{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# How To: Merge Fragmented Detections\n",
    "\n",
    "When a single colony is split into multiple objects (fragmentation),\n",
    "use refiners to merge the fragments back together."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from phenotypic.data import load_yeast_plate\n",
    "from phenotypic.enhance import GaussianBlur, CLAHE\n",
    "from phenotypic.detect import OtsuDetector\n",
    "from phenotypic.refine import NearestNeighborMerger, MaskFill, MaskCloser"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plate = load_yeast_plate()\n",
    "plate = GaussianBlur(sigma=2.0).apply(plate)\n",
    "plate = CLAHE(clip_limit=0.01).apply(plate)\n",
    "plate = OtsuDetector().apply(plate)\n",
    "print(f\"Before merging: {plate.num_objects} objects\")\n",
    "plate.dash(overlay=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Morphological Closing\n",
    "\n",
    "`MaskCloser` bridges small gaps between nearby fragments using dilation\n",
    "followed by erosion."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "closed = MaskCloser(width=5).apply(plate.copy())\n",
    "closed = MaskFill().apply(closed)\n",
    "print(f\"After closing + fill: {closed.num_objects} objects\")\n",
    "closed.dash(overlay=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Nearest-Neighbor Merging\n",
    "\n",
    "`NearestNeighborMerger` merges objects that are within a specified\n",
    "distance of each other, assigning smaller fragments to their nearest\n",
    "larger neighbor."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "merged = NearestNeighborMerger().apply(plate.copy())\n",
    "print(f\"After NN merge: {merged.num_objects} objects\")\n",
    "merged.dash(overlay=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Use `MaskCloser` for small gaps between fragments, and\n",
    "`NearestNeighborMerger` when fragments are further apart but clearly\n",
    "belong to the same colony."
   ]
  }
 ],
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