from __future__ import division, print_function, absolute_import

import numpy as np
import getpass
import time


def _fread3(fobj):
    """Read a 3-byte int from an open binary file object

    Parameters
    ----------
    fobj : file
        File descriptor

    Returns
    -------
    n : int
        A 3 byte int
    """
    b1, b2, b3 = np.fromfile(fobj, ">u1", 3)
    return (b1 << 16) + (b2 << 8) + b3


def _fread3_many(fobj, n):
    """Read 3-byte ints from an open binary file object.

    Parameters
    ----------
    fobj : file
        File descriptor

    Returns
    -------
    out : 1D array
        An array of 3 byte int
    """
    b1, b2, b3 = np.fromfile(fobj, ">u1", 3 * n).reshape(-1,
                                                    3).astype(np.int).T
    return (b1 << 16) + (b2 << 8) + b3


def read_geometry(filepath):
    """Read a triangular format Freesurfer surface mesh.

    Parameters
    ----------
    filepath : str
        Path to surface file

    Returns
    -------
    coords : numpy array
        nvtx x 3 array of vertex (x, y, z) coordinates
    faces : numpy array
        nfaces x 3 array of defining mesh triangles
    """
    with open(filepath, "rb") as fobj:
        magic = _fread3(fobj)
        if magic == 16777215:  # Quad file
            nvert = _fread3(fobj)
            nquad = _fread3(fobj)
            coords = np.fromfile(fobj, ">i2", nvert * 3).astype(np.float)
            coords = coords.reshape(-1, 3) / 100.0
            quads = _fread3_many(fobj, nquad * 4)
            quads = quads.reshape(nquad, 4)
            #
            #   Face splitting follows
            #
            faces = np.zeros((2 * nquad, 3), dtype=np.int)
            nface = 0
            for quad in quads:
                if (quad[0] % 2) == 0:
                    faces[nface] = quad[0], quad[1], quad[3]
                    nface += 1
                    faces[nface] = quad[2], quad[3], quad[1]
                    nface += 1
                else:
                    faces[nface] = quad[0], quad[1], quad[2]
                    nface += 1
                    faces[nface] = quad[0], quad[2], quad[3]
                    nface += 1

        elif magic == 16777214:  # Triangle file
            create_stamp = fobj.readline()
            _ = fobj.readline()
            vnum = np.fromfile(fobj, ">i4", 1)[0]
            fnum = np.fromfile(fobj, ">i4", 1)[0]
            coords = np.fromfile(fobj, ">f4", vnum * 3).reshape(vnum, 3)
            faces = np.fromfile(fobj, ">i4", fnum * 3).reshape(fnum, 3)
        else:
            raise ValueError("File does not appear to be a Freesurfer surface")

    coords = coords.astype(np.float)  # XXX: due to mayavi bug on mac 32bits
    return coords, faces


def write_geometry(filepath, coords, faces, create_stamp=None):
    """Write a triangular format Freesurfer surface mesh.

    Parameters
    ----------
    filepath : str
        Path to surface file
    coords : numpy array
        nvtx x 3 array of vertex (x, y, z) coordinates
    faces : numpy array
        nfaces x 3 array of defining mesh triangles
    create_stamp : str
        User/time stamp (default: "created by <user> on <ctime>")
    """
    magic_bytes = np.array([255, 255, 254], dtype=np.uint8)

    if create_stamp is None:
        create_stamp = "created by %s on %s" % (getpass.getuser(),
            time.ctime())

    with open(filepath, 'wb') as fobj:
        magic_bytes.tofile(fobj)
        fobj.write("%s\n\n" % create_stamp)

        np.array([coords.shape[0], faces.shape[0]], dtype='>i4').tofile(fobj)

        # Coerce types, just to be safe
        coords.astype('>f4').reshape(-1).tofile(fobj)
        faces.astype('>i4').reshape(-1).tofile(fobj)


def read_morph_data(filepath):
    """Read a Freesurfer morphometry data file.

    This function reads in what Freesurfer internally calls "curv" file types,
    (e.g. ?h. curv, ?h.thickness), but as that has the potential to cause
    confusion where "curv" also refers to the surface curvature values,
    we refer to these files as "morphometry" files with PySurfer.

    Parameters
    ----------
    filepath : str
        Path to morphometry file

    Returns
    -------
    curv : numpy array
        Vector representation of surface morpometry values

    """
    with open(filepath, "rb") as fobj:
        magic = _fread3(fobj)
        if magic == 16777215:
            vnum = np.fromfile(fobj, ">i4", 3)[0]
            curv = np.fromfile(fobj, ">f4", vnum)
        else:
            vnum = magic
            _ = _fread3(fobj)
            curv = np.fromfile(fobj, ">i2", vnum) / 100
    return curv


def read_annot(filepath, orig_ids=False):
    """Read in a Freesurfer annotation from a .annot file.

    Parameters
    ----------
    filepath : str
        Path to annotation file
    orig_ids : bool
        Whether to return the vertex ids as stored in the annotation
        file or the positional colortable ids

    Returns
    -------
    labels : n_vtx numpy array
        Annotation id at each vertex
    ctab : numpy array
        RGBA + label id colortable array

    """
    with open(filepath, "rb") as fobj:
        dt = ">i4"
        vnum = np.fromfile(fobj, dt, 1)[0]
        data = np.fromfile(fobj, dt, vnum * 2).reshape(vnum, 2)
        labels = data[:, 1]
        ctab_exists = np.fromfile(fobj, dt, 1)[0]
        if not ctab_exists:
            raise Exception('Color table not found in annotation file')
        n_entries = np.fromfile(fobj, dt, 1)[0]
        if n_entries > 0:
            length = np.fromfile(fobj, dt, 1)[0]
            orig_tab = np.fromfile(fobj, '>c', length)
            orig_tab = orig_tab[:-1]

            names = list()
            ctab = np.zeros((n_entries, 5), np.int)
            for i in xrange(n_entries):
                name_length = np.fromfile(fobj, dt, 1)[0]
                name = np.fromfile(fobj, "|S%d" % name_length, 1)[0]
                names.append(name)
                ctab[i, :4] = np.fromfile(fobj, dt, 4)
                ctab[i, 4] = (ctab[i, 0] + ctab[i, 1] * (2 ** 8) +
                              ctab[i, 2] * (2 ** 16) +
                              ctab[i, 3] * (2 ** 24))
        else:
            ctab_version = -n_entries
            if ctab_version != 2:
                raise Exception('Color table version not supported')
            n_entries = np.fromfile(fobj, dt, 1)[0]
            ctab = np.zeros((n_entries, 5), np.int)
            length = np.fromfile(fobj, dt, 1)[0]
            _ = np.fromfile(fobj, "|S%d" % length, 1)[0]  # Orig table path
            entries_to_read = np.fromfile(fobj, dt, 1)[0]
            names = list()
            for i in xrange(entries_to_read):
                _ = np.fromfile(fobj, dt, 1)[0]  # Structure
                name_length = np.fromfile(fobj, dt, 1)[0]
                name = np.fromfile(fobj, "|S%d" % name_length, 1)[0]
                names.append(name)
                ctab[i, :4] = np.fromfile(fobj, dt, 4)
                ctab[i, 4] = (ctab[i, 0] + ctab[i, 1] * (2 ** 8) +
                                ctab[i, 2] * (2 ** 16))
        ctab[:, 3] = 255
    if not orig_ids:
        ord = np.argsort(ctab[:, -1])
        labels = ord[np.searchsorted(ctab[ord, -1], labels)]
    return labels, ctab, names


def read_label(filepath, read_scalars=False):
    """Load in a Freesurfer .label file.

    Parameters
    ----------
    filepath : str
        Path to label file
    read_scalars : bool
        If true, read and return scalars associated with each vertex

    Returns
    -------
    label_array : numpy array
        Array with indices of vertices included in label
    scalar_array : numpy array (floats)
        If read_scalars is True, array of scalar data for each vertex

    """
    label_array = np.loadtxt(filepath, dtype=np.int, skiprows=2, usecols=[0])
    if read_scalars:
        scalar_array = np.loadtxt(filepath, skiprows=2, usecols=[-1])
        return label_array, scalar_array
    return label_array
