/**
* 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.IntegerCondition;
import org.apache.ctakes.core.fsm.condition.NegateCondition;
import org.apache.ctakes.core.fsm.condition.NumberCondition;
import org.apache.ctakes.core.fsm.condition.PunctuationValueCondition;
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.drugner.fsm.elements.conditions.FractionStrengthCondition;
import org.apache.ctakes.drugner.fsm.elements.conditions.RangeStrengthCondition;
import org.apache.ctakes.drugner.fsm.elements.conditions.StrengthUnitCombinedCondition;
import org.apache.ctakes.drugner.fsm.elements.conditions.StrengthUnitCondition;
import org.apache.ctakes.drugner.fsm.output.elements.StrengthToken;
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 StrengthFSM {
// text fractions
//Mayo SPM 2/20/2012 Changed due to separation of strength tokens
//Set iv_fullTextSet = new HashSet();
Set iv_numberTextSet = new HashSet();
// Set iv_oneOfTwoTextSet = new HashSet();
// Set iv_twoOfTwoTextSet = new HashSet();
private Machine iv_strengthMachine;
private Set iv_machineSet = new HashSet();
/**
*
* Constructor
*
*/
public StrengthFSM() {
iv_numberTextSet.add("one");
iv_numberTextSet.add("two");
iv_numberTextSet.add("three");
iv_numberTextSet.add("four");
iv_numberTextSet.add("five");
iv_numberTextSet.add("six");
iv_numberTextSet.add("seven");
iv_numberTextSet.add("eight");
iv_numberTextSet.add("nine");
//Mayo SPM 2/20/2012 Changed due to separation of strength tokens
iv_strengthMachine = getStrengthMachine();
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>0.4mg</li>
* <li>0.51milligrams</li>
* <li>25.7/30.4mg</li>
* <li>15.5 mg</li>
* <li>25.7-30.2 mg</li>
* <li>two-3.5mg</li>
* </ol>
*/
private Machine getStrengthMachine(){
State startState = new NamedState("START");
State endState = new NamedState("END");
State connectState = new NamedState("CONNECT");
State unitState = new NamedState("UNIT");
State decimalState = new NamedState("DOT");
State complexState = new NamedState("COMPLEX");
State hyphenState = new NamedState("HYPHEN");
State dateState = new NamedState("DATE");
State ntEndState = new NonTerminalEndState("NON TERMINAL END");
State ntEndHyphState = new NonTerminalEndState("NON TERMINAL HYPH END");
endState.setEndStateFlag(true);
ntEndState.setEndStateFlag(true);
ntEndHyphState.setEndStateFlag(true);
startState.addTransition(new RangeStrengthCondition(), endState);
startState.addTransition(new FractionStrengthCondition(), dateState);
startState.addTransition(new NumberCondition(), connectState);
startState.addTransition(new IntegerCondition(), connectState);
startState.addTransition(new DecimalCondition(), connectState);
startState.addTransition(new WordSetCondition(iv_numberTextSet, false), connectState);
//Mayo SPM 2/20/2012 Changed due to separation of strength tokens
// startState.addTransition(new StrengthUnitCondition(), ntEndState);
startState.addTransition(new StrengthUnitCombinedCondition(), endState);
startState.addTransition(new AnyCondition(), startState);
dateState.addTransition(new NegateCondition( new PunctuationValueCondition('/')), connectState);
dateState.addTransition(new AnyCondition(), startState);
//Mayo SPM 2/20/2012 Changed due to separation of strength tokens
connectState.addTransition(new StrengthUnitCondition(), ntEndState);
connectState.addTransition(new StrengthUnitCombinedCondition(), endState);
connectState.addTransition(new PunctuationValueCondition('-'), unitState);
connectState.addTransition(new PunctuationValueCondition('.'), decimalState);
connectState.addTransition(new AnyCondition(), startState);
//Mayo SPM 2/20/2012 Changed due to separation of strength tokens
decimalState.addTransition(new StrengthUnitCondition(), ntEndState);
decimalState.addTransition(new StrengthUnitCombinedCondition(), endState);
decimalState.addTransition(new PunctuationValueCondition('-'), unitState);
decimalState.addTransition(new NumberCondition(), complexState);
decimalState.addTransition(new AnyCondition(), startState);
//Mayo SPM 2/20/2012 Changed due to separation of strength tokens
unitState.addTransition(new StrengthUnitCondition(), ntEndHyphState);
unitState.addTransition(new StrengthUnitCombinedCondition(), endState);
unitState.addTransition(new AnyCondition(), startState);
complexState.addTransition(new PunctuationValueCondition('-'), hyphenState);
complexState.addTransition(new AnyCondition(), startState);
//Mayo SPM 2/20/2012 Changed due to separation of strength tokens
hyphenState.addTransition(new StrengthUnitCondition(), ntEndHyphState);
hyphenState.addTransition(new AnyCondition() , startState);
ntEndHyphState.addTransition(new AnyCondition(), startState);
ntEndState.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 = (BaseToken) tokens.get(tokenStartIndex);
BaseToken endToken = null;
if (currentState instanceof NonTerminalEndState && i > 0) {
if (!currentState.getName().contentEquals("NON TERMINAL HYPH END"))
endToken = (BaseToken) tokens.get(i - 1);
else if (i > 1)
endToken = (BaseToken) tokens.get(i - 2);
} else {
endToken = token;
}
/*if (fsm.equals(iv_strengthMachine)){
startToken = (BaseToken) tokens .get(tokenStartIndex+1);
} else {*/
// startToken = (BaseToken) tokens.get(tokenStartIndex);
//}
StrengthToken measurementToken = new StrengthToken(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 = (BaseToken) tokens
.get(tokenStartIndex);
BaseToken endToken = null;
if (currentState instanceof NonTerminalEndState && i > 0) {
if (!currentState.getName().contentEquals("NON TERMINAL HYPH END"))
endToken = (BaseToken) tokens.get(i - 1);
else if (i > 0)
endToken = (BaseToken) tokens.get(i - 2);
} else {
endToken = token;
}
/*if (fsm.equals(iv_strengthMachine)){
startToken = (BaseToken) tokens .get(tokenStartIndex+1);
} else {*/
// startToken = (BaseToken) tokens.get(tokenStartIndex);
//}
StrengthToken measurementToken = new StrengthToken(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) throws Exception {
Set measurementSet = new HashSet();
// maps a fsm to a token start index
// key = fsm , value = token start index
Map tokenStartMap = new HashMap();
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());
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());
tokenStartIndex = ((Integer) o).intValue() + tokenMap.intValue();
// skip ahead over single token we don't want
tokenStartIndex++;
}
BaseToken startToken = (BaseToken) tokens
.get(tokenStartIndex);
BaseToken endToken = null;
if (currentState instanceof NonTerminalEndState && i > 0) {
if (!currentState.getName().contentEquals("NON TERMINAL HYPH END"))
endToken = (BaseToken) tokens.get(i - 1);
else if (i > 0)
endToken = (BaseToken) tokens.get(i - 2);
} else {
endToken = token;
}
/*if (fsm.equals(iv_strengthMachine)){
startToken = (BaseToken) tokens .get(tokenStartIndex+1);
} else {*/
// startToken = (BaseToken) tokens.get(tokenStartIndex);
//}
StrengthToken measurementToken = new StrengthToken(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;
}
}