{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# imports\n",
    "import pathlib\n",
    "import random\n",
    "import napari\n",
    "import numpy as np\n",
    "from coda_visual.datasets.raw_hamamatsu_file import RawHamamatsuFile"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "RAW_IMAGE_DIR = pathlib.Path().resolve().parent.parent / \"sample_dataset\" / \"20x files\"\n",
    "raw_image_list = sorted(list(RAW_IMAGE_DIR.glob(\"*.ndpi\")), key=lambda x: x.name)\n",
    "random_raw_image_path = random.choice(raw_image_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "raw_file = RawHamamatsuFile(random_raw_image_path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "pyramid = raw_file.get_dask_image_pyramid()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "tissue_mask_polygons = raw_file.get_tissue_outline_polygons()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "outlines_points = [(np.array(poly.exterior.xy).T[:, [1,0]])[:-1] for poly in tissue_mask_polygons]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Shapes layer 'Tissue Outline' at 0x12e4f2d70>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "viewer = napari.Viewer()\n",
    "viewer.add_image(\n",
    "    pyramid,\n",
    "    name=raw_file.filename,\n",
    "    contrast_limits=[0, 255],\n",
    "    multiscale=True,\n",
    "    rgb=True,\n",
    ")\n",
    "viewer.add_shapes(\n",
    "    outlines_points,\n",
    "    name=\"Tissue Outline\",\n",
    "    shape_type=\"polygon\",\n",
    "    edge_color=\"red\",\n",
    "    face_color=\"transparent\",\n",
    "    edge_width=50,\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "coda_scratch",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.15"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}