void VolumeCrop::crop() {
if (!inport_.hasData())
return;
const VolumeHandleBase* inputHandle = inport_.getData();
VolumeHandle* outputVolume = 0;
tgt::ivec3 start, dimensions;
start.x = clipRight_.get();
start.y = clipFront_.get();
start.z = clipBottom_.get();
dimensions.x = clipLeft_.get() - clipRight_.get() + 1;
dimensions.y = clipBack_.get() - clipFront_.get() + 1;
dimensions.z = clipTop_.get() - clipBottom_.get() + 1;
outputVolume = VolumeOperatorSubset::APPLY_OP(inport_.getData(), start, dimensions, progressBar_);
outputVolume->setSpacing(inputHandle->getSpacing());
// assign computed volume to outport
if (outputVolume) {
if(preserveLocation_.get()) {
outputVolume->setPhysicalToWorldMatrix(inputHandle->getPhysicalToWorldMatrix());
}
else {
oldVolumePosition(outputVolume);
outputVolume->setPhysicalToWorldMatrix(tgt::mat4::identity);
}
outport_.setData(outputVolume);
}
else
outport_.setData(0);
}
voreen::VolumeCollection* VolumeCollection::selectOriginTimestep(const VolumeOrigin& origin, float timestep) const {
VolumeCollection* collection = new VolumeCollection();
for (size_t i=0; i<volumeHandles_.size(); ++i) {
VolumeHandle* vh = dynamic_cast<VolumeHandle*>(volumeHandles_[i]);
if (vh && vh->getOrigin() == origin && vh->getTimestep() == timestep)
collection->add(volumeHandles_[i]);
}
return collection;
}
void VolumeHandlePropertyWidget::volumeAdded(const VolumeCollection* /*source*/, const VolumeHandle* /*handle*/) {
int i = volumeContainer_->size()-1;
VolumeHandle* handle = volumeContainer_->at(i);
volumeSelectorBox_->addItem(VolumeViewHelper::generateBorderedPreview(handle->getVolume(), 30, 1),
QString::fromStdString(VolumeViewHelper::getStrippedVolumeName(handle)),
QString::fromStdString(VolumeViewHelper::getVolumeName(handle)));
// disable selector box, when no volume available
volumeSelectorBox_->setEnabled(volumeSelectorBox_->count() > 1);
emit modified();
}
void VolumeHandlePropertyWidget::updateFromContainer() {
if (!volumeContainer_)
return;
volumeSelectorBox_->clear();
QPixmap white = QPixmap(30, 30);
white.fill();
volumeSelectorBox_->addItem(white, tr("Select volume ..."));
for (size_t i = 0; i < volumeContainer_->size(); i++) {
VolumeHandle* handle = volumeContainer_->at(i);
volumeSelectorBox_->addItem(VolumeViewHelper::generateBorderedPreview(handle->getVolume(), 30, 1),
QString::fromStdString(VolumeViewHelper::getStrippedVolumeName(handle)),
QString::fromStdString(VolumeViewHelper::getVolumeName(handle)));
}
// disable selector box, when no volume available
volumeSelectorBox_->setEnabled(volumeSelectorBox_->count() > 1);
}
VolumeCollection* FlowReader::read(const std::string& url)
throw(tgt::FileException, std::bad_alloc)
{
VolumeOrigin origin(url);
std::string fileName = origin.getPath();
LINFO("reading flow file '" << fileName << "'...");
// try to open the file
//
std::fstream ifs(fileName.c_str(), std::ios_base::in | std::ios_base::binary);
if (ifs.good() == false)
throw tgt::IOException("Unable to open flow file for reading", fileName);
// read the magic number (string "VOREENFLOW")
//
char magicNumber[11] = {0};
ifs.read(magicNumber, 11);
std::string temp(magicNumber);
if (temp != "VOREENFLOW")
throw tgt::IOException("Missing magic number in flow file", fileName);
// read file version (must currently be 1 or 2)
//
unsigned int fileVersion = 0;
ifs.read(reinterpret_cast<char*>(&fileVersion), sizeof(unsigned int));
LINFO("file version: " << fileVersion);
if ((fileVersion < 1) || (fileVersion > 2))
throw tgt::IOException("Unsupported file version of flow file", fileName);
// read flow dimension (usually 3 for 3D flows)
//
unsigned int flowDimension = 0;
ifs.read(reinterpret_cast<char*>(&flowDimension), sizeof(unsigned int));
LINFO("flow dimension: " << flowDimension << "D");
if (flowDimension != 3)
throw tgt::IOException("Unsupported flow dimension in flow file", fileName);
unsigned char dataOrientation = 0;
unsigned char reverseSlicesMask = 0;
ifs.read(reinterpret_cast<char*>(&dataOrientation), sizeof(unsigned char));
if (fileVersion > 1) {
ifs.read(reinterpret_cast<char*>(&reverseSlicesMask), sizeof(unsigned char));
}
// read the dimension of the volume data containing the flow
//
tgt::ivec3 dimensions;
ifs.read(reinterpret_cast<char*>(&dimensions), sizeof(tgt::ivec3));
LINFO("volume dimensions: " << dimensions);
unsigned int byteSize = 0;
ifs.read(reinterpret_cast<char*>(&byteSize), sizeof(unsigned int));
LINFO("expected size of vector field: " << byteSize << " byte");
VolumeFlow3D* volume = readConvert(dimensions, dataOrientation, ifs);
ifs.close();
if (volume == 0) {
LERROR("an error occured during reading flow data! Proceeding impossible.");
return 0;
}
if (reverseSlicesMask != 0)
reverseSlices(volume, reverseSlicesMask);
// TODO: volume container merge
/*VolumeSet* volumeSet = new VolumeSet(fileName);
VolumeSeries* volumeSeries = new VolumeSeries(Modality::MODALITY_FLOW.getName(),
Modality::MODALITY_FLOW);
volumeSet->addSeries(volumeSeries);
VolumeHandle* volumeHandle = new VolumeHandle(volume, 0.0f);
volumeSeries->addVolumeHandle(volumeHandle); */
VolumeCollection* collection = new VolumeCollection();
VolumeHandle* volumeHandle = new VolumeHandle(volume, tgt::vec3(1.0f), tgt::vec3(0.0f));//FIXME: spacing?
oldVolumePosition(volumeHandle);
volumeHandle->setModality(Modality::MODALITY_FLOW);
collection->add(volumeHandle);
// TODO: origin does not save series and timestamp anymore
//volumeHandle->setOrigin(fileName, Modality::MODALITY_FLOW.getName(), 0.0f);
volumeHandle->setOrigin(fileName);
return collection;
}
VolumeCollection* PVMVolumeReader::read(const std::string &url)
throw (tgt::FileException, tgt::IOException, std::bad_alloc)
{
VolumeOrigin origin(url);
std::string fileName = origin.getPath();
uint8_t* data;
uint8_t* tmpData;
unsigned int width, height, depth, components;
float scalex, scaley, scalez;
unsigned char *description;
unsigned char *courtesy;
unsigned char *parameter;
unsigned char *comment;
LINFO("Reading PVM volume " << fileName);
/*
TODO This subroutine returns an array created with malloc but it should
be created with 'new[]' because this chunk of data will be deleted with 'delete[]'.
This can cause hard to find errors.
As a temporary workaround the data are copied over into a new array
and the c-array is deleted with 'free'.
Because of some c-pointer vodoo done in ddsbase.cpp free must be invoked
after the use of all other returned pointers. (roland)
*/
tmpData = readPVMvolume(const_cast<char*>(fileName.c_str()), getProgressBar(),
&width, &height, &depth, &components,
&scalex, &scaley, &scalez, &description, &courtesy,
¶meter, &comment);
if (!tmpData) {
LERROR("PVM Reading failed");
return 0;
}
data = new uint8_t[width * height * depth * components];
memcpy(data, tmpData, width * height * depth * components);
Volume* dataset = 0;
if (!data) {
throw tgt::IOException();
}
else {
LINFO("Size: " << width << " x " << height << " x " << depth);
LINFO("Spacing: " << scalex << " x " << scaley << " x " << scalez);
LINFO("Components: " << components);
if (description)
LINFO("Description: " << description);
if (courtesy)
LINFO("Courtesy: " << courtesy);
if (parameter)
LINFO("Parameter: " << parameter);
if (comment)
LINFO("Comment: " << comment);
if (components == 1) {
LINFO("Create 8 bit data set.");
dataset = new VolumeUInt8(data, tgt::ivec3(width, height, depth),
tgt::vec3(scalex, scaley, scalez));
}
else if (components == 2) {
// the endianness conversion in ddsbase.cpp seem to be broken,
// so we perform it here instead
uint16_t* data16 = reinterpret_cast<uint16_t*>(data);
int numElements = width * height * depth;
uint16_t maxValue = 0;
for (int i=0; i < numElements; i++) {
endian_swap(data16[i]);
if (data16[i] > maxValue)
maxValue = data16[i];
}
int bits;
if (maxValue < 4096) {
LINFO("Create 12 bit data set.");
bits = 12;
} else {
LINFO("Create 16 bit data set.");
bits = 16;
}
dataset = new VolumeUInt16((uint16_t*)data,
tgt::ivec3(width, height, depth),
tgt::vec3(scalex, scaley, scalez),
tgt::mat4::identity,
bits);
}
else LERROR("Bit depth not supported.");
}
// TODO now it is safe to free
free(tmpData);
VolumeCollection* volumeCollection = new VolumeCollection();
if (dataset) {
VolumeHandle* volumeHandle = new VolumeHandle(dataset, 0.0f);
volumeHandle->setOrigin(VolumeOrigin(fileName));
volumeCollection->add(volumeHandle);
}
return volumeCollection;
}
void CoordinateTransformation::process() {
// do nothing, if neither input data nor coordinate system selection has changed
if (!geometryInport_.hasChanged() && !volumeInport_.hasChanged() && !forceUpdate_)
return;
// clear output
delete geometryOutport_.getData();
geometryOutport_.setData(0);
forceUpdate_ = false;
// return if no input data present
if (!geometryInport_.hasData() || !volumeInport_.hasData())
return;
// retrieve and check geometry from inport
PointListGeometryVec3* geometrySrc = dynamic_cast<PointListGeometryVec3*>(geometryInport_.getData());
PointSegmentListGeometryVec3* geometrySegmentSrc = dynamic_cast<PointSegmentListGeometryVec3*>(geometryInport_.getData());
if (!geometrySrc && !geometrySegmentSrc) {
LWARNING("Geometry of type TGTvec3PointListGeometry or TGTvec3PointSegmentListGeometry expected");
return;
}
// retrieve volume handle from inport
VolumeHandle* volumeHandle = volumeInport_.getData();
tgtAssert(volumeHandle, "No volume handle");
tgtAssert(volumeHandle->getVolume(), "No volume");
// create output geometry object
PointListGeometryVec3* geometryConv = 0;
PointSegmentListGeometryVec3* geometrySegmentConv = 0;
if (geometrySrc)
geometryConv = new PointListGeometryVec3();
else if (geometrySegmentSrc)
geometrySegmentConv = new PointSegmentListGeometryVec3();
//
// convert points
//
// voxel coordinates (no transformation necessary)
if (targetCoordinateSystem_.isSelected("voxel-coordinates")) {
// pointlist
if (geometrySrc) {
std::vector<tgt::vec3> geomPointsConv = std::vector<tgt::vec3>(geometrySrc->getData());
geometryConv->setData(geomPointsConv);
}
// segmentlist
else if (geometrySegmentSrc) {
std::vector< std::vector<tgt::vec3> >geomPointsConv = std::vector< std::vector<tgt::vec3> >(geometrySegmentSrc->getData());
geometrySegmentConv->setData(geomPointsConv);
}
}
// volume coordinates
else if (targetCoordinateSystem_.isSelected("volume-coordinates")) {
tgt::vec3 dims(volumeHandle->getVolume()->getDimensions());
tgt::vec3 cubeSize = volumeHandle->getVolume()->getCubeSize();
// pointlist
if (geometrySrc) {
std::vector<tgt::vec3> geomPointsConv = std::vector<tgt::vec3>(geometrySrc->getData());
for (size_t i=0; i<geomPointsConv.size(); i++)
geomPointsConv[i] = ((geomPointsConv[i]/dims) - 0.5f) * cubeSize;
geometryConv->setData(geomPointsConv);
}
// segmentlist
else if (geometrySegmentSrc) {
std::vector< std::vector<tgt::vec3> >geomPointsConv = std::vector< std::vector<tgt::vec3> >(geometrySegmentSrc->getData());
for (size_t i=0; i<geomPointsConv.size(); ++i) {
for (size_t j=0; j<geomPointsConv[i].size(); ++j) {
geomPointsConv[i][j] = ((geomPointsConv[i][j]/dims) - 0.5f) * cubeSize;
}
geometrySegmentConv->addSegment(geomPointsConv[i]);
}
}
}
// world coordinates
else if (targetCoordinateSystem_.isSelected("world-coordinates")) {
tgt::mat4 voxelToWorldTrafo = volumeHandle->getVolume()->getVoxelToWorldMatrix();
// pointlist
if (geometrySrc) {
std::vector<tgt::vec3> geomPointsConv = std::vector<tgt::vec3>(geometrySrc->getData());
for (size_t i=0; i<geomPointsConv.size(); i++)
geomPointsConv[i] = voxelToWorldTrafo * geomPointsConv[i];
geometryConv->setData(geomPointsConv);
}
// segmentlist
else if (geometrySegmentSrc) {
std::vector< std::vector<tgt::vec3> >geomPointsConv = std::vector< std::vector<tgt::vec3> >(geometrySegmentSrc->getData());
for (size_t i=0; i<geomPointsConv.size(); ++i) {
for (size_t j=0; j<geomPointsConv[i].size(); ++j) {
geomPointsConv[i][j] = voxelToWorldTrafo * geomPointsConv[i][j];
}
geometrySegmentConv->addSegment(geomPointsConv[i]);
}
}
}
// texture coordinates: [0:1.0]^3
else if (targetCoordinateSystem_.isSelected("texture-coordinates")) {
tgt::vec3 dims(volumeHandle->getVolume()->getDimensions());
// pointlist
if (geometrySrc) {
std::vector<tgt::vec3> geomPointsConv = std::vector<tgt::vec3>(geometrySrc->getData());
for (size_t i=0; i<geomPointsConv.size(); i++)
geomPointsConv[i] /= dims;
geometryConv->setData(geomPointsConv);
}
// segmentlist
else if (geometrySegmentSrc) {
std::vector< std::vector<tgt::vec3> >geomPointsConv = std::vector< std::vector<tgt::vec3> >(geometrySegmentSrc->getData());
for (size_t i=0; i<geomPointsConv.size(); ++i) {
for (size_t j=0; j<geomPointsConv[i].size(); ++j) {
geomPointsConv[i][j] /= dims;
}
geometrySegmentConv->addSegment(geomPointsConv[i]);
}
}
}
// assign result to outport
if (geometrySrc)
geometryOutport_.setData(geometryConv);
else if (geometrySegmentSrc)
geometryOutport_.setData(geometrySegmentConv);
else {
LWARNING("No geometry object created");
}
}
void VolumeHandlePropertyWidget::updateFromProperty() {
VolumeHandle* handle = getVolume();
if (handle) {
dimensionLabel_->show();
pathLabel_->show();
spacingLabel_->show();
memSizeLabel_->show();
previewLabel_->show();
std::string name = VolumeViewHelper::getStrippedVolumeName(handle);
std::string path = VolumeViewHelper::getVolumePath(handle);
if(name.size() > 30) {
volumeNameLabel_->setToolTip(QString::fromStdString(name));
int end = name.size();
std::string startString;
std::string endString;
for(size_t i = 0; i < 14; i++){
startString += name.at(i);
endString += name.at(end-14+i);
}
name = startString+"..."+endString;
}
if (path.size() > 30) {
pathLabel_->setToolTip(QString::fromStdString(path));
int end = path.size();
std::string startString;
std::string endString;
for(size_t i = 0; i < 14; i++){
startString += path.at(i);
endString += path.at(end-14+i);
}
path = startString+"..."+endString;
}
volumeNameLabel_->setText(QString::fromStdString(" " + name+ " ("+ VolumeViewHelper::getVolumeType(handle->getVolume())+") "));
pathLabel_->setText(QString::fromStdString(" "+path));
dimensionLabel_->setText(QString::fromStdString(VolumeViewHelper::getVolumeDimension(handle->getVolume())));
spacingLabel_->setText(QString::fromStdString(VolumeViewHelper::getVolumeSpacing(handle->getVolume())));
memSizeLabel_->setText(QString::fromStdString(VolumeViewHelper::getVolumeMemorySize(handle->getVolume())));
previewLabel_->setPixmap(VolumeViewHelper::generateBorderedPreview(handle->getVolume(), 70, 0));
// adjust selected index of volume selector box to currently assigned volume
volumeSelectorBox_->setCurrentIndex(0);
if (volumeContainer_) {
tgtAssert(volumeContainer_->size()+1 == static_cast<size_t>(volumeSelectorBox_->count()),
"Sizes of volume container and volume selector box do not match");
for (size_t i=0; i < volumeContainer_->size(); ++i) {
if (handle == volumeContainer_->at(i)) {
volumeSelectorBox_->setCurrentIndex(i+1);
break;
}
}
}
}
else {
volumeNameLabel_->setText(tr(" no volume"));
volumeNameLabel_->adjustSize();
pathLabel_->hide();
previewLabel_->setPixmap(QPixmap());
dimensionLabel_->hide();
spacingLabel_->hide();
memSizeLabel_->hide();
previewLabel_->hide();
}
}