Napari_Volume_Plots.ipynb

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    "#do some imports\n",
    "\n",
    "import os\n",
    "import sys\n",
    "import enum\n",
    "from scipy.signal import savgol_filter\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "import pickle\n",
    "import napari\n",
    "from magicgui import magicgui\n",
    "from qtpy.QtCore import Qt\n",
    "\n",
    "#%run D:\\\\Segment\\\\Scripts\\\\newFunctions.py\n",
    "from matplotlib.backends.backend_qt5agg import FigureCanvas\n",
    "\n",
    "base_dir = 'D:\\\\Segment'\n",
    "project_name = 'WT_01_05_19'\n",
    "\n",
    "path = os.path.join(base_dir, project_name)\n",
    "%gui qt\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "#load the labels and the dictionary containing label dtaa\n",
    "\n",
    "labs = np.load(os.path.join(path, 'labs', 'cell_labs.npz'))\n",
    "labs = labs['arr_0']\n",
    "\n",
    "with open (os.path.join(path, 'dicts', 'cell_dict'), 'rb') as fp:\n",
    "    cell_dict = pickle.load(fp)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "#initialize napari viewer\n",
    "viewer = napari.Viewer()\n",
    "\n",
    "#generate a matplotlib plot\n",
    "plot_fig = plt.figure()\n",
    "ax = plot_fig.add_subplot(1, 1, 1)\n",
    "\n",
    "#dock the plot to the napari window\n",
    "viewer.window.add_dock_widget(FigureCanvas(plot_fig), area=\"bottom\")\n",
    "\n",
    "#add the labels\n",
    "layer = viewer.add_labels(labs.astype(int), name='labs')\n",
    "\n",
    "#initialize the plot\n",
    "(myPlot,) = ax.plot(0, 0, linewidth=5)\n",
    "(smoothed,) = ax.plot(0, 0, color='r', alpha = 0.5, linestyle='--', linewidth=5)\n",
    "myPlot.figure.canvas.draw()\n",
    "smoothed.figure.canvas.draw()\n",
    "\n",
    "#set axis limits and colors\n",
    "axes = plt.gca()\n",
    "#axes.set_xlim(np.min(timepoints), np.max(timepoints))\n",
    "#axes.set_ylim(0, np.max(area) * (1.15))\n",
    "axes.set_xlabel('time')\n",
    "axes.set_ylabel('volume (px  )')\n",
    "axes.spines['bottom'].set_color('white')\n",
    "axes.xaxis.label.set_color('white')\n",
    "axes.tick_params(axis='x', colors='white')\n",
    "axes.spines['left'].set_color('white')\n",
    "axes.yaxis.label.set_color('white')\n",
    "axes.tick_params(axis='y', colors='white')\n",
    "\n",
    "\n",
    "#update the plot on mouse click\n",
    "@layer.mouse_drag_callbacks.append\n",
    "def update_layer(layer, event):\n",
    "    im = viewer.layers['labs'].data\n",
    "    #get the click position in world coordinates and convert those to image coordinates\n",
    "    pos = viewer.cursor.position\n",
    "    pos_layer = layer.world_to_data(pos)\n",
    "    #get the value of the label at that image coordinate\n",
    "    value = im[pos_layer[0].astype(int), pos_layer[1].astype(int), pos_layer[2].astype(int), pos_layer[3].astype(int)]\n",
    "    #pass this value to GetVolume\n",
    "    try:\n",
    "        GetVolume(value, smooth=True)\n",
    "    except:\n",
    "        ValueError\n",
    "\n",
    "        \n",
    "#function to get the volume over time from a dict and update the plot\n",
    "@magicgui(call_button='Get Volume')\n",
    "def GetVolume(cell:int=0, smooth:bool=False):\n",
    "    \n",
    "    #make a list of the timepoints and volumes to plot\n",
    "    area = []\n",
    "    timepoints = []\n",
    "    for tp in cell_dict.keys():\n",
    "        if cell in cell_dict[tp].keys():\n",
    "            area.append(cell_dict[tp][cell]['Area'])\n",
    "            timepoints.append(tp)\n",
    "    \n",
    "    #pass these to the plot\n",
    "    myPlot.set_data(timepoints, area)\n",
    "    #rescale the axes\n",
    "    axes.set_xlim(np.min(timepoints), np.max(timepoints))\n",
    "    axes.set_ylim(0, np.max(area) * (1.15))\n",
    "    #draw the plot\n",
    "    myPlot.figure.canvas.draw()\n",
    "\n",
    "    #add a smoothed line, if wanted\n",
    "    if smooth:\n",
    "        area_filtered = savgol_filter(area, 11, 3)\n",
    "        smoothed.set_data(timepoints, area_filtered)\n",
    "        smoothed.figure.canvas.draw()\n",
    "\n",
    "    if not smooth:\n",
    "        smoothed.set_data(0, 0)\n",
    "        smoothed.figure.canvas.draw()\n",
    "        \n",
    "       \n",
    "viewer.window.add_dock_widget(GetVolume, area='right')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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