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"SOCIAL HISTORY: Patient is reticent and withdrawn .".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();
jcas.setDocumentText(note);
AggregateBuilder builder = new AggregateBuilder();
builder.add..........
.........
.........
SimplePipeline.runPipeline(jcas,
builder.createAggregateDescription());
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,
Kishore.
On Fri, Dec 29, 2017 at 9:45 PM, Finan, Sean <
[email protected]> 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 SOCIAL HISTORY: Patient is reticent and withdrawn ...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.
>
> 1) SOCIAL HISTORY:
> Patient is reticent and withdrawn ...
>
> 2) REVIEW OF SYMPTOMS:
> ...
>
> 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:[email protected]]
> Sent: Friday, December 29, 2017 4:46 AM
> To: [email protected]
> 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.
>
