{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "f2299629",
   "metadata": {},
   "source": [
    "# It is a template for applying CPICANN to X-ray powder diffraction phase identification"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cad44131",
   "metadata": {},
   "source": [
    "### 1: install WPEMPhase package "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "af59fa9d",
   "metadata": {},
   "source": [
    "pip install WPEMPhase"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7d9d6d02",
   "metadata": {},
   "source": [
    "### 2: The first time you execute CPICANN on your computer, you should initialize the system documents. After that, you do not need to do any additional execution to run CPICANN."
   ]
  },
  {
   "cell_type": "raw",
   "id": "4787c1b4",
   "metadata": {},
   "source": [
    "Signature:\n",
    "CPICANN.PhaseIdentifier(\n",
    "    FilePath,\n",
    "    Task='single-phase',\n",
    "    Model='default',\n",
    "    ElementsSystem='',\n",
    "    ElementsContained='',\n",
    "    Device='cuda:0',\n",
    ")\n",
    "Docstring:\n",
    "CPICANN : Crystallographic Phase Identifier of Convolutional self-Attention Neural Network\n",
    "\n",
    "Contributors : Shouyang Zhang & Bin Cao\n",
    "================================================================\n",
    "    Please feel free to open issues in the Github :\n",
    "    https://github.com/WPEM/CPICANN\n",
    "    or\n",
    "    contact Mr.Bin Cao (bcao686@connect.hkust-gz.edu.cn)\n",
    "    in case of any problems/comments/suggestions in using the code.\n",
    "==================================================================\n",
    "\n",
    ":param FilePath\n",
    "\n",
    ":param Task, type=str, default='single-phase'\n",
    "    if Task = 'single-phase', CPICANN executes a single phase identification task\n",
    "    if Task = 'di-phase', CPICANN executes a dual phase identification task\n",
    "\n",
    ":param Model, type=str, default='default'\n",
    "    if Model = 'noise_model', CPICANN executes a single phase identification by noise-contained model\n",
    "    if Model = 'bca_model', CPICANN executes a single phase identification by background-contained model\n",
    "\n",
    ":param ElementsSystem, type=str, default=''\n",
    "    Specifies the elements to be included at least in the prediction, example: 'Fe'.\n",
    "\n",
    ":param ElementsContained, type=str, default=''\n",
    "    Specifies the elements to be included, with at least one of them in the prediction, example: 'O_C_S'.\n",
    "\n",
    ":param Device, type=str, default='cuda:0',\n",
    "    Which device to run the CPICANN, example: 'cuda:0', 'cpu'.\n",
    "\n",
    "examples:\n",
    "from WPEMPhase import CPICANN\n",
    "CPICANN.PhaseIdentifier(FilePath='./single-phase',Device='cpu')\n",
    "File:      ~/miniconda3/lib/python3.9/site-packages/WPEMPhase/CPICANN.py\n",
    "Type:      function"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "0922c99d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "Successfully installed WPEMPhase-0.1.0\n",
      "Note: you may need to restart the kernel to use updated packages.\n"
     ]
    }
   ],
   "source": [
    "pip install WPEMPhase"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "8e1680a6",
   "metadata": {},
   "outputs": [],
   "source": [
    "from WPEMPhase import CPICANN"
   ]
  },
  {
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      "`--NotebookApp.iopub_msg_rate_limit`.\n",
      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "NotebookApp.rate_limit_window=3.0 (secs)\n",
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      "To change this limit, set the config variable\n",
      "`--NotebookApp.iopub_msg_rate_limit`.\n",
      "\n",
      "Current values:\n",
      "NotebookApp.iopub_msg_rate_limit=1000.0 (msgs/sec)\n",
      "NotebookApp.rate_limit_window=3.0 (secs)\n",
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      "to the client in order to avoid crashing it.\n",
      "To change this limit, set the config variable\n",
      "`--NotebookApp.iopub_msg_rate_limit`.\n",
      "\n",
      "Current values:\n",
      "NotebookApp.iopub_msg_rate_limit=1000.0 (msgs/sec)\n",
      "NotebookApp.rate_limit_window=3.0 (secs)\n",
      "\n"
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     "text": [
      "Downloading: 100% [776454342 / 776454342] bytes  ____  ____   ___   ____     _     _   _  _   _ \n",
      " / ___||  _ \\ |_ _| / ___|   / \\   | \\ | || \\ | |\n",
      "| |    | |_) | | | | |      / _ \\  |  \\| ||  \\| |\n",
      "| |___ |  __/  | | | |___  / ___ \\ | |\\  || |\\  |\n",
      " \\____||_|    |___| \\____|/_/   \\_\\|_| \\_||_| \\_|\n",
      "                                                 \n",
      "\n",
      "The phase identification module of WPEM\n",
      "URL : https://github.com/WPEM/CPICANN\n",
      "Executed on : 2024-04-21 14:14:25  | Have a great day.\n",
      "================================================================================\n",
      "loaded model from /Users/jacob/miniconda3/lib/python3.9/site-packages/WPEMPhase/pretrained/CPICANN_single-phase_back3.pth\n",
      "\n",
      ">>>>>> RUNNING: ./testdata/.DS_Store\n",
      "\n",
      ">>>>>> RUNNING: ./testdata/PbSO4.csv\n",
      "pred cls_id : 2475  confidence : 98.89%\n",
      "pred cod_id : 9009622  formula : Pb2 S2 O6\n",
      "pred space group No: 11    space group : P2_1/m\n",
      "\n",
      "inference result saved in infResults_testdata.csv\n",
      "inference figures saved at figs/\n",
      "THE END\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Here, illustrate the system requirements and how to initialize the system files at the first time of execution.\n",
    "\n",
    "CPICANN.PhaseIdentifier(FilePath='./testdata',Model='bca_model',Task='single-phase',Device='cpu',)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "304b62b5",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  ____  ____   ___   ____     _     _   _  _   _ \n",
      " / ___||  _ \\ |_ _| / ___|   / \\   | \\ | || \\ | |\n",
      "| |    | |_) | | | | |      / _ \\  |  \\| ||  \\| |\n",
      "| |___ |  __/  | | | |___  / ___ \\ | |\\  || |\\  |\n",
      " \\____||_|    |___| \\____|/_/   \\_\\|_| \\_||_| \\_|\n",
      "                                                 \n",
      "\n",
      "The phase identification module of WPEM\n",
      "URL : https://github.com/WPEM/CPICANN\n",
      "Executed on : 2024-04-21 14:14:53  | Have a great day.\n",
      "================================================================================\n",
      "loaded model from /Users/jacob/miniconda3/lib/python3.9/site-packages/WPEMPhase/pretrained/CPICANN_single-phase_noise3.pth\n",
      "\n",
      ">>>>>> RUNNING: ./testdata/.DS_Store\n",
      "\n",
      ">>>>>> RUNNING: ./testdata/PbSO4.csv\n",
      "pred cls_id : 3378  confidence : 100.00%\n",
      "pred cod_id : 9004484  formula : Pb4 S4 O16\n",
      "pred space group No: 62    space group : Pnma\n",
      "\n",
      "inference result saved in infResults_testdata.csv\n",
      "inference figures saved at figs/\n",
      "THE END\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from WPEMPhase import CPICANN\n",
    "# Here, illustrate the system requirements and how to initialize the system files at the first time of execution.\n",
    "\n",
    "CPICANN.PhaseIdentifier(FilePath='./testdata',Model='noise_model',Task='single-phase',ElementsContained='Pb_S_O',Device='cpu',)"
   ]
  },
  {
   "cell_type": "raw",
   "id": "977ede12",
   "metadata": {},
   "source": [
    "For inquiries or assistance, please don't hesitate to contact us at bcao686@connect.hkust-gz.edu.cn (Dr. CAO Bin)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "bb101480",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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