{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "06270b57",
   "metadata": {},
   "outputs": [],
   "source": [
    "# imports\n",
    "import pathlib\n",
    "import numpy as np\n",
    "from scipy import ndimage\n",
    "import skimage.measure\n",
    "import dask.array as da\n",
    "import napari"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "4c2bbccb",
   "metadata": {},
   "outputs": [],
   "source": [
    "class_names_colors = {\n",
    "    \"bronchioles\": [150, 99, 23, 255],  # brown\n",
    "    \"alveoli\": [23, 80, 150, 255],  # dark blue\n",
    "    #\"alveoli\": [23, 80, 150, 0],  # dark blue\n",
    "    \"vasculature\": [150, 31, 23, 255],  # dark red\n",
    "    \"cancer\": [199, 196, 147, 255],  # v dark purple\n",
    "    \"nonexpanded\": [23, 80, 150, 255],  # dark blue\n",
    "    #\"nonexpanded\": [23, 80, 150, 0],  # dark blue\n",
    "    #\"whitespace\": [255, 255, 255, 255],  # white\n",
    "    \"whitespace\": [255, 255, 255, 0],  # white\n",
    "    \"collagen\": [242, 167, 227, 255],  # light pink\n",
    "    #\"collagen\": [242, 167, 227, 0],  # light pink\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "4b3114b9",
   "metadata": {},
   "outputs": [],
   "source": [
    "registered_labels_zarr_path = (\n",
    "    pathlib.Path().resolve().parent.parent\n",
    "    / \"testing_python_FULL_20250929\"\n",
    "    / \"registered_class_labels.zarr\"\n",
    "    # / \"registered_class_labels_2_mpp.zarr\"\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "695184c7",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/margareteminizer/miniconda3/envs/coda-visual/lib/python3.10/site-packages/zarr/creation.py:614: UserWarning: ignoring keyword argument 'read_only'\n",
      "  compressor, fill_value = _kwargs_compat(compressor, fill_value, kwargs)\n"
     ]
    }
   ],
   "source": [
    "labels_data = da.from_zarr(str(registered_labels_zarr_path/\"arr_0\"))\n",
    "labels_data = labels_data.transpose(2, 0, 1)  # Change shape from (y, x, z) to (z, y, x)\n",
    "labels_data = labels_data.compute()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5c4067c5",
   "metadata": {},
   "outputs": [],
   "source": [
    "colors = {\n",
    "    i: tuple([v / 255.0 for v in color])\n",
    "    for i, color in enumerate(class_names_colors.values(), start=1)\n",
    "}\n",
    "colors[0] = (0, 0, 0, 0)  # Make background transparent\n",
    "colors[None] = (0, 0, 0, 0)  # Also make None transparent\n",
    "\n",
    "labels = dict(enumerate(class_names_colors.keys(), start=1))\n",
    "labels[0] = \"unassigned\"\n",
    "\n",
    "viewer = napari.Viewer()\n",
    "viewer.add_labels(\n",
    "    labels_data,\n",
    "    name=\"Registered Class Labels\",\n",
    "    colormap=colors,\n",
    "    axis_labels=(\"z\", \"y\", \"x\"),\n",
    "    opacity=1.0,\n",
    "    scale=(2.0, 1.0, 1.0),\n",
    ")\n",
    "napari.run()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "5dd373ea",
   "metadata": {},
   "outputs": [],
   "source": [
    "surface_meshes = {}\n",
    "for i_class, class_name in enumerate(class_names_colors.keys(), start=1):\n",
    "    if class_name in (\"whitespace\", \"alveoli\", \"nonexpanded\"):\n",
    "        continue  # Skip whitespace class\n",
    "    class_mask = labels_data == i_class\n",
    "    verts, faces, _, _ = skimage.measure.marching_cubes(class_mask, level=0.5)\n",
    "    surface_meshes[class_name] = (verts, faces)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "150ce1c2",
   "metadata": {},
   "outputs": [],
   "source": [
    "viewer = napari.Viewer()\n",
    "for class_name, (verts, faces) in surface_meshes.items():\n",
    "    color = tuple([v / 255.0 for v in class_names_colors[class_name]])\n",
    "    viewer.add_surface((verts, faces), name=class_name, colormap=color)\n",
    "napari.run()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "cd848e2b",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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