{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# How To: Enhance Low-Contrast Images\n",
    "\n",
    "When colonies are faint or the agar background is uneven, detection suffers.\n",
    "Use `CLAHE`, `ContrastStretching`, or `HomomorphicFilter` to boost local\n",
    "contrast in `detect_mat` before detection."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from phenotypic.data import load_yeast_plate\n",
    "from phenotypic.enhance import CLAHE, ContrastStretching, HomomorphicFilter"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plate = load_yeast_plate()\n",
    "plate.detect_mat.dash()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Option 1: CLAHE\n",
    "\n",
    "Adaptive histogram equalization that boosts local contrast. Best for plates\n",
    "with locally varying brightness."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "enhanced = CLAHE(clip_limit=0.02).apply(plate.copy())\n",
    "enhanced.detect_mat.dash()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Option 2: Contrast Stretching\n",
    "\n",
    "Linearly maps the intensity range to fill the full dynamic range. Simple\n",
    "and effective when the histogram is narrow but unimodal."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "enhanced2 = ContrastStretching().apply(plate.copy())\n",
    "enhanced2.detect_mat.dash()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Option 3: Homomorphic Filter\n",
    "\n",
    "Separates illumination from reflectance in the frequency domain.\n",
    "Best for correcting uneven illumination gradients across the plate."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "enhanced3 = HomomorphicFilter(sigma=200.0, gamma_low=0.5, gamma_high=1.5).apply(plate.copy())\n",
    "enhanced3.detect_mat.dash()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Choose based on the root cause: CLAHE for general low contrast,\n",
    "`ContrastStretching` for narrow histograms, `HomomorphicFilter` for\n",
    "uneven illumination."
   ]
  }
 ],
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