> void LinearFilterWx1<PixelType>::applyTo(const Image::Image<PixelType> & srcImage,Image::Image<PixelType> & dstImage) const {
typedef typename PixelType::DataType PixelDataType;
typedef typename PixelType::ComputationType PixelComputationType;
BaseLinearFilterParametersType<PixelDataType,PixelComputationType> parameters(
getFilterData().getDataView(),
getXoffset(),
getYoffset(),
srcImage.getWidth(),
getTotalColor()
);
Algorithm::AlgorithmWx1<
SimpleWx1dataOperationBaseAlgorithm<
BaseLinearFilterAlgorithm<
PixelDataType,
PixelComputationType,
BaseLinearFilterParametersType<PixelDataType,PixelComputationType>,
Algorithm::BaseOperationTempType<PixelDataType,PixelComputationType>
>,
PixelDataType,
PixelComputationType,
BaseLinearFilterParametersType<PixelDataType,PixelComputationType>,
Algorithm::BaseOperationTempType<PixelDataType,PixelComputationType>
>,
PixelDataType,
BaseLinearFilterParametersType<PixelDataType,PixelComputationType>
>(
srcImage.getDataView(),
dstImage.getDataView(),
parameters
);
}
bool CSPhysXObject_Character::create(CSPhysXWorld* world, IPhysicsObjectData data)
{
if (!CSPhysXObject::create(world)) return false;
#define SKINWIDTH 0.0001f
PxF32 gInitialRadius = data.scale.X;
PxF32 gInitialHeight = data.scale.Y;
if (data.node)
{
gInitialRadius = data.node->getBoundingBox().getExtent().X / 2 * data.scale.X ;
gInitialHeight = data.node->getBoundingBox().getExtent().Y / 2 * data.scale.Y ;
}
PxCapsuleControllerDesc desc;
desc.position.x = data.position.X;
desc.position.y = data.position.Y;
desc.position.z = data.position.Z;
desc.radius = gInitialRadius;
desc.height = gInitialHeight;
desc.upDirection = PxVec3(0,1,0);
desc.slopeLimit = cosf(degToRad(45.0f));
desc.stepOffset = 0.02f;
desc.callback = &gControllerHitReport;
desc.userData = (void*)data.userdata;
desc.scaleCoeff = 0.9f;
desc.volumeGrowth = 1.2f;
desc.density = 10;
desc.material = getWorld()->getPhysXManager()->m_DefaultMaterial;
m_Controller = world->getControllerManager()->createController(*getWorld()->getPhysXManager()->m_PhysicsSDK, getWorld()->getScene(), desc);
m_Controller->setUserData((void*)data.userdata);
m_Controller->getActor()->userData = (void*)data.userdata;
PxShape* shapes[10];
PxU32 nShapes = m_Controller->getActor()->getShapes(shapes, 10);
while (nShapes--)
{
shapes[nShapes]->setSimulationFilterData(getFilterData(data.objecttype));
}
CS_CHECK_NULL(m_Controller, CSLOGTYPE::CSL_WARNING, "CSPhysXObject_Character::create() Controller creaation failed");
// everything went fine
return true;
}
static int updateSurvTable(Settings *s, SurvTable **sts, CifData *cif_data,
size_t spot_num, int tile, int x, int y, int read, int *read_mismatch,
char *read_seq, int *read_qual, char *read_ref, samfile_t *fp, bam1_t *bam, FILE *fp_caldata) {
int cstart = s->cstart[read];
int read_length = s->read_length[read];
int iregion = -1;
int c, b;
assert((cstart + read_length) <= cif_data->ncycles);
if (s->spatial_filter) iregion = xy2region(x, y, s->region_size, s->nregions_x, s->nregions_y);
#ifdef CALDATA
{
int dir = BAM_FREVERSE & bam->core.flag ? 1 : 0;
char *chrom = fp->header->target_name[bam->core.tid];
int pos = bam->core.pos;
fprintf(fp_caldata, "%d\t%d\t%d\t%s\t%d\t", x, y, dir, chrom, pos);
}
#endif
/* update survival table */
for (c = cstart, b = 0; b < read_length; c++, b++) {
CifCycleData *cycle = cif_data->cycles + c;
SurvTable *st;
int channel;
int bin[cycle->num_channels];
float purity = -1.0;
int ibin;
/* set cycle ct */
if (s->spatial_filter) {
int state = (getFilterData(tile, read, b, iregion) & REGION_STATE_MISMATCH) ? 1 : 0;
st = sts[state*N_READS+read] + b;
}else{
st = sts[read] + b;
}
read_cif_chunk(cycle, spot_num);
for (channel = 0; channel < cycle->num_channels; channel++) {
size_t base_pos = spot_num - cycle->chunk_start;
switch (cycle->data_type) {
case 1:
bin[channel] = cycle->chan_data[channel].i8[base_pos];
break;
case 2:
bin[channel] = cycle->chan_data[channel].i16[base_pos];
break;
case 4:
bin[channel] = cycle->chan_data[channel].i32[base_pos];
if (bin[channel] > 65535) {
bin[channel] = 65535;
} else if (bin[channel] < -65535) {
bin[channel] = -65535;
}
break;
default:
abort();
}
}
purity = GetPu(cycle->num_channels, bin);
ibin = st->scale * (purity - st->offset) + 0.5;
if( read_mismatch[b] & BASE_KNOWN_SNP ) {
// don't count these
} else{
if( read_mismatch[b] & BASE_ALIGN )
st->num_bases[ibin]++;
if( read_mismatch[b] & BASE_MISMATCH )
st->num_errors[ibin]++;
}
#ifdef CALDATA
{
char bases[] = "ACGTNDIS";
char base = strchr(bases, read_seq[b]);
int seq_base, ref_base;
if( NULL == base ){
fprintf(stderr, "Unknown base %c\n", read_seq[b]);
exit(EXIT_FAILURE);
}
seq_base = base - bases + 1;
base = strchr(bases, read_ref[b]);
if( NULL == base ){
fprintf(stderr, "Unknown ref %c\n", read_ref[b]);
exit(EXIT_FAILURE);
}
ref_base = base - bases + 1;
fprintf(fp_caldata, "%d %d %d %d %d %d %d %d\t",
ref_base, seq_base, read_qual[b], bin[0], bin[1], bin[2], bin[3], read_mismatch[b]);
}
#endif
#ifdef CHECK_BASECALL
{
int Imax = bin[0];
int i;
for (i=1; i<cycle->num_channels; i++)
if(Imax <= bin[i])
Imax = bin[i];
if (Imax > 0 ){
char bases[] = "ACGTN", flags[] = " ";
for (i=0; i<cycle->num_channels; i++)
{
flags[i] = ' ';
if(bin[i] == Imax)
{
flags[i] = '*';
if(read_seq[b] == bases[i])
break;
}
}
if( i == cycle->num_channels )
fprintf(stderr,"%lu %d %d %d %c %c %d %d%c %d%c %d%c %d%c %f\n", spot_num, x, y, c, read_ref[b], read_seq[b], read_qual[b],
bin[0], flags[0], bin[1], flags[1], bin[2], flags[2], bin[3], flags[3], purity);
}
}
#endif
}
#ifdef CALDATA
fprintf(fp_caldata, "\n");
#endif
return 0;
}
