OK thanks, that clarifies it (including Sean's concern) for me. I think
calling it getSortedLookupTokens is the right idea. Then it makes it
clear to the implementing class that at some point sorting has to be
done, and if its not implicit/free in the implementation (as it is if
you base it on Annotations), then it needs to be explicit. Since that
can be a substantial performance penalty, putting the onus on the
implementation will hopefully lead to better implementations.
So to summarize the changes to make sure we're on the same page:
* the interface will add a method:
public List getSortedLookupTokens(JCas, Annotation);
* getLookupTokenIterator() will be reverted to its old version.
* FirstTokenPermLookupInitializerImpl will have its
getLookupTokenIterator method reverted, and my changes
will go in the implementation of getSortedLookupTokens() modulo the
unnecessary iterator inside.
* DictionaryLookupAnnotator will be changed to call
getSortedLookupTokens instead of
getLookupTokenIterator/constrainToWindow
* Other LookupInitializer's will be implemented to simply call
existing getLookupTokenIterator and do post-processing to constrain
to the window (?)
Does this match what you had in mind James? Any objections or things
I'm missing anyone?
On 02/05/2013 10:38 AM, Masanz, James J. wrote:
First, about the loop - I had been looking too quickly at the diff and didn't
notice the logic about punctuation etc
Second, what I remember when I looked at it before, was seeing interface named
LookupInitializer, which being old enough, doesn't have Iterator parameterized
in the definition of the getLookupTokenIterator:
public Iterator getLookupTokenIterator(JCas jcas)
throws AnnotatorInitializationException;
and that ends up being effectively an Iterator<LookupToken> and LookupToken
does not inherit from Annotation, and I stopped at that point.
But now looking farther, it looks to me that that's fine because in
FirstTokenPermLookupInitializerImpl, we look through the BaseTokens and create
the list of LookupTokens based on the (sorted) BaseTokens, so the LookupTokens
will be sorted too.
so maybe we should call the new method getSortedLookupTokens to make it clear
they too are sorted
________________________________________
From: ctakes-dev-return-1146-Masanz.James=mayo....@incubator.apache.org
[ctakes-dev-return-1146-Masanz.James=mayo....@incubator.apache.org] on behalf
of Tim Miller [[email protected]]
Sent: Tuesday, February 05, 2013 9:10 AM
To: [email protected]
Subject: Re: assistance with dictionary lookup issue
Yeah, if you mean just change the loop to iterate over the list instead
of getting an iterator that makes sense. There is still some logic in
there to leave out punctuation tokens but I think you were implying that
to be in your mockup diff.
As for sorting, the AnnotationIndex defines a sort order for its iterators:
http://uima.apache.org/d/uimaj-2.4.0/apidocs/org/apache/uima/cas/text/AnnotationIndex.html
so we are safe assuming that anything extending Annotation will be
iterated in sorted order. Does that answer the questions we had? Or was
I missing something subtle in that discussion?
Tim
On 02/05/2013 09:44 AM, Masanz, James J. wrote:
Looks good to me, with one question.
Instead of getting an iterator and then building a new list, can we just skip
getting the iterator and use the list that selectCovered returns?
I will mock up a diff here of what I mean:
- Iterator btaItr = org.uimafit.util.JCasUtil.selectCovered(jcas,
BaseToken.class, covering).iterator();
- while (btaItr.hasNext())
- {
- BaseToken bta = (BaseToken) btaItr.next();
- ltList.add(lt);
- }
- }
+ ltList = org.uimafit.util.JCasUtil.selectCovered(jcas, BaseToken.class,
covering);
return ltList;
I know you said it was quick and dirty at the moment - my 2 cents - unless
someone comes up with a better engineered solution, I think we could add the
new method (with a name like getLookupTokens) and leave the old one so we don't
have to deprecate anything. And phase in the change to the various
*LookupInitializerImpl classes if needed.
-- James
-----Original Message-----
From: ctakes-dev-return-1138-Masanz.James=mayo....@incubator.apache.org
[mailto:ctakes-dev-return-1138-Masanz.James=mayo....@incubator.apache.org]
On Behalf Of Masanz, James J.
Sent: Monday, February 04, 2013 4:01 PM
To: [email protected]
Subject: RE: assistance with dictionary lookup issue
I'll take a look at the patch. Also be aware of
https://issues.apache.org/jira/browse/CTAKES-31 which talks about a way of
enhancing performance -- if willing to assume annotations (BaseTokens
currently) are sorted. Currently it's always BaseToken and always sorted,
just not sure if we want to code to that assumption.
________________________________________
From: ctakes-dev-return-1137-Masanz.James=mayo....@incubator.apache.org
[ctakes-dev-return-1137-Masanz.James=mayo....@incubator.apache.org] on
behalf of Tim Miller [[email protected]]
Sent: Monday, February 04, 2013 3:43 PM
To: [email protected]
Subject: assistance with dictionary lookup issue
Pei helped me track down an issue with performance I'd noticed in the
dictionary annotator, and I have filed the issue here:
https://issues.apache.org/jira/browse/CTAKES-143
I implemented a quick and dirty proof of concept fix and noticed dramatic
performance improvement. I attached the patch to the issue, but it
involves changing an interface (currently does not try to fix other
implementing classes so obviously not ready for primetime), so I wanted to
solicit the list first in case anyone with better knowledge of that module
has some better engineering ideas than what I came up with.
Thanks,
--
Tim Miller, PhD
Postdoctoral Research Fellow
Children's Hospital Informatics Program
Children's Hospital Boston and Harvard Medical School
617-919-1223
