mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllSegmentationsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const
{
if (SemanticRelationsInference::InstanceExists(caseID, lesion))
{
// lesion exists, retrieve all case segmentations from the storage
DataNodeVector allSegmentationsOfLesion = GetAllSegmentationsOfCase(caseID);
// filter all segmentations: check for semantic relation with the given lesion using a lambda function
auto lambda = [&lesion, this](DataNode::Pointer segmentation)
{
try
{
SemanticTypes::Lesion representedLesion = SemanticRelationsInference::GetLesionOfSegmentation(segmentation);
return lesion.UID != representedLesion.UID;
}
catch (const SemanticRelationException&)
{
return true;
}
};
allSegmentationsOfLesion.erase(std::remove_if(allSegmentationsOfLesion.begin(), allSegmentationsOfLesion.end(), lambda), allSegmentationsOfLesion.end());
return allSegmentationsOfLesion;
}
else
{
mitkThrowException(SemanticRelationException) << "Could not find an existing lesion instance for the given caseID " << caseID << " and lesion " << lesion.UID << ".";
}
}
mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllSpecificImages(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const
{
if (SemanticRelationsInference::InstanceExists(caseID, controlPoint))
{
if (SemanticRelationsInference::InstanceExists(caseID, informationType))
{
// control point exists, information type exists, retrieve all images from the storage
DataNodeVector allImagesOfCase = GetAllImagesOfCase(caseID);
// filter all images to remove the ones with a different control point and information type using a lambda function
auto lambda = [&controlPoint, &informationType, this](DataNode::Pointer imageNode)
{
return (informationType != SemanticRelationsInference::GetInformationTypeOfImage(imageNode))
|| (controlPoint.date != SemanticRelationsInference::GetControlPointOfImage(imageNode).date);
};
allImagesOfCase.erase(std::remove_if(allImagesOfCase.begin(), allImagesOfCase.end(), lambda), allImagesOfCase.end());
return allImagesOfCase;
}
else
{
mitkThrowException(SemanticRelationException) << "Could not find an existing information type for the given caseID " << caseID << " and information type " << informationType;
}
}
else
{
mitkThrowException(SemanticRelationException) << "Could not find an existing control point for the given caseID " << caseID << " and control point " << controlPoint.UID;
}
}
mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllImagesOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const
{
if (m_DataStorage.IsExpired())
{
mitkThrowException(SemanticRelationException) << "Not a valid data storage.";
}
DataNodeVector allImagesOfLesion;
// 1. get all segmentations that define the lesion
// 2. retrieve the parent node (source) of the found segmentation node
DataNodeVector allSegmentationsOfLesion = GetAllSegmentationsOfLesion(caseID, lesion);
for (const auto& segmentationNode : allSegmentationsOfLesion)
{
// get parent node of the current segmentation node with the node predicate
DataStorage::SetOfObjects::ConstPointer parentNodes = m_DataStorage.Lock()->GetSources(segmentationNode, NodePredicates::GetImagePredicate(), false);
for (auto it = parentNodes->Begin(); it != parentNodes->End(); ++it)
{
DataNode::Pointer dataNode = it->Value();
allImagesOfLesion.push_back(it->Value());
}
}
std::sort(allImagesOfLesion.begin(), allImagesOfLesion.end());
allImagesOfLesion.erase(std::unique(allImagesOfLesion.begin(), allImagesOfLesion.end()), allImagesOfLesion.end());
return allImagesOfLesion;
}
mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllSpecificSegmentations(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const
{
if (m_DataStorage.IsExpired())
{
mitkThrow() << "Not a valid data storage.";
}
DataNodeVector allSpecificImages = GetAllSpecificImages(caseID, controlPoint, informationType);
DataNodeVector allSpecificSegmentations;
for (const auto& imageNode : allSpecificImages)
{
DataStorage::SetOfObjects::ConstPointer segmentationNodes = m_DataStorage.Lock()->GetDerivations(imageNode, NodePredicates::GetSegmentationPredicate(), false);
for (auto it = segmentationNodes->Begin(); it != segmentationNodes->End(); ++it)
{
allSpecificSegmentations.push_back(it->Value());
}
}
return allSpecificSegmentations;
}
bool mitk::SceneReaderV1::LoadScene( TiXmlDocument& document, const std::string& workingDirectory, DataStorage* storage )
{
assert(storage);
bool error(false);
// TODO prepare to detect errors (such as cycles) from wrongly written or edited xml files
//Get number of elements to initialze progress bar
// 1. if there is a <data type="..." file="..."> element,
// - construct a name for the appropriate serializer
// - try to instantiate this serializer via itk object factory
// - if serializer could be created, use it to read the file into a BaseData object
// - if successful, call the new node's SetData(..)
// create a node for the tag "data" and test if node was created
typedef std::vector<mitk::DataNode::Pointer> DataNodeVector;
DataNodeVector DataNodes;
unsigned int listSize = 0;
for( TiXmlElement* element = document.FirstChildElement("node"); element != NULL; element = element->NextSiblingElement("node") )
{
++listSize;
}
ProgressBar::GetInstance()->AddStepsToDo(listSize * 2);
for (TiXmlElement* element = document.FirstChildElement("node"); element != NULL; element = element->NextSiblingElement("node"))
{
DataNodes.push_back(LoadBaseDataFromDataTag(element->FirstChildElement("data"), workingDirectory, error));
ProgressBar::GetInstance()->Progress();
}
// iterate all nodes
// first level nodes should be <node> elements
DataNodeVector::iterator nit = DataNodes.begin();
for( TiXmlElement* element = document.FirstChildElement("node"); element != NULL || nit != DataNodes.end(); element = element->NextSiblingElement("node"), ++nit )
{
mitk::DataNode::Pointer node = *nit;
// in case dataXmlElement is valid test whether it containts the "properties" child tag
// and process further if and only if yes
TiXmlElement *dataXmlElement = element->FirstChildElement("data");
if( dataXmlElement && dataXmlElement->FirstChildElement("properties") )
{
TiXmlElement *baseDataElement = dataXmlElement->FirstChildElement("properties");
if ( node->GetData() )
{
DecorateBaseDataWithProperties( node->GetData(), baseDataElement, workingDirectory);
}
else
{
MITK_WARN << "BaseData properties stored in scene file, but BaseData could not be read" << std::endl;
}
}
// 2. check child nodes
const char* uida = element->Attribute("UID");
std::string uid("");
if (uida)
{
uid = uida;
m_NodeForID[uid] = node.GetPointer();
m_IDForNode[ node.GetPointer() ] = uid;
}
else
{
MITK_ERROR << "No UID found for current node. Node will have no parents.";
error = true;
}
// 3. if there are <properties> nodes,
// - instantiate the appropriate PropertyListDeSerializer
// - use them to construct PropertyList objects
// - add these properties to the node (if necessary, use renderwindow name)
bool success = DecorateNodeWithProperties(node, element, workingDirectory);
if (!success)
{
MITK_ERROR << "Could not load properties for node.";
error = true;
}
// remember node for later adding to DataStorage
m_OrderedNodePairs.push_back( std::make_pair( node, std::list<std::string>() ) );
// 4. if there are <source> elements, remember parent objects
for( TiXmlElement* source = element->FirstChildElement("source"); source != NULL; source = source->NextSiblingElement("source") )
{
const char* sourceUID = source->Attribute("UID");
if (sourceUID)
{
m_OrderedNodePairs.back().second.push_back( std::string(sourceUID) );
}
}
ProgressBar::GetInstance()->Progress();
} // end for all <node>
// sort our nodes by their "layer" property
// (to be inserted in that order)
m_OrderedNodePairs.sort( &NodeSortByLayerIsLessThan );
// remove all unknown parent UIDs
for (OrderedNodesList::iterator nodesIter = m_OrderedNodePairs.begin();
nodesIter != m_OrderedNodePairs.end();
++nodesIter)
{
for (std::list<std::string>::iterator parentsIter = nodesIter->second.begin();
parentsIter != nodesIter->second.end();)
{
if (m_NodeForID.find( *parentsIter ) == m_NodeForID.end())
{
parentsIter = nodesIter->second.erase( parentsIter );
MITK_WARN << "Found a DataNode with unknown parents. Will add it to DataStorage without any parent objects.";
error = true;
}
else
{
++parentsIter;
}
}
}
// repeat the following loop ...
// ... for all created nodes
unsigned int lastMapSize(0);
while ( lastMapSize != m_OrderedNodePairs.size()) // this is to prevent infinite loops; each iteration must at least add one node to DataStorage
{
lastMapSize = m_OrderedNodePairs.size();
// iterate (layer) ordered nodes backwards
// we insert the highest layers first
for (OrderedNodesList::iterator nodesIter = m_OrderedNodePairs.begin();
nodesIter != m_OrderedNodePairs.end();
++nodesIter)
{
bool addThisNode(true);
// if any parent node is not yet in DataStorage, skip node for now and check later
for (std::list<std::string>::iterator parentsIter = nodesIter->second.begin();
parentsIter != nodesIter->second.end();
++parentsIter)
{
if ( !storage->Exists( m_NodeForID[ *parentsIter ] ) )
{
addThisNode = false;
break;
}
}
if (addThisNode)
{
DataStorage::SetOfObjects::Pointer parents = DataStorage::SetOfObjects::New();
for ( std::list<std::string>::iterator parentsIter = nodesIter->second.begin();
parentsIter != nodesIter->second.end();
++parentsIter )
{
parents->push_back(m_NodeForID[*parentsIter]);
}
// if all parents are found in datastorage (or are unknown), add node to DataStorage
storage->Add(nodesIter->first, parents);
// remove this node from m_OrderedNodePairs
m_OrderedNodePairs.erase( nodesIter );
// break this for loop because iterators are probably invalid
break;
}
}
}
// All nodes that are still in m_OrderedNodePairs at this point are not part of a proper directed graph structure. We'll add such nodes without any parent information.
for (OrderedNodesList::iterator nodesIter = m_OrderedNodePairs.begin();
nodesIter != m_OrderedNodePairs.end();
++nodesIter)
{
storage->Add( nodesIter->first );
MITK_WARN << "Encountered node that is not part of a directed graph structure. Will be added to DataStorage without parents.";
error = true;
}
return !error;
}