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.doctrees/nbsphinx/_examples/Configuration.ipynb

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+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Configuration\n",
+    "\n",
+    "PyDicer provides various options which you may configure to change the behaviour of the tool."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-12-13T06:22:48.919921Z",
+     "iopub.status.busy": "2023-12-13T06:22:48.919723Z",
+     "iopub.status.idle": "2023-12-13T06:22:53.670045Z",
+     "shell.execute_reply": "2023-12-13T06:22:53.669389Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "try:\n",
+    "    from pydicer import PyDicer\n",
+    "except ImportError:\n",
+    "    !pip install pydicer\n",
+    "    from pydicer import PyDicer\n",
+    "\n",
+    "import logging\n",
+    "\n",
+    "from pydicer.utils import fetch_converted_test_data\n",
+    "\n",
+    "working_directory = fetch_converted_test_data(\"./testdata_lctsc\", dataset=\"LCTSC\")\n",
+    "\n",
+    "pydicer = PyDicer(working_directory)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Getting and Setting Options\n",
+    "\n",
+    "Use the `get_config` and `set_config` functions of the `config` module to get and set configuration\n",
+    "options respectively."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-12-13T06:22:53.672967Z",
+     "iopub.status.busy": "2023-12-13T06:22:53.672664Z",
+     "iopub.status.idle": "2023-12-13T06:22:53.677340Z",
+     "shell.execute_reply": "2023-12-13T06:22:53.676730Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Current logging verbosity: 0\n",
+      "New logging verbosity: 10\n"
+     ]
+    }
+   ],
+   "source": [
+    "logging_verbosity = pydicer.config.get_config(\"verbosity\")\n",
+    "print(f\"Current logging verbosity: {logging_verbosity}\")\n",
+    "\n",
+    "# Set to logging level DEBUG\n",
+    "pydicer.config.set_config(\"verbosity\", logging.DEBUG)\n",
+    "\n",
+    "logging_verbosity = pydicer.config.get_config(\"verbosity\")\n",
+    "print(f\"New logging verbosity: {logging_verbosity}\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Options Available\n",
+    "\n",
+    "### Logging Verbosity\n",
+    "\n",
+    "Level of output for standard out. Value indicates the Python built-in log level. A value of 0\n",
+    "(not set) will display the process bar. Logs of all levels are available in the .pydicer directory.\n",
+    "\n",
+    "Valid options are: `[logging.NOTSET, logging.DEBUG, logging.INFO, logging.WARNING, logging.ERROR]`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-12-13T06:22:53.680268Z",
+     "iopub.status.busy": "2023-12-13T06:22:53.680027Z",
+     "iopub.status.idle": "2023-12-13T06:22:53.683466Z",
+     "shell.execute_reply": "2023-12-13T06:22:53.682863Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "pydicer.config.set_config(\"verbosity\", logging.DEBUG)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Frame of Reference Fallback Linkage\n",
+    "\n",
+    "Determine whether to fallback on linking objects via their Frame of Reference if no more stable\n",
+    "link exists.\n",
+    "\n",
+    "Valid options are: `True` or `False`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-12-13T06:22:53.686045Z",
+     "iopub.status.busy": "2023-12-13T06:22:53.685542Z",
+     "iopub.status.idle": "2023-12-13T06:22:53.688927Z",
+     "shell.execute_reply": "2023-12-13T06:22:53.688295Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "pydicer.config.set_config(\"for_fallback_linkage\", True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Enforce `.dcm` file extension\n",
+    "\n",
+    "If True only files with the .dcm or .DCM extension will be preprocessed. Otherwise any file in the\n",
+    "DICOM directory will be preprocessed.\n",
+    "\n",
+    "Valid options are: `True` or `False`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-12-13T06:22:53.691553Z",
+     "iopub.status.busy": "2023-12-13T06:22:53.691344Z",
+     "iopub.status.idle": "2023-12-13T06:22:53.695216Z",
+     "shell.execute_reply": "2023-12-13T06:22:53.694667Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "pydicer.config.set_config(\"enforce_dcm_ext\", True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Interpolate Missing Slices\n",
+    "\n",
+    "When missing slices are detected these will be interpolated if True. Otherwise these cases will be\n",
+    "sent to quarantine.\n",
+    "\n",
+    "Valid options are: `True` or `False`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-12-13T06:22:53.697853Z",
+     "iopub.status.busy": "2023-12-13T06:22:53.697469Z",
+     "iopub.status.idle": "2023-12-13T06:22:53.700946Z",
+     "shell.execute_reply": "2023-12-13T06:22:53.700342Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "pydicer.config.set_config(\"interp_missing_slices\", True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Ignore Duplicate Slices\n",
+    "\n",
+    "If two slices at the same location with different pixel data are found then the first slice is used\n",
+    "if ignore_duplicate_slices is True. Otherwise an error is raised and these images are sent to\n",
+    "quarantine.\n",
+    "\n",
+    "Valid options are: `True` or `False`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-12-13T06:22:53.703403Z",
+     "iopub.status.busy": "2023-12-13T06:22:53.703207Z",
+     "iopub.status.idle": "2023-12-13T06:22:53.706596Z",
+     "shell.execute_reply": "2023-12-13T06:22:53.705970Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "pydicer.config.set_config(\"ignore_duplicate_slices\", False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Generate NRRD\n",
+    "\n",
+    "Whether or not to generate an additional NRRD file when converting RTSTRUCT. This allows loading\n",
+    "easily into 3D slicer, but it takes up more disk space and takes time to generate the file.\n",
+    "\n",
+    "Valid options are: `True` or `False`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-12-13T06:22:53.709235Z",
+     "iopub.status.busy": "2023-12-13T06:22:53.708841Z",
+     "iopub.status.idle": "2023-12-13T06:22:53.712240Z",
+     "shell.execute_reply": "2023-12-13T06:22:53.711693Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "pydicer.config.set_config(\"generate_nrrd\", False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### NRRD Colormap\n",
+    "\n",
+    "If NRRD files are to be generated, this defines the Matplotlib colormap to use when saving NRRD\n",
+    "file of structures.\n",
+    "\n",
+    "Valid options are any [Matplotlib colormap](https://matplotlib.org/stable/users/explain/colors/colormaps.html)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-12-13T06:22:53.714796Z",
+     "iopub.status.busy": "2023-12-13T06:22:53.714333Z",
+     "iopub.status.idle": "2023-12-13T06:22:53.717874Z",
+     "shell.execute_reply": "2023-12-13T06:22:53.717323Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "pydicer.config.set_config(\"nrrd_colormap\", \"rainbow\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "interpreter": {
+   "hash": "814af119db7f8f2860617be3dcd1d37c560587d11c65bd58c45b1679d3ee6ea4"
+  },
+  "kernelspec": {
+   "display_name": "Python 3.8.0 64-bit ('pydicer': pyenv)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.18"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}