void checkCrop3D(struct data *d)
{
int fn3, startd3, cropd3;
checkCrop(d); // set 2D parameters
fn3=d->fn3;
/* Check that either fn3 is active */
/* If so, make sure it is divisible by 4 */
if (!fn3) fn3 = d->nv3*2;
else { fn3 /=4; fn3 *=4; }
fn3 /= 2;
startd3 = d->startd3;
cropd3 = d->cropd3;
if((startd3 < 0) || (startd3 > fn3-2)){
d->startd3=0;
fprintf(stderr,"Warning: setting start of crop 3 to 1\n");
}
if(cropd3 < 1) {
d->cropd3=fn3;
fprintf(stderr,"Warning: setting crop 3 to %d \n",d->cropd3);
}
if(d->startd3 + d->cropd3 > fn3){
d->cropd3 = fn3-d->startd3;
fprintf(stderr,"Warning: setting crop 3 to %d \n",d->cropd3);
}
}
BufferMapper* OverlayPlaneBase::getTTMMapper(BufferMapper& grallocMapper, struct VideoPayloadBuffer *payload)
{
buffer_handle_t khandle;
uint32_t w, h;
uint32_t yStride, uvStride;
stride_t stride;
int srcX, srcY, srcW, srcH;
int tmp;
DataBuffer *buf;
ssize_t index;
TTMBufferMapper *mapper;
bool ret;
if (!payload) {
ETRACE("invalid payload buffer");
return 0;
}
srcX = grallocMapper.getCrop().x;
srcY = grallocMapper.getCrop().y;
srcW = grallocMapper.getCrop().w;
srcH = grallocMapper.getCrop().h;
// init ttm buffer
if (mUseScaledBuffer) {
khandle = payload->scaling_khandle;
} else {
khandle = payload->rotated_buffer_handle;
}
index = mTTMBuffers.indexOfKey(khandle);
if (index < 0) {
VTRACE("unmapped TTM buffer, will map it");
if (mUseScaledBuffer) {
w = payload->scaling_width;
h = payload->scaling_height;
} else {
w = payload->rotated_width;
h = payload->rotated_height;
checkCrop(srcX, srcY, srcW, srcH, payload->coded_width, payload->coded_height);
}
uint32_t format = grallocMapper.getFormat();
// this is for sw decode with tiled buffer in landscape mode
if (payload->tiling)
format = OMX_INTEL_COLOR_FormatYUV420PackedSemiPlanar_Tiled;
// calculate stride
switch (format) {
case HAL_PIXEL_FORMAT_YV12:
case HAL_PIXEL_FORMAT_I420:
uint32_t yStride_align;
yStride_align = DisplayQuery::getOverlayLumaStrideAlignment(grallocMapper.getFormat());
if (yStride_align > 0)
{
yStride = align_to(align_to(w, 32), yStride_align);
}
else
{
yStride = align_to(align_to(w, 32), 64);
}
uvStride = align_to(yStride >> 1, 64);
stride.yuv.yStride = yStride;
stride.yuv.uvStride = uvStride;
break;
case HAL_PIXEL_FORMAT_NV12:
yStride = align_to(align_to(w, 32), 64);
uvStride = yStride;
stride.yuv.yStride = yStride;
stride.yuv.uvStride = uvStride;
break;
case OMX_INTEL_COLOR_FormatYUV420PackedSemiPlanar:
case OMX_INTEL_COLOR_FormatYUV420PackedSemiPlanar_Tiled:
if (mUseScaledBuffer) {
stride.yuv.yStride = payload->scaling_luma_stride;
stride.yuv.uvStride = payload->scaling_chroma_u_stride;
} else {
yStride = align_to(align_to(w, 32), 64);
uvStride = yStride;
stride.yuv.yStride = yStride;
stride.yuv.uvStride = uvStride;
}
break;
case HAL_PIXEL_FORMAT_YUY2:
case HAL_PIXEL_FORMAT_UYVY:
yStride = align_to((align_to(w, 32) << 1), 64);
uvStride = 0;
stride.yuv.yStride = yStride;
stride.yuv.uvStride = uvStride;
break;
}
DataBuffer buf(khandle);
// update buffer
buf.setStride(stride);
buf.setWidth(w);
buf.setHeight(h);
buf.setCrop(srcX, srcY, srcW, srcH);
buf.setFormat(format);
// create buffer mapper
bool res = false;
do {
mapper = new TTMBufferMapper(*mWsbm, buf);
if (!mapper) {
ETRACE("failed to allocate mapper");
break;
}
// map ttm buffer
ret = mapper->map();
if (!ret) {
ETRACE("failed to map");
invalidateTTMBuffers();
ret = mapper->map();
if (!ret) {
ETRACE("failed to remap");
break;
}
}
if (mTTMBuffers.size() >= OVERLAY_DATA_BUFFER_COUNT) {
invalidateTTMBuffers();
}
// add mapper
index = mTTMBuffers.add(khandle, mapper);
if (index < 0) {
ETRACE("failed to add TTMMapper");
break;
}
// increase mapper refCount since it is added to mTTMBuffers
mapper->incRef();
res = true;
} while (0);
if (!res) {
// error handling
if (mapper) {
mapper->unmap();
delete mapper;
mapper = NULL;
}
return 0;
}
} else {
void
DistanceMapFilter::applyDistanceMapFilter(QString flnm,
QList<Vec> clipPos,
QList<Vec> clipNormal,
QList<CropObject> crops,
QList<PathObject> paths,
uchar *lut,
int chan)
{
int bpv = 1;
if (m_voxelType > 0) bpv = 2;
int nbytes = bpv*m_nY*m_nZ;
bool trim = (qRound(m_dataSize.x) < m_height ||
qRound(m_dataSize.y) < m_width ||
qRound(m_dataSize.z) < m_depth);
bool clipPresent = (clipPos.count() > 0);
m_cropPresent = false;
m_tearPresent = false;
m_blendPresent = false;
for(int ci=0; ci<m_crops.count(); ci++)
{
if (crops[ci].cropType() < CropObject::Tear_Tear)
m_cropPresent = true;
else if (crops[ci].cropType() < CropObject::View_Tear)
m_tearPresent = true;
else if (m_crops[ci].cropType() > CropObject::Displace_Displace &&
m_crops[ci].cropType() < CropObject::Glow_Ball)
m_blendPresent = true;
}
m_pathCropPresent = false;
m_pathBlendPresent = false;
for (int i=0; i<m_paths.count(); i++)
{
if (m_paths[i].blend()) m_pathBlendPresent = true;
if (m_paths[i].crop()) m_pathCropPresent = true;
}
m_meshLog->moveCursor(QTextCursor::End);
int d0 = 0;
int d1 = m_nX-1;
int d0z = d0 + qRound(m_dataMin.z);
int d1z = d1 + qRound(m_dataMin.z);
uchar *opacityVol = new uchar[m_nX*m_nY*m_nZ];
uchar *cropped = new uchar[nbytes];
uchar *tmp = new uchar[nbytes];
int i0 = 0;
for(int i=d0z; i<=d1z; i++)
{
m_meshProgress->setValue((int)(100.0*(float)i0/(float)m_nX));
qApp->processEvents();
int iv = qBound(0, i, m_depth-1);
uchar *vslice = m_vfm->getSlice(iv);
memset(cropped, 0, nbytes);
if (!trim)
memcpy(tmp, vslice, nbytes);
else
{
int wmin = qRound(m_dataMin.y);
int hmin = qRound(m_dataMin.x);
if (m_voxelType == 0)
{
for(int w=0; w<m_nY; w++)
for(int h=0; h<m_nZ; h++)
tmp[w*m_nZ + h] = vslice[(wmin+w)*m_height + (hmin+h)];
}
else
{
for(int w=0; w<m_nY; w++)
for(int h=0; h<m_nZ; h++)
((ushort*)tmp)[w*m_nZ + h] = ((ushort*)vslice)[(wmin+w)*m_height + (hmin+h)];
}
}
int jk = 0;
for(int j=0; j<m_nY; j++)
for(int k=0; k<m_nZ; k++)
{
Vec po = Vec(m_dataMin.x+k, m_dataMin.y+j, iv);
bool ok = true;
// we don't want to scale before pruning
int mop = 0;
{
Vec pp = po - m_dataMin;
int ppi = pp.x/m_pruneLod;
int ppj = pp.y/m_pruneLod;
int ppk = pp.z/m_pruneLod;
ppi = qBound(0, ppi, m_pruneX-1);
ppj = qBound(0, ppj, m_pruneY-1);
ppk = qBound(0, ppk, m_pruneZ-1);
int mopidx = ppk*m_pruneY*m_pruneX + ppj*m_pruneX + ppi;
mop = m_pruneData[3*mopidx + chan];
ok = (mop > 0);
}
po *= m_samplingLevel;
if (ok && clipPresent)
ok = StaticFunctions::getClip(po, clipPos, clipNormal);
if (ok && m_cropPresent)
ok = checkCrop(po);
if (ok && m_pathCropPresent)
ok = checkPathCrop(po);
if (ok && m_blendPresent)
{
ushort v;
if (m_voxelType == 0)
v = tmp[j*m_nZ + k];
else
v = ((ushort*)tmp)[j*m_nZ + k];
ok = checkBlend(po, v, lut);
}
if (ok && m_pathBlendPresent)
{
ushort v;
if (m_voxelType == 0)
v = tmp[j*m_nZ + k];
else
v = ((ushort*)tmp)[j*m_nZ + k];
ok = checkPathBlend(po, v, lut);
}
if (ok)
cropped[jk] = mop;
else
cropped[jk] = 0;
jk ++;
}
if (m_voxelType == 0)
{
for(int j=0; j<m_nY*m_nZ; j++)
{
if (cropped[j] == 0)
tmp[j] = 0;
}
}
else
{
for(int j=0; j<m_nY*m_nZ; j++)
{
if (cropped[j] == 0)
((ushort*)tmp)[j] = 0;
}
}
applyOpacity(iv, cropped, lut, tmp);
memcpy(opacityVol + i0*m_nY*m_nZ, tmp, m_nY*m_nZ);
i0++;
}
delete [] tmp;
delete [] cropped;
m_meshProgress->setValue(100);
qApp->processEvents();
//------------
if (m_tearPresent)
{
uchar *data0 = new uchar[m_nX*m_nY*m_nZ];
memcpy(data0, opacityVol, m_nX*m_nY*m_nZ);
applyTear(d0, d1, 0,
data0, opacityVol, false);
delete [] data0;
}
typedef uchar PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
ImageType::IndexType start;
start.Fill(0);
ImageType::SizeType size;
size[0] = m_nZ;
size[1] = m_nY;
size[2] = m_nX;
ImageType::RegionType region(start, size);
ImageType::Pointer image = ImageType::New();
image->SetRegions(region);
image->Allocate();
image->FillBuffer(0);
uchar *iptr = (uchar*)image->GetBufferPointer();
memcpy(iptr, opacityVol, m_nX*m_nY*m_nZ);
typedef itk::Image< float, 3 > OutputImageType;
typedef itk::SignedMaurerDistanceMapImageFilter<ImageType, OutputImageType> DistanceMapFilter;
DistanceMapFilter::Pointer filter = DistanceMapFilter::New();
filter->SetInput( image );
filter->SetSquaredDistance(0);
filter->SetUseImageSpacing(0);
filter->SetInsideIsPositive(1);
filter->Update();
QFile fp;
fp.setFileName(flnm);
fp.open(QFile::WriteOnly);
uchar vt = 8;
fp.write((char*)&vt, 1);
fp.write((char*)&m_nX, 4);
fp.write((char*)&m_nY, 4);
fp.write((char*)&m_nZ, 4);
OutputImageType *dimg = filter->GetOutput();
char *tdata = (char*)(dimg->GetBufferPointer());
fp.write(tdata, 4*m_nX*m_nY*m_nZ);
fp.close();
m_meshLog->moveCursor(QTextCursor::End);
m_meshLog->insertPlainText("Signed Distance Map data saved in "+flnm);
QMessageBox::information(0, "", QString("Signed Distance Map saved in "+flnm));
}
void
MeshGenerator::generateMesh(int nSlabs,
QStringList volumeFiles,
QString flnm,
int depth,
QGradientStops vstops,
int fillValue,
bool checkForMore,
bool lookInside,
Vec voxelScaling,
QList<Vec> clipPos,
QList<Vec> clipNormal,
QList<CropObject> crops,
QList<PathObject> paths,
uchar *lut,
int chan,
bool avgColor)
{
bool saveIntermediate = false;
int bpv = 1;
if (m_voxelType > 0) bpv = 2;
int nbytes = bpv*m_nY*m_nZ;
// if (nSlabs > 1)
// {
// QStringList sl;
// sl << "No";
// sl << "Yes";
// bool ok;
// QString okstr = QInputDialog::getItem(0, "Save slab files",
// "Save slab files in .ply format.\nFiles will not be collated together to create a unified mesh for the whole sample.",
// sl, 0, false, &ok);
// if (ok && okstr == "Yes")
// saveIntermediate = true;
// }
QGradientStops lutstops;
for(int i=0; i<255; i++)
{
QColor col(lut[4*i+0], lut[4*i+1], lut[4*i+2], lut[4*i+3]);
lutstops << QGradientStop((float)i/(float)255.0f, col);
}
bool trim = (qRound(m_dataSize.x) < m_height ||
qRound(m_dataSize.y) < m_width ||
qRound(m_dataSize.z) < m_depth);
bool clipPresent = (clipPos.count() > 0);
m_cropPresent = false;
m_tearPresent = false;
m_blendPresent = false;
for(int ci=0; ci<m_crops.count(); ci++)
{
if (crops[ci].cropType() < CropObject::Tear_Tear)
m_cropPresent = true;
else if (crops[ci].cropType() < CropObject::View_Tear)
m_tearPresent = true;
else if (m_crops[ci].cropType() > CropObject::Displace_Displace &&
m_crops[ci].cropType() < CropObject::Glow_Ball)
m_blendPresent = true;
}
m_pathCropPresent = false;
m_pathBlendPresent = false;
for (int i=0; i<m_paths.count(); i++)
{
if (m_paths[i].blend()) m_pathBlendPresent = true;
if (m_paths[i].crop()) m_pathCropPresent = true;
}
int nextra = depth;
int blockStep = m_nX/nSlabs;
//-----------------------------
int nvols = volumeFiles.count();
//-----------------------------
for (int volnum=0; volnum < nvols; volnum++)
{
//if (nvols > 1)
{
m_vfm->setBaseFilename(volumeFiles[volnum]);
uchar *vslice = m_vfm->getSlice(0);
}
m_meshLog->moveCursor(QTextCursor::End);
m_meshLog->insertPlainText(QString("\nProcessing file %1 of %2 : %3\n").\
arg(volnum+1).arg(nvols).arg(m_vfm->fileName()));
for (int nb=0; nb<nSlabs; nb++)
{
m_meshLog->moveCursor(QTextCursor::End);
m_meshLog->insertPlainText(QString(" Processing slab %1 of %2\n").arg(nb+1).arg(nSlabs));
int d0 = nb*blockStep;
int d1 = qMin(m_nX-1, (nb+1)*blockStep);
int dlen = d1-d0+1;
int d0z = d0 + qRound(m_dataMin.z);
int d1z = d1 + qRound(m_dataMin.z);
uchar *extData;
if (m_voxelType == 0)
extData = new uchar[(dlen+2*nextra)*m_nY*m_nZ];
else
extData = new uchar[2*(dlen+2*nextra)*m_nY*m_nZ]; // ushort
uchar *cropped = new uchar[nbytes];
uchar *tmp = new uchar[nbytes];
int i0 = 0;
for(int i=d0z-nextra; i<=d1z+nextra; i++)
{
m_meshProgress->setValue((int)(100.0*(float)(i0/(float)(dlen+2*nextra))));
qApp->processEvents();
int iv = qBound(0, i, m_depth-1);
uchar *vslice = m_vfm->getSlice(iv);
memset(cropped, 0, nbytes);
if (!trim)
memcpy(tmp, vslice, nbytes);
else
{
int wmin = qRound(m_dataMin.y);
int hmin = qRound(m_dataMin.x);
if (m_voxelType == 0)
{
for(int w=0; w<m_nY; w++)
for(int h=0; h<m_nZ; h++)
tmp[w*m_nZ + h] = vslice[(wmin+w)*m_height + (hmin+h)];
}
else
{
for(int w=0; w<m_nY; w++)
for(int h=0; h<m_nZ; h++)
((ushort*)tmp)[w*m_nZ + h] = ((ushort*)vslice)[(wmin+w)*m_height + (hmin+h)];
}
}
int jk = 0;
for(int j=0; j<m_nY; j++)
for(int k=0; k<m_nZ; k++)
{
Vec po = Vec(m_dataMin.x+k, m_dataMin.y+j, iv);
bool ok = true;
// we don't want to scale before pruning
// no mop pruning
po *= m_samplingLevel;
if (ok && clipPresent)
ok = StaticFunctions::getClip(po, clipPos, clipNormal);
if (ok && m_cropPresent)
ok = checkCrop(po);
if (ok && m_pathCropPresent)
ok = checkPathCrop(po);
if (ok && m_blendPresent)
{
ushort v;
if (m_voxelType == 0)
v = tmp[j*m_nZ + k];
else
v = ((ushort*)tmp)[j*m_nZ + k];
ok = checkBlend(po, v, lut);
}
if (ok && m_pathBlendPresent)
{
ushort v;
if (m_voxelType == 0)
v = tmp[j*m_nZ + k];
else
v = ((ushort*)tmp)[j*m_nZ + k];
ok = checkPathBlend(po, v, lut);
}
if (ok)
//cropped[jk] = mop; // nop mop pruning
cropped[jk] = 255;
else
cropped[jk] = 0;
jk ++;
}
if (m_voxelType == 0)
{
for(int j=0; j<m_nY*m_nZ; j++)
{
if (cropped[j] == 0)
tmp[j] = 0;
}
}
else
{
for(int j=0; j<m_nY*m_nZ; j++)
{
if (cropped[j] == 0)
((ushort*)tmp)[j] = 0;
}
}
// tmp now clipped and contains raw data
memcpy(extData + bpv*i0*m_nY*m_nZ, tmp, nbytes);
i0++;
}
delete [] tmp;
delete [] cropped;
m_meshProgress->setValue(100);
qApp->processEvents();
//------------
if (m_tearPresent)
{
uchar *data0 = new uchar[(dlen+2*nextra)*m_nY*m_nZ];
uchar *data1 = extData;
memcpy(data0, data1, (dlen+2*nextra)*m_nY*m_nZ);
applyTear(d0, d1, nextra,
data0, data1, true);
delete [] data0;
}
//------------
//--------------------------------
// ---- set border voxels to fillValue
if (fillValue >= 0)
{
uchar *v = extData;
i0 = 0;
for(int i=d0z-nextra; i<=d1z+nextra; i++)
{
int iv = qBound(0, i, m_depth-1);
int i0dx = i0*m_nY*m_nZ;
if (iv <= qRound(m_dataMin.z) || iv >= qRound(m_dataMax.z))
{
if (m_voxelType == 0)
memset(v + i0dx, fillValue, m_nY*m_nZ);
else
{
for(int fi=0; fi<m_nY*m_nZ; fi++)
((ushort*)v)[i0*m_nY*m_nZ + fi] = fillValue;
}
}
else
{
if (m_voxelType == 0)
{
for(int j=0; j<m_nY; j++)
v[i0dx + j*m_nZ] = fillValue;
for(int j=0; j<m_nY; j++)
v[i0dx + j*m_nZ + m_nZ-1] = fillValue;
for(int k=0; k<m_nZ; k++)
v[i0dx + k] = fillValue;
for(int k=0; k<m_nZ; k++)
v[i0dx + (m_nY-1)*m_nZ + k] = fillValue;
}
else
{
for(int j=0; j<m_nY; j++)
((ushort*)v)[i0dx + j*m_nZ] = fillValue;
for(int j=0; j<m_nY; j++)
((ushort*)v)[i0dx + j*m_nZ + m_nZ-1] = fillValue;
for(int k=0; k<m_nZ; k++)
((ushort*)v)[i0dx + k] = fillValue;
for(int k=0; k<m_nZ; k++)
((ushort*)v)[i0dx + (m_nY-1)*m_nZ + k] = fillValue;
}
}
i0++;
}
}
//--------------------------------
m_meshLog->moveCursor(QTextCursor::End);
m_meshLog->insertPlainText(" Generating Color ...\n");
for(int ni=0; ni<m_nverts; ni++)
{
m_meshProgress->setValue((int)(100.0*(float)ni/(float)m_nverts));
qApp->processEvents();
float v[3];
v[0] = m_vlist[ni]->x/voxelScaling.x/m_scaleModel;
v[1] = m_vlist[ni]->y/voxelScaling.y/m_scaleModel;
v[2] = m_vlist[ni]->z/voxelScaling.z/m_scaleModel;
if (v[2] > d0 && v[2] <= d1)
{
// QMessageBox::information(0, "", QString("%1 %2 %3\n%4 %5 %6\n%7 %8"). \
// arg(v[0]).arg(v[1]).arg(v[2]). \
// arg(m_vlist[ni]->x).arg(m_vlist[ni]->y).arg(m_vlist[ni]->z). \
// arg(d0).arg(d1));
uchar *volData = extData;
QColor col;
QVector3D pos, normal;
pos = QVector3D(v[0], v[1], v[2]-d0 + nextra);
normal = QVector3D(-m_vlist[ni]->nx,
-m_vlist[ni]->ny,
-m_vlist[ni]->nz);
col = getVRLutColor(volData,
dlen,
depth, nextra,
pos, normal,
lut,
lookInside,
QVector3D(v[0], v[1], v[2]));
if (col.alphaF() > 0)
{
float r = col.red()/255.0f;
float g = col.green()/255.0f;
float b = col.blue()/255.0f;
float a = col.alphaF();
// tinge with lutcolor
QColor col0 = vstops[255*(float)(volnum+1)/(float)nvols].second;
float aa = col0.alphaF();
float tr = col0.red()/255.0f;
float tg = col0.green()/255.0f;
float tb = col0.blue()/255.0f;
r = (1.0-aa)*r + aa*a*tr;
g = (1.0-aa)*g + aa*a*tg;
b = (1.0-aa)*b + aa*a*tb;
vcolor[3*ni+0] = (1-a)*vcolor[3*ni+0] + r;
vcolor[3*ni+1] = (1-a)*vcolor[3*ni+1] + g;
vcolor[3*ni+2] = (1-a)*vcolor[3*ni+2] + b;
}
}
}
m_meshProgress->setValue(100);
delete [] extData;
} // loop over slabs
// if (nvols > 1) // save intermediate files
// {
// QString plyflnm = flnm;
// plyflnm.chop(3);
// plyflnm += QString("%1.ply").arg((int)volnum, (int)nvols/10+2, 10, QChar('0'));
//
// for(int ni=0; ni<m_nverts; ni++)
// {
// m_vlist[ni]->r = 255*vcolor[3*ni+0];
// m_vlist[ni]->g = 255*vcolor[3*ni+1];
// m_vlist[ni]->b = 255*vcolor[3*ni+2];
// }
// savePLY(plyflnm);
// }
}// loop over files
for(int ni=0; ni<m_nverts; ni++)
{
m_vlist[ni]->r = 255*vcolor[3*ni+0];
m_vlist[ni]->g = 255*vcolor[3*ni+1];
m_vlist[ni]->b = 255*vcolor[3*ni+2];
}
savePLY(flnm);
m_meshLog->moveCursor(QTextCursor::End);
m_meshLog->insertPlainText("Mesh saved in "+flnm);
QMessageBox::information(0, "", QString("Mesh saved in "+flnm));
}
