imjoy-app-engine-demo.ipynb

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 "cells": [
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
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     "text": [
      "ERROR:ImJoy-RPC:{'type': 'error', 'message': 'Traceback (most recent call last):\\n  File \"/Users/wei.ouyang/miniconda3/lib/python3.7/site-packages/imjoy_rpc/rpc.py\", line 354, in _call_method\\n    result = method(*args)\\n  File \"/Users/wei.ouyang/workspace/ImJoy-Engine/imjoy/core/interface.py\", line 46, in get_plugin\\n    raise Exception(f\"Plugin {name} not found\")\\nException: Plugin c2d69288-383d-45e5-a313-c2a704fe68b8 not found\\n', 'peer_id': '13038ba2-3d8f-43a5-9d56-a7f587bb84a5'}\n",
      "ERROR:ImJoy-RPC:{'type': 'error', 'message': 'Traceback (most recent call last):\\n  File \"/Users/wei.ouyang/miniconda3/lib/python3.7/site-packages/imjoy_rpc/rpc.py\", line 354, in _call_method\\n    result = method(*args)\\n  File \"/Users/wei.ouyang/workspace/ImJoy-Engine/imjoy/core/interface.py\", line 46, in get_plugin\\n    raise Exception(f\"Plugin {name} not found\")\\nException: Plugin c2d69288-383d-45e5-a313-c2a704fe68b8 not found\\n', 'peer_id': '13038ba2-3d8f-43a5-9d56-a7f587bb84a5'}\n"
     ]
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    {
     "ename": "Exception",
     "evalue": "Traceback (most recent call last):\n  File \"/Users/wei.ouyang/workspace/ImJoy-Engine/imjoy/core/interface.py\", line 46, in get_plugin\n    raise Exception(f\"Plugin {name} not found\")\nException: Plugin c2d69288-383d-45e5-a313-c2a704fe68b8 not found",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mException\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-9-22550a7c66b0>\u001b[0m in \u001b[0;36masync-def-wrapper\u001b[0;34m()\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0mlocations\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mawait\u001b[0m \u001b[0mplugin\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlocalize\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mones\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m100\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m100\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      6\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlocations\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mException\u001b[0m: Traceback (most recent call last):\n  File \"/Users/wei.ouyang/workspace/ImJoy-Engine/imjoy/core/interface.py\", line 46, in get_plugin\n    raise Exception(f\"Plugin {name} not found\")\nException: Plugin c2d69288-383d-45e5-a313-c2a704fe68b8 not found"
     ]
    }
   ],
   "source": [
    "import numpy as np\n",
    "from imjoy import connect_to_server\n",
    "ws = await connect_to_server(server_url=\"http://127.0.0.1:9527\", workspace=\"b54481bc-8685-46ca-8a4c-e2bd9bda9d08\", token=\"imjoy@eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJzY29wZXMiOlsiYjU0NDgxYmMtODY4NS00NmNhLThhNGMtZTJiZDliZGE5ZDA4Il0sImV4cGlyZXNfYXQiOm51bGwsInVzZXJfaWQiOiI2NjczMGRmZC1jZmNlLTRjMDYtOTdmYi1hYTM5MTFlZTVmODYiLCJwYXJlbnQiOiJiNTQ0ODFiYy04Njg1LTQ2Y2EtOGE0Yy1lMmJkOWJkYTlkMDgiLCJlbWFpbCI6bnVsbCwicm9sZXMiOltdfQ.Qbt0J7f4XJccVNH4726tf0sPPq-jPUsz_B888_rrcgg\")\n",
    "localize_plugin = await ws.getPlugin(\"localization\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "locations = await localize_plugin.localize(np.ones([100,100]))\n",
    "print(locations)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "from imjoy import api\n",
    "\n",
    "class ImJoyPlugin():\n",
    "    def __init__(self,image):\n",
    "        self._image = image\n",
    "        \n",
    "    async def setup(self):\n",
    "        pass\n",
    "\n",
    "    async def run(self, ctx):\n",
    "        # load the ImageJ.JS window\n",
    "        cellpose = await api.showDialog(src=\"https://cellpose.imjoy.io\")\n",
    "        # read the image\n",
    "        result = await cellpose.segment({\"input\": self._image, \"diam\": 300, \"net\": \"cyto\", \"chan1\": 1, \"chan2\": 3, \"keep_size\": True, \"outputs\": \"flow,mask,outline_plot,flow_plot\"})\n",
    "        # we will get mask and flow as numpy array\n",
    "        flow = result[\"flow\"]\n",
    "        mask = result[\"mask\"]\n",
    "        await api.alert(str(result[\"mask\"].shape))\n",
    "\n",
    "def segment(image):\n",
    "    api.export(ImJoyPlugin(image))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "window.connectPlugin && window.connectPlugin(\"65088bd1-0d92-408d-9685-b01d393fbb7c\")"
      ],
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       "<IPython.core.display.Javascript object>"
      ]
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   "source": [
    "locations = await localize_plugin.localize(np.ones([100,100]))\n",
    "segment(locations)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": [
       "window.connectPlugin && window.connectPlugin(\"65088bd1-0d92-408d-9685-b01d393fbb7c\")"
      ],
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       "<IPython.core.display.Javascript object>"
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      "text/plain": [
       "<Future finished result=[]>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from imjoy import api\n",
    "import numpy as np\n",
    "\n",
    "class ImJoyPlugin():\n",
    "    def setup(self):\n",
    "        api.log('plugin initialized')\n",
    "\n",
    "    async def run(self, ctx):\n",
    "        # here the itk_image will be encoded via the registered encoder function (i.e.: itkimage_to_json)\n",
    "        api.showDialog(type=\"itk-vtk-viewer\", src=\"https://oeway.github.io/itk-vtk-viewer/\", data={\"image\": locations})\n",
    "\n",
    "api.export(ImJoyPlugin())\n"
   ]
  }
 ],
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