{
 "cells": [
  {
   "cell_type": "markdown",
   "source": [
    "# Support mask\n",
    "\n",
    "This page explains the `mask` aspects of the Julia package\n",
    "[`ImageGeoms`](https://github.com/JuliaImageRecon/ImageGeoms.jl)."
   ],
   "metadata": {}
  },
  {
   "cell_type": "markdown",
   "source": [
    "### Setup"
   ],
   "metadata": {}
  },
  {
   "cell_type": "markdown",
   "source": [
    "Packages needed here."
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "using ImageGeoms: ImageGeom, MaskCircle, MaskAllButEdge\n",
    "using ImageGeoms: maskit, embed, embed!, getindex! # +jim +size\n",
    "using ImageGeoms: mask_outline\n",
    "using MIRTjim: jim, prompt\n",
    "using Unitful: mm"
   ],
   "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": [
    "## Mask overview\n",
    "\n",
    "In tomographic image reconstruction, patients are usually more \"round\"\n",
    "than \"square\" so often we only want to estimate the pixels inside some\n",
    "support `mask`: a `Bool` array indicating which pixels are to be estimated.\n",
    "(The rest are constrained to be zero.)\n",
    "The `ImageGeom` struct has an entry to store this `mask`.\n",
    "The default is `Trues(dims)` which is a \"lazy\" Bool `AbstractArray`\n",
    "from the `FillArrays` package that is conceptually similar to `trues(dims)`\n",
    "but requires `O(1)` storage.  So there is essentially no memory penalty\n",
    "to storing this entry in the `ImageGeom` for users who do not want\n",
    "to think about a `mask`.\n",
    "For users who do want a `mask`, fortunately Julia uses a special `BitArray`\n",
    "type to store `Bool` arrays, so the storage is 8× less than using bytes\n",
    "in most other languages.\n",
    "\n",
    "Often we use a \"circle inscribed in the square\" as a generic support mask,\n",
    "and one of the built-in constructors can generate such a circular mask:"
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "ig = ImageGeom(MaskCircle() ; dims=(40,32), deltas=(1mm,1mm))"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "That last line shows that 716 of 1280=40*32 mask pixels are nonzero."
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "jim(ig)"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "Note that `jim` displays the axes with the units naturally;\n",
    "see [MIRTjim.jl](https://github.com/JeffFessler/MIRTjim.jl).\n",
    "\n",
    "A 3D mask can be hard to visualize, so there is a `mask_or` method\n",
    "that collapses it to 2D:"
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "ig = ImageGeom(MaskAllButEdge() ; dims=(32,32,16))\n",
    "\n",
    "jim(ig)"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "## Mask operations"
   ],
   "metadata": {}
  },
  {
   "cell_type": "markdown",
   "source": [
    "Often we need to extract the pixel values within a mask:"
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "ig = ImageGeom(MaskAllButEdge() ; dims=(6,4))\n",
    "x = 1:size(ig,1)\n",
    "y = 1:size(ig,2)\n",
    "ramp = x .+ 10*y'\n",
    "\n",
    "ig.mask\n",
    "\n",
    "core = ramp[ig.mask]"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "Or equivalently:"
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "maskit(ramp, ig.mask)"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "Conversely, we can `embed` that list of pixels back into an array:"
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "array = embed(core, ig.mask)"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "There are in-place versions of these two operations:"
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "core = Array{Float32}(undef, sum(ig.mask))\n",
    "getindex!(core, ramp, ig.mask)"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "array = collect(zeros(Float16, ig))\n",
    "embed!(array, core, ig.mask)"
   ],
   "metadata": {},
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "## Mask outline\n",
    "Sometimes we need the outline of the mask."
   ],
   "metadata": {}
  },
  {
   "outputs": [],
   "cell_type": "code",
   "source": [
    "ig = ImageGeom(MaskCircle() ; dims=(40,32))\n",
    "outline = mask_outline(ig.mask)\n",
    "jim(\n",
    " jim(ig.mask, \"Mask\"; prompt=false),\n",
    " jim(outline, \"Outline\"; prompt=false),\n",
    ")"
   ],
   "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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