{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6269c1d6-fa76-4919-ae26-f150d7d9f536",
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "np.float = float\n",
    "\n",
    "import defdap.hrdic as hrdic\n",
    "import defdap.ebsd as ebsd\n",
    "from defdap.quat import Quat\n",
    "\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d7025973-752f-4f75-a66e-b12e875c3749",
   "metadata": {},
   "outputs": [],
   "source": [
    "ebsd_map = ebsd.Map('../tests/data/testDataEBSD')\n",
    "ebsd_map.buildQuatArray()\n",
    "ebsd_map.findBoundaries(boundDef=8)\n",
    "ebsd_map.findGrains(minGrainSize=10)\n",
    "ebsd_map.calcGrainAvOris()\n",
    "ebsd_map.buildNeighbourNetwork()\n",
    "ebsd_map.homogPoints = [\n",
    "    (68, 95),\n",
    "    (308, 45),\n",
    "    (191, 187),\n",
    "    (89, 174)\n",
    "]\n",
    "\n",
    "dic_map = hrdic.Map('../tests/data/', 'testDataDIC.txt')\n",
    "dic_map.setScale(20 / 2048)\n",
    "dic_map.homogPoints = [\n",
    "    (36, 72),\n",
    "    (279, 27),\n",
    "    (162, 174),\n",
    "    (60, 157)\n",
    "]\n",
    "dic_map.linkEbsdMap(ebsd_map, transformType=\"affine\")\n",
    "dic_map.findGrains(minGrainSize=10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "976b7e11-6909-4f57-9f7a-6cf73499ec7b",
   "metadata": {},
   "outputs": [],
   "source": [
    "# find twin boundaries\n",
    "misori_twin = Quat.fromAxisAngle([1, 1, 1], 60*np.pi/180)\n",
    "misori_twin_tol = 5*np.pi/180\n",
    "\n",
    "# create all symmetric equivalent misorientations\n",
    "misori_twin_all = []\n",
    "syms = ebsd_map.primaryPhase.crystalStructure.symmetries\n",
    "for sym_i in syms:\n",
    "    for sym_j in syms:\n",
    "        misori_twin_all.append(sym_i.conjugate * misori_twin * sym_j)\n",
    "# get rid of any duplicates\n",
    "misori_twin_all = list(set(misori_twin_all))\n",
    "\n",
    "# loop over all grain boundary segments and check if the misorientation between\n",
    "# the two grains is within tolerance of the twin misorientation\n",
    "twin_lines = []\n",
    "for grain1, grain2, b_seg in ebsd_map.neighbourNetwork.edges.data('boundary'):\n",
    "    twin = False\n",
    "    misori = grain2.refOri * grain1.refOri.conjugate\n",
    "    for misori_twin in misori_twin_all:\n",
    "        if 2 * np.arccos(misori_twin.dot(misori)) < misori_twin_tol:\n",
    "            twin = True\n",
    "            break\n",
    "    \n",
    "    if not twin:\n",
    "        continue\n",
    "    \n",
    "    twin_lines += b_seg.boundaryLines"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0c76eb93-44fe-493a-9d94-3411475e1bf6",
   "metadata": {},
   "outputs": [],
   "source": [
    "plot = ebsd_map.plotEulerMap(plotGBs='line')\n",
    "plot.addGrainBoundaries(boundaries=twin_lines, kind='line', colour='limegreen')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "04770a4f-a267-4060-acbe-53cf89525d5b",
   "metadata": {},
   "outputs": [],
   "source": [
    "plot = dic_map.plotMaxShear(vmin=0, vmax=0.05, plotGBs='line')\n",
    "plot.addGrainBoundaries(\n",
    "    boundaries=dic_map.warp_lines_to_dic_frame(twin_lines), \n",
    "    kind='line', colour='limegreen', lw=3\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "aa26f342-2ec4-4263-bb01-0fbe9224051d",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "097ab2f9-2389-4b3e-86b9-de996d9b59c7",
   "metadata": {},
   "source": [
    "## Colour grain boundaries by misorientation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6ed39a19-6470-4705-9a8e-cbe3db042ba0",
   "metadata": {},
   "outputs": [],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "import matplotlib as mpl\n",
    "import defdap.plotting"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "64370d47-86fa-431d-9b0f-93e693e9e95f",
   "metadata": {},
   "outputs": [],
   "source": [
    "def oris_to_col(ori_1: Quat, ori_2: Quat, sym_group: str) -> float:\n",
    "    return ori_1.misOri(ori_2, sym_group)\n",
    "\n",
    "sym_group = ebsd_map.primaryPhase.crystalStructure.name\n",
    "gb_lines = []\n",
    "gb_cols = []\n",
    "for grain1, grain2, b_seg in ebsd_map.neighbourNetwork.edges.data('boundary'):\n",
    "    line_col = oris_to_col(grain1.refOri, grain2.refOri, sym_group)\n",
    "    gb_lines += b_seg.boundaryLines\n",
    "    gb_cols += [line_col] * len(b_seg.boundaryLines)\n",
    "\n",
    "# Convert values to colours\n",
    "gb_cols = 2 * np.arccos(gb_cols)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "aa49a105-def4-4d04-937a-b5d9f0dd4975",
   "metadata": {},
   "outputs": [],
   "source": [
    "plot = ebsd_map.plotEulerMap()\n",
    "img = plot.addGrainBoundaries(\n",
    "    kind='line',\n",
    "    boundaries=gb_lines,\n",
    "    colour=gb_cols,\n",
    "    cmap=mpl.colormaps['gray'],\n",
    "    norm=mpl.colors.Normalize(vmin=gb_cols.min(), vmax=gb_cols.max()),\n",
    ")\n",
    "plt.colorbar(mappable=img, label=\"Boundary misorientation\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d95f6f54-c177-48ec-9608-949c2643e200",
   "metadata": {},
   "outputs": [],
   "source": [
    "plot = defdap.plotting.MapPlot.create(dic_map, np.zeros(dic_map.shape))\n",
    "img = plot.addGrainBoundaries(\n",
    "    kind='line',\n",
    "    boundaries=dic_map.warp_lines_to_dic_frame(gb_lines),\n",
    "    colour=gb_cols,\n",
    "    cmap=mpl.colormaps['viridis'],\n",
    "    norm=mpl.colors.Normalize(vmin=gb_cols.min(), vmax=gb_cols.max()),\n",
    ")\n",
    "plt.colorbar(mappable=img, label=\"Boundary misorientation\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e6cd018a-b87a-48bd-9344-5e6516fb9a4d",
   "metadata": {},
   "outputs": [],
   "source": [
    "plot = dic_map.plotMaxShear(vmin=0, vmax=0.05)\n",
    "img = plot.addGrainBoundaries(\n",
    "    kind='line',\n",
    "    boundaries=dic_map.warp_lines_to_dic_frame(gb_lines),\n",
    "    colour=gb_cols,\n",
    "    cmap=mpl.colormaps['gray'],\n",
    "    norm=mpl.colors.Normalize(vmin=gb_cols.min(), vmax=gb_cols.max()),\n",
    ")\n",
    "plt.colorbar(mappable=img, label=\"Boundary misorientation\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4366d01f-1c8a-4dc2-b589-e8055aa7d01d",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "61fe241b-2178-4f39-998d-ac3f6e13b070",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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