diff toolboxes/FullBNT-1.0.7/bnt/inference/static/@quickscore_inf_engine/private/C_quickscore.c @ 0:e9a9cd732c1e tip

first hg version after svn

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolboxes/FullBNT-1.0.7/bnt/inference/static/@quickscore_inf_engine/private/C_quickscore.c	Tue Feb 10 15:05:51 2015 +0000
@@ -0,0 +1,164 @@
+/* To compile, type "mex C_quickscore.c" */
+
+#include <stdio.h>
+#include "nrutil.h"
+#include "nrutil.c"
+#include <math.h>
+#include "mex.h"
+
+#define MAX(X,Y) (X)>(Y)?(X):(Y)
+
+int two_to_the(int n)
+{
+  return 1 << n;
+}
+
+void int2bin(int num, int nbits, int bits[])
+{
+  int i, mask;
+  mask = 1 << (nbits-1); /* mask = 0010...0 , where the 1 is in col nbits (rightmost = col 1) */
+  for (i = 0; i < nbits; i++) {
+    bits[i] = ((num & mask) == 0) ? 0 : 1;
+    num <<= 1;
+  }
+}
+
+
+void quickscore(int ndiseases, int nfindings, const double *fpos, int npos, const double *fneg, int nneg,
+                  const double *inhibit, const double *prior, const double *leak, double *prob)
+{
+  double *Pon, *Poff, **Uon, **Uoff, **post, *pterm, *ptermOff, *ptermOn, temp, p, myp;
+  int *bits, nsubsets, *fmask;
+  int f, d, i, j, si, size_subset, sign;
+
+  Pon = dvector(0, ndiseases);
+  Poff = dvector(0, ndiseases);
+  Pon[0] = 1;
+  Poff[0] = 0;
+  for (i=1; i <= ndiseases; i++) {
+    Pon[i] = prior[i-1];
+    Poff[i] = 1-Pon[i];
+  }
+
+  Uon = dmatrix(0, nfindings-1, 0, ndiseases);
+  Uoff = dmatrix(0, nfindings-1, 0, ndiseases);
+  d = 0;
+  for (f=0; f < nfindings; f++) {
+    Uon[f][d] = leak[f];
+    Uoff[f][d] = leak[f];
+  }
+  for (f=0; f < nfindings; f++) {
+    for (d=1; d <= ndiseases; d++) {
+      Uon[f][d] = inhibit[f + nfindings*(d-1)];
+      Uoff[f][d] = 1;
+    }
+  }
+  
+  post = dmatrix(0, ndiseases, 0, 1);
+  for (d = 0; d <= ndiseases; d++) {
+    post[d][0] = 0;
+    post[d][1] = 0;
+  }
+  
+  bits = ivector(0, npos-1);
+  fmask = ivector(0, nfindings-1);
+  pterm = dvector(0, ndiseases);
+  ptermOff = dvector(0, ndiseases);
+  ptermOn = dvector(0, ndiseases);
+
+  nsubsets = two_to_the(npos);
+
+  for (si = 0; si < nsubsets; si++) {
+    int2bin(si, npos, bits);
+    for (i=0; i < nfindings; i++) fmask[i] = 0;
+    for (i=0; i < nneg; i++) fmask[(int)fneg[i]-1] = 1;
+    size_subset = 0;
+    for (i=0; i < npos; i++) {
+      if (bits[i]) {
+	size_subset++;
+	fmask[(int)fpos[i]-1] = 1;
+      }
+    }
+    p = 1;
+    for (d=0; d <= ndiseases; d++) {
+      temp = 1;
+      for (j = 0; j < nfindings; j++) {
+	if (fmask[j]) temp *= Uoff[j][d];
+      }
+      ptermOff[d] = temp;
+
+      temp = 1;
+      for (j = 0; j < nfindings; j++) {
+	if (fmask[j]) temp *= Uon[j][d];
+      }
+      ptermOn[d] = temp;
+
+      pterm[d] = Poff[d]*ptermOff[d] + Pon[d]*ptermOn[d];
+      p *= pterm[d];
+    }
+    sign = (int) pow(-1, size_subset);
+    for (d=0; d <= ndiseases; d++) {
+      myp = p / pterm[d];
+      post[d][0] += sign*(myp * ptermOff[d]);
+      post[d][1] += sign*(myp * ptermOn[d]);
+    }
+  } /* next si */
+
+  
+  for (d=0; d <= ndiseases; d++) {
+    post[d][0] *= Poff[d];
+    post[d][1] *= Pon[d];
+  }
+  for (d=0; d <= ndiseases; d++) {
+    temp = post[d][0] + post[d][1];
+    post[d][0] /= temp;
+    post[d][1] /= temp;
+    if (d>0) { prob[d-1] = post[d][1]; }
+  }
+
+  
+  free_dvector(Pon, 0, ndiseases);
+  free_dvector(Poff, 0, ndiseases);
+  free_dmatrix(Uon, 0, nfindings-1, 0, ndiseases);
+  free_dmatrix(Uoff, 0, nfindings-1, 0, ndiseases);
+  free_dmatrix(post, 0, ndiseases, 0, 1);
+  free_ivector(bits, 0, npos-1);
+  free_ivector(fmask, 0, nfindings-1);
+  free_dvector(pterm, 0, ndiseases);
+  free_dvector(ptermOff, 0, ndiseases);
+  free_dvector(ptermOn, 0, ndiseases);
+}
+
+
+void mexFunction(
+                 int nlhs,       mxArray *plhs[],
+                 int nrhs, const mxArray *prhs[]
+                 )
+{
+  double *fpos, *fneg, *inhibit, *prior, *leak, *prob;
+  int npos, nneg, ndiseases, nfindings;
+  double *p;
+
+  /* read the input args */
+  fpos = mxGetPr(prhs[0]);
+  npos = MAX(mxGetM(prhs[0]), mxGetN(prhs[0]));
+
+  fneg = mxGetPr(prhs[1]);
+  nneg = MAX(mxGetM(prhs[1]), mxGetN(prhs[1]));
+
+  inhibit = mxGetPr(prhs[2]); /* inhibit(finding, disease) */
+  nfindings = mxGetM(prhs[2]);
+  ndiseases = mxGetN(prhs[2]);
+
+  prior = mxGetPr(prhs[3]);
+
+  leak = mxGetPr(prhs[4]);
+
+
+ /* set the output pointers */
+  plhs[0] = mxCreateDoubleMatrix(1, ndiseases, mxREAL);
+  prob = mxGetPr(plhs[0]);
+
+  quickscore(ndiseases, nfindings, fpos, npos, fneg, nneg, inhibit, prior, leak, prob);
+}
+