{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Working with NumPy Array Images"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import itk\n",
    "import numpy as np\n",
    "import imageio\n",
    "from itkwidgets import view, compare, checkerboard"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Images as NumPy arrays can be registered.\n",
    "\n",
    "Convert them to floating point arrays for registration."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "numpy.ndarray"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fixed = imageio.imread('data/CT_2D_head_fixed.mha')\n",
    "fixed = np.asarray(fixed).astype(np.float32)\n",
    "type(fixed)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "numpy.ndarray"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "moving = imageio.imread('data/CT_2D_head_moving.mha')\n",
    "moving = np.asarray(moving).astype(np.float32)\n",
    "type(moving)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "73d7960ef9194b41823abc916f85fad9",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=False, description='cmap'), Checkbox(v…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "compare(fixed, moving, ui_collapsed=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Before registration, the moving image is not aligned with the fixed image."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "6885b56476d74c1db2a58cedfe4da230",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(Viewer(annotations=False, interpolation=False, rendered_image=<itkImagePython.itkImageF2; proxy…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "checkerboard(fixed, moving, pattern=10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "numpy.ndarray"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Register!\n",
    "registered = itk.elastix_registration_method(fixed, moving)\n",
    "type(registered)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "b743e0733f84453db820d32a3ad9e718",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=False, description='cmap'), Checkbox(v…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "compare(fixed, registered, ui_collapsed=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The registered moving image is aligned with the fixed image"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "33eb1427d33a4c9293ac5c60ad74c2d3",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(Viewer(annotations=False, interpolation=False, rendered_image=<itkImagePython.itkImageF2; proxy…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "checkerboard(fixed, registered, pattern=10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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