static void gather(const communicator& comm, const std::vector<T>& in, std::vector< std::vector<T> >& out, int root)
{
std::vector<int> counts(comm.size());
Collectives<int,void*>::gather(comm, (int) in.size(), counts, root);
std::vector<int> offsets(comm.size(), 0);
for (unsigned i = 1; i < offsets.size(); ++i)
offsets[i] = offsets[i-1] + counts[i-1];
std::vector<T> buffer(offsets.back() + counts.back());
MPI_Gatherv(Datatype::address(const_cast<T&>(in[0])),
in.size(),
Datatype::datatype(),
Datatype::address(buffer[0]),
&counts[0],
&offsets[0],
Datatype::datatype(),
root, comm);
out.resize(comm.size());
size_t cur = 0;
for (unsigned i = 0; i < (unsigned)comm.size(); ++i)
{
out[i].reserve(counts[i]);
for (unsigned j = 0; j < (unsigned)counts[i]; ++j)
out[i].push_back(buffer[cur++]);
}
}
void HexView::paintOffsets(QPainter *painter, int &left,int first, int last)
{
QPen pen;
for (int i=first; i<=last ; ++i) {
QRect offsets(left,rowHeight() * i,offsetsWidth(),rowHeight());
if (showGuidelines_) {
pen.setColor(Qt::green);
painter->setPen(pen);
painter->drawRect(offsets);
}
pen.setColor(Qt::black);
painter->setPen(pen);
QString offset = getHexNumber(i * bytesPerRow(),offsetLen(),true);
painter->drawText( offsets ,Qt::AlignCenter ,offset );
}
left += offsetsWidth();
if (showGuidelines_) {
QRect space(left,0,spacer() ,contentHeight());
pen.setColor(Qt::blue);
painter->setPen(pen);
painter->drawRect(space);
}
left += spacer();
}
void StringFile::readHeader()
{
if(_compressed) {
std::vector<uint16_t> offsets(_strings.size());
for(uint16_t i = 0; i < _strings.size(); i++)
offsets[i] = _stream.getU16LE();
for(uint16_t i = 0; i < _strings.size(); i++)
_strings[i] = decodeString(offsets[i]);
}
else {
_strings.push_back("");
while(!_stream.eof()) {
uint8_t byte = _stream.get();
//TODO: Figure out what these non-alpha numeric characters are for,
// some sort of formatting perhaps? Let's just treat them as
// separators for now...
if(byte >= 0x20 && byte <= 0x7e)
_strings.back() += byte;
else if(_strings.back().size() != 0)
_strings.push_back("");
}
}
}
/*
double Network::_dfs_cal_famscore_with_prior(const node_pointer_t &p,condition_t &condition,const int idx){
if(idx<0){
vector<size_t> offsets;
size_t total=_get_data_offsets(offsets,condition);
// condition_t data_condition(condition);
double res=log(math::tgamma_delta_ratio(get_alpha2(p,condition),total));
for(size_t i=0;i<p->get_n_states() && res!=DOUBLE_NEG_INF;i++){
// data_condition[p]=i;
// res/=math::tgamma_delta_ratio(get_alpha3(p,condition,i),_get_data_count(data_condition));
res-=log(math::tgamma_delta_ratio(get_alpha3(p,condition,i),_get_data_count(offsets,p,i)));
}
//return res*math::tgamma_delta_ratio(get_alpha2(p,condition),_get_data_count(condition));
return res;
}
double res=0.0;
node_pointer_t node=p->get_parent(idx);
for(size_t i=0;i<node->get_n_states();i++){
condition[node]=i;
res+=_dfs_cal_famscore_with_prior(p,condition,idx-1);
}
return res;
}
double Network::_dfs_cal_famscore_with_prior(
const node_pointer_t &p,condition_t &condition,const vector<size_t> &offset_base,const size_t idx)
{
if(idx>=p->get_n_parents()){
//more fast: divide each part together and log once.
//more accurate: log each part and minus together.
size_t total=offset_base.size();
// double res=math::tgamma_delta_ratio(get_alpha2(p,condition),total); //fast
double res=log(math::tgamma_delta_ratio(get_alpha2(p,condition),total)); //accurate
for(size_t i=0;i<p->get_n_states() && res!=DOUBLE_NEG_INF;i++){
// res/=math::tgamma_delta_ratio(get_alpha3(p,condition,i),_get_data_count(offset_base,p,i)); //fast
res-=log(math::tgamma_delta_ratio(get_alpha3(p,condition,i),_get_data_count(offset_base,p,i))); //accurate
}
// return log(res); //fast
return res; //accurate
}
double res=0.0;
node_pointer_t node=p->get_parent(idx);
vector<size_t> offsets;
for(size_t i=0;i<node->get_n_states() && res!=DOUBLE_NEG_INF;i++){
//prepare the data offsets
condition[node]=i;
_get_data_offsets(offsets,offset_base,node,i);
res+=_dfs_cal_famscore_with_prior(p,condition,offsets,idx+1);
offsets.clear();
}
return res;
}
*/
double Network::_dfs_cal_famscore_without_prior(
const node_pointer_t &p,condition_t &condition,const vector<size_t> &offset_base,const size_t idx)
{
if(offset_base.empty()){//shortcut
static const double none_data_score=0.0;//log(gamma(1.0))==0.0
return none_data_score;
}
if(idx>=p->get_n_parents()){
//more fast: divide each part together and log once.
//more accurate: log each part and minus together.
size_t N=offset_base.size();
double res=-lgamma(N+1.0);
vector<size_t> offset_temp=offset_base;
for(size_t i=0;i<p->get_n_states() && res!=DOUBLE_NEG_INF;i++){
// res+=math::lgamma(pdata->_get_data_count(offset_base,p,i)+1.0);
res+=lgamma(pdata->_get_data_count_and_exclude(offset_temp,p,i)+1.0);
}
return res;
}
double res=0.0;
node_pointer_t node=p->get_parent(idx);
// vector<size_t> offsets;
vector<vector<size_t> > offsets(node->get_n_states());
pdata->_get_data_offsets_split(offsets,offset_base,node);
for(size_t i=0;i<node->get_n_states() && res!=DOUBLE_NEG_INF;i++){
//prepare the data offsets
condition[node]=i;
// pdata->_get_data_offsets(offsets,offset_base,node,i);
res+=_dfs_cal_famscore_without_prior(p,condition,offsets[i],idx+1);
// offsets.clear();
}
return res;
}
int main( int argc, char* argv[] ) {
const int N = 100;
std::vector<int> a(N), b(N);
std::vector<int> offsets(3);
offsets[0] = 3;
offsets[1] = 94;
offsets[2] = 50;
{
for (int j = 0; j < (int)offsets.size(); ++j) {
for (int i = 0; i < N; ++i) {
a[i] = i;
b[i] = (i + offsets[j]) % N;
}
rotate1(a, offsets[j]);
eq(j, a, b);
}
}
{
for (int j = 0; j < (int)offsets.size(); ++j) {
for (int i = 0; i < N; ++i) {
a[i] = i;
b[i] = (i + offsets[j]) % N;
}
rotate2(a, offsets[j]);
eq(j, a, b);
}
}
}
int main(int argc, char **argv)
{
char *inputFilename;
char *outputFilename;
if (!parseCmdLineSimple(argc, argv, "ss", &inputFilename, &outputFilename))
{
printf("Usage: mtx2gr input output\n");
exit(1);
}
int nVertices;
std::vector<int> srcs;
std::vector<int> dsts;
std::vector<int> edgeValues;
loadGraph(inputFilename, nVertices, srcs, dsts, &edgeValues);
printf("Read input file with %d vertices and %zd edges\n", nVertices, dsts.size());
printf("Converting to CSR\n");
std::vector<int> offsets(nVertices + 1);
std::vector<int> csrDsts(dsts.size());
std::vector<int> sortIndices(dsts.size());
std::vector<int> sortedEdgeValues(dsts.size());
edgeListToCSR<int>(nVertices, dsts.size(), &srcs[0], &dsts[0]
, &offsets[0], &csrDsts[0], &sortIndices[0]);
for (size_t i = 0; i < sortIndices.size(); ++i)
sortedEdgeValues[i] = edgeValues[sortIndices[i]];
printf("writing output\n");
writeGraph_binaryCSR(outputFilename, nVertices, dsts.size()
, &offsets[0], &csrDsts[0], &sortedEdgeValues[0]);
}
void mouseHandler(int event, int x, int y, int flags, void* data) {
if (event == CV_EVENT_LBUTTONDOWN) {
SurgicalGUI* gui = (SurgicalGUI *) data;
pcl::PointCloud<pcl::PointXYZRGB>::Ptr
cloud_ptr = gui->get_image_communicator()->get_cloud_ptr();
int cloud_height = cloud_ptr->height;
int off[] = {0,1,-1,2,-2,-3,3,-4,4,-5,5};
std::vector<int> offsets(off, off+sizeof(off)/sizeof(int));
for (int x_idx = 0; x_idx < offsets.size(); x_idx += 1) {
for (int y_idx = 0; y_idx < offsets.size(); y_idx += 1) {
int x_new = round(x/ZOOM_FACTOR) + offsets[x_idx];
int y_new = round(y/ZOOM_FACTOR) + offsets[y_idx];
if ( ( (0 <= x_new) && (x_new < cloud_ptr->width))
&& ( (0 <= y_new) && (y_new < cloud_ptr->height)) ) {
pcl::PointXYZRGB pt = cloud_ptr->at(x_new,y_new);
if (pointIsFinite(pt)) {
gui->interact(&pt, x_new, y_new);
return;
}
}
}
}
}
}
// Returns a vector of cube offsets
static std::vector<Mat4f> MakeCubeMatrices(GLuint count, float max_dist)
{
std::srand(59039);
std::vector<Mat4f> offsets(count);
for(GLuint i=0; i!=count; ++i)
{
float x = float(std::rand())/RAND_MAX;
float y = float(std::rand())/RAND_MAX;
float z = float(std::rand())/RAND_MAX;
float sx = std::rand()%2 ? 1.0f: -1.0f;
float sy = std::rand()%2 ? 1.0f: -1.0f;
float sz = std::rand()%2 ? 1.0f: -1.0f;
offsets[i] =
ModelMatrixf::Translation(
sx*(1.0f + std::pow(x, 0.9f) * max_dist),
sy*(1.0f + std::pow(y, 1.5f) * max_dist),
sz*(1.0f + std::pow(z, 0.7f) * max_dist)
) *
ModelMatrixf::RotationZ(
RightAngles(float(std::rand())/RAND_MAX)
) *
ModelMatrixf::RotationY(
RightAngles(float(std::rand())/RAND_MAX)
) *
ModelMatrixf::RotationX(
RightAngles(float(std::rand())/RAND_MAX)
);
}
return offsets;
}
/**
* Creates a massvector representing the centre of gravity from a given list of mass vectors
* \param masses: The mass vectors, that will be combined
*/
static BITBOTS_INLINE Eigen::Vector4d create_mass_offset(const Eigen::Matrix4Xd& masses) {
Eigen::Matrix4Xd offsets(4,masses.cols());
for(uint i = 0; i < (uint)masses.cols(); ++i) {
offsets.col(i) << masses(3, i) * masses.col(i).head<3>(), masses(3, i);
}
return mass_from_offsets(offsets);
}
/*
* load the offsets of the user binary into memory
*/
void IBBL_LargeFile::load_user_offsets()
{
int num_users;
user_offsets.clear();
ifstream offsets(get_user_offset_filename().c_str(), ifstream::binary);
offsets.read((char*)&num_users, 4);
if (num_users == 0)
{
cerr << "Couldn't read user offset file: "
<< get_user_offset_filename();
assert(false);
}
int id;
int offset;
for (int i = 0; i < num_users; ++i)
{
offsets.read((char*)&id, 4);
offsets.read((char*)&offset, 4);
user_offsets.insert(pair<int, int>(id, offset));
}
offsets.close();
}
TYPED_TEST_P(TcTest, ShuffledRdWr)
{
const char *PATH = "TcTest-ShuffledRdWr.dat";
const int N = 8; /* size of iovs */
struct tc_iovec iovs[N];
const int S = 4096;
tc_touch(PATH, N * S);
char *data1 = getRandomBytes(N * S);
char *data2 = (char *)malloc(N * S);
std::vector<int> offsets(N);
std::iota(offsets.begin(), offsets.end(), 0);
std::mt19937 rng(8887);
for (int i = 0; i < 10; ++i) { // repeat for 10 times
for (int n = 0; n < N; ++n) {
tc_iov2path(&iovs[n], PATH, offsets[n] * S, S,
data1 + offsets[n] * S);
}
EXPECT_OK(tc_writev(iovs, N, false));
for (int n = 0; n < N; ++n) {
iovs[n].data = data2 + offsets[n] * S;
}
EXPECT_OK(tc_readv(iovs, N, false));
EXPECT_EQ(0, memcmp(data1, data2, N * S));
std::shuffle(offsets.begin(), offsets.end(), rng);
}
free(data1);
free(data2);
}
// static
PassRefPtrWillBeRawPtr<SpellCheckRequest> SpellCheckRequest::create(TextCheckingTypeMask textCheckingOptions, TextCheckingProcessType processType, const EphemeralRange& checkingRange, const EphemeralRange& paragraphRange, int requestNumber)
{
if (checkingRange.isNull())
return nullptr;
if (!checkingRange.startPosition().computeContainerNode()->rootEditableElement())
return nullptr;
String text = plainText(checkingRange, TextIteratorEmitsObjectReplacementCharacter);
if (text.isEmpty())
return nullptr;
RefPtrWillBeRawPtr<Range> checkingRangeObject = createRange(checkingRange);
RefPtrWillBeRawPtr<Range> paragraphRangeObject = nullptr;
// Share identical Range objects.
if (checkingRange == paragraphRange)
paragraphRangeObject = checkingRangeObject;
else
paragraphRangeObject = createRange(paragraphRange);
const DocumentMarkerVector& markers = checkingRangeObject->ownerDocument().markers().markersInRange(checkingRange, DocumentMarker::SpellCheckClientMarkers());
Vector<uint32_t> hashes(markers.size());
Vector<unsigned> offsets(markers.size());
for (size_t i = 0; i < markers.size(); ++i) {
hashes[i] = markers[i]->hash();
offsets[i] = markers[i]->startOffset();
}
return adoptRefWillBeNoop(new SpellCheckRequest(checkingRangeObject, paragraphRangeObject, text, textCheckingOptions, processType, hashes, offsets, requestNumber));
}
void HeapRegion::add_continuingHumongousRegion(HeapRegion* cont) {
// Must join the blocks of the current H region seq with the block of the
// added region.
offsets()->join_blocks(bottom(), cont->bottom());
arrayOop obj = (arrayOop)(bottom());
obj->set_length((int) (obj->length() + cont->capacity()/jintSize));
set_end(cont->end());
set_top(cont->end());
}
//#################### FUNCTIONS ####################
std::vector<itk::Offset<2> > make_4_connected_offsets()
{
std::vector<itk::Offset<2> > offsets(4);
offsets[0][0] = 0; offsets[0][1] = -1; // above
offsets[1][0] = -1; offsets[1][1] = 0; // left
offsets[2][0] = 1; offsets[2][1] = 0; // right
offsets[3][0] = 0; offsets[3][1] = 1; // below
return offsets;
}
static std::vector<size_t> offsetsFromParts(const std::vector<c_atable_ptr_t>& parts) {
std::vector<size_t> offsets(parts.size());
auto total_size = 0;
size_t i = 0;
for (const auto& part: parts) {
offsets[i++] = total_size;
total_size += part->size();
}
return offsets;
}
static std::vector<table_id_t> tableIdOffsets(const std::vector<c_atable_ptr_t>& parts) {
std::vector<table_id_t> offsets(parts.size()+1, 0);
std::transform(std::begin(parts), std::end(parts),
std::begin(offsets) + 1,
[] (const c_atable_ptr_t& part) {
return part->subtableCount();
});
std::partial_sum(std::begin(offsets), std::end(offsets), std::begin(offsets));
return offsets;
}
double Dnds::change(void) {
// update conditional likelihood and transition probability flags
Topology* t = modelPtr->getActiveTopology();
t->updateAllCls(true);
t->updateAllTis(true);
t->flipAllActiveCls();
t->flipAllActiveTis();
// set the maximum distance of the move
double x = 0.1;
// propose new values for all of the omegas
bool isValid = true;
std::vector<double> newVals(numCategories);
std::vector<double> offsets(numCategories);
do
{
// pick the values for each of the categories
for (int i=0; i<numCategories; i++)
offsets[i] = x*(ranPtr->uniformRv()-0.5);
// calculate the new points
for (int i=0; i<numCategories; i++)
newVals[i] = dndsVals[i] + offsets[i];
// decide if the new point is valid
isValid = true;
for (int i=0; i<numCategories; i++)
{
if (newVals[i] < 0.0)
{
isValid = false;
break;
}
for (int j=i+1; j<numCategories; j++)
{
if (newVals[i] > newVals[j])
{
isValid = false;
break;
}
}
if (isValid == false)
break;
}
} while (isValid == false);
// commit the change
for (int i=0; i<numCategories; i++)
dndsVals[i] = newVals[i];
return 0.0;
}
void QTextEngine::shape( int item ) const
{
assert( item < items.size() );
QScriptItem &si = items[item];
if ( si.num_glyphs )
return;
QFont::Script script = (QFont::Script)si.analysis.script;
si.glyph_data_offset = used;
if ( !si.fontEngine )
si.fontEngine = fnt->engineForScript( script );
si.fontEngine->ref();
si.ascent = si.fontEngine->ascent();
si.descent = si.fontEngine->descent();
si.num_glyphs = 0;
if ( si.fontEngine && si.fontEngine != (QFontEngine*)-1 ) {
QShaperItem shaper_item;
shaper_item.script = si.analysis.script;
shaper_item.string = &string;
shaper_item.from = si.position;
shaper_item.length = length(item);
shaper_item.font = si.fontEngine;
shaper_item.num_glyphs = QMAX(int(num_glyphs - used), shaper_item.length);
shaper_item.flags = si.analysis.bidiLevel % 2 ? RightToLeft : 0;
while (1) {
// qDebug(" . num_glyphs=%d, used=%d, item.num_glyphs=%d", num_glyphs, used, shaper_item.num_glyphs);
ensureSpace(shaper_item.num_glyphs);
shaper_item.num_glyphs = num_glyphs - used;
// qDebug(" .. num_glyphs=%d, used=%d, item.num_glyphs=%d", num_glyphs, used, shaper_item.num_glyphs);
shaper_item.glyphs = glyphs(&si);
shaper_item.advances = advances(&si);
shaper_item.offsets = offsets(&si);
shaper_item.attributes = glyphAttributes(&si);
shaper_item.log_clusters = logClusters(&si);
if (scriptEngines[shaper_item.script].shape(&shaper_item))
break;
}
si.num_glyphs = shaper_item.num_glyphs;
}
((QTextEngine *)this)->used += si.num_glyphs;
si.width = 0;
advance_t *advances = this->advances( &si );
advance_t *end = advances + si.num_glyphs;
while ( advances < end )
si.width += *(advances++);
return;
}
void MemoryWatcher::ParseLine(const std::string& line)
{
m_values[line] = 0;
m_addresses[line] = std::vector<u32>();
std::stringstream offsets(line);
offsets >> std::hex;
u32 offset;
while (offsets >> offset)
m_addresses[line].push_back(offset);
}
std::vector<itk::Offset<3> > make_6_connected_offsets()
{
std::vector<itk::Offset<3> > offsets(6);
offsets[0][0] = 0; offsets[0][1] = 0; offsets[0][2] = -1;
offsets[1][0] = 0; offsets[1][1] = -1; offsets[1][2] = 0;
offsets[2][0] = -1; offsets[2][1] = 0; offsets[2][2] = 0;
offsets[3][0] = 1; offsets[3][1] = 0; offsets[3][2] = 0;
offsets[4][0] = 0; offsets[4][1] = 1; offsets[4][2] = 0;
offsets[5][0] = 0; offsets[5][1] = 0; offsets[5][2] = 1;
return offsets;
}
/// Read the string values. This function processes the data produced by
/// version 0x01000000 of the write function. On successful completion, it
/// returns 0.
int ibis::dictionary::readKeys1(const char *evt, FILE *fptr) {
uint32_t nkeys;
int ierr = fread(&nkeys, 4, 1, fptr);
if (ierr != 1) {
LOGGER(ibis::gVerbose > 1)
<< "Warning -- " << evt
<< " failed to read the number of keys, fread returned " << ierr;
return -6;
}
clear();
array_t<uint64_t> offsets(nkeys+1);
ierr = fread(offsets.begin(), 8, nkeys+1, fptr);
if (ierr != (int)(1+nkeys)) {
LOGGER(ibis::gVerbose > 1)
<< "Warning -- " << evt << " failed to read the string positions, "
"expected fread to return " << nkeys+1 << ", but got " << ierr;
return -8;
}
buffer_.resize(1);
buffer_[0] = new char[offsets.back()-offsets.front()];
ierr = fread(buffer_[0], 1, offsets.back()-offsets.front(), fptr);
if (ierr != (int)(offsets.back()-offsets.front())) {
LOGGER(ibis::gVerbose > 1)
<< "Warning -- " << evt << " failed to read the strings, "
"expected fread to return " << (offsets.back()-offsets.front())
<< ", but got " << ierr;
return -9;
}
raw_.resize(nkeys+1);
raw_[0] = 0;
#if __GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 7)
key_.reserve(nkeys+nkeys); // older version does not have reserve
#endif
for (unsigned j = 0; j < nkeys; ++ j) {
raw_[j+1] = buffer_[0] + (offsets[j] - offsets[0]);
key_[raw_[j+1]] = j+1;
#if DEBUG+0 > 2 || _DEBUG+0 > 2
LOGGER(ibis::gVerbose > 0)
<< "DEBUG -- " << evt << " raw_[" << j+1 << "] = \"" << raw_[j+1]
<< '"';
#endif
}
#if DEBUG+0 > 2 || _DEBUG+0 > 2
ibis::util::logger lg;
lg() << "DEBUG -- " << evt << " got the following keys";
for (MYMAP::const_iterator it = key_.begin(); it != key_.end(); ++ it)
lg() << "\n\t" << it->second << ": " << it->first;
#endif
return 0;
} // ibis::dictionary::readKeys1
void updateOffsets(jintArray javaOffsets) {
ScopedIntArrayRW offsets(mEnv, javaOffsets);
if (offsets.get() == NULL) {
return;
}
for (size_t i = 0, groupCount = mMatcher->groupCount(); i <= groupCount; ++i) {
offsets[2*i + 0] = mMatcher->start(i, mStatus);
offsets[2*i + 1] = mMatcher->end(i, mStatus);
}
}
size_t getImportList(
const PartitioningSolution<SolutionAdapter> &solution,
const DataAdapter * const data,
ArrayRCP<typename DataAdapter::zgid_t> &imports // output
)
{
typedef typename PartitioningSolution<SolutionAdapter>::part_t part_t;
typedef typename PartitioningSolution<SolutionAdapter>::gno_t gno_t;
typedef typename DataAdapter::zgid_t zgid_t;
size_t numParts = solution.getActualGlobalNumberOfParts();
int numProcs = solution.getCommunicator()->getSize();
if (numParts > size_t(numProcs)) {
char msg[256];
sprintf(msg, "Number of parts %lu exceeds number of ranks %d; "
"%s requires a MappingSolution for this case\n",
numParts, numProcs, __func__);
throw std::logic_error(msg);
}
size_t localNumIds = data->getLocalNumIDs();
const zgid_t *gids = NULL;
data->getIDsView(gids);
const part_t *parts = solution.getPartListView();
// How many ids to each process?
Array<int> counts(numProcs, 0);
for (size_t i=0; i < localNumIds; i++)
counts[parts[i]]++;
Array<gno_t> offsets(numProcs+1, 0);
for (int i=1; i <= numProcs; i++){
offsets[i] = offsets[i-1] + counts[i-1];
}
Array<typename DataAdapter::zgid_t> gidList(localNumIds);
for (size_t i=0; i < localNumIds; i++) {
gno_t idx = offsets[parts[i]];
gidList[idx] = gids[i];
offsets[parts[i]] = idx + 1;
}
Array<int> recvCounts(numProcs, 0);
try {
AlltoAllv<zgid_t>(*(solution.getCommunicator()),
*(solution.getEnvironment()),
gidList(), counts(), imports, recvCounts());
}
Z2_FORWARD_EXCEPTIONS;
return imports.size();
}
static std::vector<Offset> generate(const Lattice& lattice) {
Vid dx = OffsetCat::dx_max(lattice);
Vid dy = OffsetCat::dy_max(lattice);
Vid n = std::min(dx, dy);
std::vector<Offset> offsets(n);
for (Vid i=0; i<n; i++) {
//offsets[i] = {i+1, i+1};
offsets[i].dx = i+1;
offsets[i].dy = i+1;
}
return offsets;
}
HexFindResult HexSearcher::FindOffsets(std::vector<unsigned char> const& pattern, size_t limit, ADDRESS& address, const char* func, bool displayError)
{
if (address)
return HexFindResult(ERR_ALREADY_EXISTS, func, displayError);
Offsets offsets(FindOffsets(pattern, limit));
if (offsets.empty())
return HexFindResult(ERR_NOTFOUND, func, displayError);
if (offsets.size() > 1)
return HexFindResult(ERR_MULTIPLE, func, displayError);
address = STATIC_REBASE(*offsets.begin());
return HexFindResult(ERR_OK, func, displayError);
}
/*
* load the offsets from the movie binary into memory
*/
void IBBL_LargeFile::load_movie_offsets()
{
movie_offsets.clear();
movie_offsets.push_back(0);
ifstream offsets(get_movie_offset_filename().c_str(), ifstream::binary);
int offset = 0;
for (int i = 1; i <= NUM_MOVIES; ++i)
{
offsets.read((char*)&offset, 4);
movie_offsets.push_back(offset);
}
offsets.close();
}
Rcpp::List reTrms::condVar(double scale) {
if (scale < 0 || !R_finite(scale))
throw runtime_error("scale must be non-negative and finite");
int nf = d_flist.size();
IntegerVector nc = ncols(), nl = nlevs(), nct = nctot(), off = offsets();
List ans(nf);
CharacterVector nms = d_flist.names();
ans.names() = clone(nms);
for (int i = 0; i < nf; i++) {
int ncti = nct[i], nli = nl[i];
IntegerVector trms = terms(i);
int *cset = new int[ncti], nct2 = ncti * ncti;
NumericVector ansi(Dimension(ncti, ncti, nli));
ans[i] = ansi;
double *ai = ansi.begin();
for (int j = 0; j < nli; j++) {
int kk = 0;
for (int jj = 0; jj < trms.size(); jj++) {
int tjj = trms[jj];
for (int k = 0; k < nc[tjj]; k++)
cset[kk++] = off[tjj] + j * nc[tjj] + k;
}
CHM_SP cols =
M_cholmod_submatrix(&d_Lambda, (int*)NULL, -1, cset, ncti,
1/*values*/, 1/*sorted*/, &c);
CHM_SP sol = d_L.spsolve(CHOLMOD_A, cols);
CHM_SP tcols = M_cholmod_transpose(cols, 1/*values*/, &c);
M_cholmod_free_sparse(&cols, &c);
CHM_SP var = M_cholmod_ssmult(tcols, sol, 0/*stype*/,
1/*values*/, 1/*sorted*/, &c);
M_cholmod_free_sparse(&sol, &c);
M_cholmod_free_sparse(&tcols, &c);
CHM_DN dvar = M_cholmod_sparse_to_dense(var, &c);
M_cholmod_free_sparse(&var, &c);
Memcpy(ai + j * nct2, (double*)dvar->x, nct2);
M_cholmod_free_dense(&dvar, &c);
}
delete[] cset;
transform(ansi.begin(), ansi.end(), ansi.begin(),
bind2nd(multiplies<double>(), scale * scale));
}
return ans;
}
/// Read the ordered strings. This function process the data produced by
/// the write function. On successful completion, it returns 0.
int ibis::dictionary::readKeys(const char *evt, FILE *fptr) {
uint32_t nkeys;
int ierr = fread(&nkeys, 4, 1, fptr);
if (ierr != 1) {
LOGGER(ibis::gVerbose > 1)
<< "Warning -- " << evt
<< " failed to read the number of keys, fread returned " << ierr;
return -6;
}
clear();
code_.resize(nkeys);
ierr = fread(code_.begin(), 4, nkeys, fptr);
if (ierr != (int)nkeys) {
LOGGER(ibis::gVerbose > 1)
<< "Warning -- " << evt << " failed to read the code values, "
"expected fread to return " << nkeys << ", but got " << ierr;
return -7;
}
array_t<uint32_t> offsets(nkeys+1);
ierr = fread(offsets.begin(), 4, nkeys+1, fptr);
if (ierr != (int)(1+nkeys)) {
LOGGER(ibis::gVerbose > 1)
<< "Warning -- " << evt << " failed to read the string positions, "
"expected fread to return " << nkeys+1 << ", but got " << ierr;
return -8;
}
buffer_.resize(1);
buffer_[0] = new char[offsets.back()-offsets.front()];
ierr = fread(buffer_[0], 1, offsets.back()-offsets.front(), fptr);
if (ierr != (int)(offsets.back()-offsets.front())) {
LOGGER(ibis::gVerbose > 1)
<< "Warning -- " << evt << " failed to read the strings, "
"expected fread to return " << (offsets.back()-offsets.front())
<< ", but got " << ierr;
return -9;
}
raw_.resize(nkeys+1);
key_.resize(nkeys);
for (unsigned j = 0; j < nkeys; ++ j)
key_[j] = buffer_[0] + (offsets[j] - offsets[0]);
for (unsigned j = 0; j < nkeys; ++ j)
raw_[code_[j]] = key_[j];
return 0;
} // ibis::dictionary::readKeys
void convolve_3d(SrcIterT src_begin, ExtentT* src_extents,
KernIterT kernel_begin, ExtentT* kernel_extents,
OutIterT out_begin)
{
std::vector<ExtentT> image_shape(src_extents,src_extents+3);
std::vector<ExtentT> kernel_shape(kernel_extents,kernel_extents+3);
anyfold::image_stack_cref image(src_begin, image_shape);
anyfold::image_stack_cref kernel(kernel_begin, kernel_shape);
anyfold::image_stack_ref output(out_begin, image_shape);
std::vector<ExtentT> offsets(3);
for (unsigned i = 0; i < offsets.size(); ++i)
offsets[i] = kernel_shape[i]/2;
return convolve(image,kernel,output,offsets);
}
//==============================================================================
int load_BC_data(FEI* fei, PoissonData& poissonData)
{
//first, have the data object generate the BC data
poissonData.calculateBCs();
int numBCNodes = poissonData.getNumBCNodes();
GlobalID* nodeIDs = poissonData.getBCNodeIDs();
int fieldID = poissonData.getBCFieldID();
double* values = poissonData.getBCValues();
std::vector<int> offsets(numBCNodes, 0);
CHK_ERR( fei->loadNodeBCs(numBCNodes, nodeIDs, fieldID,
&offsets[0], values) );
return(0);
}
