BNW using Octave instead of Matlab.

This version of BNW should perform the same as the original version. The only difference is that it uses Octave instead of Matlab when running BayesNet Toolbox during parameter learning.

I am calling this BNW_1.02. It can be accessed at:
compbio.uthsc.edu/BNW_1.02

1 files changed, 147 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/KPMtools/rectintSparseLoopC.c b/sourcecodes/bnt-master/KPMtools/rectintSparseLoopC.c
new file mode 100644
index 00000000..38ed08d5
--- /dev/null
+++ b/sourcecodes/bnt-master/KPMtools/rectintSparseLoopC.c
@@ -0,0 +1,147 @@
+/* This is based on
+http://www.mathworks.com/access/helpdesk/help/techdoc/matlab_external/ch04cr12.shtml
+
+See rectintSparse.m for the matlab version of this code.
+
+*/
+
+#include <math.h> /* Needed for the ceil() prototype. */
+#include "mex.h"
+#include <stdio.h>
+
+/* If you are using a compiler that equates NaN to be zero, you 
+ * must compile this example using the flag  -DNAN_EQUALS_ZERO.
+ * For example:
+ *
+ *     mex -DNAN_EQUALS_ZERO fulltosparse.c
+ *
+ * This will correctly define the IsNonZero macro for your C
+ * compiler.
+ */
+
+#if defined(NAN_EQUALS_ZERO)
+#define IsNonZero(d) ((d) != 0.0 || mxIsNaN(d))
+#else
+#define IsNonZero(d) ((d) != 0.0)
+#endif
+
+#define MAX(x,y)  ((x)>(y) ? (x) : (y))
+#define MIN(x,y)  ((x)<(y) ? (x) : (y))
+
+void mexFunction(
+        int nlhs,       mxArray *plhs[],
+        int nrhs, const mxArray *prhs[]
+        )
+{
+  /* Declare variables. */
+  int j,k,m,n,nzmax,*irs,*jcs, *irs2, *jcs2;
+  double *overlap, *overlap2, tmp, areaA, areaB;
+  double percent_sparse;
+  double *leftA, *rightA, *topA, *bottomA;
+  double *leftB, *rightB, *topB, *bottomB;
+  double *verbose;
+
+  /* Get the size and pointers to input data. */
+  m = MAX(mxGetM(prhs[0]), mxGetN(prhs[0]));
+  n = MAX(mxGetM(prhs[4]), mxGetN(prhs[4]));
+  /* printf("A=%d, B=%d\n", m, n); */
+
+  leftA = mxGetPr(prhs[0]);
+  rightA = mxGetPr(prhs[1]);
+  topA = mxGetPr(prhs[2]);
+  bottomA = mxGetPr(prhs[3]);
+
+  leftB = mxGetPr(prhs[4]);
+  rightB = mxGetPr(prhs[5]);
+  topB = mxGetPr(prhs[6]);
+  bottomB = mxGetPr(prhs[7]);
+
+  verbose = mxGetPr(prhs[8]);
+
+    /* Allocate space for sparse matrix. 
+     * NOTE:  Assume at most 20% of the data is sparse.  Use ceil
+     * to cause it to round up. 
+     */
+
+  percent_sparse = 0.01;
+  nzmax = (int)ceil((double)m*(double)n*percent_sparse);
+
+  plhs[0] = mxCreateSparse(m,n,nzmax,0);
+  overlap  = mxGetPr(plhs[0]);
+  irs = mxGetIr(plhs[0]);
+  jcs = mxGetJc(plhs[0]);
+
+  plhs[1] = mxCreateSparse(m,n,nzmax,0);
+  overlap2  = mxGetPr(plhs[1]);
+  irs2 = mxGetIr(plhs[1]);
+  jcs2 = mxGetJc(plhs[1]);
+
+    
+  /* Assign nonzeros. */
+  k = 0; 
+  for (j = 0; (j < n); j++) {
+    int i;
+    jcs[j] = k; 
+    jcs2[j] = k; 
+    for (i = 0; (i < m); i++) {
+      tmp = (MAX(0, MIN(rightA[i], rightB[j]) - MAX(leftA[i], leftB[j]) )) * 
+	(MAX(0, MIN(topA[i], topB[j]) - MAX(bottomA[i], bottomB[j]) ));
+      
+      if (*verbose) {
+	printf("j=%d,i=%d,tmp=%5.3f\n", j,i,tmp);
+      }
+
+      if (IsNonZero(tmp)) {
+
+        /* Check to see if non-zero element will fit in 
+         * allocated output array.  If not, increase
+         * percent_sparse by 20%, recalculate nzmax, and augment
+         * the sparse array.
+         */
+        if (k >= nzmax) {
+          int oldnzmax = nzmax;
+          percent_sparse += 0.2;
+          nzmax = (int)ceil((double)m*(double)n*percent_sparse);
+
+          /* Make sure nzmax increases atleast by 1. */
+          if (oldnzmax == nzmax) 
+            nzmax++;
+	  printf("reallocating from %d to %d\n", oldnzmax, nzmax);
+
+          mxSetNzmax(plhs[0], nzmax); 
+          mxSetPr(plhs[0], mxRealloc(overlap, nzmax*sizeof(double)));
+          mxSetIr(plhs[0], mxRealloc(irs, nzmax*sizeof(int)));
+          overlap  = mxGetPr(plhs[0]);
+          irs = mxGetIr(plhs[0]);
+
+          mxSetNzmax(plhs[1], nzmax); 
+          mxSetPr(plhs[1], mxRealloc(overlap2, nzmax*sizeof(double)));
+          mxSetIr(plhs[1], mxRealloc(irs2, nzmax*sizeof(int)));
+          overlap2  = mxGetPr(plhs[1]);
+          irs2 = mxGetIr(plhs[1]);
+        }
+
+        overlap[k] = tmp;
+        irs[k] = i;
+	
+	areaA = (rightA[i]-leftA[i])*(topA[i]-bottomA[i]);
+	areaB = (rightB[j]-leftB[j])*(topB[j]-bottomB[j]);
+	overlap2[k] = MIN(tmp/areaA, tmp/areaB);
+	irs2[k] = i;
+
+        k++;
+      } /* IsNonZero */
+    } /* for i */
+  }
+  jcs[n] = k;
+  jcs2[n] = k;
+  
+}
+
+
+
+
+
+
+
+