# Buggy code
def binned_statistic(x, values, statistic="mean", bins=10, range=None):
    """
    Compute a binned statistic for one or more sets of data.

    This is a generalization of a histogram function.  A histogram divides
    the space into bins, and returns the count of the number of points in
    each bin.  This function allows the computation of the sum, mean, median,
    or other statistic of the values (or set of values) within each bin.

    Parameters
    ----------
    x : (N,) array_like
        A sequence of values to be binned.
    values : (N,) array_like or list of (N,) array_like
        The data on which the statistic will be computed.  This must be
        the same shape as `x`, or a set of sequences - each the same shape as
        `x`.  If `values` is a set of sequences, the statistic will be computed
        on each independently.
    statistic : string or callable, optional
        The statistic to compute (default is 'mean').
        The following statistics are available:

          * 'mean' : compute the mean of values for points within each bin.
            Empty bins will be represented by NaN.
          * 'std' : compute the standard deviation within each bin. This
            is implicitly calculated with ddof=0.
          * 'median' : compute the median of values for points within each
            bin. Empty bins will be represented by NaN.
          * 'count' : compute the count of points within each bin.  This is
            identical to an unweighted histogram.  `values` array is not
            referenced.
          * 'sum' : compute the sum of values for points within each bin.
            This is identical to a weighted histogram.
          * 'min' : compute the minimum of values for points within each bin.
            Empty bins will be represented by NaN.
          * 'max' : compute the maximum of values for point within each bin.
            Empty bins will be represented by NaN.
          * function : a user-defined function which takes a 1D array of
            values, and outputs a single numerical statistic. This function
            will be called on the values in each bin.  Empty bins will be
            represented by function([]), or NaN if this returns an error.

    bins : int or sequence of scalars, optional
        If `bins` is an int, it defines the number of equal-width bins in the
        given range (10 by default).  If `bins` is a sequence, it defines the
        bin edges, including the rightmost edge, allowing for non-uniform bin
        widths.  Values in `x` that are smaller than lowest bin edge are
        assigned to bin number 0, values beyond the highest bin are assigned to
        ``bins[-1]``.  If the bin edges are specified, the number of bins will
        be, (nx = len(bins)-1).
    range : (float, float) or [(float, float)], optional
        The lower and upper range of the bins.  If not provided, range
        is simply ``(x.min(), x.max())``.  Values outside the range are
        ignored.

    Returns
    -------
    statistic : array
        The values of the selected statistic in each bin.
    bin_edges : array of dtype float
        Return the bin edges ``(length(statistic)+1)``.
    binnumber: 1-D ndarray of ints
        Indices of the bins (corresponding to `bin_edges`) in which each value
        of `x` belongs.  Same length as `values`.  A binnumber of `i` means the
        corresponding value is between (bin_edges[i-1], bin_edges[i]).

    See Also
    --------
    numpy.digitize, numpy.histogram, binned_statistic_2d, binned_statistic_dd

    Notes
    -----
    All but the last (righthand-most) bin is half-open.  In other words, if
    `bins` is ``[1, 2, 3, 4]``, then the first bin is ``[1, 2)`` (including 1,
    but excluding 2) and the second ``[2, 3)``.  The last bin, however, is
    ``[3, 4]``, which *includes* 4.

    .. versionadded:: 0.11.0

    Examples
    --------
    >>> from scipy import stats
    >>> import matplotlib.pyplot as plt

    First some basic examples:

    Create two evenly spaced bins in the range of the given sample, and sum the
    corresponding values in each of those bins:

    >>> values = [1.0, 1.0, 2.0, 1.5, 3.0]
    >>> stats.binned_statistic([1, 1, 2, 5, 7], values, 'sum', bins=2)
    (array([ 4. ,  4.5]), array([ 1.,  4.,  7.]), array([1, 1, 1, 2, 2]))

    Multiple arrays of values can also be passed.  The statistic is calculated
    on each set independently:

    >>> values = [[1.0, 1.0, 2.0, 1.5, 3.0], [2.0, 2.0, 4.0, 3.0, 6.0]]
    >>> stats.binned_statistic([1, 1, 2, 5, 7], values, 'sum', bins=2)
    (array([[ 4. ,  4.5], [ 8. ,  9. ]]), array([ 1.,  4.,  7.]),
        array([1, 1, 1, 2, 2]))

    >>> stats.binned_statistic([1, 2, 1, 2, 4], np.arange(5), statistic='mean',
    ...                        bins=3)
    (array([ 1.,  2.,  4.]), array([ 1.,  2.,  3.,  4.]),
        array([1, 2, 1, 2, 3]))

    As a second example, we now generate some random data of sailing boat speed
    as a function of wind speed, and then determine how fast our boat is for
    certain wind speeds:

    >>> windspeed = 8 * np.random.rand(500)
    >>> boatspeed = .3 * windspeed**.5 + .2 * np.random.rand(500)
    >>> bin_means, bin_edges, binnumber = stats.binned_statistic(windspeed,
    ...                 boatspeed, statistic='median', bins=[1,2,3,4,5,6,7])
    >>> plt.figure()
    >>> plt.plot(windspeed, boatspeed, 'b.', label='raw data')
    >>> plt.hlines(bin_means, bin_edges[:-1], bin_edges[1:], colors='g', lw=5,
    ...            label='binned statistic of data')
    >>> plt.legend()

    Now we can use ``binnumber`` to select all datapoints with a windspeed
    below 1:

    >>> low_boatspeed = boatspeed[binnumber == 0]

    As a final example, we will use ``bin_edges`` and ``binnumber`` to make a
    plot of a distribution that shows the mean and distribution around that
    mean per bin, on top of a regular histogram and the probability
    distribution function:

    >>> x = np.linspace(0, 5, num=500)
    >>> x_pdf = stats.maxwell.pdf(x)
    >>> samples = stats.maxwell.rvs(size=10000)

    >>> bin_means, bin_edges, binnumber = stats.binned_statistic(x, x_pdf,
    ...         statistic='mean', bins=25)
    >>> bin_width = (bin_edges[1] - bin_edges[0])
    >>> bin_centers = bin_edges[1:] - bin_width/2

    >>> plt.figure()
    >>> plt.hist(samples, bins=50, density=True, histtype='stepfilled',
    ...          alpha=0.2, label='histogram of data')
    >>> plt.plot(x, x_pdf, 'r-', label='analytical pdf')
    >>> plt.hlines(bin_means, bin_edges[:-1], bin_edges[1:], colors='g', lw=2,
    ...            label='binned statistic of data')
    >>> plt.plot((binnumber - 0.5) * bin_width, x_pdf, 'g.', alpha=0.5)
    >>> plt.legend(fontsize=10)
    >>> plt.show()

    """
    try:
        N = len(bins)
    except TypeError:
        N = 1

    if N != 1:
        bins = [np.asarray(bins, float)]

    if range is not None:
        if len(range) == 2:
            range = [range]

    medians, edges, binnumbers = binned_statistic_dd(
        [x], values, statistic, bins, range
    )

    return BinnedStatisticResult(medians, edges[0], binnumbers)


# Traceback (OverflowError)
---------------------------------------------------------------------------
OverflowError                             Traceback (most recent call last)
<ipython-input-86-0811ef0d48f7> in <module>()
16         sl = SpectrumList([x for x in spectrum_list if x.id in ids])
17         print sl.tolist()
---> 18         sl_df = make_spectrumlist(sl)
19
20         pls_df = pd.concat([sl_df, mtd["Diagnosis"]], axis=1).dropna(axis=0)

<ipython-input-63-51c201b1e4f9> in make_spectrumlist(sl)
1 def make_spectrumlist(sl):
----> 2     sl.binning(bin_size=0.5, mass_statistic="max")
3     sl.value_imputation(method="basic", threshold=0.1)
4     sl.normalise(method="tic")
5     sl.transform(method="log10")

/home/keo7/ProjectsNew/metabolomics/denisa-saliva/env/local/lib/python2.7/site-packages/dimepy/SpectrumList.pyc in binning(self, bin_size, int_statistic, mass_statistic, inplace)
174
175         for spectrum in self._spectrum:
--> 176             bins, intensities = _apply_binning(spectrum, bins)
177             if inplace:
178                 spectrum.masses = bins

/home/keo7/ProjectsNew/metabolomics/denisa-saliva/env/local/lib/python2.7/site-packages/dimepy/SpectrumList.pyc in _apply_binning(spectrum, bins)
160                 spectrum.intensities,
161                 bins=bins,
--> 162                 statistic=int_statistic)
163             indx = np.invert(np.isnan(b_i))
164

/home/keo7/ProjectsNew/metabolomics/denisa-saliva/env/local/lib/python2.7/site-packages/scipy/stats/_binned_statistic.pyc in binned_statistic(x, values, statistic, bins, range)
177
178     medians, edges, binnumbers = binned_statistic_dd(
--> 179         [x], values, statistic, bins, range)
180
181     return BinnedStatisticResult(medians, edges[0], binnumbers)

/home/keo7/ProjectsNew/metabolomics/denisa-saliva/env/local/lib/python2.7/site-packages/scipy/stats/_binned_statistic.pyc in binned_statistic_dd(sample, values, statistic, bins, range, expand_binnumbers)
534     for i in xrange(Ndim):
535         # Find the rounding precision
--> 536         decimal = int(-np.log10(dedges[i].min())) + 6
537         # Find which points are on the rightmost edge.
538         on_edge = np.where(np.around(sample[:, i], decimal) ==

OverflowError: cannot convert float infinity to integer

# Fixed code
def binned_statistic(x, values, statistic="mean", bins=10, range=None):
    """
    Compute a binned statistic for one or more sets of data.

    This is a generalization of a histogram function.  A histogram divides
    the space into bins, and returns the count of the number of points in
    each bin.  This function allows the computation of the sum, mean, median,
    or other statistic of the values (or set of values) within each bin.

    Parameters
    ----------
    x : (N,) array_like
        A sequence of values to be binned.
    values : (N,) array_like or list of (N,) array_like
        The data on which the statistic will be computed.  This must be
        the same shape as `x`, or a set of sequences - each the same shape as
        `x`.  If `values` is a set of sequences, the statistic will be computed
        on each independently.
    statistic : string or callable, optional
        The statistic to compute (default is 'mean').
        The following statistics are available:

          * 'mean' : compute the mean of values for points within each bin.
            Empty bins will be represented by NaN.
          * 'std' : compute the standard deviation within each bin. This
            is implicitly calculated with ddof=0.
          * 'median' : compute the median of values for points within each
            bin. Empty bins will be represented by NaN.
          * 'count' : compute the count of points within each bin.  This is
            identical to an unweighted histogram.  `values` array is not
            referenced.
          * 'sum' : compute the sum of values for points within each bin.
            This is identical to a weighted histogram.
          * 'min' : compute the minimum of values for points within each bin.
            Empty bins will be represented by NaN.
          * 'max' : compute the maximum of values for point within each bin.
            Empty bins will be represented by NaN.
          * function : a user-defined function which takes a 1D array of
            values, and outputs a single numerical statistic. This function
            will be called on the values in each bin.  Empty bins will be
            represented by function([]), or NaN if this returns an error.

    bins : int or sequence of scalars, optional
        If `bins` is an int, it defines the number of equal-width bins in the
        given range (10 by default).  If `bins` is a sequence, it defines the
        bin edges, including the rightmost edge, allowing for non-uniform bin
        widths.  Values in `x` that are smaller than lowest bin edge are
        assigned to bin number 0, values beyond the highest bin are assigned to
        ``bins[-1]``.  If the bin edges are specified, the number of bins will
        be, (nx = len(bins)-1).
    range : (float, float) or [(float, float)], optional
        The lower and upper range of the bins.  If not provided, range
        is simply ``(x.min(), x.max())``.  Values outside the range are
        ignored.

    Returns
    -------
    statistic : array
        The values of the selected statistic in each bin.
    bin_edges : array of dtype float
        Return the bin edges ``(length(statistic)+1)``.
    binnumber: 1-D ndarray of ints
        Indices of the bins (corresponding to `bin_edges`) in which each value
        of `x` belongs.  Same length as `values`.  A binnumber of `i` means the
        corresponding value is between (bin_edges[i-1], bin_edges[i]).

    See Also
    --------
    numpy.digitize, numpy.histogram, binned_statistic_2d, binned_statistic_dd

    Notes
    -----
    All but the last (righthand-most) bin is half-open.  In other words, if
    `bins` is ``[1, 2, 3, 4]``, then the first bin is ``[1, 2)`` (including 1,
    but excluding 2) and the second ``[2, 3)``.  The last bin, however, is
    ``[3, 4]``, which *includes* 4.

    .. versionadded:: 0.11.0

    Examples
    --------
    >>> from scipy import stats
    >>> import matplotlib.pyplot as plt

    First some basic examples:

    Create two evenly spaced bins in the range of the given sample, and sum the
    corresponding values in each of those bins:

    >>> values = [1.0, 1.0, 2.0, 1.5, 3.0]
    >>> stats.binned_statistic([1, 1, 2, 5, 7], values, 'sum', bins=2)
    BinnedStatisticResult(statistic=array([4. , 4.5]), bin_edges=array([1., 4., 7.]), binnumber=array([1, 1, 1, 2, 2]))

    Multiple arrays of values can also be passed.  The statistic is calculated
    on each set independently:

    >>> values = [[1.0, 1.0, 2.0, 1.5, 3.0], [2.0, 2.0, 4.0, 3.0, 6.0]]
    >>> stats.binned_statistic([1, 1, 2, 5, 7], values, 'sum', bins=2)
    BinnedStatisticResult(statistic=array([[4. , 4.5],
           [8. , 9. ]]), bin_edges=array([1., 4., 7.]), binnumber=array([1, 1, 1, 2, 2]))

    >>> stats.binned_statistic([1, 2, 1, 2, 4], np.arange(5), statistic='mean',
    ...                        bins=3)
    BinnedStatisticResult(statistic=array([1., 2., 4.]), bin_edges=array([1., 2., 3., 4.]), binnumber=array([1, 2, 1, 2, 3]))

    As a second example, we now generate some random data of sailing boat speed
    as a function of wind speed, and then determine how fast our boat is for
    certain wind speeds:

    >>> windspeed = 8 * np.random.rand(500)
    >>> boatspeed = .3 * windspeed**.5 + .2 * np.random.rand(500)
    >>> bin_means, bin_edges, binnumber = stats.binned_statistic(windspeed,
    ...                 boatspeed, statistic='median', bins=[1,2,3,4,5,6,7])
    >>> plt.figure()
    >>> plt.plot(windspeed, boatspeed, 'b.', label='raw data')
    >>> plt.hlines(bin_means, bin_edges[:-1], bin_edges[1:], colors='g', lw=5,
    ...            label='binned statistic of data')
    >>> plt.legend()

    Now we can use ``binnumber`` to select all datapoints with a windspeed
    below 1:

    >>> low_boatspeed = boatspeed[binnumber == 0]

    As a final example, we will use ``bin_edges`` and ``binnumber`` to make a
    plot of a distribution that shows the mean and distribution around that
    mean per bin, on top of a regular histogram and the probability
    distribution function:

    >>> x = np.linspace(0, 5, num=500)
    >>> x_pdf = stats.maxwell.pdf(x)
    >>> samples = stats.maxwell.rvs(size=10000)

    >>> bin_means, bin_edges, binnumber = stats.binned_statistic(x, x_pdf,
    ...         statistic='mean', bins=25)
    >>> bin_width = (bin_edges[1] - bin_edges[0])
    >>> bin_centers = bin_edges[1:] - bin_width/2

    >>> plt.figure()
    >>> plt.hist(samples, bins=50, density=True, histtype='stepfilled',
    ...          alpha=0.2, label='histogram of data')
    >>> plt.plot(x, x_pdf, 'r-', label='analytical pdf')
    >>> plt.hlines(bin_means, bin_edges[:-1], bin_edges[1:], colors='g', lw=2,
    ...            label='binned statistic of data')
    >>> plt.plot((binnumber - 0.5) * bin_width, x_pdf, 'g.', alpha=0.5)
    >>> plt.legend(fontsize=10)
    >>> plt.show()

    """
    try:
        N = len(bins)
    except TypeError:
        N = 1

    if N != 1:
        bins = [np.asarray(bins, float)]

    if range is not None:
        if len(range) == 2:
            range = [range]

    medians, edges, binnumbers = binned_statistic_dd(
        [x], values, statistic, bins, range
    )

    return BinnedStatisticResult(medians, edges[0], binnumbers)