templates/3b_extract_images_from_bin.ipynb

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   "source": [
    "# Extract Bin Files\n",
    "\n",
    "This notebook will check for the previously extracted FOVs in an image directory and proceed to extract any remaining FOVs from the provided base directory."
   ]
  },
  {
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   "id": "57186f2e-8030-436d-85ff-b4a3aa4a446f",
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   "outputs": [],
   "source": [
    "import sys\n",
    "sys.path.append('../')"
   ]
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  {
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   "id": "641739e1-2f6f-485e-8c8b-7fd9b09a023b",
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   "source": [
    "import os\n",
    "\n",
    "from toffy.panel_utils import load_panel\n",
    "from toffy.bin_extraction import extract_missing_fovs"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e2ba233e-6904-409c-b324-162dc9ff10e7",
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   "source": [
    "## Required variables\n",
    "You will need to define the following two arguments for this notebook.\n",
    " - `run_name` should contain the exact name of the MIBI run to extract from\n",
    " - `panel_path` should point to a panel csv specifying the targets on your panel. You can download your panel online from the Ionpath MibiTracker and then copy the file to the `C:\\\\Users\\\\Customer.ION\\\\Documents\\panel_files` directory (see [panel format](https://github.com/angelolab/toffy#panel-format) for more information)"
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   "source": [
    "# set up args for current run\n",
    "run_name = 'YYYY-MM-DD_run_name'\n",
    "panel_path = 'C:\\\\Users\\\\Customer.ION\\\\Documents\\\\panel_files\\\\my_cool_panel.csv'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4491bec6",
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   "source": [
    "Everything necessary for and subsequently outputted from this notebook is stored in the automatic directories established in `1_set_up_toffy.ipynb`. More information on the uses and locations of the directories in toffy can be found in the [README](https://github.com/angelolab/toffy#directory-structure)."
   ]
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   "source": [
    "# read in panel information\n",
    "panel = load_panel(panel_path)\n",
    "\n",
    "# path to the directory containing the FOV bin files\n",
    "base_dir = os.path.join('D:\\\\Data', run_name) \n",
    "\n",
    "# path to directory containing extracted files\n",
    "extraction_dir = os.path.join('D:\\\\Extracted_Images', run_name)    \n",
    "if not os.path.exists(extraction_dir):\n",
    "    os.makedirs(extraction_dir)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8767f85a-6c91-4e4e-9fe1-2a1603fdf384",
   "metadata": {},
   "source": [
    "## Extract FOV bin files\n",
    "The function below will skip any previously extracted FOVs and print \"Extraction completed!\" when done. If you receive a warning message stating \"no viable bin files were found\", then all of the necessary FOVs have already been extracted."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "cd6eda88-3003-496f-8c66-1697d570f05d",
   "metadata": {},
   "outputs": [],
   "source": [
    "extract_missing_fovs(base_dir, extraction_dir, panel)"
   ]
  }
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