{
 "cells": [
  {
   "cell_type": "markdown",
   "source": [
    "# Fan-beam tomography: flat detector\n",
    "\n",
    "This page describes fan-beam tomographic image reconstruction\n",
    "using the Julia package\n",
    "[`Sinograms.jl`](https://github.com/JuliaImageRecon/Sinograms.jl).\n",
    "\n",
    "This page focuses on fan-beam with a \"flat\" detector,\n",
    "i.e., one row of a flat-panel detector\n",
    "as used in many cone-beam CT (CBCT) systems."
   ],
   "metadata": {}
  },
  {
   "cell_type": "markdown",
   "source": [
    "### Setup"
   ],
   "metadata": {}
  },
  {
   "cell_type": "markdown",
   "source": [
    "Packages needed here."
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "using Plots: plot, gui\n",
    "using Unitful: cm\n",
    "using Sinograms: SinoFanFlat, rays, plan_fbp, Window, Hamming, fbp, sino_geom_plot!\n",
    "using ImageGeoms: ImageGeom, fovs, MaskCircle\n",
    "using ImagePhantoms: SheppLogan, shepp_logan, radon, phantom\n",
    "using MIRTjim: jim, prompt"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "The following line is helpful when running this file as a script;\n",
    "this way it will prompt user to hit a key after each figure is displayed."
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "isinteractive() ? jim(:prompt, true) : prompt(:draw);"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "## Fan-beam sinogram of Shepp-Logan phantom\n",
    "\n",
    "For illustration,\n",
    "we start by synthesizing\n",
    "a fan-beam sinogram\n",
    "of the Shepp-Logan phantom.\n",
    "\n",
    "For completeness,\n",
    "we use units (from Unitful),\n",
    "but units are optional."
   ],
   "metadata": {}
  },
  {
   "cell_type": "markdown",
   "source": [
    "Use `ImageGeom` to define the image geometry."
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "ig = ImageGeom(MaskCircle(); dims=(128,126), deltas = (0.2cm,0.2cm) )"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "Use `SinoFanFlat` to define the sinogram geometry."
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "rg = SinoFanFlat( ; nb = 130, d = 0.3cm, na = 100, dsd = 50cm, dod = 14cm)"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "Examine the geometry to verify the FOV:"
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "jim(axes(ig), ig.mask; prompt=false)\n",
    "sino_geom_plot!(rg, ig)"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "prompt()"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "Ellipse parameters for Shepp-Logan phantom:"
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "μ = 0.1 / cm # typical linear attenuation coefficient\n",
    "ob = shepp_logan(SheppLogan(); fovs = fovs(ig), u = (1, 1, μ))"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "Arc fan-beam sinogram for Shepp-Logan phantom:"
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "sino = radon(rays(rg), ob)\n",
    "jim(axes(rg), sino; title=\"Shepp-Logan sinogram\", xlabel=\"r\", ylabel=\"ϕ\")"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "## Image reconstruction via FBP\n",
    "Here we start with a \"plan\",\n",
    "which would save work if we were reconstructing many images.\n",
    "For illustration we include `Hamming` window."
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "plan = plan_fbp(rg, ig; window = Window(Hamming(), 1.0))\n",
    "fbp_image = fbp(plan, sino)"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "A narrow color window is needed to see the soft tissue structures:"
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "clim = (0.9, 1.1) .* μ\n",
    "jim(axes(ig), fbp_image, \"FBP image for flat case\"; clim)"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "For comparison, here is the ideal phantom image"
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "true_image = phantom(axes(ig)..., ob, 2)\n",
    "jim(axes(ig)..., true_image, \"True phantom image\"; clim)"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "---\n",
    "\n",
    "*This notebook was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).*"
   ],
   "metadata": {}
  }
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