Cut-resample.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a694e51a",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Use a virtual environment, since the notebook install these packages \n",
    "!pip install itkwidgets simpleitk"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c818de9e",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os.path\n",
    "import urllib.request\n",
    "if not os.path.isfile(\"ct_example.nii.gz\"):\n",
    "    print(\"image not found. downloading now.\")\n",
    "    urllib.request.urlretrieve(\"https://raw.githubusercontent.com/dave3d/dicom2stl/main/examples/Data/ct_example.nii.gz\", \"ct_example.nii.gz\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4dbf5526",
   "metadata": {},
   "outputs": [],
   "source": [
    "import SimpleITK as sitk\n",
    "\n",
    "# Example volume: https://raw.githubusercontent.com/dave3d/dicom2stl/main/examples/Data/ct_example.nii.gz\"\n",
    "img = sitk.ReadImage(\"ct_example.nii.gz\")\n",
    "\n",
    "cut = sitk.Image([300,300,1], sitk.sitkUInt16)\n",
    "\n",
    "rotate = sitk.Euler3DTransform()\n",
    "\n",
    "# 15 degree rotation about X axis\n",
    "rotate.SetRotation(.2618, 0.0, 0.0)\n",
    "\n",
    "cut.SetDirection(rotate.GetMatrix())\n",
    "\n",
    "cut2 = sitk.Resample(img, cut)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3f3e8cfe",
   "metadata": {},
   "outputs": [],
   "source": [
    "#sitk.Show(cut2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b9f3d0a6",
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "import itkwidgets\n",
    "\n",
    "itkwidgets.view(cut2, axes=True, slicing_planes=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4502bfea",
   "metadata": {},
   "outputs": [],
   "source": [
    "sitk.WriteImage(cut2, \"cut.nrrd\")"
   ]
  }
 ],
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