{
 "cells": [
  {
   "cell_type": "markdown",
   "source": [
    "# FBP Overview\n",
    "\n",
    "This example illustrates how to perform filtered back-projection (FBP)\n",
    "image reconstruction in CT\n",
    "using the Julia language.\n",
    "\n",
    "This is under construction.\n",
    "See the demos in the Sinograms.jl package instead."
   ],
   "metadata": {}
  },
  {
   "cell_type": "markdown",
   "source": [
    "First we add the Julia packages that are need for these examples.\n",
    "Change `false` to `true` in the following code block\n",
    "if you are using any of the following packages for the first time."
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "if false\n",
    "    import Pkg\n",
    "    Pkg.add([\n",
    "        \"ImagePhantoms\"\n",
    "        \"Unitful\"\n",
    "        \"Plots\"\n",
    "        \"LaTeXStrings\"\n",
    "        \"MIRTjim\"\n",
    "        \"MIRT\"\n",
    "        \"Sinograms\"\n",
    "        \"InteractiveUtils\"\n",
    "    ])\n",
    "end"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "Now tell this Julia session to use the following packages for this example.\n",
    "Run `Pkg.add()` in the preceding code block first, if needed."
   ],
   "metadata": {}
  },
  {
   "cell_type": "markdown",
   "source": [
    "using ImagePhantoms: shepp_logan, SheppLogan, radon, phantom\n",
    "using Unitful: mm\n",
    "using Plots; default(label=\"\", markerstrokecolor=:auto)\n",
    "using LaTeXStrings\n",
    "using MIRT: diffl_map, ncg\n",
    "using Sinograms: todo"
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "using MIRTjim: jim, prompt\n",
    "using InteractiveUtils: versioninfo"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "The following line is helpful when running this jl-file as a script;\n",
    "this way it will prompt user to hit a key after each image is displayed."
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "isinteractive() && jim(:prompt, true);"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "isinteractive() && prompt();"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "Get the ellipse parameters for a CT-suitable version of the Shepp-Logan phantom\n",
    "and calculate (analytically) its sinogram."
   ],
   "metadata": {}
  },
  {
   "cell_type": "markdown",
   "source": [
    "if false\n",
    "object = shepp_logan(SheppLogan(); fovs=(FOV,FOV))\n",
    "sino = radon(object).(r,ϕ')\n",
    "data = data / oneunit(eltype(data)) # abandon units at this point\n",
    "jim(kr, kϕ, abs.(data), title=\"k-space data magnitude\",\n",
    "    xlabel=L\"k_r\",\n",
    "    ylabel=L\"k_{\\phi}\",\n",
    "    xticks = (-1:1) .* maximum(abs, kr),\n",
    "    yticks = (0,π),\n",
    "    ylims = (0,π),\n",
    "    aspect_ratio = :none,\n",
    ")\n",
    "end"
   ],
   "metadata": {}
  },
  {
   "cell_type": "markdown",
   "source": [
    "---\n",
    "\n",
    "*This notebook was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).*"
   ],
   "metadata": {}
  }
 ],
 "nbformat_minor": 3,
 "metadata": {
  "language_info": {
   "file_extension": ".jl",
   "mimetype": "application/julia",
   "name": "julia",
   "version": "1.9.1"
  },
  "kernelspec": {
   "name": "julia-1.9",
   "display_name": "Julia 1.9.1",
   "language": "julia"
  }
 },
 "nbformat": 4
}