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From "Sean Finan (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-450) CDASegmentAnnotator misses all headings after empty segment
Date Thu, 28 Sep 2017 13:46:00 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-450?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16184195#comment-16184195
] 

Sean Finan commented on CTAKES-450:
-----------------------------------

Hi Kean,  Have you had a chance to test the patch?

> CDASegmentAnnotator misses all headings after empty segment
> -----------------------------------------------------------
>
>                 Key: CTAKES-450
>                 URL: https://issues.apache.org/jira/browse/CTAKES-450
>             Project: cTAKES
>          Issue Type: Bug
>          Components: ctakes-core
>            Reporter: Kean Kaufmann
>         Attachments: CDASegmentAnnotator.diff, CDASegmentAnnotator-empty-segment.CTAKES-450.svn.patch
>
>
> If the CDASegmentAnnotator encounters an empty segment, it throws away everything after
that in the document.  You can see this in the test document provided for TestCDASegmentAnnotator.
The heading "CURRENT HEALTH STATUS" is followed immediately by the heading "Medications";
the test case misses the "Medications" heading, and "FAMILY HISTORY" after that. The sorted_segments
loop is only incrementing the index variable for non-empty segments.
> Patch attached.
> TestCDASegmentAnnotator output before fix (with getPreferredText()):
> Segment:2.16.840.1.113883.10.20.22.1.1 Begin:92 End:159: Header
> Segment:1.3.6.1.4.1.19376.1.5.3.1.1.13.2.1 Begin:176 End:1612: CHIEF COMPLAINT
> Segment:2.16.840.1.113883.10.20.22.2.20 Begin:1634 End:1696: HISTORY OF PAST ILLNESS
> Segment:2.16.840.1.113883.10.20.22.2.2.1 Begin:1711 End:2271: History of immunizations
> After fix:
> Segment:2.16.840.1.113883.10.20.22.1.1 Begin:92 End:159: Header
> Segment:1.3.6.1.4.1.19376.1.5.3.1.1.13.2.1 Begin:176 End:1612: CHIEF COMPLAINT
> Segment:2.16.840.1.113883.10.20.22.2.20 Begin:1634 End:1696: HISTORY OF PAST ILLNESS
> Segment:2.16.840.1.113883.10.20.22.2.2.1 Begin:1711 End:2271: History of immunizations
> Segment:2.16.840.1.113883.10.20.22.2.1.1 Begin:2307 End:3506: HISTORY OF MEDICATION USE
> Segment:2.16.840.1.113883.10.20.22.2.15 Begin:3522 End:5608: Family History



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