Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
VertexMeshOperationRecorder.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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10This file is part of Chaste.
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12Redistribution and use in source and binary forms, with or without
13modification, are permitted provided that the following conditions are met:
14 * Redistributions of source code must retain the above copyright notice,
15 this list of conditions and the following disclaimer.
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19 * Neither the name of the University of Oxford nor the names of its
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23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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34*/
35
36#include "VertexMeshOperationRecorder.hpp"
37
38#include "EdgeRemapInfo.hpp"
39
40template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
45
46template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
50
51template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
53{
54 mpEdgeHelper = pEdgeHelper;
55}
56
57template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
59{
60 mT1Swaps.push_back(rSwapInfo);
61}
62
63template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
65{
66 return mT1Swaps;
67}
68
69template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
74
75template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
77{
78 mT2Swaps.push_back(rSwapInfo);
79}
80
81template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
83{
84 return mT2Swaps;
85}
86
87template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
92
93template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
95{
96 mT3Swaps.push_back(rSwapInfo);
97}
98
99template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
101{
102 return mT3Swaps;
103}
104
105template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
110
111template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
113{
114 mCellDivisions.push_back(rDivisionInfo);
115}
116
117template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
119{
120 return mCellDivisions;
121}
122
123template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
128
129template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
131{
132 return mEdgeOperations;
133}
134
135template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
140
141template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
144 const std::pair<unsigned, unsigned> merged_nodes_pair,
145 const bool elementIndexIsRemapped)
146{
147 const unsigned element_index = pElement->GetIndex();
148 const unsigned element_num_edges = pElement->GetNumEdges();
149 std::vector<long> edge_mapping(element_num_edges, -1);
150 std::vector<unsigned> edge_status(element_num_edges, 0);
151
152 // Marking unaffected edges
153 for (unsigned i = 0; i < oldIds.size(); ++i)
154 {
155 long index = pElement->GetLocalEdgeIndex((*mpEdgeHelper)[oldIds[i]]);
156 if (index >= 0)
157 {
158 edge_mapping[index] = i;
159 edge_status[index] = 0;
160 }
161 }
162 // Checking whether the deleted node is upper or lower node
163 const unsigned node_A_index = merged_nodes_pair.first;
164 const unsigned node_B_index = merged_nodes_pair.second;
165
166 // Node B is also considered upper node if the last two nodes are merged
167 bool is_B_upper = node_B_index > node_A_index;
168 if (node_A_index == 0)
169 {
170 is_B_upper = node_B_index == 1;
171 }
172 if (node_B_index == 0)
173 {
174 // This line is excluded from coverage, as it is very difficult to test this case
175 // This case becomes relevant in long time simulations of proliferating tissue
176 // and difficult to reproduce
177 is_B_upper = node_A_index != 1; // LCOV_EXCL_LINE
178 }
179
180 unsigned lower_node = node_A_index;
181 unsigned upper_node = node_B_index;
182 if (!is_B_upper)
183 {
184 lower_node = node_B_index;
185 upper_node = node_A_index;
186 }
187 // Previous edge denotes the edge below the lower node index
188 // and next_edge denotes the edge above the upper node index
189 unsigned prev_edge = 0;
190 if (is_B_upper)
191 {
192 if (upper_node == 0)
193 {
194 // This line is excluded from coverage, as it is very difficult to test this case
195 // This case becomes relevant in long time simulations of proliferating tissue
196 // and difficult to reproduce
197 prev_edge = element_num_edges - 2; // LCOV_EXCL_LINE
198 }
199 else if (upper_node == 1)
200 {
201 prev_edge = element_num_edges - 1;
202 }
203 else
204 {
205 prev_edge = upper_node - 2;
206 }
207 }
208 else
209 {
210 if (upper_node == 0 || upper_node == 1)
211 {
212 prev_edge = element_num_edges - 1;
213 }
214 else
215 {
216 prev_edge = upper_node - 2;
217 }
218 }
219 const unsigned next_edge = (prev_edge + 1) % element_num_edges;
220
221 // Marking edges below and above the deleted edge
222 edge_status[prev_edge] = 3;
223 edge_status[next_edge] = 3;
224
225 // 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
226 // Because node deletion during node merging also removes the pair of edges associated to it,
227 // we need to make sure the edges associated with nodes about to be merges correctly map to the old element edges
228 if (is_B_upper)
229 {
230 edge_mapping[next_edge] = node_B_index;
231 }
232 else
233 {
234 if (lower_node == 0)
235 {
236 // This line is excluded from coverage, as it is very difficult to test this case
237 // This case becomes relevant in long time simulations of proliferating tissue
238 // and difficult to reproduce
239 edge_mapping[prev_edge] = element_num_edges; // LCOV_EXCL_LINE
240 }
241 else
242 {
243 edge_mapping[prev_edge] = lower_node - 1;
244 }
245 }
246 // Sanity check
247 for (unsigned i = 0; i < edge_mapping.size(); ++i)
248 {
249 assert(edge_mapping[i] >= 0);
250 }
251
252 const EdgeRemapInfo remap_info(edge_mapping, edge_status);
253 mEdgeOperations.emplace_back(EDGE_OPERATION_NODE_MERGE, element_index, remap_info, elementIndexIsRemapped);
254}
255
256template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
258 const unsigned edgeIndex,
259 const double insertedNodeRelPosition,
260 const bool elementIndexIsRemapped)
261{
262 const unsigned element_index = pElement->GetIndex();
263 const unsigned element_num_edges = pElement->GetNumEdges();
264 std::vector<double> thetas(element_num_edges);
265 std::vector<long> edge_mapping(element_num_edges);
266 std::vector<unsigned> edge_status(element_num_edges, 0);
267
268 // Daughter edge indices
269 const unsigned split_1 = edgeIndex;
270 const unsigned split_2 = edgeIndex + 1;
271 edge_status[split_1] = 1;
272 edge_status[split_2] = 1;
273 thetas[split_1] = insertedNodeRelPosition;
274 thetas[split_2] = 1.0 - insertedNodeRelPosition;
275 unsigned count = 0;
276 for (unsigned i = 0; i < element_num_edges; ++i)
277 {
278 edge_mapping[i] = i - count;
279 if (edge_status[i] == 1)
280 {
281 count = 1;
282 }
283 }
284
285 EdgeRemapInfo remap_info(edge_mapping, edge_status);
286 remap_info.SetSplitProportions(thetas);
287 mEdgeOperations.emplace_back(EDGE_OPERATION_SPLIT, element_index, remap_info, elementIndexIsRemapped);
288}
289
290template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
294{
295 const unsigned num_edges_1 = pElement1->GetNumEdges();
296 const unsigned num_edges_2 = pElement2->GetNumEdges();
297 std::vector<long> edge_mapping_1(num_edges_1, -2);
298 std::vector<long> edge_mapping_2(num_edges_2, -2);
299 std::vector<unsigned> edge_status_1(num_edges_1);
300 std::vector<unsigned> edge_status_2(num_edges_2);
301
302 std::vector<unsigned> old_split_edges(rOldIds.size());
303 // Keeps track of parent edges that are NOT retained in daughter cells
304 for (unsigned i = 0; i < rOldIds.size(); ++i)
305 {
306 old_split_edges[i] = i;
307 }
308
309 // These are maybe unused because in release builds the asserts below will be compiled out
310 [[maybe_unused]] unsigned counter_1 = 0;
311 [[maybe_unused]] unsigned counter_2 = 0;
312
313 // First find parent edges that correspond directly to daughter cells' edges
314 // At the end of the loop, old_split_edges contains parent edge indices that are split
315 for (unsigned i = 0; i < rOldIds.size(); ++i)
316 {
317 // Index of parent edge corresponding to daughter cell's edge.
318 //-1 if not found.
319 long index_1 = pElement1->GetLocalEdgeIndex((*mpEdgeHelper)[rOldIds[i]]);
320 long index_2 = pElement2->GetLocalEdgeIndex((*mpEdgeHelper)[rOldIds[i]]);
321 auto position = std::find(old_split_edges.begin(), old_split_edges.end(), i);
322
323 // Modify edge map and status
324 if (index_1 >= 0)
325 {
326 edge_mapping_1[index_1] = i;
327 edge_status_1[index_1] = 0;
328 old_split_edges.erase(position);
329 counter_1++;
330 }
331 if (index_2 >= 0)
332 {
333 edge_mapping_2[index_2] = i;
334 edge_status_2[index_2] = 0;
335 old_split_edges.erase(position);
336 counter_2++;
337 }
338 }
339 // Two parent edges are split
340 assert(old_split_edges.size() == 2);
341
342 // Three edges in daughter cells are unmapped
343 assert(counter_1 == num_edges_1 - 3);
344 assert(counter_2 == num_edges_2 - 3);
345
346 // Edge split proportions.
347 std::vector<double> thetas_1(num_edges_1);
348 std::vector<double> thetas_2(num_edges_2);
349
350 // Go through unmapped edges of daughter cell to find a mapping between parent split edge and
351 // daughter edge
352 std::vector<unsigned> old_split_edges_1(old_split_edges);
353 for (unsigned i = 0; i < num_edges_1; ++i)
354 {
355 if (edge_mapping_1[i] == -2)
356 {
357 auto p_node_1 = pElement1->GetEdge(i)->GetNode(0);
358 auto p_node_2 = pElement1->GetEdge(i)->GetNode(1);
359 bool split_edge_found = false;
360 for (unsigned j = 0; j < old_split_edges_1.size(); ++j)
361 {
362 auto old_edge = (*mpEdgeHelper)[rOldIds[old_split_edges_1[j]]];
363 if (old_edge->ContainsNode(p_node_1) || old_edge->ContainsNode(p_node_2))
364 {
365 edge_mapping_1[i] = old_split_edges_1[j];
366 edge_status_1[i] = 1;
367 counter_1++;
368 split_edge_found = true;
369 thetas_1[i] = pElement1->GetEdge(i)->rGetLength() / old_edge->rGetLength();
370 old_split_edges_1.erase(old_split_edges_1.begin() + j);
371 break;
372 }
373 }
374 if (!split_edge_found)
375 {
376 edge_mapping_1[i] = -1;
377 edge_status_1[i] = 2;
378 counter_1++;
379 }
380 }
381 }
382
383 for (unsigned i = 0; i < num_edges_2; ++i)
384 {
385 if (edge_mapping_2[i] == -2)
386 {
387 auto p_node_1 = pElement2->GetEdge(i)->GetNode(0);
388 auto p_node_2 = pElement2->GetEdge(i)->GetNode(1);
389 bool split_edge_found = false;
390 for (unsigned j = 0; j < old_split_edges.size(); ++j)
391 {
392 auto old_edge = (*mpEdgeHelper)[rOldIds[old_split_edges[j]]];
393 if (old_edge->ContainsNode(p_node_1) || old_edge->ContainsNode(p_node_2))
394 {
395 edge_mapping_2[i] = old_split_edges[j];
396 edge_status_2[i] = 1;
397 counter_2++;
398 split_edge_found = true;
399 thetas_2[i] = pElement2->GetEdge(i)->rGetLength() / old_edge->rGetLength();
400 old_split_edges.erase(old_split_edges.begin() + j);
401 break;
402 }
403 }
404 if (!split_edge_found)
405 {
406 edge_mapping_2[i] = -1;
407 edge_status_2[i] = 2;
408 counter_2++;
409 }
410 }
411 }
412 assert(old_split_edges_1.empty());
413 assert(old_split_edges.empty());
414
415 // Checking if all edges of daughter cells have been mapped.
416 assert(counter_1 == num_edges_1);
417 assert(counter_2 == num_edges_2);
418
419 EdgeRemapInfo remap_info_1(edge_mapping_1, edge_status_1);
420 EdgeRemapInfo remap_info_2(edge_mapping_2, edge_status_2);
421 remap_info_1.SetSplitProportions(thetas_1);
422 remap_info_2.SetSplitProportions(thetas_2);
423 mEdgeOperations.emplace_back(pElement1->GetIndex(), pElement2->GetIndex(), remap_info_1, remap_info_2);
424}
425
426template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
428 const unsigned edgeIndex)
429{
430 const unsigned element_index = pElement->GetIndex();
431 const unsigned num_edges = pElement->GetNumEdges();
432 std::vector<long> edge_mapping(num_edges, 0);
433 std::vector<unsigned> edge_status(num_edges);
434 for (unsigned i = 0; i < edgeIndex; ++i)
435 {
436 edge_mapping[i] = i;
437 edge_status[i] = 0;
438 }
439 edge_mapping[edgeIndex] = -1;
440 edge_status[edgeIndex] = 2;
441 for (unsigned i = edgeIndex + 1; i < num_edges; ++i)
442 {
443 edge_mapping[i] = i - 1;
444 edge_status[i] = 0;
445 }
446
447 const EdgeRemapInfo remap_info(edge_mapping, edge_status);
448 mEdgeOperations.emplace_back(EDGE_OPERATION_ADD, element_index, remap_info);
449}
450
451template<unsigned ELEMENT_DIM,unsigned SPACE_DIM>
453 const unsigned nodeIndex)
454{
455 const unsigned element_index = pElement->GetIndex();
456 const unsigned num_edges = pElement->GetNumEdges();
457 std::vector<long> edge_mapping(num_edges, 0);
458 std::vector<unsigned> edge_status(num_edges, 0);
459
460 // Here we find the edge with the lower index.
461 // High index edge is merged into low edge index
462 unsigned low_edge = (nodeIndex + num_edges) % (num_edges + 1);
463 unsigned high_edge = nodeIndex;
464
465 // If the first edge was merged into the last edge
466 if (low_edge > high_edge)
467 {
468 edge_status[low_edge - 1] = 4;
469 for (unsigned i = 0; i < num_edges; ++i)
470 {
471 edge_mapping[i] = i + 1;
472 }
473 edge_mapping[low_edge - 1] = low_edge;
474 }
475 else
476 {
477 edge_status[low_edge] = 4;
478 for (unsigned i = 0; i < high_edge; ++i)
479 {
480 edge_mapping[i] = i;
481 }
482 for (unsigned i = high_edge; i < num_edges; ++i)
483 {
484 edge_mapping[i] = i + 1;
485 }
486 }
487
488 const EdgeRemapInfo remap_info(edge_mapping, edge_status);
489 mEdgeOperations.emplace_back(EDGE_OPERATION_MERGE, element_index, remap_info);
490}
491
498
499// Serialization for Boost >= 1.36
#define EXPORT_TEMPLATE_CLASS_ALL_DIMS(CLASS)
unsigned GetIndex() const
void SetSplitProportions(const std::vector< double > proportions)
long GetLocalEdgeIndex(const Edge< SPACE_DIM > *pEdge) const
Edge< SPACE_DIM > * GetEdge(unsigned localIndex) const
unsigned GetNumEdges() const
void RecordNewEdgeOperation(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, const unsigned edgeIndex)
void SetEdgeHelper(EdgeHelper< SPACE_DIM > *pEdgeHelper)
void RecordT1Swap(T1SwapInfo< SPACE_DIM > &rSwapInfo)
std::vector< CellDivisionInfo< SPACE_DIM > > GetCellDivisionInfo() const
const std::vector< EdgeOperation > & GetEdgeOperations()
void RecordEdgeMergeOperation(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, const unsigned nodeIndex)
void RecordCellDivisionInfo(CellDivisionInfo< SPACE_DIM > &rDivisionInfo)
void RecordEdgeSplitOperation(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, const unsigned edgeIndex, const double insertedNodeRelPosition, const bool elementIndexIsRemapped=false)
std::vector< T1SwapInfo< SPACE_DIM > > GetT1SwapsInfo() const
void RecordCellDivideOperation(const std::vector< unsigned > &rOldIds, VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement1, VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement2)
std::vector< T3SwapInfo< SPACE_DIM > > GetT3SwapsInfo() const
void RecordT3Swap(T3SwapInfo< SPACE_DIM > &rSwapInfo)
void RecordNodeMergeOperation(const std::vector< unsigned > oldIds, VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, const std::pair< unsigned, unsigned > mergedNodesPair, const bool elementIndexIsRemapped=false)
std::vector< T2SwapInfo< SPACE_DIM > > GetT2SwapsInfo() const
void RecordT2Swap(T2SwapInfo< SPACE_DIM > &rSwapInfo)