> We also had issues in cTAKES 2.5.
> Here is the patch for 2.5. Before I got the patch to 3.0 Sean made his
> changes.
Thanks for verifying,
Sean
________________________________________
From: Kim Ebert [kim.eb...@perfectsearchcorp.com]
Sent: Friday, September 05, 2014 12:28 PM
To: dev@ctakes.apache.org; Finan, Sean
Subject: Re: Permutations
Hi Pei and Sean,
Sean, any thoughts about this would be helpful.
We also had issues in cTAKES 2.5.
Here is the patch for 2.5. Before I got the patch to 3.0 Sean made his
changes.
=== modified file
'src/edu/mayo/bmi/lookup/algorithms/FirstTokenPermutationImpl.java'
--- src/edu/mayo/bmi/lookup/algorithms/FirstTokenPermutationImpl.java
2012-11-28 01:56:50 +0000
+++ src/edu/mayo/bmi/lookup/algorithms/FirstTokenPermutationImpl.java
2013-02-06 16:39:37 +0000
@@ -294,14 +294,16 @@
Iterator mdhIterator = mdhSet.iterator();
while (mdhIterator.hasNext())
{
- MetaDataHit mdh = (MetaDataHit)
mdhIterator.next();
+ MetaDataHit mdh = (MetaDataHit)
mdhIterator.next();
+
+ List permutationSorted = (List)
((ArrayList)permutation).clone();
// figure out start and end offsets
- Collections.sort(permutation);
+ Collections.sort(permutationSorted);
int startOffset;
- if (permutation.size() > 0)
+ if (permutationSorted.size() > 0)
{
- int firstIdx = ((Integer)
permutation.get(0)).intValue();
+ int firstIdx = ((Integer)
permutationSorted.get(0)).intValue();
if (firstIdx <= firstTokenIndex.intValue())
{
firstIdx--;
@@ -322,9 +324,9 @@
}
int endOffset;
- if (permutation.size() > 0)
+ if (permutationSorted.size() > 0)
{
- int lastIdx = ((Integer)
permutation.get(permutation.size() - 1)).intValue();
+ int lastIdx = ((Integer)
permutationSorted.get(permutationSorted.size() - 1)).intValue();
if (lastIdx <= firstTokenIndex.intValue())
{
lastIdx--;
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 09/05/2014 10:17 AM, Pei Chen wrote:
> Hi Kim,
> Thanks for pointing that out.
> https://issues.apache.org/jira/browse/CTAKES-310 has been opened for
> this.
> If you commit the changes, we can see if we can include in the 3.2.1
> patch release.
> I was looking at the changelist for this file, and it may look like
> some of these optimizations may have been intentional by Sean so he
> may have some more insight in this bit of the logic.
>
> On Thu, Sep 4, 2014 at 6:22 PM, Kim Ebert
> <kim.eb...@perfectsearchcorp.com> wrote:
>> Hi All,
>>
>> I was reviewing the use of permutations, and I noticed that we sorted
>> the permutation list before creating the string to do the concept lookup
>> with. It also appears that we were sorting the object that was stored in
>> the parent list.
>>
>> I've made a few changes, and now it appears I can discover some
>> additional concepts based upon the permutations.
>>
>> Let me know what you think of the following changes.
>>
>> Thanks,
>>
>> Kim
>>
>> === modified file
>> 'ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java'
>> ---
>> ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java
>> 2014-07-31 22:00:48 +0000
>> +++
>> ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java
>> 2014-09-04 18:39:59 +0000
>> @@ -210,11 +210,12 @@
>> final List<List<Integer>> permutationList = iv_permCacheMap.get(
>> permutationIndex );
>> for ( List<Integer> permutations : permutationList ) {
>> // Moved sort and offset calculation from inner (per
>> MetaDataHit) iteration 2-21-2013 spf
>> - Collections.sort( permutations );
>> + List<Integer> permutationsSorted = (List)
>> ((ArrayList)permutations).clone();
>> + Collections.sort( permutationsSorted );
>> int startOffset = firstWordStartOffset;
>> int endOffset = firstWordEndOffset;
>> - if ( !permutations.isEmpty() ) {
>> - int firstIdx = permutations.get( 0 );
>> + if ( !permutationsSorted.isEmpty() ) {
>> + int firstIdx = permutationsSorted.get( 0 );
>> if ( firstIdx <= firstTokenIndex ) {
>> firstIdx--;
>> }
>> @@ -222,7 +223,7 @@
>> if ( firstToken.getStartOffset() < firstWordStartOffset ) {
>> startOffset = firstToken.getStartOffset();
>> }
>> - int lastIdx = permutations.get( permutations.size() - 1 );
>> + int lastIdx = permutationsSorted.get(
>> permutationsSorted.size() - 1 );
>> if ( lastIdx <= firstTokenIndex ) {
>> lastIdx--;
>> }
>>
>>
>> --
>> Kim Ebert
>> 1.801.669.7342
>> Perfect Search Corp
>> http://www.perfectsearchcorp.com/
>>
