base.py

# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
    # changing to temporary directories
    >>> tmp = getfixture('tmpdir')
    >>> old = tmp.chdir()
"""
import os
import re
import numpy as np

from ..base import (
    traits,
    TraitedSpec,
    DynamicTraitedSpec,
    File,
    Undefined,
    isdefined,
    OutputMultiPath,
    InputMultiPath,
    BaseInterface,
    BaseInterfaceInputSpec,
    Str,
    SimpleInterface,
)
from ..io import IOBase, add_traits
from ...utils.filemanip import ensure_list, copyfile, split_filename


class IdentityInterface(IOBase):
    """Basic interface class generates identity mappings

    Examples
    --------

    >>> from nipype.interfaces.utility import IdentityInterface
    >>> ii = IdentityInterface(fields=['a', 'b'], mandatory_inputs=False)
    >>> ii.inputs.a
    <undefined>

    >>> ii.inputs.a = 'foo'
    >>> out = ii._outputs()
    >>> out.a
    <undefined>

    >>> out = ii.run()
    >>> out.outputs.a
    'foo'

    >>> ii2 = IdentityInterface(fields=['a', 'b'], mandatory_inputs=True)
    >>> ii2.inputs.a = 'foo'
    >>> out = ii2.run() # doctest: +SKIP
    ValueError: IdentityInterface requires a value for input 'b' because it was listed in 'fields' Interface IdentityInterface failed to run.
    """

    input_spec = DynamicTraitedSpec
    output_spec = DynamicTraitedSpec

    def __init__(self, fields=None, mandatory_inputs=True, **inputs):
        super(IdentityInterface, self).__init__(**inputs)
        if fields is None or not fields:
            raise ValueError("Identity Interface fields must be a non-empty list")
        # Each input must be in the fields.
        for in_field in inputs:
            if in_field not in fields:
                raise ValueError(
                    "Identity Interface input is not in the fields: %s" % in_field
                )
        self._fields = fields
        self._mandatory_inputs = mandatory_inputs
        add_traits(self.inputs, fields)
        # Adding any traits wipes out all input values set in superclass initialization,
        # even it the trait is not in the add_traits argument. The work-around is to reset
        # the values after adding the traits.
        self.inputs.trait_set(**inputs)

    def _add_output_traits(self, base):
        return add_traits(base, self._fields)

    def _list_outputs(self):
        # manual mandatory inputs check
        if self._fields and self._mandatory_inputs:
            for key in self._fields:
                value = getattr(self.inputs, key)
                if not isdefined(value):
                    msg = (
                        "%s requires a value for input '%s' because it was listed in 'fields'. \
                    You can turn off mandatory inputs checking by passing mandatory_inputs = False to the constructor."
                        % (self.__class__.__name__, key)
                    )
                    raise ValueError(msg)

        outputs = self._outputs().get()
        for key in self._fields:
            val = getattr(self.inputs, key)
            if isdefined(val):
                outputs[key] = val
        return outputs


class MergeInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
    axis = traits.Enum(
        "vstack",
        "hstack",
        usedefault=True,
        desc="direction in which to merge, hstack requires same number of elements in each input",
    )
    no_flatten = traits.Bool(
        False,
        usedefault=True,
        desc="append to outlist instead of extending in vstack mode",
    )
    ravel_inputs = traits.Bool(
        False, usedefault=True, desc="ravel inputs when no_flatten is False"
    )


class MergeOutputSpec(TraitedSpec):
    out = traits.List(desc="Merged output")


def _ravel(in_val):
    if not isinstance(in_val, list):
        return in_val
    flat_list = []
    for val in in_val:
        raveled_val = _ravel(val)
        if isinstance(raveled_val, list):
            flat_list.extend(raveled_val)
        else:
            flat_list.append(raveled_val)
    return flat_list


class Merge(IOBase):
    """Basic interface class to merge inputs into a single list

    ``Merge(1)`` will merge a list of lists

    Examples
    --------

    >>> from nipype.interfaces.utility import Merge
    >>> mi = Merge(3)
    >>> mi.inputs.in1 = 1
    >>> mi.inputs.in2 = [2, 5]
    >>> mi.inputs.in3 = 3
    >>> out = mi.run()
    >>> out.outputs.out
    [1, 2, 5, 3]

    >>> merge = Merge(1)
    >>> merge.inputs.in1 = [1, [2, 5], 3]
    >>> out = merge.run()
    >>> out.outputs.out
    [1, [2, 5], 3]

    >>> merge = Merge(1)
    >>> merge.inputs.in1 = [1, [2, 5], 3]
    >>> merge.inputs.ravel_inputs = True
    >>> out = merge.run()
    >>> out.outputs.out
    [1, 2, 5, 3]

    >>> merge = Merge(1)
    >>> merge.inputs.in1 = [1, [2, 5], 3]
    >>> merge.inputs.no_flatten = True
    >>> out = merge.run()
    >>> out.outputs.out
    [[1, [2, 5], 3]]
    """

    input_spec = MergeInputSpec
    output_spec = MergeOutputSpec

    def __init__(self, numinputs=0, **inputs):
        super(Merge, self).__init__(**inputs)
        self._numinputs = numinputs
        if numinputs >= 1:
            input_names = ["in%d" % (i + 1) for i in range(numinputs)]
        else:
            input_names = []
        add_traits(self.inputs, input_names)

    def _list_outputs(self):
        outputs = self._outputs().get()
        out = []

        if self._numinputs < 1:
            return outputs
        else:
            getval = lambda idx: getattr(self.inputs, "in%d" % (idx + 1))
            values = [
                getval(idx) for idx in range(self._numinputs) if isdefined(getval(idx))
            ]

        if self.inputs.axis == "vstack":
            for value in values:
                if isinstance(value, list) and not self.inputs.no_flatten:
                    out.extend(_ravel(value) if self.inputs.ravel_inputs else value)
                else:
                    out.append(value)
        else:
            lists = [ensure_list(val) for val in values]
            out = [[val[i] for val in lists] for i in range(len(lists[0]))]
        outputs["out"] = out
        return outputs


class RenameInputSpec(DynamicTraitedSpec):
    in_file = File(exists=True, mandatory=True, desc="file to rename")
    keep_ext = traits.Bool(
        desc=("Keep in_file extension, replace " "non-extension component of name")
    )
    format_string = Str(
        mandatory=True, desc="Python formatting string for output template"
    )
    parse_string = Str(
        desc="Python regexp parse string to define " "replacement inputs"
    )
    use_fullpath = traits.Bool(
        False, usedefault=True, desc="Use full path as input to regex parser"
    )


class RenameOutputSpec(TraitedSpec):
    out_file = File(exists=True, desc="softlink to original file with new name")


class Rename(SimpleInterface, IOBase):
    """Change the name of a file based on a mapped format string.

    To use additional inputs that will be defined at run-time, the class
    constructor must be called with the format template, and the fields
    identified will become inputs to the interface.

    Additionally, you may set the parse_string input, which will be run
    over the input filename with a regular expressions search, and will
    fill in additional input fields from matched groups. Fields set with
    inputs have precedence over fields filled in with the regexp match.

    Examples
    --------

    >>> from nipype.interfaces.utility import Rename
    >>> rename1 = Rename()
    >>> rename1.inputs.in_file = os.path.join(datadir, "zstat1.nii.gz") # datadir is a directory with exemplary files, defined in conftest.py
    >>> rename1.inputs.format_string = "Faces-Scenes.nii.gz"
    >>> res = rename1.run()          # doctest: +SKIP
    >>> res.outputs.out_file         # doctest: +SKIP
    'Faces-Scenes.nii.gz"            # doctest: +SKIP

    >>> rename2 = Rename(format_string="%(subject_id)s_func_run%(run)02d")
    >>> rename2.inputs.in_file = os.path.join(datadir, "functional.nii")
    >>> rename2.inputs.keep_ext = True
    >>> rename2.inputs.subject_id = "subj_201"
    >>> rename2.inputs.run = 2
    >>> res = rename2.run()          # doctest: +SKIP
    >>> res.outputs.out_file         # doctest: +SKIP
    'subj_201_func_run02.nii'        # doctest: +SKIP

    >>> rename3 = Rename(format_string="%(subject_id)s_%(seq)s_run%(run)02d.nii")
    >>> rename3.inputs.in_file = os.path.join(datadir, "func_epi_1_1.nii")
    >>> rename3.inputs.parse_string = r"func_(?P<seq>\w*)_.*"
    >>> rename3.inputs.subject_id = "subj_201"
    >>> rename3.inputs.run = 2
    >>> res = rename3.run()          # doctest: +SKIP
    >>> res.outputs.out_file         # doctest: +SKIP
    'subj_201_epi_run02.nii'         # doctest: +SKIP

    """

    input_spec = RenameInputSpec
    output_spec = RenameOutputSpec

    def __init__(self, format_string=None, **inputs):
        super(Rename, self).__init__(**inputs)
        if format_string is not None:
            self.inputs.format_string = format_string
            self.fmt_fields = re.findall(r"%\((.+?)\)", format_string)
            add_traits(self.inputs, self.fmt_fields)
        else:
            self.fmt_fields = []

    def _rename(self):
        fmt_dict = dict()
        if isdefined(self.inputs.parse_string):
            if isdefined(self.inputs.use_fullpath) and self.inputs.use_fullpath:
                m = re.search(self.inputs.parse_string, self.inputs.in_file)
            else:
                m = re.search(
                    self.inputs.parse_string, os.path.split(self.inputs.in_file)[1]
                )
            if m:
                fmt_dict.update(m.groupdict())
        for field in self.fmt_fields:
            val = getattr(self.inputs, field)
            if isdefined(val):
                fmt_dict[field] = getattr(self.inputs, field)
        if self.inputs.keep_ext:
            fmt_string = "".join(
                [self.inputs.format_string, split_filename(self.inputs.in_file)[2]]
            )
        else:
            fmt_string = self.inputs.format_string
        return fmt_string % fmt_dict

    def _run_interface(self, runtime):
        runtime.returncode = 0
        out_file = os.path.join(runtime.cwd, self._rename())
        _ = copyfile(self.inputs.in_file, out_file)
        self._results["out_file"] = out_file
        return runtime


class SplitInputSpec(BaseInterfaceInputSpec):
    inlist = traits.List(traits.Any, mandatory=True, desc="list of values to split")
    splits = traits.List(
        traits.Int,
        mandatory=True,
        desc="Number of outputs in each split - should add to number of inputs",
    )
    squeeze = traits.Bool(
        False, usedefault=True, desc="unfold one-element splits removing the list"
    )


class Split(IOBase):
    """Basic interface class to split lists into multiple outputs

    Examples
    --------

    >>> from nipype.interfaces.utility import Split
    >>> sp = Split()
    >>> _ = sp.inputs.trait_set(inlist=[1, 2, 3], splits=[2, 1])
    >>> out = sp.run()
    >>> out.outputs.out1
    [1, 2]

    """

    input_spec = SplitInputSpec
    output_spec = DynamicTraitedSpec

    def _add_output_traits(self, base):
        undefined_traits = {}
        for i in range(len(self.inputs.splits)):
            key = "out%d" % (i + 1)
            base.add_trait(key, traits.Any)
            undefined_traits[key] = Undefined
        base.trait_set(trait_change_notify=False, **undefined_traits)
        return base

    def _list_outputs(self):
        outputs = self._outputs().get()
        if isdefined(self.inputs.splits):
            if sum(self.inputs.splits) != len(self.inputs.inlist):
                raise RuntimeError("sum of splits != num of list elements")
            splits = [0]
            splits.extend(self.inputs.splits)
            splits = np.cumsum(splits)
            for i in range(len(splits) - 1):
                val = np.array(self.inputs.inlist)[splits[i] : splits[i + 1]].tolist()
                if self.inputs.squeeze and len(val) == 1:
                    val = val[0]
                outputs["out%d" % (i + 1)] = val
        return outputs


class SelectInputSpec(BaseInterfaceInputSpec):
    inlist = InputMultiPath(
        traits.Any, mandatory=True, desc="list of values to choose from"
    )
    index = InputMultiPath(
        traits.Int, mandatory=True, desc="0-based indices of values to choose"
    )


class SelectOutputSpec(TraitedSpec):
    out = OutputMultiPath(traits.Any, desc="list of selected values")


class Select(IOBase):
    """Basic interface class to select specific elements from a list

    Examples
    --------

    >>> from nipype.interfaces.utility import Select
    >>> sl = Select()
    >>> _ = sl.inputs.trait_set(inlist=[1, 2, 3, 4, 5], index=[3])
    >>> out = sl.run()
    >>> out.outputs.out
    4

    >>> _ = sl.inputs.trait_set(inlist=[1, 2, 3, 4, 5], index=[3, 4])
    >>> out = sl.run()
    >>> out.outputs.out
    [4, 5]

    """

    input_spec = SelectInputSpec
    output_spec = SelectOutputSpec

    def _list_outputs(self):
        outputs = self._outputs().get()
        out = np.array(self.inputs.inlist)[np.array(self.inputs.index)].tolist()
        outputs["out"] = out
        return outputs


class AssertEqualInputSpec(BaseInterfaceInputSpec):
    volume1 = File(exists=True, mandatory=True)
    volume2 = File(exists=True, mandatory=True)


class AssertEqual(BaseInterface):
    input_spec = AssertEqualInputSpec

    def _run_interface(self, runtime):
        import nibabel as nb

        data1 = np.asanyarray(nb.load(self.inputs.volume1))
        data2 = np.asanyarray(nb.load(self.inputs.volume2))

        if not np.array_equal(data1, data2):
            raise RuntimeError("Input images are not exactly equal")
        return runtime