/**
* 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.WordSetCondition;
import org.apache.ctakes.core.fsm.state.NamedState;
import org.apache.ctakes.core.fsm.token.BaseToken;
import org.apache.ctakes.drugner.fsm.output.elements.FormToken;
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 form tokens in the given
* input of tokens.
* @author Mayo Clinic
*/
public class FormFSM {
// text fractions
Set iv_fullTextSet = new HashSet();
// contains the finite state machines
private Set iv_machineSet = new HashSet();
/**
*
* Constructor
*
*/
public FormFSM() {
iv_fullTextSet.add("cream");
iv_fullTextSet.add("creams");
iv_fullTextSet.add("patch");
iv_fullTextSet.add("patches");
iv_fullTextSet.add("tablet");
iv_fullTextSet.add("tablets");
iv_fullTextSet.add("capsules");
iv_fullTextSet.add("capsule");
iv_fullTextSet.add("caplets");
iv_fullTextSet.add("nebulizer");
iv_fullTextSet.add("supplementation");
iv_fullTextSet.add("supplement");
iv_fullTextSet.add("cap");
iv_fullTextSet.add("caps");
iv_fullTextSet.add("tabs");
iv_fullTextSet.add("tab");
iv_fullTextSet.add("aerosol");
iv_fullTextSet.add("elixir");
iv_fullTextSet.add("emulsion");
iv_fullTextSet.add("enema");
iv_fullTextSet.add("gel");
iv_fullTextSet.add("implant");
iv_fullTextSet.add("inhalant");
iv_fullTextSet.add("injection");
iv_fullTextSet.add("liquid");
iv_fullTextSet.add("lotion");
iv_fullTextSet.add("lozenge");
iv_fullTextSet.add("lozenges");
iv_fullTextSet.add("ointment");
iv_fullTextSet.add("packet");
iv_fullTextSet.add("packets");
iv_fullTextSet.add("pill");
iv_fullTextSet.add("pills");
iv_fullTextSet.add("powder");
iv_fullTextSet.add("shampoo");
iv_fullTextSet.add("soap");
iv_fullTextSet.add("unit");
iv_fullTextSet.add("units");
iv_fullTextSet.add("solution");
iv_fullTextSet.add("spray");
iv_fullTextSet.add("suppository");
iv_fullTextSet.add("syrup");
iv_fullTextSet.add("drop");
iv_fullTextSet.add("drops");
iv_fullTextSet.add("dl");
iv_fullTextSet.add("cl");
iv_fullTextSet.add("cc");
iv_fullTextSet.add("ml");
iv_fullTextSet.add("liter");
iv_fullTextSet.add("liters");
iv_fullTextSet.add("centiliter");
iv_fullTextSet.add("centiliters");
iv_fullTextSet.add("milliliter");
iv_fullTextSet.add("milliliters");
iv_machineSet.add(getFormMachine());
}
/**
- * Gets a finite state machine that detects the following:
* <ol>
* <li>tablet</li>
* <li>caps</li>
* </ol>
* @return
*/
private Machine getFormMachine() {
State startState = new NamedState("START");
State endState = new NamedState("END");
endState.setEndStateFlag(true);
Machine m = new Machine(startState);
Condition fullTextCondition = new WordSetCondition(iv_fullTextSet,
false);
startState.addTransition(fullTextCondition, endState);
startState.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 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 = (BaseToken) tokens
.get(tokenStartIndex);
BaseToken endToken = token;
FormToken measurementToken = new FormToken(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 FractionToken objects.
* @throws Exception
*/
public List execute(List tokens) throws Exception {
// maps a fsm to a token start index
// key = fsm , value = token start index
Map tokenStartMap = new HashMap();
for (int i = 0; i < tokens.size(); i++) {
Object token = tokens.get(i);
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++;
}
tokens.remove(o);
fsm.reset();
}
}
}
// cleanup
tokenStartMap.clear();
// reset machines
Iterator itr = iv_machineSet.iterator();
while (itr.hasNext()) {
Machine fsm = (Machine) itr.next();
fsm.reset();
}
return tokens;
}
}