"""
Transformations that primarily involve numerical computation on variables.
"""
from __future__ import division
import math
import numpy as np
import pandas as pd
from bids.utils import listify
from .base import Transformation
from bids.analysis import hrf
from bids.variables import SparseRunVariable,  DenseRunVariable


class Convolve(Transformation):
    """Convolve the input variable with an HRF.

    Parameters
    ----------
    var : Variable
        The variable to convolve.
    model : str
        The name of the HRF model to apply. Must be one of 'spm',
        'glover', or 'fir'.
    derivative : bool
        Whether or not to include the temporal derivative.
    dispersion : bool
        Whether or not to include the dispersion derivative.
    fir_delays : iterable
        A list or iterable of delays to use if model is
        'fir' (ignored otherwise). Spacing between delays must be fixed.

    Notes
    -----
    Uses the HRF convolution functions implemented in nistats.
    """

    _input_type = 'variable'
    _return_type = 'variable'

    def _transform(self, var, model='spm', derivative=False, dispersion=False,
                   fir_delays=None):

        model = model.lower()

        df = var.to_df(entities=False)

        if isinstance(var, SparseRunVariable):
            sampling_rate = self.collection.sampling_rate
            dur = var.get_duration()
            resample_frames = np.linspace(
                0, dur, int(math.ceil(dur * sampling_rate)), endpoint=False)

        else:
            resample_frames = df['onset'].values
            sampling_rate = var.sampling_rate

        vals = df[['onset', 'duration', 'amplitude']].values.T

        if model in ['spm', 'glover']:
            if derivative:
                model += ' + derivative'
            if dispersion:
                model += ' + dispersion'
        elif model != 'fir':
            raise ValueError("Model must be one of 'spm', 'glover', or 'fir'.")

        # Minimum interval between event onsets/duration
        # Used to compute oversampling factor to prevent information loss
        unique_onsets = np.unique(np.sort(df.onset))
        if len(unique_onsets) > 1:
            min_interval = min(np.ediff1d(unique_onsets).min(),
                               df.duration.min())
            oversampling = np.ceil(2*(1 / (min_interval * sampling_rate)))
        else:
            oversampling = 2
        convolved = hrf.compute_regressor(
            vals, model, resample_frames, fir_delays=fir_delays, min_onset=0,
            oversampling=oversampling
            )

        return DenseRunVariable(
            name=var.name, values=convolved[0], run_info=var.run_info,
            source=var.source, sampling_rate=sampling_rate)


class Demean(Transformation):

    def _transform(self, data):
        return data - data.mean()


class Orthogonalize(Transformation):

    _variables_used = ('variables', 'other')
    _densify = ('variables', 'other')
    _align = ('other')

    def _transform(self, var, other):

        other = listify(other)

        # Set up X matrix and slice into it based on target variable indices
        X = np.array([self._variables[c].values.values.squeeze()
                      for c in other]).T
        X = X[var.index, :]
        assert len(X) == len(var)
        y = var.values
        _aX = np.c_[np.ones(len(y)), X]
        coefs, resids, rank, s = np.linalg.lstsq(_aX, y)
        result = pd.DataFrame(y - X.dot(coefs[1:]), index=var.index)
        return result


class Product(Transformation):

    _loopable = False
    _groupable = False
    _align = True
    _output_required = True

    def _transform(self, data):
        data = pd.concat(data, axis=1, sort=True)
        return data.product(1)


class Scale(Transformation):
    """Scale a variable.

    Parameters
    ----------
    data : :obj:`pandas.Series` or :obj:`pandas.DataFrame`
        The variables to scale.
    demean : bool
        If True, demean each column.
    rescale : bool
        If True, divide variables by their standard deviation.
    replace_na : str
        Whether/when to replace missing values with 0. If
        None, no replacement is performed. If 'before', missing values are
        replaced with 0's before scaling. If 'after', missing values are
        replaced with 0 after scaling.
    """

    def _transform(self, data, demean=True, rescale=True, replace_na=None):
        if replace_na == 'before':
            data = data.fillna(0.)
        if demean:
            data -= data.mean()
        if rescale:
            data /= data.std()
        if replace_na == 'after':
            data = data.fillna(0.)
        return data


class Sum(Transformation):

    _loopable = False
    _groupable = False
    _align = True
    _output_required = True

    def _transform(self, data, weights=None):
        data = pd.concat(data, axis=1, sort=True)
        if weights is None:
            weights = np.ones(data.shape[1])
        else:
            weights = np.array(weights)
            if len(weights.ravel()) != data.shape[1]:
                raise ValueError("If weights are passed to sum(), the number "
                                 "of elements must equal number of variables"
                                 "being summed.")
        return (data * weights).sum(axis=1)



class Threshold(Transformation):
    """Threshold and/or binarize a variable.

    Parameters
    ----------
    data :obj:`pandas.Series` or :obj:`pandas.DataFrame`
        The pandas structure to threshold.
    threshold : float
        The value to binarize around (values above will
        be assigned 1, values below will be assigned 0).
    binarize : bool
        If True, binarizes all non-zero values (i.e., every
        non-zero value will be set to 1).
    above : bool
        Specifies which values to retain with respect to the
        cut-off. If True, all value above the threshold will be kept; if
        False, all values below the threshold will be kept. Defaults to
        True.
    signed : bool
        Specifies whether to treat the threshold as signed
        (default) or unsigned. For example, when passing above=True and
        threshold=3, if signed=True, all and only values above +3 would be
        retained. If signed=False, all absolute values > 3 would be retained
        (i.e.,values in  the range -3 < X < 3 would be set to 0).
    """

    _groupable = False

    def _transform(self, data, threshold=0., binarize=False, above=True,
                   signed=True):
        if not signed:
            threshold = np.abs(threshold)
            data = data.abs()
        keep = data >= threshold if above else data <= threshold
        data[~keep] = 0
        if binarize:
            data[keep] = 1
        return data


class And(Transformation):
    """Logical AND on two or more variables.

    Parameters
    ----------
    dfs : list of :obj:`pandas.DataFrame`
        variables to enter into the conjunction.
    """

    _loopable = False
    _groupable = False
    _output_required = True

    def _transform(self, dfs):
        df = pd.concat(dfs, axis=1, sort=True)
        return df.all(axis=1).astype(int)


class Not(Transformation):
    """Logical negation of a variable.

    Parameters
    ----------
    var : :obj:`pandas.Series`
        Variable to negate. Must be convertible to bool.
    """

    _loopable = True
    _groupable = False

    def _transform(self, var):
        return ~var.astype(bool)


class Or(Transformation):
    """Logical OR (inclusive) on two or more variables.

    Parameters
    ----------
    dfs : list of :obj:`pandas.DataFrame`
        variables to enter into the disjunction.
    """

    _loopable = False
    _groupable = False
    _output_required = True

    def _transform(self, dfs):
        df = pd.concat(dfs, axis=1, sort=True)
        return df.any(axis=1).astype(int)

@@ -3444,16 +3444,28 @@
 q(_aX, y
+, rcond=None
 )%0A      

Remove future warning