{
 "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
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      "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": "markdown",
   "metadata": {},
   "source": [
    "### License (BSD 2-Clause)\n",
    "Copyright (c) 2021, University of Dundee All rights reserved.\n",
    "\n",
    "Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:\n",
    "\n",
    "Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
   ]
  }
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