# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.spm.base import SPMCommandInputSpec, SPMCommand, Info, scans_for_fnames, scans_for_fname
from nipype.interfaces.matlab import MatlabCommand
from nipype.interfaces.base import (TraitedSpec, BaseInterface,
                                    BaseInterfaceInputSpec, isdefined,
                                    OutputMultiPath, InputMultiPath)
from nipype.interfaces.base import File, traits
from nipype.utils.filemanip import split_filename, fname_presuffix, filename_to_list,list_to_filename
import os
import numpy as np

class Analyze2niiInputSpec(SPMCommandInputSpec):
    analyze_file = File(exists=True, mandatory=True)

class Analyze2niiOutputSpec(SPMCommandInputSpec):
    nifti_file = File(exists=True)

class Analyze2nii(SPMCommand):

    input_spec = Analyze2niiInputSpec
    output_spec = Analyze2niiOutputSpec

    def _make_matlab_command(self, _):
        script = "V = spm_vol('%s');\n"%self.inputs.analyze_file
        _, name,_ = split_filename(self.inputs.analyze_file)
        self.output_name = os.path.join(os.getcwd(), name + ".nii")
        script += "[Y, XYZ] = spm_read_vols(V);\n"
        script += "V.fname = '%s';\n"%self.output_name
        script += "spm_write_vol(V, Y);\n"

        return script

    def _list_outputs(self):
        outputs = self._outputs().get()
        outputs['nifti_file'] = self.output_name
        return outputs

class CalcCoregAffineInputSpec(SPMCommandInputSpec):
    target = File( exists = True, mandatory = True,
                   desc = 'target for generating affine transform')
    moving = File( exists = True, mandatory = True, copyfile=False,
                   desc = 'volume transform can be applied to register with target')
    mat = File( desc = 'Filename used to store affine matrix')
    invmat = File( desc = 'Filename used to store inverse affine matrix')


class CalcCoregAffineOutputSpec(TraitedSpec):
    mat = File(exists = True, desc = 'Matlab file holding transform')
    invmat = File( desc = 'Matlab file holding inverse transform')


class CalcCoregAffine(SPMCommand):
    """ Uses SPM (spm_coreg) to calculate the transform mapping
    moving to target. Saves Transform in mat (matlab binary file)
    Also saves inverse transform

    Examples
    --------

    >>> import nipype.interfaces.spm.utils as spmu
    >>> coreg = spmu.CalcCoregAffine(matlab_cmd='matlab-spm8')
    >>> coreg.inputs.target = 'structural.nii'
    >>> coreg.inputs.moving = 'functional.nii'
    >>> coreg.inputs.mat = 'func_to_struct.mat'
    >>> coreg.run() # doctest: +SKIP

    .. note::

     * the output file mat is saves as a matlab binary file
     * calculating the transforms does NOT change either input image
       it does not **move** the moving image, only calculates the transform
       that can be used to move it
    """

    input_spec = CalcCoregAffineInputSpec
    output_spec = CalcCoregAffineOutputSpec

    def _make_inv_file(self):
        """ makes filename to hold inverse transform if not specified"""
        invmat = fname_presuffix(self.inputs.mat, prefix = 'inverse_')
        return invmat

    def _make_mat_file(self):
        """ makes name for matfile if doesn exist"""
        pth, mv, _  = split_filename(self.inputs.moving)
        _, tgt, _ = split_filename(self.inputs.target)
        mat = os.path.join(pth, '%s_to_%s.mat'%(mv,tgt))
        return mat

    def _make_matlab_command(self, _):
        """checks for SPM, generates script"""
        if not isdefined(self.inputs.mat):
            self.inputs.mat = self._make_mat_file()
        if not isdefined(self.inputs.invmat):
            self.inputs.invmat = self._make_inv_file()
        script = """
        target = '%s';
        moving = '%s';
        targetv = spm_vol(target);
        movingv = spm_vol(moving);
        x = spm_coreg(targetv, movingv);
        M = spm_matrix(x);
        save('%s' , 'M' );
        M = inv(M);
        save('%s','M')
        """%(self.inputs.target,
             self.inputs.moving,
             self.inputs.mat,
             self.inputs.invmat)
        return script

    def _list_outputs(self):
        outputs = self._outputs().get()
        outputs['mat'] = os.path.abspath(self.inputs.mat)
        outputs['invmat'] = os.path.abspath(self.inputs.invmat)
        return outputs

class ApplyTransformInputSpec(SPMCommandInputSpec):
    in_file = File( exists = True, mandatory = True, copyfile=True,
                   desc='file to apply transform to, (only updates header)')
    mat = File( exists = True, mandatory = True,
                desc='file holding transform to apply')


class ApplyTransformOutputSpec(TraitedSpec):
    out_file = File(exists = True, desc = 'File with updated header')


class ApplyTransform(SPMCommand):
    """ Uses spm to apply transform stored in a .mat file to given file

    Examples
    --------

    >>> import nipype.interfaces.spm.utils as spmu
    >>> applymat = spmu.ApplyTransform(matlab_cmd='matlab-spm8')
    >>> applymat.inputs.in_file = 'functional.nii'
    >>> applymat.inputs.mat = 'func_to_struct.mat'
    >>> applymat.run() # doctest: +SKIP

    .. warning::

       CHANGES YOUR INPUT FILE (applies transform by updating the header)
       except when used with nipype caching or workflow.
    """
    input_spec = ApplyTransformInputSpec
    output_spec = ApplyTransformOutputSpec

    def _make_matlab_command(self, _):
        """checks for SPM, generates script"""
        script = """
        infile = '%s';
        transform = load('%s');
        M  = inv(transform.M);
        img_space = spm_get_space(infile);
        spm_get_space(infile, M * img_space);
        """%(self.inputs.in_file,
             self.inputs.mat)
        return script

    def _list_outputs(self):
        outputs = self._outputs().get()
        outputs['out_file'] = os.path.abspath(self.inputs.in_file)
        return outputs

class ResliceInputSpec(SPMCommandInputSpec):
    in_file = File( exists = True, mandatory=True,
                    desc='file to apply transform to, (only updates header)')
    space_defining = File ( exists = True, mandatory = True,
                            desc = 'Volume defining space to slice in_file into')

    interp = traits.Range(low = 0, high = 7, usedefault = True,
                          desc='degree of b-spline used for interpolation'\
                                '0 is nearest neighbor (default)')


    out_file = File(desc = 'Optional file to save resliced volume')

class ResliceOutputSpec(TraitedSpec):
    out_file = File( exists = True, desc = 'resliced volume')

class Reslice(SPMCommand):
    """ uses  spm_reslice to resample in_file into space of space_defining"""

    input_spec = ResliceInputSpec
    output_spec = ResliceOutputSpec

    def _make_matlab_command(self, _):
        """ generates script"""
        if not isdefined(self.inputs.out_file):
            self.inputs.out_file = fname_presuffix(self.inputs.in_file,
                                                   prefix = 'r')
        script = """
        flags.mean = 0;
        flags.which = 1;
        flags.mask = 0;
        flags.interp = %d;
        infiles = strvcat(\'%s\', \'%s\');
        invols = spm_vol(infiles);
        spm_reslice(invols, flags);
        """%(self.inputs.interp,
             self.inputs.space_defining,
             self.inputs.in_file)
        return script

    def _list_outputs(self):
        outputs = self._outputs().get()
        outputs['out_file'] = os.path.abspath(self.inputs.out_file)
        return outputs

class ApplyInverseDeformationInput(SPMCommandInputSpec):
    in_files = InputMultiPath(
        File(exists=True), mandatory=True, field='fnames',
        desc='Files on which deformation is applied')
    target = File(
        exists=True,
        field='comp{1}.inv.space',
        desc='File defining target space')
    deformation = File(
        exists=True,
        field='comp{1}.inv.comp{1}.sn2def.matname',
        desc='SN SPM deformation file',
        xor=['deformation_field'])
    deformation_field = File(
        exists=True,
        field='comp{1}.inv.comp{1}.def',
        desc='SN SPM deformation file',
        xor=['deformation'])
    interpolation = traits.Range(
        low=0, high=7, field='interp',
        desc='degree of b-spline used for interpolation')

    bounding_box = traits.List(
        traits.Float(),
        field='comp{1}.inv.comp{1}.sn2def.bb',
        minlen=6, maxlen=6,
        desc='6-element list (opt)')
    voxel_sizes = traits.List(
        traits.Float(),
        field='comp{1}.inv.comp{1}.sn2def.vox',
        minlen=3, maxlen=3,
        desc='3-element list (opt)')


class ApplyInverseDeformationOutput(TraitedSpec):
    out_files = OutputMultiPath(File(exists=True),
                                desc='Transformed files')


class ApplyInverseDeformation(SPMCommand):
    """ Uses spm to apply inverse deformation stored in a .mat file or a
    deformation field to a given file

    Examples
    --------

    >>> import nipype.interfaces.spm.utils as spmu
    >>> inv = spmu.ApplyInverseDeformation()
    >>> inv.inputs.in_files = 'functional.nii'
    >>> inv.inputs.deformation = 'struct_to_func.mat'
    >>> inv.inputs.target = 'structural.nii'
    >>> inv.run() # doctest: +SKIP
    """

    input_spec = ApplyInverseDeformationInput
    output_spec = ApplyInverseDeformationOutput

    _jobtype = 'util'
    _jobname = 'defs'

    def _format_arg(self, opt, spec, val):
        """Convert input to appropriate format for spm
        """
        if opt == 'in_files':
            return scans_for_fnames(filename_to_list(val))
        if opt == 'target':
            return scans_for_fname(filename_to_list(val))
        if opt == 'deformation':
            return np.array([list_to_filename(val)], dtype=object)
        if opt == 'deformation_field':
            return np.array([list_to_filename(val)], dtype=object)
        return val

    def _list_outputs(self):
        outputs = self._outputs().get()
        outputs['out_files'] = []
        for filename in self.inputs.in_files:
            _, fname = os.path.split(filename)
            outputs['out_files'].append(os.path.realpath('w%s' % fname))
        return outputs


class ResliceToReferenceInput(SPMCommandInputSpec):
    in_files = InputMultiPath(
        File(exists=True), mandatory=True, field='fnames',
        desc='Files on which deformation is applied')
    target = File(
        exists=True,
        field='comp{1}.id.space',
        desc='File defining target space')
    interpolation = traits.Range(
        low=0, high=7, field='interp',
        desc='degree of b-spline used for interpolation')

    bounding_box = traits.List(
        traits.Float(),
        field='comp{2}.idbbvox.bb',
        minlen=6, maxlen=6,
        desc='6-element list (opt)')
    voxel_sizes = traits.List(
        traits.Float(),
        field='comp{2}.idbbvox.vox',
        minlen=3, maxlen=3,
        desc='3-element list (opt)')


class ResliceToReferenceOutput(TraitedSpec):
    out_files = OutputMultiPath(File(exists=True),
                                desc='Transformed files')


class ResliceToReference(SPMCommand):
    """ Uses spm to reslice a volume to a target image space or to a provided voxel size and bounding box

    Examples
    --------

    >>> import nipype.interfaces.spm.utils as spmu
    >>> r2ref = spmu.ResliceToReference()
    >>> r2ref.inputs.in_files = 'functional.nii'
    >>> r2ref.inputs.target = 'structural.nii'
    >>> r2ref.run() # doctest: +SKIP
    """

    input_spec = ResliceToReferenceInput
    output_spec = ResliceToReferenceOutput

    _jobtype = 'util'
    _jobname = 'defs'

    def _format_arg(self, opt, spec, val):
        """Convert input to appropriate format for spm
        """
        if opt == 'in_files':
            return scans_for_fnames(filename_to_list(val))
        if opt == 'target':
            return scans_for_fname(filename_to_list(val))
        if opt == 'deformation':
            return np.array([list_to_filename(val)], dtype=object)
        if opt == 'deformation_field':
            return np.array([list_to_filename(val)], dtype=object)
        return val

    def _list_outputs(self):
        outputs = self._outputs().get()
        outputs['out_files'] = []
        for filename in self.inputs.in_files:
            _, fname = os.path.split(filename)
            outputs['out_files'].append(os.path.realpath('w%s' % fname))
        return outputs

class DicomImportInputSpec(SPMCommandInputSpec):
    in_files = InputMultiPath(
        File(exists=True),
        mandatory=True,
        field='data',
        desc='dicom files to be converted')
    output_dir_struct = traits.Enum(
        'flat', 'series', 'patname', 'patid_date', 'patid', 'date_time',
        field='root',
        usedefault=True,
        desc='directory structure for the output.')
    output_dir = traits.Str('./converted_dicom',
        field='outdir',
        usedefault=True,
        desc='output directory.')
    format = traits.Enum(
        'nii', 'img',
        field='convopts.format',
        usedefault=True,
        desc='output format.')
    icedims = traits.Bool(False,
        field='convopts.icedims',
        usedefault=True,
        desc='If image sorting fails, one can try using the additional\
              SIEMENS ICEDims information to create unique filenames.\
              Use this only if there would be multiple volumes with\
              exactly the same file names.')

class DicomImportOutputSpec(TraitedSpec):
    out_files = OutputMultiPath(File(exists=True),
                                desc='converted files')

class DicomImport(SPMCommand):
    """ Uses spm to convert DICOM files to nii or img+hdr.

    Examples
    --------

    >>> import nipype.interfaces.spm.utils as spmu
    >>> di = spmu.DicomImport()
    >>> di.inputs.in_files = ['functional_1.dcm', 'functional_2.dcm']
    >>> di.run() # doctest: +SKIP
    """

    input_spec = DicomImportInputSpec
    output_spec = DicomImportOutputSpec

    _jobtype = 'util'
    _jobname = 'dicom'

    def _format_arg(self, opt, spec, val):
        """Convert input to appropriate format for spm
        """
        if opt == 'in_files':
            return np.array(val, dtype=object)
        if opt == 'output_dir':
            return np.array([val], dtype=object)
        if opt == 'output_dir':
            return os.path.abspath(val)
        if opt == 'icedims':
            if val:
                return 1
            return 0
        return super(DicomImport, self)._format_arg(opt, spec, val)

    def _run_interface(self, runtime):
        od = os.path.abspath(self.inputs.output_dir)
        if not os.path.isdir(od):
            os.mkdir(od)
        return super(DicomImport, self)._run_interface(runtime)

    def _list_outputs(self):
        from glob import glob
        outputs = self._outputs().get()
        od = os.path.abspath(self.inputs.output_dir)
        outputs['out_files'] = glob(os.path.join(od, '*'))
        return outputs
