[Midas] midas batchmake plugin error

Fri May 20 15:59:04 EDT 2011

Hi J,

At this time, executing locally (without Condor) isn't fully supported on
Midas, so you should be using

$MIDAS_BATCHMAKE_USE_CONDOR = 1

in your config_batchmake.php or config.batchmake.local.php files.

Do you have your Condor grid setup?

Since these are just example applications, you don't need to have them
running to use Midas and BatchMake.  If you have the PixelCounter
application running this should give you an example for sending files into a
BatchMake application/script from within Midas.  These examples just give
you a basis for developing your own BatchMake scripts and applications.

As far as debugging, once you have the MIDAS_BATCHMAKE_USE_CONDOR option set
to 1, there should appear some condor outputs and logs in your BatchMake
temporary (batchmake-basedir temp) execution directory, which you can use to
see any problems.

One problem in this case, judging from your output of "Error: SetAppOption:
Cannot find parameter: GaussianBlur.", is probably that incorrect .bmm files
(or none at all) were packaged with Midas.  I'm attaching the appropriate
.bmm file for the ImageMath application.  Place this in the directory you
have defined for MIDAS_BATCHMAKE_APPLICATION_DIRECTORY, and change the path
in the .bmm file to the correct path to the ImageMath application.

I hope this helps.

On Wed, May 18, 2011 at 6:55 AM, <j at dicomfly.com> wrote:

> Hi Michael,
>   following your info I was able to successfully execute PixelCounter
> (without and with condor=execute_in_server). I saw the following echo
> and I found output xml:
>
> #use_condor=0
> Executing ...
> Status: Start /var/www/opt/batchmake/bin/PixelCounter
> /var/www/BASEDIR-batchmake/data/user_1/cart_2/10_AddTest_DOUBLE.mha 10
> --ofxml 10_AddTest_DOUBLE.output.xml
> run: '/var/www/opt/batchmake/bin/PixelCounter'
> '''/var/www/BASEDIR-batchmake/data/user_1/cart_2/10_AddTest_DOUBLE.mha'
> '10' --ofxml '10_AddTest_DOUBLE.output.xml'''
> Status: Finish: Execution time 315ms
>
> Unfortunately, trying to run ImageMathAdder (following rigorously the info
> in the bms file: i.e. png filenames in cart1 and cart2, etc.), something
> goes wrong: I cannot find any output image.
>
> I saw the following echo (only one line):
> Executing ...
>
> I tried to understand what happens checking in logs and in
> batchmake-basedir temp folder but without success (apparently no
> errors...)
>
> For ImageMath a different error is returned:
> Executing ...
> Error: SetAppOption: Cannot find parameter: GaussianBlur.
>
>
> Any advice?
>
> Thanks in advance...
>
> 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
> >
>
>
>

-- 
Thanks,
Michael Grauer
R & D Engineer
Kitware, Inc.
919 969 6990 x322
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