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From kishore <kasaraneni.kish...@gmail.com>
Subject Re: Sectionheadings are not coming properly [EXTERNAL]
Date Tue, 02 Jan 2018 11:43:32 GMT
Hi Sean,
            Thanks allot, as you mentioned I have document like this
"SOCIAL HISTORY:  Patient is reticent and withdrawn .". I removed eol($),
now its working. I am able to read annotations section wise.
            I have another question. Right now my code is like this
            String note = "Hello World!  I feel no pain.  My father takes
aspirin.  My sister might have a headache.";
            JCas jcas = JCasFactory.createJCas();
            AggregateBuilder builder = new AggregateBuilder();
            Map<Segment,Collection<IdentifiedAnnoation>> annotationSections

JCasUtil.indexCovered( jCas, Segment.class, IdentifiedAnnotation.class );

for ( Map.Entry<Segment,Collection<IdentifiedAnnotation>> entry :
annotationSections.entrySet() ){



          I am able to run this code for single document. can we run this
for Multiple documents. How can we get JCas object for each document to
pass it for JCasUtil.indexCovered(....);
Thank you,

On Fri, Dec 29, 2017 at 9:45 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi Kishore,
> From what you can tell, is there anything in your section headers that may
> not fit the regex?  Are they all on a line by themselves?  That is one
> requirement for section headers in that pipeline.  For instance, this will
> not work:
> SOCIAL HISTORY:  Patient is reticent and withdrawn ...
> If this is the case then you can try making a copy of the regex bsv file
> and remove the eol requirement in each section regex.  If this is the
> problem then we should probably consider adding the second regex (no eol)
> type as an option.
> Another thing that wouldn't work is if the section headers have a prefix
> of some sort, for instance an enumeration.
> Patient is reticent and withdrawn ...
> ...
> Another possibility is that the regex requires an empty line above each
> section header.  I am not sure if this is the case or not - I don't have
> ctakes open at this moment.
> Lastly, do you see any "regex timed out" messages in your log?  If the
> note is particularly long then the regex may time out on more complex
> patterns.  If that is the case then we can make the timeout variable and
> you can retry with different values.
> Sean
> -----Original Message-----
> From: kishore [mailto:kasaraneni.kishore@gmail.com]
> Sent: Friday, December 29, 2017 4:46 AM
> To: dev@ctakes.apache.org
> Subject: Sectionheadings are not coming properly [EXTERNAL]
> Hello All,
>         I am new to the community. to identify Sectionheadings I am using
> AdvancedTokenizerPipeline.piper in my program. In segment annotation, it
> is showing "Family History:" only. In my document I have many other
> headings like "REVIEW OF SYSTEMS:","SOCIAL HISTORY:". I have seen regex
> pattern for them in DefaultSectionRegex.bsv. Can anyone help me in this.
> Thanks and Regards,
> Kishore.

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