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Posted to commits@ctakes.apache.org by bl...@apache.org on 2012/11/15 20:29:00 UTC
svn commit: r1409941 -
/incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext
Author: bleeker
Date: Thu Nov 15 19:28:59 2012
New Revision: 1409941
URL: http://svn.apache.org/viewvc?rev=1409941&view=rev
Log:
CMS commit to ctakes by bleeker
Modified:
incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext
Modified: incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext
URL: http://svn.apache.org/viewvc/incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext?rev=1409941&r1=1409940&r2=1409941&view=diff
==============================================================================
--- incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext (original)
+++ incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext Thu Nov 15 19:28:59 2012
@@ -110,9 +110,9 @@ and
edu.mayo.bmi.uima.core.type.textsem.EventMention
edu.mayo.bmi.uima.core.type.textsem.EventMention.MedicationEventMention
</pre>
-7. Then select **edu.mayo.bmi.uima.core.type.****textsem.****EntityMention** or *
-*edu.mayo.bmi.uima.core.type.****textsem.****EventMention.****Medication****Ev
-entMention**.This will show an Annotation Index in the lower frame. Select any
+7. Then select **edu.mayo.bmi.uima.core.type.textsem.EntityMention** or
+**edu.mayo.bmi.uima.core.type.textsem.EventMention.MedicationEventMention**.
+This will show an Annotation Index in the lower frame. Select any
annotation in that lower frame and you will see the text discovered in the
Text frame on the right.
@@ -145,62 +145,48 @@ Close the results window.
7. Close the CPE application. You may be prompted to save changes. Since this
was just a test you may click the **No** button.
-8. Open a new command prompt and change to the <cTAKES_HOME> directory.
-
-9. To test the results, you will use a comparison tool that will help show that the
-results match expectations with the following syntax:
-
-Where: **_<First File>_** is the first file to compare; **_<Second File>_** is
-the second file to compare; **_<diff-html>_** is where the results are written
-to
-
-
-Copy and paste the example at the right (next cell) which has had our example
-files already substituted into a command prompt to run. In this case we have
-shipped an example of what the output should be for you to compare against.
+### Validate CPE Results
+1. Open a command prompt and change to the cTAKES_HOME directory.
+**Windows**: <code>cd \cTAKES-3.0</code> **Linux**: <code>cd /usr/bin/cTAKES-3.0</code>
+2. To test the results, you will use a comparison tool that will help show that the
+results match expectations. Enter this command:
+<pre>
+java -cp cTAKES.jar edu.mayo.bmi.utils.xcas_comparison.Compare <First File> <Second File> <diff-html>
+</pre>
+Where: **_<First File>_** is the first file to compare; **_<Second File>_** is
+the second file to compare; **_<diff-html>_** is where the results are written
+to. For example:
**Windows**:
-
+<pre>
+java -cp cTAKES.jar edu.mayo.bmi.utils.xcas_comparison.Compare ^
+"testdata\cdptest\testoutput\plaintext\sample_note_plaintext.xml" ^
+"testdata\cdptest\testsampleoutput\plaintext\sample_note_plaintext.xml" ^
+c:\stuff\diff-html.html
+</pre>
**Linux**:
+<pre>
+java edu.mayo.bmi.utils.xcas_comparison.Compare \
+"/usr/bin/cTAKES2.5/testdata/cdptest/testoutput/plaintext\sample_note_plaintext.xml" \
+"/usr/bin/cTAKES2.5/testdata/cdptest/testsampleoutput/plaintext/sample_note_plaintext.xml" \
+/tmp/diff-html.html
+</pre>
+Copy and paste the example above, which has had our example
+files already substituted, into a command prompt to run. In this case we have
+shipped an example of what the output should be for you to compare against.
-10. The resulting file will open for you. Look at the comparison to see the
+3. The resulting file will open for you. Look at the comparison to see the
annotations resulting from this pipeline.
-
-**Windows:**
-
-**Linux**:
-
-
+**Windows**: <code>c:\stuff\diff-html.html</code> **Linux**: <code>/tmp/diff-html.html</code>
Using the same CVD and CPE programs in the manner described above, you can
test all the other components. The analysis engines and collection processing
engines shipped with cTAKES for some of the annotators are described in the
following table.
-Annotator
-
-Description
-
-Abbreviated
-
-Example Analysis Engine (AE)
-
-Example Collection processing Engine (CPE)
-
-Example test data
-
-Clinical Document Pipeline
-
-the complete cTAKES pipeline to obtain majority of cTAKES annotations
-
-cdp
-
-cTAKES_HOME/cTAKESdesc/cdpdesc/analysis_engine/AggregatePlaintextProcessor.xml
-
-cTAKES_HOME/cTAKESdesc/cdpdesc/collection_processing_engine/test_plaintext.xml
-
-cTAKES_HOME/testdata/cdptest
+|Annotator|Description|Abbreviated|Example Analysis Engine (AE)|Example Collection processing Engine (CPE)|Example test data|
+|---------|-----------|-----------|----------------------------|------------------------------------------|-----------------|
+|Clinical Document Pipeline|the complete cTAKES pipeline to obtain majority of cTAKES annotations|cdp|cTAKES_HOME/cTAKESdesc/cdpdesc/analysis_engine/AggregatePlaintextProcessor.xml|cTAKES_HOME/cTAKESdesc/cdpdesc/collection_processing_engine/test_plaintext.xml|cTAKES_HOME/testdata/cdptest|
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