cellpose_tuning.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "import napari\n",
    "import numpy as np\n",
    "import scipy.ndimage as ndi\n",
    "import yaml\n",
    "import h5py\n",
    "from pathlib import Path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "settings_path = Path(r\"Y:\\PhD\\Code\\Python\\lca\\scripts\\settings\\20211126_Sec16_live_settings.yml\")\n",
    "site = 1\n",
    "\n",
    "with open(settings_path, 'r') as stream:\n",
    "    settings = yaml.safe_load(stream)\n",
    "    \n",
    "hdf5_path = Path(settings['paths']['hdf5_path'])\n",
    "\n",
    "nuclei_channel = settings['cellpose']['nuclei']['channel']\n",
    "cells_channel = settings['cellpose']['cells']['channel']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# load hdf5 file of site\n",
    "with h5py.File(hdf5_path.joinpath('site_%04d.hdf5' % site), \"r\") as file:\n",
    "    img_nuc = file[f'intensity_images/{nuclei_channel}'][0, :, :]\n",
    "    img_cells = file[f'intensity_images/{cells_channel}'][0, :, :]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "img_nuc_filtered = ndi.median_filter(img_nuc, 10)\n",
    "img_cells_filtered = ndi.median_filter(img_cells, 10)\n",
    "\n",
    "merged = np.stack([img_nuc_filtered, img_cells_filtered])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Image layer 'merged' at 0x2c15b655c40>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "viewer = napari.Viewer()\n",
    "viewer.add_image(img_nuc, colormap=settings['channel_colors'][nuclei_channel])\n",
    "viewer.add_image(merged, colormap=settings['channel_colors'][cells_channel])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Image layer 'img_nuc' at 0x1b21d181fa0>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Exception in callback BaseAsyncIOLoop._handle_events(7184, 1)\n",
      "handle: <Handle BaseAsyncIOLoop._handle_events(7184, 1)>\n",
      "Traceback (most recent call last):\n",
      "  File \"C:\\Users\\Adrian\\miniconda3\\envs\\lca\\lib\\asyncio\\events.py\", line 80, in _run\n",
      "    self._context.run(self._callback, *self._args)\n",
      "  File \"C:\\Users\\Adrian\\miniconda3\\envs\\lca\\lib\\site-packages\\tornado\\platform\\asyncio.py\", line 189, in _handle_events\n",
      "    handler_func(fileobj, events)\n",
      "  File \"C:\\Users\\Adrian\\miniconda3\\envs\\lca\\lib\\site-packages\\zmq\\eventloop\\zmqstream.py\", line 452, in _handle_events\n",
      "    self._handle_recv()\n",
      "  File \"C:\\Users\\Adrian\\miniconda3\\envs\\lca\\lib\\site-packages\\zmq\\eventloop\\zmqstream.py\", line 481, in _handle_recv\n",
      "    self._run_callback(callback, msg)\n",
      "  File \"C:\\Users\\Adrian\\miniconda3\\envs\\lca\\lib\\site-packages\\zmq\\eventloop\\zmqstream.py\", line 431, in _run_callback\n",
      "    callback(*args, **kwargs)\n",
      "  File \"C:\\Users\\Adrian\\miniconda3\\envs\\lca\\lib\\site-packages\\jupyter_client\\threaded.py\", line 121, in _handle_recv\n",
      "    msg_list = self.ioloop._asyncio_event_loop.run_until_complete(get_msg(future_msg))\n",
      "  File \"C:\\Users\\Adrian\\miniconda3\\envs\\lca\\lib\\asyncio\\base_events.py\", line 618, in run_until_complete\n",
      "    self._check_running()\n",
      "  File \"C:\\Users\\Adrian\\miniconda3\\envs\\lca\\lib\\asyncio\\base_events.py\", line 580, in _check_running\n",
      "    raise RuntimeError(\n",
      "RuntimeError: Cannot run the event loop while another loop is running\n"
     ]
    }
   ],
   "source": [
    "viewer = napari.Viewer()\n",
    "viewer.add_image(img_nuc, colormap=settings['channel_colors'][nuclei_channel])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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