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  {
   "cell_type": "markdown",
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    "collapsed": true
   },
   "source": [
    "### Basic example on how to use OMERO Python language bindings\n",
    "See https://docs.openmicroscopy.org/latest/omero/developers/Python.html"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Import Packages required to connect to OMERO"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from omero.gateway import BlitzGateway\n",
    "from getpass import getpass"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Create a connection to an OMERO server"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Username: trainer-1\n",
      "OMERO Password: ········\n",
      "Connected as trainer-1\n"
     ]
    }
   ],
   "source": [
    "def connect(hostname, username, password):\n",
    "    \"\"\"\n",
    "    Connect to an OMERO server\n",
    "    :param hostname: Host name\n",
    "    :param username: User\n",
    "    :param password: Password\n",
    "    :return: Connected BlitzGateway\n",
    "    \"\"\"\n",
    "    conn = BlitzGateway(username, password,\n",
    "                        host=hostname, secure=True)\n",
    "    conn.connect()\n",
    "    conn.c.enableKeepAlive(60)\n",
    "    return conn\n",
    "\n",
    "HOST = 'wss://workshop.openmicroscopy.org/omero-ws'\n",
    "conn = connect(HOST, input(\"Username: \"),\n",
    "               getpass(\"OMERO Password: \"))\n",
    "print(\"Connected as {}\".format(conn.getUser().getName()))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Load images in a specified dataset method"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dataset ID: 2391\n",
      "---- Processing image 28662\n",
      "---- Processing image 57226\n",
      "---- Processing image 28663\n",
      "---- Processing image 57227\n",
      "---- Processing image 28664\n",
      "---- Processing image 57228\n",
      "---- Processing image 28665\n",
      "---- Processing image 28666\n",
      "---- Processing image 28667\n",
      "---- Processing image 28668\n",
      "---- Processing image 57229\n",
      "---- Processing image 28669\n",
      "---- Processing image 57230\n",
      "---- Processing image 28670\n",
      "---- Processing image 57231\n",
      "---- Processing image 28671\n",
      "---- Processing image 28672\n",
      "---- Processing image 28673\n",
      "---- Processing image 28674\n",
      "---- Processing image 28675\n",
      "object #0 (::omero::RLong)\n",
      "{\n",
      "    _val = 28662\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "def load_images(conn, dataset_id):\n",
    "    \"\"\"\n",
    "    Load the images in the specified dataset\n",
    "    :param conn: The BlitzGateway\n",
    "    :param dataset_id: The dataset's id\n",
    "    :return: The Images or None\n",
    "    \"\"\"\n",
    "    dataset = conn.getObject(\"Dataset\", dataset_id)\n",
    "    images = []\n",
    "    for image in dataset.listChildren():\n",
    "        images.append(image)\n",
    "    if len(images) == 0:\n",
    "        return None\n",
    "\n",
    "    for image in images:\n",
    "        print(\"---- Processing image\", image.id)\n",
    "    return images\n",
    "\n",
    "images = load_images(conn, input(\"Dataset ID: \"))\n",
    "print(images[0]._obj.id)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Close the connection to the OMERO server"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "conn.close()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "### License\n",
    "Copyright (C) 2019-2020 University of Dundee. All Rights Reserved.\n",
    "This program is free software; you can redistribute it and/or modify it\n",
    "under the terms of the GNU General Public License as published by the\n",
    "Free Software Foundation; either version 2 of the License, or\n",
    "(at your option) any later version.\n",
    "This program is distributed in the hope that it will be useful, but\n",
    "WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY\n",
    "or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for\n",
    "more details. You should have received a copy of the GNU General\n",
    "Public License along with this program; if not, write to the\n",
    "Free Software Foundation,\n",
    "Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA."
   ]
  }
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