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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: passing information through pipleline.process
Date Tue, 14 Feb 2017 14:33:58 GMT
Go into resources/org/apache/ctakes/dictionary/lookup/fast/ and edit your xml configuration
file.  Comment out the 2 lines that have icd9 listed as desired schemes.  That should do it.

The configuration file basically tells ctakes what is in your dictionary database.  If you
comment those lines then it will think that there is no icd9 table in your database.  It won't
bother to look up icd9 codes or store icd9 codes in the cas.  So, icd9 codes will not be in
the array - no filtering is necessary and the iteration is shorter.

Sean

-----Original Message-----
From: Alaa al Barari [mailto:alaa.albarari@gmail.com] 
Sent: Tuesday, February 14, 2017 9:29 AM
To: dev@ctakes.apache.org
Subject: Re: passing information through pipleline.process

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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