/**
* 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.PunctuationValueCondition;
import org.apache.ctakes.core.fsm.condition.SymbolValueCondition;
import org.apache.ctakes.core.fsm.condition.WordSetCondition;
import org.apache.ctakes.core.fsm.state.NamedState;
import org.apache.ctakes.core.fsm.token.BaseToken;
import org.apache.ctakes.drugner.fsm.elements.conditions.ContainsSetTextValueCondition;
import org.apache.ctakes.drugner.fsm.output.elements.StrengthUnitCombinedToken;
import org.apache.ctakes.drugner.fsm.output.elements.StrengthUnitToken;
import org.apache.ctakes.drugner.fsm.states.util.IndentStartState;
import net.openai.util.fsm.AnyCondition;
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 StrengthUnitFSM {
// text fractions
Set<String> iv_fullTextSet = new HashSet();
Set iv_oneOfTwoTextSet = new HashSet();
Set iv_twoOfTwoTextSet = new HashSet();
private Machine iv_strengthMachine;
private Machine iv_strengthCombinedMachine;
private Set iv_machineSet = new HashSet();
/**
*
* Constructor
*
*/
public StrengthUnitFSM() {
iv_oneOfTwoTextSet.add("international");
iv_twoOfTwoTextSet.add("units");
iv_fullTextSet.add("micrograms");
iv_fullTextSet.add("microgram");
iv_fullTextSet.add("teaspoon");
iv_fullTextSet.add("teaspoons");
iv_fullTextSet.add("tablespoon");
iv_fullTextSet.add("tablespoons");
iv_fullTextSet.add("gram");
iv_fullTextSet.add("grams");
iv_fullTextSet.add("centigram");
iv_fullTextSet.add("centigrams");
iv_fullTextSet.add("milligram");
iv_fullTextSet.add("milligrams");
iv_fullTextSet.add("grain");
iv_fullTextSet.add("grains");
iv_fullTextSet.add("puffs");
iv_fullTextSet.add("puff");
iv_fullTextSet.add("unit");
iv_fullTextSet.add("units");
iv_fullTextSet.add("gtts");
iv_fullTextSet.add("ui");
iv_fullTextSet.add("iu");
iv_fullTextSet.add("meq");
iv_fullTextSet.add("mcg");
iv_fullTextSet.add("gr");
iv_fullTextSet.add("gm");
iv_fullTextSet.add("tsp");
iv_fullTextSet.add("tbsp");
iv_fullTextSet.add("g");
iv_fullTextSet.add("mg");
iv_fullTextSet.add("ou");
iv_strengthMachine = getStrengthMachine();
iv_strengthCombinedMachine = getStrengthCombinedMachine();
iv_machineSet.add(iv_strengthCombinedMachine);
iv_machineSet.add(iv_strengthMachine);
}
/**
* Handles a complex range of strength representations for the discovery of the combined
* quantity and unit value for this element. The following represents the range of strength
* types which are discovered:
* <ol>
* <li>250-mg</li>
* <li>two-puffs</li>
* <li>1-cc</li>
* <li>15.5 mg</li>
* <li>25.7-30.2 mg</li>
* </ol>
*/
private Machine getStrengthMachine(){
State startState = new NamedState("START");
State endState = new NamedState("END");
State unitState = new NamedState("UNIT");
State ntFalseTermState = new IndentStartState("NON TERMINAL START");
endState.setEndStateFlag(true);
ntFalseTermState.setEndStateFlag(true);
// startState.addTransition(new ContainsSetTextValueCondition(
// iv_fullTextSet, false), endState);
// startState.addTransition(new WordSetCondition(
// iv_fullTextSet, false), endState);
startState.addTransition(new WordSetCondition(iv_fullTextSet, false), endState);
startState.addTransition(new PunctuationValueCondition('-'), unitState);
startState.addTransition(new SymbolValueCondition('%'), endState);
startState.addTransition(new AnyCondition(), startState);
unitState.addTransition(new WordSetCondition(iv_fullTextSet, false), ntFalseTermState);
unitState.addTransition(new SymbolValueCondition('%'), endState);
unitState.addTransition(new AnyCondition(), startState);
ntFalseTermState.addTransition(new AnyCondition(), startState);
endState.addTransition(new AnyCondition(), startState);
Machine m = new Machine(startState);
return m;
}
/**
* Handles a complex range of strength representations for the discovery of the combined
* quantity and unit value for this element. The following represents the range of strength
* types which are discovered:
* <ol>
* <li>250mg</li>
* <li>1-cc</li>
* <li>0.4mg</li>
* <li>two-3.5mg</li>
* </ol>
*/
private Machine getStrengthCombinedMachine(){
State startState = new NamedState("START");
State endState = new NamedState("END");
State unitState = new NamedState("UNIT");
State ntFalseTermState = new IndentStartState("NON TERMINAL START");
endState.setEndStateFlag(true);
ntFalseTermState.setEndStateFlag(true);
startState.addTransition(new ContainsSetTextValueCondition(
iv_fullTextSet, false), endState);
// startState.addTransition(new WordSetCondition(
// iv_fullTextSet, false), endState);
//
// startState.addTransition(new WordSetCondition(iv_fullTextSet, false), endState);
startState.addTransition(new PunctuationValueCondition('-'), unitState);
startState.addTransition(new SymbolValueCondition('%'), endState);
startState.addTransition(new AnyCondition(), startState);
unitState.addTransition(new ContainsSetTextValueCondition(iv_fullTextSet, false), ntFalseTermState);
unitState.addTransition(new SymbolValueCondition('%'), endState);
unitState.addTransition(new AnyCondition(), startState);
ntFalseTermState.addTransition(new AnyCondition(), startState);
endState.addTransition(new AnyCondition(), startState);
Machine m = new Machine(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();
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) {
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) {
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 tokenStartIndex;
int globalOffset = 0;
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;
BaseToken endToken = token;
if (currentState instanceof IndentStartState) {
startToken = (BaseToken) tokens
.get(tokenStartIndex + 1);
} else {
startToken = (BaseToken) tokens.get(tokenStartIndex);
}
StrengthUnitToken measurementToken = null;
StrengthUnitCombinedToken measurementCombinedToken = null;
if (fsm.equals(iv_strengthCombinedMachine)) {
measurementCombinedToken = new StrengthUnitCombinedToken(startToken
.getStartOffset(), endToken.getEndOffset());
measurementSet.add(measurementCombinedToken);
}
else {
measurementToken = new StrengthUnitToken(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();
Map overrideBeginTokenMap = 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;
int tokenOffset = 0;
int anchorKey = 0;
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) {
if (tokenOffset > 0)
overrideBeginTokenMap.put(new Integer(anchorKey), new Integer(tokenOffset));
overrideOn = false;
overrideEndOffset = -1;
} else {
tokenOffset++;
// step to next iteration of for loop
continue;
}
} else {
if (overrideTokenMap.containsKey(key)) {
// override one or more tokens until the override
// token is complete
anchorKey = key.intValue();
token = (BaseToken) overrideTokenMap.get(key);
overrideOn = true;
overrideEndOffset = token.getEndOffset();
tokenOffset = 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));
tokenOffset = 0;
}
if (currentState.getEndStateFlag()) {
Object o = tokenStartMap.get(fsm);
int tokenStartIndex;
if (o == null) {
// By default, all machines start with
// token zero.
tokenStartIndex = 0;
} else {
Integer tokenMap = new Integer(0);
BaseToken lookUpOffset = (BaseToken) tokens.get(((Integer) o).intValue());
if (overrideBeginTokenMap.get(new Integer(lookUpOffset.getStartOffset())) != null){
Integer offSet = (Integer) (overrideBeginTokenMap.get(new Integer(lookUpOffset.getStartOffset())));
tokenMap = new Integer(offSet.intValue() + tokenMap.intValue());
}
tokenStartIndex = ((Integer) o).intValue() + tokenMap.intValue();
// skip ahead over single token we don't want
tokenStartIndex++;
}
BaseToken startToken = null;
BaseToken endToken = token;
if (currentState instanceof IndentStartState) {
startToken = (BaseToken) tokens
.get(tokenStartIndex + 1);
} else {
startToken = (BaseToken) tokens.get(tokenStartIndex);
}
StrengthUnitToken measurementToken = null;
StrengthUnitCombinedToken measurementCombinedToken = null;
if (fsm.equals(iv_strengthCombinedMachine)) {
measurementCombinedToken = new StrengthUnitCombinedToken(startToken
.getStartOffset(), endToken.getEndOffset());
measurementSet.add(measurementCombinedToken);
}
else {
measurementToken = new StrengthUnitToken(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;
}
}