/**
* 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.padtermspotter.fsm.pad.machine;
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.TextSetCondition;
import org.apache.ctakes.core.fsm.condition.WordValueCondition;
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.padtermspotter.fsm.output.SubSectionIndicator;
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 sub-sections in the given input of
* tokens.
* - terms; "smh","rmh","gonda","romayo" are indicative of names of buildings on the Mayo campus which are used to mark
* subsection begin/end
* - terms; "indications","bleindications","exam","showing" are special terms which often contain the terms being screened for
* relating to PAD, but since they are titles of examinations, revision sections, and generalized screenings they are to be
* ignored in the Mayo cohort.
*
* @author Mayo Clinic
*/
public class SubSectionPadIdFSM {
// contains the finite state machines
private Set<Machine>iv_machineSet = new HashSet<Machine>();
private Set<String>iv_probableSubSet = new HashSet<String>();
private Set<String>iv_probableSubSetNL = new HashSet<String>();
private Set<String>iv_probableSubBeginSet = new HashSet<String>();
private Set<String>iv_probableSubEndSet = new HashSet<String>();
private Set<String>iv_negateSubSet = new HashSet<String>();
private Set<String>iv_confirmedSubBeginSet = new HashSet<String>();
private Set<String>iv_confirmedSubNextSet = new HashSet<String>();
private Set<String>iv_confirmedSubTailSet = new HashSet<String>();
private Set<String> iv_confirmedSpecialFirstSubSet = new HashSet<String>();
private Set<String> iv_confirmedSpecialNextSubSet = new HashSet<String>();
private Machine iv_subSectionIDConfirmMachine = new Machine();
private Machine iv_subSectionIDProbableMachine = new Machine();
private Machine iv_subSectionIDNegateMachine = new Machine();
/**
*
* Constructor
*
*/
public SubSectionPadIdFSM() {
iv_probableSubSet.add("left");
iv_probableSubSet.add("right");
iv_probableSubSet.add("cta");
iv_probableSubSet.add("reconstructions");
iv_probableSubSet.add("pelvis");
iv_probableSubSet.add("impression");
iv_probableSubSet.add("summary");
iv_probableSubSet.add("analysis");
iv_probableSubSetNL.add("smh");// Mayo Clinic specific term *Site*
iv_probableSubSetNL.add("rmh");// Mayo Clinic specific term *Site*
iv_probableSubSetNL.add("gonda");// Mayo Clinic specific term *Site*
iv_probableSubSetNL.add("romayo");// Mayo Clinic specific term *Site*
iv_probableSubBeginSet.add("original");
iv_probableSubBeginSet.add("additional");
iv_probableSubEndSet.add("report");
iv_probableSubEndSet.add("findings");
iv_negateSubSet.add("indications");// Mayo Clinic specific term *Header*
iv_negateSubSet.add("bleindications");// Mayo Clinic specific term *Header*
iv_negateSubSet.add("exam");// Mayo Clinic specific term *Header*
iv_negateSubSet.add("showing");// Mayo Clinic specific term *Header*
iv_confirmedSubBeginSet.add("right");
iv_confirmedSubBeginSet.add("left");
iv_confirmedSubBeginSet.add("runoff");
iv_confirmedSubBeginSet.add("bilateral");
iv_confirmedSubBeginSet.add("lower");
iv_confirmedSubBeginSet.add("ultrasound");
iv_confirmedSubBeginSet.add("v");
iv_confirmedSubNextSet.add("&");
iv_confirmedSubNextSet.add("leg");
iv_confirmedSubNextSet.add("lower");
iv_confirmedSubNextSet.add("extremity");
iv_confirmedSubNextSet.add("extrem");
iv_confirmedSubNextSet.add("examination");
iv_confirmedSubNextSet.add("evaluation");
iv_confirmedSubTailSet.add("extremity");
iv_confirmedSubTailSet.add("extremities");
iv_confirmedSubTailSet.add("extrem");
iv_confirmedSubTailSet.add("artery");
iv_confirmedSubTailSet.add("art");
iv_confirmedSubTailSet.add("of");
iv_confirmedSubTailSet.add("irad");
iv_confirmedSpecialFirstSubSet.add("graft");
iv_confirmedSpecialNextSubSet.add("art");
iv_subSectionIDConfirmMachine = getConfirmSubSectionMachine();
iv_subSectionIDNegateMachine = getNegateSubSectionMachine();
iv_subSectionIDProbableMachine = getProbableSubSectionMachine();
iv_machineSet.add(iv_subSectionIDConfirmMachine);
iv_machineSet.add(iv_subSectionIDNegateMachine);
iv_machineSet.add(iv_subSectionIDProbableMachine);
}
public Set<SubSectionIndicator> execute(List<? extends BaseToken> tokens) throws Exception {
Set<SubSectionIndicator> outSet = new HashSet<SubSectionIndicator>();
// maps a fsm to a token start index
// key = fsm , value = token start index
Map<Machine, Integer> tokenStartMap = new HashMap<Machine, Integer> ();
for (int i = 0; i < tokens.size(); i++) {
BaseToken token = (BaseToken) tokens.get(i);
Iterator<Machine> 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));
}
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 endToken = null;
if (currentState instanceof NonTerminalEndState) {
endToken = (BaseToken) tokens.get(i - 1);
} else {
endToken = token;
}
BaseToken startToken = (BaseToken) tokens
.get(tokenStartIndex);
SubSectionIndicator subs = null;
if (fsm.equals(iv_subSectionIDConfirmMachine)) {
subs = new SubSectionIndicator(startToken
.getStartOffset(), endToken.getEndOffset(),
SubSectionIndicator.CONFIRMED_STATUS);
} else if (fsm.equals(iv_subSectionIDNegateMachine)) {
subs = new SubSectionIndicator(startToken
.getStartOffset(), endToken.getEndOffset(),
SubSectionIndicator.NEGATED_STATUS);
} else if (fsm.equals(iv_subSectionIDProbableMachine)) {
subs = new SubSectionIndicator(startToken
.getStartOffset(), endToken.getEndOffset(),
SubSectionIndicator.PROBABLE_STATUS);
}
outSet.add(subs);
fsm.reset();
}
}
}
// cleanup
tokenStartMap.clear();
// reset machines
Iterator<Machine> itr = iv_machineSet.iterator();
while (itr.hasNext()) {
Machine fsm = (Machine) itr.next();
fsm.reset();
}
return outSet;
}
private Machine getConfirmSubSectionMachine() {
State startState = new NamedState("START");
State endState = new NamedState("END");
State medState = new NamedState("MED");
State tailState = new NamedState("TAIL");
State caseState = new NamedState("COLON");
State nonCaseState = new NamedState("NOCOLON");
State fslashState = new NamedState("FSLASH");
State orState = new NamedState("OR");
State altTailState = new NamedState("ALTTAIL");
State finishAltState = new NamedState("EXTREMITY");
State ntEndState = new NonTerminalEndState("NON TERMINAL END");
endState.setEndStateFlag(true);
ntEndState.setEndStateFlag(true);
Machine m = new Machine(startState);
Condition subFirstBegin = new TextSetCondition(iv_confirmedSubBeginSet,
false);
Condition subFirstNext = new TextSetCondition(iv_confirmedSubNextSet,
false);
Condition subFirstTail = new TextSetCondition(iv_confirmedSubTailSet,
false);
Condition altSubFirstBegin = new TextSetCondition(iv_confirmedSubBeginSet,
false);
Condition altSubFirstNext = new TextSetCondition(iv_confirmedSubNextSet,
false);
Condition altSubFirstTail = new TextSetCondition(iv_confirmedSubTailSet,
false);
Condition subSecondBegin = new TextSetCondition(iv_confirmedSpecialFirstSubSet,
false);
Condition subSecondNext = new TextSetCondition(iv_confirmedSpecialNextSubSet,
false);
startState.addTransition(subFirstBegin, medState);
startState.addTransition(new AnyCondition(), startState);
medState.addTransition(new PunctuationValueCondition(':'), endState);
medState.addTransition(subFirstNext, tailState);
medState.addTransition(new SymbolValueCondition('&'), tailState);
medState.addTransition(new PunctuationValueCondition('&'), tailState);
medState.addTransition(new AnyCondition(), startState);
tailState.addTransition(new PunctuationValueCondition(':'), endState);
tailState.addTransition(subFirstTail, caseState);
tailState.addTransition(new AnyCondition(), startState);
caseState.addTransition(new WordValueCondition("and", false), nonCaseState);
caseState.addTransition(new WordValueCondition("the", false), nonCaseState);
caseState.addTransition(new PunctuationValueCondition(':'), endState);
caseState.addTransition(new PunctuationValueCondition('-'), endState);
caseState.addTransition(new AnyCondition(), startState);
nonCaseState.addTransition(new PunctuationValueCondition('/'), fslashState);
nonCaseState.addTransition(altSubFirstBegin, altTailState);
nonCaseState.addTransition(new AnyCondition(), startState);
altTailState.addTransition(altSubFirstNext, finishAltState);
altTailState.addTransition(new AnyCondition(), startState);
finishAltState.addTransition(altSubFirstTail, endState);
finishAltState.addTransition(new AnyCondition(), startState);
fslashState.addTransition(new WordValueCondition("or", false), orState);
fslashState.addTransition(subSecondBegin, orState);
fslashState.addTransition(new AnyCondition(), startState);
orState.addTransition(subSecondNext, endState);
orState.addTransition(new AnyCondition(), startState);
endState.addTransition(new AnyCondition(), startState);
return m;
}
private Machine getProbableSubSectionMachine() {
State startState = new NamedState("START");
State endState = new NamedState("END");
State nonCaseState = new NamedState("NOCOLON");
State casenState = new NamedState("COLON");
State ntEndState = new NonTerminalEndState("NON TERMINAL END");
endState.setEndStateFlag(true);
ntEndState.setEndStateFlag(true);
Machine m = new Machine(startState);
Condition subFirstSolo = new TextSetCondition(iv_probableSubSet,
false);
Condition subFirstBegin = new TextSetCondition(iv_probableSubBeginSet,
false);
Condition subFirstEnd = new TextSetCondition(iv_probableSubEndSet,
false);
Condition subFirstSoloNL = new TextSetCondition(iv_probableSubSetNL,
false);
startState.addTransition(subFirstSolo, casenState);
startState.addTransition(subFirstBegin, nonCaseState);
startState.addTransition(subFirstSoloNL, ntEndState);
startState.addTransition(new AnyCondition(), startState);
nonCaseState.addTransition(subFirstEnd, endState);
nonCaseState.addTransition(new AnyCondition(), startState);
casenState.addTransition(new PunctuationValueCondition(':'), endState);
casenState.addTransition(new AnyCondition(), startState);
endState.addTransition(new AnyCondition(), startState);
return m;
}
private Machine getNegateSubSectionMachine() {
State startState = new NamedState("START");
State endState = new NamedState("END");
State caseState = new NamedState("COLON");
State nonCaseState = new NamedState("NOCOLON");
State ntEndState = new NonTerminalEndState("NON TERMINAL END");
endState.setEndStateFlag(true);
ntEndState.setEndStateFlag(true);
Machine m = new Machine(startState);
Condition subFirstBegin = new TextSetCondition(iv_negateSubSet,
false);
startState.addTransition(subFirstBegin, caseState);
startState.addTransition(new AnyCondition(), startState);
caseState.addTransition(new PunctuationValueCondition(':'), endState);
caseState.addTransition(new WordValueCondition("revision", false), nonCaseState);
caseState.addTransition(new AnyCondition(), startState);
nonCaseState.addTransition(new WordValueCondition("changes", false), endState);
nonCaseState.addTransition(new AnyCondition(), startState);
endState.addTransition(new AnyCondition(), startState);
return m;
}
}