VertexMeshOperationRecorder.cpp

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*/
 
#include "VertexMeshOperationRecorder.hpp"
 
#include "EdgeRemapInfo.hpp"
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::VertexMeshOperationRecorder()
    : mpEdgeHelper(nullptr)
{
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::~VertexMeshOperationRecorder()
{
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::SetEdgeHelper(EdgeHelper<SPACE_DIM>* pEdgeHelper)
{
    mpEdgeHelper = pEdgeHelper;
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::RecordT1Swap(T1SwapInfo<SPACE_DIM>& rSwapInfo)
{
    mT1Swaps.push_back(rSwapInfo);
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
std::vector<T1SwapInfo<SPACE_DIM> > VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::GetT1SwapsInfo() const
{
    return mT1Swaps;
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::ClearT1SwapsInfo()
{
    mT1Swaps.clear();
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::RecordT2Swap(T2SwapInfo<SPACE_DIM>& rSwapInfo)
{
    mT2Swaps.push_back(rSwapInfo);
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
std::vector<T2SwapInfo<SPACE_DIM> > VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::GetT2SwapsInfo() const
{
    return mT2Swaps;
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::ClearT2SwapsInfo()
{
    mT2Swaps.clear();
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::RecordT3Swap(T3SwapInfo<SPACE_DIM>& rSwapInfo)
{
    mT3Swaps.push_back(rSwapInfo);
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
std::vector<T3SwapInfo<SPACE_DIM> > VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::GetT3SwapsInfo() const
{
    return mT3Swaps;
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::ClearT3SwapsInfo()
{
    mT3Swaps.clear();
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::RecordCellDivisionInfo(CellDivisionInfo<SPACE_DIM>& rDivisionInfo)
{
    mCellDivisions.push_back(rDivisionInfo);
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
std::vector<CellDivisionInfo<SPACE_DIM> > VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::GetCellDivisionInfo() const
{
    return mCellDivisions;
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::ClearCellDivisionInfo()
{
    mCellDivisions.clear();
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
const std::vector<EdgeOperation>& VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::GetEdgeOperations()
{
    return mEdgeOperations;
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::ClearEdgeOperations()
{
    mEdgeOperations.clear();
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::RecordNodeMergeOperation(const std::vector<unsigned> oldIds,
                                                                                   VertexElement<ELEMENT_DIM, SPACE_DIM>* pElement,
                                                                                   const std::pair<unsigned, unsigned> merged_nodes_pair,
                                                                                   const bool elementIndexIsRemapped)
{
    const unsigned element_index = pElement->GetIndex();
    const unsigned element_num_edges = pElement->GetNumEdges();
    std::vector<long> edge_mapping(element_num_edges, -1);
    std::vector<unsigned> edge_status(element_num_edges, 0);
 
    // Marking unaffected edges
    for (unsigned i = 0; i < oldIds.size(); ++i)
    {
        long index = pElement->GetLocalEdgeIndex((*mpEdgeHelper)[oldIds[i]]);
        if (index >= 0)
        {
            edge_mapping[index] = i;
            edge_status[index] = 0;
        }
    }
    // Checking whether the deleted node is upper or lower node
    const unsigned node_A_index = merged_nodes_pair.first;
    const unsigned node_B_index = merged_nodes_pair.second;
 
    // Node B is also considered upper node if the last two nodes are merged
    bool is_B_upper = node_B_index > node_A_index;
    if (node_A_index == 0)
    {
        is_B_upper = node_B_index == 1;
    }
    if (node_B_index == 0)
    {
        // This line is excluded from coverage, as it is very difficult to test this case
        // This case becomes relevant in long time simulations of proliferating tissue
        // and difficult to reproduce
        is_B_upper = node_A_index != 1; // LCOV_EXCL_LINE
    }
 
    unsigned lower_node = node_A_index;
    unsigned upper_node = node_B_index;
    if (!is_B_upper)
    {
        lower_node = node_B_index;
        upper_node = node_A_index;
    }
    // Previous edge denotes the edge below the lower node index
    // and next_edge denotes the edge above the upper node index
    unsigned prev_edge = 0;
    if (is_B_upper)
    {
        if (upper_node == 0)
        {
            // This line is excluded from coverage, as it is very difficult to test this case
            // This case becomes relevant in long time simulations of proliferating tissue
            // and difficult to reproduce
            prev_edge = element_num_edges - 2; // LCOV_EXCL_LINE
        }
        else if (upper_node == 1)
        {
            prev_edge = element_num_edges - 1;
        }
        else
        {
            prev_edge = upper_node - 2;
        }
    }
    else
    {
        if (upper_node == 0 || upper_node == 1)
        {
            prev_edge = element_num_edges - 1;
        }
        else
        {
            prev_edge = upper_node - 2;
        }
    }
    const unsigned next_edge = (prev_edge + 1) % element_num_edges;
 
    // Marking edges below and above the deleted edge
    edge_status[prev_edge] = 3;
    edge_status[next_edge] = 3;
 
    // The edge below node A is in the old element if node B is upper node, and marked with status 0 in the loop above
    // Because node deletion during node merging also removes the pair of edges associated to it,
    // we need to make sure the edges associated with nodes about to be merges correctly map to the old element edges
    if (is_B_upper)
    {
        edge_mapping[next_edge] = node_B_index;
    }
    else
    {
        if (lower_node == 0)
        {
            // This line is excluded from coverage, as it is very difficult to test this case
            // This case becomes relevant in long time simulations of proliferating tissue
            // and difficult to reproduce
            edge_mapping[prev_edge] = element_num_edges; // LCOV_EXCL_LINE
        }
        else
        {
            edge_mapping[prev_edge] = lower_node - 1;
        }
    }
    // Sanity check
    for (unsigned i = 0; i < edge_mapping.size(); ++i)
    {
        assert(edge_mapping[i] >= 0);
    }
 
    const EdgeRemapInfo remap_info(edge_mapping, edge_status);
    mEdgeOperations.emplace_back(EDGE_OPERATION_NODE_MERGE, element_index, remap_info, elementIndexIsRemapped);
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::RecordEdgeSplitOperation(VertexElement<ELEMENT_DIM, SPACE_DIM>* pElement,
                                                                                   const unsigned edgeIndex,
                                                                                   const double insertedNodeRelPosition,
                                                                                   const bool elementIndexIsRemapped)
{
    const unsigned element_index = pElement->GetIndex();
    const unsigned element_num_edges = pElement->GetNumEdges();
    std::vector<double> thetas(element_num_edges);
    std::vector<long> edge_mapping(element_num_edges);
    std::vector<unsigned> edge_status(element_num_edges, 0);
 
    // Daughter edge indices
    const unsigned split_1 = edgeIndex;
    const unsigned split_2 = edgeIndex + 1;
    edge_status[split_1] = 1;
    edge_status[split_2] = 1;
    thetas[split_1] = insertedNodeRelPosition;
    thetas[split_2] = 1.0 - insertedNodeRelPosition;
    unsigned count = 0;
    for (unsigned i = 0; i < element_num_edges; ++i)
    {
        edge_mapping[i] = i - count;
        if (edge_status[i] == 1)
        {
            count = 1;
        }
    }
 
    EdgeRemapInfo remap_info(edge_mapping, edge_status);
    remap_info.SetSplitProportions(thetas);
    mEdgeOperations.emplace_back(EDGE_OPERATION_SPLIT, element_index, remap_info, elementIndexIsRemapped);
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::RecordCellDivideOperation(const std::vector<unsigned>& rOldIds,
                                                                                    VertexElement<ELEMENT_DIM, SPACE_DIM>* pElement1,
                                                                                    VertexElement<ELEMENT_DIM, SPACE_DIM>* pElement2)
{
    const unsigned num_edges_1 = pElement1->GetNumEdges();
    const unsigned num_edges_2 = pElement2->GetNumEdges();
    std::vector<long> edge_mapping_1(num_edges_1, -2);
    std::vector<long> edge_mapping_2(num_edges_2, -2);
    std::vector<unsigned> edge_status_1(num_edges_1);
    std::vector<unsigned> edge_status_2(num_edges_2);
 
    std::vector<unsigned> old_split_edges(rOldIds.size());
    // Keeps track of parent edges that are NOT retained in daughter cells
    for (unsigned i = 0; i < rOldIds.size(); ++i)
    {
        old_split_edges[i] = i;
    }
    unsigned counter_1 = 0;
    unsigned counter_2 = 0;
 
    // First find parent edges that correspond directly to daughter cells' edges
    // At the end of the loop, old_split_edges contains parent edge indices that are split
    for (unsigned i = 0; i < rOldIds.size(); ++i)
    {
        // Index of parent edge corresponding to daughter cell's edge.
        //-1 if not found.
        long index_1 = pElement1->GetLocalEdgeIndex((*mpEdgeHelper)[rOldIds[i]]);
        long index_2 = pElement2->GetLocalEdgeIndex((*mpEdgeHelper)[rOldIds[i]]);
        auto position = std::find(old_split_edges.begin(), old_split_edges.end(), i);
 
        // Modify edge map and status
        if (index_1 >= 0)
        {
            edge_mapping_1[index_1] = i;
            edge_status_1[index_1] = 0;
            old_split_edges.erase(position);
            counter_1++;
        }
        if (index_2 >= 0)
        {
            edge_mapping_2[index_2] = i;
            edge_status_2[index_2] = 0;
            old_split_edges.erase(position);
            counter_2++;
        }
    }
    // Two parent edges are split
    assert(old_split_edges.size() == 2);
 
    // Three edges in daughter cells are unmapped
    assert(counter_1 == num_edges_1 - 3);
    assert(counter_2 == num_edges_2 - 3);
 
    // Edge split proportions.
    std::vector<double> thetas_1(num_edges_1);
    std::vector<double> thetas_2(num_edges_2);
 
    // Go through unmapped edges of daughter cell to find a mapping between parent split edge and
    // daughter edge
    std::vector<unsigned> old_split_edges_1(old_split_edges);
    for (unsigned i = 0; i < num_edges_1; ++i)
    {
        if (edge_mapping_1[i] == -2)
        {
            auto p_node_1 = pElement1->GetEdge(i)->GetNode(0);
            auto p_node_2 = pElement1->GetEdge(i)->GetNode(1);
            bool split_edge_found = false;
            for (unsigned j = 0; j < old_split_edges_1.size(); ++j)
            {
                auto old_edge = (*mpEdgeHelper)[rOldIds[old_split_edges_1[j]]];
                if (old_edge->ContainsNode(p_node_1) || old_edge->ContainsNode(p_node_2))
                {
                    edge_mapping_1[i] = old_split_edges_1[j];
                    edge_status_1[i] = 1;
                    counter_1++;
                    split_edge_found = true;
                    thetas_1[i] = pElement1->GetEdge(i)->rGetLength() / old_edge->rGetLength();
                    old_split_edges_1.erase(old_split_edges_1.begin() + j);
                    break;
                }
            }
            if (!split_edge_found)
            {
                edge_mapping_1[i] = -1;
                edge_status_1[i] = 2;
                counter_1++;
            }
        }
    }
 
    for (unsigned i = 0; i < num_edges_2; ++i)
    {
        if (edge_mapping_2[i] == -2)
        {
            auto p_node_1 = pElement2->GetEdge(i)->GetNode(0);
            auto p_node_2 = pElement2->GetEdge(i)->GetNode(1);
            bool split_edge_found = false;
            for (unsigned j = 0; j < old_split_edges.size(); ++j)
            {
                auto old_edge = (*mpEdgeHelper)[rOldIds[old_split_edges[j]]];
                if (old_edge->ContainsNode(p_node_1) || old_edge->ContainsNode(p_node_2))
                {
                    edge_mapping_2[i] = old_split_edges[j];
                    edge_status_2[i] = 1;
                    counter_2++;
                    split_edge_found = true;
                    thetas_2[i] = pElement2->GetEdge(i)->rGetLength() / old_edge->rGetLength();
                    old_split_edges.erase(old_split_edges.begin() + j);
                    break;
                }
            }
            if (!split_edge_found)
            {
                edge_mapping_2[i] = -1;
                edge_status_2[i] = 2;
                counter_2++;
            }
        }
    }
    assert(old_split_edges_1.empty());
    assert(old_split_edges.empty());
 
    // Checking if all edges of daughter cells have been mapped.
    assert(counter_1 == num_edges_1);
    assert(counter_2 == num_edges_2);
 
    EdgeRemapInfo remap_info_1(edge_mapping_1, edge_status_1);
    EdgeRemapInfo remap_info_2(edge_mapping_2, edge_status_2);
    remap_info_1.SetSplitProportions(thetas_1);
    remap_info_2.SetSplitProportions(thetas_2);
    mEdgeOperations.emplace_back(pElement1->GetIndex(), pElement2->GetIndex(), remap_info_1, remap_info_2);
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::RecordNewEdgeOperation(VertexElement<ELEMENT_DIM, SPACE_DIM>* pElement,
                                                                                 const unsigned edgeIndex)
{
    const unsigned element_index = pElement->GetIndex();
    const unsigned num_edges = pElement->GetNumEdges();
    std::vector<long> edge_mapping(num_edges, 0);
    std::vector<unsigned> edge_status(num_edges);
    for (unsigned i = 0; i < edgeIndex; ++i)
    {
        edge_mapping[i] = i;
        edge_status[i] = 0;
    }
    edge_mapping[edgeIndex] = -1;
    edge_status[edgeIndex] = 2;
    for (unsigned i = edgeIndex + 1; i < num_edges; ++i)
    {
        edge_mapping[i] = i - 1;
        edge_status[i] = 0;
    }
 
    const EdgeRemapInfo remap_info(edge_mapping, edge_status);
    mEdgeOperations.emplace_back(EDGE_OPERATION_ADD, element_index, remap_info);
}
 
template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
void VertexMeshOperationRecorder<ELEMENT_DIM, SPACE_DIM>::RecordEdgeMergeOperation(VertexElement<ELEMENT_DIM, SPACE_DIM>* pElement,
                                                                                   const unsigned nodeIndex)
{
    const unsigned element_index = pElement->GetIndex();
    const unsigned num_edges = pElement->GetNumEdges();
    std::vector<long> edge_mapping(num_edges, 0);
    std::vector<unsigned> edge_status(num_edges, 0);
 
    // Here we find the edge with the lower index.
    // High index edge is merged into low edge index
    unsigned low_edge = (nodeIndex + num_edges) % (num_edges + 1);
    unsigned high_edge = nodeIndex;
 
    // If the first edge was merged into the last edge
    if (low_edge > high_edge)
    {
        edge_status[low_edge - 1] = 4;
        for (unsigned i = 0; i < num_edges; ++i)
        {
            edge_mapping[i] = i + 1;
        }
        edge_mapping[low_edge - 1] = low_edge;
    }
    else
    {
        edge_status[low_edge] = 4;
        for (unsigned i = 0; i < high_edge; ++i)
        {
            edge_mapping[i] = i;
        }
        for (unsigned i = high_edge; i < num_edges; ++i)
        {
            edge_mapping[i] = i + 1;
        }
    }
 
    const EdgeRemapInfo remap_info(edge_mapping, edge_status);
    mEdgeOperations.emplace_back(EDGE_OPERATION_MERGE, element_index, remap_info);
}
 
template class VertexMeshOperationRecorder<1, 1>;
template class VertexMeshOperationRecorder<1, 2>;
template class VertexMeshOperationRecorder<1, 3>;
template class VertexMeshOperationRecorder<2, 2>;
template class VertexMeshOperationRecorder<2, 3>;
template class VertexMeshOperationRecorder<3, 3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(VertexMeshOperationRecorder)