# Source code for spacepy.datamanager

    #!/usr/bin/env python
    # -*- coding: utf-8 -*-
    """
    The datamanager classes and functions are useful for locating the correct
    data file for a particular day and manipulating data and subsets in a generic
    way.

    Authors: Jon Niehof

    Institution: University of New Hampshire

    Contact: Jonathan.Niehof@unh.edu

    Copyright 2015

    About datamanager
    -----------------

    Examples
    --------
    Examples go here

    .. currentmodule:: spacepy.datamanager

    .. rubric:: Classes

    .. autosummary::
        :template: clean_class.rst

        DataManager

    .. rubric:: Functions

    .. autosummary::

        apply_index
        array_interleave
        axis_index
        flatten_idx
        insert_fill
        rev_index
        values_to_steps
    """

    __all__ = ["DataManager", "apply_index", "array_interleave", "axis_index",
               "flatten_idx", "insert_fill", "rev_index", "values_to_steps"]

    import datetime
    import operator
    import os.path
    import re

    import numpy

    class DataManager(object):
        """
        THIS CLASS IS NOT YET COMPLETE, doesn't do much useful.

        Will have to do something that allows the config file to specify regex
        and other things, and then just the directory to be changed (since
        regex, etc.

        Parameters
        ==========
        directories : list
            A list of directories that might contain the data
        file_fmt : string
            Regular expression that matches the files desired. Will also recognize
            strftime parameters %w %d %m %y %Y %H %M %s %j %U %W, all zero-pad.
            https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior
            Can have subdirectory reference, but separator should be unix-style,
            with no leading slash.

        period : string
            Size of file; can be a number followed by one of d, m, y, H, M, s.
            Anything else is assumed to be "irregular" and files treated
            as if there are neither gaps nor overlaps in the sequence.
            If not specified, will be assumed to match one count of the
            smallest unit in the format string.

        Examples
        =======
        """
        def __init__(self, directories, file_fmt, descend=False, period=None):
            """
            """
            #Duplicate from class docstring. Consider autoclass_content = "both"
            #Convert to system path format
            directories = [os.path.expandvars(os.path.expanduser(
                os.path.normpath(d))) for d in directories]
            file_fmt = os.path.normpath(file_fmt)
            #The period matching might go into RePath
            if period is None:
                period = next(
                    ('1{0}'.format(i) for i in 'sMHdmyY' if i in file_fmt),
                    None)
            elif not re.match(r'^\d+[yYmdHMs]$', period):
                period = None #irregular, fun!
            self.directories = directories
            self.descend = descend
            self.period = period
            self.file_fmt = RePath(file_fmt)

        def get_filename(self, dt):
            """
            Returns the filename corresponding to a particular point in time
            """
            if self.period:
                flist = self.files_matching(dt)
            else:
                raise NotImplementedError
            #Now figure out the priority..

        def files_matching(self, dt=None):
            """
            Return all the files matching this file format
            """
            #Use os.walk. If descend is False, only continue for matching
            #the re to this point. If True, compare branch to entire re but
            #walk everything
            for d in self.directories:
                for (dirpath, dirnames, filenames) in \
                    os.walk(d, topdown=True, followlinks=True):
                    #dirpath is FULL DIRECTORY to this point
                    relpath = dirpath[len(d) + 1:]
                    if not self.descend:
                        if relpath and not \
                           self.file_fmt.match(relpath, dt, 'start'):
                            continue
                        for i in range(-len(dirnames), 0):
                            if not self.file_fmt.match(os.path.join(
                                    relpath, dirnames[i]), dt, 'start'):
                                del dirnames[i]
                    for f in filenames:
                        if self.file_fmt.match(os.path.join(relpath, f), dt,
                                               'end' if self.descend else None):
                            yield os.path.join(dirpath, f)

    class RePath(object):
        """
        A path based on a regular expression + time format

        Parameters
        ==========
        expression : string
            Regular expression that matches the files desired. Will also recognize
            strftime parameters %w %d %m %y %Y %H %M %s %j %U %W, all zero-pad.
            https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior
            Can have subdirectory reference, but separator should be unix-style,
            with no leading slash.
            Matching is normally done against entire string, anchors should NOT
            be included.
        """
        fmt_to_re = { 'd': r'[0-3]\d', 'm': r'[0-2]\d', 'y': r'\d\d', 'Y': r'\d{4}',
                      'H': r'[0-5]\d', 'M': r'[0-5]\d', 's': r'[0-6]\d',
                      'j': r'[0-3]\d\d', 'U': r'[0-5]\d', 'W': r'[0-5]\d'
                      }
        def __init__(self, expression):
            self.file_fmt = expression
            #This should have backrefs where the same format occurs twice
            #(year in both directory and file, for example)
            self.file_re = re.sub(r'(?!(?:%%)+)%([wdmyYHMsjUW])',
                                 lambda x: self.fmt_to_re[x.group(1)],
                                  expression)
            self.file_fmt_split = self.path_split(self.file_fmt)
            self.file_re_split = self.path_split(self.file_re)

        def match(self, string, dt=None, where=None):
            """
            Matches a string against a path or part thereof, optionally anchored
            at a particular date/time

            Other Parameters
            ================
            dt : datetime.datetime
                The time to specifically match; otherwise matches all files.
            where : str
                Where to match: None to match the string to the entire path
                (default); ``'start'`` to match entire string against the start
                of the path; ``'end'`` to match entire path against end of string.
                Note this matches the last elements of the string, not just
                the last characters, i.e., ``oo/bar`` will not match ``foo/bar``.
                Similarly, ``'start'`` matches the first elements of the path,
                i.e., ``foo/ba`` will not match ``foo/bar``
                ``start`` matches subset of path, i.e., the string is a directory
                that may contain full matches further down the tree. ``end``
                matches a subset of the string, i.e, the string is a
                path to a file that would be a complete match except it has
                additional path elements leading. This is the order that tends to
                be useful.

            Returns
            =======
            out : re.MatchObject
                The result of the match.
            """
            datestr = (datetime.datetime.strftime(dt, self.file_fmt)
                       if dt else self.file_re)
            if where is None:
                pat = datestr
            elif where.lower() == 'end': #Cut down string to match path pattern
                pat = datestr
                string = self.path_slice(string, -len(self.file_re_split), None, 1)
            elif where.lower() == 'start': #Does path pattern start like string?
                pat = self.path_slice(datestr,
                                      0, len(self.path_split(string)))
            else:
                raise(ValueError("where must be 'start', 'stop', or None, not {0}".
                                 format(where)))
            return re.match('^' + pat + '$', string)

        @staticmethod
        def path_split(path):
            """
            Break a path apart into a list for each path element.

            Parameters
            ==========
            path : str
                Path to split

            Returns
            =======
            out : list of str
                One path element (directory or file) per item
            """
            res = []
            while path:
                path, tail = os.path.split(path)
                res.insert(0, tail)
                if path == '/':
                    res.insert(0, '/')
                    break
            return res

        @staticmethod
        def path_slice(path, start, stop=None, step=None):
            """
            Slice a path by elements, as in getitem or []

            Parameters
            ==========
            path : str
                Path to slice
            start : int
                First path element to return, or the only element if
                stop and step are not specified.

            Other Parameters
            ================
            stop : int
                First path element to NOT return, i.e., one past the last.
                If ``stop`` is not specified but ``step`` is, return to end.
            step : int
                Increment between each.

            Returns
            =======
            out : str
                Selection of the path

            Examples
            ========
            >>> path = "foo/bar/baz"
            >>> spacepy.datamanager.DataManager.path_slice(path, 1)
            "bar"
            >>> spacepy.datamanager.DataManager.path_slice(path, 0, step=2)
            "foo/baz"
            >>> spacepy.datamanager.DataManager.path_slice(path, 1, 3)
            "bar/baz"
            """
            if stop is None and step is None:
                return RePath.path_split(path)[start]
            else:
                return os.path.join(*RePath.path_split(path)[start:stop:step])

    def insert_fill(times, data, fillval=numpy.nan, tol=1.5, absolute=None, doTimes=True):
        """Populate gaps in data with fill.

        Continuous data are often treated differently from discontinuous data,
        e.g., matplotlib will draw lines connecting data points but break the line
        at fill. Often data will be irregularly sampled but also contain large
        gaps that are not explicitly marked as fill. This function adds a single
        record of explicit fill to each gap, defined as places where the spacing
        between input times is a certain multiple of the median spacing.

        Parameters
        ==========
        times : sequence
            Values representing when the data were taken. Must be one-dimensional,
            i.e., each value must be scalar. Not modified
        data : sequence
            Input data.

        Other Parameters
        ================
        fillval :
            Fill value, same type as ``data``. Default is ``numpy.nan``. If scalar,
            will be repeated to match the shape of ``data`` (minus the time axis).

            .. note::
                The default value of ``nan`` will not produce good results with
                integer input.

        tol : float
            Tolerance. A single fill value is inserted between adjacent
            values where the spacing in ``times`` is strictly greater than
            ``tol`` times the median of the spacing across all
            ``times``. The inserted time for fill is halfway between the
            time on each side. (Default 1.5)
        absolute :
            An absolute value for maximum spacing, of a type that would result from
            a difference in ``times``. If specified, ``tol`` is ignored and any gap
            strictly larger than ``absolute`` will have fill inserted.
        doTimes : boolean
            If True (default), will return a tuple of the times (with new values
            inserted for the fill records) and the data with new fill values.
            If False, will only return the data -- useful for applying fill to
            multiple arrays of data on the same timebase.

        Raises
        ======
        ValueError : if can't identify the time axis of data
            Try using :func:`numpy.rollaxis` to put the time axis first in both
            ``data`` and ``times``.

        Returns
        =======
        times, data : tuple of sequence
            Copies of input times and data, fill added in gaps (``doTimes`` True)
        data : sequence
            Copy of input data, with fill added in gaps (``doTimes`` False)

        Examples
        ========
        This example shows simple hourly data with a gap, populated with fill.
        Note that only a single fill value is inserted, to break the sequence
        of valid data rather than trying to match the existing cadence.

        >>> import datetime
        >>> import numpy
        >>> import spacepy.datamanager
        >>> t = [datetime.datetime(2012, 1, 1, 0),
                 datetime.datetime(2012, 1, 1, 1),
                 datetime.datetime(2012, 1, 1, 2),
                 datetime.datetime(2012, 1, 1, 5),
                 datetime.datetime(2012, 1, 1, 6)]
        >>> temp = [30.0, 28, 27, 32, 35]
        >>> filled_t, filled_temp = spacepy.datamanager.insert_fill(t, temp)
        >>> filled_t
        array([datetime.datetime(2012, 1, 1, 0, 0),
               datetime.datetime(2012, 1, 1, 1, 0),
               datetime.datetime(2012, 1, 1, 2, 0),
               datetime.datetime(2012, 1, 1, 3, 30),
               datetime.datetime(2012, 1, 1, 5, 0),
               datetime.datetime(2012, 1, 1, 6, 0)], dtype=object)
        >>> filled_temp
        array([ 30.,  28.,  27.,  nan,  32.,  35.])

        .. plot::
           :include-source:

           This example plots "gappy" data with and without explicit fill values.

           >>> import matplotlib.pyplot as plt
           >>> import numpy
           >>> import spacepy.datamanager
           >>> x = numpy.append(numpy.arange(0, 6, 0.1), numpy.arange(12, 18, 0.1))
           >>> y = numpy.sin(x)
           >>> xf, yf = spacepy.datamanager.insert_fill(x, y)
           >>> fig = plt.figure()
           >>> ax0 = fig.add_subplot(211)
           >>> ax0.plot(x, y)
           >>> ax1 = fig.add_subplot(212)
           >>> ax1.plot(xf, yf)
           >>> plt.show()

        """
        times = numpy.asanyarray(times)
        data = numpy.asanyarray(data)
        assert(len(times.shape) == 1)
        if len(times) == data.shape[0]:
            timeaxis = 0
        else:
            matches = numpy.nonzero(numpy.asanyarray(data.shape) == len(times))[0]
            if len(matches) != 1:
                raise ValueError(
                    "Unable to uniquely match shape of data to count of times.")
            timeaxis = matches[0]
        fillshape = numpy.delete(data.shape, timeaxis) #shape of data w/o time axis
        if numpy.shape(fillval) != fillshape:
            if numpy.shape(fillval) == ():
                fillval = numpy.tile(fillval, fillshape)
            else:
                raise ValueError("Cannot match shape of fill to shape of data")
        diff = numpy.diff(times)
        if hasattr(diff[0], 'seconds'): #datetime
            diff = numpy.vectorize(lambda x: x.days * 86400.0 + x.seconds +
                                   x.microseconds / 1.0e6)(diff)
            if absolute is not None:
                absolute = absolute.days * 86400.0 + absolute.seconds + \
                           absolute.microseconds / 1.0e6
        if absolute is None:
            idx = numpy.nonzero(diff > (numpy.median(diff) * tol))[0] + 1
        else:
            idx = numpy.nonzero(diff > absolute)[0] + 1
        data = numpy.insert(data, idx, numpy.repeat(fillval, len(idx)),
                            axis=timeaxis) #NOOP if no fill
        if not doTimes:
            return data
        try:
            filltimes = (times[idx] + times[idx - 1]) / 2.0
        except TypeError:
            filltimes = times[idx - 1] + numpy.vectorize(lambda x: datetime.timedelta(seconds=x / 2.0))(diff[idx - 1])
        times = numpy.insert(times, idx, filltimes)
        return times, data

    def apply_index(data, idx):
        """Apply an array of indices to data.

        Most useful in dealing with the output from :func:`numpy.argsort`, and
        best explained by the example.

        Parameters
        ==========
        data : array
            Input data, at least two dimensional. The 0th dimension is treated as
            a "time" or "record" dimension.
        idx : sequence
            2D index to apply to the import data. The 0th dimension must be the
            same size as ``data``'s 0th dimension. Dimension 1 must be the same
            size as one other dimension in data (the first match found is used);
            this is referred to as the "index dimension."

        Raises
        ======
        ValueError : if can't match the shape of data and indices

        Returns
        =======
        data : sequence
            View of ``data``, with index applied. For each index of the 0th
            dimension, the values along the index dimension are obtained by applying
            the value of ``idx`` at the same index in the 0th dimension. This is
            repeated across any other dimensions in ``data``.

            .. warning::
                No guarantee is made whether the returned data is a copy
                of the input data. Modifying values in the input may change
                the values of the input. Call :meth:`~numpy.ndarray.copy` if
                a copy is required.

        Examples
        ========
        Assume ``flux`` is a 3D array of fluxes, with a value for each of
        time, pitch angle, and energy. Assume energy is not necessarily
        constant in time, nor is ordered in the energy dimension. If
        ``energy`` is a 2D array of the energies as a function of energy
        step for each time, then the following will sort the flux at each
        time and pitch angle in energy order.

        >>> idx = numpy.argsort(energy, axis=1)
        >>> flux_sorted = spacepy.datamanager.apply_index(flux, idx)
        """
        data = numpy.asanyarray(data)
        idx = numpy.asanyarray(idx)
        if len(idx.shape) != 2:
            raise ValueError("idx must have dimensions 2, not {0}".format(
                len(idx.shape)))
        if len(data.shape) < 2:
            raise ValueError("data must have at least dimensions 2")
        if idx.shape[0] != data.shape[0]:
            raise ValueError("data and idx must have same size in "
                             "0th dimension")
        if not idx.shape[1] in data.shape[1:]:
            raise ValueError("Size of idx dimension 1 must match a dimension in "
                             "data")
        idx_dim = data.shape[1:].index(idx.shape[1]) + 1
        return numpy.rollaxis(
            numpy.rollaxis(data, idx_dim, 1) #make time and index dim adjacent
            #get a 2d array where every element matches index of first axis
            [numpy.mgrid[0:idx.shape[0], slice(idx.shape[1])][0],
             idx, #2d array, every element is desired index of second axis
             ...] #and the other axes come along for the ride
            , 1, idx_dim + 1) #and put index dim back in place

    def array_interleave(array1, array2, idx):
        """Create an array containing all elements of both array1 and array2

        ``idx`` is an index on the output array which indicates which elements will
        be populated from ``array1``, i.e., ``out[idx] == array1`` (in order.)
        The other elements of ``out`` will be filled, in order, from ``array2``.

        Parameters
        ==========
        array1 : array
            Input data.
        array2 : array
            Input data. Must have same number of dimensions as ``array1``, and all
            dimensions except the zeroth must also have the same length.
        idx : array
            A 1D array of indices on the zeroth dimension of the output array. Must
            have the same length as the zeroth dimension of ``array1``.

        Returns
        =======
        out : array
            All elements from ``array1`` and ``array2``, interleaved according
            to ``idx``.

        Examples
        ========
        >>> import numpy
        >>> import spacepy.datamanager
        >>> a = numpy.array([10, 20, 30])
        >>> b = numpy.array([1, 2])
        >>> idx = numpy.array([1, 2, 4])
        >>> spacepy.datamanager.array_interleave(a, b, idx)
        array([ 1, 10, 20,  2, 30])
        """
        array1 = numpy.asanyarray(array1)
        array2 = numpy.asanyarray(array2)
        idx = numpy.asanyarray(idx)
        assert(len(array1.shape) == len(array2.shape))
        assert(array1.shape[1:] == array2.shape[1:])
        assert(array1.dtype == array2.dtype)
        outarray = numpy.empty(dtype=array1.dtype,
            shape=((array1.shape[0] + array2.shape[0],) + array1.shape[1:]))
        outarray[idx, ...] = array1
        idx_comp = numpy.ones((outarray.shape[0],), dtype=numpy.bool)
        idx_comp[idx] = False
        outarray[idx_comp, ...] = array2
        return outarray

    def values_to_steps(array, axis=-1):
        """Transform values along an axis to their order in a unique sequence.

        Useful in, e.g., converting a list of energies to their steps.

        Parameters
        ==========
        array : array
            Input data.

        Other Parameters
        ================
        axis : int
            Axis along which to find the steps.

        Returns
        =======
        steps : array
            An array, the same size as ``array``, with values along ``axis``
            corresponding to the position of the value in ``array`` in a unique,
            sorted, set of the values in ``array`` along that axis. Differs from
            :func:`~numpy.argsort` in that identical values will have identical
            step numbers in the output.

        Examples
        ========
        >>> import numpy
        >>> import spacepy.datamanager
        >>> data = [[10., 12., 11., 9., 10., 12., 11., 9.],
                    [10., 12., 11., 9., 14., 16., 15., 13.]]
        >>> spacepy.datamanager.values_to_steps(data)
        array([[1, 3, 2, 0, 1, 3, 2, 0],
               [1, 3, 2, 0, 5, 7, 6, 4]])
        """
        array = numpy.asanyarray(array)
        sortidx = array.argsort(axis=axis)
        steps = rev_index(sortidx, axis=axis)
        d = numpy.diff(apply_index(array, sortidx), axis=axis)
        #Everywhere in SORTED array that the VALUE is same as one before
        same = numpy.insert(d==0, 0, False, axis=axis)
        #Number of duplicate indices BEFORE current index, in SORTED array
        delta = numpy.cumsum(same, axis=-1)
        #Get delta into the unsorted frame, and correct for uniqueness
        return steps - delta.ravel()[
            flatten_idx(rev_index(sortidx, axis=axis), axis=axis)]\
            .reshape(steps.shape)

    def flatten_idx(idx, axis=-1):
        """Convert multidimensional index into index on flattened array.

        Convert a multidimensional index, that is values along a particular axis,
        so that it can derefence the flattened array properly. Note this is not
        the same as :func:`~numpy.ravel_multi_index`.

        Parameters
        ==========
        idx : array
            Input index, i.e. a list of elements along a particular axis,
            in the style of :func:`~numpy.argsort`.

        Other Parameters
        ================
        axis : int
            Axis along which ``idx`` operates, defaults to the last axis.

        Returns
        =======
        flat : array
            A 1D array of indices suitable for indexing the flat version of the
            array

        See Also
        ========
        apply_index

        Examples
        ========
        >>> import numpy
        >>> import spacepy.datamanager
        >>> data = numpy.array([[3, 1, 2], [3, 2, 1]])
        >>> idx = numpy.argsort(data, -1)
        >>> idx_flat = spacepy.datamanager.flatten_idx(idx)
        >>> data.ravel() #flat array
        array([3, 1, 2, 3, 2, 1])
        >>> idx_flat #indices into the flat array
        array([1, 2, 0, 5, 4, 3])
        >>> data.ravel()[idx_flat] #index applied to the flat array
        array([1, 2, 3, 1, 2, 3])
        """
        idx = numpy.asanyarray(idx)
        if not idx.dtype.kind in ('i', 'u'):
            idx = idx.astype(int)
        preshape = idx.shape[:axis]
        postshape = idx.shape[axis:]
        stride = int(numpy.product(postshape[1:])) #1 if applied to empty
        #The index on this axis moves stride elements in flat
        outidx = idx.flatten() * stride #makes a copy
        #First add the offsets to get us to [..., idx @ axis = 0, 0...)
        outidx += numpy.repeat(
            numpy.arange(0, len(outidx), int(numpy.product(postshape)),
                         dtype=idx.dtype),
            numpy.product(postshape))
        #Now offsets for non-zero on the trailing axes [0, 0, ... 0@axis, ...]
        outidx += numpy.tile(numpy.arange(0, stride, dtype=idx.dtype),
                               int(numpy.product(preshape)) * idx.shape[axis])
        return outidx

    def axis_index(shape, axis=-1):
        """Returns array of indices along axis, for all other axes

        Parameters
        ==========
        shape : tuple
            Shape of the output array

        Other Parameters
        ================
        axis : int
            Axis along which to return indices, defaults to the last axis.

        Returns
        =======
        idx : array
            An array of indices. The value of each element is that element's index
            along ``axis``.

        See Also
        ========
        numpy.mgrid : This function is a special case

        Examples
        ========
        For a shape of ``(i, j, k, l)`` and ``axis`` = -1,
        ``idx[i, j, k, :] = range(l)`` for all ``i``, ``j``, ``k``.

        Similarly, for the same shape and ``axis = 1``,
        ``idx[i, :, k, l] = range(j)`` for all ``i``, ``k``, ``l``.

        >>> import numpy
        >>> import spacepy.datamanager
        >>> spacepy.datamanager.axis_index((5, 3))
        array([[0, 1, 2],
               [0, 1, 2],
               [0, 1, 2],
               [0, 1, 2],
               [0, 1, 2]])
        >>> spacepy.datamanager.axis_index((5, 3), 0)
            array([[0, 0, 0],
                   [1, 1, 1],
                   [2, 2, 2],
                   [3, 3, 3],
                   [4, 4, 4]])
    """
        return operator.getitem(numpy.mgrid, [slice(i) for i in shape])[axis]

    def rev_index(idx, axis=-1):
        """From an index, return an index that reverses the action of that index

        Essentially, ``a[idx][rev_index(idx)] == a``

        .. note::
            This becomes more complicated in multiple dimensions, due to the
            vagaries of applying a multidimensional index.

        Parameters
        ==========
        idx : array
            Indices onto an array, often the output of :func:`~numpy.argsort`.

        Other Parameters
        ================
        axis : int
            Axis along which to return indices, defaults to the last axis.

        Returns
        =======
        rev_idx : array
            Indices that, when applied to an array after ``idx``, will return
            the original array (before the application of ``idx``).

        See Also
        ========
        apply_index

        Examples
        ========
        >>> import numpy
        >>> import spacepy.datamanager
        >>> data = numpy.array([7, 2, 4, 6, 3])
        >>> idx = numpy.argsort(data)
        >>> data[idx] #sorted
        array([2, 3, 4, 6, 7])
        >>> data[idx][spacepy.datamanager.rev_index(idx)] #original
        array([7, 2, 4, 6, 3])
    """
        #Want an idx2 such that x[idx][idx2] == x
        #idx is position to value map
        #Populate every POSITION in idx2 with the POSITION in idx that
        #has the VALUE of the idx2 position
        #searchsorted on range?
        idx_out = numpy.empty_like(idx).ravel()
        idx_out[flatten_idx(idx, axis)] = axis_index(idx.shape, axis).ravel()
        return idx_out.reshape(idx.shape)