Re: [base] how can i interact with the spot creator plugin from outside the system

2007-04-12 Thread Nicklas Nordborg 
Chad Matsalla wrote:
 
 Nicklas Nordborg wrote:
 Can you tell me how to create the appropriate file objects when the files
 are here and not connected to the base datbaase?
 This is not possible. The plugin expects net.sf.basedb.core.File objects
 not java.io.File object. And you can't work with XxxxData (FileData,
 SpotImagesData) objects. These are only used internally in BASE. You
 must use the corresponding objects from the net.sf.basedb.core package
 (File, SpotImages, etc.)
  
 Can you please tell me the best way to do that? I've been looking through
 the plugin and test code and I'm mystified.
 
 I've uploaded the files into the BASE2 directory Root/chad/13298608_532.tif
 and Root/chad/images/13298608_635.tif.
  
 Somehow, I need to build a connection to the BASE2 server running on the
 host base2server' using the base2 username 'chad' and some password. Then I
 need to get a reference to those files and pass it to the spot finder.
  
 Is there some documentation I can read or can you give me some example code?
 
 I tried to mimic the 'ExampleAnalyzer.java' class but I think it's designed
 to work in the gui. I'm now trying to mimic the migrator because it runs on
 the commandline. I see that it reads a base.config so I started by copying
 the base.config from the server named base2server.
 
 I think I'm on the wrong track because I need to connect to a running base2
 server to ask for the files. Is this the case?
 

You can check the src/test/TestSpotImages.java file. It contains 
everything that is needed to create the spot images using our test data. 
It shouldn't be to hard to modify this code to use your files instead. 
You will of course have to download the source distribution or check it 
out from the subversion repository. How to do that is described on the 
download page. Another useful document is: 
http://base.thep.lu.se/chrome/site/doc/development/build.html

You can also check the code for the SpotImageCreator plugin.

The ExampleAnalyzer is a plugin and must run on the server.

If you are going to run it from the command line it is best to use the 
same server as your BASE is running on. Otherwise you will need to open 
up MySQL and the file system so it becomes accessible from the other 
computer. This is how job agents works (used for running plugins on 
external computers). How to set this up is rather complex and is 
documented at http://base.thep.lu.se/chrome/site/doc/admin/jobagent.html

/Nicklas

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[base] how can i interact with the spot creator plugin from outside the system

2007-04-11 Thread Chad Matsalla 

Greetings!

I'm trying to understand the genepix tiff spotfinding problem I described
earlier.

I want to interact with the spotfinder plugin with my own program but I
can't create files.

I have this:
images/
|-- 13298608_532-uncompressed.tif
`-- 13298608_635-uncompressed.tif

I want to do something like this:

public class TestImageProblem {
 SpotImagesData data;
 FileData red;
 FileData green;

 TestImageProblem() {
  data = new SpotImagesData();
  data.setGamma(new Float(1.8));
  data.setXOffset(2000);
  data.setYOffset(2400);
  data.setXScale(10);
  data.setYScale(10);
  data.setSpotsize(24);
  java.io.File redfile = new
java.io.File(images/13298608_635-uncompressed.tif);
  java.io.File greenfile = new
java.io.File(images/13298608_532-uncompressed.tif);


Pass the data to the spot image creator ( SpotImages.createSpotImages )


}

Can you tell me how to create the appropriate file objects when the files
are here and not connected to the base datbaase?

Thanks!

Chad


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