{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Crop OMERO Image using Fiji\n",
    "\n",
    "\n",
    "This notebook shows how to crop an OMERO image using the crop functionality available in [Fiji](https://imagej.net/Fiji).\n",
    "\n",
    "Fiji has been installed with few other plugins including the omero_ij plugin to allow to connect to an OMERO server."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Description\n",
    "\n",
    "The following section shows:\n",
    " * how to connect to OMERO\n",
    " * how to open an OMERO image using Bio-Formats\n",
    " * how to crop an image using Fiji\n",
    " * how to save the generated image as OME-TIFF\n",
    " * how to import the created OME-TIFF to OMERO"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup: start the [desktop](../../desktop) if it is not already up\n",
    "The link should open in a different window. If you see an error message try refreshing the window."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup: Add plugins to Classpath\n",
    "First we had Fiji and the plugins to the classpath."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "43d1d91f-f79a-4623-a886-61d38508c0a0",
       "version_major": 2,
       "version_minor": 0
      },
      "method": "display_data"
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "700b97a3-b91f-4642-accb-91b0d66539d0",
       "version_major": 2,
       "version_minor": 0
      },
      "method": "display_data"
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "//Add dependencies to the classpath\n",
    "%classpath add jar /srv/conda/vnc/Fiji.app/jars/*\n",
    "%classpath add jar /srv/conda/vnc/Fiji.app/plugins/*"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Enter credentials. Do not re-run this cell."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "cc3d14a2-a6e0-4ae7-8dd7-ccfc7fc41c07",
       "version_major": 2,
       "version_minor": 0
      },
      "method": "display_data"
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "g = new EasyForm(\"Enter credentials and continue to the next cell. Do not re-run this cell\")\n",
    "g.addTextField(\"Server\").onInit({g['Server'] = \"wss://workshop.openmicroscopy.org/omero-ws\"})\n",
    "g.addTextField(\"UserName\")\n",
    "g.addPasswordField(\"Password\")\n",
    "g"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Connect to OMERO"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "connecting...\n",
      "connected...\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "null"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import omero.gateway.Gateway\n",
    "import omero.gateway.LoginCredentials\n",
    "import omero.log.SimpleLogger\n",
    "\n",
    "// Method to connect to OMERO\n",
    "def connect_to_omero() {\n",
    "    \"Connect to OMERO\"\n",
    "\n",
    "    credentials = new LoginCredentials()\n",
    "    credentials.getServer().setHostname(g['Server'])\n",
    "    credentials.getUser().setUsername(g['UserName'].trim())\n",
    "    credentials.getUser().setPassword(g['Password'].trim())\n",
    "    simpleLogger = new SimpleLogger()\n",
    "    gateway = new Gateway(simpleLogger)\n",
    "    gateway.connect(credentials)\n",
    "    return gateway\n",
    "\n",
    "}\n",
    "\n",
    "// Connect to OMERO\n",
    "println \"connecting...\"\n",
    "gateway = connect_to_omero()\n",
    "println \"connected...\"\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Select the Image. Do not re-run this cell."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "44ae2872-73e3-4d84-8e42-3bcd9aaad137",
       "version_major": 2,
       "version_minor": 0
      },
      "method": "display_data"
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "//Move to the next cell after entering a value\n",
    "ga = new EasyForm(\"Select the Image to analyze\")\n",
    "ga.addTextField(\"ImageID\")\n",
    "ga"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Collect parameters "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-1"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "//Connection information\n",
    "HOST = g['Server']\n",
    "USERNAME = g['UserName'].trim()\n",
    "PASSWORD = g['Password'].trim()\n",
    "\n",
    "//Image to analyze\n",
    "image_id = ga['ImageID'].toLong()\n",
    "group_id = \"-1\"\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Open the image using Bio-Formats and crop it"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "opening Image...\n",
      "cropping...\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "null"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import ij.IJ\n",
    "//Function to Open an OMERO image using Bio-Formats\n",
    "def open_image_plus(host, username, password, group_id, image_id) {\n",
    "    \"Open the image using the Bio-Formats Importer\"\n",
    "\n",
    "    StringBuilder options = new StringBuilder()\n",
    "    options.append(\"location=[OMERO] open=[omero:server=\")\n",
    "    options.append(host)\n",
    "    options.append(\"\\nuser=\")\n",
    "    options.append(username)\n",
    "    options.append(\"\\nport=\")\n",
    "    options.append(443)\n",
    "    options.append(\"\\npass=\")\n",
    "    options.append(password)\n",
    "    options.append(\"\\ngroupID=\")\n",
    "    options.append(group_id)\n",
    "    options.append(\"\\niid=\")\n",
    "    options.append(image_id)\n",
    "    options.append(\"] \")\n",
    "    options.append(\"windowless=true view=Hyperstack \")\n",
    "    IJ.runPlugIn(\"loci.plugins.LociImporter\", options.toString())\n",
    "}\n",
    "\n",
    "println \"opening Image...\"\n",
    "// Open the Image using Bio-Formats\n",
    "open_image_plus(HOST, USERNAME, PASSWORD, group_id, String.valueOf(image_id))\n",
    "\n",
    "// Crop the image\n",
    "println \"cropping...\"\n",
    "IJ.makeRectangle(0, 0, 200, 200)\n",
    "IJ.run(\"Crop\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Save the cropped image as OME-TIFF"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/tmp/33676-EB1_dsRed_(red)_tracking_along_peripheral_SEPT2-YFP_fila...(green)._Spinning_disc_confocal_microscopy..ome.tiff_kymograph4297281605584244054.ome.tiff\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "null"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import ij.IJ\n",
    "import java.io.File\n",
    "\n",
    "// Save modified image as OME-TIFF using Bio-Formats Exporter\n",
    "imp = IJ.getImage()\n",
    "name = imp.getTitle().replaceAll(\"\\\\s\",\"\")\n",
    "file = File.createTempFile(name, \".ome.tiff\")\n",
    "path_to_file = file.getAbsolutePath()\n",
    "println  path_to_file\n",
    "options = \"outfile=\" + path_to_file + \" export compression=Uncompressed windowless=true\"\n",
    "IJ.runPlugIn(\"loci.plugins.LociExporter\", options.toString())\n",
    "imp.changes = false\n",
    "imp.close()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Import the OME-TIFF  into a new dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "importing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "May 25, 2020 7:22:49 AM java.util.prefs.FileSystemPreferences$1 run\n",
      "INFO: Created user preferences directory.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Image:57239\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Other imported objects:\n",
      "Fileset:39953\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "imported\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "null"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import java.lang.reflect.Array\n",
    "\n",
    "import omero.gateway.SecurityContext\n",
    "import omero.gateway.facility.BrowseFacility\n",
    "import omero.gateway.facility.DataManagerFacility\n",
    "import omero.gateway.model.DatasetData\n",
    "\n",
    "import ome.formats.importer.ImportConfig\n",
    "import ome.formats.importer.OMEROWrapper\n",
    "import ome.formats.importer.ImportLibrary\n",
    "import ome.formats.importer.ImportCandidates\n",
    "import ome.formats.importer.cli.ErrorHandler\n",
    "import ome.formats.importer.cli.LoggingImportMonitor\n",
    "\n",
    "import loci.formats.in.DefaultMetadataOptions\n",
    "import loci.formats.in.MetadataLevel\n",
    "\n",
    "//Find the dataset matching the specified ID\n",
    "def find_dataset(gateway, dataset_id) {\n",
    "    \"Load the Dataset\"\n",
    "    browse = gateway.getFacility(BrowseFacility)\n",
    "    user = gateway.getLoggedInUser()\n",
    "    ctx = new SecurityContext(user.getGroupId())\n",
    "    return browse.findIObject(ctx, \"omero.model.Dataset\", dataset_id)\n",
    "}\n",
    "\n",
    "//Upload the generated image\n",
    "def upload_image(paths, gateway, id) {\n",
    "    \"Upload an image to OMERO\"\n",
    "\n",
    "    user = gateway.getLoggedInUser()\n",
    "    sessionKey = gateway.getSessionId(user)\n",
    "\n",
    "    config = new ImportConfig()\n",
    "    config.debug.set('false')\n",
    "    config.hostname.set(HOST)\n",
    "    config.sessionKey.set(sessionKey)\n",
    "    config.port.set(443)\n",
    "    dataset = find_dataset(gateway, id)\n",
    "\n",
    "    store = config.createStore()\n",
    "    reader = new OMEROWrapper(config)\n",
    "\n",
    "    library = new ImportLibrary(store, reader)\n",
    "    error_handler = new ErrorHandler(config)\n",
    "\n",
    "    library.addObserver(new LoggingImportMonitor())\n",
    "    candidates = new ImportCandidates(reader, paths, error_handler)\n",
    "    containers = candidates.getContainers()\n",
    "    containers.each() { c ->\n",
    "        c.setTarget(dataset)\n",
    "    }\n",
    "    reader.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.ALL))\n",
    "    return library.importCandidates(config, candidates)\n",
    "}\n",
    "\n",
    "// Create a Dataset\n",
    "d = new DatasetData()\n",
    "d.setName(\"Cropped Image\")\n",
    "dm = gateway.getFacility(DataManagerFacility)\n",
    "user = gateway.getLoggedInUser()\n",
    "ctx = new SecurityContext(user.getGroupId())\n",
    "d = dm.createDataset(ctx, d, null)\n",
    "\n",
    "// Import the generated OME-TIFF to OMERO\n",
    "println \"importing...\"\n",
    "str2d = new String[1]\n",
    "str2d[0] = path_to_file\n",
    "success = upload_image(str2d, gateway, d.getId())\n",
    "println \"imported\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Close the connection and delete local file "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Done\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "true"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "// Close the connection\n",
    "gateway.disconnect()\n",
    "println \"Done\"\n",
    "// delete the local OME-TIFF image\n",
    "file.delete()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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