# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft = python sts = 4 ts = 4 sw = 4 et:
"""Afni svm interfaces

    Change directory to provide relative paths for doctests
    >>> import os
    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
    >>> os.chdir(datadir)
"""
import warnings

import os
import re

from ..base import (Directory, TraitedSpec,
                    traits, isdefined, File, InputMultiPath, Undefined)
from ...utils.filemanip import (load_json, save_json, split_filename)
from nipype.utils.filemanip import fname_presuffix
from .base import AFNICommand, AFNICommandInputSpec,\
    AFNICommandOutputSpec
from nipype.interfaces.base import CommandLineInputSpec, CommandLine,\
    OutputMultiPath

warn = warnings.warn
warnings.filterwarnings('always', category=UserWarning)

class SVMTrainInputSpec(AFNICommandInputSpec):
    #training options
    ttype = traits.Str(desc='tname: classification or regression',
                argstr='-type %s',
                mandatory=True)
    in_file = File(desc='A 3D+t AFNI brik dataset to be used for training.',
                argstr='-trainvol %s',
                mandatory=True,
                exists=True,
                copyfile=False)
    out_file = File(name_template="%s_vectors",
                desc='output sum of weighted linear support vectors file name',
                argstr='-bucket %s',
                suffix='_bucket',
                name_source="in_file")
    model = File(name_template="%s_model",
                desc='basename for the brik containing the SVM model',
                argstr='-model %s',
                suffix='_model',
                name_source="in_file")
    alphas = File(name_template="%s_alphas",
                desc='output alphas file name',
                argstr='-alpha %s',
                suffix='_alphas',
                name_source="in_file")
    mask = File(desc='byte-format brik file used to mask voxels in the analysis',
                argstr='-mask %s',
                position=-1,
                exists=True,
                copyfile=False)
    nomodelmask = traits.Bool(desc='Flag to enable the omission of a mask file',
                argstr='-nomodelmask')
    trainlabels = File(desc='.1D labels corresponding to the stimulus paradigm for the training data.',
                argstr='-trainlabels %s',
                exists=True)
    censor = File(desc='.1D censor file that allows the user to ignore certain samples in the training data.',
                argstr='-censor %s',
                exists=True)
    kernel = traits.Str(desc='string specifying type of kernel function:linear, polynomial, rbf, sigmoid',
                argstr='-kernel %s')
    max_iterations = traits.Int(desc='Specify the maximum number of iterations for the optimization.',
                argstr='-max_iterations %d')
    w_out = traits.Bool(desc='output sum of weighted linear support vectors',
                argstr='-wout')
    options = traits.Str(desc='additional options for SVM-light', argstr='%s')

class SVMTrainOutputSpec(TraitedSpec):
    out_file = File(desc='sum of weighted linear support vectors file name')
    model = File(desc='brik containing the SVM model file name')
    alphas = File(desc='output alphas file name')

class SVMTrain(AFNICommand):
    """Temporally predictive modeling with the support vector machine
    SVM Train Only
    For complete details, see the `3dsvm Documentation.
    <http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dsvm.html>`_

    Examples
    ========

    >>> from nipype.interfaces import afni as afni
    >>> svmTrain = afni.SVMTrain()
    >>> svmTrain.inputs.in_file = 'run1+orig'
    >>> svmTrain.inputs.trainlabels = 'run1_categories.1D'
    >>> svmTrain.inputs.ttype = 'regression'
    >>> svmTrain.inputs.mask = 'mask.nii'
    >>> svmTrain.inputs.model = 'model_run1'
    >>> svmTrain.inputs.alphas = 'alphas_run1'
    >>> res = svmTrain.run() # doctest: +SKIP

    """

    _cmd = '3dsvm'
    input_spec = SVMTrainInputSpec
    output_spec = SVMTrainOutputSpec
    _additional_metadata = ['suffix']

    def _format_arg(self, name, trait_spec, value):
        return super(SVMTrain, self)._format_arg(name, trait_spec, value)

class SVMTestInputSpec(AFNICommandInputSpec):
    #testing options
    model = traits.Str(desc='modname is the basename for the brik containing the SVM model',
                argstr='-model %s',
                mandatory=True)
    in_file = File(desc='A 3D or 3D+t AFNI brik dataset to be used for testing.',
                argstr='-testvol %s',
                exists=True,
                mandatory=True)
    out_file = File(name_template="%s_predictions",
                desc='filename for .1D prediction file(s).',
                argstr='-predictions %s')
    testlabels = File(desc='*true* class category .1D labels for the test dataset. It is used to calculate the prediction accuracy performance',
                exists=True,
                argstr='-testlabels %s')
    classout = traits.Bool(desc='Flag to specify that pname files should be integer-valued, corresponding to class category decisions.',
                argstr='-classout')
    nopredcensord = traits.Bool(desc='Flag to prevent writing predicted values for censored time-points',
                argstr='-nopredcensord')
    nodetrend = traits.Bool(desc='Flag to specify that pname files should not be linearly detrended',
                argstr='-nodetrend')
    multiclass = traits.Bool(desc='Specifies multiclass algorithm for classification',
                argstr='-multiclass %s')
    options = traits.Str(desc='additional options for SVM-light', argstr='%s')

class SVMTest(AFNICommand):
    """Temporally predictive modeling with the support vector machine
    SVM Test Only
    For complete details, see the `3dsvm Documentation.
    <http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dsvm.html>`_

    Examples
    ========

    >>> from nipype.interfaces import afni as afni
    >>> svmTest = afni.SVMTest()
    >>> svmTest.inputs.in_file= 'run2+orig'
    >>> svmTest.inputs.model= 'run1+orig_model'
    >>> svmTest.inputs.testlabels= 'run2_categories.1D'
    >>> svmTest.inputs.out_file= 'pred2_model1'
    >>> res = svmTest.run() # doctest: +SKIP

    """
    _cmd = '3dsvm'
    input_spec = SVMTestInputSpec
    output_spec = AFNICommandOutputSpec
