ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Andy McMurry <mcmurry.a...@gmail.com>
Subject Re: docs on running Clinical Document Pipeline from Java?
Date Wed, 19 Jun 2013 21:30:32 GMT
Note: The WEKA gui reports the command line arguments for any GUI task. 
It could be a very helpful timesaver if cTAKES had a similar feature. 

Otherwise, I fear we will be writing Main methods and docs for each and every cTAKES task.

What do you all think? 

-------

Real world example of how this works in Weka. 
Say you wanted to run Adaboost on a C4.5 decision tree with cost sensitive classification.

Weka reports the arguments, which I can re-run from command line 

Classifier csc = new CostSensitiveClassifier();

        String[] adaboost = {
                "-cost-matrix", costMatrix,
                "-S", "1",
                "-W", "weka.classifiers.meta.AdaBoostM1",
                "--",
                "-P", "100",
                "-S", "1",
                "-I", "30",
                //
                "-W", "weka.classifiers.trees.J48",
                "--",
                "-C", String.valueOf(j48Confidence),
                "-M", String.valueOf(j48MinObjects)
        };

csc.setOptions(adaboost); 








On Jun 19, 2013, at 5:20 PM, "Chen, Pei" <Pei.Chen@childrens.harvard.edu> wrote:

> Also,
> Tim recently just checked in a Main class that essentially could be the beginnings of
a Driver program.
> Check the main() out at:
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java
> 
> --Pei
> 
> 
>> -----Original Message-----
>> From: Girivaraprasad Nambari [mailto:girinambari@gmail.com]
>> Sent: Wednesday, June 19, 2013 3:47 PM
>> To: dev@ctakes.apache.org
>> Subject: Re: docs on running Clinical Document Pipeline from Java?
>> 
>> Hi,
>> 
>> Welcome to ctakes.
>> 
>> There was a similar discussion initiated by me few months ago (you may be
>> able to find out if you browse through old discussions) . Here is response
>> form Pei Chen & ctakes community:
>> 
>> It is not quite prime time ready but, take a look peek at the below (It uses
>> uimaFIT to do the above):
>> 
>> **
>> 
>> http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-
>> gui/src/main/java/org/chboston/cnlp/ctakes/gui/service/LauncherService.ja
>> va
>> ****
>> 
>> ** Essentially, it boils down to a few lines of code:
>> 
>> AnalysisEngine aggregateAE = AnalysisEngineFactory.createAggregate(****
>> 
>>               engines, componentNames, typeSystemDescription, null,****
>> 
>>               new SofaMapping[0]);****
>> 
>>              ****
>> 
>> JCas jcas = aggregateAE.newJCas();****
>> 
>> jcas.setDocumentText(doc.getText());****
>> 
>> aggregateAE.process(jcas);
>> 
>> 
>> We need to start from UIMA and UIMAfit to get some basic understanding,
>> then using ctakes component will be easy.
>> 
>> Good luck!
>> 
>> Thank you,
>> 
>> Giri
>> 
>> 
>> On Wed, Jun 19, 2013 at 3:17 PM, Sandy Ryza <sandy.ryza@cloudera.com>
>> wrote:
>> 
>>> Hi cTAKES folks,
>>> 
>>> I am trying to figure out how to run the Clinical Document Pipeline
>>> from Java.  All the documentation I have found so far has been about
>>> how to do this through a GUI.  Is there anything on how to run the
>>> pipeline programmatically?
>>> 
>>> thanks for any help!
>>> Sandy
>>> 


Mime
View raw message