org.apache.ctakes.ytex.kernel.model.ConcRel Maven / Gradle / Ivy
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*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing,
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*/
package org.apache.ctakes.ytex.kernel.model;
import com.google.common.collect.ImmutableSet;
import org.apache.ctakes.ytex.kernel.metric.LCSPath;
import java.util.*;
import java.util.logging.Level;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class ConcRel implements java.io.Serializable {
private static final Logger LOGGER = LoggerFactory.getLogger( "ConcRel" );
/**
*
*/
private static final long serialVersionUID = 1L;
public static List crListToString(List crList) {
if (crList != null) {
List path = new ArrayList(crList.size());
for (ConcRel cr : crList)
path.add(cr.getConceptID());
return path;
} else {
return null;
}
}
/**
* get least common subsumer of the specified concepts and its distance from
* root.
*
* @deprecated
*
* @param c1
* @param c2
* @return
*/
public static ObjPair getLeastCommonConcept(ConcRel c1,
ConcRel c2) {
LOGGER.debug("getLeastCommonConcept(" + c1 + "," + c2 + ")");
// result
ObjPair res = new ObjPair(null,
Integer.MAX_VALUE);
// concept 1's parent distance map
Map cand1 = new HashMap();
// concept 2's parent distance map
Map cand2 = new HashMap();
// parents of concept 1
HashSet parC1 = new HashSet();
parC1.add(c1);
// parents of concept 2
HashSet parC2 = new HashSet();
parC2.add(c2);
HashSet tmp = new HashSet();
HashSet tmp2;
int dist = 0;
// changed to start distance with 1 - we increment at the end of the
// loop
// we always look at the parents, so the distance has to start with 1
// if one concept is the parent of the other, this would return 0 if
// dist starts with 0
// int dist = 1;
// while there are parents
// this does a dual-breadth first search
// parC1 are the dist'th ancestors of concept 1
// parC2 are the dist'th ancestors of concept 2
while (!parC1.isEmpty() || !parC2.isEmpty()) {
// grandparents
tmp.clear();
// go through parents of concept1
for (Iterator it = parC1.iterator(); it.hasNext();) {
ConcRel cr = it.next();
// checkif it's in the map concept2's parent distance map
// - map of distances from concept 1
if (cand2.containsKey(cr)) {
res.v1 = cr;
res.v2 = dist + cand2.get(cr).intValue();
// return
return res;
}
// not in the map - add it to the concept-distance map
cand1.put(cr, dist);
// add the grandparents to the tmp set
tmp.addAll(cr.parents);
}
// remove concepts already in concept1's parent distance map from
// the grandparent map
tmp.removeAll(cand1.keySet());
// tmp2 becomes the parents of c1
tmp2 = parC1;
// par c1 becomes grandparents minus parents
parC1 = tmp;
// tmp becomes tmp2, which is going to be killed in the next line
tmp = tmp2;
tmp.clear();
// repeat everything for concept2 - go up one level
for (Iterator it = parC2.iterator(); it.hasNext();) {
ConcRel cr = it.next();
if (cand1.containsKey(cr)) {
res.v1 = cr;
res.v2 = dist + cand1.get(cr).intValue();
return res;
}
cand2.put(cr, dist);
tmp.addAll(cr.parents);
}
tmp.removeAll(cand2.keySet());
tmp2 = parC2;
parC2 = tmp;
tmp = tmp2;
++dist;
}
return res;
}
/**
*
* @param c1
* concept1
* @param c2
* concept2
* @param lcses
* least common subsumers, required
* @param paths
* paths between concepts via lcses, optional. Key - lcs. Value -
* 2 element list corresponding to paths to lcs from c1 and c2
* @return path length, -1 if no lcs
*/
public static int getLeastCommonConcept(ConcRel c1, ConcRel c2,
Set lcses, Map paths) {
LOGGER.debug("getLeastCommonConcept(" + c1 + "," + c2 + ")");
// concept 1's parent distance map
Map cand1 = new HashMap();
// concept 2's parent distance map
Map cand2 = new HashMap();
// paths corresponding to parents
// we only calculate these if they are asked of us
Map> paths1 = paths != null ? new HashMap>()
: null;
Map> paths2 = paths != null ? new HashMap>()
: null;
// parents of concept 1
HashSet parC1 = new HashSet();
parC1.add(c1);
// parents of concept 2
HashSet parC2 = new HashSet();
parC2.add(c2);
// temporary hashset for scratch work
// not clear if this really reduces memory overhead
HashSet tmp = new HashSet();
HashSet candidateLCSes = new HashSet();
int maxIter = -1;
int dist = 0;
int minDist = Integer.MAX_VALUE - 1;
// continue the search while there are parents left
// check maxIter - if this is some non-negative number
// then it must be greater than 0
while ((!parC1.isEmpty() || !parC2.isEmpty())
&& (maxIter < 0 || maxIter != 0)) {
// get next iteration of ancestors, save them
updateParent(cand1, parC1, tmp, dist, paths1);
updateParent(cand2, parC2, tmp, dist, paths2);
// get the intersection across the ancestors
tmp.clear();
tmp.addAll(cand1.keySet());
tmp.retainAll(cand2.keySet());
tmp.removeAll(candidateLCSes);
// if there is something in the intersection, we have a potential
// winner. however, we can't stop here
// example: ascites/hepatoma in snomed C2239176 C0003962
// e.g. one path could be 3-3, but a shorter path could be 4-1
// we would only find the 4-1 path after 4 iterations
if (!tmp.isEmpty()) {
// add candidates so we don't have to look at them in future
// iterations
candidateLCSes.addAll(tmp);
// remove candidates' parents from the parent collections for
// the next iterations
removeParents(tmp, parC1);
removeParents(tmp, parC2);
// add the lcs candidates and their path length
// even though we have a hit, we can't stop here
// there could be uneven path lengths.
// to account for this, the 1st time we find an lcs
// we set maxIter to the minimum path length to either concept
// from the lcs. if we can't find a match after maxIter
// iterations, then we know that what we've found is a winner
for (ConcRel lcs : tmp) {
// path length for current lcs
int distTmp = cand1.get(lcs) + cand2.get(lcs) + 1;
// only add it to the list of lcses if it is less than or
// equal to the current minimal path length
if (distTmp <= minDist) {
if (distTmp < minDist) {
// we have a new best minimal path length
// clear the current lcses
lcses.clear();
}
minDist = distTmp;
lcses.add(lcs);
}
// all additional lcses must be found within maxIter
// iterations. maxIter is the shortest path between
// the lcs and a concept
int minLcsToConceptLen = Math.min(cand1.get(lcs),
cand2.get(lcs));
if (maxIter < 0 || maxIter > minLcsToConceptLen) {
maxIter = minLcsToConceptLen;
}
}
}
// reduce maximum number of iterations left
maxIter--;
++dist;
}
if (lcses.isEmpty())
return -1;
else {
if (paths != null) {
for (ConcRel lcs : lcses) {
LCSPath lcsPath = new LCSPath();
lcsPath.setLcs(lcs.getConceptID());
lcsPath.setConcept1Path(crListToString(paths1.get(lcs)));
lcsPath.setConcept2Path(crListToString(paths2.get(lcs)));
paths.put(lcs, lcsPath);
}
}
return minDist;
}
}
/**
* remove the parents of candidate lcses from the list of parents we were
* planning on looking at in the next iteration
*
* @param lcses
* @param parents
*/
private static void removeParents(HashSet lcses,
HashSet parents) {
for (ConcRel lcs : lcses) {
parents.removeAll(lcs.parents);
}
}
/**
* perform 1 iteration of breadth-first search on lcs. update the various
* collections with the next iteration of ancestors.
*
* @param cand1
* @param parC1
* @param tmp
* @param dist
*/
private static void updateParent(Map cand1,
HashSet parC1, HashSet tmp, int dist,
Map> paths) {
tmp.clear();
// go through parents of concept1
for (Iterator it = parC1.iterator(); it.hasNext();) {
ConcRel cr = it.next();
if (!cand1.containsKey(cr)) {
// not in the map - add it to the concept-distance map
cand1.put(cr, dist);
// add the grandparents to the tmp set
tmp.addAll(cr.parents);
if (paths != null) {
// add the path to the parent to the map of paths
List pathCR = paths.get(cr);
for (ConcRel parent : cr.parents) {
if (!paths.containsKey(parent)) {
// path to parent = path to child + child
List path = new ArrayList(
pathCR != null ? pathCR.size() + 1 : 1);
if (pathCR != null)
path.addAll(pathCR);
path.add(cr);
paths.put(parent, path);
}
}
}
}
}
// remove concepts already in concept1's parent distance map from
// the grandparent map
tmp.removeAll(cand1.keySet());
// parents for the next iteration
parC1.clear();
parC1.addAll(tmp);
}
/**
* children of this concept
*/
private Set children;
private int[] childrenArray;
private short depth;
private double intrinsicInfoContent;
/**
* id of this concept
*/
private String nodeCUI;
private int nodeIndex;
/**
* parents of this concept
*/
private Set parents;
/**
* for java object serialization, need to avoid default serializer behavior
* of writing out entire object graph. just write the parent/children object
* ids and resolve the connections after loading this object.
*/
private int[] parentsArray;
public ConcRel(String cui, int nodeIndex) {
nodeCUI = cui;
parents = new HashSet();
children = new HashSet();
parentsArray = null;
childrenArray = null;
this.nodeIndex = nodeIndex;
}
/**
* reconstruct the relationships to other ConcRel objects
*
* @param db
*/
public void constructRel(List db) {
ImmutableSet.Builder pBuilder = new ImmutableSet.Builder();
for (int c : parentsArray)
pBuilder.add(db.get(c));
parents = pBuilder.build();
parentsArray = null;
ImmutableSet.Builder cBuilder = new ImmutableSet.Builder();
for (int c : childrenArray)
cBuilder.add(db.get(c));
children = cBuilder.build();
childrenArray = null;
}
public int depthMax() {
int d = 0;
for (Iterator it = children.iterator(); it.hasNext();) {
ConcRel child = it.next();
int dm = child.depthMax() + 1;
if (dm > d)
d = dm;
}
return d;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
ConcRel other = (ConcRel) obj;
if (nodeIndex != other.nodeIndex)
return false;
return true;
}
public Set getChildren() {
return children;
}
public int[] getChildrenArray() {
return childrenArray;
}
public String getConceptID() {
return nodeCUI;
}
public short getDepth() {
return depth;
}
public double getIntrinsicInfoContent() {
return intrinsicInfoContent;
}
public int getNodeIndex() {
return nodeIndex;
}
public Set getParents() {
return parents;
}
public int[] getParentsArray() {
return parentsArray;
}
/**
* recursively build all paths to root from a concept - add elements from
* set of parents.
*
* @param lpath
* current path from children to this concept
* @param allPaths
* list of all paths
* @param depth
* current depth
* @param depthMax
*/
public void getPath(List lpath, List> allPaths,
int depth, int depthMax) {
if (depth >= depthMax)
return;
if (lpath == null)
lpath = new ArrayList();
lpath.add(this);
if (isRoot()) {
// add a copy to the list of all paths
allPaths.add(new ArrayList(lpath));
} else {
// recurse
for (ConcRel p : parents) {
p.getPath(lpath, allPaths, depth + 1, depthMax);
}
}
lpath.remove(lpath.size() - 1);
}
/**
* is the specified concept an ancestor of this concept?
*
* @param cui
* @return
*/
public boolean hasAncestor(String cui) {
if (nodeCUI.equals(cui))
return true;
for (ConcRel c : parents) {
if (c.hasAncestor(cui))
return true;
}
return false;
}
@Override
public int hashCode() {
return nodeIndex;
}
public boolean isLeaf() {
return children.isEmpty();
}
public boolean isRoot() {
return parents.isEmpty();
}
/**
* read parent/children concept ids, not the objects
*/
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException, ClassNotFoundException {
nodeCUI = (String) in.readObject();
this.nodeIndex = in.readInt();
this.intrinsicInfoContent = in.readDouble();
this.depth = in.readShort();
parentsArray = (int[]) in.readObject();
childrenArray = (int[]) in.readObject();
parents = new HashSet(parentsArray.length);
children = new HashSet(childrenArray.length);
}
// public static ObjPair getLeastCommonConcept(
// Vector> allPaths1, Vector> allPaths2) {
// ObjPair res = new ObjPair(null,
// Integer.MAX_VALUE);
// ObjPair tmp = new ObjPair(null,
// Integer.MAX_VALUE);
//
// int n = 0;
// for (Vector path1 : allPaths1) {
// // if(n++>200)
// // break;
// int n2 = 0;
// for (Vector path2 : allPaths2) {
// // if(n2++>200)
// // break;
// if (getCommonConcept(path1, path2, tmp) != null) {
// if (tmp.v2.intValue() < res.v2.intValue()) {
// res.v1 = tmp.v1;
// res.v2 = tmp.v2;
// }
// }
// }
// }
//
// return res;
// }
// public static ConcRel getCommonConcept(Vector path1,
// Vector path2, ObjPair oVals) {
// ConcRel common = null;
// int dist = Integer.MAX_VALUE;
// int index1 = path1.size() - 1;
// int index2 = path2.size() - 1;
// while (index1 >= 0 && index2 >= 0) {
// ConcRel r1 = path1.get(index1);
// if (r1.equals(path2.get(index2))) {
// common = r1;
// dist = index1 + index2;
// --index1;
// --index2;
// } else
// break;
// }
//
// oVals.v1 = common;
// oVals.v2 = dist;
//
// return common;
// }
public void setChildrenArray(int[] childrenArray) {
this.childrenArray = childrenArray;
}
public void setConceptID(String nodeCUI) {
this.nodeCUI = nodeCUI;
}
public void setDepth(short depth) {
this.depth = depth;
}
public void setIntrinsicInfoContent(double intrinsicInfoContent) {
this.intrinsicInfoContent = intrinsicInfoContent;
}
public void setNodeIndex(int nodeIndex) {
this.nodeIndex = nodeIndex;
}
public void setParentsArray(int[] parentsArray) {
this.parentsArray = parentsArray;
}
@Override
public String toString() {
return "ConcRel [nodeCUI=" + nodeCUI + "]";
}
/**
* serialize parent/children concept ids, not the objects
*/
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException {
out.writeObject(nodeCUI);
out.writeInt(this.nodeIndex);
out.writeDouble(this.intrinsicInfoContent);
out.writeShort(this.depth);
if (parentsArray == null) {
parentsArray = new int[parents.size()];
int i = 0;
for (ConcRel c : parents)
parentsArray[i++] = c.getNodeIndex();
}
if (childrenArray == null) {
childrenArray = new int[children.size()];
int i = 0;
for (ConcRel c : children)
childrenArray[i++] = c.getNodeIndex();
}
out.writeObject(parentsArray);
out.writeObject(childrenArray);
parentsArray = null;
childrenArray = null;
}
// public static void main(String[] args) {
// int c1 = 18563; // 4903;
// int c2 = 18670; // 175695;
//
// ConcRel r1 = MetaDB.concRelDB.cuiRelDB.get(c1);
// ConcRel r2 = MetaDB.concRelDB.cuiRelDB.get(c2);
// if (r1 == null)
// System.out.println("No rel for " + c1);
// if (r2 == null)
// System.out.println("No rel for " + c2);
//
// if (r1 == null || r2 == null)
// return;
//
// Vector> allPaths1 = new Vector>();
// Vector> allPaths2 = new Vector>();
//
// r1.getPath(null, allPaths1, 0, 1000);
// r2.getPath(null, allPaths2, 0, 1000);
//
// int i = 0;
// System.out.println("***Paths for " + c1);
// i = 0;
// for (Vector vc : allPaths1) {
// System.out.print("#P" + (i++) + ": ");
// i++;
// for (ConcRel cr : vc) {
// System.out.print("->" + cr.nodeCUI);
// }
// System.out.println("");
// }
//
// System.out.println("***Paths for " + c2);
// i = 0;
// for (Vector vc : allPaths2) {
// System.out.print("##P" + (i++) + ": ");
// for (ConcRel cr : vc) {
// System.out.print("->" + cr.nodeCUI);
// }
// System.out.println("");
// }
//
// ObjPair obp = getLeastCommonConcept(allPaths1,
// allPaths2);
// System.out.println("Common concept :"
// + (obp.v1 == null ? "none" : obp.v1.nodeCUI));
// System.out.println("dist: " + obp.v2);
//
// obp = getLeastCommonConcept(r1, r2);
// System.out.println("Common concept2 :"
// + (obp.v1 == null ? "none" : obp.v1.nodeCUI));
// System.out.println("dist: " + obp.v2);
//
// }
}
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