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From Alaa al Barari <alaa.albar...@gmail.com>
Subject Re: passing information through pipleline.process
Date Tue, 14 Feb 2017 14:28:56 GMT
Thanks for your answer!

Do you want ctakes to never find codes from certain schemes during
processing?  yes exactly this is what I am shooting for, if I dont need
them at the moment I dont want them found. suppose I have icd10 and icd9, I
want it to not find icd9 when I am looking for 10 and nice versa.


On Tue, Feb 14, 2017 at 4:13 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi Alaa,
>
> I have a question for you.  Do you want ctakes to never find codes from
> certain schemes during processing?  Or do you want it to find them, but
> only return them when you request them explicitly after processing?
>
> > can I override process(final JCas jcas)
> That depends.  If you are subclassing an AE that declares it final you
> cannot override it. If it is declared final then there may be a reason.  In
> that case use composition.  If you need help, web search "composition over
> inheritance".  You may want to use composition anyway ...
>
> > its from UIMA library right
> Very close.  Process( JCas ) is from UimaFit while process (CAS ) is from
> uima.  Web search UimaFit or go to uima.apache.org for more information.
>
> > how can I pass an information like final ConceptCode ... createConcepts(
> final Collection<Long> cuiCodes, final ConceptCode
> conceptCode)
> Now you are getting into the fast-dictionary-lookup code that is in
> ctakes.  You probably don't want to override this.  Look at my question
> above.  What I am getting at is, if you only want ctakes to maintain a
> small list of schemes then you should just change the dictionary
> configuration file instead of delving into coding.  The configuration file
> is xml and lists the schemes in your database, one per line.  Just comment
> out the schemes that you don't want.
>
> As for a faster way to get codes of a different scheme, you are pretty
> much out of luck.  This is because the uima cas stores everything in an
> array.  To get items of interest ctakes has to go through the array and
> filter out whatever you don't want.  We try to do that as efficiently as
> possible, but we are tied to this array storage mechanism.
>
> Sean
>
>
>
> -----Original Message-----
> From: Alaa al Barari [mailto:alaa.albarari@gmail.com]
> Sent: Monday, February 13, 2017 3:40 AM
> To: dev@ctakes.apache.org
> Subject: passing information through pipleline.process
>
> Hi,
>
> I have around 16 different schemes, and the way I see it through ctakes,
> it gets the information for all schemes then filter the un wanted ones
> afterwards, this is a performance concern for me, so I am trying to modify
> ctakes to suite my needs.
>
> can I override process(final JCas jcas)  if yes then where and how ?  its
> from UIMA library right ? if not how can I pass an information like final
> ConceptCode from pipeline.process to createConcepts, my createConcepts now
> look like below :
> createConcepts( final Collection<Long> cuiCodes, final ConceptCode
> conceptCode) ?
>
> --
> Eng Alaa Al-Barari
> phone 0599297470
>



-- 
Eng Alaa Al-Barari
phone 0599297470

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