{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Epithelium Visualization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import tyssue\n",
    "\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "\n",
    "import matplotlib.pylab as plt\n",
    "%matplotlib inline\n",
    "import ipyvolume as ipv\n",
    "\n",
    "\n",
    "from tyssue import Sheet, SheetGeometry  as geom\n",
    "from tyssue.generation import three_faces_sheet\n",
    "from tyssue.draw import sheet_view\n",
    "from tyssue import config\n",
    "from tyssue import Monolayer, config\n",
    "from tyssue.generation import extrude\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "datasets, specs = three_faces_sheet()\n",
    "sheet = Sheet('3cells_2D', datasets, specs)\n",
    "\n",
    "\n",
    "geom.update_all(sheet)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sheet.vert_df.describe().head(3)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Matplotlib based representation\n",
    "\n",
    "### Custom settings\n",
    "\n",
    "These might go in a config file latter on."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Ploting itself"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Epithelial sheet representation\n",
    "\n",
    "\n",
    "### The  default"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "draw_specs = tyssue.config.draw.sheet_spec()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fig, ax = sheet_view(sheet, ['x', 'y'])\n",
    "\n",
    "\n",
    "ax.set_xlim(-3, 2.5)\n",
    "ax.set_ylim(-2.75, 2.75)\n",
    "fig.set_size_inches((8, 8))\n",
    "    \n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Coloring"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "## Let's add a column to sheet.vert_df\n",
    "sheet.vert_df['rand'] = np.linspace(0.0, 1.0, num=sheet.vert_df.shape[0])\n",
    "\n",
    "cmap = plt.cm.get_cmap('viridis')\n",
    "color_cmap = cmap(sheet.vert_df.rand)\n",
    "draw_specs['vert']['visible'] = True\n",
    "\n",
    "draw_specs['vert']['color'] = color_cmap\n",
    "draw_specs['vert']['alpha'] = 0.5\n",
    "draw_specs['vert']['s'] = 500"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "coords = ['x', 'y']\n",
    "fig, ax = sheet_view(sheet, coords, **draw_specs)\n",
    "\n",
    "ax.set_xlim(-3, 2.5)\n",
    "ax.set_ylim(-2.75, 2.75)\n",
    "fig.set_size_inches((8, 8))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Filling the cells\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sheet.face_df['col'] = np.linspace(0.0, 1.0, \n",
    "                                    num=sheet.face_df.shape[0])\n",
    "\n",
    "cmap = plt.cm.get_cmap('viridis')\n",
    "color_cmap = cmap(sheet.face_df.col)\n",
    "\n",
    "draw_specs['edge']['visible'] = False\n",
    "\n",
    "draw_specs['face']['visible'] = True\n",
    "draw_specs['face']['color'] = sheet.face_df['col']\n",
    "draw_specs['face']['alpha'] = 0.5\n",
    "\n",
    "\n",
    "fig, ax = sheet_view(sheet, coords, **draw_specs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "draw_specs['edge']['visible'] = True\n",
    "\n",
    "#draw_specs['face']['visible'] = False\n",
    "draw_specs['face']['color'] = color_cmap\n",
    "draw_specs['face']['alpha'] = 0.5\n",
    "\n",
    "edge_color = np.linspace(0.0, 1.0, \n",
    "                        num=sheet.edge_df.shape[0])\n",
    "\n",
    "cmap = plt.cm.get_cmap('viridis')\n",
    "edge_cmap = cmap(edge_color)\n",
    "draw_specs['edge']['color'] = edge_cmap #[0, 0, 0, 1]\n",
    "#draw_specs['edge']['color'] = [0, 0, 0, 0.2]\n",
    "\n",
    "draw_specs['edge']['width'] = 8. * np.linspace(0.0, 1.0, \n",
    "                        num=sheet.edge_df.shape[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fig, ax = sheet_view(sheet, coords, **draw_specs)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Ipyvolume based"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "extruded = extrude(sheet.datasets, method='translation')\n",
    "specs = config.geometry.bulk_spec()\n",
    "monolayer = Monolayer('mono', extruded, specs)\n",
    "\n",
    "\n",
    "\n",
    "ipv.clear()\n",
    "fig2, mesh = sheet_view(monolayer, mode=\"3D\")\n",
    "fig2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Vertex based color"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "color = (monolayer.vert_df.x**2\n",
    "         + monolayer.vert_df.y**2\n",
    "         + monolayer.vert_df.z**2)\n",
    "\n",
    "\n",
    "ipv.clear()\n",
    "fig2, mesh = sheet_view(monolayer, edge={\"color\":color}, mode=\"3D\")\n",
    "fig2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Edge based color"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "color = monolayer.edge_df['dy']\n",
    "ipv.clear()\n",
    "fig2, mesh = sheet_view(monolayer, edge={\"color\":color}, mode=\"3D\")\n",
    "fig2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Displaying faces"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "draw_specs = config.draw.sheet_spec()\n",
    "\n",
    "draw_specs['face']['visible'] = True\n",
    "\n",
    "\n",
    "\n",
    "#draw_specs['face']['visible'] = False\n",
    "draw_specs['face']['color'] = np.random.random(monolayer.face_df.shape[0])\n",
    "\n",
    "draw_specs['face']['alpha'] = 0.5\n",
    "\n",
    "ipv.clear()\n",
    "fig2, mesh = sheet_view(monolayer, mode=\"3D\", **draw_specs)\n",
    "fig2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Higlighting faces"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from tyssue.draw import highlight_cells, highlight_faces"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "highlight_faces(monolayer.face_df, [0, 2, 3], reset_visible=True)\n",
    "\n",
    "ipv.clear()\n",
    "fig2, mesh = sheet_view(monolayer, mode=\"3D\", **draw_specs)\n",
    "fig2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "highlight_cells(monolayer, 1, reset_visible=True)\n",
    "\n",
    "ipv.clear()\n",
    "fig2, mesh = sheet_view(monolayer, mode=\"3D\", **draw_specs)\n",
    "fig2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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