Squashed commit of the sb-vbs branch.

Includes the SD-VBS benchmarks modified to:
- Use libextra to loop as realtime jobs
- Preallocate memory before starting their main computation
- Accept input via stdin instead of via argc

Does not include the SD-VBS matlab code.

Fixes libextra execution in LITMUS^RT.

9 files changed, 765 insertions, 0 deletions

diff --git a/SD-VBS/benchmarks/stitch/src/c/dist2.c b/SD-VBS/benchmarks/stitch/src/c/dist2.c
new file mode 100644
index 0000000..d76fcb2
--- /dev/null
+++ b/SD-VBS/benchmarks/stitch/src/c/dist2.c
@@ -0,0 +1,76 @@
+/********************************
+Author: Sravanthi Kota Venkata
+********************************/
+
+#include "stitch.h"
+
+F2D* dist2(I2D* x, F2D* c)
+{
+    int ndata, dimx, ncentres, dimc, i, j, k;
+    F2D *n2, *t1, *t2;
+    float temp;
+    F2D *s1, *s2, *ctrans;
+    F2D *mult1, *mult2, *mult3;
+
+    ndata = x->height;
+    dimx = x->width;
+
+    ncentres = c->height;
+    dimc = c->width;
+
+    if(dimx != dimc)
+        return NULL;
+
+    s1 = fSetArray(ncentres, 1, 1);
+    s2 = fSetArray(ndata, 1, 1);
+    t1 = fMallocHandle(1, x->height);
+
+    for(j=0; j<t1->width; j++)
+    {
+        temp = 0;
+        for(i=0; i<t1->height; i++)
+        {
+            temp += subsref(x,j,i) * subsref(x,j,i);
+        }
+
+        asubsref(t1,j) = temp;
+    }
+
+    mult1 = fMtimes(s1, t1);
+    t2 = fMallocHandle(1, c->height);
+
+    for(j=0; j<t2->width; j++)
+    {
+        temp = 0;
+        for(i=0; i<t2->height; i++)
+        {
+            temp += subsref(c,j,i) * subsref(c,j,i);
+        }
+
+        asubsref(t2,j) = temp;
+    }
+
+    mult2 = fMtimes(s2, t2);
+    ctrans = fTranspose(c);
+    mult3 = ifMtimes(x, ctrans);
+
+    for(i=0; i<(mult3->height * mult3->width); i++)
+        asubsref(mult3,i) = asubsref(mult3,i) * 2;
+
+    free(t1);
+    free(t2);
+    free(s1);
+    free(s2);
+    free(ctrans);
+
+    n2 = fMallocHandle(ndata, ncentres);
+    for(i=0; i<(ndata*ncentres); i++)
+        asubsref(n2,i) = asubsref(mult1,i) + asubsref(mult2,i) - asubsref(mult3,i);
+
+    free(mult1);
+    free(mult2);
+    free(mult3);
+
+    return n2;
+
+}
diff --git a/SD-VBS/benchmarks/stitch/src/c/extractFeatures.c b/SD-VBS/benchmarks/stitch/src/c/extractFeatures.c
new file mode 100644
index 0000000..ea574e4
--- /dev/null
+++ b/SD-VBS/benchmarks/stitch/src/c/extractFeatures.c
@@ -0,0 +1,181 @@
+/********************************
+Author: Sravanthi Kota Venkata
+********************************/
+
+#include "stitch.h"
+#include <math.h>
+
+#define min(a,b) (a<b)?a:b
+
+F2D* extractFeatures(I2D* I, F2D* x, F2D* y)
+{
+    int n, i, j, k;
+    F2D* I1;
+    F2D *Iconv;
+    F2D *Isub;
+    int nr, nc;
+    F2D *w, *wt, *vecF;
+    I2D *Xsub, *Ysub;
+    float temp, mean, std;
+    int m;
+    F2D *g1, *g;
+
+    g1 = fSetArray(5,5,0);
+
+    asubsref(g1,0) = 1;
+    asubsref(g1,1) = 4;
+    asubsref(g1,2) = 6;
+    asubsref(g1,3) = 4;
+    asubsref(g1,4) = 1;
+
+    asubsref(g1,5) = 4;
+    asubsref(g1,6) = 16;
+    asubsref(g1,7) = 24;
+    asubsref(g1,8) = 16;
+    asubsref(g1,9) = 4;
+
+    asubsref(g1,10) = 6;
+    asubsref(g1,11) = 24;
+    asubsref(g1,12) = 36;
+    asubsref(g1,13) = 24;
+    asubsref(g1,14) = 6;
+
+    asubsref(g1,15) = 4;
+    asubsref(g1,16) = 16;
+    asubsref(g1,17) = 24;
+    asubsref(g1,18) = 16;
+    asubsref(g1,19) = 4;
+
+    asubsref(g1,20) = 1;
+    asubsref(g1,21) = 4;
+    asubsref(g1,22) = 6;
+    asubsref(g1,23) = 4;
+    asubsref(g1,24) = 1;
+
+    g = fDivide(g1, 256);
+    n = x->height;
+
+    vecF = fMallocHandle(n, 64);
+    I1 = fiDeepCopy(I);
+
+    Iconv = ffConv2(I1, g);
+    fFreeHandle(I1);
+    I1 = ffConv2(Iconv, g);
+    fFreeHandle(Iconv);
+    Iconv = fDeepCopy(I1);
+
+    {
+        int i = (Iconv->height/5);
+        int j = (Iconv->width/5);
+        Isub = fMallocHandle(i, j);
+    }
+
+    for(i=0, m=0; m<Isub->height; i+=5, m++)
+    {
+        for(j=0, k=0; k<Isub->width; j+=5, k++)
+        {
+            subsref(Isub,m,k) = subsref(Iconv,i,j);
+        }
+    }
+
+    fFreeHandle(Iconv);
+    fFreeHandle(g1);
+    fFreeHandle(g);
+    fFreeHandle(I1);
+
+    nr = Isub->height;
+    nc = Isub->width;
+
+    Xsub = iMallocHandle(x->height, x->width);
+    Ysub = iMallocHandle(y->height, y->width);
+        
+//    printf("Sizes = %d\t%d\t%d\t%d\n", Isub->height, Isub->width, x->height, x->width);
+   
+    for(i=0; i<(x->height*x->width); i++)
+    {
+        asubsref(Xsub,i) = min( ( asubsref(x,i) /5), nc-4 );
+        asubsref(Ysub,i) = min( ( asubsref(y,i) /5), nr-4 );
+    }
+
+    {
+        int maxX, maxY;
+        maxX = Xsub->height>Xsub->width?Xsub->height:Xsub->width;
+        maxY = Ysub->height>Ysub->width?Ysub->height:Ysub->width;
+        if(maxX < 6 || maxY < 10)
+        {