Merge pull request #434 from WilhelmusLab/433-add-notebook-with-tilin…

…g-illustrations

docs: add nb for image tiling workflow

notebooks/preprocessing-workflow/tiling.ipynb

@@ -0,0 +1,286 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Tiling Utilities"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This notebook contains a demo of the tiling utilities included in `IceFloeTracker.jl`. In particular, the following workflows are illustrated:\n",
+    "\n",
+    "- Getting tiling with tiles of a given size\n",
+    "- Getting the optimal tile size given an initial tile side length\n",
+    "\n",
+    "Run the cell below to set up the computation environment."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "HOME = \"../..\" # path to the root of the project two levels up\n",
+    "\n",
+    "# Activate the environment\n",
+    "using Pkg\n",
+    "Pkg.activate(HOME)\n",
+    "Pkg.precompile()\n",
+    "\n",
+    "using IceFloeTracker: get_tiles, get_tile_dims, load\n",
+    "using ColorTypes: RGBA"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Load the image"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "imgpath = \"test/test_inputs/NE_Greenland_truecolor.2020162.aqua.250m.tiff\"\n",
+    "img = load(joinpath(HOME,imgpath))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Estimate tile size\n",
+    "\n",
+    "Say we want to split the image into roughly 8x8 tiles."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "prelim_sizes = size(img) .÷ 8"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Choosing tile size and building tilings\n",
+    "\n",
+    "The `get_tiles` function builds a tiling given an image (array) and a tile side length.\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Let's view the documentation for the function\n",
+    "@info @doc get_tiles"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tiles = get_tiles(img, prelim_sizes[1] + 1) # deliberately using a size that is too large"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Top left tile dimensions\n",
+    "get_tile_dims(tiles[1])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Note that the bottom right tile has been extended to cover the rest of the image as a uniform tiling of side length `prelim_sizes[1] + 1` fails to cover the full image."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# View the first tile\n",
+    "img[tiles[1]...]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Further, note that the tiles on the right and bottom edges are slightly bigger."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Bottom right tile dimensions\n",
+    "get_tile_dims(tiles[end])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### View the full tiling"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "function build_tiling_illustration(img, side_length)\n",
+    "\n",
+    "    # Create new canvas to draw on\n",
+    "    newimg = similar(img, RGBA{Float64})\n",
+    "\n",
+    "    # Apply transparency to the tiles\n",
+    "    for tile_coords in get_tiles(img, side_length)\n",
+    "        tile = @view img[tile_coords...]\n",
+    "        alpha = rand(0.5:0.05:1)\n",
+    "        transparent_tile = map(c -> RGBA(c.r, c.g, c.b, alpha), tile)\n",
+    "        newimg[tile_coords...] .= transparent_tile\n",
+    "    end\n",
+    "\n",
+    "    # View the image\n",
+    "    newimg\n",
+    "end\n",
+    "\n",
+    "build_tiling_illustration(img, prelim_sizes[1] + 1)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Optimal tile side length\n",
+    "\n",
+    "Perhaps there is a fitter tiling that is close to the originally desired tiling. We can use the `get_optimal_tile_size` function to determine whether this is possible."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "using IceFloeTracker: get_optimal_tile_size\n",
+    "\n",
+    "@info @doc get_optimal_tile_size"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "best_side_length = get_optimal_tile_size(prelim_sizes[1] + 1, size(img))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "As expected, a tile size of 1016 is not optimal for this image. The function `get_optimal_tile_size` suggests a fitter tiling is possible using tiles of 1015 pixels in side length for this image."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "build_tiling_illustration(img, best_side_length)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Area of corner tile with optimal side length\n",
+    "get_tile_dims(get_tiles(img, best_side_length)[end]) |> prod"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Note that the area of the corner tile for the suboptimal tiling is larger."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "get_tile_dims(get_tiles(img, prelim_sizes[1] + 1)[end]) |> prod"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The proportion of pixels missed by a uniform tiling can be computed with `get_area_missed`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "using IceFloeTracker: get_area_missed\n",
+    "areamissed_optimal = get_area_missed(best_side_length, size(img))\n",
+    "@show areamissed_optimal\n",
+    "@assert get_area_missed(prelim_sizes[1] + 1, size(img)) > get_area_missed(best_side_length, size(img))"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Julia 1.9.3",
+   "language": "julia",
+   "name": "julia-1.9"
+  },
+  "language_info": {
+   "file_extension": ".jl",
+   "mimetype": "application/julia",
+   "name": "julia"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}