[Midas] midas batchmake plugin error

[j at dicomfly.com]

Hi Michael,
   in short, what we are working on is to build a midas-based website to
provide a medical and biological repository of data and image
processing and analysis methods. We would like, as a first step, to
give to the website guests the possibility to upload your own data, to
run some processing (via batchmake, with or without condor) and to
view/download the results...

Thanks

J





> Hi J,
>
> Can you tell me more about what you are trying to accomplish with Midas?
> I
> might be able to give you some better advice if I know this.
>
>
>
> PixelCounter won't work with DICOM images, it is really more of an example
> or demo application for testing out the BatchMake/Condor infrastructure.
>  This is useful to test before you do any other development, so you can be
> sure the infrastructure works correctly.
>
>
> Here is a link that covers some of this information.  If anything is
> unclear
> or you would like more details in a particular area, please let us know as
> we are always trying to improve the documentation.
>
> http://www.kitware.com/midaswiki/index.php/Plugins:BatchMake#Adding_a_BatchMake_script_to_the_Midas_BatchMake_Plugin
>
>
>
> For the PixelCounter application, you can use some sphere image files as
> inputs.  In the BatchMake build directory, under bin, if you configured
> BatchMake with BUILD_EXAMPLES = on, you should have a GenerateSpheres
> executable.  If you run this, it will generate several sphere images files
> for you.  You can upload some of these to Midas, then create a cart and
> add
> the images to the cart.  Use this cart as the input to the PixelCounter
> application.
>
>
>
> Once you run the PixelCounter, you can use the Midas logs to help debug
> problems.  Also, look in the directory defined for
>
> $MIDAS_BATCHMAKE_TEMP_DIRECTORY
>
> in your BatchMake Midas plugin configuration file.  Here you will see the
> temporary directories associated with BatchMake processing in Midas, and
> the
> generated Condor output files there can help you debug further problems.
>
>
>
> I think the development version of Midas taken out of the Git repository
> (2.8.1) is the best one to use for doing BatchMake plugin development, as
> this area of Midas is under active development.
>
>
>
>
>
>
>
>
> On Sat, May 7, 2011 at 12:26 PM, J <j at dicomfly.com> wrote:
>
>>  Hi Michael,
>>         batchmake plugin now seems to work even if PixelCounter example
>> runs but does not produce any output: any idea? I tried to process DICOM
>> images...
>>
>> Which is the better Midas version to use? (2.8.1, 2.9, ??)
>>
>> Thanks in advance
>>
>> J
>>
>>
>>
>> At 16.48 05/05/2011, you wrote:
>>
>> Hi J,
>>
>> First off, you will want to upgrade your BatchMake to the current
>> development version to take advantage of integration with Midas and
>> Condor:
>>
>>  http://batchmake.org/batchmake/resources/software.html
>>
>> You can clone from git and then build the source using Cmake.
>>
>>
>>
>>
>> A couple things to think about before running any BatchMake applications
>> from within Midas:
>>
>> -Is your condor grid status correctly viewable from the "Midas Grid
>> Status"
>> link of the BatchMake plugin?
>> -Are all of the configuration settings correct (green colored) from the
>> "Check Configuration" link of the BatchMake plugin?
>>
>>
>>
>> There should be more detailed error messages available in the Midas
>> logs.
>> Look in the MIDAS_INSTALL_DIR/midas/tmp/logs/error.log , this will help
>> you
>> with your specific problem.
>>
>>
>> Let me know if this helps.
>>
>>
>>
>>
>
>
> --
> Thanks,
> Michael Grauer
> R & D Engineer
> Kitware, Inc.
> 919 969 6990 x322
>