{
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    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "%matplotlib inline"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "\n# Surface seeding for tractography\n\nSurface seeding is a way to generate initial position for tractography\nfrom cortical surfaces position [Stonge2018]_.\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "import numpy as np\n\nfrom dipy.viz import window, actor\nfrom dipy.data import get_fnames\nfrom dipy.tracking.mesh import (random_coordinates_from_surface,\n                                seeds_from_surface_coordinates)\n\nfrom fury.io import load_polydata\nfrom fury.utils import (get_polydata_triangles, get_polydata_vertices,\n                        get_actor_from_polydata, normals_from_v_f)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Fetch and load a surface\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "brain_lh = get_fnames(\"fury_surface\")\npolydata = load_polydata(brain_lh)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Extract the triangles and vertices\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "triangles = get_polydata_triangles(polydata)\nvts = get_polydata_vertices(polydata)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "## Display the surface\n\nFirst, create an actor from the polydata, to display in the scene\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "scene = window.Scene()\nsurface_actor = get_actor_from_polydata(polydata)\n\nscene.add(surface_actor)\nscene.set_camera(position=(-500, 0, 0),\n                 view_up=(0.0, 0.0, 1))\n\n# Uncomment the line below to show to display the window\n# window.show(scene, size=(600, 600), reset_camera=False)\nwindow.record(scene, out_path='surface_seed1.png', size=(600, 600))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        ".. figure:: surface_seed1.png\n   :align: center\n\n   **Initial cortical surface**\n\n\n## Generate a list of seeding positions\n\nChoose the number of seed\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "nb_seeds = 100000\nnb_triangles = len(triangles)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Get a list of triangles indices and trilinear coordinates for each seed\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "tri_idx, trilin_co = random_coordinates_from_surface(nb_triangles, nb_seeds)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Get the 3d cartesian position from triangles indices and trilinear coordinates\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "seed_pts = seeds_from_surface_coordinates(triangles, vts, tri_idx, trilin_co)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Compute normal and get the normal direction for each seeds\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "normals = normals_from_v_f(vts, triangles)\nseed_n = seeds_from_surface_coordinates(triangles, normals, tri_idx, trilin_co)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Create dot actor for seeds (blue)\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "seed_actors = actor.dot(seed_pts, colors=(0, 0, 1), dot_size=4.0)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Create line actors for seeds normals (green outside, red inside)\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "normal_length = 0.5\nnormal_in = np.tile(seed_pts[:, np.newaxis, :], (1, 2, 1))\nnormal_out = np.tile(seed_pts[:, np.newaxis, :], (1, 2, 1))\nnormal_in[:, 0] -= seed_n * normal_length\nnormal_out[:, 1] += seed_n * normal_length\n\nnormal_in_actor = actor.line(normal_in, colors=(1, 0, 0))\nnormal_out_actor = actor.line(normal_out, colors=(0, 1, 0))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Visualise seeds and normals along the surface\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "scene = window.Scene()\nscene.add(surface_actor)\nscene.add(seed_actors)\nscene.add(normal_in_actor)\nscene.add(normal_out_actor)\nscene.set_camera(position=(-500, 0, 0),\n                 view_up=(0.0, 0.0, 1))\n\n# Uncomment the line below to show to display the window\n# window.show(scene, size=(600, 600), reset_camera=False)\nwindow.record(scene, out_path='surface_seed2.png', size=(600, 600))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        ".. figure:: surface_seed2.png\n   :align: center\n\n   **Surface seeds with normal orientation**\n\n\n### References\n.. [Stonge2018] St-Onge, E., Daducci, A., Girard, G., & Descoteaux, M.\n    Surface-enhanced tractography (SET). NeuroImage, 169, 524-539, 2018.\n\n.. include:: ../links_names.inc\n\n\n"
      ]
    }
  ],
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