int main()
{
struct node node_dat[NODES];
int matrix[NODES][NODES];
int times;
int start = 0;
int end = 5;
int i;
if( adjacency("graph2.dat", matrix) == -1 ) {
fprintf(stderr, "Can't open file: graph2.dat\n");
return -1;
}
for( i = 0; i < NODES; i++ ) {
node_dat[i].dist = INF;
node_dat[i].flag = 0;
}
times = dijkstra(start, end, node_dat, matrix);
printf("%d : Distance = %d\n", end, node_dat[end].dist);
printf(" Comparison %d\n", times);
return 0;
}
void prim()
{
auto V = std::vector<Vertex>(N);
auto E = std::vector<Edge>{ };
auto T = std::vector<Vertex>{ };
// generate city graph based on distance table
createGraph(E, V);
for(int t = V.size()-1; t >= 0; t--){
V[t].key = Vertex::max_key;
V[t].parent_index = Vertex::undef;
}
//int randomIndex = rand() % V.size();
//V[randomIndex].key = 0;
V[0].key = 0;
auto Q = V;
auto A = std::vector<Edge>{ };
while(Q.size()-1 > 0){
int smallest = Vertex::max_key;
int erase = 0;
int pos = 0;
for (int x = 0; x < Q.size(); x++) {
if (Q[x].key < smallest) {
smallest = Q[x].key;
pos = x;
}
}
auto u = Q[pos];
Q.erase(Q.begin()+pos);
if(u.parent_index != Vertex::undef){
A.push_back(Edge(u.index, u.parent_index));
}
adjacency(E,u.index,T);
int smallestEdge = Vertex::max_key;
int indicator = 0;
for(int j = 0; j < T.size(); j++){
if(weight(u.index,T[j].index) < smallestEdge){
smallestEdge = weight(u.index,T[j].index);
indicator = j;
}
}
T[indicator].parent_index = u.index;
T[indicator].key = weight(u.index,T[indicator].index);
A.push_back(Edge(u.index, T[indicator].index));
eraseEdge(E,u.index,T[indicator].index);
}
std::cout << "Minimal graph: E = {";
for (int i = 0; i < A.size(); i++){
std::cout << "(" << A[i].vi1 << "," << A[i].vi2 << ")" << ",";
}
std::cout << "\b" << "}";
std::cout << "\n" << "Minimal costs: " << totalWeight(A) << "\n";
}
void testAdjacency(double * expr, int * nSamples, int * nGenes, int * corType, int * adjType,
double * power, double * maxPOutliers, double * quick, int * fallback, int * cosine,
double * adj,
int * errCode, int * warn, int * nThreads)
{
adjacency(expr, * nSamples, * nGenes, * corType, * adjType, * power,
*maxPOutliers, *quick, *fallback, *cosine, 0,
adj, errCode, warn, nThreads, 1, 0);
}
int
SwapHeavierToLighterNeighbours::balance(Graph &theWeightedGraph)
{
// check to see a domain partitioner has been set
DomainPartitioner *thePartitioner = this->getDomainPartitioner();
if (thePartitioner == 0) {
opserr << "SwapHeavierToLighterNeighbours::balance";
opserr << "- No DomainPartitioner has been set\n";
return -1;
}
int res = 0;
for (int ii=0; ii<numReleases; ii++) {
VertexIter &theVertices = theWeightedGraph.getVertices();
Vertex *vertexPtr;
while ((vertexPtr = theVertices()) != 0) {
int vertexTag = vertexPtr->getTag();
double vertexLoad = vertexPtr->getWeight();
const ID &adjacency = vertexPtr->getAdjacency();
int size = adjacency.Size();
for (int j=0; j<size; j++) {
int otherVertexTag = adjacency(j);
Vertex *otherVertexPtr
= theWeightedGraph.getVertexPtr(otherVertexTag);
double otherVertexLoad = otherVertexPtr->getWeight();
if (vertexLoad > otherVertexLoad && otherVertexLoad != 0)
if (vertexLoad/otherVertexLoad > factorGreater) {
res = thePartitioner->
swapBoundary(vertexTag,otherVertexTag);
if (res < 0) {
opserr << "WARNING SwapHeavierToLighterNeighbours";
opserr << "::balance - DomainPartitioner returned ";
opserr << res << endln;
return res;
}
}
if (vertexLoad != 0 && otherVertexLoad == 0) {
res = thePartitioner->
swapBoundary(vertexTag,otherVertexTag);
if (res < 0) {
opserr << "WARNING SwapHeavierToLighterNeighbours";
opserr << "::balance - DomainPartitioner returned ";
opserr << res << endln;
return res;
}
}
}
}
}
return res;
}
bool Digraph<T, Allocator>::is_linked(T v1, T v2)
{
vector<T> neighbors = adjacency(v1);
for (typename vector<T>::iterator it = neighbors.begin(); it != neighbors.end(); ++it)
{
if (v2 == *it) return true;
}
return false;
}
bool Digraph<T, Allocator>::is_reach(T start, T finish)
{
if (start == finish) return true;
vector<T> neighbors = adjacency(start);
queue<T> achievable;
fill_achievable(neighbors, achievable);
while (!achievable.empty())
{
T v = achievable.front();
achievable.pop();
if (finish == v) return true;
else
{
vector<T> neighbors = adjacency(v);
fill_achievable(neighbors, achievable);
}
}
return false;
}
AbstractDigraph<T, Allocator> *Digraph<T, Allocator>::get_transpose()
{
AbstractDigraph<T, Allocator>* tr_graph = new Digraph<T, Allocator>();
for(AbstractIterator<T> *v = begin(VERTEX); *v != &*end(VERTEX); ++*v)
{
Vertex<T>& verticle = static_cast<Vertex<T>&>(**v);
vector<T> adjVerticles = adjacency(verticle.getValue());
typename vector<T>::iterator it;
for (it = adjVerticles.begin(); it != adjVerticles.end(); ++it) {
tr_graph->add_link(*it, verticle.getValue());
}
}
return tr_graph;
}
// On copy apply for type matrix<int>!
bool labelAdjacencyMap::apply(const matrix<int>& src,image& dest) const {
sparseMatrix<int> adj;
usePalette colorizer;
if (adjacency(src,adj)) {
const parameters& par = getParameters();
palette pal;
if (par.minColors) {
computeMinPalette(adj,pal);
} else {
computeMaxPalette(adj,pal);
}
return colorizer.apply(src,pal,dest);
}
return false;
};
void Goodfellow::Create( uint32_t numCompartments ) {
N = numCompartments;
stateDim = 2*N;
mu.setZero(N);
double muMin = 0.2;
double muMax = 0.3;
mu(0) = 0.6;
if( N >= 2 ) {
mu(1) = muMax;
for(uint32_t i=2;i<N;++i)
mu(i) = muMax - ((muMax-muMin)*i)/(N-1);
}
adjacency.setZero(N,N);
for(uint32_t i=0;i<N;++i)
for(uint32_t j=0;j<N;++j)
adjacency(i,j) = (i==j)?0.0:1.0;
}
bool graph<V,E>::isConnected()
{
if(vertices.size()==0) return true;
matrix<int> adjacency = adjacency_matrix();
bool discovered[vertices.size()]; for(int i=0;i<vertices.size();i++) discovered[i]=false;
stack<int> DFSstack; DFSstack.push(0);
while(DFSstack.size())
{
int now = DFSstack.top();
DFSstack.pop();
if(!discovered[now])
{
discovered[now] = true;
for(int i=0;i<vertices.size();i++) if(adjacency(now,i)==1) DFSstack.push(i);
}
}
for(int i=0;i<vertices.size();i++) if(!discovered[i]) return false;
return true;
}
int
main (int argc, char **argv) {
graph *g = gengraph(7);
g = adjacency(g, 0, 1);
g = adjacency(g, 0, 2);
g = adjacency(g, 1, 5);
g = adjacency(g, 2, 3);
g = adjacency(g, 2, 4);
g = adjacency(g, 3, 6);
printf("bfs\n");
bfs(g, 0, printnode, NULL);
printf("dfs\n");
dfs(g, 0, printnode, NULL);
exit(0);
}
int
Metis::partition(Graph &theGraph, int numPart)
{
// first we check that the options are valid
if (checkOptions() == false)
return -1;
// now we get room for the data structures metis needs
int numVertex = theGraph.getNumVertex();
int numEdge = theGraph.getNumEdge();
int *options = new int [5];
int *partition = new int [numVertex+1];
int *xadj = new int [numVertex+2];
int *adjncy = new int [2*numEdge];
int *vwgts = 0;
int *ewgts = 0;
int numbering = 0;
int weightflag = 0; // no weights on our graphs yet
if (START_VERTEX_NUM == 0)
numbering = 0;
else if (START_VERTEX_NUM == 1)
numbering = 1;
else {
opserr << "WARNING Metis::partition - No partitioning done";
opserr << " vertex numbering must start at 0 or 1\n";
return (-2);
}
int edgecut;
if ((options == 0) || (partition == 0) || (xadj == 0) || (adjncy == 0)) {
opserr << "WARNING Metis::partition - No partitioning done";
opserr << " as ran out of memory\n";
return (-2);
}
// we build these data structures
int indexEdge = 0;
xadj[0] = 0;
Vertex *vertexPtr;
for (int vertex =0; vertex<numVertex; vertex++) {
vertexPtr = theGraph.getVertexPtr(vertex+START_VERTEX_NUM);
// check we don't have an invalid vertex numbering scheme
// if so WARNING message, clean up and return -2
if (vertexPtr == 0) {
opserr << "WARNING Metis::partition - No partitioning done";
opserr << " Metis requires consequtive Vertex Numbering\n";
delete [] options;
delete [] partition;
delete [] xadj;
delete [] adjncy;
return -2;
}
const ID&adjacency = vertexPtr->getAdjacency();
int degree = adjacency.Size();
for (int i=0; i<degree; i++) {
adjncy[indexEdge++] = adjacency(i)-START_VERTEX_NUM;
}
xadj[vertex+1] = indexEdge;
}
if (defaultOptions == true)
options[0] = 0;
else {
options[0] =1;
options[1] = myCoarsenTo;
options[2] = myMtype;
options[3] = myIPtype;
options[4] = myRtype;
}
int j;
// we now the metis routines
if (myPtype == 1)
PMETIS(&numVertex, xadj, adjncy, vwgts, ewgts, &weightflag, &numPart,
options, &numbering, &edgecut, partition);
else
KMETIS(&numVertex, xadj, adjncy, vwgts, ewgts, &weightflag, &numPart,
options, &numbering, &edgecut, partition);
// we set the vertex colors to correspond to the partitioned scheme
for (int vert =0; vert<numVertex; vert++) {
vertexPtr = theGraph.getVertexPtr(vert+START_VERTEX_NUM);
vertexPtr->setColor(partition[vert]+1); // start colors at 1
}
// clean up the space and return
delete [] options;
delete [] partition;
delete [] xadj;
delete [] adjncy;
return 0;
}
/**
* Evaluates the Levenshtein distance between the strings `a` and `b` using the
* Wagner-Fischer algorithm. This is the number of single-character edits
* required to change the first string into the second.
*
* @param a[in]
* the first string
* @param b[in]
* the second string
* @param ignore_case[in,opt]
* ignore differences in character case
* @param print_matrix[in,opt]
* print the matrix holding prefix distances to stdout
* @return
* the Levenshtein distance between `a` and `b`
*/
size_t levenshtein(char const* a, char const* b, bool ignore_case, bool print_matrix)
{
size_t len_a = strlen(a); //!< Length of string `a`
size_t len_b = strlen(b); //!< Length of string `b`
//! Adjacency matrix for holding edit distances between prefix strings.
std::vector<size_t> adjacency((len_a + 1) * (len_b + 1), 0);
//! Convenience function for setting and retreiving data in the matrix.
auto idx = [&](size_t x, size_t y) -> size_t& {
return adjacency[(len_a + 1) * y + x];
};
// Initialize the first row with the edit distance from the substring
// prefixes of `a` to an empty string.
for (size_t ii = 1; ii <= len_a; ++ii) {
idx(ii, 0) = ii;
}
// Initialize the first column with the edit distance from the substring
// prefixes of `b` to an empty string.
for (size_t jj = 1; jj <= len_b; ++jj) {
idx(0, jj) = jj;
}
for (size_t ii = 0; ii < len_a; ++ii) {
for (size_t jj = 0; jj < len_b; ++jj) {
//! Convert both characters to upper case if ignoring case.
int ch_a = ignore_case ? std::toupper(a[ii]) : a[ii];
int ch_b = ignore_case ? std::toupper(b[jj]) : b[jj];
// If the characters match then there is no edit and the cost
// is unchanged from the previous characters in both strings.
if (ch_a == ch_b) {
idx(ii + 1, jj + 1) = idx(ii, jj);
}
// Otherwise the cost is the minimum of the cost of deletion,
// insertion, or substitution.
else {
size_t deletion_cost = idx(ii, jj + 1) + 1;
size_t insertion_cost = idx(ii + 1, jj) + 1;
size_t substitution_cost = idx(ii, jj) + 1;
idx(ii + 1, jj + 1) = std::min({deletion_cost,
insertion_cost,
substitution_cost});
}
}
}
// Print the adjacency matrix to stdout.
if (print_matrix) {
fprintf(stdout, " ");
for (size_t jj = 0; jj < len_b; ++jj) {
fprintf(stdout, " %1.1s ", b + jj);
}
fprintf(stdout, "\n");
for (size_t ii = 0; ii <= len_a; ++ii) {
fprintf(stdout, " %1.1s ", ii ? a + ii - 1 : "");
for (size_t jj = 0; jj <= len_b; ++jj) {
fprintf(stdout, "%2llu ", (unsigned long long)idx(ii, jj));
}
fprintf(stdout, "\n");
}
fprintf(stdout, "\n");
}
// Return the edit distance from `a` to `b`.
return idx(len_a, len_b);
}
int main(void) {
std::string filePath = "CNN-DocTermCountMatrix.txt";
Matrix& X_Ori = loadMatrix(filePath);
int NSample = min(20, X_Ori.getRowDimension());
Matrix& X = X_Ori.getSubMatrix(0, NSample - 1, 0, X_Ori.getColumnDimension() - 1);
// disp(X.getSubMatrix(0, 10, 0, 100));
println(sprintf("%d samples loaded", X.getRowDimension()));
GraphOptions& options = *new GraphOptions();
options.graphType = "nn";
std::string type = options.graphType;
double NN = options.graphParam;
fprintf("Graph type: %s with NN: %d\n", type.c_str(), (int)NN);
// Parameter setting for text data
options.kernelType = "cosine";
options.graphDistanceFunction = "cosine";
// Parameter setting for image data
/*options.kernelType = "rbf";
options.graphDistanceFunction = "euclidean";*/
options.graphNormalize = true;
options.graphWeightType = "heat";
bool show = true && !false;
// Test adjacency function - pass
tic();
std::string DISTANCEFUNCTION = options.graphDistanceFunction;
Matrix& A = adjacency(X, type, NN, DISTANCEFUNCTION);
fprintf("Elapsed time: %.2f seconds.\n", toc());
std::string adjacencyFilePath = "adjacency.txt";
saveMatrix(adjacencyFilePath, A);
if (show)
disp(A.getSubMatrix(0, 4, 0, 4));
// Test laplacian function - pass
tic();
Matrix& L = laplacian(X, type, options);
fprintf("Elapsed time: %.2f seconds.\n", toc());
std::string LaplacianFilePath = "Laplacian.txt";
saveMatrix(LaplacianFilePath, L);
if (show)
disp(L.getSubMatrix(0, 4, 0, 4));
// Test local learning regularization - pass
NN = options.graphParam;
std::string DISTFUNC = options.graphDistanceFunction;
std::string KernelType = options.kernelType;
double KernelParam = options.kernelParam;
double lambda = 0.001;
tic();
Matrix& LLR_text = calcLLR(X, NN, DISTFUNC, KernelType, KernelParam, lambda);
fprintf("Elapsed time: %.2f seconds.\n", toc());
std::string LLRFilePath = "localLearningRegularization.txt";
saveMatrix(LLRFilePath, LLR_text);
if (show)
display(LLR_text.getSubMatrix(0, 4, 0, 4));
return EXIT_SUCCESS;
}
int
DomainPartitioner::partition(int numParts, bool usingMain, int mainPartitionTag, int specialElementTag)
{
usingMainDomain = usingMain;
mainPartition = mainPartitionTag;
// first we ensure the partitioned domain has numpart subdomains
// with tags 1 through numparts
for (int i=1; i<=numParts; i++) {
if (i != mainPartition) {
Subdomain *subdomainPtr = myDomain->getSubdomainPtr(i);
if (subdomainPtr == 0) {
opserr << "DomainPartitioner::partition - No Subdomain: ";
opserr << i << " exists\n";
return -1;
}
}
}
// we get the ele graph from the domain and partition it
// Graph &theEleGraph = myDomain->getElementGraph();
// theElementGraph = new Graph(myDomain->getElementGraph());
theElementGraph = &(myDomain->getElementGraph());
int theError = thePartitioner.partition(*theElementGraph, numParts);
if (theError < 0) {
opserr << "DomainPartitioner::partition";
opserr << " - the graph partioner failed to partition the ";
opserr << "element graph\n";
return -10+theError;
}
/* print graph */
// opserr << "DomainPartitioner::partition - eleGraph: \n";
// theElementGraph->Print(opserr, 4);
VertexIter &theVertices1 = theElementGraph->getVertices();
Vertex *vertexPtr = 0;
bool moreThanOne = false;
vertexPtr = theVertices1();
int vertexOnePartition = 0;
if (vertexPtr != 0)
vertexOnePartition = vertexPtr->getColor();
while ((moreThanOne == false) && ((vertexPtr = theVertices1()) != 0)) {
int partition = vertexPtr->getColor();
if (partition != vertexOnePartition ) {
moreThanOne = true;
}
}
if (moreThanOne == false) {
opserr <<"DomainPartitioner::partition - too few elements for model to be partitioned\n";
return -1;
}
int specialElementColor = 1;
if (specialElementTag != 0) {
bool found = false;
VertexIter &theVerticesSpecial = theElementGraph->getVertices();
while ((found == false) && ((vertexPtr = theVerticesSpecial()) != 0)) {
int eleTag = vertexPtr->getRef();
if (eleTag == specialElementTag) {
found = true;
int vertexColor = vertexPtr->getColor();
if (vertexColor != 1)
// specialElementColor = vertexColor;
vertexPtr->setColor(1);
}
}
}
// we create empty graphs for the numParts subdomains,
// in the graphs we place the vertices for the elements on the boundaries
// we do not invoke the destructor on the individual graphs as
// this would invoke the destructor on the individual vertices
if (theBoundaryElements != 0)
delete [] theBoundaryElements;
theBoundaryElements = new Graph * [numParts];
if (theBoundaryElements == 0) {
opserr << "DomainPartitioner::partition(int numParts)";
opserr << " - ran out of memory\n";
numPartitions = 0;
return -1;
}
for (int l=0; l<numParts; l++) {
theBoundaryElements[l] = new Graph(2048); // graphs can grow larger; just an estimate
if (theBoundaryElements[l] == 0) {
opserr << "DomainPartitioner::partition(int numParts)";
opserr << " - ran out of memory\n";
numPartitions = 0;
return -1;
}
}
numPartitions = numParts;
// opserr << "DomainPartitioner::partition() - nodes \n";
// we now create a MapOfTaggedObjectStorage to store the NodeLocations
// and create a new NodeLocation for each node; adding it to the map object
theNodeLocations = new MapOfTaggedObjects();
if (theNodeLocations == 0) {
opserr << "DomainPartitioner::partition(int numParts)";
opserr << " - ran out of memory creating MapOfTaggedObjectStorage for node locations\n";
numPartitions = 0;
return -1;
}
NodeIter &theNodes = myDomain->getNodes();
Node *nodePtr;
while ((nodePtr = theNodes()) != 0) {
NodeLocations *theNodeLocation = new NodeLocations(nodePtr->getTag());
if (theNodeLocation == 0) {
opserr << "DomainPartitioner::partition(int numParts)";
opserr << " - ran out of memory creating NodeLocation for node: " << nodePtr->getTag() << endln;
numPartitions = 0;
return -1;
}
if (theNodeLocations->addComponent(theNodeLocation) == false) {
opserr << "DomainPartitioner::partition(int numParts)";
opserr << " - failed to add NodeLocation to Map for Node: " << nodePtr->getTag() << endln;
numPartitions = 0;
return -1;
}
}
//
// we now iterate through the vertices of the element graph
// to see if the vertex is a boundary vertex or not - if it is
// we add to the appropriate graph created above. We also set the
// value the color variable of each of the external nodes connected
// to the element to a value which will indicate that that node will
// have to be added to the subdomain.
//
VertexIter &theVertexIter = theElementGraph->getVertices();
while ((vertexPtr = theVertexIter()) != 0) {
int eleTag = vertexPtr->getRef();
int vertexColor = vertexPtr->getColor();
const ID &adjacency = vertexPtr->getAdjacency();
int size = adjacency.Size();
for (int i=0; i<size; i++) {
Vertex *otherVertex = theElementGraph->getVertexPtr(adjacency(i));
if (otherVertex->getColor() != vertexColor) {
theBoundaryElements[vertexColor-1]->addVertex(vertexPtr,false);
i = size;
}
}
Element *elePtr = myDomain->getElement(eleTag);
const ID &nodes = elePtr->getExternalNodes();
size = nodes.Size();
for (int j=0; j<size; j++) {
int nodeTag = nodes(j);
TaggedObject *theTaggedObject = theNodeLocations->getComponentPtr(nodeTag);
if (theTaggedObject == 0) {
opserr << "DomainPartitioner::partition(int numParts)";
opserr << " - failed to find NodeLocation in Map for Node: " << nodePtr->getTag() << " -- A BUG!!\n";
numPartitions = 0;
return -1;
}
NodeLocations *theNodeLocation = (NodeLocations *)theTaggedObject;
theNodeLocation->addPartition(vertexColor);
}
}
// now go through the MP_Constraints and ensure the retained node is in every
// partition the constrained node is in
MP_ConstraintIter &theMPs = myDomain->getMPs();
MP_Constraint *mpPtr;
while ((mpPtr = theMPs()) != 0) {
int retained = mpPtr->getNodeRetained();
int constrained = mpPtr->getNodeConstrained();
TaggedObject *theRetainedObject = theNodeLocations->getComponentPtr(retained);
TaggedObject *theConstrainedObject = theNodeLocations->getComponentPtr(constrained);
if (theRetainedObject == 0 || theConstrainedObject == 0) {
opserr << "DomainPartitioner::partition(int numParts)";
if (theRetainedObject == 0)
opserr << " - failed to find NodeLocation in Map for Node: " << retained << " -- A BUG!!\n";
if (theConstrainedObject == 0)
opserr << " - failed to find NodeLocation in Map for Node: " << constrained << " -- A BUG!!\n";
numPartitions = 0;
return -1;
}
NodeLocations *theRetainedLocation = (NodeLocations *)theRetainedObject;
NodeLocations *theConstrainedLocation = (NodeLocations *)theConstrainedObject;
ID &theConstrainedNodesPartitions = theConstrainedLocation->nodePartitions;
int numPartitions = theConstrainedNodesPartitions.Size();
for (int i=0; i<numPartitions; i++) {
theRetainedLocation->addPartition(theConstrainedNodesPartitions(i));
}
}
// we now add the nodes,
TaggedObjectIter &theNodeLocationIter = theNodeLocations->getComponents();
TaggedObject *theNodeObject;
while ((theNodeObject = theNodeLocationIter()) != 0) {
NodeLocations *theNodeLocation = (NodeLocations *)theNodeObject;
int nodeTag = theNodeLocation->getTag();
ID &nodePartitions = theNodeLocation->nodePartitions;
int numPartitions = theNodeLocation->numPartitions;
for (int i=0; i<numPartitions; i++) {
int partition = nodePartitions(i);
if (partition != mainPartition) {
Subdomain *theSubdomain = myDomain->getSubdomainPtr(partition);
if (numPartitions == 1) {
Node *nodePtr = myDomain->removeNode(nodeTag);
theSubdomain->addNode(nodePtr);
} else {
Node *nodePtr = myDomain->getNode(nodeTag);
theSubdomain->addExternalNode(nodePtr);
}
}
}
}
// we now move the elements
VertexIter &theVertices = theElementGraph->getVertices();
while ((vertexPtr = theVertices()) != 0) {
// move the element
int partition = vertexPtr->getColor();
if (partition != mainPartition) {
int eleTag = vertexPtr->getRef();
// opserr << "removing ele: " << eleTag << endln;
Element *elePtr = myDomain->removeElement(eleTag);
// opserr << *elePtr;
if (elePtr != 0) {
// opserr << "adding ele - start\n";
Subdomain *theSubdomain = myDomain->getSubdomainPtr(partition);
theSubdomain->addElement(elePtr);
// opserr << "adding ele - done\n";
} else {
opserr << "DomainPartitioner::partioner - element GONE! - eleTag " << eleTag << endln;
}
}
}
// now we go through the load patterns and move NodalLoad
// 1) make sure each subdomain has a copy of the partitioneddomains load patterns.
// 2) move nodal loads
// 3) move SP_Constraints
LoadPatternIter &theLoadPatterns = myDomain->getLoadPatterns();
LoadPattern *theLoadPattern;
while ((theLoadPattern = theLoadPatterns()) != 0) {
int loadPatternTag = theLoadPattern->getTag();
// check that each subdomain has a loadPattern with a similar tag and class tag
for (int i=1; i<=numParts; i++) {
if (i != mainPartition) {
Subdomain *theSubdomain = myDomain->getSubdomainPtr(i);
LoadPattern *loadPatternCopy = theSubdomain->getLoadPattern(loadPatternTag);
if (loadPatternCopy == 0) {
LoadPattern *newLoadPattern = theLoadPattern->getCopy();
if (newLoadPattern == 0) {
opserr << "DomaiPartitioner::partition - out of memory creating LoadPatterns\n";
return -1;
}
theSubdomain->addLoadPattern(newLoadPattern);
}
}
}
// now remove any nodal loads that correspond to internal nodes in a subdomain
// and add them to the appropriate loadpattern in the subdomain
NodalLoadIter &theNodalLoads = theLoadPattern->getNodalLoads();
NodalLoad *theNodalLoad;
while ((theNodalLoad = theNodalLoads()) != 0) {
int nodeTag = theNodalLoad->getNodeTag();
TaggedObject *theTaggedObject = theNodeLocations->getComponentPtr(nodeTag);
if (theTaggedObject == 0) {
opserr << "DomainPartitioner::partition(int numParts)";
opserr << " - failed to find NodeLocation in Map for Node: " << nodeTag << " -- A BUG!!\n";
numPartitions = 0;
return -1;
}
NodeLocations *theNodeLocation = (NodeLocations *)theTaggedObject;
ID &nodePartitions = theNodeLocation->nodePartitions;
int numPartitions = theNodeLocation->numPartitions;
for (int i=0; i<numPartitions; i++) {
int partition = nodePartitions(i);
if (partition != mainPartition) {
if (numPartitions == 1) {
Subdomain *theSubdomain = myDomain->getSubdomainPtr(partition);
theLoadPattern->removeNodalLoad(theNodalLoad->getTag());
if ((theSubdomain->addNodalLoad(theNodalLoad, loadPatternTag)) != true)
opserr << "DomainPartitioner::partition() - failed to add Nodal Load\n";
}
}
}
}
SP_ConstraintIter &theSPs = theLoadPattern->getSPs();
SP_Constraint *spPtr;
while ((spPtr = theSPs()) != 0) {
int nodeTag = spPtr->getNodeTag();
TaggedObject *theTaggedObject = theNodeLocations->getComponentPtr(nodeTag);
if (theTaggedObject == 0) {
opserr << "DomainPartitioner::partition(int numParts)";
opserr << " - failed to find NodeLocation in Map for Node: " << nodeTag << " -- A BUG!!\n";
numPartitions = 0;
return -1;
}
NodeLocations *theNodeLocation = (NodeLocations *)theTaggedObject;
ID &nodePartitions = theNodeLocation->nodePartitions;
int numPartitions = theNodeLocation->numPartitions;
for (int i=0; i<numPartitions; i++) {
int partition = nodePartitions(i);
if (partition != mainPartition) {
Subdomain *theSubdomain = myDomain->getSubdomainPtr(partition);
if (numPartitions == 1)
theLoadPattern->removeSP_Constraint(spPtr->getTag());
int res = theSubdomain->addSP_Constraint(spPtr, loadPatternTag);
if (res < 0)
opserr << "DomainPartitioner::partition() - failed to add SP Constraint\n";
}
}
}
ElementalLoadIter &theLoads = theLoadPattern->getElementalLoads();
ElementalLoad *theLoad;
while ((theLoad = theLoads()) != 0) {
int loadEleTag = theLoad->getElementTag();
SubdomainIter &theSubdomains = myDomain->getSubdomains();
Subdomain *theSub;
bool added = false;
while (((theSub = theSubdomains()) != 0) && (added == false)) {
bool res = theSub->hasElement(loadEleTag);
if (res == true) {
theLoadPattern->removeElementalLoad(theLoad->getTag());
theSub->addElementalLoad(theLoad, loadPatternTag);
if (res < 0)
opserr << "DomainPartitioner::partition() - failed to add ElementalLoad\n";
added = true;
}
}
}
}
// add the single point constraints,
SP_ConstraintIter &theDomainSP = myDomain->getSPs();
SP_Constraint *spPtr;
while ((spPtr = theDomainSP()) != 0) {
int nodeTag = spPtr->getNodeTag();
TaggedObject *theTaggedObject = theNodeLocations->getComponentPtr(nodeTag);
if (theTaggedObject == 0) {
opserr << "DomainPartitioner::partition(int numParts)";
opserr << " - failed to find NodeLocation in Map for Node: " << nodeTag << " -- A BUG!!\n";
numPartitions = 0;
return -1;
}
NodeLocations *theNodeLocation = (NodeLocations *)theTaggedObject;
ID &nodePartitions = theNodeLocation->nodePartitions;
int numPartitions = theNodeLocation->numPartitions;
for (int i=0; i<numPartitions; i++) {
int partition = nodePartitions(i);
if (partition != mainPartition) {
Subdomain *theSubdomain = myDomain->getSubdomainPtr(partition);
if (numPartitions == 1) {
myDomain->removeSP_Constraint(spPtr->getTag());
}
int res = theSubdomain->addSP_Constraint(spPtr);
if (res < 0)
opserr << "DomainPartitioner::partition() - failed to add SP Constraint\n";
}
}
}
// move MP_Constraints - add an MP_Constraint to every partition a constrained node is in
MP_ConstraintIter &moreMPs = myDomain->getMPs();
while ((mpPtr = moreMPs()) != 0) {
int constrained = mpPtr->getNodeConstrained();
TaggedObject *theConstrainedObject = theNodeLocations->getComponentPtr(constrained);
NodeLocations *theConstrainedLocation = (NodeLocations *)theConstrainedObject;
ID &theConstrainedNodesPartitions = theConstrainedLocation->nodePartitions;
int numPartitions = theConstrainedLocation->numPartitions;
for (int i=0; i<numPartitions; i++) {
int partition = theConstrainedNodesPartitions(i);
if (partition != mainPartition) {
Subdomain *theSubdomain = myDomain->getSubdomainPtr(partition);
if (numPartitions == 1)
myDomain->removeMP_Constraint(mpPtr->getTag());
int res = theSubdomain->addMP_Constraint(mpPtr);
if (res < 0)
opserr << "DomainPartitioner::partition() - failed to add MP Constraint\n";
}
}
}
// now we go through all the subdomains and tell them to update
// their analysis for the new layouts
SubdomainIter &theSubDomains = myDomain->getSubdomains();
Subdomain *theSubDomain;
while ((theSubDomain = theSubDomains()) != 0)
theSubDomain->domainChange();
// we invoke change on the PartitionedDomain
myDomain->domainChange();
myDomain->clearElementGraph();
// we are done
partitionFlag = true;
return 0;
}
void tomSimilarity(double * expr, int * nSamples, int * nGenes,
int * corType,
int * adjType,
double * power,
int * tomType,
int * denomType,
double * maxPOutliers,
double * quick,
int * fallback,
int * cosine,
int * replaceMissing,
double * tom,
int * warn,
int * nThreads,
int * verbose, int * indent)
{
// Rprintf("Starting tomSimilarity...\n");
double * adj;
int ng = *nGenes, ns = *nSamples;
size_t matSize = ( (size_t)ng) * ( (size_t) ng);
int err = 0;
char spaces[2* *indent+1];
for (int i=0; i<2* *indent; i++) spaces[i] = ' ';
spaces[2* *indent] = '\0';
/*
int size=4000;
int success = 0;
double * pt;
while ( (pt=malloc(size*size*sizeof(double)))!=NULL )
{
size+=1000;
success = 1;
free(pt);
}
size -= 1000;
if ((*verbose > 0) && success)
Rprintf("%sRough guide to maximum array size: about %d x %d array of doubles..\n",
spaces, size, size);
*/
if (*verbose > 0) Rprintf("%sTOM calculation: adjacency..\n", spaces);
if (* tomType==TomTypeNone) // just calculate adjacency.
{
adjacency(expr, ns, ng, *corType, *adjType, *power, *maxPOutliers, *quick, *fallback, *cosine,
*replaceMissing, tom, &err, warn, nThreads, *verbose, *indent);
if (*verbose > 0) Rprintf("\n");
if (err) error(AdjErrors[err]);
return;
}
if ((adj = malloc(matSize * sizeof(double))) == NULL)
error("Memmory allocation error.");
if ((* tomType == TomTypeSigned) && (* adjType == AdjTypeUnsigned))
* adjType = AdjTypeUnsignedKeepSign;
if ((* tomType == TomTypeUnsigned) && (* adjType == AdjTypeUnsignedKeepSign))
* adjType = AdjTypeUnsigned;
adjacency(expr, ns, ng, * corType, * adjType, * power, * maxPOutliers, * quick, *fallback, *cosine,
*replaceMissing, adj, & err, warn, nThreads, *verbose, *indent);
// Rprintf("TOM 1\n");
if (err)
{
Rprintf("TOM: exit because 'adjacency' reported an error.\n");
free(adj);
error(AdjErrors[err]);
} else {
tomSimilarityFromAdj(adj, nGenes, tomType, denomType, tom, verbose, indent);
free(adj);
}
}
const ID &
MyRCM::number(Graph &theGraph, int startVertex)
{
// first check our size, if not same make new
if (numVertex != theGraph.getNumVertex()) {
// delete the old
if (theRefResult != 0)
delete theRefResult;
numVertex = theGraph.getNumVertex();
theRefResult = new ID(numVertex);
if (theRefResult == 0) {
opserr << "ERROR: MyRCM::number - Out of Memory\n";
theRefResult = new ID(0);
numVertex = 0;
return *theRefResult;
}
}
// see if we can do quick return
if (numVertex == 0)
return *theRefResult;
// we first set the Tmp of all vertices to -1, indicating
// they have not yet been added.
Vertex *vertexPtr;
VertexIter &vertexIter = theGraph.getVertices();
while ((vertexPtr = vertexIter()) != 0)
vertexPtr->setTmp(-1);
// we now set up; setting our markers and getting first vertex
if (startVertex != -1)
startVertexTag = startVertex;
if (startVertexTag != -1) {
vertexPtr = theGraph.getVertexPtr(startVertexTag);
if (vertexPtr == 0) {
opserr << "WARNING: MyRCM::number - No vertex with tag ";
opserr << startVertexTag << "Exists - using first come from iter\n";
startVertexTag = -1;
}
}
// if no starting vertex use the first one we get from the VertexIter
VertexIter &vertexIter2 = theGraph.getVertices();
if (startVertexTag == -1)
vertexPtr = vertexIter2();
int currentMark = numVertex-1; // marks current vertex visiting.
int nextMark = currentMark -1; // indiactes where to put next Tag in ID.
(*theRefResult)(currentMark) = vertexPtr->getTag();
vertexPtr->setTmp(currentMark);
// we continue till the ID is full
while (nextMark >= 0) {
// get the current vertex and its adjacency
vertexPtr = theGraph.getVertexPtr((*theRefResult)(currentMark));
const ID &adjacency = vertexPtr->getAdjacency();
// go through the vertices adjacency and add vertices which
// have not yet been Tmp'ed to the (*theRefResult)
int size = adjacency.Size();
for (int i=0; i<size; i++) {
int vertexTag = adjacency(i);
vertexPtr = theGraph.getVertexPtr(vertexTag);
if ((vertexPtr->getTmp()) == -1) {
vertexPtr->setTmp(nextMark);
(*theRefResult)(nextMark--) = vertexTag;
}
}
// go to the next vertex
// we decrement because we are doing reverse Cuthill-McKee
currentMark--;
// check to see if graph is disconneted
if ((currentMark == nextMark) && (currentMark >= 0)) {
opserr << "WARNING: MyRCM::number - Disconnected graph\n";
// loop over iter till we get a vertex not yet Tmped
while (((vertexPtr = vertexIter2()) != 0) &&
(vertexPtr->getTmp() != -1))
;
nextMark--;
vertexPtr->setTmp(currentMark);
(*theRefResult)(currentMark) = vertexPtr->getTag();
}
}
// now set the vertex references instead of the vertex tags
// in the result, we change the Tmp to indicate number and return
for (int i=0; i<numVertex; i++) {
int vertexTag = (*theRefResult)(i);
vertexPtr = theGraph.getVertexPtr(vertexTag);
vertexPtr->setTmp(i+1); // 1 through numVertex
(*theRefResult)(i) = vertexPtr->getTag();
}
theGraph.Print(opserr, 3);
opserr << *theRefResult;
return *theRefResult;
}
const ID &
MyRCM::number(Graph &theGraph, const ID &startVertices)
{
// first check our size, if not same make new
if (numVertex != theGraph.getNumVertex()) {
// delete the old
if (theRefResult != 0)
delete theRefResult;
numVertex = theGraph.getNumVertex();
theRefResult = new ID(numVertex);
if (theRefResult == 0) {
opserr << "ERROR: MyRCM::number - Out of Memory\n";
theRefResult = new ID(0);
numVertex = 0;
return *theRefResult;
}
}
// see if we can do quick return
if (numVertex == 0)
return *theRefResult;
ID copyStart(startVertices);
// we determine which node to start with
int minStartVertexTag =0;
int minAvgProfile = 0;
int startVerticesSize = startVertices.Size();
for (int j=0; j<startVerticesSize; j++) {
// we first set the Tmp of all vertices to -1, indicating
// they have not yet been added.
Vertex *vertexPtr;
VertexIter &vertexIter = theGraph.getVertices();
while ((vertexPtr = vertexIter()) != 0)
vertexPtr->setTmp(-1);
// we now set up; setting our markers and set first vertices
VertexIter &vertexIter2 = theGraph.getVertices();
int currentMark = numVertex-1; // marks current vertex visiting.
int nextMark = currentMark-1;
for (int k=0; k<startVerticesSize; k++)
if (k != j)
copyStart(k) = 0;
else
copyStart(k) = 1;
vertexPtr = theGraph.getVertexPtr(startVertices(j));
(*theRefResult)(currentMark) = vertexPtr->getTag();
vertexPtr->setTmp(currentMark);
int numFromStart = 1;
int avgProfile = 1;
while (numFromStart < startVerticesSize) {
// get the current vertex and its adjacency
vertexPtr = theGraph.getVertexPtr((*theRefResult)(currentMark));
const ID &adjacency = vertexPtr->getAdjacency();
// go through the vertices adjacency and add vertices which
// have not yet been Tmp'ed to the (*theRefResult)
int size = adjacency.Size();
for (int i=0; i<size; i++) {
int vertexTag = adjacency(i);
int loc =startVertices.getLocation(vertexTag);
if (loc >= 0) {
vertexPtr = theGraph.getVertexPtr(vertexTag);
if ((vertexPtr->getTmp()) == -1) {
vertexPtr->setTmp(nextMark);
copyStart(loc) = 1;
numFromStart++;
avgProfile += currentMark - nextMark;
(*theRefResult)(nextMark--) = vertexTag;
}
}
}
// go to the next vertex
// we decrement because we are doing reverse Cuthill-McKee
currentMark--;
// check to see if graph is disconneted
if (currentMark == nextMark && numFromStart < startVerticesSize) {
// loop over iter till we get a vertex not yet included
for (int l=0; l<startVerticesSize; l++)
if (copyStart(l) == 0) {
int vertexTag = startVertices(l);
vertexPtr = theGraph.getVertexPtr(vertexTag);
nextMark--;
copyStart(l) = 1;
vertexPtr->setTmp(currentMark);
numFromStart++;
(*theRefResult)(currentMark) = vertexPtr->getTag();
l =startVerticesSize;
}
}
}
currentMark = numVertex-1; // set current to the first again
nextMark = numVertex - startVerticesSize -1;
// we continue till the ID is full
while (nextMark >= 0) {
// get the current vertex and its adjacency
vertexPtr = theGraph.getVertexPtr((*theRefResult)(currentMark));
const ID &adjacency = vertexPtr->getAdjacency();
// go through the vertices adjacency and add vertices which
// have not yet been Tmp'ed to the (*theRefResult)
int size = adjacency.Size();
for (int i=0; i<size; i++) {
int vertexTag = adjacency(i);
vertexPtr = theGraph.getVertexPtr(vertexTag);
if ((vertexPtr->getTmp()) == -1) {
vertexPtr->setTmp(nextMark);
avgProfile += currentMark - nextMark;
(*theRefResult)(nextMark--) = vertexTag;
}
}
// go to the next vertex
// we decrement because we are doing reverse Cuthill-McKee
currentMark--;
// check to see if graph is disconneted
if ((currentMark == nextMark) && (currentMark >= 0)) {
// loop over iter till we get a vertex not yet Tmped
while (((vertexPtr = vertexIter2()) != 0) &&
(vertexPtr->getTmp() != -1))
;
nextMark--;
vertexPtr->setTmp(currentMark);
(*theRefResult)(currentMark) = vertexPtr->getTag();
}
}
if (j == 0 || minAvgProfile > avgProfile) {
minStartVertexTag = startVertices(j);
minAvgProfile = avgProfile;
}
}
// now we numebr based on minStartVErtexTag
// we first set the Tmp of all vertices to -1, indicating
// they have not yet been added.
Vertex *vertexPtr;
VertexIter &vertexIter = theGraph.getVertices();
while ((vertexPtr = vertexIter()) != 0)
vertexPtr->setTmp(-1);
// we now set up; setting our markers and set first vertices
VertexIter &vertexIter2 = theGraph.getVertices();
int currentMark = numVertex-1; // marks current vertex visiting.
int nextMark = currentMark-1;
vertexPtr = theGraph.getVertexPtr(minStartVertexTag);
(*theRefResult)(currentMark) = vertexPtr->getTag();
vertexPtr->setTmp(currentMark);
currentMark--;
int loc = startVertices.getLocation(minStartVertexTag);
for (int k=0; k<startVerticesSize; k++)
if (k != loc)
copyStart(k) = 0;
int numFromStart = 1;
while (numFromStart < startVerticesSize) {
// get the current vertex and its adjacency
vertexPtr = theGraph.getVertexPtr((*theRefResult)(currentMark));
const ID &adjacency = vertexPtr->getAdjacency();
// go through the vertices adjacency and add vertices which
// have not yet been Tmp'ed to the (*theRefResult)
int size = adjacency.Size();
for (int i=0; i<size; i++) {
int vertexTag = adjacency(i);
int loc =startVertices.getLocation(vertexTag);
if (loc >= 0) {
vertexPtr = theGraph.getVertexPtr(vertexTag);
if ((vertexPtr->getTmp()) == -1) {
vertexPtr->setTmp(nextMark);
copyStart(loc) = 1;
numFromStart++;
(*theRefResult)(nextMark--) = vertexTag;
}
}
}
// go to the next vertex
// we decrement because we are doing reverse Cuthill-McKee
currentMark--;
// check to see if graph is disconneted
if (currentMark == nextMark && numFromStart < startVerticesSize) {
// loop over iter till we get a vertex not yet included
for (int l=0; l<startVerticesSize; l++)
if (copyStart(l) == 0) {
int vertexTag = startVertices(l);
vertexPtr = theGraph.getVertexPtr(vertexTag);
nextMark--;
copyStart(l) = 1;
vertexPtr->setTmp(currentMark);
numFromStart++;
(*theRefResult)(currentMark) = vertexPtr->getTag();
l =startVerticesSize;
}
}
}
currentMark = numVertex-1; // set current to the first again
nextMark = numVertex - startVerticesSize -1;
currentMark = numVertex-1; // set current to the first again
// we continue till the ID is full
while (nextMark >= 0) {
// get the current vertex and its adjacency
vertexPtr = theGraph.getVertexPtr((*theRefResult)(currentMark));
const ID &adjacency = vertexPtr->getAdjacency();
// go through the vertices adjacency and add vertices which
// have not yet been Tmp'ed to the (*theRefResult)
int size = adjacency.Size();
for (int i=0; i<size; i++) {
int vertexTag = adjacency(i);
vertexPtr = theGraph.getVertexPtr(vertexTag);
if ((vertexPtr->getTmp()) == -1) {
vertexPtr->setTmp(nextMark);
(*theRefResult)(nextMark--) = vertexTag;
}
}
// go to the next vertex
// we decrement because we are doing reverse Cuthill-McKee
currentMark--;
// check to see if graph is disconneted
if ((currentMark == nextMark) && (currentMark >= 0)) {
opserr << "WARNING: MyRCM::number - Disconnected graph ";
// loop over iter till we get a vertex not yet Tmped
while (((vertexPtr = vertexIter2()) != 0) &&
(vertexPtr->getTmp() != -1))
;
nextMark--;
vertexPtr->setTmp(currentMark);
(*theRefResult)(currentMark) = vertexPtr->getTag();
}
}
// now set the vertex references instead of the vertex tags
// in the result, we change the Tmp to indicate number and return
for (int m=0; m<numVertex; m++) {
int vertexTag = (*theRefResult)(m);
vertexPtr = theGraph.getVertexPtr(vertexTag);
vertexPtr->setTmp(m+1); // 1 through numVertex
(*theRefResult)(m) = vertexPtr->getTag();
}
return *theRefResult;
}
