f54d790f5e9ba6e34d018f9e9b0af4b94e88c681 kent Mon Aug 25 08:03:56 2014 -0700 Adding childDistance diff --git src/lib/hacTree.c src/lib/hacTree.c index 6752a70..3196d82 100644 --- src/lib/hacTree.c +++ src/lib/hacTree.c @@ -1,382 +1,384 @@ /* hacTree - Hierarchical Agglomerative Clustering a list of inputs into a binary tree */ /* Copyright (C) 2011 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "dlist.h" #include "hash.h" #include "hacTree.h" static struct hacTree *leafNodesFromItems(const struct slList *itemList, int itemCount, struct lm *localMem) /* Allocate & initialize leaf nodes that contain only items. */ { struct hacTree *leafNodes = lmAlloc(localMem, itemCount * sizeof(struct hacTree)); int i = 0; const struct slList *item = itemList; while (item != NULL && i < itemCount) { // needMem zeroes the memory, so initialize only non-NULL stuff. struct hacTree *node = &(leafNodes[i]); if (i < itemCount-1) node->next = &(leafNodes[i+1]); node->itemOrCluster = (struct slList *)item; i++; item = item->next; } return leafNodes; } struct sortWrapper /* We need to compare nodes' itemOrClusters using cmpF and extraData; * qsort's comparison function doesn't have a way to pass in extraData, * so we need to point to it from each qsort element. */ { struct hacTree *node; // contains itemOrCluster to be compared hacCmpFunction *cmpF; // user-provided itemOrCluster comparison function void *extraData; // user-provided aux data for cmpF }; static int sortWrapCmp(const void *v1, const void *v2) /* Unpack sortWrappers and run cmpF on nodes' itemOrClusters with extraData. */ { const struct sortWrapper *w1 = v1, *w2 = v2; return w1->cmpF(w1->node->itemOrCluster, w2->node->itemOrCluster, w1->extraData); } static struct sortWrapper *makeSortedWraps(struct hacTree *leafNodes, int itemCount, struct lm *localMem, hacCmpFunction cmpF, void *extraData) /* Use cmpF and extraData to sort wrapped leaves so that identical leaves will be adjacent. */ { struct sortWrapper *leafWraps = lmAlloc(localMem, itemCount * sizeof(struct sortWrapper)); int i; for (i=0; i < itemCount; i++) { leafWraps[i].node = &(leafNodes[i]); leafWraps[i].cmpF = cmpF; leafWraps[i].extraData = extraData; } qsort(leafWraps, itemCount, sizeof(struct sortWrapper), sortWrapCmp); return leafWraps; } INLINE void initNode(struct hacTree *node, const struct hacTree *left, const struct hacTree *right, hacDistanceFunction *distF, hacMergeFunction *mergeF, void *extraData) /* Initialize node to have left and right as its children. Leave parent pointers * alone -- they would be unstable during tree construction. */ { node->left = (struct hacTree *)left; node->right = (struct hacTree *)right; if (left != NULL && right != NULL) { node->childDistance = distF(left->itemOrCluster, right->itemOrCluster, extraData); node->itemOrCluster = mergeF(left->itemOrCluster, right->itemOrCluster, extraData); } } INLINE struct hacTree preClusterNodes(const struct sortWrapper *leafWraps, int i, int runLength, hacDistanceFunction *distF, hacMergeFunction *mergeF, void *extraData, struct lm *localMem) /* Caller has allocated a node, and this returns what to store there: * a recursively constructed cluster of nodes extracted from wrapped * leafNodes (leafWraps) starting at i, for runLength items. */ { struct hacTree ret = {NULL, NULL, NULL, NULL, 0, NULL}; if (runLength > 2) { struct hacTree *newClusters = lmAlloc(localMem, 2 * sizeof(struct hacTree)); int halfLength = runLength/2; newClusters[0] = preClusterNodes(leafWraps, i, halfLength, distF, mergeF, extraData, localMem); newClusters[1] = preClusterNodes(leafWraps, i+halfLength, runLength-halfLength, distF, mergeF, extraData, localMem); initNode(&ret, &(newClusters[0]), &(newClusters[1]), distF, mergeF, extraData); } else if (runLength == 2) { initNode(&ret, leafWraps[i].node, leafWraps[i+1].node, distF, mergeF, extraData); } else ret = *(leafWraps[i].node); return ret; } static struct hacTree *sortAndPreCluster(struct hacTree *leafNodes, int *retItemCount, struct lm *localMem, hacDistanceFunction *distF, hacMergeFunction *mergeF, hacCmpFunction *cmpF, void *extraData) /* Use cmpF and extraData to sort wrapped leaf nodes so that identical leaves will be adjacent, * then replace leaves with clusters of identical leaves where possible. Place new * (hopefully smaller) item count in retItemCount. */ { int itemCount = *retItemCount; struct sortWrapper *leafWraps = makeSortedWraps(leafNodes, itemCount, localMem, cmpF, extraData); struct hacTree *newLeaves = lmAlloc(localMem, itemCount * sizeof(struct hacTree)); int i=0, newI=0; while (i < itemCount) { int nextRunStart; for (nextRunStart = i+1; nextRunStart < itemCount; nextRunStart++) if (distF(leafWraps[i].node->itemOrCluster, leafWraps[nextRunStart].node->itemOrCluster, extraData) != 0) break; int runLength = nextRunStart - i; newLeaves[newI] = preClusterNodes(leafWraps, i, runLength, distF, mergeF, extraData, localMem); i = nextRunStart; newI++; } *retItemCount = newI; return newLeaves; } static struct hacTree *pairUpItems(const struct slList *itemList, int itemCount, int *retPairCount, struct lm *localMem, hacDistanceFunction *distF, hacMergeFunction *mergeF, hacCmpFunction *cmpF, void *extraData) /* Allocate & initialize leaf nodes and all possible pairings of leaf nodes * which will be our seed clusters. If cmpF is given, pre-sort the leaf nodes * and pre-cluster identical leaves before generating seed clusters. */ { struct hacTree *leafNodes = leafNodesFromItems(itemList, itemCount, localMem); if (cmpF != NULL) leafNodes = sortAndPreCluster(leafNodes, &itemCount, localMem, distF, mergeF, cmpF, extraData); int pairCount = (itemCount == 1) ? 1 : (itemCount * (itemCount-1) / 2); struct hacTree *pairPool = lmAlloc(localMem, pairCount * sizeof(struct hacTree)); if (itemCount == 1) initNode(pairPool, leafNodes, NULL, distF, mergeF, extraData); else { int i, j, pairIx; for (i=0, pairIx=0; i < itemCount-1; i++) for (j=i+1; j < itemCount; j++, pairIx++) initNode(&(pairPool[pairIx]), &(leafNodes[i]), &(leafNodes[j]), distF, mergeF, extraData); } *retPairCount = pairCount; return pairPool; } struct hacTree *hacTreeFromItems(const struct slList *itemList, struct lm *localMem, hacDistanceFunction *distF, hacMergeFunction *mergeF, hacCmpFunction *cmpF, void *extraData) /* Using distF, mergeF, optionally cmpF and binary tree operations, * perform a hierarchical agglomerative (bottom-up) clustering of * items. To free the resulting tree, lmCleanup(&localMem). */ // // Implementation: // // Create a pool containing all pairs of items (N*(N-1)/2), and build // a hierarchical binary tree of items from the bottom up. In each // iteration, first we find the closest pair and swap it into the head // of the pool; then we advance the head pointer, so the closest pair // now has a stable location in memory. Next, for all pairs still in // the pool, we replace references to the elements of the closest pair // with the closest pair itself, but delete half of such pairs because // they would be duplicates. Specifically, we keep pairs that had the // left element of the closest pair, and delete pairs that had the // right element of the closest pair. We rescore the pairs that have // the closest pair swapped in for an element. The code to do all // this is surprisingly simple -- in the second for loop below. Note // that with each iteration, the pool will reduce in size, by N-2 the // first iteration, N-3 the second, and so forth. // // An example may help: say we start with items A, B, C and D. Initially // the pool contains all pairs: // (A, B) (A, C) (A, D) (B, C) (B, D) (C, D) // // If (A, B) is the closest pair, we pop it from the pool and the pool // becomes // (A, C) (A, D) (B, C) (B, D) (C, D) // // Now we substitute (A, B) for pool pairs containing A, and delete pool // pairs contining B because they would be duplicates of those containing // A. [X] shows where a pair was deleted: // // ((A, B), C) ((A, B), D) [X] [X] (C, D) // // Now say ((A, B), D) is the closest remaining pair, and is popped from // the head of the pool. We substitute into pairs containing (A, B) and // delete pairs containing D. After the replacement step, the pool is // down to a single element: // // (((A, B), D), C) [X] { if (itemList == NULL) return NULL; struct hacTree *root = NULL; int itemCount = slCount(itemList); int pairCount = 0; struct hacTree *leafPairs = pairUpItems(itemList, itemCount, &pairCount, localMem, distF, mergeF, cmpF, extraData); int *nodesToDelete = needMem(pairCount * sizeof(int)); struct hacTree *poolHead = leafPairs; int poolLength = pairCount; while (poolLength > 0) { // Scan pool for node with lowest childDistance; swap that node w/head int bestIx = 0; double minScore = poolHead[0].childDistance; int i; for (i=1; i < poolLength; i++) if (poolHead[i].childDistance < minScore) { minScore = poolHead[i].childDistance; bestIx = i; } if (bestIx != 0) swapBytes((char *)&(poolHead[0]), (char *)&(poolHead[bestIx]), sizeof(struct hacTree)); // Pop the best (lowest-distance) node from poolHead, make it root (for now). root = poolHead; poolHead = &(poolHead[1]); poolLength--; // Where root->left is found in the pool, replace it with root. // Where root->right is found, drop that node so it doesn't become // a duplicate of the replacement cases. int numNodesToDelete = 0; for (i=0; i < poolLength; i++) { struct hacTree *node = &(poolHead[i]); if (node->left == root->left) // found root->left; replace node->left with root (merge root with node->right): initNode(node, root, node->right, distF, mergeF, extraData); else if (node->right == root->left) // found root->left; replace node->right with root (merge root with node->left): initNode(node, node->left, root, distF, mergeF, extraData); else if (node->left == root->right || node->right == root->right) // found root->right; mark this node for deletion: nodesToDelete[numNodesToDelete++] = i; } if (numNodesToDelete > 0) { int newPoolLen = nodesToDelete[0]; // This will be "next node to delete" for the last marked node: nodesToDelete[numNodesToDelete] = poolLength; for (i = 0; i < numNodesToDelete; i++) { int nodeToDel = nodesToDelete[i]; int nextNodeToDel = nodesToDelete[i+1]; int blkSize = nextNodeToDel - (nodeToDel+1); if (blkSize == 0) continue; struct hacTree *fromNode = &(poolHead[nodeToDel+1]); struct hacTree *toNode = &(poolHead[newPoolLen]); memmove(toNode, fromNode, blkSize * sizeof(struct hacTree)); newPoolLen += blkSize; } poolLength = newPoolLen; } // root now has a stable address, unlike nodes still in the pool, so set parents here: if (root->left != NULL) root->left->parent = root; if (root->right != NULL) root->right->parent = root; } // This shouldn't be necessary as long as initNode leaves parent pointers alone, // but just in case that changes: root->parent = NULL; return root; } /** The code from here on down is an alternative implementation that calls the merge ** function and for that matter the distance function much less than the function ** above. */ -static void findClosestPair(struct dlList *list, struct hash *distanceHash, +static double findClosestPair(struct dlList *list, struct hash *distanceHash, hacDistanceFunction *distF, void *extraData, struct dlNode **retNodeA, struct dlNode **retNodeB) /* Loop through list returning closest two nodes */ { struct dlNode *aNode; double closestDistance = BIGDOUBLE; struct dlNode *closestA = NULL, *closestB = NULL; for (aNode = list->head; !dlEnd(aNode); aNode = aNode->next) { struct hacTree *aHt = aNode->val; struct slList *a = aHt->itemOrCluster; struct dlNode *bNode; for (bNode = aNode->next; !dlEnd(bNode); bNode = bNode->next) { struct hacTree *bHt = bNode->val; char key[64]; safef(key, sizeof(key), "%p %p", aHt, bHt); double *pd = hashFindVal(distanceHash, key); if (pd == NULL) { lmAllocVar(distanceHash->lm, pd); *pd = distF(a, bHt->itemOrCluster, extraData); hashAdd(distanceHash, key, pd); } double d = *pd; if (d < closestDistance) { closestDistance = d; closestA = aNode; closestB = bNode; } } } *retNodeA = closestA; *retNodeB = closestB; +return closestDistance; } static void lmDlAddValTail(struct lm *lm, struct dlList *list, void *val) /* Allocate new dlNode out of lm, initialize it with val, and add it to end of list */ { struct dlNode *node; lmAllocVar(lm, node); node->val = val; dlAddTail(list, node); } struct hacTree *hacTreeForCostlyMerges(struct slList *itemList, struct lm *localMem, hacDistanceFunction *distF, hacMergeFunction *mergeF, void *extraData) /* Construct hacTree using a method that will minimize the number of calls to * the distance and merge functions, assuming they are expensive. Do a lmCleanup(localMem) * to free the returned tree. */ { /* Make up a doubly-linked list in 'remaining' with all items in it */ struct dlList remaining; dlListInit(&remaining); struct slList *item; int count = 0; struct hash *distanceHash = hashNew(0); for (item = itemList; item != NULL; item = item->next) { struct hacTree *ht; lmAllocVar(localMem, ht); ht->itemOrCluster = item; lmDlAddValTail(localMem, &remaining, ht); count += 1; } /* Loop through finding closest and merging until only one node left on remaining. */ int i; for (i=1; i<count; ++i) { /* Find closest pair and take them off of remaining list */ struct dlNode *aNode, *bNode; - findClosestPair(&remaining, distanceHash, distF, extraData, &aNode, &bNode); + double distance = findClosestPair(&remaining, distanceHash, distF, extraData, &aNode, &bNode); dlRemove(aNode); dlRemove(bNode); /* Allocated new hacTree item for them and fill it in with a merged value. */ struct hacTree *ht; lmAllocVar(localMem, ht); struct hacTree *left = ht->left = aNode->val; struct hacTree *right = ht->right = bNode->val; left->parent = right->parent = ht; ht->itemOrCluster = mergeF(left->itemOrCluster, right->itemOrCluster, extraData); + ht->childDistance = distance; /* Put merged item onto remaining list. */ lmDlAddValTail(localMem, &remaining, ht); } /* Clean up and go home. */ hashFree(&distanceHash); struct dlNode *lastNode = dlPopHead(&remaining); return lastNode->val; }