{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5768eedc-f8be-442d-b93c-4377f6a923bc",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": [
     "remove-input"
    ]
   },
   "outputs": [],
   "source": ""
  },
  {
   "cell_type": "markdown",
   "id": "bd120f126071e47c",
   "metadata": {},
   "source": [
    "# Tiles in `wsidata`\n",
    "\n",
    "Tiles in wsidata is stored as a `GeoDataFrame` with an associated `TileSpec` object.\n",
    "\n",
    "To extract tiles from a non-existing magnification level, the tiling operation in `wsidata` is recorded with following information:\n",
    "\n",
    "- User specifies the tile size and magnification level.\n",
    "- The actual tile size and magnification level are used to create the tiles.\n",
    "- The tile size at the level 0.\n",
    "\n",
    "Noted that `wsidata` cannot create tiles, it can only record the information for generating tiles. Please use LazySlide to create tiles."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "44be3d819edfcf81",
   "metadata": {},
   "outputs": [],
   "source": [
    "from huggingface_hub import hf_hub_download\n",
    "\n",
    "s = hf_hub_download(\"RendeiroLab/LazySlide-data\", \"sample.svs\", repo_type=\"dataset\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5cbd0d5ea5df7e59",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-03-15T10:30:10.026711Z",
     "start_time": "2025-03-15T10:30:09.828212Z"
    }
   },
   "outputs": [],
   "source": [
    "from wsidata import TileSpec, open_wsi\n",
    "\n",
    "wsi = open_wsi(s)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9d730457bec9c405",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-03-15T10:28:56.364064Z",
     "start_time": "2025-03-15T10:28:56.359520Z"
    }
   },
   "outputs": [],
   "source": [
    "wsi.properties"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b44082cf-c4cc-4919-850f-b4392f6a26b5",
   "metadata": {},
   "source": [
    "Here we have a wsi with only one level with mpp=0.5\n",
    "\n",
    "If we want to request a tile size of 100x100 at level 0, the tile operation will be performed at level 0 with a tile size of 100x100."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2b12afbe09ff3524",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-03-15T10:32:04.097263Z",
     "start_time": "2025-03-15T10:32:04.094399Z"
    }
   },
   "outputs": [],
   "source": [
    "TileSpec.from_wsidata(wsi, 100)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7193229098adaee3",
   "metadata": {},
   "source": [
    "However, if we request a tile size of 100x100 at mpp=1, but mpp=1 doesn't exist in the original image.\n",
    "The tile operation will be performed at level 0 with a tile size of 200x200 and rescaled to 100x100."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "46d30d5ae9855bad",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-03-15T10:30:44.003204Z",
     "start_time": "2025-03-15T10:30:44.000219Z"
    }
   },
   "outputs": [],
   "source": [
    "TileSpec.from_wsidata(wsi, 100, mpp=1)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "57f2ff1d-6785-4708-864e-ddffb80d622b",
   "metadata": {},
   "source": [
    "Of course, tiles with overlapping is also supported"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "131db596377edbdd",
   "metadata": {},
   "outputs": [],
   "source": [
    "TileSpec.from_wsidata(wsi, 100, stride_px=50)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b3440d59-b388-4547-a0b1-53d9f34bd7dc",
   "metadata": {},
   "outputs": [],
   "source": [
    "TileSpec.from_wsidata(wsi, 100, overlap=0.1)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cf86c92f4c8b8eda",
   "metadata": {},
   "source": "If you want to create a new tile table manually, please remember to synchronize the `TileSpec` with it.\n"
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": [
    "import numpy as np\n",
    "\n",
    "from wsidata.io import add_tiles, sync_tile_spec\n",
    "\n",
    "add_tiles(\n",
    "    wsi,\n",
    "    \"tiles\",\n",
    "    np.random.randint(0, 255, (100, 2), dtype=np.int32),\n",
    "    tile_spec=TileSpec.from_wsidata(wsi, 25),\n",
    "    tissue_ids=np.random.randint(0, 2, 100),\n",
    ")\n",
    "\n",
    "wsi[\"new_tiles\"] = wsi[\"tiles\"].sample(10)\n",
    "sync_tile_spec(wsi, \"tiles\", \"new_tiles\")"
   ],
   "id": "b413a546eacb4b5d"
  }
 ],
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