{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Calculate fibre orientation from a photograph"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "# from skimage.color import rgb2gray\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "from pynamix import io, data, measure, color, plotting, exposure\n",
    "virino = color.virino()\n",
    "\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load example data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "io.download_file('https://thumbs.dreamstime.com/b/hypnos-circles-concentric-abstract-texture-vector-illustration-hypnotic-swirl-spiral-background-137959483.jpg','spiral.jpg') # download an image from the internet\n",
    "ims, logfile = io.load_image('spiral.jpg')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Show example data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plt.imshow(ims[0],cmap='gray') # show the first 'frame' in the video (i.e. the only image)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## (Optionally) apply an ROI"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# ims, logfile = exposure.apply_ROI(ims, logfile, left=600)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Calculate orientation field"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "patchw=8\n",
    "X,Y,orient,dzeta = measure.orientation_map(ims,logfile,patchw=patchw,xstep=patchw//4,ystep=patchw//4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fig = plt.figure(figsize=[14,4])\n",
    "\n",
    "plt.subplot(131)\n",
    "plt.title('Original image')\n",
    "plt.imshow(ims[0],origin='lower',cmap='gray')\n",
    "\n",
    "plt.subplot(132)\n",
    "plt.title(r'$\\theta$')\n",
    "plt.pcolormesh(X,Y,orient[0],cmap=virino,vmin=0,vmax=np.pi)\n",
    "cb = plt.colorbar()\n",
    "cb.set_ticks([0,np.pi/2.,np.pi])\n",
    "cb.set_ticklabels([r'$0$',r'$\\pi/2$',r'$\\pi$'])\n",
    "\n",
    "plt.subplot(133)\n",
    "plt.title(r'$||T||$')\n",
    "plt.pcolormesh(X,Y,dzeta[0],vmin=0,vmax=1)\n",
    "plt.colorbar()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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