void NonGradient::optimize_vertex_positions(PatchData &pd,
MsqError &err)
{
MSQ_FUNCTION_TIMER( "NonGradient::optimize_vertex_positions" );
int numRow = getDimension();
int numCol = numRow+1;
std::vector<double> height(numCol);
for(int col = 0; col < numCol; col++)
{
height[col] = evaluate(&simplex[col*numRow], pd, err);// eval patch stuff
}
if(mNonGradDebug > 0)
{
printSimplex( simplex, height );
}
// standardization
TerminationCriterion* term_crit=get_inner_termination_criterion();
int maxNumEval = getMaxNumEval();
double threshold = getThreshold();
// double ftol = getTolerance();
int ilo = 0; //height[ilo]<=...
int inhi = 0; //...<=height[inhi]<=
int ihi = 0; //<=height[ihi]
// double rtol = 2.*ftol;
double ysave;
double ytry;
bool afterEvaluation = false;
std::vector<double> rowSum(numRow);
getRowSum( numRow, numCol, simplex, rowSum);
while( !( term_crit->terminate() ) )
{
if(mNonGradDebug > 0)
{
printSimplex( simplex, height );
}
//std::cout << "rtol " << rtol << " ftol " << ftol << " MesquiteIter " << term_crit->get_iteration_count() << " Done " << term_crit->terminate() << std::endl;
if( afterEvaluation )
{
// reflect highPt through opposite face
// height[0] may vanish
/*
if( !testRowSum( numRow, numCol, &simplex[0], &rowSum[0]) )
{
// Before uncommenting here and ...
//MSQ_SETERR(err)("Internal check sum test A failed", MsqError::INTERNAL_ERROR);
//MSQ_ERRRTN(err);
}
*/
ytry=amotry(simplex,height,&rowSum[0],ihi,-1.0, pd, err);
/*
if( !testRowSum( numRow, numCol, &simplex[0], &rowSum[0]) )
{
// ... here, determine a maxVal majorizing the previous as well as the current simplex.
//MSQ_SETERR(err)("Internal check sum test B failed", MsqError::INTERNAL_ERROR);
//MSQ_ERRRTN(err);
}
*/
/*
if( height[0] == 0.)
{
MSQ_SETERR(err)("(B) Zero objective function value", MsqError::INTERNAL_ERROR);
exit(-1);
}
*/
if (ytry <= height[ilo])
{
ytry=amotry(simplex,height,&rowSum[0],ihi,-2.0,pd,err);
if( mNonGradDebug >= 3 )
{
std::cout << "Reflect and Expand from highPt " << ytry << std::endl;
}
//MSQ_PRINT(3)("Reflect and Expand from highPt : %e\n",ytry);
}
else
{
if (ytry >= height[inhi])
{
ysave=height[ihi]; // Contract along highPt
ytry=amotry(simplex,height,&rowSum[0],ihi,0.5,pd,err);
if (ytry >= ysave)
{ // contract all directions toward lowPt
for (int col=0;col<numCol;col++)
{
if (col != ilo)
{
for (int row=0;row<numRow;row++)
{
rowSum[row]=0.5*(simplex[row+col*numRow]+simplex[row+ilo*numRow]);
simplex[row+col*numRow]=rowSum[row];
}
height[col] = evaluate(&rowSum[0], pd, err);
if( mNonGradDebug >= 3 )
{
std::cout << "Contract all directions toward lowPt value( " << col << " ) = " << height[col] << " ilo = " << ilo << std::endl;
}
//MSQ_PRINT(3)("Contract all directions toward lowPt value( %d ) = %e ilo = %d\n", col, height[col], ilo);
}
}
}
}
} // ytri > h(ilo)
} // after evaluation
ilo=1; // conditional operator or inline if
ihi = height[0] > height[1] ? (inhi=1,0) : (inhi=0,1);
for (int col=0;col<numCol;col++)
{
if (height[col] <= height[ilo])
{
ilo=col; // ilo := argmin height
}
if (height[col] > height[ihi])
{
inhi=ihi;
ihi=col;
}
else // height[ihi] >= height[col]
if (col != ihi && height[col] > height[inhi] ) inhi=col;
}
// rtol=2.0*fabs( height[ihi]-height[ilo] )/
// ( fabs(height[ihi])+fabs(height[ilo])+threshold );
afterEvaluation = true;
} // while not converged
// Always set to current best mesh.
{
if( ilo != 0 )
{
double yTemp = height[0];
height[0] = height[ilo]; // height dimension numCol
height[ilo] = yTemp;
for (int row=1;row<numRow;row++)
{
yTemp = simplex[row];
simplex[row] = simplex[row+ilo*numRow];
simplex[row+ilo*numRow] = yTemp;
}
}
}
if( pd.num_free_vertices() > 1 )
{
MSQ_SETERR(err)("Only one free vertex per patch implemented", MsqError::NOT_IMPLEMENTED);
}
Vector3D newPoint( &simplex[0] );
size_t vertexIndex = 0; // fix c.f. freeVertexIndex
pd.set_vertex_coordinates( newPoint, vertexIndex, err );
pd.snap_vertex_to_domain( vertexIndex, err );
if( term_crit->terminate() )
{
if( mNonGradDebug >= 1 )
{
std::cout << "Optimization Termination OptStatus: Max Iter Exceeded" << std::endl;
}
//MSQ_PRINT(1)("Optimization Termination OptStatus: Max Iter Exceeded\n");
}
}
void GaborFilter::getIntegral(const cv::Mat& matrix, cv::Mat& integral) {
integral.create(matrix.size(), CV_32F);
cv::Mat rowSum(matrix.size(), CV_32F);
float* prevRowSumPtr = NULL;
for (int y = 0; y < matrix.rows; ++y) {
const float* matrixPtr = matrix.ptr<float> (y);
float* rowSumPtr = rowSum.ptr<float> (y);
float* integralPtr = integral.ptr<float> (y);
for (int x = 0; x < matrix.cols; ++x) {
rowSumPtr[x] = matrixPtr[x];
if (prevRowSumPtr) {
rowSumPtr[x] += prevRowSumPtr[x];
}
integralPtr[x] = rowSumPtr[x];
if (x > 0) {
integralPtr[x] += integralPtr[x - 1];
}
}
prevRowSumPtr = rowSumPtr;
}
}
bool
NonGradient::testRowSum( int numRow, int numCol, double* matrix, double* oldRowSum)
{
bool same = true;
std::vector<double> rowSum(numRow,0.);
double maxVal = 0.;
for (int col=0;col<numCol;col++)
{
for (int row=0;row<numRow;row++)
{
rowSum[row] += matrix[row+col*numRow];
if( fabs( matrix[row+col*numRow] ) > maxVal )
{
maxVal = fabs( matrix[row+col*numRow] );
}
}
}
double machEps = 1.e-14 * static_cast<double>(numRow); // better to use system parameters
double upperBound = machEps * maxVal + 1.e-15;
for (int row=0;row<numRow;row++)
{
if( fabs( rowSum[row] - oldRowSum[row]) > upperBound )
{
same = false;
if( mNonGradDebug >= 2 )
{
std::cout << " Warning: NonGradient Row Sum " << row << " Test: value " << rowSum[row] << " Discrepancy " << rowSum[row] - oldRowSum[row] << " maxVal " << maxVal << " numRow " << numRow << " numCol " << numCol <<std::endl;
}
MSQ_PRINT(2)("NonGradient Row Sum [%d] Test failure: value %22.15e difference %22.15e \n", row, rowSum[row], rowSum[row] - oldRowSum[row]);
}
}
return(same);
}
void ConfusionMatrix::printPrecisionRecall(const char *header) const {
if (header == NULL) {
LOG(INFO) << "--- class-specific recall/precision ---";
} else {
LOG(INFO) << header;
}
// recall
LOG(INFO) << ROW_BEGIN;
for (size_t i = 0; i < _matrix.size(); i++) {
if (i > 0) {
LOG(INFO) << COL_SEP;
}
double r = (_matrix[i].size() > i) ?
(double)_matrix[i][i] / (double)rowSum(i) : 0.0;
LOG(INFO) << r;
}
LOG(INFO) << ROW_END;
// precision
LOG(INFO) << ROW_BEGIN;
for (size_t i = 0; i < _matrix.size(); i++) {
if (i > 0) {
LOG(INFO) << COL_SEP;
}
double p = (_matrix[i].size() > i) ?
(double)_matrix[i][i] / (double)colSum(i) : 1.0;
LOG(INFO) << p;
}
LOG(INFO) << ROW_END;
}
double ConfusionMatrix::jaccard(int n) const {
CHECK((_matrix.size() > (size_t)n) && (_matrix[n].size() > (size_t)n));
const double intersectionSize = (double)_matrix[n][n];
const double unionSize = (double)(rowSum(n) + colSum(n) - _matrix[n][n]);
return (intersectionSize == unionSize) ? 1.0 :
intersectionSize / unionSize;
}
float smallTable::getMarkov(int row, int col)
{
float sum = rowSum(row);
float ratio(0);
if(sum)
ratio = (float)(myTable[row][col]/sum);
return ratio;
}
int minimumTotal(vector<vector<int>>& triangle) {
if (triangle.size() == 0)
return 0;
vector<vector<int> > minSum;
for (int i = 0; i < triangle.size(); ++i)
{
vector<int> rowSum(triangle[i].size(), INT_MAX);
minSum.push_back(rowSum);
}
minPathSum(0, triangle, 0, minSum);
return minSum[0][0];
}
typename MaxNorm<VectorType, MatrixType>::ScalarType
MaxNorm<VectorType, MatrixType>::operator()(const MatrixType &A) const {
ScalarType maximum(0.);
for(int i=0;i<A.numberOfRows();i++) {
// Computes sum of absolute values of entries in given row
ScalarType rowSum(0.);
for(int j=0; j<A.numberOfColumns(); ++j){
rowSum += capd::abs(A[i][j]);
}
maximum = capd::max(maximum, rowSum);
}
return maximum;
}
double ConfusionMatrix::avgJaccard() const {
double totalJaccard = 0.0;
for (size_t i = 0; i < _matrix.size(); i++) {
if (_matrix[i].size() <= i) continue;
const double intersectionSize = (double)_matrix[i][i];
const double unionSize = (double)(rowSum(i) + colSum(i) - _matrix[i][i]);
if (intersectionSize == unionSize) {
// avoid divide by zero
totalJaccard += 1.0;
} else {
totalJaccard += intersectionSize / unionSize;
}
}
return totalJaccard / (double)_matrix.size();
}
void ConfusionMatrix::printJaccard(const char *header) const {
if (header == NULL) {
LOG(INFO) << "--- class-specific Jaccard coefficient ---";
} else {
LOG(INFO) << header;
}
LOG(INFO) << ROW_BEGIN;
for (size_t i = 0; i < _matrix.size(); i++) {
if (i > 0) {
LOG(INFO) << COL_SEP;
}
double p = (_matrix[i].size() > i) ? (double)_matrix[i][i] /
(double)(rowSum(i) + colSum(i) - _matrix[i][i]) : 0.0;
LOG(INFO) << p;
}
LOG(INFO) << ROW_END;
}
void ConfusionMatrix::printRowNormalized(const char *header) const {
if (header == NULL) {
LOG(INFO) << "--- confusion matrix: (actual, predicted) ---";
} else {
LOG(INFO) << header;
}
for (size_t i = 0; i < _matrix.size(); i++) {
double total = rowSum(i);
LOG(INFO) << ROW_BEGIN;
for (size_t j = 0; j < _matrix[i].size(); j++) {
if (j > 0) {
LOG(INFO) << COL_SEP;
}
LOG(INFO) << ((double)_matrix[i][j] / total);
}
LOG(INFO) << ROW_END;
}
}
void SystemMatrix::makeZeroRowSums(double* left_over)
{
const dim_t n = pattern->getNumOutput();
const dim_t nblk = block_size;
const dim_t blk = row_block_size;
const index_t* main_ptr = borrowMainDiagonalPointer();
rowSum(left_over);
// left_over now holds the row sum
#pragma omp parallel for
for (index_t ir=0; ir<n; ir++) {
for (index_t ib=0; ib<blk; ib++) {
const index_t irow = ib+blk*ir;
const double rtmp2 = mainBlock->val[main_ptr[ir]*nblk+ib+blk*ib];
const double rtmp1 = rtmp2-left_over[irow];
mainBlock->val[main_ptr[ir]*nblk+ib+blk*ib] = rtmp1;
left_over[irow]=rtmp2-rtmp1;
}
}
}
void ConfusionMatrix::printF1Score(const char *header) const {
if (header == NULL) {
LOG(INFO) << "--- class-specific F1 score ---";
} else {
LOG(INFO) << header;
}
LOG(INFO) << ROW_BEGIN;
for (size_t i = 0; i < _matrix.size(); i++) {
if (i > 0) {
LOG(INFO) << COL_SEP;
}
// recall
double r = (_matrix[i].size() > i) ?
(double)_matrix[i][i] / (double)rowSum(i) : 0.0;
// precision
double p = (_matrix[i].size() > i) ?
(double)_matrix[i][i] / (double)colSum(i) : 1.0;
LOG(INFO) << ((2.0 * p * r) / (p + r));
}
LOG(INFO) << ROW_END;
}
double ConfusionMatrix::avgRecall(const bool strict) const {
double totalRecall = 0.0;
int numClasses = 0;
for (size_t i = 0; i < _matrix.size(); i++) {
if (_matrix[i].size() > i) {
const double classSize = (double)rowSum(i);
if (classSize > 0.0) {
totalRecall += (double)_matrix[i][i] / classSize;
numClasses += 1;
}
}
}
if (strict && numClasses != (int)_matrix.size()) {
LOG(FATAL) << "not all classes represented in avgRecall()";
}
if (numClasses == 0) {
return 0;
} else {
return totalRecall / (double)numClasses;
}
}
boolean isCassette(struct altGraphX *ag, bool **em, int vs, int ve1, int ve2,
int *altBpStartV, int *altBpEndV, int *startV, int *endV)
/* Return TRUE if SIMPLE cassette exon.
Looking for pattern:
he--->hs---->he---->hs
\----------------/
Use edgesInArea() to investigate that encompasses the common hard
end and common hard start. Should only be 4 edges in area defined by
splicing.
sesese
012345
0
1 + +
2 +
3 +
4
5
*/
{
unsigned char *vTypes = ag->vTypes;
int i=0;
int numAltVerts = 4;
int *vPos = ag->vPositions;
/* Quick check. */
if(vTypes[vs] != ggHardEnd || vTypes[ve1] != ggHardStart || vTypes[ve2] != ggHardStart)
return FALSE;
if(em[vs][ve1] && em[vs][ve2])
{
/* Try to find a hard end that connects ve1 and ve2. */
for(i=0; i<ag->vertexCount; i++)
{
if(vTypes[i] == ggHardEnd && em[ve1][i] && em[i][ve2])
{
/* Make sure that our cassette only connect to downstream. otherwise not
so simple...*/
if(rowSum(em[i],ag->vTypes,ag->vertexCount) == 1 &&
rowSum(em[ve1],ag->vTypes,ag->vertexCount) == 1 &&
colSum(em, ag->vTypes, ag->vertexCount, ve1) == 1 &&
edgesInArea(ag,em,ve2-1,vs+1) == numAltVerts)
{
struct bed bedUp, bedDown, bedAlt;
/* Initialize some beds for reporting. */
*startV = findClosestUpstreamVertex(ag, em, vs);
*endV = findClosestDownstreamVertex(ag, em, ve2);
bedUp.chrom = bedDown.chrom = bedAlt.chrom = ag->tName;
bedUp.name = bedDown.name = bedAlt.name = ag->name;
bedUp.score = bedDown.score = bedAlt.score = altCassette;
safef(bedUp.strand, sizeof(bedUp.strand), "%s", ag->strand);
safef(bedDown.strand, sizeof(bedDown.strand), "%s", ag->strand);
safef(bedAlt.strand, sizeof(bedDown.strand), "%s", ag->strand);
/* Alt spliced region. */
bedAlt.chromStart = vPos[ve1];
bedAlt.chromEnd = vPos[i];
/* Upstream/down stream */
if(sameString(ag->strand, "+"))
{
bedUp.chromStart = vPos[ve1] - flankingSize;
bedUp.chromEnd = vPos[ve1];
bedDown.chromStart = vPos[i];
bedDown.chromEnd = vPos[i] + flankingSize;
}
else
{
bedDown.chromStart = vPos[ve1] - flankingSize;
bedDown.chromEnd = vPos[ve1];
bedUp.chromStart = vPos[i];
bedUp.chromEnd = vPos[i] + flankingSize;
}
if(altRegion != NULL)
{
bedOutputN(&bedAlt, 6, altRegion, '\t','\n');
bedOutputN(&bedUp, 6, upStream100, '\t', '\n');
bedOutputN(&bedDown, 6, downStream100, '\t', '\n');
}
*altBpStartV = ve1;
*altBpEndV = i;
return TRUE;
}
}
}
}
return FALSE;
}
boolean isAlt5Prime(struct altGraphX *ag, bool **em, int vs, int ve1, int ve2,
int *altBpStart, int *altBpEnd, int *termExonStart, int *termExonEnd)
/* Return TRUE if we have an edge pattern of:
hs->he----->hs
\-->he--/
Which indicates two possible ends to an exon (alt 5' intron starts).
Use edgesInArea() to investigate an area that begins in the rows with the common
hard end and finishes with common hard end.
esees
01234 (4 vertices involved in alt splicing)
0
1 ++
2 +
3 +
4
*/
{
unsigned char *vTypes = ag->vTypes;
int i=0;
int numAltVerts = 4;
/* Quick check. */
if(vTypes[vs] != ggHardStart || vTypes[ve1] != ggHardEnd || vTypes[ve2] != ggHardEnd)
return FALSE;
if(em[vs][ve1] && em[vs][ve2])
{
/* Try to find common start for the two hard ends. */
for(i=0; i<ag->vertexCount; i++)
{
if(vTypes[i] == ggHardStart && em[ve1][i] && em[ve2][i])
{
/* Make sure that they only connect to that one hard start. */
if(rowSum(em[ve1],ag->vTypes,ag->vertexCount) == 1 &&
rowSum(em[ve2],ag->vTypes,ag->vertexCount) == 1 &&
edgesInArea(ag,em,i-1,vs+1) == numAltVerts)
{
int *vPos = ag->vPositions;
struct bed bedUp, bedDown, bedAlt, bedConst;
/* Report the first and last vertexes. */
*termExonStart = i;
*termExonEnd = findClosestDownstreamVertex(ag, em, i);
/* Initialize some beds for reporting. */
bedConst.chrom = bedUp.chrom = bedDown.chrom = bedAlt.chrom = ag->tName;
bedConst.name = bedUp.name = bedDown.name = bedAlt.name = ag->name;
if(sameString(ag->strand, "+"))
bedConst.score = bedUp.score = bedDown.score = bedAlt.score = alt5Prime;
else
bedConst.score = bedUp.score = bedDown.score = bedAlt.score = alt3Prime;
safef(bedConst.strand, sizeof(bedConst.strand), "%s", ag->strand);
safef(bedUp.strand, sizeof(bedUp.strand), "%s", ag->strand);
safef(bedDown.strand, sizeof(bedDown.strand), "%s", ag->strand);
safef(bedAlt.strand, sizeof(bedDown.strand), "%s", ag->strand);
/* Alt spliced region. */
bedAlt.chromStart = vPos[ve1];
bedAlt.chromEnd = vPos[ve2];
bedConst.chromStart = vPos[vs];
bedConst.chromEnd = vPos[ve1];
/* Upstream/down stream */
if(sameString(ag->strand, "+"))
{
bedDown.chromStart = vPos[ve2];
bedDown.chromEnd = vPos[ve2]+flankingSize;
bedUp.chromStart = vPos[vs]-flankingSize;
bedUp.chromEnd = vPos[vs];
}
else
{
bedUp.chromStart = vPos[ve2];
bedUp.chromEnd = vPos[ve2]+flankingSize;
bedDown.chromStart = vPos[vs]-flankingSize;
bedDown.chromEnd = vPos[vs];
}
if(altRegion)
{
bedOutputN(&bedConst, 6, constRegion, '\t','\n');
bedOutputN(&bedAlt, 6, altRegion, '\t','\n');
bedOutputN(&bedDown, 6, downStream100, '\t', '\n');
bedOutputN(&bedUp, 6, upStream100, '\t', '\n');
}
*altBpStart = ve1;
*altBpEnd = ve2;
return TRUE;
}
}
}
}
return FALSE;
}
void lookForAltSplicing(char *db, struct altGraphX *ag, struct altSpliceSite **aSpliceList,
int *altSpliceSites, int *altSpliceLoci, int *totalSpliceSites)
/* Walk throught the altGraphX graph and look for evidence of altSplicing. */
{
struct altSpliceSite *notAlt = NULL, *notAltList = NULL;
bool **em = altGraphXCreateEdgeMatrix(ag);
int vCount = ag->vertexCount;
unsigned char *vTypes = ag->vTypes;
int altSpliceSitesOrig = *altSpliceSites;
int i,j,k;
int altCount = 0;
occassionalDot();
totalLoci++;
for(i=0; i<vCount; i++)
{
struct altSpliceSite *aSplice = NULL;
for(j=0; j<vCount; j++)
{
if(em[i][j] && areConsSplice(em, vCount, vTypes,i,j) &&
(agxEvCount(ag, i,j) >= minConfidence))
{
for(k=j+1; k<vCount; k++)
{
if(em[i][k] && areConsSplice(em, vCount, vTypes, i, k) &&
(agxEvCount(ag, i,k) >= minConfidence))
{
totalSplices++;
if(aSplice == NULL)
{
splicedLoci++;
aSplice = initASplice(ag, em, i, j, k);
(*altSpliceSites)++;
}
else
addSpliceSite(ag, em, aSplice, k);
}
}
}
/* Only want non alt-spliced exons for our controls. Some of
these checks are historical and probably redundant....*/
if(em[i][j] &&
rowSum(em[i], ag->vTypes, ag->vertexCount) == 1 &&
rowSum(em[j], ag->vTypes, ag->vertexCount) == 1 &&
colSum(em, ag->vTypes, ag->vertexCount, j) == 1 &&
colSum(em, ag->vTypes, ag->vertexCount, j) == 1 &&
altGraphXEdgeVertexType(ag, i, j) == ggExon &&
areHard(ag, i, j) &&
areConstitutive(ag, em, i, j))
{
notAlt = initASplice(ag, em, i, j, j);
if(altRegion != NULL)
outputControlExonBeds(ag, i, j);
slAddHead(¬AltList, notAlt);
}
}
if(aSplice != NULL)
{
if(altLogFile)
fprintf(altLogFile, "%s\n", ag->name);
slAddHead(aSpliceList, aSplice);
}
/* If we have a simple splice classfy it and log it. */
if(aSplice != NULL && aSplice->altCount == 2)
{
altTotalCount++;
fixOtherStrand(aSplice);
logSpliceType(aSplice->spliceTypes[1], abs(aSplice->altBpEnds[1] - aSplice->altBpStarts[1]));
if(aSplice->spliceTypes[1] == alt3Prime && (aSplice->altBpEnds[1] - aSplice->altBpStarts[1] == 3))
reportThreeBpBed(aSplice);
if(doSScores)
fillInSscores(db, aSplice, 1);
if(RData != NULL)
{
outputForR(aSplice, 1, RData);
}
}
/* Otherwise log it as altOther. Start at 1 as 0->1 is the first
* splice, 1->2 is the first alt spliced.*/
else if(aSplice != NULL)
{
for(altCount=1; altCount<aSplice->altCount; altCount++)
{
altTotalCount++;
altOtherCount++;
}
}
}
for(notAlt = notAltList; notAlt != NULL; notAlt = notAlt->next)
{
if(doSScores)
fillInSscores(db, notAlt, 1);
if(RData != NULL)
{
fixOtherStrand(notAlt);
outputForR(notAlt, 1, RDataCont);
}
}
if(*altSpliceSites != altSpliceSitesOrig)
(*altSpliceLoci)++;
altGraphXFreeEdgeMatrix(&em, vCount);
}
double ConfusionMatrix::recall(int n) const {
CHECK(_matrix.size() > (size_t)n);
return (_matrix[n].size() > (size_t)n) ?
(double)_matrix[n][n] / (double)rowSum(n) : 0.0;
}
void Confusion_getEntropies (Confusion me, double *p_h, double *p_hx, double *p_hy, double *p_hygx, double *p_hxgy, double *p_uygx, double *p_uxgy, double *p_uxy) {
double h = 0.0, hx = 0.0, hy = 0.0, hxgy = 0.0, hygx = 0.0, uygx = 0.0, uxgy = 0.0, uxy = 0.0;
autoNUMvector<double> rowSum (1, my numberOfRows);
autoNUMvector<double> colSum (1, my numberOfColumns);
double sum = 0.0;
for (long i = 1; i <= my numberOfRows; i++) {
for (long j = 1; j <= my numberOfColumns; j++) {
rowSum[i] += my data[i][j];
colSum[j] += my data[i][j];
sum += my data[i][j];
}
}
for (long i = 1; i <= my numberOfRows; i++) {
if (rowSum[i] > 0.0) {
hy -= rowSum[i] / sum * NUMlog2 (rowSum[i] / sum);
}
}
for (long j = 1; j <= my numberOfColumns; j++) {
if (colSum[j] > 0.0) {
hx -= colSum[j] / sum * NUMlog2 (colSum[j] / sum);
}
}
for (long i = 1; i <= my numberOfRows; i++) {
for (long j = 1; j <= my numberOfColumns; j++) {
if (my data[i][j] > 0.0) {
h -= my data[i][j] / sum * NUMlog2 (my data[i][j] / sum);
}
}
}
hygx = h - hx;
hxgy = h - hy;
uygx = (hy - hygx) / (hy + TINY);
uxgy = (hx - hxgy) / (hx + TINY);
uxy = 2.0 * (hx + hy - h) / (hx + hy + TINY);
if (p_h) {
*p_h = h;
}
if (p_hx) {
*p_hx = hx;
}
if (p_hy) {
*p_hy = hy;
}
if (p_hygx) {
*p_hygx = hygx;
}
if (p_hxgy) {
*p_hxgy = hxgy;
}
if (p_uygx) {
*p_uygx = uygx;
}
if (p_uxgy) {
*p_uxgy = uxgy;
}
if (p_uxy) {
*p_uxy = uxy;
}
}
int main (){
int array[][3] = { {1}, {2, 3}, {3, 4, 5}};
printArray(array);
rowSum (array, 2);
return 0;
}