STYLE: Clean up generate_classes.py
squash
ENH: Added more input traits for Allineate()
BUG: Fixed afni.preprocess.to3D funcparams to not use the undocumented template for the argstr
ENH: Adding tpattern reading functionality to To3D()
BUG: Fixed bug for To3D() for output, To3D only returns AFNI output type (AFNI implementation)
STYLE: fixed typo in documentation and made more PEP8-compliant
BUG: Fixed file rename bug when copyfile is used for AFNI
STYLE: Removed attempt to use base class for prefix and suffix inputs
BUG: Fixed Refit() to correctly accept the output from To3D()
ENH: Added more options for Refit()
ENH: Added Deconvolve() to AFNI and all doctests pass
ENH: Added Zeropad
ENH: Doctests now pass with ELLIPSIS flag
STYLE: Removed unrelated files from pull topic
BUG: DeconvolveInputSpec() inheritance must include DynamicTraitedSpec FIRST or you get weird errors running the pipeline
BUG: Fixed bug with Zeropad's out_file and misspelling with Deconvolve's in_file
BUG: Deconvolve typo for input argstr(s)
squash! Waiting for Jatin's help on Deconvolve errts output
squash! REVIEW THESE COMMITS
TODO: AFNI's Calc function fails to run with dynamic traits for 'in_file_*'.  Contact mailing list about the add_traits() function and how it should be correctly implemented.  Doctesting and pipeline testing pass the cmdline generation, but the pipeline fails to add the argstr for the pipeline run (causing failure)
ENH: Added include_volumes input_spec to Despike
BUG: Fixed all calls to super(AFNICommand, self) to super(CLASSNAME, self)
ENH: Changed command line for ROIStats such that the output file is generated by the stdout, not by the json file handling
ENH: Added support to ApplyTransform for all interpolation methods
ENH:Added start and end volume indices for Despike
BUG: Deconvolve.inputs.ignoreWarnings formatted correctly
HACK: cPickle complains about no __getstate__ method with a function using PyDicom