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   "source": [
    "# Polarimetric Refined Lee speckle filter\n",
    "\n",
    "This tutorial shows how to:\n",
    "- Open the ALOS dataset and convert the S matrix to T3 coherency matrix\n",
    "- Pre-process the data by applying a 4-look decimation in azimuth\n",
    "- Apply the Refined Lee speckle filter to the 3x3 coherency matrix\n",
    "- Write the results to a file\n",
    "- Visualize the results as an RGB image\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "\n",
    "import os\n",
    "\n",
    "import xarray as xr\n",
    "\n",
    "from pathlib import Path\n",
    "from polsarpro.io import open_netcdf_beam, polmat_to_netcdf\n",
    "from polsarpro.speckle_filters import refined_lee\n",
    "from polsarpro.util import S_to_T3, multilook, pauli_rgb\n",
    "\n",
    "# optional import for progress bar\n",
    "from dask.diagnostics import ProgressBar\n",
    "\n",
    "\n",
    "# change to your data paths\n",
    "# original dataset\n",
    "input_alos_data = Path(\"/data/psp/test_files/SAN_FRANCISCO_ALOS1_slc.nc\")\n",
    "\n",
    "# output files from C\n",
    "output_test_dir = Path(\"/data/psp/res/\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load ALOS data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "S = open_netcdf_beam(input_alos_data)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Apply the filter to T3 matrices"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "if os.path.exists(output_test_dir / \"T3_refined_lee.nc\"):\n",
    "    os.remove(output_test_dir / \"T3_refined_lee.nc\")\n",
    "\n",
    "with ProgressBar():\n",
    "    # convert S to T3\n",
    "    T3 = S_to_T3(S)\n",
    "    # apply 4-look multilook along lines\n",
    "    T3 = multilook(T3, dim_az=4, dim_rg=1)\n",
    "    # apply the filter\n",
    "    T3_flt = refined_lee(T3, window_size=7, num_looks=4)\n",
    "    # use custom function that writes complex matrices and preserves chunks\n",
    "    polmat_to_netcdf(T3_flt, output_test_dir / f\"T3_refined_lee.nc\")\n",
    "    "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Open the file and visualize the results as an RBG image"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# open the file\n",
    "T3_flt = open_netcdf_beam(output_test_dir / f\"T3_refined_lee.nc\")\n",
    "\n",
    "pauli_rgb(T3_flt).plot.imshow(figsize=(5, 7))"
   ]
  }
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