VolumeCollection* RawVoxVolumeReader::read(const std::string &url)
throw (tgt::CorruptedFileException, tgt::IOException, std::bad_alloc)
{
VolumeURL origin(url);
std::string fileName = origin.getPath();
LINFO("Reading file " << fileName);
std::fstream fin(fileName.c_str(), std::ios::in | std::ios::binary);
if (!fin.good())
throw tgt::IOException();
RawVoxHeader header;
fin.read(reinterpret_cast<char*>(&header), sizeof(header));
svec3 dimensions = svec3(header.sizeX_, header.sizeY_, header.sizeZ_);
if(header.magic_ != 1381388120) {
throw tgt::CorruptedFileException("Wrong magic number.");
}
VolumeRAM* dataset;
switch(header.bitsPerVoxel_) {
case 8:
LINFO("Reading 8 bit dataset");
dataset = new VolumeRAM_UInt8(dimensions);
break;
case 16:
LINFO("Reading 16 bit dataset");
dataset = new VolumeRAM_UInt16(dimensions);
break;
case 32:
LINFO("Reading 32 bit (float) dataset");
dataset = new VolumeRAM_Float(dimensions);
break;
default:
LERROR("Unknown bpp!");
throw tgt::UnsupportedFormatException("Unexpected bpp.");
}
fin.read(reinterpret_cast<char*>(dataset->getData()), dataset->getNumBytes());
if ( fin.eof() ) {
delete dataset;
throw tgt::CorruptedFileException();
}
fin.close();
VolumeCollection* volumeCollection = new VolumeCollection();
Volume* volumeHandle = new Volume(dataset, vec3(1.0f), vec3(0.0f));
oldVolumePosition(volumeHandle);
volumeHandle->setOrigin(fileName);
volumeCollection->add(volumeHandle);
return volumeCollection;
}
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[] )
{ mxArray *blk_cell_pr;
double *A, *B, *AI, *BI, *blksize;
mwIndex *irA, *jcA, *irB, *jcB;
int *cumblksize, *blknnz;
int mblk, isspA, isspB, iscmpA;
mwIndex subs[2];
mwSize nsubs=2;
int m, n, n2, nsub, k, index, numblk, NZmax, type;
double r2;
/* CHECK FOR PROPER NUMBER OF ARGUMENTS */
if (nrhs < 2){
mexErrMsgTxt("mexsvec: requires at least 2 input arguments."); }
if (nlhs > 1){
mexErrMsgTxt("mexsvec: requires 1 output argument."); }
/* CHECK THE DIMENSIONS */
mblk = mxGetM(prhs[0]);
if (mblk > 1) {
mexErrMsgTxt("mexsvec: blk can have only 1 row."); }
m = mxGetM(prhs[1]);
n = mxGetN(prhs[1]);
if (m != n) {
mexErrMsgTxt("mexsvec: matrix must be square."); }
subs[0] = 0; subs[1] = 1;
index = mxCalcSingleSubscript(prhs[0],nsubs,subs);
blk_cell_pr = mxGetCell(prhs[0],index);
numblk = mxGetN(blk_cell_pr);
blksize = mxGetPr(blk_cell_pr);
if (numblk == 1) {
n2 = n*(n+1)/2;
} else {
cumblksize = mxCalloc(numblk+1,sizeof(int));
blknnz = mxCalloc(numblk+1,sizeof(int));
cumblksize[0] = 0; blknnz[0] = 0;
n = 0; n2 = 0;
for (k=0; k<numblk; ++k) {
nsub = (int) blksize[k];
n += nsub;
n2 += nsub*(nsub+1)/2;
cumblksize[k+1] = n;
blknnz[k+1] = n2; }
}
/***** assign pointers *****/
A = mxGetPr(prhs[1]);
isspA = mxIsSparse(prhs[1]);
iscmpA = mxIsComplex(prhs[1]);
if (isspA) { irA = mxGetIr(prhs[1]);
jcA = mxGetJc(prhs[1]);
NZmax = mxGetNzmax(prhs[1]);
} else {
NZmax = n2;
}
if (iscmpA) { AI = mxGetPi(prhs[1]); }
if ((numblk > 1) & (!isspA)) {
mexErrMsgTxt("mexsvec: matrix must be sparse for numblk > 1"); }
if (nrhs > 2) {
if (mxGetM(prhs[2])>1) { isspB = (int)*mxGetPr(prhs[2]); }
else if (NZmax < n2/2) { isspB = 1; }
else { isspB = 0; }
} else {
if (NZmax < n2/2) { isspB = 1; }
else { isspB = 0; }
}
if (nrhs > 3) { type = (int)*mxGetPr(prhs[3]); }
else { type = 0; }
/***** create return argument *****/
if (isspB) {
if (iscmpA) {
plhs[0] = mxCreateSparse(n2,1,NZmax,mxCOMPLEX);
} else {
plhs[0] = mxCreateSparse(n2,1,NZmax,mxREAL);
}
B = mxGetPr(plhs[0]);
irB = mxGetIr(plhs[0]);
jcB = mxGetJc(plhs[0]);
jcB[0] = 0;
} else {
if (iscmpA) {
plhs[0] = mxCreateDoubleMatrix(n2,1,mxCOMPLEX);
} else {
plhs[0] = mxCreateDoubleMatrix(n2,1,mxREAL);
}
B = mxGetPr(plhs[0]);
}
if (iscmpA) { BI = mxGetPi(plhs[0]); }
/***** Do the computations in a subroutine *****/
r2 = sqrt(2);
if (type == 0) {
if (iscmpA) {
if (numblk == 1) {
svec1cmp(n,r2,A,irA,jcA,isspA,B,irB,jcB,isspB,AI,BI); }
else {
svec2cmp(n,numblk,cumblksize,blknnz,r2,A,irA,jcA,isspA,B,irB,jcB,isspB,AI,BI);
}
} else {
if (numblk == 1) {
svec1(n,r2,A,irA,jcA,isspA,B,irB,jcB,isspB); }
else {
svec2(n,numblk,cumblksize,blknnz,r2,A,irA,jcA,isspA,B,irB,jcB,isspB);
}
}
} else {
if (iscmpA) {
if (numblk == 1) {
svec3cmp(n,r2,A,irA,jcA,isspA,B,irB,jcB,isspB,AI,BI); }
else {
svec4cmp(n,numblk,cumblksize,blknnz,r2,A,irA,jcA,isspA,B,irB,jcB,isspB,AI,BI);
}
} else {
if (numblk == 1) {
svec3(n,r2,A,irA,jcA,isspA,B,irB,jcB,isspB); }
else {
svec4(n,numblk,cumblksize,blknnz,r2,A,irA,jcA,isspA,B,irB,jcB,isspB);
}
}
}
return;
}
void VolumeGL::generateTexture(const Volume* volume)
throw (VoreenException, std::bad_alloc)
{
if (!tgt::hand(tgt::greaterThan(volume->getDimensions(), svec3(1)))) {
std::stringstream message;
message << "OpenGL volumes must have a size greater than one in all dimensions. Actual size: " << volume->getDimensions();
LERROR(message.str());
throw VoreenException(message.str());
}
if (!GpuCaps.is3DTexturingSupported()) {
std::string message = "3D textures apparently not supported by the OpenGL driver";
LERROR(message);
throw VoreenException(message);
}
if (!GpuCaps.isNpotSupported() && !isPowerOfTwo(getDimensions())) {
std::string message = "Non-power-of-two textures apparently not supported by the OpenGL driver";
LERROR(message);
throw VoreenException(message);
}
//
// Determine GL format
//
GLint format; ///< The format of textures which will are created.
GLint internalFormat; ///< The internal format of the textures which are created.
GLenum dataType; ///< The data type of the textures which are created.
// scalar
if (dynamic_cast<const VolumeAtomic<uint8_t>*>(volume)) {
format = GL_ALPHA;
internalFormat = GL_ALPHA8;
dataType = GL_UNSIGNED_BYTE;
}
else if (dynamic_cast<const VolumeAtomic<int8_t>*>(volume)) {
format = GL_ALPHA;
internalFormat = GL_ALPHA8;
dataType = GL_BYTE;
}
else if (dynamic_cast<const VolumeAtomic<uint16_t>*>(volume)) {
format = GL_ALPHA;
internalFormat = GL_ALPHA16;
dataType = GL_UNSIGNED_SHORT;
}
else if (dynamic_cast<const VolumeAtomic<int16_t>*>(volume)) {
format = GL_ALPHA;
internalFormat = GL_ALPHA16;
dataType = GL_SHORT;
}
else if (dynamic_cast<const VolumeAtomic<uint32_t>*>(volume)) {
format = GL_ALPHA;
internalFormat = GL_ALPHA;
dataType = GL_UNSIGNED_INT;
}
else if (dynamic_cast<const VolumeAtomic<int32_t>*>(volume)) {
format = GL_ALPHA;
internalFormat = GL_ALPHA;
dataType = GL_INT;
}
else if (dynamic_cast<const VolumeAtomic<uint64_t>*>(volume)) {
std::string message = "VolumeUInt64 not supported as OpenGL volume.";
LERROR(message);
throw VoreenException(message);
}
else if (dynamic_cast<const VolumeAtomic<int64_t>*>(volume)) {
std::string message = "VolumeInt64 not supported as OpenGL volume.";
LERROR(message);
throw VoreenException(message);
}
else if (dynamic_cast<const VolumeAtomic<float>*>(volume)) {
format = GL_ALPHA;
internalFormat = GL_ALPHA;
dataType = GL_FLOAT;
}
else if (dynamic_cast<const VolumeAtomic<double>*>(volume)) {
std::string message = "VolumeDouble not supported as OpenGL volume.";
LERROR(message);
throw VoreenException(message);
}
// vec2
else if (dynamic_cast<const VolumeAtomic<tgt::Vector2<uint8_t> >*>(volume)) {
format = GL_LUMINANCE_ALPHA;
internalFormat = GL_LUMINANCE_ALPHA;
dataType = GL_UNSIGNED_BYTE;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector2<int8_t> >*>(volume)) {
format = GL_LUMINANCE_ALPHA;
internalFormat = GL_LUMINANCE_ALPHA;
dataType = GL_BYTE;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector2<uint16_t> >*>(volume)) {
format = GL_LUMINANCE_ALPHA;
internalFormat = GL_LUMINANCE_ALPHA;
dataType = GL_UNSIGNED_SHORT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector2<int16_t> >*>(volume)) {
format = GL_LUMINANCE_ALPHA;
internalFormat = GL_LUMINANCE_ALPHA;
dataType = GL_SHORT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector2<uint32_t> >*>(volume)) {
format = GL_LUMINANCE_ALPHA;
internalFormat = GL_LUMINANCE_ALPHA;
dataType = GL_UNSIGNED_INT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector2<int32_t> >*>(volume)) {
format = GL_LUMINANCE_ALPHA;
internalFormat = GL_LUMINANCE_ALPHA;
dataType = GL_INT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector2<uint64_t> >*>(volume)) {
std::string message = "Volume2xUInt64 not supported as OpenGL volume.";
LERROR(message);
throw VoreenException(message);
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector2<int64_t> >*>(volume)) {
std::string message = "Volume2xInt64 not supported as OpenGL volume.";
LERROR(message);
throw VoreenException(message);
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector2<float> >*>(volume)) {
format = GL_LUMINANCE_ALPHA;
internalFormat = GL_LUMINANCE_ALPHA;
dataType = GL_FLOAT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector2<double> >*>(volume)) {
std::string message = "Volume2xDouble not supported as OpenGL volume.";
LERROR(message);
throw VoreenException(message);
}
// vec3
else if (dynamic_cast<const VolumeAtomic<tgt::Vector3<uint8_t> >*>(volume)) {
format = GL_RGB;
internalFormat = GL_RGB8;
dataType = GL_UNSIGNED_BYTE;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector3<int8_t> >*>(volume)) {
format = GL_RGB;
internalFormat = GL_RGB8;
dataType = GL_BYTE;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector3<uint16_t> >*>(volume)) {
format = GL_RGB;
internalFormat = GL_RGB16;
dataType = GL_UNSIGNED_SHORT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector3<int16_t> >*>(volume)) {
format = GL_RGB;
internalFormat = GL_RGB16;
dataType = GL_SHORT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector3<uint32_t> >*>(volume)) {
format = GL_RGB;
internalFormat = GL_RGB;
dataType = GL_UNSIGNED_INT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector3<int32_t> >*>(volume)) {
format = GL_RGB;
internalFormat = GL_RGB;
dataType = GL_INT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector3<uint64_t> >*>(volume)) {
std::string message = "Volume3xUInt64 not supported as OpenGL volume.";
LERROR(message);
throw VoreenException(message);
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector3<int64_t> >*>(volume)) {
std::string message = "Volume3xInt64 not supported as OpenGL volume.";
LERROR(message);
throw VoreenException(message);
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector3<float> >*>(volume)) {
format = GL_RGB;
internalFormat = GL_RGB;
dataType = GL_FLOAT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector3<double> >*>(volume)) {
std::string message = "Volume3xDouble not supported as OpenGL volume.";
LERROR(message);
throw VoreenException(message);
}
// vec4
else if (dynamic_cast<const VolumeAtomic<tgt::Vector4<uint8_t> >*>(volume)) {
format = GL_RGBA;
internalFormat = GL_RGBA8;
dataType = GL_UNSIGNED_BYTE;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector4<int8_t> >*>(volume)) {
format = GL_RGBA;
internalFormat = GL_RGBA8;
dataType = GL_BYTE;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector4<uint16_t> >*>(volume)) {
format = GL_RGBA;
internalFormat = GL_RGBA16;
dataType = GL_UNSIGNED_SHORT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector4<int16_t> >*>(volume)) {
format = GL_RGBA;
internalFormat = GL_RGBA16;
dataType = GL_SHORT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector4<uint32_t> >*>(volume)) {
format = GL_RGBA;
internalFormat = GL_RGBA;
dataType = GL_UNSIGNED_INT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector4<int32_t> >*>(volume)) {
format = GL_RGBA;
internalFormat = GL_RGBA;
dataType = GL_INT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector4<uint64_t> >*>(volume)) {
std::string message = "Volume4xUInt64 not supported as OpenGL volume.";
LERROR(message);
throw VoreenException(message);
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector4<int64_t> >*>(volume)) {
std::string message = "Volume4xInt64 not supported as OpenGL volume.";
LERROR(message);
throw VoreenException(message);
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector4<float> >*>(volume)) {
format = GL_RGBA;
internalFormat = GL_RGBA;
dataType = GL_FLOAT;
}
else if (dynamic_cast<const VolumeAtomic<tgt::Vector4<double> >*>(volume)) {
std::string message = "Volume4xDouble not supported as OpenGL volume.";
LERROR(message);
throw VoreenException(message);
}
// special types (TODO: extract from here)
#ifdef VRN_MODULE_FLOWREEN
else if (dynamic_cast<const VolumeFlow3D*>(volume)) {
format = GL_RGB;
internalFormat = GL_RGB16;
dataType = GL_FLOAT;
}
#endif
else {
LERROR("unknown or unsupported volume type");
}
//
// Create texture
//
glPixelStorei(GL_UNPACK_ALIGNMENT, 1);
VolumeTexture* vTex = 0;
tgt::vec3* temp2 = 0;
#ifdef VRN_MODULE_FLOWREEN
// Textures containing flow data need to contain data
// within range [0.0, 1.0], so the values have to be mapped
const VolumeFlow3D* flowTex = dynamic_cast<const VolumeFlow3D*>(volume);
if (flowTex) {
const float minValue = flowTex->getMinValue();
const float maxValue = flowTex->getMaxValue();
const float range = (maxValue - minValue);
const tgt::vec3* const voxels = flowTex->voxel();
temp2 = new tgt::vec3[volume->getNumVoxels()];
for (size_t i = 0; i < volume->getNumVoxels(); ++i) {
if (voxels[i] != tgt::vec3::zero) {
temp2[i].x = (voxels[i].x - minValue) / range;
temp2[i].y = (voxels[i].y - minValue) / range;
temp2[i].z = (voxels[i].z - minValue) / range;
}
}
}
#endif
// use temp data if this was created
if (temp2) {
vTex = new VolumeTexture(reinterpret_cast<GLubyte*>(temp2), volume->getDimensionsWithBorder(),
format, internalFormat, dataType, tgt::Texture::LINEAR);
}
else {
vTex = new VolumeTexture(static_cast<const GLubyte*>(volume->getData()),
volume->getDimensionsWithBorder(),
format, internalFormat, dataType, tgt::Texture::LINEAR);
}
LGL_ERROR;
vTex->bind();
if (volume->getData())
vTex->uploadTexture();
// set texture wrap to clamp
vTex->setWrapping(tgt::Texture::CLAMP);
LGL_ERROR;
// delete temporary data that has eventually be created
delete[] temp2;
// prevent deleting twice
vTex->setPixelData(0);
// append to internal data structure
texture_ = vTex;
LGL_ERROR;
}
