// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ScaleVolume::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
if (m_ApplyToVoxelVolume == true)
{
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
ImageGeom::Pointer image = m->getGeometryAs<ImageGeom>();
float resolution[3] = { 0.0f, 0.0f, 0.0f };
image->getResolution(resolution);
resolution[0] *= m_ScaleFactor.x;
resolution[1] *= m_ScaleFactor.y;
resolution[2] *= m_ScaleFactor.z;
image->setResolution(resolution);
}
if (m_ApplyToSurfaceMesh == true)
{
updateSurfaceMesh();
}
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void CropImageGeometry::dataCheck()
{
if(getErrorCondition() < 0) { return; }
setErrorCondition(0);
// Validate the incoming DataContainer, Geometry, and AttributeMatrix ; bail if any do not exist since we plan on using them later on in the dataCheck
// Error messages are handled by the getPrereq functions
DataContainer::Pointer srcCellDataContainer = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getCellAttributeMatrixPath().getDataContainerName());
ImageGeom::Pointer image = getDataContainerArray()->getPrereqGeometryFromDataContainer<ImageGeom, AbstractFilter>(this, getCellAttributeMatrixPath().getDataContainerName());
AttributeMatrix::Pointer srcCellAttrMat = getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, getCellAttributeMatrixPath(), -301);
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer destCellDataContainer = srcCellDataContainer;
AttributeMatrix::Pointer destCellAttrMat;
if (m_SaveAsNewDataContainer == true)
{
float ox = 0.0f, oy = 0.0f, oz = 0.0f, rx = 0.0f, ry = 0.0f, rz = 0.0f;
size_t dx = 0, dy = 0, dz = 0;
image->getOrigin(ox, oy, oz);
image->getResolution(rx, ry, rz);
image->getDimensions(dx, dy, dz);
destCellDataContainer = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getNewDataContainerName());
if(NULL == destCellDataContainer.get() || getErrorCondition() < 0)
{
return;
}
IGeometry::Pointer imageCopy = image->deepCopy();
destCellDataContainer->setGeometry(imageCopy);
destCellAttrMat = srcCellAttrMat->deepCopy();
destCellDataContainer->addAttributeMatrix(destCellAttrMat->getName(), destCellAttrMat);
}
else
{
destCellAttrMat = srcCellAttrMat;
}
if(NULL == destCellDataContainer.get() || NULL == destCellAttrMat.get() || getErrorCondition() < 0)
{
return;
}
if (getXMax() < getXMin())
{
QString ss = QObject::tr("X Max (%1) less than X Min (%2)").arg(getXMax()).arg(getXMin());
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getYMax() < getYMin())
{
QString ss = QObject::tr("Y Max (%1) less than Y Min (%2)").arg(getYMax()).arg(getYMin());
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getZMax() < getZMin())
{
QString ss = QObject::tr("Z Max (%1) less than Z Min (%2)").arg(getZMax()).arg(getZMin());
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getXMin() < 0)
{
QString ss = QObject::tr("X Min (%1) less than 0").arg(getXMin());
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getYMin() < 0)
{
QString ss = QObject::tr("Y Min (%1) less than 0").arg(getYMin());
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getZMin() < 0)
{
QString ss = QObject::tr("Z Min (%1) less than 0").arg(getZMin());
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getXMax() > (static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getXPoints()) - 1))
{
QString ss = QObject::tr("The X Max (%1) is greater than the Image Geometry X extent (%2)").arg(getXMax()).arg(static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getXPoints()) - 1);
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getYMax() > (static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getYPoints()) - 1))
{
QString ss = QObject::tr("The Y Max (%1) is greater than the Image Geometry Y extent (%2)").arg(getYMax()).arg(static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getYPoints()) - 1);
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getZMax() > (static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getZPoints()) - 1))
{
QString ss = QObject::tr("The Z Max (%1) is greater than the Image Geometry Z extent (%2)").arg(getZMax()).arg(static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getZPoints()) - 1);
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
QVector<size_t> tDims(3, 0);
if (getXMax() - getXMin() < 0) { setXMax(getXMin() + 1); }
if (getYMax() - getYMin() < 0) { setYMax(getYMin() + 1); }
if (getZMax() - getZMin() < 0) { setZMax(getZMin() + 1); }
tDims[0] = (getXMax() - getXMin()) + 1;
tDims[1] = (getYMax() - getYMin()) + 1;
tDims[2] = (getZMax() - getZMin()) + 1;
destCellDataContainer->getGeometryAs<ImageGeom>()->setDimensions(tDims[0], tDims[1], tDims[2]);
// If any of the sanity checks fail above then we should NOT attempt to go any further.
if (getErrorCondition() < 0) { return; }
size_t totalPoints = 1;
for(int i = 0; i < 3; i++) {
if(tDims[i] != 0) { totalPoints *= tDims[i]; }
}
AttributeMatrix::Pointer newCellAttrMat = AttributeMatrix::New(tDims, destCellAttrMat->getName(), destCellAttrMat->getType());
QList<QString> voxelArrayNames = destCellAttrMat->getAttributeArrayNames();
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = destCellAttrMat->getAttributeArray(*iter);
//
IDataArray::Pointer data = p->createNewArray(totalPoints, p->getComponentDimensions(), p->getName(), false);
destCellAttrMat->removeAttributeArray(*iter);
newCellAttrMat->addAttributeArray(*iter, data);
}
destCellDataContainer->removeAttributeMatrix(destCellAttrMat->getName());
destCellDataContainer->addAttributeMatrix(newCellAttrMat->getName(), newCellAttrMat);
if(m_RenumberFeatures == true)
{
QVector<size_t> cDims(1, 1);
m_FeatureIdsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getFeatureIdsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FeatureIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{
m_FeatureIds = m_FeatureIdsPtr.lock()->getPointer(0);
} /* Now assign the raw pointer to data from the DataArray<T> object */
AttributeMatrix::Pointer cellFeatureAttrMat = srcCellDataContainer->getAttributeMatrix(getCellFeatureAttributeMatrixPath().getAttributeMatrixName());
if(NULL == cellFeatureAttrMat.get()) { return; }
QVector<bool> activeObjects(cellFeatureAttrMat->getNumTuples(), true);
cellFeatureAttrMat->removeInactiveObjects(activeObjects, m_FeatureIdsPtr.lock());
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ReadImage::dataCheck()
{
setErrorCondition(0);
//check file name exists
if(getInputFileName().isEmpty())
{
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), "The input file name must be set before executing this filter.", getErrorCondition());
return;
}
//read image metadata
itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(getInputFileName().toLocal8Bit().constData(), itk::ImageIOFactory::ReadMode);
if(NULL == imageIO)
{
setErrorCondition(-2);
QString message = QObject::tr("Unable to read image '%1'").arg(getInputFileName());
notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
return;
}
imageIO->SetFileName(getInputFileName().toLocal8Bit().data());
imageIO->ReadImageInformation();
//get size of image
const size_t numDimensions = imageIO->GetNumberOfDimensions();
int xdim = imageIO->GetDimensions(0);
int ydim = imageIO->GetDimensions(1);
int zdim = 1;
if(3 != numDimensions)
{
if(2 == numDimensions)
{
//allow 2 dimensional images (as 3d image with size 1 in the z direction)
}
else
{
QString message = QObject::tr("3 dimensional image required (slected image dimensions: %1)").arg(numDimensions);
setErrorCondition(-3);
notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
return;
}
}
else
{
zdim = imageIO->GetDimensions(2);
}
//determine if container/attribute matrix already exist. if so check size compatibility
DataArrayPath createdPath;
DataContainer::Pointer m;
AttributeMatrix::Pointer cellAttrMat;
createdPath.update(getDataContainerName(), getCellAttributeMatrixName(), getImageDataArrayName() );
m = getDataContainerArray()->getDataContainer(getDataContainerName());
bool createAttributeMatrix = false;
if(NULL == m.get()) //datacontainer doesn't exist->create
{
m = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getDataContainerName());
ImageGeom::Pointer image = ImageGeom::CreateGeometry(DREAM3D::Geometry::ImageGeometry);
m->setGeometry(image);
m->getGeometryAs<ImageGeom>()->setDimensions(xdim, ydim, zdim);
double zRes = 1;
double zOrigin = 0;
if(3 == numDimensions)
{
zRes = imageIO->GetSpacing(2);
zOrigin = imageIO->GetOrigin(2);
}
m->getGeometryAs<ImageGeom>()->setResolution(imageIO->GetSpacing(0), imageIO->GetSpacing(0), zRes);
m->getGeometryAs<ImageGeom>()->setOrigin(imageIO->GetOrigin(0), imageIO->GetOrigin(1), zOrigin);
createAttributeMatrix = true;
if(getErrorCondition() < 0) { return; }
}
else //datacontainer exists, check if attribute matrix exists
{
bool dcExists = m->doesAttributeMatrixExist(getCellAttributeMatrixName());
ImageGeom::Pointer image = m->getPrereqGeometry<ImageGeom, AbstractFilter>(this);
if(getErrorCondition() < 0) { return; }
size_t iDims[3] = { 0, 0, 0 };
float iRes[3] = { 0.0f, 0.0f, 0.0f };
float iOrigin[4] = { 0.0f, 0.0f, 0.0f };
image->getDimensions(iDims);
image->getResolution(iRes);
image->getOrigin(iOrigin);
if(dcExists && NULL != image.get())//attribute matrix exists, check compatibility
{
//get matrix
cellAttrMat = m->getPrereqAttributeMatrix<AbstractFilter>(this, getCellAttributeMatrixName(), false);
if(getErrorCondition() < 0) { return; }
//check dimension compatibility
QVector<size_t> tDims = cellAttrMat->getTupleDimensions();
if(tDims[0] != xdim || iDims[0] != xdim)
{
QString message = QObject::tr("The x size of '%1' (%2) does not match the x size of '%3' (%4)").arg(getInputFileName()).arg(xdim).arg(getDataContainerName() + "/" + getCellAttributeMatrixName()).arg(tDims[0]);
setErrorCondition(-4);
notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
return;
}
if(tDims[1] != ydim || iDims[1] != ydim)
{
QString message = QObject::tr("The y size of '%1' (%2) does not match the x size of '%3' (%4)").arg(getInputFileName()).arg(ydim).arg(getDataContainerName() + "/" + getCellAttributeMatrixName()).arg(tDims[1]);
setErrorCondition(-5);
notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
return;
}
if(3 == numDimensions)
{
if(tDims[2] != zdim || iDims[2] != zdim)
{
QString message = QObject::tr("The z size of '%1' (%2) does not match the x size of '%3' (%4)").arg(getInputFileName()).arg(zdim).arg(getDataContainerName() + "/" + getCellAttributeMatrixName()).arg(tDims[2]);
setErrorCondition(-6);
notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
return;
}
}
else
{
if(tDims[2] != 1 || iDims[2] != 1)
{
QString message = QObject::tr("The z size of '%1' (%2) does not match the x size of '%3' (1)").arg(getInputFileName()).arg(zdim).arg(getDataContainerName() + "/" + getCellAttributeMatrixName());
setErrorCondition(-7);
notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
return;
}
}
}
else //attribute matrix doesn't exist, create
{
createAttributeMatrix = true;
}
}
//image/attribute matrix dimensions
QVector<size_t> tDims(3, 0);
tDims[0] = xdim;
tDims[1] = ydim;
tDims[2] = zdim;
//create attribute matrix if needed
if(createAttributeMatrix)
{
//create attribute matrix
cellAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Cell);
if(getErrorCondition() < 0) { return; }
}
//check pixel type (scalar, vector, etc) for support
QVector<size_t> componentDims(1, 0);
itk::ImageIOBase::IOPixelType pixelType = imageIO->GetPixelType();
switch(pixelType)
{
case itk::ImageIOBase::SCALAR:
componentDims[0] = 1;
break;
case itk::ImageIOBase::RGB:
componentDims[0] = 3;
break;
case itk::ImageIOBase::RGBA:
componentDims[0] = 4;
break;
default:
setErrorCondition(-80001);
notifyErrorMessage(getHumanLabel(), "The Pixel Type of the image is not supported with DREAM3D.", getErrorCondition());
}
// Check to make sure everything is OK with reading the image
if(getErrorCondition() < 0)
{
std::string pixelTypeName = itk::ImageIOBase::GetPixelTypeAsString(pixelType);
QString message = QObject::tr("The pixel type of '%1' (%2) is unsupported").arg(getInputFileName()).arg(QString::fromStdString(pixelTypeName));
notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
return;
}
//Now get how the actual image data is stored.
IDataArray::Pointer data;
itk::ImageIOBase::IOComponentType componentType = imageIO->GetComponentType();
if(itk::ImageIOBase::CHAR == componentType)
{
data = Int8ArrayType::CreateArray(0, "Temp", false);
}
else if(itk::ImageIOBase::UCHAR == componentType)
{
data = UInt8ArrayType::CreateArray(0, "Temp", false);
}
else if(itk::ImageIOBase::SHORT == componentType)
{
data = Int16ArrayType::CreateArray(0, "Temp", false);
}
else if(itk::ImageIOBase::USHORT == componentType)
{
data = UInt16ArrayType::CreateArray(0, "Temp", false);
}
else if(itk::ImageIOBase::INT == componentType)
{
data = Int32ArrayType::CreateArray(0, "Temp", false);
}
else if(itk::ImageIOBase::UINT == componentType)
{
data = UInt32ArrayType::CreateArray(0, "Temp", false);
}
else if(itk::ImageIOBase::LONG == componentType)
{
data = Int64ArrayType::CreateArray(0, "Temp", false);
}
else if(itk::ImageIOBase::ULONG == componentType)
{
data = UInt64ArrayType::CreateArray(0, "Temp", false);
}
else if(itk::ImageIOBase::FLOAT == componentType)
{
data = FloatArrayType::CreateArray(0, "Temp", false);
}
else if(itk::ImageIOBase::DOUBLE == componentType)
{
data = DoubleArrayType::CreateArray(0, "Temp", false);
}
else
{
std::string componentTypeName = itk::ImageIOBase::GetComponentTypeAsString(componentType);
QString message = QObject::tr("The component type type of '%1' (%2) is unsupported").arg(getInputFileName()).arg(QString::fromStdString(componentTypeName));
setErrorCondition(-9);
notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
return;
}
if(getErrorCondition() < 0) { return; }
m_ImageDataPtr = TemplateHelpers::CreateNonPrereqArrayFromArrayType()(this, createdPath, componentDims, data);
if( NULL != m_ImageDataPtr.lock().get() )
{
m_ImageData = m_ImageDataPtr.lock()->getVoidPointer(0);
}
}