{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "444ee591",
   "metadata": {},
   "source": [
    "# 3D Elliptic Fourier Analysis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "37d7c848",
   "metadata": {},
   "outputs": [],
   "source": [
    "import urllib\n",
    "\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "\n",
    "import matplotlib.pyplot as plt\n",
    "import seaborn as sns\n",
    "import plotly.express as px\n",
    "\n",
    "from ktch.outline import EllipticFourierAnalysis"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f12966fd",
   "metadata": {},
   "source": [
    "## 3D coordinate values of a leaf edge"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b7320a0a",
   "metadata": {},
   "outputs": [],
   "source": [
    "resp = urllib.request.urlopen(\"https://strata.morphometrics.jp/examples/rolling_alpha_016_nIntervals_64.csv\")\n",
    "arr_coord = np.loadtxt(resp)\n",
    "df_coord = pd.DataFrame(arr_coord, columns=[\"x\", \"y\", \"z\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "eb1bb8b2",
   "metadata": {},
   "outputs": [],
   "source": [
    "fig = px.line_3d(df_coord, x=\"x\", y=\"y\", z=\"z\")\n",
    "fig.update_layout(\n",
    "    scene=dict(\n",
    "                 aspectmode='data'\n",
    "         )\n",
    ")\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3a36631a",
   "metadata": {},
   "source": [
    "## 3D EFA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c7fa9f54",
   "metadata": {},
   "outputs": [],
   "source": [
    "efa3d = EllipticFourierAnalysis(n_harmonics=20, n_dim=3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0cd0c812",
   "metadata": {},
   "outputs": [],
   "source": [
    "coef = efa3d.fit_transform([arr_coord], norm=False).reshape(-1, 6, 21)\n",
    "print(\"coefficients (a, b, c, d, e, f) x (n_harmonics + 1)\", coef[0].shape)\n",
    "coef[0]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d8f327b1",
   "metadata": {},
   "source": [
    "## Reconstruction of 3D coordinate values from Fourier coefficients"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7c4d55ae",
   "metadata": {},
   "outputs": [],
   "source": [
    "arr_coord_recon = efa3d.inverse_transform(coef,t_num=600)\n",
    "df_coord_recon = pd.DataFrame(arr_coord_recon[0], columns=[\"x\", \"y\", \"z\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d5f9067b",
   "metadata": {},
   "outputs": [],
   "source": [
    "fig = px.line_3d(df_coord_recon, x=\"x\", y=\"y\", z=\"z\")\n",
    "fig.update_layout(\n",
    "    scene=dict(\n",
    "                 aspectmode='data'\n",
    "         )\n",
    ")\n",
    "fig.show()"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}