{
 "cells": [
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "# Example notebook `neuralib.atlas`",
   "id": "d554af79863e6491"
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": [
    "import matplotlib.pyplot as plt\n",
    "\n",
    "from neuralib.atlas.data import get_children\n",
    "from neuralib.atlas.view import get_slice_view"
   ],
   "id": "caf8ddaf8dde6427"
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": [
    "%load_ext autoreload\n",
    "%autoreload"
   ],
   "id": "8dd2102aed296798"
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": [
    "### Example of ML offset in coronal slice\n",
    "\n",
    "- Use `plane.with_angle_offset(deg_x=...)` for ML axis offset in a reference view"
   ],
   "id": "cce8e8f856205935"
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": [
    "slice_index = 700\n",
    "plane = get_slice_view('reference', plane_type='coronal', resolution=10).plane_at(slice_index)\n",
    "\n",
    "_, ax = plt.subplots(ncols=2, figsize=(20, 10))\n",
    "\n",
    "plane.plot(ax=ax[0], boundaries=True)\n",
    "ax[0].set_title('without offset')\n",
    "\n",
    "plane.with_angle_offset(deg_x=10).plot(ax=ax[1], boundaries=True)\n",
    "ax[1].set_title('+10 degree ML offset')"
   ],
   "id": "24f641c7fdf95ab2"
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": [
    "### Example of DV offset in sagittal slice\n",
    "\n",
    "- Use `plane.with_angle_offset(deg_y=...)` for DV axis offset in an annotation view"
   ],
   "id": "d015c4495a3a8240"
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": [
    "slice_index = 500\n",
    "plane = get_slice_view('annotation', plane_type='sagittal', resolution=10).plane_at(slice_index)\n",
    "\n",
    "_, ax = plt.subplots(ncols=2, figsize=(20, 10))\n",
    "plane.plot(ax=ax[0], boundaries=True)\n",
    "ax[0].set_title('without offset')\n",
    "\n",
    "plane.with_angle_offset(deg_y=20).plot(ax=ax[1], boundaries=True)\n",
    "ax[1].set_title('+20 degree DV offset')"
   ],
   "id": "d4bc3a2e2a2d6b2d"
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": [
    "### Example of Annotate regions\n",
    "- Annotation Hippocampal CA1 and Primary Visual Cortex (VISp)\n",
    "- Also works in offset view and detailed tree regions"
   ],
   "id": "a10e63243ddb47e4"
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": [
    "slice_index = 900\n",
    "plane = get_slice_view('reference', plane_type='coronal', resolution=10).plane_at(slice_index)\n",
    "\n",
    "_, ax = plt.subplots(ncols=2, figsize=(20, 10))\n",
    "plane.plot(ax=ax[0], boundaries=True, annotation_region=['CA1', 'VISp'])\n",
    "\n",
    "#\n",
    "primary_visual_layers = get_children('VISp', dataframe=False)\n",
    "print(primary_visual_layers)\n",
    "plane.with_angle_offset(deg_x=10).plot(ax=ax[1], boundaries=True, annotation_region=['CA1'] + primary_visual_layers)\n"
   ],
   "id": "edd06789ed9e063a"
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "### Example of Annotate regions in transverse view",
   "id": "29c226a118d26723"
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": [
    "slice_index = 300\n",
    "plane = get_slice_view('reference', plane_type='transverse', resolution=10).plane_at(slice_index)\n",
    "\n",
    "_, ax = plt.subplots(ncols=2, figsize=(20, 10))\n",
    "plane.plot(ax=ax[0], annotation_region=['ACA', 'LP'])\n",
    "plane.plot(ax=ax[1], annotation_region=['SS', 'MO'], annotation_cmap='PiYG', boundaries=True)"
   ],
   "id": "b4dd56e9f9e0d915"
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": [
    "### Example of max projection\n",
    "- All visual areas max projection in transverse section plane\n"
   ],
   "id": "1fea0394fbb7ad0d"
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": [
    "view = get_slice_view('reference', plane_type='transverse', resolution=10)\n",
    "\n",
    "_, ax = plt.subplots()\n",
    "regions = get_children('VIS')\n",
    "print(regions)\n",
    "view.plot_max_projection(ax, annotation_regions=regions)"
   ],
   "id": "4ebc4138e85eafcd"
  }
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