From 1d97e50f7fdca907e3dead928a362d4842f84032 Mon Sep 17 00:00:00 2001
From: Christian Evenhuis <christian.evenhuis@gmail.com>
Date: Wed, 20 Mar 2019 23:38:22 +1100
Subject: [PATCH 1/2] ext changed by Fiji script added script params to replace
 hard coded USERNAME, HOST etc

---
 practical/jython/open_image.py | 96 ++++++++++++++++++++++++++++++++++
 1 file changed, 96 insertions(+)
 create mode 100644 practical/jython/open_image.py

diff --git a/practical/jython/open_image.py b/practical/jython/open_image.py
new file mode 100644
index 00000000..10059cd6
--- /dev/null
+++ b/practical/jython/open_image.py
@@ -0,0 +1,96 @@
+#@ String(label="Username") USERNAME
+#@ String(label="Password", style='password') PASSWORD
+#@ String(label="Host",value='outreach.openmicroscopy.org') HOST
+#@ Integer(label="Port",value=4064) PORT
+#@ Integer(label="ImageId" ) image_id
+
+
+# -----------------------------------------------------------------------------
+#  Copyright (C) 2017 University of Dundee. All rights reserved.
+#
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+#  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# ------------------------------------------------------------------------------
+
+# This script downloads a file and opens it in ImageJ using Bio-Formats
+# importer.
+# Use this script in the Scripting Dialog of Fiji (File > New > Script).
+# Select Python as language in the Scripting Dialog.
+# Error handling is omitted to ease the reading of the script but this
+# should be added if used in production to make sure the services are closed
+# Information can be found at
+# https://docs.openmicroscopy.org/omero/5.4.1/developers/Java.html
+
+import tempfile
+import shutil
+
+from java.lang import Long
+
+
+# OMERO Dependencies
+from omero.gateway import Gateway
+from omero.gateway import LoginCredentials
+from omero.gateway import SecurityContext
+from omero.gateway.facility import TransferFacility
+from omero.log import SimpleLogger
+
+from ij import IJ
+
+
+# Setup
+# =====
+
+
+
+def connect_to_omero():
+    "Connect to OMERO"
+
+    credentials = LoginCredentials()
+    credentials.getServer().setHostname(HOST)
+    credentials.getServer().setPort(PORT)
+    credentials.getUser().setUsername(USERNAME.strip())
+    credentials.getUser().setPassword(PASSWORD.strip())
+    simpleLogger = SimpleLogger()
+    gateway = Gateway(simpleLogger)
+    gateway.connect(credentials)
+    return gateway
+
+
+def download_image(gateway, image_id, path):
+    "Download the files composing the image"
+
+    transfer = gateway.getFacility(TransferFacility)
+    user = gateway.getLoggedInUser()
+    ctx = SecurityContext(user.getGroupId())
+    return transfer.downloadImage(ctx, path, Long(image_id))
+
+
+# Connect to OMERO
+gateway = connect_to_omero()
+
+# Download the image. This could be composed of several files
+tmp_dir = tempfile.mkdtemp()
+print(tmp_dir)
+
+files = download_image(gateway, image_id, tmp_dir)
+for f in files:
+    options = "open=" + f.getAbsolutePath()
+    options += " autoscale color_mode=Default "
+    options += "view=[Standard ImageJ] stack_order=Default"
+    IJ.run("Bio-Formats Importer", options)
+    break
+
+shutil.rmtree(tmp_dir)
+gateway.disconnect()

From bfaf3b583ee3a06f3d1471942542056642be3e93 Mon Sep 17 00:00:00 2001
From: Christian Evenhuis <christian.evenhuis@gmail.com>
Date: Wed, 20 Mar 2019 23:41:08 +1100
Subject: [PATCH 2/2] made smae changes to open_image.jy so that diffs can be
 compared

---
 practical/jython/open_image.jy | 17 ++++++-----------
 1 file changed, 6 insertions(+), 11 deletions(-)

diff --git a/practical/jython/open_image.jy b/practical/jython/open_image.jy
index bf98f674..8463aaea 100644
--- a/practical/jython/open_image.jy
+++ b/practical/jython/open_image.jy
@@ -1,3 +1,9 @@
+#@ String(label="Username") USERNAME
+#@ String(label="Password", style='password') PASSWORD
+#@ String(label="Host",value='outreach.openmicroscopy.org') HOST
+#@ Integer(label="Port",value=4064) PORT
+#@ Integer(label="ImageId" ) image_id
+
 # -----------------------------------------------------------------------------
 #  Copyright (C) 2017 University of Dundee. All rights reserved.
 #
@@ -42,17 +48,6 @@ from omero.log import SimpleLogger
 from ij import IJ
 
 
-# Setup
-# =====
-
-# OMERO Server details
-HOST = "outreach.openmicroscopy.org"
-PORT = 4064
-#  parameters to edit
-image_id = "1001"
-USERNAME = "username"
-PASSWORD = "password"
-
 
 def connect_to_omero():
     "Connect to OMERO"