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 "cells": [
  {
   "cell_type": "markdown",
   "id": "91860fae-a8ce-4c4d-9687-15f41bd9023b",
   "metadata": {},
   "source": [
    "# Atlas Free Slice Alignment Example"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8204ee94-b057-4e08-8386-468edbc17e04",
   "metadata": {},
   "source": [
    "The below cells show an example use case of the atlas-free slice alignment package."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d87cc448-5903-437f-bc1b-f6c5dc80d103",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import matplotlib.pyplot as plt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "dcfcc4c2-674e-4aaf-a8d4-d8b003c17b26",
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "# Location of the script on your local device\n",
    "script_path = '/home/abenneck/Desktop/atlas_free_slice_alignment/slice_alignment.py'\n",
    "cmd_str = f'python3 {script_path}'\n",
    "\n",
    "# Directory where all outputs should be stored\n",
    "outdir = '/home/abenneck/Desktop/atlas_free_slice_alignment_outputs'\n",
    "cmd_str += f' {outdir}'\n",
    "\n",
    "# Directory containing all files to be registered + the relevant fnames\n",
    "indir = '/home/abenneck/Desktop/atlas_free_slice_alignment/images'\n",
    "filesmoon=['frame_1_delay-0.2s[1].png','frame_0_delay-0.2s[1].png','frame_0_delay-0.2s[1].png','frame_1_delay-0.2s[1].png','frame_2_delay-0.2s[1].png','frame_3_delay-0.2s[1].png','frame_4_delay-0.2s[1].png','frame_5_delay-0.2s[1].png','frame_6_delay-0.2s[1].png','frame_7_delay-0.2s[1].png','frame_7_delay-0.2s[1].png','frame_6_delay-0.2s[1].png']\n",
    "cmd_str += ' -fnames'\n",
    "for fname in filesmoon:\n",
    "    fname = os.path.join(indir, fname)\n",
    "    cmd_str += f' {fname}'\n",
    "\n",
    "# NOTE: All of the scalar and torch-specific arguments are not included in this example\n",
    "\n",
    "# Include boolean flag for removing artifacts in input images\n",
    "cmd_str += ' --remove_artifacts'\n",
    "\n",
    "# Include boolean flag for saving all figures\n",
    "cmd_str += ' --saveAllFigs'\n",
    "\n",
    "print(cmd_str)\n",
    "os.system(cmd_str)\n",
    "plt.close('all')"
   ]
  }
 ],
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