 
+    double *x, *b, *s;
+    mwSize sz[3], stepsize[3], n[3], ndims;
+    mwIndex i, j, k, l, m, t, blocknum;
+    
+    
+    /* Check for proper number of arguments */
+    
+    if (nrhs < 3 || nrhs > 4) {
+      mexErrMsgTxt("Invalid number of input arguments."); 
+    } else if (nlhs > 1) {
+      mexErrMsgTxt("Too many output arguments."); 
+    } 
+    
+    
+    /* Check the the input dimensions */ 
+    
+    if (!mxIsDouble(B_IN) || mxIsComplex(B_IN) || mxGetNumberOfDimensions(B_IN)>2) {
+      mexErrMsgTxt("B should be a double matrix.");
+    }
+    if (!mxIsDouble(N_IN) || mxIsComplex(N_IN) || mxGetNumberOfDimensions(N_IN)>2) {
+      mexErrMsgTxt("Invalid output matrix size.");
+    }
+    ndims = mxGetM(N_IN)*mxGetN(N_IN);
+    if (ndims<2 || ndims>3) {
+      mexErrMsgTxt("Output matrix can only be 2-D or 3-D.");
+    }
+    if (!mxIsDouble(SZ_IN) || mxIsComplex(SZ_IN) || mxGetNumberOfDimensions(SZ_IN)>2 || mxGetM(SZ_IN)*mxGetN(SZ_IN)!=ndims) {
+      mexErrMsgTxt("Invalid block size.");
+    }
+    if (nrhs == 4) {
+      if (!mxIsDouble(S_IN) || mxIsComplex(S_IN) || mxGetNumberOfDimensions(S_IN)>2 || mxGetM(S_IN)*mxGetN(S_IN)!=ndims) {
+        mexErrMsgTxt("Invalid step size.");
+      }
+    }
+    
+    
+    /* Get parameters */
+    
+    s = mxGetPr(N_IN);
+    if (s[0]<1 || s[1]<1 || (ndims==3 && s[2]<1)) {
+      mexErrMsgTxt("Invalid output matrix size.");
+    }
+    n[0] = (mwSize)(s[0] + 0.01);
+    n[1] = (mwSize)(s[1] + 0.01);
+    n[2] = ndims==3 ? (mwSize)(s[2] + 0.01) : 1;
+    
+    s = mxGetPr(SZ_IN);
+    if (s[0]<1 || s[1]<1 || (ndims==3 && s[2]<1)) {
+      mexErrMsgTxt("Invalid block size.");
+    }
+    sz[0] = (mwSize)(s[0] + 0.01);
+    sz[1] = (mwSize)(s[1] + 0.01);
+    sz[2] = ndims==3 ? (mwSize)(s[2] + 0.01) : 1;
+    
+    if (nrhs == 4) {
+      s = mxGetPr(S_IN);
+      if (s[0]<1 || s[1]<1 || (ndims==3 && s[2]<1)) {
+        mexErrMsgTxt("Invalid step size.");
+      }
+      stepsize[0] = (mwSize)(s[0] + 0.01);
+      stepsize[1] = (mwSize)(s[1] + 0.01);
+      stepsize[2] = ndims==3 ? (mwSize)(s[2] + 0.01) : 1;
+    }
+    else {
+      stepsize[0] = stepsize[1] = stepsize[2] = 1;
+    }
+    
+    if (n[0]<sz[0] || n[1]<sz[1] || (ndims==3 && n[2]<sz[2])) {
+      mexErrMsgTxt("Block size too large.");
+    }
+
+    if (mxGetN(B_IN) != ((n[0]-sz[0])/stepsize[0]+1)*((n[1]-sz[1])/stepsize[1]+1)*((n[2]-sz[2])/stepsize[2]+1)) {
+      mexErrMsgTxt("Invalid number of columns in B. Please use IM2COLSTEP to compute B.");
+    }
+    
+    
+    /* Create a matrix for the return argument */
+    
+    X_OUT = mxCreateNumericArray(ndims, n, mxDOUBLE_CLASS, mxREAL);
+    
+    
+    /* Assign pointers */
+    
+    b = mxGetPr(B_IN);
+    x = mxGetPr(X_OUT);
+            
+    
+    /* Do the actual computation */
+    
+    blocknum = 0;
+    
+    /* iterate over all blocks */
+    for (k=0; k<=n[2]-sz[2]; k+=stepsize[2]) {
+      for (j=0; j<=n[1]-sz[1]; j+=stepsize[1]) {
+        for (i=0; i<=n[0]-sz[0]; i+=stepsize[0]) {
+          
+          /* add single block */
+          for (m=0; m<sz[2]; m++) {
+            for (l=0; l<sz[1]; l++) {
+              for (t=0; t<sz[0]; t++) {
+                (x+(k+m)*n[0]*n[1]+(j+l)*n[0]+i)[t] += (b + blocknum*sz[0]*sz[1]*sz[2] + m*sz[0]*sz[1] + l*sz[0])[t];
+              }
+            }
+          }
+          blocknum++;
+          
+        }
+      }
+    }
+    
+    return;
+}
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/col2imstep.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/col2imstep.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,25 @@
+%COL2IMSTEP Rearrange matrix columns into blocks.
+%  A = COL2IMSTEP(B,[MM NN],[N1 N2]) rearranges the columns of B into
+%  sliding N1-by-N2 blocks producing the matrix A of size MM-by-NN. B is
+%  usually the result of calling IM2COLSTEP(...) with a stepsize of 1, or
+%  using Matlab's IM2COL(..,'sliding'). Overlapping blocks are summed in A.
+%
+%  A = COL2IMSTEP(B,[MM NN],[N1 N2],[S1 S2]) arranges the blocks in A with
+%  a step size of (S1,S2) between them. The first block is at A(1:N1,1:N2),
+%  and the rest are at A((1:N1)+i*S1,(1:N2)+j*S2). Overlapping blocks are
+%  summed in A. Note that B is usually the result of calling
+%  IM2COLSTEP(...) with a stepsize of [S1 S2].
+%
+%  A = IM2COLSTEP(B,[MM NN KK],[N1 N2 N3],[S1 S2 S3]) generates a 3-D
+%  output matrix A. The step size [S1 S2 S3] may be ommitted, and defaults
+%  to [1 1 1].
+%
+%  See also IM2COLSTEP, IM2COL, COUNTCOVER.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  August 2009
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/collincomb.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/collincomb.c	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,165 @@
+/**************************************************************************
+ *
+ * File name: collincomb.c
+ *
+ * Ron Rubinstein
+ * Computer Science Department
+ * Technion, Haifa 32000 Israel
+ * ronrubin@cs
+ *
+ * Last Updated: 21.5.2009
+ *
+ *************************************************************************/
+
+
+#include "mex.h"
+
+
+/* Input Arguments */
+
+#define	A_IN	   prhs[0]
+#define ROWS_IN  prhs[1]
+#define COLS_IN1 prhs[1]
+#define COLS_IN2 prhs[2]
+#define X_IN1    prhs[2]
+#define X_IN2    prhs[3]
+
+
+/* Output Arguments */
+
+#define	Y_OUT	plhs[0]
+
+
+void mexFunction(int nlhs, mxArray *plhs[],
+int nrhs, const mxArray*prhs[])
+
+{
+  double *A, *x, *y, *rows, *cols;
+  mwSize m,n,m1,n1,m2,n2,rownum,colnum;
+  mwIndex col_id,*row_ids,i,j;
+  int rownumspecified=0;
+  
+  
+  /* Check for proper number of arguments */
+  
+  if (nrhs!=3 && nrhs!=4) {
+    mexErrMsgTxt("Invalid number of arguments.");
+  } else if (nlhs > 1) {
+    mexErrMsgTxt("Too many output arguments.");
+  }
+  
+  
+  /* Check the input dimensions */
+  
+  m = mxGetM(A_IN);
+  n = mxGetN(A_IN);
+  if (!mxIsDouble(A_IN) || mxIsComplex(A_IN) || mxGetNumberOfDimensions(A_IN)>2) {
+    mexErrMsgTxt("COLLINCOMB requires that A be a double matrix.");
+  }
+  
+  if (nrhs==3) {
+    
+    m1 = mxGetM(COLS_IN1);
+    n1 = mxGetN(COLS_IN1);
+    if (!mxIsDouble(COLS_IN1) || mxIsComplex(COLS_IN1) || (m1!=1 && n1!=1)) {
+      mexErrMsgTxt("COLLINCOMB requires that COLS be an index vector of type double.");
+    }
+    colnum = (m1 > n1) ? m1 : n1;   /* the number of columns in the linear combination */
+    
+    m2 = mxGetM(X_IN1);
+    n2 = mxGetN(X_IN1);
+    if (!mxIsDouble(X_IN1) || mxIsComplex(X_IN1) || (m2!=1 && n2!=1)) {
+      mexErrMsgTxt("COLLINCOMB requires that X be a double vector.");
+    }
+    
+    if (m2!=colnum && n2!=colnum) {
+      mexErrMsgTxt("The length of X does not match the number of columns in COLS.");
+    }
+    
+    rows = 0;
+    Y_OUT = mxCreateDoubleMatrix(m, 1, mxREAL);
+    cols = mxGetPr(COLS_IN1);
+    x = mxGetPr(X_IN1);
+  }
+  else {
+    
+    m1 = mxGetM(ROWS_IN);
+    n1 = mxGetN(ROWS_IN);
+    if (!mxIsDouble(ROWS_IN) || mxIsComplex(ROWS_IN) || (m1!=1 && n1!=1)) {
+      mexErrMsgTxt("COLLINCOMB requires that ROWS be an index vector of type double.");
+    }
+    rownum = (m1 > n1) ? m1 : n1;   /* the number of rows in the linear combination */
+    rownumspecified = 1;
+    rows = mxGetPr(ROWS_IN);
+    
+    m1 = mxGetM(COLS_IN2);
+    n1 = mxGetN(COLS_IN2);
+    if (!mxIsDouble(COLS_IN2) || mxIsComplex(COLS_IN2) || (m1!=1 && n1!=1)) {
+      mexErrMsgTxt("COLLINCOMB requires that COLS be an index vector of type double.");
+    }
+    colnum = (m1 > n1) ? m1 : n1;   /* the number of columns in the linear combination */
+    
+    m2 = mxGetM(X_IN2);
+    n2 = mxGetN(X_IN2);
+    if (!mxIsDouble(X_IN2) || mxIsComplex(X_IN2) || (m2!=1 && n2!=1)) {
+      mexErrMsgTxt("COLLINCOMB requires that X be a double vector.");
+    }
+    
+    if (m2!=colnum && n2!=colnum) {
+      mexErrMsgTxt("The length of X does not match the number of columns in COLS.");
+    }
+    
+    Y_OUT = mxCreateDoubleMatrix(rownum, 1, mxREAL);
+    cols = mxGetPr(COLS_IN2);
+    x = mxGetPr(X_IN2);
+  }
+  
+  
+  /* Assign pointers to the various parameters */
+  A = mxGetPr(A_IN);
+  y = mxGetPr(Y_OUT);
+  
+  
+  if (rownumspecified) {
+    
+     /* check row indices */
+    
+    row_ids = (mwIndex*)mxMalloc(rownum*sizeof(mwIndex));
+    
+    for (i=0; i<rownum; ++i) {
+      row_ids[i] = (mwIndex)(rows[i]+0.1)-1;
+      if (row_ids[i]<0 || row_ids[i]>=m) {
+        mexErrMsgTxt("Row index in ROWS is out of range.");
+      }
+    }
+    
+    /* Do the actual computation */
+    for (i=0; i<colnum; ++i) {
+      col_id = (mwIndex)(cols[i]+0.1)-1;
+      if (col_id<0 || col_id>=n) {
+        mexErrMsgTxt("Column index in COLS is out of range.");
+      }
+      for (j=0; j<rownum; ++j) {
+        y[j] += A[m*col_id+row_ids[j]]*x[i];
+      }
+    }
+    
+    mxFree(row_ids);
+  }
+  
+  else {
+    
+    /* Do the actual computation */
+    for (i=0; i<colnum; ++i) {
+      col_id = (mwIndex)(cols[i]+0.1)-1;
+      if (col_id<0 || col_id>=n) {
+        mexErrMsgTxt("Column index in COLS is out of range.");
+      }
+      for (j=0; j<m; ++j) {
+        y[j] += A[m*col_id+j]*x[i];
+      }
+    }
+  }
+  
+  return;
+}
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/collincomb.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/collincomb.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,27 @@
+%COLLINCOMB Linear combination of matrix columns.
+%  Y = COLLINCOMB(A,COLS,X) computes a linear combination of the columns of
+%  the matrix A. The column indices are specified in the vector COLS, and
+%  the correspoinding coefficients are specified in the vector X. The
+%  vectors COLS and X must be of the same length. 
+%  
+%  The call Y = COLLINCOMB(A,COLS,X) is essentially equivalent to
+%
+%         Y = A(:,COLS)*X .
+%
+%  However, it is implemented much more efficiently.
+%
+%  Y = COLLINCOMB(A,ROWS,COLS,X) only works on the rows of A specified
+%  in ROWS, returning a vector of length equal to ROWS. This call is
+%  essentially equivalent to the command
+%
+%         Y = A(ROWS,COLS)*X .
+%
+%  See also ROWLINCOMB.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  April 2009
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/countcover.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/countcover.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,33 @@
+function cnt = countcover(sz,blocksize,stepsize)
+%COUNTCOVER Covering of signal samples by blocks
+%  CNT = COUNTCOVER(SZ,BLOCKSIZE,STEPSIZE) assumes a p-dimensional signal
+%  of size SZ=[N1 N2 ... Np] covered by (possibly overlapping) blocks of
+%  size BLOCKSIZE=[M1 M2 ... Mp]. The blocks start at position (1,1,..,1)
+%  and are shifted between them by steps of size STEPSIZE=[S1 S2 ... Sp].
+%  COUNTCOVER returns a matrix the same size as the signal, containing in
+%  each entry the number of blocks covering that sample.
+%
+%  See also IM2COLSTEP, COL2IMSTEP, IM2COL.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  August 2008
+
+
+cnt = ones(sz);
+for k = 1:length(sz)
+  
+  % this code is modified from function NDGRID, so it computes one
+  % output argument of NDGRID at a time (to conserve memory)
+  ids = (1:sz(k))';
+  s = sz; s(k) = [];
+  ids = reshape(ids(:,ones(1,prod(s))),[length(ids) s]);
+  ids = permute(ids,[2:k 1 k+1:length(sz)]);
+  
+  cnt = cnt .* max( min(floor((ids-1)/stepsize(k)),floor((sz(k)-blocksize(k))/stepsize(k))) - ...
+                    max(ceil((ids-blocksize(k))/stepsize(k)),0) + 1 , 0 );
+end
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/dictdist.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/dictdist.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,61 @@
+function [dist,ratio] = dictdist(approxD,D,epsilon)
+%DICTDIST Distance between dictionaries.
+%  [DIST,RATIO] = DICTDIST(APPROXD,D) computes the distance between the
+%  approximate dictionary APPROXD and the true dictionary D, where APPROXD
+%  is NxK and D is NxM.
+%
+%  The distance between the dictionary APPROXD and a single atom A of D is
+%  defined as:
+%
+%      DIST(APPROXD,A) = min  { 1-abs(APPROXD(:,i)' * A) }
+%                         i
+%
+%  The distance between the dictionaries APPROXD and D is defined as:
+%
+%      DIST(APPROXD,D) = sum { dist(APPROXD, D(:,k)) } / M
+%                         k
+%
+%  Note that 0 <= DIST(APPROXD,D) <= 1, where 0 implies that all atoms in D
+%  appear in APPROXD, and 1 implies that the atoms of D are orthogonal to
+%  APPROXD.
+%
+%  The similarity ratio between APPROXD and D is defined as:
+%
+%      RATIO(APPROXD,D) = #(atoms in D that appear in APPROXD) / M
+%
+%  where two atoms are considered identical when DIST(A1,A2) < EPSILON with
+%  EPSILON=0.01 by default. Note that 0 <= RATIO(APPROXD,D) <= 1, where 0
+%  means APPROXD and D have no identical atoms, and 1 means that all atoms
+%  of D appear in APPROXD.
+%
+%  [DIST,RATIO] = DICTDIST(DICT1,DICT2,EPSILON) specifies a different value
+%  for EPSILON.
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  October 2007
+
+
+if (nargin < 3), epsilon = 0.01; end
+
+[n,m] = size(D);
+
+approxD = normcols(approxD*spdiag(sign(approxD(1,:))));
+D = normcols(D*spdiag(sign(D(1,:))));
+
+identical_atoms = 0;
+dist = 0;
+
+for i = 1:m
+  atom = D(:,i);
+  distances = 1-abs(atom'*approxD);
+  mindist = min(distances);
+  dist = dist + mindist;
+  identical_atoms = identical_atoms + (mindist < epsilon);
+end
+
+dist = dist / m;
+ratio = identical_atoms / m;
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/im2colstep.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/im2colstep.c	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,131 @@
+/**************************************************************************
+ *
+ * File name: im2colstep.c
+ *
+ * Ron Rubinstein
+ * Computer Science Department
+ * Technion, Haifa 32000 Israel
+ * ronrubin@cs
+ *
+ * Last Updated: 31.8.2009
+ *
+ *************************************************************************/
+
+
+#include "mex.h"
+#include <string.h>
+
+
+/* Input Arguments */
+
+#define	X_IN	 prhs[0]
+#define SZ_IN  prhs[1]
+#define S_IN   prhs[2]
+
+
+/* Output Arguments */
+
+#define	B_OUT	plhs[0]
+
+
+void mexFunction(int nlhs, mxArray *plhs[], 
+		             int nrhs, const mxArray*prhs[])
+     
+{ 
+    double *x, *b, *s;
+    mwSize sz[3], stepsize[3], n[3], ndims;
+    mwIndex i, j, k, l, m, blocknum;
+    
+    
+    /* Check for proper number of arguments */
+    
+    if (nrhs < 2 || nrhs > 3) {
+      mexErrMsgTxt("Invalid number of input arguments."); 
+    } else if (nlhs > 1) {
+      mexErrMsgTxt("Too many output arguments."); 
+    } 
+    
+    
+    /* Check the the input dimensions */ 
+    
+    ndims = mxGetNumberOfDimensions(X_IN);
+    
+    if (!mxIsDouble(X_IN) || mxIsComplex(X_IN) || ndims>3) {
+      mexErrMsgTxt("X should be a 2-D or 3-D double matrix.");
+    }
+    if (!mxIsDouble(SZ_IN) || mxIsComplex(SZ_IN) || mxGetNumberOfDimensions(SZ_IN)>2 || mxGetM(SZ_IN)*mxGetN(SZ_IN)!=ndims) {
+      mexErrMsgTxt("Invalid block size.");
+    }
+    if (nrhs == 3) {
+      if (!mxIsDouble(S_IN) || mxIsComplex(S_IN) || mxGetNumberOfDimensions(S_IN)>2 || mxGetM(S_IN)*mxGetN(S_IN)!=ndims) {
+        mexErrMsgTxt("Invalid step size.");
+      }
+    }
+    
+    
+    /* Get parameters */
+    
+    s = mxGetPr(SZ_IN);
+    if (s[0]<1 || s[1]<1 || (ndims==3 && s[2]<1)) {
+      mexErrMsgTxt("Invalid block size.");
+    }
+    sz[0] = (mwSize)(s[0] + 0.01);
+    sz[1] = (mwSize)(s[1] + 0.01);
+    sz[2] = ndims==3 ? (mwSize)(s[2] + 0.01) : 1;
+    
+    if (nrhs == 3) {
+      s = mxGetPr(S_IN);
+      if (s[0]<1 || s[1]<1 || (ndims==3 && s[2]<1)) {
+        mexErrMsgTxt("Invalid step size.");
+      }
+      stepsize[0] = (mwSize)(s[0] + 0.01);
+      stepsize[1] = (mwSize)(s[1] + 0.01);
+      stepsize[2] = ndims==3 ? (mwSize)(s[2] + 0.01) : 1;
+    }
+    else {
+      stepsize[0] = stepsize[1] = stepsize[2] = 1;
+    }
+    
+    n[0] = (mxGetDimensions(X_IN))[0];
+    n[1] = (mxGetDimensions(X_IN))[1];
+    n[2] = ndims==3 ? (mxGetDimensions(X_IN))[2] : 1;
+    
+    if (n[0]<sz[0] || n[1]<sz[1] || (ndims==3 && n[2]<sz[2])) {
+      mexErrMsgTxt("Block size too large.");
+    }
+    
+    
+    /* Create a matrix for the return argument */
+    
+    B_OUT = mxCreateDoubleMatrix(sz[0]*sz[1]*sz[2], ((n[0]-sz[0])/stepsize[0]+1)*((n[1]-sz[1])/stepsize[1]+1)*((n[2]-sz[2])/stepsize[2]+1), mxREAL);
+    
+    
+    /* Assign pointers */
+    
+    x = mxGetPr(X_IN);
+    b = mxGetPr(B_OUT);
+            
+    
+    /* Do the actual computation */
+    
+    blocknum = 0;
+    
+    /* iterate over all blocks */
+    for (k=0; k<=n[2]-sz[2]; k+=stepsize[2]) {
+      for (j=0; j<=n[1]-sz[1]; j+=stepsize[1]) {
+        for (i=0; i<=n[0]-sz[0]; i+=stepsize[0]) {
+          
+          /* copy single block */
+          for (m=0; m<sz[2]; m++) {
+            for (l=0; l<sz[1]; l++) {
+              memcpy(b + blocknum*sz[0]*sz[1]*sz[2] + m*sz[0]*sz[1] + l*sz[0], x+(k+m)*n[0]*n[1]+(j+l)*n[0]+i, sz[0]*sizeof(double));
+            }
+          }
+          blocknum++;
+          
+        }
+      }
+    }
+    
+    return;
+}
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/im2colstep.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/im2colstep.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,31 @@
+%IM2COLSTEP Rearrange matrix blocks into columns.
+%  B = IM2COLSTEP(A,[N1 N2]) converts each sliding N1-by-N2 block of the
+%  2-D matrix A into a column of B, with no zero padding. B has N1*N2 rows
+%  and will contain as many columns as there are N1-by-N2 neighborhoods in
+%  A. Each column of B contains a neighborhood of A reshaped as NHOOD(:),
+%  where NHOOD is a matrix containing an N1-by-N2 neighborhood of A.
+%
+%  B = IM2COLSTEP(A,[N1 N2],[S1 S2]) extracts neighborhoods of A with a
+%  step size of (S1,S2) between them. The first extracted neighborhood is
+%  A(1:N1,1:N2), and the rest are of the form A((1:N1)+i*S1,(1:N2)+j*S2).
+%  Note that to ensure coverage of all A by neighborhoods,
+%  (size(A,i)-Ni)/Si must be whole for i=1,2. The default function behavior
+%  corresponds to [S1 S2] = [1 1]. Setting S1>=N1 and S2>=N2 results in no
+%  overlap between the neighborhoods.
+%
+%  B = IM2COLSTEP(A,[N1 N2 N3],[S1 S2 S3]) operates on a 3-D matrix A. The
+%  step size [S1 S2 S3] may be ommitted, and defaults to [1 1 1].
+%
+%  Note: the call IM2COLSTEP(A,[N1 N2]) produces the same output as
+%  Matlab's IM2COL(A,[N1 N2],'sliding'). However, it is significantly
+%  faster.
+%
+%  See also COL2IMSTEP, IM2COL, COUNTCOVER.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  August 2009
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/imnormalize.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/imnormalize.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,19 @@
+function y = imnormalize(x)
+%IMNORMALIZE Normalize image values.
+%  Y = IMNORMALIZE(X) linearly transforms the intensity values of the image
+%  X to tightly cover the range [0,1]. If X has more than one channel, the
+%  channels are handled as one and normalized using the same transform.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  May 2004
+
+
+maxval = max(x(:));
+minval = min(x(:));
+
+y = (x-minval) / (maxval-minval);
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/iswhole.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/iswhole.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,17 @@
+function z = iswhole(x,epsilon)
+%ISWHOLE Determine whole numbers with finite precision.
+%  Z = ISWHOLE(X,EPSILON) returns a matrix the same size as X, containing
+%  1's where X is whole up to precision EPSILON, and 0's elsewhere. 
+%
+%  Z = ISWHOLE(X) uses the default value of EPSILON=1e-6.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  May 2005
+
+if (nargin<2), epsilon = 1e-6; end
+z = abs(round(x)-x) < epsilon;
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/make.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/make.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,40 @@
+function make
+%MAKE Build the KSVDBox MEX support files.
+%  MAKE compiles the KSVDBox supporting MEX functions, using Matlab's
+%  default MEX compiler. If the MEX compiler has not been set-up before,
+%  please run 
+%
+%    mex -setup
+%
+%  before using this MAKE file.
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  August 2009
+
+
+% detect platform 
+
+compstr = computer;
+is64bit = strcmp(compstr(end-1:end),'64');
+
+
+% compilation parameters
+
+compile_params = cell(0);
+if (is64bit)
+  compile_params{1} = '-largeArrayDims';
+end
+
+
+% Compile files %
+
+sourcefiles = {{'addtocols.c'}, {'collincomb.c'}, {'rowlincomb.c'}, {'sprow.c','mexutils.c'}, {'im2colstep.c'}, {'col2imstep.c'}};
+
+for i = 1:length(sourcefiles)
+  printf('Compiling %s...', sourcefiles{i}{1});
+  mex(sourcefiles{i}{:},compile_params{:});
+end
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/mexutils.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/mexutils.c	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,79 @@
+/**************************************************************************
+ *
+ * File name: mexutils.c
+ *
+ * Ron Rubinstein
+ * Computer Science Department
+ * Technion, Haifa 32000 Israel
+ * ronrubin@cs
+ *
+ * Last Updated: 15.8.2009
+ *
+ *************************************************************************/
+
+#include "mexutils.h"
+#include <math.h>
+
+
+
+/* verify that the mxArray contains a double matrix */
+
+void checkmatrix(const mxArray *param, char *fname, char *pname)
+{
+  char errmsg[100];
+  sprintf(errmsg, "%.15s requires that %.25s be a double matrix.", fname, pname);
+  if (!mxIsDouble(param) || mxIsComplex(param) || mxGetNumberOfDimensions(param)>2) {
+    mexErrMsgTxt(errmsg);
+  }
+}
+
+
+/* verify that the mxArray contains a 1-D double vector */
+
+void checkvector(const mxArray *param, char *fname, char *pname)
+{
+  char errmsg[100];
+  sprintf(errmsg, "%.15s requires that %.25s be a double vector.", fname, pname);
+  if (!mxIsDouble(param) || mxIsComplex(param) || mxGetNumberOfDimensions(param)>2 || (mxGetM(param)!=1 && mxGetN(param)!=1)) {
+    mexErrMsgTxt(errmsg);
+  }
+}
+
+
+/* verify that the mxArray contains a double scalar */
+
+void checkscalar(const mxArray *param, char *fname, char *pname)
+{
+  char errmsg[100];
+  sprintf(errmsg, "%.15s requires that %.25s be a double scalar.", fname, pname);
+  if (!mxIsDouble(param) || mxIsComplex(param) || mxGetNumberOfDimensions(param)>2 || 
+      mxGetM(param)!=1 || mxGetN(param)!=1) 
+  {
+    mexErrMsgTxt(errmsg);
+  }
+}
+
+
+/* verify that the mxArray contains a sparse matrix */
+
+void checksparse(const mxArray *param, char *fname, char *pname)
+{
+  char errmsg[100];
+  sprintf(errmsg, "%.15s requires that %.25s be sparse.", fname, pname);
+  if (!mxIsSparse(param)) {
+    mexErrMsgTxt(errmsg);
+  }
+}
+
+
+/* verify that the mxArray contains a 1-dimensional cell array */
+
+void checkcell_1d(const mxArray *param, char *fname, char *pname)
+{
+  char errmsg[100];
+  sprintf(errmsg, "%.15s requires that %.25s be a 1-D cell array.", fname, pname);
+  if (!mxIsCell(param) || mxGetNumberOfDimensions(param)>2 || (mxGetM(param)!=1 && mxGetN(param)!=1)) {
+    mexErrMsgTxt(errmsg);
+  }
+}
+
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/mexutils.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/mexutils.h	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,103 @@
+/**************************************************************************
+ *
+ * File name: mexutils.h
+ *
+ * Ron Rubinstein
+ * Computer Science Department
+ * Technion, Haifa 32000 Israel
+ * ronrubin@cs
+ *
+ * Last Updated: 18.8.2009
+ *
+ * Utility functions for MEX files.
+ *
+ *************************************************************************/
+
+
+#ifndef __MEX_UTILS_H__
+#define __MEX_UTILS_H__
+
+#include "mex.h"
+
+
+
+/**************************************************************************
+ * Function checkmatrix:
+ *
+ * Verify that the specified mxArray is real, of type double, and has 
+ * no more than two dimensions. If not, an error message is printed
+ * and the mex file terminates.
+ * 
+ * Parameters:
+ *   param - the mxArray to be checked
+ *   fname - the name of the function where the error occured (15 characters or less)
+ *   pname - the name of the parameter (25 characters or less)
+ *
+ **************************************************************************/
+void checkmatrix(const mxArray *param, char *fname, char *pname);
+
+
+/**************************************************************************
+ * Function checkvector:
+ *
+ * Verify that the specified mxArray is 1-D, real, and of type double. The
+ * vector may be a column or row vector. Otherwise, an error message is
+ * printed and the mex file terminates.
+ * 
+ * Parameters:
+ *   param - the mxArray to be checked
+ *   fname - the name of the function where the error occured (15 characters or less)
+ *   pname - the name of the parameter (25 characters or less)
+ *
+ **************************************************************************/
+void checkvector(const mxArray *param, char *fname, char *pname);
+
+
+/**************************************************************************
+ * Function checkscalar:
+ *
+ * Verify that the specified mxArray represents a real double scalar value. 
+ * If not, an error message is printed and the mex file terminates.
+ * 
+ * Parameters:
+ *   param - the mxArray to be checked
+ *   fname - the name of the function where the error occured (15 characters or less)
+ *   pname - the name of the parameter (25 characters or less)
+ *
+ **************************************************************************/
+void checkscalar(const mxArray *param, char *fname, char *pname);
+
+
+/**************************************************************************
+ * Function checksparse:
+ *
+ * Verify that the specified mxArray contains a sparse matrix. If not,
+ * an error message is printed and the mex file terminates.
+ * 
+ * Parameters:
+ *   param - the mxArray to be checked
+ *   fname - the name of the function where the error occured (15 characters or less)
+ *   pname - the name of the parameter (25 characters or less)
+ *
+ **************************************************************************/
+void checksparse(const mxArray *param, char *fname, char *pname);
+
+
+/**************************************************************************
+ * Function checkcell_1d:
+ *
+ * Verify that the specified mxArray is a 1-D cell array. The cell array 
+ * may be arranged as either a column or a row. If not, an error message 
+ * is printed and the mex file terminates.
+ * 
+ * Parameters:
+ *   param - the mxArray to be checked
+ *   fname - the name of the function where the error occured (15 characters or less)
+ *   pname - the name of the parameter (25 characters or less)
+ *
+ **************************************************************************/
+void checkcell_1d(const mxArray *param, char *fname, char *pname);
+
+
+#endif
+
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/normcols.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/normcols.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,17 @@
+function y = normcols(x)
+%NORMCOLS Normalize matrix columns.
+%  Y = NORMCOLS(X) normalizes the columns of X to unit length, returning
+%  the result as Y.
+%
+%  See also ADDTOCOLS.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  April 2009
+
+
+y = x*spdiag(1./sqrt(sum(x.*x)));
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/printf.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/printf.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,26 @@
+function str = printf(varargin)
+%PRINTF Print formatted text to screen.
+%  PRINTF(FMT,VAL1,VAL2,...) formats the data in VAL1,VAL2,... according to
+%  the format string FMT, and prints the result to the screen.
+%
+%  The call to PRINTF(FMT,VAL1,VAL2,...) simply invokes the call
+%  DISP(SPRINTF(FMT,VAL1,VAL2,...)). For a complete description of the
+%  format string options see function SPRINTF.
+%
+%  STR = PRINTF(...) also returns the formatted string.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  April 2008
+
+
+if (nargout>0)
+  str = sprintf(varargin{:});
+  disp(str);
+else
+  disp(sprintf(varargin{:}));
+end
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/reggrid.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/reggrid.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,136 @@
+function [varargout] = reggrid(sz,num,mode)
+%REGGRID Regular sampling grid.
+%  [I1,I2,...,Ip] = REGGRID([N1 N2 ... Np], NUM) returns the indices
+%  of a regular uniform sampling grid over a p-dimensional matrix with
+%  dimensions N1xN2x...xNp. NUM is the minimal number of required samples,
+%  and it is ensured that the actual number of samples, given by
+%  length(I1)xlength(I2)x...xlength(Ip), is at least as large as NUM.
+%
+%  [I1,I2,...,Ip] = REGGRID([N1 N2 ... Np], NUM,'MODE') specifies the
+%  method for distributing the samples along each dimension. Valid modes
+%  include 'eqdist' (the default mode) and 'eqnum'. 'eqdist' indicates an
+%  equal distance between the samples in each dimension, while 'eqnum'
+%  indicates an equal number of samples in each dimension.
+%
+%  Notes about MODE:
+%
+%    1. The 'eqnum' mode will generally fail when the p-th root of NUM
+%    (i.e. NUM^(1/p)) is larger than min([N1 N2 ... Np]). Thus 'eqdist' is
+%    the more useful choice for sampling an arbitrary number of samples
+%    from the matrix (up to the total number of matrix entries).
+%  
+%    2. In both modes, the equality (of the distance between samples, or
+%    the number of samples in each dimension) is only approximate. This is
+%    because REGGRID attempts to maintain the appropriate equality while at
+%    the same time find a sampling pattern where the total number of
+%    samples is as close as possible to NUM. In general, the larger {Ni}
+%    and NUM are, the tighter the equality.
+%
+%  Example: Sample a set of blocks uniformly from a 2D image.
+%
+%    n = 512; blocknum = 20000; blocksize = [8 8];
+%    im = rand(n,n);
+%    [i1,i2] = reggrid(size(im)-blocksize+1, blocknum);
+%    blocks = sampgrid(im, blocksize, i1, i2);
+%
+%  See also SAMPGRID.
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  November 2007
+
+dim = length(sz);
+
+if (nargin<3)
+  mode = 'eqdist';
+end
+
+if (any(sz<1))
+  error(['Invalid matrix size : [' num2str(sz) ']']);
+end
+
+if (num > prod(sz))
+  warning(['Invalid number of samples, returning maximum number of samples.']);
+elseif (num <= 0)
+  if (num < 0)
+    warning('Invalid number of samples, assuming 0 samples.');
+  end
+  for i = 1:length(sz)
+    varargout{i} = [];
+  end
+  return;
+end
+
+
+if (strcmp(mode,'eqdist'))
+  
+  % approximate distance between samples: total volume divided by number of
+  % samples gives the average volume per sample. then, taking the p-th root
+  % gives the average distance between samples
+  d = (prod(sz)/num)^(1/dim);
+  
+  % compute the initial guess for number of samples in each dimension.
+  % then, while total number of samples is too large, decrese the number of
+  % samples by one in the dimension where the samples are the most crowded.
+  % finally, do the opposite process until just passing num, so the final
+  % number of samples is the closest to num from above.
+  
+  n = min(max(round(sz/d),1),sz);   % set n so that it saturates at 1 and sz
+  
+  active_dims = find(n>1);    % dimensions where the sample num can be reduced
+  while(prod(n)>num && ~isempty(active_dims))
+    [y,id] = min((sz(active_dims)-1)./n(active_dims));
+    n(active_dims(id)) = n(active_dims(id))-1;
+    if (n(active_dims(id)) < 2)
+      active_dims = find(n>1);
+    end
+  end
+
+  active_dims = find(n<sz);    % dimensions where the sample num can be increased
+  while(prod(n)<num && ~isempty(active_dims))
+    [y,id] = max((sz(active_dims)-1)./n(active_dims));
+    n(active_dims(id)) = n(active_dims(id))+1;
+    if (n(active_dims(id)) >= sz(active_dims(id)))
+      active_dims = find(n<sz);
+    end
+  end
+
+  for i = 1:dim
+    varargout{i} = round((1:n(i))/n(i)*sz(i));
+    varargout{i} = varargout{i} - floor((varargout{i}(1)-1)/2);
+  end
+  
+elseif (strcmp(mode,'eqnum'))
+  
+  % same idea as above
+  n = min(max( ones(size(sz)) * round(num^(1/dim)) ,1),sz);
+
+  active_dims = find(n>1);
+  while(prod(n)>num && ~isempty(active_dims))
+    [y,id] = min((sz(active_dims)-1)./n(active_dims));
+    n(active_dims(id)) = n(active_dims(id))-1;
+    if (n(active_dims(id)) < 2)
+      active_dims = find(n>1);
+    end
+  end
+  
+  active_dims = find(n<sz);
+  while(prod(n)<num && ~isempty(active_dims))
+    [y,id] = max((sz(active_dims)-1)./n(active_dims));
+    n(active_dims(id)) = n(active_dims(id))+1;
+    if (n(active_dims(id)) >= sz(active_dims(id)))
+      active_dims = find(n<sz);
+    end
+  end
+  
+  for i = 1:dim
+    varargout{i} = round((1:n(i))/n(i)*sz(i));
+    varargout{i} = varargout{i} - floor((varargout{i}(1)-1)/2);
+  end
+else
+  error('Invalid sampling mode');
+end
+
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/remove_dc.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/remove_dc.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,31 @@
+function [y,dc] = remove_dc(x,columns)
+%REMOVE_DC Remove DC channel from signals.
+%   [Y,DC] = REMOVE_DC(X) removes the DC channel (i.e. the mean) from the
+%   specified (possibly multi-dimensional) signal X. Y is the DC-free
+%   signal and is the same size as X. DC is a scalar containing the mean of
+%   the signal X.
+%
+%   [Y,DC] = REMOVE_DC(X,'columns') where X is a 2D matrix, treats the
+%   columns of X as a set of 1D signals, removing the DC channel from each
+%   one individually. Y is the same size as X and contains the DC-free
+%   signals. DC is a row vector of length size(X,2) containing the means of
+%   the signals in X.
+%
+%   See also ADD_DC.
+
+
+if (nargin==2 && strcmpi(columns,'columns')), columns = 1;
+else columns = 0;
+end
+
+if (columns)
+  dc = mean(x);
+  y = addtocols(x,-dc);
+else
+  if (ndims(x)==2)  % temporary, will remove in future
+    warning('Treating 2D matrix X as a single signal and not each column individually');
+  end
+  dc = mean(x(:));
+  y = x-dc;
+end
+
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/rowlincomb.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/rowlincomb.c	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,148 @@
+/**************************************************************************
+ *
+ * File name: rowlincomb.c
+ *
+ * Ron Rubinstein
+ * Computer Science Department
+ * Technion, Haifa 32000 Israel
+ * ronrubin@cs
+ *
+ * Last Updated: 21.5.2009
+ *
+ *************************************************************************/
+
+#include "mex.h"
+
+
+/* Input Arguments */
+
+#define	X_IN	   prhs[0]
+#define A_IN     prhs[1]
+#define ROWS_IN  prhs[2]
+#define COLS_IN  prhs[3]
+
+
+/* Output Arguments */
+
+#define	Y_OUT	plhs[0]
+
+
+void mexFunction(int nlhs, mxArray *plhs[],
+int nrhs, const mxArray*prhs[])
+
+{
+  double *A, *x, *y, *rows, *cols;
+  mwSize m,n,m1,n1,m2,n2,rownum,colnum;
+  mwIndex *row_ids,*col_ids,i,j;
+  int colnumspecified=0;
+  
+  
+  /* Check for proper number of arguments */
+  
+  if (nrhs!=3 && nrhs!=4) {
+    mexErrMsgTxt("Invalid number of input arguments.");
+  } else if (nlhs > 1) {
+    mexErrMsgTxt("Too many output arguments.");
+  }
+  
+  
+  /* Check the input dimensions */
+  
+  m = mxGetM(A_IN);
+  n = mxGetN(A_IN);
+  if (!mxIsDouble(A_IN) || mxIsComplex(A_IN) || mxGetNumberOfDimensions(A_IN)>2) {
+    mexErrMsgTxt("ROWLINCOMB requires that A be a double matrix.");
+  }
+  
+  m1 = mxGetM(ROWS_IN);
+  n1 = mxGetN(ROWS_IN);
+  if (!mxIsDouble(ROWS_IN) || mxIsComplex(ROWS_IN) || (m1!=1 && n1!=1)) {
+    mexErrMsgTxt("ROWLINCOMB requires that ROWS be an index vector of type double.");
+  }
+  rownum = (m1 > n1) ? m1 : n1;   /* the number of rows in the linear combination */
+  
+  m2 = mxGetM(X_IN);
+  n2 = mxGetN(X_IN);
+  if (!mxIsDouble(X_IN) || mxIsComplex(X_IN) || ((m2!=1) && (n2!=1))) {
+    mexErrMsgTxt("ROWLINCOMB requires that X be a double vector.");
+  }
+  
+  if (m2 != rownum && n2 != rownum) {
+    mexErrMsgTxt("The length of X does not match the number of rows in ROWS.");
+  }
+  
+  if (nrhs==4) {
+    m1 = mxGetM(COLS_IN);
+    n1 = mxGetN(COLS_IN);
+    if (!mxIsDouble(COLS_IN) || mxIsComplex(COLS_IN) || (m1!=1 && n1!=1)) {
+      mexErrMsgTxt("ROWLINCOMB requires that COLS be an index vector of type double.");
+    }
+    colnum = (m1 > n1) ? m1 : n1;   /* the number of columns */
+    colnumspecified = 1;
+    cols = mxGetPr(COLS_IN);
+    
+    Y_OUT = mxCreateDoubleMatrix(1, colnum, mxREAL);
+  }
+  else {
+    cols = 0;
+    Y_OUT = mxCreateDoubleMatrix(1, n, mxREAL);
+  }
+  
+  
+  /* Assign pointers to the various parameters */
+  A = mxGetPr(A_IN);
+  rows = mxGetPr(ROWS_IN);
+  x = mxGetPr(X_IN);
+  y = mxGetPr(Y_OUT);
+  
+  
+  /* check row indices */
+  
+  row_ids = (mwIndex*)mxMalloc(rownum*sizeof(mwIndex));
+  
+  for (i=0; i<rownum; ++i) {
+    row_ids[i] = (mwIndex)(rows[i]+0.1)-1;
+    if (row_ids[i]<0 || row_ids[i]>=m) {
+      mexErrMsgTxt("Row index in ROWS is out of range.");
+    }
+  }
+  
+  
+  
+  if (colnumspecified) {
+    
+    /* check column indices */
+    col_ids = (mwIndex*)mxMalloc(colnum*sizeof(mwIndex));
+    
+    for (i=0; i<colnum; ++i) {
+      col_ids[i] = (mwIndex)(cols[i]+0.1)-1;
+      if (col_ids[i]<0 || col_ids[i]>=n) {
+        mexErrMsgTxt("Column index in COLS is out of range.");
+      }
+    }
+    
+    /* Do the actual computation */
+    for (j=0; j<colnum; ++j) {
+      for (i=0; i<rownum; ++i) {
+        y[j] += A[m*col_ids[j]+row_ids[i]]*x[i];
+      }
+    }
+    
+    mxFree(col_ids);
+  }
+  
+  else {
+    
+    /* Do the actual computation */
+    for (j=0; j<n; ++j) {
+      for (i=0; i<rownum; ++i) {
+        y[j] += A[m*j+row_ids[i]]*x[i];
+      }
+    }
+  }
+  
+  
+  mxFree(row_ids);
+  
+  return;
+}
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/rowlincomb.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/rowlincomb.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,26 @@
+%ROWLINCOMB Linear combination of matrix rows.
+%  Y = ROWLINCOMB(X,A,ROWS) computes a linear combination of the rows of
+%  the matrix A. The row indices are specified in the vector ROWS, and the
+%  correspoinding coefficients are specified in the vector X. The vectors
+%  ROWS and X must be of the same length. The call Y = ROWLINCOMB(X,A,ROWS)
+%  is essentially equivalent to the command
+%
+%         Y = X'*A(ROWS,:) .
+%
+%  However, it is implemented much more efficiently.
+%
+%  Y = ROWLINCOMB(X,A,ROWS,COLS) only works on the columns of A specified
+%  in COLS, returning a vector of length equal to COLS. This call is
+%  essentially equivalent to the command
+%
+%         Y = X'*A(ROWS,COLS) .
+%
+%  See also COLLINCOMB.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  April 2009
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/sampgrid.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/sampgrid.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,72 @@
+function y = sampgrid(x,blocksize,varargin)
+%SAMPGRID Sample a multi-dimensional matrix on a regular grid.
+%  Y = SAMPGRID(X,BLOCKSIZE,I1,I2,...,Ip) extracts block samples of size
+%  BLOCKSIZE from the p-dimensional matrix X, arranging the samples as the
+%  column vectors of the matrix Y. The locations of the (1,1,..,1)-th
+%  elements of each block are given in the index vectors I1,I2,..Ip. The
+%  total number of samples taken is length(I1)xlength(I2)x...xlength(Ip).
+%  BLOCKSIZE should either be a p-element vector of the form [N1,N2,...Np],
+%  or a scalar N which is shorthand for the square block size [N N ... N].
+%
+%  Example: Sample a set of blocks uniformly from a 2D image.
+%
+%    n = 512; blocknum = 20000; blocksize = [8 8];
+%    im = rand(n,n);
+%    [i1,i2] = reggrid(size(im)-blocksize+1, blocknum);
+%    blocks = sampgrid(im, blocksize, i1, i2);
+%
+%  See also REGGRID.
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  November 2007
+
+
+p = ndims(x);
+if (p==2 && any(size(x)==1) && length(blocksize)==1)
+  p = 1;
+end
+
+if (numel(blocksize)==1)
+  blocksize = ones(1,p)*blocksize;
+end
+
+n = zeros(1,p);
+for i = 1:p
+  n(i) = length(varargin{i});
+end
+
+nsamps = prod(n);
+
+% create y of the same class as x
+y = zeros(prod(blocksize),nsamps,class(x));
+
+% ids() contains the index of the current block in I1..Ip
+ids = ones(p,1);
+
+% block_ids contains the indices of the current block in X
+block_ids = cell(p,1);
+for j = 1:p
+  block_ids{j} = varargin{j}(1) : varargin{j}(1)+blocksize(j)-1;
+end
+
+for k = 1:nsamps
+  block = x(block_ids{:});
+  y(:,k) = block(:);
+  
+  % increment ids() and block_ids{}
+  if (k<nsamps)
+    j = 1;
+    while (ids(j) == n(j))
+      ids(j) = 1;
+      block_ids{j} = varargin{j}(1) : varargin{j}(1)+blocksize(j)-1;
+      j = j+1;
+    end
+    ids(j) = ids(j)+1;
+    block_ids{j} = varargin{j}(ids(j)) : varargin{j}(ids(j))+blocksize(j)-1;
+  end
+end
+
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/secs2hms.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/secs2hms.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,28 @@
+function [h,m,s] = secs2hms(t)
+%SECS2HMS Convert seconds to hours, minutes and seconds.
+%  [H,M,S] = SECS2HMS(T) converts the specified number of seconds T to
+%  hours, minutes and seconds. H and M are whole numbers, and S is real.
+%
+%  Example: Estimate the remaining time of a loop
+%
+%    n = 10; tic;
+%    for i = 1:n
+%      pause(1);
+%      [h,m,s] = secs2hms( (n-i)*toc/i );
+%      printf('estimated remaining time: %02d:%02d:%05.2f',h,m,s);
+%    end
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  April 2008
+
+
+s = t;
+h = fix(s/3600);
+s = rem(s,3600);
+m = fix(s/60);
+s = rem(s,60);
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/spdiag.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/spdiag.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,38 @@
+function Y = spdiag(V,K)
+%SPDIAG Sparse diagonal matrices.
+%   SPDIAG(V,K) when V is a vector with N components is a sparse square
+%   matrix of order N+ABS(K) with the elements of V on the K-th diagonal. 
+%   K = 0 is the main diagonal, K > 0 is above the main diagonal and K < 0
+%   is below the main diagonal. 
+%
+%   SPDIAG(V) is the same as SPDIAG(V,0) and puts V on the main diagonal.
+%
+%   See also DIAG, SPDIAGS.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  June 2008
+
+
+if (nargin<2)
+  K = 0;
+end
+
+n = length(V) + abs(K);
+
+if (K>0)
+  i = 1:length(V);
+  j = K+1:n;
+elseif (K<0)
+  i = -K+1:n;
+  j = 1:length(V);
+else
+  i = 1:n;
+  j = 1:n;
+end
+
+Y = sparse(i,j,V(:),n,n);
\ No newline at end of file
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/sprow.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/sprow.c	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,94 @@
+/**************************************************************************
+ *
+ * File name: sprow.c
+ *
+ * Ron Rubinstein
+ * Computer Science Department
+ * Technion, Haifa 32000 Israel
+ * ronrubin@cs
+ *
+ * Last Updated: 24.8.2009
+ *
+ *************************************************************************/
+
+
+#include "mex.h"
+#include "mexutils.h"
+
+
+/* Input Arguments */
+
+#define	A_IN	prhs[0]
+#define J_IN  prhs[1]
+
+
+/* Output Arguments */
+
+#define	X_OUT	  plhs[0]
+#define	ID_OUT	plhs[1]
+
+
+void mexFunction(int nlhs, mxArray *plhs[], 
+		             int nrhs, const mxArray*prhs[])
+     
+{ 
+  double *pr, *x, *id, rowid;
+  mwIndex *ir, *jc;
+  mwSize m, n;
+  mwIndex i, j, k, l, rowlen;
+  
+  if (nrhs != 2) {
+    mexErrMsgTxt("GETSPROW requires two input arguments.");
+  } else if (nlhs > 2) {
+    mexErrMsgTxt("Too many output arguments.");
+  }
+  
+  checkmatrix(A_IN, "GETSPROW", "A");
+  checksparse(A_IN, "GETSPROW", "A");
+  checkscalar(J_IN, "GETSPROW", "J");
+  
+  m = mxGetM(A_IN);
+  n = mxGetN(A_IN);
+  
+  rowid = mxGetScalar(J_IN);
+  if (rowid < 0) {
+    mexErrMsgTxt("Invalid row index.");
+  }
+  j = (mwIndex)(rowid + 1e-2);
+  if (j<1 || j>m) {
+    mexErrMsgTxt("Row index is out of range.");
+  }
+  j--;
+  
+  pr = mxGetPr(A_IN);
+  ir = mxGetIr(A_IN);
+  jc = mxGetJc(A_IN);
+  
+  /* Determine length of row */
+  rowlen = 0;
+  for (i=0; i<jc[n]; ++i) {
+    rowlen += (ir[i]==j);
+  }
+  
+  /* Allocate output parameters */
+  X_OUT = mxCreateDoubleMatrix(1, rowlen, mxREAL);
+  ID_OUT = mxCreateDoubleMatrix(1, rowlen, mxREAL);
+  
+  x = mxGetPr(X_OUT);
+  id = mxGetPr(ID_OUT);
+  
+  /* Compute j-th row */
+  k=0;
+  for (l=1; l<=n; ++l) {
+    i = jc[l-1];
+    while (i<jc[l] && ir[i]<j) {
+      i++;
+    }
+    if (i<jc[l] && ir[i]==j) {
+      x[k] = pr[i];
+      id[k] = l;
+      k++;
+    }
+  }
+  
+}
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/sprow.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/sprow.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,19 @@
+%SPROW Extract row of sparse matrix.
+%  X = SPROW(A,J) where A is a sparse matrix, returns the nonzero values in
+%  the row A(J,:).
+%
+%  [X,ID] = SPROW(A,J) also returns the column indices of the nonzeros.
+%
+%  Note that the call [X,ID] = SPROW(A,J) is equivalent (but more efficient
+%  than) the Matlab code
+%
+%    IDS = find(A(J,:)); 
+%    X = A(J,IDS);
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  August 2009
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/timerclear.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/timerclear.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,37 @@
+function timerclear()
+%TIMERCLEAR Clear all timers.
+%   TIMERCLEAR clears all currenly registered timers, invalidating all
+%   timer ids.
+%
+%   Note: since registered timers do not consume CPU power except for when
+%   the TIMER<*> functions are called, this function is only useful in
+%   situations where a large number of timers have been initialized, and
+%   there is a need to reclaim memory.
+%
+%   See also TIMERINIT, TIMERETA.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  June 2008
+
+
+global utiltbx_timer_start_times    % start times
+global utiltbx_time_lastdisp        % last display times
+global utiltbx_timer_iternums       % iteration numbers
+global utiltbx_timer_lastiter       % last queried iteration numbers
+global utiltbx_timer_name           % timer names
+global utiltbx_timer_callfun        % timer calling functions
+
+
+% clear all timers %
+
+utiltbx_timer_start_times = [];
+utiltbx_time_lastdisp = [];
+utiltbx_timer_iternums = [];
+utiltbx_timer_lastiter = [];
+utiltbx_timer_name = [];
+utiltbx_timer_callfun = [];
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/timereta.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/timereta.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,98 @@
+function varargout = timereta(tid,iter,delay)
+%TIMERETA Estimated remaining time.
+%   S = TIMERETA(TID,ITER) returns the estimated remaining time (in
+%   seconds) for the process associated with timer TID, assuming the
+%   process has completed ITER iterations. Note: the function will exit
+%   with an error if the timer TID does not have an associated number of
+%   iterations (see function TIMERINIT).
+%
+%   [H,M,S] = TIMERETA(TID,ITER) returns the estimated remaining time in
+%   hours, minutes and seconds.
+%
+%   TIMERETA(TID,ITER), with no output arguments, prints the estimated
+%   remaining time to the screen. The time is displayed in the format
+%
+%     TIMERNAME: iteration ITER / ITERNUM, estimated remaining time: HH:MM:SS.SS
+%
+%   If the timer has no assigned name, the display format changes to
+%
+%     Iteration ITER / ITERNUM, estimated remaining time: HH:MM:SS.SS
+%
+%   TIMERETA(TID,ITER,DELAY) only displays the remaining time if the
+%   time elapsed since the previous printout is at least DELAY seconds.
+%
+%   See also TIMERINIT, TIMERCLEAR.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  June 2008
+
+
+global utiltbx_timer_start_times 
+global utiltbx_timer_iternums
+global utiltbx_timer_lastiter
+global utiltbx_time_lastdisp
+global utiltbx_timer_name
+
+
+if (tid<1 || tid>length(utiltbx_timer_iternums))
+  error('Unknown timer id');
+end
+
+if (utiltbx_timer_iternums(tid) < 0)
+  error('Specified timer does not have an associated number of iterations');
+end
+
+% update last reported iteration number
+utiltbx_timer_lastiter(tid) = iter;
+
+% compute elapsed time
+starttime = utiltbx_timer_start_times(tid,:);
+currtime = clock;
+timediff = etime(currtime, starttime);
+
+% total iteration number
+iternum = utiltbx_timer_iternums(tid);
+
+% compute eta
+timeremain = (iternum-iter)*timediff/iter;
+
+% return eta in seconds
+if (nargout==1)
+  varargout{1} = timeremain;
+  
+% return eta in hms
+elseif (nargout==3)
+  [varargout{1}, varargout{2}, varargout{3}] = secs2hms(timeremain);
+  
+  
+% print eta
+elseif (nargout==0)
+  
+  % check last display time
+  lastdisptime = utiltbx_time_lastdisp(tid,:);
+  if (nargin>2 && etime(currtime,lastdisptime) < delay)
+    return;
+  end
+  
+  % update last display time
+  utiltbx_time_lastdisp(tid,:) = currtime;
+
+  % display timer
+  [hrs,mins,secs] = secs2hms(timeremain);
+  if (isempty(utiltbx_timer_name{tid}))
+    printf('Iteration %d / %d, estimated remaining time: %02d:%02d:%05.2f', iter, iternum, hrs, mins, secs);
+  else
+    timername = utiltbx_timer_name{tid};
+    printf('%s: iteration %d / %d, estimated remaining time: %02d:%02d:%05.2f', timername, iter, iternum, hrs, mins, secs);
+  end
+   
+% invalid number of outputs
+else
+  error('Invalid number of output arguments');
+end
+
diff -r 5f1f436057ca -r c3eca463202d util/ksvd utils/timerinit.m
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/ksvd utils/timerinit.m	Wed Mar 16 14:16:57 2011 +0000
@@ -0,0 +1,110 @@
+function tid = timerinit(par1,par2)
+%TIMERINIT Initialize a new timer.
+%   TID = TIMERINIT() initializes a new timer for counting elapsed time,
+%   and returns its id.
+%
+%   TID = TIMERINIT('TIMERNAME') sets the timer name to the specified
+%   string for display purposes.
+%
+%   TID = TIMERINIT(ITERNUM) initializes a new ETA timer for a process with
+%   ITERNUM iterations. An ETA timer can be used for both counting elapsed
+%   time and estimating remaining time.
+%
+%   TID = TIMERINIT('TIMERNAME',ITERNUM) sets the ETA timer name to the
+%   specified string for display purposes.
+%
+%   Example:
+%
+%     tid = timerinit(100); 
+%     for i = 1:100
+%       pause(0.07);
+%       timereta(tid,i,1);
+%     end
+%     timereta(tid,i);
+%
+%   See also TIMERETA, TIMERCLEAR.
+
+
+%  Ron Rubinstein
+%  Computer Science Department
+%  Technion, Haifa 32000 Israel
+%  ronrubin@cs
+%
+%  June 2008
+
+
+global utiltbx_timer_start_times    % start times
+global utiltbx_time_lastdisp        % last display times
+global utiltbx_timer_iternums       % iteration numbers
+global utiltbx_timer_lastiter       % last queried iteration numbers
+global utiltbx_timer_name           % timer names
+global utiltbx_timer_callfun        % timer calling functions
+
+
+% parse function arguments %
+
+if (nargin==0)
+
+  iternum = -1;
+  timername = '';
+
+elseif (nargin==1)
+
+  if (ischar(par1))
+    iternum = -1;
+    timername = par1;
+
+  elseif (isnumeric(par1) && numel(par1)==1 && par1>0)
+    iternum = par1;
+    timername = '';
+
+  else
+    error('Invalid number of iterations');
+  end
+
+elseif (nargin==2)
+
+  if (ischar(par1) && isnumeric(par2))
+    if (numel(par2)==1 && par2>0)
+      timername = par1;
+      iternum = par2;
+    else
+      error('Invalid number of iterations');
+    end
+  else
+    error('Invalid function syntax');
+  end
+
+else
+  error('Too many function parameters');
+end
+
+
+% register the timer %
+
+if (isempty(utiltbx_timer_start_times))
+  utiltbx_timer_start_times = clock;
+  utiltbx_time_lastdisp = utiltbx_timer_start_times;
+  utiltbx_timer_iternums = double(iternum);
+  utiltbx_timer_lastiter = 0;
+  utiltbx_timer_name = { timername };
+  utiltbx_timer_callfun = {};
+  tid = 1;
+else
+  utiltbx_timer_start_times(end+1,:) = clock;
+  utiltbx_time_lastdisp(end+1,:) = utiltbx_timer_start_times(end,:);
+  utiltbx_timer_iternums(end+1) = double(iternum);
+  utiltbx_timer_lastiter(end+1) = 0;
+  utiltbx_timer_name{end+1} = timername;
+  tid = size(utiltbx_timer_start_times,1);
+end
+
+
+% detect timer calling function %
+
+st = dbstack;
+if (length(dbstack) >= 2)
+  utiltbx_timer_callfun{end+1} = st(2).name;
+else
+  utiltbx_timer_callfun{end+1} = '';
+end