/**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
* KIND, either express or implied. See the License for the
* specific language governing permissions and limitations
* under the License.
*/
package org.apache.ctakes.drugner.fsm.machines.elements;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.ctakes.core.fsm.condition.DecimalCondition;
import org.apache.ctakes.core.fsm.condition.DisjoinCondition;
import org.apache.ctakes.core.fsm.condition.IntegerValueCondition;
import org.apache.ctakes.core.fsm.condition.NumberCondition;
import org.apache.ctakes.core.fsm.condition.PunctuationValueCondition;
import org.apache.ctakes.core.fsm.condition.TextValueCondition;
import org.apache.ctakes.core.fsm.condition.WordSetCondition;
import org.apache.ctakes.core.fsm.state.NamedState;
import org.apache.ctakes.core.fsm.state.NonTerminalEndState;
import org.apache.ctakes.core.fsm.token.BaseToken;
import org.apache.ctakes.core.fsm.token.adapter.PunctuationTokenAdapter;
import org.apache.ctakes.drugner.fsm.elements.conditions.FormCondition;
import org.apache.ctakes.drugner.fsm.elements.conditions.FractionStrengthCondition;
import org.apache.ctakes.drugner.fsm.elements.conditions.RangeStrengthCondition;
import org.apache.ctakes.drugner.fsm.elements.conditions.RouteCondition;
import org.apache.ctakes.drugner.fsm.output.elements.DosageToken;
import org.apache.ctakes.drugner.fsm.states.util.IndentStartState;
import net.openai.util.fsm.AnyCondition;
import net.openai.util.fsm.Condition;
import net.openai.util.fsm.Machine;
import net.openai.util.fsm.State;
/**
* Uses one or more finite state machines to detect dosages in the given input
* of tokens.
*
* @author Mayo Clinic
*/
public class DosagesFSM {
Set iv_soloTextSet = new HashSet();
Set iv_textNumberSet = new HashSet();
// contains the finite state machines
private Set iv_machineSet = new HashSet();
/**
*
* Constructor
*
*/
public DosagesFSM() {
iv_textNumberSet.add("one");
iv_textNumberSet.add("two");
iv_textNumberSet.add("three");
iv_textNumberSet.add("four");
iv_textNumberSet.add("five");
iv_textNumberSet.add("six");
iv_textNumberSet.add("seven");
iv_textNumberSet.add("eight");
iv_textNumberSet.add("nine");
iv_textNumberSet.add("ten");
iv_textNumberSet.add("one-half");
iv_textNumberSet.add("one-and-a-half");
iv_textNumberSet.add("one-and-a-half-tablets");
iv_textNumberSet.add("one-half-tablet");
iv_textNumberSet.add("one-fourth");
iv_textNumberSet.add("one-third");
iv_textNumberSet.add("half-tablet");
iv_textNumberSet.add("one-to-two");
iv_textNumberSet.add("two-to-three");
iv_textNumberSet.add("three-quarter");
iv_textNumberSet.add("three-quarters");
iv_textNumberSet.add("three-fourths");
iv_textNumberSet.add("one-quarter");
iv_soloTextSet.add("one-half-tablet");
iv_soloTextSet.add("half-tablet");
iv_machineSet.add(getDosageQuantityMachine());
}
/**
* - * Gets a finite state machine that detects the following:
* <ol>
* <li>one milligram</li>
* <li>one mg</li>
* <li>1 milligram</li>
* <li>1 mg</li>
* <li>10mg</li>
* <li>0.5 mg</li>
* <li>1-5 milligrams</li>
* </ol>
*
* @return
*/
private Machine getDosageQuantityMachine() {
State startState = new NamedState("START");
State endState = new NamedState("END");
State ofState = new NamedState("OF");
State aState = new NamedState("A");
State numState = new NamedState("NUMVALUE");
State formState = new NamedState("FORM");
State leftParenState = new NamedState("LEFTPAREN");
State ntFalseTermState = new IndentStartState("NON TERMINAL START");
State ntEndState = new NonTerminalEndState("NON TERMINAL END");
ntFalseTermState.setEndStateFlag(true);
endState.setEndStateFlag(true);
ntEndState.setEndStateFlag(true);
Machine m = new Machine(startState);
State hyphState = new NamedState("HYPHTERM");
State dosageState = new NamedState("DOSAGE");
Condition decimalCondition = new DecimalCondition();
Condition numberCondition = new NumberCondition();
Condition strengthFormCondition = new DisjoinCondition(
new RouteCondition(), new FormCondition());
Condition numberTextCondition = new WordSetCondition(iv_textNumberSet,
false);
Condition rangeCondition = new RangeStrengthCondition();
Condition fractionRangeCondition = new FractionStrengthCondition();
Condition decimalStart = new DisjoinCondition(
new IntegerValueCondition(0), new NumberCondition());
startState.addTransition(new WordSetCondition(iv_soloTextSet, true),
endState);
startState.addTransition(numberCondition, dosageState);
startState.addTransition(decimalCondition, dosageState);
startState.addTransition(rangeCondition, dosageState);
startState.addTransition(fractionRangeCondition, dosageState);
startState.addTransition(numberTextCondition, dosageState);
startState.addTransition(decimalStart, dosageState);
/*startState.addTransition(new DisjoinCondition(new StrengthCondition(),
new FormCondition()), formState);*/
startState.addTransition(new AnyCondition(), startState);
formState.addTransition(new WordSetCondition(iv_textNumberSet, true),
ntFalseTermState);
formState.addTransition(new AnyCondition(), startState);
dosageState.addTransition(strengthFormCondition, ntEndState);
dosageState
.addTransition(new PunctuationValueCondition('-'), hyphState);
dosageState.addTransition(new PunctuationValueCondition('('),
leftParenState);
dosageState.addTransition(new TextValueCondition("of", false), ofState);
dosageState.addTransition(new AnyCondition(), startState);
ofState.addTransition(new TextValueCondition("a", false), aState);
ofState.addTransition(new AnyCondition(), startState);
aState.addTransition(new DisjoinCondition(new RouteCondition(),
new FormCondition()), ntEndState);
aState.addTransition(new AnyCondition(), startState);
hyphState.addTransition(new WordSetCondition(iv_soloTextSet, true),
endState);
hyphState.addTransition(new NumberCondition(), numState);
hyphState.addTransition(new AnyCondition(), startState);
numState.addTransition(new DisjoinCondition(new RouteCondition(),
new FormCondition()), ntEndState);
numState.addTransition(new AnyCondition(), startState);
leftParenState.addTransition(new DisjoinCondition(
new RouteCondition(), new FormCondition()), ntEndState);
leftParenState.addTransition(new AnyCondition(), startState);
ntEndState.addTransition(new AnyCondition(), startState);
ntFalseTermState.addTransition(new AnyCondition(), startState);
endState.addTransition(new AnyCondition(), startState);
return m;
}
/**
* Executes the finite state machines.
*
* @param tokens
* @return Set of RangeToken objects.
* @throws Exception
*/
public Set execute(List tokens, Set overrideSet1, Set overrideSet2)
throws Exception {
Set measurementSet = new HashSet();
// maps a fsm to a token start index
// key = fsm , value = token start index
Map tokenStartMap = new HashMap();
Iterator overrideTokenItr1 = overrideSet1.iterator();
Iterator overrideTokenItr2 = overrideSet2.iterator();
// key = start offset, value = override BaseToken object
Map overrideTokenMap1 = new HashMap();
Map overrideTokenMap2 = new HashMap();
Map overrideBeginTokenMap1 = new HashMap();
Map overrideBeginTokenMap2 = new HashMap();
while (overrideTokenItr1.hasNext()) {
BaseToken t = (BaseToken) overrideTokenItr1.next();
Integer key = new Integer(t.getStartOffset());
overrideTokenMap1.put(key, t);
}
while (overrideTokenItr2.hasNext()) {
BaseToken t = (BaseToken) overrideTokenItr2.next();
Integer key = new Integer(t.getStartOffset());
overrideTokenMap2.put(key, t);
}
boolean overrideOn1 = false;
boolean overrideOn2 = false;
int overrideEndOffset1 = -1;
int overrideEndOffset2 = -1;
int tokenOffset1 = 0;
int tokenOffset2 = 0;
int anchorKey1 = 0;
int anchorKey2 = 0;
for (int i = 0; i < tokens.size(); i++) {
BaseToken token = (BaseToken) tokens.get(i);
Integer key = new Integer(token.getStartOffset());
if (overrideOn1 && overrideOn2) {
if (overrideEndOffset1 >= overrideEndOffset2)
overrideOn1 = false;
else
overrideOn2 = false;
}
if (overrideOn1) {
if (token.getStartOffset() >= overrideEndOffset1) {
if (tokenOffset1 > 0)
overrideBeginTokenMap1.put(new Integer(anchorKey1), new Integer(tokenOffset1));
overrideOn1 = false;
overrideEndOffset1 = -1;
} else {
tokenOffset1++;
// step to next iteration of for loop
continue;
}
} else if (overrideOn2) {
if (token.getStartOffset() >= overrideEndOffset2) {
if (tokenOffset2 > 0)
overrideBeginTokenMap2.put(new Integer(anchorKey2), new Integer(tokenOffset2));
overrideOn2 = false;
overrideEndOffset2 = -1;
} else {
tokenOffset2++;
// step to next iteration of for loop
continue;
}
} else {
if (overrideTokenMap1.containsKey(key)) {
// override one or more tokens until the override
// token is complete
anchorKey1 = key.intValue();
token = (BaseToken) overrideTokenMap1.get(key);
overrideOn1 = true;
overrideEndOffset1 = token.getEndOffset();
tokenOffset1 = 0;
}
if (overrideTokenMap2.containsKey(key)) {
// override one or more tokens until the override
// token is complete
anchorKey2 = key.intValue();
token = (BaseToken) overrideTokenMap2.get(key);
overrideOn2 = true;
overrideEndOffset2 = token.getEndOffset();
tokenOffset2 = 0;
}
}
Iterator machineItr = iv_machineSet.iterator();
while (machineItr.hasNext()) {
Machine fsm = (Machine) machineItr.next();
fsm.input(token);
State currentState = fsm.getCurrentState();
if (currentState.getStartStateFlag()) {
tokenStartMap.put(fsm, new Integer(i));
tokenOffset1 = 0;
tokenOffset2 = 0;
}
if (currentState.getEndStateFlag()) {
Object o = tokenStartMap.get(fsm);
int globalOffset = 0;
int tokenStartIndex;
if (o == null) {
// By default, all machines start with
// token zero.
tokenStartIndex = 0;
} else {
Integer tokenMap1 = new Integer(0);
Integer tokenMap2 = new Integer(0);
BaseToken lookUpOffset = (BaseToken) tokens.get(((Integer) o).intValue());
if (overrideBeginTokenMap1.get(new Integer(lookUpOffset.getStartOffset())) != null){
Integer offSet = (Integer) (overrideBeginTokenMap1.get(new Integer(lookUpOffset.getStartOffset())));
tokenMap1 = new Integer(offSet.intValue() + tokenMap1.intValue());
}
if (overrideBeginTokenMap2.get(new Integer(lookUpOffset.getStartOffset())) != null){
Integer offSet = (Integer) (overrideBeginTokenMap2.get(new Integer(lookUpOffset.getStartOffset())));
tokenMap2 = new Integer(offSet.intValue() + tokenMap2.intValue());
}
globalOffset = tokenMap1.intValue() + tokenMap2.intValue();
tokenStartIndex = ((Integer) o).intValue() + globalOffset;
// skip ahead over single token we don't want
tokenStartIndex++;
}
BaseToken startToken = null;
if (currentState instanceof IndentStartState) {
startToken = (BaseToken) tokens
.get(tokenStartIndex + 1);
} else {
startToken = (BaseToken) tokens.get(tokenStartIndex);
}
BaseToken endToken = token;
if (currentState instanceof NonTerminalEndState) {
endToken = (BaseToken) tokens.get(i - 1);
if (endToken instanceof PunctuationTokenAdapter) {
endToken = (BaseToken) tokens.get(i - 2);
}
} else {
endToken = token;
}
DosageToken measurementToken = new DosageToken(startToken
.getStartOffset(), endToken.getEndOffset());
measurementSet.add(measurementToken);
fsm.reset();
}
}
}
// cleanup
tokenStartMap.clear();
// reset machines
Iterator itr = iv_machineSet.iterator();
while (itr.hasNext()) {
Machine fsm = (Machine) itr.next();
fsm.reset();
}
return measurementSet;
}
/**
* Executes the finite state machines.
*
* @param tokens
* @return Set of RangeToken objects.
* @throws Exception
*/
public Set execute(List tokens, Set overrideSet) throws Exception {
Set measurementSet = new HashSet();
// maps a fsm to a token start index
// key = fsm , value = token start index
Map tokenStartMap = new HashMap();
Iterator overrideTokenItr = overrideSet.iterator();
// key = start offset, value = override BaseToken object
Map overrideTokenMap = new HashMap();
while (overrideTokenItr.hasNext()) {
BaseToken t = (BaseToken) overrideTokenItr.next();
Integer key = new Integer(t.getStartOffset());
overrideTokenMap.put(key, t);
}
boolean overrideOn = false;
int overrideEndOffset = -1;
for (int i = 0; i < tokens.size(); i++) {
BaseToken token = (BaseToken) tokens.get(i);
Integer key = new Integer(token.getStartOffset());
if (overrideOn) {
if (token.getStartOffset() >= overrideEndOffset) {
overrideOn = false;
overrideEndOffset = -1;
} else {
// step to next iteration of for loop
continue;
}
} else {
if (overrideTokenMap.containsKey(key)) {
// override one or more tokens until the override
// token is complete
token = (BaseToken) overrideTokenMap.get(key);
overrideOn = true;
overrideEndOffset = token.getEndOffset();
}
}
Iterator machineItr = iv_machineSet.iterator();
while (machineItr.hasNext()) {
Machine fsm = (Machine) machineItr.next();
fsm.input(token);
State currentState = fsm.getCurrentState();
if (currentState.getStartStateFlag()) {
tokenStartMap.put(fsm, Integer.valueOf(i));
}
if (currentState.getEndStateFlag()) {
Object o = tokenStartMap.get(fsm);
int tokenStartIndex;
if (o == null) {
// By default, all machines start with
// token zero.
tokenStartIndex = 0;
} else {
tokenStartIndex = ((Integer) o).intValue();
// skip ahead over single token we don't want
tokenStartIndex++;
}
BaseToken startToken = null;
if (currentState instanceof IndentStartState) {
startToken = (BaseToken) tokens
.get(tokenStartIndex + 1);
} else {
startToken = (BaseToken) tokens.get(tokenStartIndex);
}
BaseToken endToken = null;
if (currentState instanceof NonTerminalEndState) {
endToken = (BaseToken) tokens.get(i - 1);
if (endToken instanceof PunctuationTokenAdapter) {
endToken = (BaseToken) tokens.get(i - 2);
}
} else {
endToken = token;
}
// BaseToken endToken = token;
DosageToken measurementToken = new DosageToken(startToken
.getStartOffset(), endToken.getEndOffset());
measurementSet.add(measurementToken);
fsm.reset();
}
}
}
// cleanup
tokenStartMap.clear();
// reset machines
Iterator itr = iv_machineSet.iterator();
while (itr.hasNext()) {
Machine fsm = (Machine) itr.next();
fsm.reset();
}
return measurementSet;
}
}