Mipav interface via JIST

[Yasin Yazıcı]

Hi,

I'm trying to interface with mipav via JIST. The command line that I want to implement is below:

java -classpath /usr/local/mipav/plugins/:/usr/local/mipav/:`find /usr/local/mipav/ -name \*.jar | sed 's#/usr/local/mipav/#:/usr/local/mipav/#' | tr -d '\n' | sed 's/^://'`  edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmN3$AlgorithmIHN3CorrectionWrapper -inInput /new_home/intern2012/yasin/data_sink/T2_TSE_crop_rescale.hdr -outInhomogeneity /new_home/intern2012/yasin/data_sink/test1.img

there are 5 basic part in it:

java

calls java

-classpath /usr/local/mipav/plugins/:/usr/local/mipav/:`find /usr/local/mipav/ -name \*.jar | sed 's#/usr/local/mipav/#:/usr/local/mipav/#' | tr -d '\n' | sed 's/^://'`

adds all necessary paths for java to run following java classes.

edu.jhu.ece.iacl.jist.cli.run

JIST launcher for java classes

edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmN3$AlgorithmIHN3CorrectionWrapper

mipav algorithm

-inInput /new_home/intern2012/yasin/data_sink/T2_TSE_crop_rescale.hdr -outInhomogeneity /new_home/intern2012/yasin/data_sink/test1.img

input and output for the mipav algorithm

In order to use the command line in nipype, I wrapped a code below

from nipype.interfaces.base import TraitedSpec, File, traits, isdefined,CommandLine, CommandLineInputSpec, SEMLikeCommandLine
import os

class IHN3CorrectionInputSpec(CommandLineInputSpec):

    in_file = File(exists=True, desc='input file', argstr='-inInput %s', position=0, mandatory=True)

    out_file = File(exists=False, desc='output file', argstr='-outInhomogeneity %s', position=-1)

class IHN3CorrectionOutputSpec(TraitedSpec):
 
    out_file = File(desc = "output file", exists = True)
 
class IHN3Correction(SEMLikeCommandLine):

    input_spec = IHN3CorrectionInputSpec
    output_spec = IHN3CorrectionOutputSpec
    _cmd = "java -classpath /usr/local/mipav/plugins/:/usr/local/mipav/:`find /usr/local/mipav/ -name \*.jar | sed 's#/usr/local/mipav/#:/usr/local/mipav/#' | tr -d '\n' | sed 's/^://'`  edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmN3$AlgorithmIHN3CorrectionWrapper"
    _outputs_filenames = {'out_file':'T2_crop_N3rescale.img'}

if __name__ == '__main__':

    N3 = IHN3Correction()
    N3.inputs.in_file = '/new_home/intern2012/yasin/data_sink/T2_TSE_crop_rescale.img'
    N3.inputs.out_file = '/new_home/intern2012/yasin/data_sink/T2_crop_N3rescale.img'
    print N3.cmdline
    N3.run()

The command line runs without error, however the wrapped code above gets stuck at "Initializing MIPAV/JIST Framework" and can not proceed to "Interpretting command line arguments". The code above is very similar to the codes in https://github.com/chrisfilo/nipype/commit/b7286aeb91275f76f3abbc13581111a63d67eb48 The only difference is "-classpath".

Cheers
Yasin