{
 "cells": [
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "# How to extract symmetry maps from atomic resolution images",
   "id": "d3500980a70fbbf6"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-20T03:23:15.738034Z",
     "start_time": "2024-05-20T03:23:12.926074Z"
    }
   },
   "cell_type": "code",
   "source": [
    "%matplotlib qt\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "from mtflearn import ZPs"
   ],
   "id": "a7e6a89e8beda717",
   "execution_count": 1,
   "outputs": []
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-20T10:41:52.573922Z",
     "start_time": "2024-05-20T10:41:52.548902Z"
    }
   },
   "cell_type": "code",
   "source": [
    "from mtflearn.utils import normalize_image\n",
    "from skimage.transform import resize"
   ],
   "id": "f425368b13bfb9d",
   "execution_count": 17,
   "outputs": []
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "## load an image",
   "id": "fd32ef086403d1d0"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-20T10:42:50.375633Z",
     "start_time": "2024-05-20T10:42:50.317613Z"
    }
   },
   "cell_type": "code",
   "source": [
    "filename = 'data\\\\monolayer_MoSe2_80K.npy'\n",
    "img = np.load(filename)[0:800, 0:800]\n",
    "img = resize(img, (512, 512), order=0)\n",
    "img = normalize_image(img)"
   ],
   "id": "fe1ce0a08b2ef4bf",
   "execution_count": 18,
   "outputs": []
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-20T10:42:57.719652Z",
     "start_time": "2024-05-20T10:42:55.841789Z"
    }
   },
   "cell_type": "code",
   "source": [
    "zps = ZPs(n_max=10, size=72)\n",
    "m = zps.fit_transform(img)"
   ],
   "id": "27be3af3acab21b7",
   "execution_count": 19,
   "outputs": []
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-20T09:00:20.798068Z",
     "start_time": "2024-05-20T09:00:20.777087Z"
    }
   },
   "cell_type": "code",
   "source": "",
   "id": "7b41be2cb2b50f1f",
   "execution_count": 51,
   "outputs": []
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-20T10:43:46.050988Z",
     "start_time": "2024-05-20T10:43:45.933989Z"
    }
   },
   "cell_type": "code",
   "source": "m3, m6 = m.rot_maps([3, 6])",
   "id": "82d62306f686b64b",
   "execution_count": 25,
   "outputs": []
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-20T10:43:46.438978Z",
     "start_time": "2024-05-20T10:43:46.424978Z"
    }
   },
   "cell_type": "code",
   "source": "",
   "id": "9cc5d0c66a2cc0de",
   "execution_count": 25,
   "outputs": []
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-20T10:43:54.441991Z",
     "start_time": "2024-05-20T10:43:52.392847Z"
    }
   },
   "cell_type": "code",
   "source": "hh = m.mirror_map(m_unselect=[0,1])",
   "id": "9165b84596f1bd9",
   "execution_count": 27,
   "outputs": []
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-20T10:43:54.965506Z",
     "start_time": "2024-05-20T10:43:54.949506Z"
    }
   },
   "cell_type": "code",
   "source": "",
   "id": "b2b481946a1bae19",
   "execution_count": 27,
   "outputs": []
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-20T10:43:55.266217Z",
     "start_time": "2024-05-20T10:43:55.166307Z"
    }
   },
   "cell_type": "code",
   "source": "plt.imshow(hh[40:-40, 40:-40])\n",
   "id": "a58537bb55984668",
   "execution_count": 28,
   "outputs": []
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-20T10:43:09.664312Z",
     "start_time": "2024-05-20T10:43:09.548315Z"
    }
   },
   "cell_type": "code",
   "source": "plt.imshow(m3[40:-40, 40:-40])",
   "id": "25e088c02d876392",
   "execution_count": 22,
   "outputs": []
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-20T09:00:39.411083Z",
     "start_time": "2024-05-20T09:00:39.395085Z"
    }
   },
   "cell_type": "code",
   "source": "",
   "id": "8c9885424b581017",
   "execution_count": 52,
   "outputs": []
  },
  {
   "metadata": {},
   "cell_type": "code",
   "execution_count": null,
   "source": "",
   "id": "ce3c05b2d34ed100",
   "outputs": []
  }
 ],
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