[Midas] [Fwd: Re: midas batchmake plugin error] no attachment

j at dicomfly.com j at dicomfly.com
Thu May 26 10:49:03 EDT 2011 

Hi Michael,
   because I'm not sure you received my last email (too big), I resend it
removing attachment...

Sorry, if you received it twice...

Thanks for your patience...

J

---------------------------- Original Message ----------------------------
Subject: Re: [Midas] midas batchmake plugin error
From:    j at dicomfly.com
Date:    Tue, May 24, 2011 3:08 am
To:      "Michael Grauer" <michael.grauer at kitware.com>
Cc:      midas at public.kitware.com
--------------------------------------------------------------------------

Hi Michael,
   is there something that continue to goes wrong.

Following your istruction I successfully executed, outside Midas,
ImageMath on ChestCT-SHORT.mha (from VTKData/Data/MetaIO/) with the
following command:

/var/www/opt/apps/bin/ImageMath ~/data/ChestCT-SHORT.mha -b 2 -W 3
~/data/3_ChestCT-SHORT.sum.mha

and it works!

But, unfortunately, running inside Midas with $MIDAS_BATCHMAKE_USE_CONDOR = 1

[ImageMath.16.dagjob]
 Script generated by BatchMake (c) Insight Software Consortium
# (c) Kitware Inc 2009
# More information at: http://www.batchmake.org

Universe       = vanilla
Output         = bmGrid.16.out.txt
Error          = bmGrid.16.error.txt
Log            = bmGrid.16.log.txt
Notification   = NEVER
Executable    = /var/www/opt/apps/bin/ImageMath
Arguments     =
"'/var/www/BASEDIR-batchmake/data/user_1/cart_3/3_ChestCT-SHORT.mha//var/www/BASEDIR-batchmake/data/user_1/cart_3/3_ChestCT-SHORT.mha'
-b '2' -W '3' ''3_ChestCT-SHORT.sum.mha''"
transfer_input_files =
/var/www/BASEDIR-batchmake/data/user_1/cart_3/3_ChestCT-SHORT.mha//var/www/BASEDIR-batchmake/data/user_1/cart_3/3_ChestCT-SHORT.mha
should_transfer_files = yes
when_to_transfer_output = ON_EXIT_OR_EVICT
Queue 1

we have at least the following error:

[from ImageMath.dagjob.dagman.out]
05/24/11 01:04:41 From submit: ERROR: Can't open
"/var/www/BASEDIR-batchmake/data/user_1/cart_3/3_ChestCT-SHORT.mha/var/www/BASEDIR-batchmake/data/user_1/cart_3/3_ChestCT-SHORT.mha"
 with flags 00 (Not a directory)

Is there an error passing imagepath from midas/cart to
batchmake/condor/ImageMath?

How can I solve it?

In the attached file, you can find debug and error midas logs, the
complete SSP directory created by batchmake plugin to perform the
requested job(s) (#18)...

Thanks in advance

Ciao

J




> 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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