{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Elastix\n",
    "\n",
    "This notebooks show very basic image registration examples with on-the-fly generated binary images."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import itk\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Image generators"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Image generator functions\n",
    "def image_generator_2D(x1, x2, y1, y2):\n",
    "    image = np.zeros([100, 100], np.float32)\n",
    "    image[y1:y2, x1:x2] = 1\n",
    "    return image\n",
    "\n",
    "\n",
    "def image_generator_3D(x1, x2, y1, y2, z1, z2):\n",
    "    image = np.zeros([10, 10, 10], np.float32)\n",
    "    image[z1:z2, y1:y2, x1:x2] = 1\n",
    "    return image"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Groupwise Registration Test (3D registration, 2D+time)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "itkPyVectorContainerPF4 not loaded from module ITKBridgeNumPy because of exception:\n",
      " module 'itk.ITKBridgeNumPyPython' has no attribute 'itkPyVectorContainerPF4'\n"
     ]
    }
   ],
   "source": [
    "# Create a vector of images for a 2D+time example in numpy\n",
    "array_of_images = np.zeros([6, 100, 100], np.float32)\n",
    "i = 0\n",
    "for x in range(0, 30, 5):\n",
    "    image = image_generator_2D(x, x+50, x, x+50)\n",
    "    array_of_images[i] = image\n",
    "    i += 1\n",
    "\n",
    "# Convert numpy array to itk 3D image\n",
    "image_itk_3D = itk.image_view_from_array(array_of_images)\n",
    "\n",
    "# Create Groupwise Parameter Object\n",
    "parameter_object = itk.ParameterObject.New()\n",
    "groupwise_parameter_map = parameter_object.GetDefaultParameterMap('groupwise',4)\n",
    "groupwise_parameter_map['FinalBSplineInterpolationOrder'] = ['0']\n",
    "groupwise_parameter_map['Transform'] = ['EulerStackTransform']\n",
    "groupwise_parameter_map['AutomaticScalesEstimation'] = ['true']\n",
    "groupwise_parameter_map['AutomaticScalesEstimationStackTransform'] = ['true']\n",
    "\n",
    "parameter_object.AddParameterMap(groupwise_parameter_map)\n",
    "\n",
    "result_image, result_transform_parameters = itk.elastix_registration_method(\n",
    "    image_itk_3D, image_itk_3D,\n",
    "    parameter_object,\n",
    "    log_to_console=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Groupwise Registration Test Visualization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "result_image_np = np.asarray(result_image).astype(np.float32)\n",
    "\n",
    "# Plot images\n",
    "fig, axs = plt.subplots(2,3, sharey=True, figsize=[30,30])\n",
    "plt.figsize=[100,100]\n",
    "axs[0,0].imshow(array_of_images[0])\n",
    "axs[0,0].set_title('Image0', fontsize=30)\n",
    "axs[0,1].imshow(array_of_images[1])\n",
    "axs[0,1].set_title('Image1', fontsize=30)\n",
    "axs[0,2].imshow(array_of_images[2])\n",
    "axs[0,2].set_title('Image2', fontsize=30)\n",
    "axs[1,0].imshow(array_of_images[3])\n",
    "axs[1,0].set_title('Image3', fontsize=30)\n",
    "axs[1,1].imshow(array_of_images[4])\n",
    "axs[1,1].set_title('Image4', fontsize=30)\n",
    "axs[1,2].imshow(result_image_np[5])\n",
    "axs[1,2].set_title('Result', fontsize=30)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Groupwise Registration Test (4D registration, 3D+time)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Create a vector of images for a 3D+time example in numpy\n",
    "array_of_images = np.zeros([6, 10, 10, 10], np.float32)\n",
    "i = 0\n",
    "for x in range(0, 30, 5):\n",
    "    image = image_generator_3D(x, x+50, x, x+50, x, x+50)\n",
    "    array_of_images[i] = image\n",
    "    i += 1\n",
    "\n",
    "# Convert numpy array to itk 4D image\n",
    "image_itk_4D = itk.image_view_from_array(array_of_images)\n",
    "\n",
    "# Create Groupwise Parameter Object\n",
    "parameter_object = itk.ParameterObject.New()\n",
    "groupwise_parameter_map = parameter_object.GetDefaultParameterMap('groupwise',2)\n",
    "groupwise_parameter_map['FinalBSplineInterpolationOrder'] = ['0']\n",
    "groupwise_parameter_map['Transform'] = ['EulerStackTransform']\n",
    "groupwise_parameter_map['AutomaticScalesEstimation'] = ['true']\n",
    "groupwise_parameter_map['AutomaticScalesEstimationStackTransform'] = ['true']\n",
    "\n",
    "parameter_object.AddParameterMap(groupwise_parameter_map)\n",
    "\n",
    "result_image, result_transform_parameters = itk.elastix_registration_method(\n",
    "    image_itk_4D, image_itk_4D,\n",
    "    parameter_object,\n",
    "    log_to_console=True)"
   ]
  }
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