# Source code for markers

    '''
    Utilities for analyzing movement data recorded with marker-based video
    systems.
    '''

    '''
    Author: Thomas Haslwanter
    Version: 1.1
    Date: April-2016
    '''

    import numpy as np
    import scipy as sp
    import matplotlib.pyplot as plt
    import pandas as pd
    from numpy import r_, sum

    # The following construct is required since I want to run the module as a script
    # inside the thLib-directory
    import os
    import sys
    PACKAGE_PARENT = '..'
    SCRIPT_DIR = os.path.realpath(os.path.dirname(__file__))
    sys.path.append(os.path.normpath(os.path.join(SCRIPT_DIR, PACKAGE_PARENT)))

    from skinematics import quat, vector

    def analyze3Dmarkers(MarkerPos, ReferencePos):
        '''
        Take recorded positions from 3 markers, and calculate center-of-mass (COM) and orientation
        Can be used e.g. for the analysis of Optotrac data.

        Parameters
        ----------
        MarkerPos : ndarray, shape (N,9)
            x/y/z coordinates of 3 markers

        ReferencePos : ndarray, shape (1,9)
            x/y/z coordinates of markers in the reference position

        Returns
        -------
        Position : ndarray, shape (N,3)
            x/y/z coordinates of COM, relative to the reference position
        Orientation : ndarray, shape (N,3)
            Orientation relative to reference orientation, expressed as quaternion

        Example
        -------
        >>> (PosOut, OrientOut) = analyze3Dmarkers(MarkerPos, ReferencePos)

        '''

        # Specify where the x-, y-, and z-position are located in the data
        cols = {'x' : r_[(0,3,6)]}
        cols['y'] = cols['x'] + 1
        cols['z'] = cols['x'] + 2

        # Calculate the position
        cog = np.vstack(( sum(MarkerPos[:,cols['x']], axis=1),
                          sum(MarkerPos[:,cols['y']], axis=1),
                          sum(MarkerPos[:,cols['z']], axis=1) )).T/3.

        cog_ref = np.vstack(( sum(ReferencePos[cols['x']]),
                              sum(ReferencePos[cols['y']]),
                              sum(ReferencePos[cols['z']]) )).T/3.

        position = cog - cog_ref

        # Calculate the orientation
        numPoints = len(MarkerPos)
        orientation = np.ones((numPoints,3))

        refOrientation = vector.plane_orientation(ReferencePos[:3], ReferencePos[3:6], ReferencePos[6:])

        for ii in range(numPoints):
            '''The three points define a triangle. The first rotation is such
            that the orientation of the reference-triangle, defined as the
            direction perpendicular to the triangle, is rotated along the shortest
            path to the current orientation.
            In other words, this is a rotation outside the plane spanned by the three
            marker points.'''

            curOrientation = vector.plane_orientation( MarkerPos[ii,:3], MarkerPos[ii,3:6], MarkerPos[ii,6:])
            alpha = vector.angle(refOrientation, curOrientation)

            if alpha > 0:
                n1 = vector.normalize( np.cross(refOrientation, curOrientation) )
                q1 = n1 * np.sin(alpha/2)
            else:
                q1 = r_[0,0,0]

            # Now rotate the triangle into this orientation ...
            refPos_after_q1 = vector.rotate_vector(np.reshape(ReferencePos,(3,3)), q1)

            '''Find which further rotation in the plane spanned by the three marker points
    	is necessary to bring the data into the measured orientation.'''

            Marker_0 = MarkerPos[ii,:3]
            Marker_1 = MarkerPos[ii,3:6]
            Vector10 = Marker_0 - Marker_1
            vector10_ref = refPos_after_q1[0]-refPos_after_q1[1]
            beta = vector.angle(Vector10, vector10_ref)

            q2 = curOrientation * np.sin(beta/2)

            if np.cross(vector10_ref,Vector10).dot(curOrientation)<=0:
                q2 = -q2
            orientation[ii,:] = quat.quatmult(q2, q1)

        return (position, orientation)

    def findTrajectory(r0, Position, Orientation):
        '''
        Movement trajetory of a point on an object, from the position and
        orientation of a sensor, and the relative position of the point at t=0.

        Parameters
        ----------
        r0 : ndarray (3,)
            Position of point relative to center of markers, when the object is
            in the reference position.
        Position : ndarray, shape (N,3)
            x/y/z coordinates of COM, relative to the reference position
        Orientation : ndarray, shape (N,3)
            Orientation relative to reference orientation, expressed as quaternion

        Returns
        -------
        mov : ndarray, shape (N,3)
            x/y/z coordinates of the position on the object, relative to the
            reference position of the markers

        Notes
        -----

          .. math::

              \\vec C(t) = \\vec M(t) + \\vec r(t) = \\vec M(t) +
              {{\\bf{R}}_{mov}}(t) \\cdot \\vec r({t_0})

        Examples
        --------
        >>> t = np.arange(0,10,0.1)
        >>> translation = (np.c_[[1,1,0]]*t).T
        >>> M = np.empty((3,3))
        >>> M[0] = np.r_[0,0,0]
        >>> M[1]= np.r_[1,0,0]
        >>> M[2] = np.r_[1,1,0]
        >>> M -= np.mean(M, axis=0)
        >>> q = np.vstack((np.zeros_like(t), np.zeros_like(t),quat.deg2quat(100*t))).T
        >>> M0 = vector.rotate_vector(M[0], q) + translation
        >>> M1 = vector.rotate_vector(M[1], q) + translation
        >>> M2 = vector.rotate_vector(M[2], q) + translation
        >>> data = np.hstack((M0,M1,M2))
        >>> (pos, ori) = signals.analyze3Dmarkers(data, data[0])
        >>> r0 = np.r_[1,2,3]
        >>> movement = movement_from_markers(r0, pos, ori)

        '''

        return Position + vector.rotate_vector(r0, Orientation)

    if __name__ == '__main__':
        # Here a marker-test is required

        print('Done')