[med-svn] [orthanc-imagej] 08/12: Imported Upstream version 1.1+dfsg
Andreas Tille
tille at debian.org
Tue Apr 19 12:57:54 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository orthanc-imagej.
commit 2afd8442272b089907cbdf0af2133aa0c277e6e2
Author: Andreas Tille <tille at debian.org>
Date: Tue Apr 19 14:54:08 2016 +0200
Imported Upstream version 1.1+dfsg
---
.hg_archival.txt | 5 +
AUTHORS | 5 +
CMakeLists.txt | 44 ++
COPYING | 674 ++++++++++++++++++++++
INSTALL | 36 ++
NEWS | 15 +
README | 57 ++
com/orthancserver/DicomDecoder.java | 427 ++++++++++++++
com/orthancserver/GridLayout2.java | 167 ++++++
com/orthancserver/HttpsTrustModifier.java | 84 +++
com/orthancserver/Orthanc.java | 51 ++
com/orthancserver/OrthancConfigurationDialog.java | 170 ++++++
com/orthancserver/OrthancConnection.java | 242 ++++++++
com/orthancserver/PreviewPanel.java | 82 +++
com/orthancserver/SelectImageDialog.java | 580 +++++++++++++++++++
debian/README.Debian | 7 -
debian/changelog | 12 -
debian/compat | 1 -
debian/control | 35 --
debian/copyright | 29 -
debian/dirs | 1 -
debian/install | 1 -
debian/patches/json-simple | 38 --
debian/patches/series | 1 -
debian/rules | 19 -
debian/source/format | 1 -
debian/upstream/metadata | 6 -
debian/watch | 3 -
plugins.config | 1 +
29 files changed, 2640 insertions(+), 154 deletions(-)
diff --git a/.hg_archival.txt b/.hg_archival.txt
new file mode 100644
index 0000000..58db48f
--- /dev/null
+++ b/.hg_archival.txt
@@ -0,0 +1,5 @@
+repo: 1092b2dca366ed837f03d51f1a1b6002d52c4c12
+node: 4c6bba5f44e778f26f9bd45d0c3ce0167e921280
+branch: OrthancImageJ-1.1
+latesttag: null
+latesttagdistance: 10
diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 0000000..8ae3946
--- /dev/null
+++ b/AUTHORS
@@ -0,0 +1,5 @@
+Orthanc - A Lightweight, RESTful DICOM Server
+=============================================
+
+* Sebastien Jodogne <s.jodogne at gmail.com>
+ Department of Medical Physics, CHU of Liege, Belgium
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..54dc06f
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,44 @@
+cmake_minimum_required (VERSION 2.8)
+
+project(Orthanc_Import)
+
+find_package(Java REQUIRED)
+include(UseJava)
+
+set(CMAKE_JAVA_COMPILE_FLAGS "-source" "1.6" "-target" "1.6")
+set(CMAKE_JAVA_INCLUDE_PATH /usr/share/java/ij.jar)
+
+# The name of an ImageJ plugin must contain an underscore
+# http://imagejdocu.tudor.lu/doku.php?id=howto:plugins:howto_create_an_imagej_plugin_jar_file
+add_jar(Orthanc_Import
+ # Sources of the plugin
+ ${CMAKE_SOURCE_DIR}/com/orthancserver/DicomDecoder.java
+ ${CMAKE_SOURCE_DIR}/com/orthancserver/Orthanc.java
+ ${CMAKE_SOURCE_DIR}/com/orthancserver/OrthancConfigurationDialog.java
+ ${CMAKE_SOURCE_DIR}/com/orthancserver/OrthancConnection.java
+ ${CMAKE_SOURCE_DIR}/com/orthancserver/PreviewPanel.java
+ ${CMAKE_SOURCE_DIR}/com/orthancserver/SelectImageDialog.java
+ ${CMAKE_SOURCE_DIR}/com/orthancserver/HttpsTrustModifier.java
+
+ # Sources of the "json-simple" toolkit
+ ${CMAKE_SOURCE_DIR}/org/json/simple/ItemList.java
+ ${CMAKE_SOURCE_DIR}/org/json/simple/JSONArray.java
+ ${CMAKE_SOURCE_DIR}/org/json/simple/JSONAware.java
+ ${CMAKE_SOURCE_DIR}/org/json/simple/JSONObject.java
+ ${CMAKE_SOURCE_DIR}/org/json/simple/JSONStreamAware.java
+ ${CMAKE_SOURCE_DIR}/org/json/simple/JSONValue.java
+ ${CMAKE_SOURCE_DIR}/org/json/simple/parser/ContainerFactory.java
+ ${CMAKE_SOURCE_DIR}/org/json/simple/parser/ContentHandler.java
+ ${CMAKE_SOURCE_DIR}/org/json/simple/parser/JSONParser.java
+ ${CMAKE_SOURCE_DIR}/org/json/simple/parser/ParseException.java
+ ${CMAKE_SOURCE_DIR}/org/json/simple/parser/Yylex.java
+ ${CMAKE_SOURCE_DIR}/org/json/simple/parser/Yytoken.java
+ )
+
+# Add the "plugins.config" file that is expected by ImageJ in the JAR file
+add_custom_command(TARGET Orthanc_Import
+ POST_BUILD
+ COMMAND jar uf ${CMAKE_CURRENT_BINARY_DIR}/Orthanc_Import.jar plugins.config
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+ COMMENT "Packaging the configuration file" VERBATIM
+ )
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000..94a9ed0
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
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+then you must either (1) cause the Corresponding Source to be so
+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients. "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.
+
+ If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+
+ A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
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+parties who would receive the covered work from you, a discriminatory
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+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Use with the GNU Affero General Public License.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ 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 3 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, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/INSTALL b/INSTALL
new file mode 100644
index 0000000..d8c13ae
--- /dev/null
+++ b/INSTALL
@@ -0,0 +1,36 @@
+Installing pre-compiled binaries
+================================
+
+Pre-compiled binaries of this plugin are available at:
+http://sourceforge.net/projects/orthancserver/files/ImageJ/
+
+
+Windows Installation
+--------------------
+
+Download the most recent ".jar" file, then put it into the "plugins"
+folder of the ImageJ distribution. By default, this folder is:
+
+C:\Program Files\ImageJ\plugins\
+
+
+Linux Installation
+------------------
+
+Download the most recent ".jar" file, then put it into the following
+folder:
+
+~/.imagej/plugins/
+
+
+Building from source
+====================
+
+You will first have to install CMake (http://www.cmake.org/) and, of
+course, ImageJ. Here are the commands to build from source under
+Linux:
+
+# mkdir Build
+# cd Build
+# cmake ..
+# make
diff --git a/NEWS b/NEWS
new file mode 100644
index 0000000..748cb9a
--- /dev/null
+++ b/NEWS
@@ -0,0 +1,15 @@
+Pending changes in the mainline
+===============================
+
+
+Version 1.1 (2016/04/15)
+========================
+
+* Fix issue #9 ("Error while importing this image: null")
+* Fix issue #10 ("Cannot access an Orthanc running with a self-signed HTTPS certificate")
+
+
+Version 1.0.0 (2014/12/08)
+==========================
+
+* Initial release
diff --git a/README b/README
new file mode 100644
index 0000000..3a282c4
--- /dev/null
+++ b/README
@@ -0,0 +1,57 @@
+Orthanc - A Lightweight, RESTful DICOM Server
+=============================================
+
+
+General Information
+-------------------
+
+This repository contains an ImageJ plugin that allows to easily access
+DICOM images that are stored in some Orthanc server. This plugin might
+be useful to medical physicists for QA tasks, as well as for
+pedagogical purpose.
+
+Demonstration: http://youtu.be/wsslVhE-R1Q
+
+The instructions for building/installing the plugin can be found in
+the "INSTALL" file.
+
+
+Licensing
+---------
+
+Orthanc and this plugin are licensed under the GPLv3 license.
+
+We also kindly ask scientific works and clinical studies that make use
+of this plugin or of Orthanc, to cite Orthanc in their associated
+publications. Similarly, we ask open-source and closed-source products
+that make use of Orthanc to warn us about this use. You can cite our
+work using the following BibTeX entry:
+
+ at inproceedings{Jodogne:ISBI2013,
+ author = {Jodogne, S. and Bernard, C. and Devillers, M. and Lenaerts, E. and Coucke, P.},
+ title = {Orthanc -- {A} Lightweight, {REST}ful {DICOM} Server for Healthcare and Medical Research},
+ booktitle={Biomedical Imaging ({ISBI}), {IEEE} 10th International Symposium on},
+ year={2013},
+ pages={190-193},
+ ISSN={1945-7928},
+ month=apr,
+ url={http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6556444},
+ address={San Francisco, {CA}, {USA}}
+}
+
+
+Disclaimer
+----------
+
+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.
+
+
+Dependencies
+------------
+
+* This plugin depends upon the "json-simple" toolkit
+ (http://code.google.com/p/json-simple/), version 1.1.1, that is
+ released under the Apache License 2.0. The source of this dependency
+ is located in the "org/" folder.
diff --git a/com/orthancserver/DicomDecoder.java b/com/orthancserver/DicomDecoder.java
new file mode 100644
index 0000000..36c3f5e
--- /dev/null
+++ b/com/orthancserver/DicomDecoder.java
@@ -0,0 +1,427 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ *
+ * 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 3 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, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+package com.orthancserver;
+
+import ij.ImagePlus;
+import ij.ImageStack;
+import ij.process.ImageProcessor;
+import ij.process.ShortProcessor;
+import ij.process.ColorProcessor;
+import ij.io.FileInfo;
+import ij.measure.Calibration;
+import org.json.simple.*;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.io.IOException;
+import javax.swing.SwingWorker;
+import java.util.concurrent.ExecutionException;
+
+import javax.swing.JFrame;
+import javax.swing.JProgressBar;
+import java.awt.BorderLayout;
+import javax.swing.JPanel;
+import javax.swing.JButton;
+import java.awt.FlowLayout;
+import javax.swing.border.EmptyBorder;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+
+
+public class DicomDecoder
+{
+ private static class ProgressDialog extends JFrame
+ {
+ private JProgressBar bar_ = new JProgressBar();
+ private boolean canceled_ = false;
+
+ public ProgressDialog(int count)
+ {
+ getContentPane().setLayout(new BorderLayout());
+ bar_.setBorder(new EmptyBorder(20, 20, 20, 20));
+ getContentPane().add(bar_, BorderLayout.NORTH);
+
+ JPanel buttonPane = new JPanel();
+ buttonPane.setLayout(new FlowLayout(FlowLayout.RIGHT));
+ getContentPane().add(buttonPane, BorderLayout.SOUTH);
+
+ JButton cancelButton = new JButton("Cancel");
+ cancelButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg) {
+ canceled_ = true;
+ }
+ });
+ buttonPane.add(cancelButton);
+
+ bar_.setMaximum(0);
+ bar_.setMaximum(count);
+
+ setSize(500, 150);
+ setTitle("Importing series from Orthanc");
+ setLocationRelativeTo(null); // Center dialog on screen
+ }
+
+ public void SetProgress(int value)
+ {
+ bar_.setValue(value);
+ }
+
+ public boolean IsCanceled()
+ {
+ return canceled_;
+ }
+ };
+
+ private static void ExtractCalibration(ImagePlus image,
+ JSONObject tags)
+ {
+ JSONObject rescaleIntercept = (JSONObject) tags.get("0028,1052");
+ JSONObject rescaleSlope = (JSONObject) tags.get("0028,1053");
+ if (rescaleIntercept != null &&
+ rescaleSlope != null)
+ {
+ double[] coeff = {
+ Float.valueOf((String) rescaleIntercept.get("Value")),
+ Float.valueOf((String) rescaleSlope.get("Value"))
+ };
+ image.getCalibration().setFunction(Calibration.STRAIGHT_LINE, coeff, "Gray Value");
+ }
+ }
+
+ private static void ExtractPixelSpacing(ImagePlus image,
+ JSONObject tags)
+ {
+ JSONObject pixelSpacing = (JSONObject) tags.get("0028,0030");
+ if (pixelSpacing != null)
+ {
+ String[] tokens = ((String) pixelSpacing.get("Value")).split("\\\\");
+ if (tokens.length == 2)
+ {
+ FileInfo fi = image.getFileInfo();
+ fi.pixelWidth = Float.valueOf(tokens[0]);
+ fi.pixelHeight = Float.valueOf(tokens[1]);
+ fi.unit = "mm";
+
+ image.setFileInfo(fi);
+ image.getCalibration().pixelWidth = fi.pixelWidth;
+ image.getCalibration().pixelHeight = fi.pixelHeight;
+ image.getCalibration().setUnit(fi.unit);
+ }
+ }
+ }
+
+ private static void ExtractDicomInfo(ImagePlus image,
+ JSONObject tags)
+ {
+ String info = new String();
+
+ ArrayList<String> tagsIndex = new ArrayList<String>();
+ for (Object tag : tags.keySet())
+ {
+ tagsIndex.add((String) tag);
+ }
+
+ Collections.sort(tagsIndex);
+ for (String tag : tagsIndex)
+ {
+ JSONObject value = (JSONObject) tags.get(tag);
+
+ if (((String) value.get("Type")).equals("String"))
+ {
+ info += (tag + " " + (String) value.get("Name") +
+ ": " + (String) value.get("Value") + "\n");
+ }
+ }
+
+ image.setProperty("Info", info);
+ }
+
+ private static ImageProcessor DecodeInstance(OrthancConnection c,
+ String uuid) throws IOException
+ {
+ try
+ {
+ String uri = "/instances/" + uuid + "/image-uint16";
+ ShortProcessor slice = new ShortProcessor(c.ReadImage(uri));
+ return slice;
+ }
+ catch (IllegalArgumentException e)
+ {
+ // Color image
+ String uri = "/instances/" + uuid + "/preview";
+ ColorProcessor slice = new ColorProcessor(c.ReadImage(uri));
+ return slice;
+ }
+ }
+
+ private static ImageStack AddSlice(ImageStack stack,
+ OrthancConnection c,
+ String uuid) throws IOException
+ {
+ ImageProcessor slice = DecodeInstance(c, uuid);
+
+ if (stack == null)
+ {
+ stack = new ImageStack(slice.getWidth(), slice.getHeight());
+ }
+
+ stack.addSlice("", slice);
+ return stack;
+ }
+
+
+ static private class Slice implements Comparable
+ {
+ private Float index_;
+ private String uuid_;
+
+ Slice(float index,
+ String uuid)
+ {
+ index_ = index;
+ uuid_ = uuid;
+ }
+
+ @Override
+ public int compareTo(Object other)
+ {
+ return index_.compareTo(((Slice) other).index_);
+ }
+
+ public String GetUuid()
+ {
+ return uuid_;
+ }
+ }
+
+
+
+ private String[] SortSlices(List<Slice> slices)
+ {
+ Collections.sort(slices);
+
+ String[] result = new String[slices.size()];
+
+ for (int i = 0; i < slices.size(); i++)
+ {
+ result[i] = slices.get(i).GetUuid();
+ }
+
+ return result;
+ }
+
+
+
+ private String[] SortSlicesBy3D(OrthancConnection c,
+ JSONArray instances) throws IOException
+ {
+ ArrayList<Slice> slices = new ArrayList<Slice>();
+ float normal[] = null;
+
+ float minDistance = Float.POSITIVE_INFINITY;
+ float maxDistance = Float.NEGATIVE_INFINITY;
+
+ for (int i = 0; i < instances.size(); i++)
+ {
+ String uuid = (String) instances.get(i);
+ JSONObject instance = (JSONObject) c.ReadJson("/instances/" + uuid + "/tags?simplify");
+ if (!instance.containsKey("ImageOrientationPatient") ||
+ !instance.containsKey("ImagePositionPatient"))
+ {
+ return null;
+ }
+
+ if (i == 0)
+ {
+ String[] tokens = ((String) instance.get("ImageOrientationPatient")).split("\\\\");
+ if (tokens.length != 6)
+ {
+ return null;
+ }
+
+ float cosines[] = new float[6];
+ for (int j = 0; j < 6; j++)
+ {
+ cosines[j] = Float.parseFloat(tokens[j]);
+ }
+
+ normal = new float[] {
+ cosines[1] * cosines[5] - cosines[2] * cosines[4],
+ cosines[2] * cosines[3] - cosines[0] * cosines[5],
+ cosines[0] * cosines[4] - cosines[1] * cosines[3]
+ };
+ }
+
+ String[] tokens = ((String) instance.get("ImagePositionPatient")).split("\\\\");
+ if (tokens.length != 3)
+ {
+ return null;
+ }
+
+ float distance = 0;
+ for (int j = 0; j < 3; j++)
+ {
+ distance += normal[j] * Float.parseFloat(tokens[j]);
+ }
+
+ minDistance = Math.min(minDistance, distance);
+ maxDistance = Math.max(minDistance, distance);
+ slices.add(new Slice(distance, uuid));
+ }
+
+ if (maxDistance - minDistance < 0.001)
+ {
+ return null;
+ }
+
+ return SortSlices(slices);
+ }
+
+
+ private String[] SortSlicesByNumber(OrthancConnection c,
+ JSONArray instances) throws IOException
+ {
+ ArrayList<Slice> slices = new ArrayList<Slice>();
+
+ for (int i = 0; i < instances.size(); i++)
+ {
+ String uuid = (String) instances.get(i);
+ JSONObject instance = (JSONObject) c.ReadJson("/instances/" + uuid);
+ Long index = (Long) instance.get("IndexInSeries");
+ slices.add(new Slice((float) index, uuid));
+ }
+
+ return SortSlices(slices);
+ }
+
+
+
+ private String[] GetSlices(OrthancConnection c,
+ JSONArray instances) throws IOException
+ {
+ String[] result;
+
+ result = SortSlicesBy3D(c, instances);
+ if (result != null && result.length == instances.size())
+ {
+ return result;
+ }
+
+ result = SortSlicesByNumber(c, instances);
+ if (result != null && result.length == instances.size())
+ {
+ return result;
+ }
+
+ throw new IOException("Not a 3D image");
+ }
+
+
+
+
+ private ImagePlus image_;
+
+ public DicomDecoder(final OrthancConnection c,
+ boolean isInstance,
+ String uuid) throws IOException, InterruptedException, ExecutionException
+ {
+ ImageStack stack = null;
+ JSONObject tags = null;
+ String tagsUri, name;
+
+ if (isInstance)
+ {
+ name = "Instance " + uuid;
+ tags = (JSONObject) c.ReadJson("/instances/" + uuid + "/tags");
+ stack = AddSlice(stack, c, uuid);
+ }
+ else
+ {
+ name = "Series " + uuid;
+
+ JSONObject series = (JSONObject) c.ReadJson("/series/" + uuid);
+ JSONArray instances = (JSONArray) series.get("Instances");
+
+ try
+ {
+ tags = (JSONObject) c.ReadJson("/series/" + uuid + "/shared-tags");
+ }
+ catch (Exception e)
+ {
+ // Fallback for old versions of Orthanc, without "shared-tags"
+ tags = (JSONObject) c.ReadJson("/instances/" + (String) instances.get(0) + "/tags");
+ }
+
+ final String[] slices = GetSlices(c, instances);
+ final ProgressDialog progress = new ProgressDialog(slices.length);
+
+ try
+ {
+ progress.setVisible(true);
+ SwingWorker<ImageStack, Float> worker = new SwingWorker<ImageStack, Float>() {
+ @Override
+ protected ImageStack doInBackground()
+ {
+ try
+ {
+ ImageStack stack = null;
+
+ for (int i = 0; i < slices.length; i++)
+ {
+ if (progress.IsCanceled())
+ {
+ return null;
+ }
+
+ progress.SetProgress(i);
+ stack = AddSlice(stack, c, slices[i]);
+ }
+
+ return stack;
+ }
+ catch (IOException e)
+ {
+ return null;
+ }
+ }
+ };
+
+ worker.execute();
+ stack = worker.get();
+ }
+ finally
+ {
+ progress.setVisible(false);
+ }
+ }
+
+ image_ = new ImagePlus(name, stack);
+
+ ExtractCalibration(image_, tags);
+ ExtractPixelSpacing(image_, tags);
+ ExtractDicomInfo(image_, tags);
+ }
+
+ public ImagePlus GetImage()
+ {
+ return image_;
+ }
+}
diff --git a/com/orthancserver/GridLayout2.java b/com/orthancserver/GridLayout2.java
new file mode 100644
index 0000000..86beedb
--- /dev/null
+++ b/com/orthancserver/GridLayout2.java
@@ -0,0 +1,167 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ *
+ * 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 3 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, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+package com.orthancserver;
+
+import java.awt.*;
+
+public class GridLayout2 extends GridLayout
+{
+ public GridLayout2() {
+ this(1, 0, 0, 0);
+ }
+
+ public GridLayout2(int rows, int cols) {
+ this(rows, cols, 0, 0);
+ }
+
+ public GridLayout2(int rows, int cols, int hgap, int vgap) {
+ super(rows, cols, hgap, vgap);
+ }
+
+ public Dimension preferredLayoutSize(Container parent) {
+ synchronized (parent.getTreeLock()) {
+ Insets insets = parent.getInsets();
+ int ncomponents = parent.getComponentCount();
+ int nrows = getRows();
+ int ncols = getColumns();
+ if (nrows > 0) {
+ ncols = (ncomponents + nrows - 1) / nrows;
+ }
+ else {
+ nrows = (ncomponents + ncols - 1) / ncols;
+ }
+ int[] w = new int[ncols];
+ int[] h = new int[nrows];
+ for (int i = 0; i < ncomponents; i ++) {
+ int r = i / ncols;
+ int c = i % ncols;
+ Component comp = parent.getComponent(i);
+ Dimension d = comp.getPreferredSize();
+ if (w[c] < d.width) {
+ w[c] = d.width;
+ }
+ if (h[r] < d.height) {
+ h[r] = d.height;
+ }
+ }
+ int nw = 0;
+ for (int j = 0; j < ncols; j ++) {
+ nw += w[j];
+ }
+ int nh = 0;
+ for (int i = 0; i < nrows; i ++) {
+ nh += h[i];
+ }
+ return new Dimension(insets.left + insets.right + nw + (ncols-1)*getHgap(),
+ insets.top + insets.bottom + nh + (nrows-1)*getVgap());
+ }
+ }
+
+ public Dimension minimumLayoutSize(Container parent) {
+ synchronized (parent.getTreeLock()) {
+ Insets insets = parent.getInsets();
+ int ncomponents = parent.getComponentCount();
+ int nrows = getRows();
+ int ncols = getColumns();
+ if (nrows > 0) {
+ ncols = (ncomponents + nrows - 1) / nrows;
+ }
+ else {
+ nrows = (ncomponents + ncols - 1) / ncols;
+ }
+ int[] w = new int[ncols];
+ int[] h = new int[nrows];
+ for (int i = 0; i < ncomponents; i ++) {
+ int r = i / ncols;
+ int c = i % ncols;
+ Component comp = parent.getComponent(i);
+ Dimension d = comp.getMinimumSize();
+ if (w[c] < d.width) {
+ w[c] = d.width;
+ }
+ if (h[r] < d.height) {
+ h[r] = d.height;
+ }
+ }
+ int nw = 0;
+ for (int j = 0; j < ncols; j ++) {
+ nw += w[j];
+ }
+ int nh = 0;
+ for (int i = 0; i < nrows; i ++) {
+ nh += h[i];
+ }
+ return new Dimension(insets.left + insets.right + nw + (ncols-1)*getHgap(),
+ insets.top + insets.bottom + nh + (nrows-1)*getVgap());
+ }
+ }
+
+ public void layoutContainer(Container parent) {
+ synchronized (parent.getTreeLock()) {
+ Insets insets = parent.getInsets();
+ int ncomponents = parent.getComponentCount();
+ int nrows = getRows();
+ int ncols = getColumns();
+ if (ncomponents == 0) {
+ return;
+ }
+ if (nrows > 0) {
+ ncols = (ncomponents + nrows - 1) / nrows;
+ }
+ else {
+ nrows = (ncomponents + ncols - 1) / ncols;
+ }
+ int hgap = getHgap();
+ int vgap = getVgap();
+ // scaling factors
+ Dimension pd = preferredLayoutSize(parent);
+ double sw = (1.0 * parent.getWidth()) / pd.width;
+ double sh = (1.0 * parent.getHeight()) / pd.height;
+ // scale
+ int[] w = new int[ncols];
+ int[] h = new int[nrows];
+ for (int i = 0; i < ncomponents; i ++) {
+ int r = i / ncols;
+ int c = i % ncols;
+ Component comp = parent.getComponent(i);
+ Dimension d = comp.getPreferredSize();
+ d.width = (int) (sw * d.width);
+ d.height = (int) (sh * d.height);
+ if (w[c] < d.width) {
+ w[c] = d.width;
+ }
+ if (h[r] < d.height) {
+ h[r] = d.height;
+ }
+ }
+ for (int c = 0, x = insets.left; c < ncols; c ++) {
+ for (int r = 0, y = insets.top; r < nrows; r ++) {
+ int i = r * ncols + c;
+ if (i < ncomponents) {
+ parent.getComponent(i).setBounds(x, y, w[c], h[r]);
+ }
+ y += h[r] + vgap;
+ }
+ x += w[c] + hgap;
+ }
+ }
+ }
+}
diff --git a/com/orthancserver/HttpsTrustModifier.java b/com/orthancserver/HttpsTrustModifier.java
new file mode 100644
index 0000000..0295063
--- /dev/null
+++ b/com/orthancserver/HttpsTrustModifier.java
@@ -0,0 +1,84 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ *
+ * 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 3 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, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+package com.orthancserver;
+
+import java.net.*;
+import javax.net.ssl.*;
+import java.security.*;
+import java.security.cert.*;
+
+public class HttpsTrustModifier
+{
+ private static final AlwaysTrustHostname trustHostname_ = new AlwaysTrustHostname();
+ private static SSLSocketFactory trustSocket_;
+
+ private static synchronized SSLSocketFactory GetAlwaysTrustSocket(HttpsURLConnection httpsConnection)
+ throws NoSuchAlgorithmException, KeyStoreException, KeyManagementException
+ {
+ // Singleton pattern to create one single trust manager
+ if (trustSocket_ == null)
+ {
+ SSLContext ctx = SSLContext.getInstance("TLS");
+ ctx.init(null, new TrustManager[] { new AlwaysTrustManager() }, null);
+ trustSocket_ = ctx.getSocketFactory();
+ }
+
+ return trustSocket_;
+ }
+
+
+ private static final class AlwaysTrustHostname implements HostnameVerifier
+ {
+ public boolean verify(String hostname, SSLSession session)
+ {
+ return true;
+ }
+ }
+
+
+ private static class AlwaysTrustManager implements X509TrustManager
+ {
+ public void checkClientTrusted(X509Certificate[] arg0, String arg1) throws CertificateException
+ {
+ }
+
+ public void checkServerTrusted(X509Certificate[] arg0, String arg1) throws CertificateException
+ {
+ }
+
+ public X509Certificate[] getAcceptedIssuers()
+ {
+ return null;
+ }
+ }
+
+
+ public static void Trust(URLConnection conn)
+ throws KeyManagementException, NoSuchAlgorithmException, KeyStoreException
+ {
+ if (conn instanceof HttpsURLConnection)
+ {
+ HttpsURLConnection httpsConnection = (HttpsURLConnection) conn;
+ httpsConnection.setSSLSocketFactory(GetAlwaysTrustSocket(httpsConnection));
+ httpsConnection.setHostnameVerifier(trustHostname_);
+ }
+ }
+}
diff --git a/com/orthancserver/Orthanc.java b/com/orthancserver/Orthanc.java
new file mode 100644
index 0000000..abe2d47
--- /dev/null
+++ b/com/orthancserver/Orthanc.java
@@ -0,0 +1,51 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ *
+ * 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 3 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, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+package com.orthancserver;
+
+import ij.plugin.PlugIn;
+import ij.Prefs;
+import javax.swing.JOptionPane;
+
+public class Orthanc implements PlugIn
+{
+ public void run(String arg)
+ {
+ SelectImageDialog d = new SelectImageDialog();
+ d.Unserialize(Prefs.get("orthanc.servers", ""));
+
+ boolean success = d.ShowModal();
+ Prefs.set("orthanc.servers", d.Serialize());
+
+ if (success)
+ {
+ try
+ {
+ DicomDecoder decoder = new DicomDecoder(d.GetSelectedConnection(), d.IsInstanceSelected(), d.GetSelectedUuid());
+ decoder.GetImage().show();
+ }
+ catch (Exception e)
+ {
+ JOptionPane.showMessageDialog(null, "Error while importing this image: " + e.getMessage());
+ //e.printStackTrace(System.out);
+ }
+ }
+ }
+}
diff --git a/com/orthancserver/OrthancConfigurationDialog.java b/com/orthancserver/OrthancConfigurationDialog.java
new file mode 100644
index 0000000..35ddfd1
--- /dev/null
+++ b/com/orthancserver/OrthancConfigurationDialog.java
@@ -0,0 +1,170 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ *
+ * 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 3 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, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+package com.orthancserver;
+
+import java.awt.BorderLayout;
+import java.awt.Canvas;
+import java.awt.FlowLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.io.IOException;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPasswordField;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.JTextField;
+import javax.swing.JTree;
+import javax.swing.SwingWorker;
+import javax.swing.border.EmptyBorder;
+
+import org.json.simple.JSONObject;
+
+
+public class OrthancConfigurationDialog extends JDialog
+{
+ private JTextField name_ = new JTextField("Orthanc");
+ private JTextField url_ = new JTextField("http://localhost:8042/");
+ private JTextField username_ = new JTextField("");
+ private JTextField password_ = new JPasswordField("");
+ private boolean isSuccess_;
+
+ private OrthancConnection CreateConnection()
+ {
+ OrthancConnection orthanc = new OrthancConnection();
+ orthanc.SetInsecure(true); // Fix issue 9 (cannot connect to self-signed certificates)
+ orthanc.SetName(name_.getText());
+ orthanc.SetBaseUrl(url_.getText());
+
+ if (username_.getText().length() != 0)
+ {
+ orthanc.SetCredentials(username_.getText(), password_.getText());
+ }
+
+ return orthanc;
+ }
+
+ public OrthancConfigurationDialog()
+ {
+ final JPanel contentPanel = new JPanel();
+ contentPanel.setBorder(new EmptyBorder(20, 5, 5, 5));
+ contentPanel.setLayout(new GridLayout2(0, 2, 20, 5));
+
+ JLabel label = new JLabel("Name:");
+ label.setHorizontalAlignment(JLabel.RIGHT);
+ contentPanel.add(label);
+ contentPanel.add(name_);
+
+ label = new JLabel("URL:");
+ label.setHorizontalAlignment(JLabel.RIGHT);
+ contentPanel.add(label);
+ contentPanel.add(url_);
+
+ label = new JLabel("Username:");
+ label.setHorizontalAlignment(JLabel.RIGHT);
+ contentPanel.add(label);
+ contentPanel.add(username_);
+
+ label = new JLabel("Password:");
+ label.setHorizontalAlignment(JLabel.RIGHT);
+ contentPanel.add(label);
+ contentPanel.add(password_);
+
+ getContentPane().setLayout(new BorderLayout());
+ getContentPane().add(contentPanel, BorderLayout.NORTH);
+
+ JPanel buttonPane = new JPanel();
+ buttonPane.setLayout(new FlowLayout(FlowLayout.RIGHT));
+ getContentPane().add(buttonPane, BorderLayout.SOUTH);
+ {
+ {
+ JButton test = new JButton("Test connection");
+ test.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg) {
+ OrthancConnection orthanc = CreateConnection();
+ try
+ {
+ JSONObject system = (JSONObject) orthanc.ReadJson("system");
+ JOptionPane.showMessageDialog(null, "Successfully connected to this Orthanc server " +
+ "(version: " + (String) system.get("Version") + ")!",
+ "Success", JOptionPane.INFORMATION_MESSAGE);
+ }
+ catch (IOException e)
+ {
+ JOptionPane.showMessageDialog(null, "Cannot connect to this Orthanc server!",
+ "Error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ });
+ buttonPane.add(test);
+ }
+ {
+ JButton okButton = new JButton("Add");
+ okButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg) {
+ isSuccess_ = true;
+ setVisible(false);
+ }
+ });
+ buttonPane.add(okButton);
+ getRootPane().setDefaultButton(okButton);
+ }
+ {
+ JButton cancelButton = new JButton("Cancel");
+ cancelButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg) {
+ setVisible(false);
+ }
+ });
+ buttonPane.add(cancelButton);
+ }
+ }
+
+ setUndecorated(false);
+ setSize(500,500);
+ setTitle("Add new server");
+ setModal(true);
+ }
+
+
+
+ public OrthancConnection ShowModal()
+ {
+ isSuccess_ = false;
+ setVisible(true);
+ if (isSuccess_)
+ {
+ return CreateConnection();
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+}
diff --git a/com/orthancserver/OrthancConnection.java b/com/orthancserver/OrthancConnection.java
new file mode 100644
index 0000000..c7f622a
--- /dev/null
+++ b/com/orthancserver/OrthancConnection.java
@@ -0,0 +1,242 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ *
+ * 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 3 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, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+package com.orthancserver;
+
+import java.awt.image.BufferedImage;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.ConnectException;
+import java.net.URL;
+import java.net.URLConnection;
+import javax.imageio.ImageIO;
+import javax.xml.bind.DatatypeConverter;
+import org.json.simple.JSONObject;
+import org.json.simple.JSONValue;
+
+public class OrthancConnection
+{
+ private String baseUrl_;
+ private String authentication_;
+ private String name_;
+ private boolean insecure_;
+
+ OrthancConnection()
+ {
+ baseUrl_ = "http://localhost:8042/";
+ authentication_ = null;
+ name_ = "Default Orthanc server";
+ insecure_ = false;
+ }
+
+
+ private static InputStream OpenUrl(String urlString,
+ boolean isInsecure,
+ String authentication,
+ String accept) throws IOException
+ {
+ URL url = new URL(urlString);
+
+ URLConnection uc = url.openConnection();
+
+ if (isInsecure)
+ {
+ try
+ {
+ HttpsTrustModifier.Trust(uc);
+ }
+ catch (Exception e)
+ {
+ throw new IOException("Cannot allow self-signed certificates");
+ }
+ }
+
+ if (authentication != null)
+ {
+ // http://blogs.deepal.org/2008/01/sending-basic-authentication-using-url.html
+ uc.setRequestProperty("Authorization", "Basic " + authentication);
+ }
+
+ if (accept != null)
+ {
+ uc.setRequestProperty("Accept", accept);
+ }
+
+ try
+ {
+ return uc.getInputStream();
+ }
+ catch (ConnectException e)
+ {
+ throw new IOException("Cannot read URL: " + urlString);
+ }
+ }
+
+
+ private static String ComputeAuthentication(String username,
+ String password)
+ {
+ String auth = (new StringBuffer(username).append(":").append(password)).toString();
+ // http://stackoverflow.com/a/14413290/881731
+ return DatatypeConverter.printBase64Binary(auth.getBytes());
+ }
+
+
+ public InputStream OpenStream(String uri,
+ String acceptHeader) throws IOException
+ {
+ String url = baseUrl_ + uri;
+ return OpenUrl(url, insecure_, authentication_, acceptHeader);
+ }
+
+
+ public void SetCredentials(String username,
+ String password)
+ {
+ authentication_ = ComputeAuthentication(username, password);
+ }
+
+ public void SetBaseUrl(String url)
+ {
+ if (url.endsWith("/"))
+ {
+ baseUrl_ = url;
+ }
+ else
+ {
+ baseUrl_ = url + "/";
+ }
+ }
+
+ public String GetBaseUrl()
+ {
+ return baseUrl_;
+ }
+
+ public void SetInsecure(boolean insecure)
+ {
+ insecure_ = true;
+ }
+
+ public boolean IsInsecure()
+ {
+ return insecure_;
+ }
+
+ public String ReadString(String uri) throws IOException
+ {
+ InputStream stream = OpenStream(uri, null);
+
+ BufferedReader reader = null;
+ try
+ {
+ reader = new BufferedReader(new InputStreamReader(stream));
+
+ StringBuffer buffer = new StringBuffer();
+ int read;
+ char[] chars = new char[1024 * 16];
+ while ((read = reader.read(chars)) != -1)
+ {
+ buffer.append(chars, 0, read);
+ }
+
+ return buffer.toString();
+ }
+ finally
+ {
+ try
+ {
+ if (reader != null)
+ {
+ reader.close();
+ }
+ }
+ catch (IOException e)
+ {
+ }
+ }
+ }
+
+ public Object ReadJson(String uri) throws IOException
+ {
+ String content = ReadString(uri);
+ Object json = JSONValue.parse(content);
+
+ if (json == null)
+ {
+ throw new IOException();
+ }
+ else
+ {
+ return json;
+ }
+ }
+
+ public BufferedImage ReadImage(String uri) throws IOException
+ {
+ // Ask the download of "image/png", otherwise an "image/jpeg" is negociated
+ return ImageIO.read(OpenStream(uri, "image/png"));
+ }
+
+ public String GetName()
+ {
+ return name_;
+ }
+
+ public void SetName(String name)
+ {
+ name_ = name;
+ }
+
+ public JSONObject Serialize()
+ {
+ JSONObject json = new JSONObject();
+ json.put("Name", name_);
+ json.put("Url", baseUrl_);
+
+ if (authentication_ != null)
+ {
+ json.put("Authentication", authentication_);
+ }
+
+ return json;
+ }
+
+ public static OrthancConnection Unserialize(JSONObject json)
+ {
+ OrthancConnection c = new OrthancConnection();
+ c.SetInsecure(true); // Fix issue 9 (cannot connect to self-signed certificates)
+ c.SetName((String) json.get("Name"));
+ c.SetBaseUrl((String) json.get("Url"));
+
+ if (json.containsKey("Authentication"))
+ {
+ c.authentication_ = (String) json.get("Authentication");
+ }
+ else
+ {
+ c.authentication_ = null;
+ }
+
+ return c;
+ }
+}
diff --git a/com/orthancserver/PreviewPanel.java b/com/orthancserver/PreviewPanel.java
new file mode 100644
index 0000000..f56315d
--- /dev/null
+++ b/com/orthancserver/PreviewPanel.java
@@ -0,0 +1,82 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ *
+ * 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 3 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, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+package com.orthancserver;
+
+import java.awt.Graphics;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.ByteArrayInputStream;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import javax.swing.JPanel;
+
+public class PreviewPanel extends JPanel
+{
+ private BufferedImage image_ = null;
+
+ public void Reset()
+ {
+ image_ = null;
+ repaint();
+ }
+
+ public void Load(OrthancConnection orthanc,
+ String uri)
+ {
+ try
+ {
+ image_ = orthanc.ReadImage(uri);
+ repaint();
+ }
+ catch (IOException e)
+ {
+ Reset();
+ }
+ }
+
+ @Override
+ protected void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+
+ if (image_ != null)
+ {
+ float scaleX = (float) getWidth() / (float) image_.getWidth();
+ float scaleY = (float) getHeight() / (float) image_.getHeight();
+ float scale = Math.min(scaleX, scaleY);
+ if (scale > 1)
+ {
+ // Do not upscale the image
+ scale = 1;
+ }
+
+ int width = Math.round((float) image_.getWidth() * scale);
+ int height = Math.round((float) image_.getHeight() * scale);
+
+ int dx = (getWidth() - width) / 2;
+ int dy = (getHeight() - height) / 2;
+ g.drawImage(image_, dx, dy, dx + width, dy + height,
+ 0, 0, image_.getWidth(), image_.getHeight(), null);
+ }
+ }
+}
diff --git a/com/orthancserver/SelectImageDialog.java b/com/orthancserver/SelectImageDialog.java
new file mode 100644
index 0000000..9fc96a5
--- /dev/null
+++ b/com/orthancserver/SelectImageDialog.java
@@ -0,0 +1,580 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ *
+ * 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 3 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, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+package com.orthancserver;
+
+import org.json.simple.JSONValue;
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Collections;
+import java.util.Enumeration;
+
+
+import java.awt.Canvas;
+import java.awt.GridLayout;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.JScrollPane;
+import javax.swing.JTree;
+import javax.swing.SwingWorker;
+import javax.swing.border.EmptyBorder;
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+
+import javax.xml.bind.DatatypeConverter;
+import javax.swing.event.TreeExpansionEvent;
+import javax.swing.event.TreeWillExpandListener;
+import javax.swing.event.TreeSelectionEvent;
+import javax.swing.event.TreeSelectionListener;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.DefaultTreeModel;
+import javax.swing.tree.ExpandVetoException;
+import javax.swing.tree.MutableTreeNode;
+import javax.swing.tree.TreePath;
+
+
+public class SelectImageDialog extends JDialog
+{
+ private enum ResourceType {
+ ROOT,
+ SERVER,
+ PATIENT,
+ STUDY,
+ SERIES,
+ INSTANCE,
+ INFO;
+ }
+
+
+ private static class MyTreeNode extends DefaultMutableTreeNode implements Comparable
+ {
+ private OrthancConnection orthanc_;
+ private boolean loaded_ = false;
+ private ResourceType type_;
+ private String uuid_;
+
+
+ public String GetUuid()
+ {
+ return uuid_;
+ }
+
+ public ResourceType GetResourceType()
+ {
+ return type_;
+ }
+
+ public OrthancConnection GetConnection()
+ {
+ return orthanc_;
+ }
+
+ public boolean UpdatePreview(PreviewPanel preview)
+ {
+ if (type_ == ResourceType.INSTANCE)
+ {
+ preview.Load(orthanc_, "/instances/" + uuid_ + "/preview");
+ return true;
+ }
+ else if (type_ == ResourceType.SERIES)
+ {
+ try
+ {
+ JSONObject series = (JSONObject) orthanc_.ReadJson("series/" + uuid_);
+ JSONArray instances = (JSONArray) series.get("Instances");
+ if (instances.size() > 0)
+ {
+ preview.Load(orthanc_, "/instances/" + instances.get(0) + "/preview");
+ return true;
+ }
+ }
+ catch (IOException e)
+ {
+ }
+ }
+
+ preview.Reset();
+ return false;
+ }
+
+
+ private String AddComponent(String source, String component)
+ {
+ if (component == null ||
+ component.length() == 0)
+ {
+ return source;
+ }
+
+ if (source.length() == 0)
+ {
+ return component;
+ }
+ else
+ {
+ return source + " - " + component;
+ }
+ }
+
+
+ private List<MyTreeNode> LoadPatients() throws IOException
+ {
+ List<MyTreeNode> children = new ArrayList<MyTreeNode>();
+
+ JSONArray patients = (JSONArray) orthanc_.ReadJson("patients");
+ for (int i = 0; i < patients.size(); i++)
+ {
+ String uuid = (String) patients.get(i);
+ JSONObject patient = (JSONObject) orthanc_.ReadJson("patients/" + uuid);
+ JSONObject main = (JSONObject) patient.get("MainDicomTags");
+
+ String s = new String();
+ s = AddComponent(s, (String) main.get("PatientID"));
+ s = AddComponent(s, (String) main.get("PatientName"));
+ children.add(new MyTreeNode(orthanc_, ResourceType.PATIENT, uuid, s));
+ }
+
+ return children;
+ }
+
+
+ private List<MyTreeNode> LoadStudies() throws IOException
+ {
+ List<MyTreeNode> children = new ArrayList<MyTreeNode>();
+
+ JSONObject patient = (JSONObject) orthanc_.ReadJson("patients/" + uuid_);
+ JSONArray studies = (JSONArray) patient.get("Studies");
+ for (int i = 0; i < studies.size(); i++)
+ {
+ String uuid = (String) studies.get(i);
+ JSONObject study = (JSONObject) orthanc_.ReadJson("studies/" + uuid);
+ JSONObject main = (JSONObject) study.get("MainDicomTags");
+
+ String s = new String();
+ s = AddComponent(s, (String) main.get("StudyDescription"));
+ s = AddComponent(s, (String) main.get("StudyDate"));
+ children.add(new MyTreeNode(orthanc_, ResourceType.STUDY, uuid, s));
+ }
+
+ return children;
+ }
+
+
+ private List<MyTreeNode> LoadSeries() throws IOException
+ {
+ List<MyTreeNode> children = new ArrayList<MyTreeNode>();
+
+ JSONObject study = (JSONObject) orthanc_.ReadJson("studies/" + uuid_);
+ JSONArray seriesSet = (JSONArray) study.get("Series");
+ for (int i = 0; i < seriesSet.size(); i++)
+ {
+ String uuid = (String) seriesSet.get(i);
+ JSONObject series = (JSONObject) orthanc_.ReadJson("series/" + uuid);
+ JSONObject main = (JSONObject) series.get("MainDicomTags");
+
+ String s = new String();
+ s = AddComponent(s, (String) main.get("Modality"));
+ s = AddComponent(s, (String) main.get("SeriesDescription"));
+ children.add(new MyTreeNode(orthanc_, ResourceType.SERIES, uuid, s));
+ }
+
+ return children;
+ }
+
+
+ private List<MyTreeNode> LoadInstances() throws IOException
+ {
+ List<MyTreeNode> children = new ArrayList<MyTreeNode>();
+
+ JSONObject series = (JSONObject) orthanc_.ReadJson("series/" + uuid_);
+ JSONArray instances = (JSONArray) series.get("Instances");
+ for (int i = 0; i < instances.size(); i++)
+ {
+ String uuid = (String) instances.get(i);
+ JSONObject instance = (JSONObject) orthanc_.ReadJson("instances/" + uuid);
+ Long index = (Long) instance.get("IndexInSeries");
+ String s;
+ if (index == null)
+ {
+ s = uuid;
+ }
+ else
+ {
+ s = String.valueOf(index);
+ }
+
+ children.add(new MyTreeNode(orthanc_, ResourceType.INSTANCE, uuid, s));
+ }
+
+ return children;
+ }
+
+
+ public MyTreeNode() // Create root node
+ {
+ loaded_ = true;
+ orthanc_ = null;
+ type_ = ResourceType.ROOT;
+ uuid_ = "";
+ setAllowsChildren(true);
+ }
+
+ public MyTreeNode(OrthancConnection orthanc,
+ ResourceType type,
+ String id,
+ String name)
+ {
+ orthanc_ = orthanc;
+ type_ = type;
+ uuid_ = id;
+ add(new DefaultMutableTreeNode("Loading...", false));
+ setAllowsChildren(true);
+ setUserObject(name);
+ }
+
+ @Override
+ public int compareTo(Object other)
+ {
+ String a = (String) getUserObject();
+ String b = (String) ((MyTreeNode) other).getUserObject();
+ return a.compareTo(b);
+ }
+
+ private void SetChildren(List<MyTreeNode> children)
+ {
+ Collections.sort(children);
+
+ removeAllChildren();
+ setAllowsChildren(children.size() > 0);
+ for (MutableTreeNode node : children)
+ {
+ add(node);
+ }
+ loaded_ = true;
+ }
+
+ @Override
+ public boolean isLeaf()
+ {
+ return type_ == ResourceType.INSTANCE || type_ == ResourceType.INFO;
+ }
+
+ public void LoadChildren(final DefaultTreeModel model)
+ {
+ if (loaded_)
+ {
+ return;
+ }
+
+ SwingWorker<List<MyTreeNode>, Void> worker = new SwingWorker<List<MyTreeNode>, Void>() {
+ @Override
+ protected List<MyTreeNode> doInBackground()
+ {
+ List<MyTreeNode> children = null;
+
+ try
+ {
+ switch (type_)
+ {
+ case SERVER: children = LoadPatients(); break;
+ case PATIENT: children = LoadStudies(); break;
+ case STUDY: children = LoadSeries(); break;
+ case SERIES: children = LoadInstances(); break;
+ default:
+ break;
+ }
+ }
+ catch (IOException e)
+ {
+ children = null;
+ }
+
+ if (children == null)
+ {
+ children = new ArrayList<MyTreeNode>();
+ children.add(new MyTreeNode(orthanc_, ResourceType.INFO, "", "Orthanc is not running, or bad credentials"));
+ }
+
+ return children;
+ }
+
+ @Override
+ protected void done()
+ {
+ try
+ {
+ SetChildren(get());
+ model.nodeStructureChanged(MyTreeNode.this);
+ }
+ catch (Exception e)
+ {
+ }
+
+ super.done();
+ }
+ };
+
+ worker.execute();
+ }
+
+ }
+
+
+ private MyTreeNode root_ = new MyTreeNode();
+ private JTree tree_ = null;
+ private boolean isSuccess_;
+ private String selectedUuid_;
+ private ResourceType selectedType_;
+ private OrthancConnection selectedConnection_;
+ private JButton okButton_ = new JButton("Open");
+ private JButton removeServer_ = new JButton("Remove server");
+ private PreviewPanel preview_ = new PreviewPanel();
+
+ public SelectImageDialog()
+ {
+ tree_ = new JTree();
+
+ tree_.addTreeWillExpandListener(new TreeWillExpandListener()
+ {
+ @Override
+ public void treeWillExpand(TreeExpansionEvent event) throws ExpandVetoException {
+ TreePath path = event.getPath();
+ if (path.getLastPathComponent() instanceof MyTreeNode) {
+ MyTreeNode node = (MyTreeNode) path.getLastPathComponent();
+ node.LoadChildren((DefaultTreeModel) tree_.getModel());
+ }
+ }
+
+ @Override
+ public void treeWillCollapse(TreeExpansionEvent event) throws ExpandVetoException {
+ }
+ });
+
+
+ tree_.addTreeSelectionListener(new TreeSelectionListener()
+ {
+ @Override
+ public void valueChanged(TreeSelectionEvent e) {
+ TreePath path = e.getNewLeadSelectionPath();
+ if (path != null)
+ {
+ MyTreeNode node = (MyTreeNode) path.getLastPathComponent();
+ if (node.UpdatePreview(preview_))
+ {
+ selectedType_ = node.GetResourceType();
+ selectedUuid_ = node.GetUuid();
+ selectedConnection_ = node.GetConnection();
+ okButton_.setEnabled(true);
+ }
+
+ removeServer_.setEnabled(node.GetResourceType() == ResourceType.SERVER);
+ }
+ }
+ });
+
+
+ tree_.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent e) {
+ TreePath path = tree_.getPathForLocation(e.getX(), e.getY());
+ if (path != null) {
+ MyTreeNode node = (MyTreeNode) path.getLastPathComponent();
+ if (e.getClickCount() == 2 &&
+ node.GetResourceType() == ResourceType.INSTANCE) {
+ // Double click on an instance, close the dialog
+ isSuccess_ = true;
+ setVisible(false);
+ }
+ }
+ }
+ });
+
+
+ final JPanel contentPanel = new JPanel();
+ getContentPane().setLayout(new BorderLayout());
+ contentPanel.setBorder(new EmptyBorder(5, 5, 5, 5));
+ getContentPane().add(contentPanel, BorderLayout.CENTER);
+ contentPanel.setLayout(new BorderLayout(0, 0));
+ {
+ JSplitPane splitPane = new JSplitPane();
+ splitPane.setResizeWeight(0.6);
+ contentPanel.add(splitPane);
+
+ splitPane.setLeftComponent(new JScrollPane(tree_));
+ splitPane.setRightComponent(preview_);
+ }
+ {
+ JPanel buttonPane = new JPanel();
+ buttonPane.setLayout(new FlowLayout(FlowLayout.RIGHT));
+ getContentPane().add(buttonPane, BorderLayout.SOUTH);
+ {
+ JButton btnAddServer = new JButton("Add server");
+ btnAddServer.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg) {
+ OrthancConfigurationDialog dd = new OrthancConfigurationDialog();
+ dd.setLocationRelativeTo(null); // Center dialog on screen
+
+ OrthancConnection orthanc = dd.ShowModal();
+ if (orthanc != null) {
+ AddOrthancServer(orthanc);
+ ((DefaultTreeModel) tree_.getModel()).reload();
+ }
+ }
+ });
+ buttonPane.add(btnAddServer);
+ }
+
+ {
+ buttonPane.add(removeServer_);
+ removeServer_.setEnabled(false);
+
+ removeServer_.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg) {
+ MyTreeNode selected = (MyTreeNode) tree_.getLastSelectedPathComponent();
+ if (selected.GetResourceType() == ResourceType.SERVER &&
+ JOptionPane.showConfirmDialog(null, "Remove server \"" + selected.getUserObject() + "\"?",
+ "WARNING", JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
+ {
+ ((DefaultTreeModel) tree_.getModel()).removeNodeFromParent(selected);
+ }
+ }
+ });
+ }
+
+ {
+ okButton_.setEnabled(false);
+ okButton_.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg) {
+ isSuccess_ = true;
+ setVisible(false);
+ }
+ });
+ buttonPane.add(okButton_);
+ getRootPane().setDefaultButton(okButton_);
+ }
+ {
+ JButton cancelButton = new JButton("Cancel");
+ cancelButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg) {
+ setVisible(false);
+ }
+ });
+ buttonPane.add(cancelButton);
+ }
+ }
+
+ setUndecorated(false);
+ setSize(500,500);
+ setTitle("Select some series or some instance in Orthanc");
+ setModal(true);
+ }
+
+
+ public void AddOrthancServer(OrthancConnection orthanc)
+ {
+ root_.add(new MyTreeNode(orthanc, ResourceType.SERVER, "", orthanc.GetName()));
+ }
+
+ public boolean ShowModal()
+ {
+ final DefaultTreeModel model = new DefaultTreeModel(root_);
+ root_.LoadChildren(model);
+ tree_.setRootVisible(false);
+ tree_.setShowsRootHandles(true);
+ tree_.setModel(model);
+
+ isSuccess_ = false;
+ setVisible(true);
+ return isSuccess_;
+ }
+
+ public String GetSelectedUuid()
+ {
+ return selectedUuid_;
+ }
+
+ public boolean IsSeriesSelected()
+ {
+ return selectedType_ == ResourceType.SERIES;
+ }
+
+ public boolean IsInstanceSelected()
+ {
+ return selectedType_ == ResourceType.INSTANCE;
+ }
+
+ public OrthancConnection GetSelectedConnection()
+ {
+ return selectedConnection_;
+ }
+
+ public void Select(OrthancConnection c, boolean isInstance, String uuid) // For test
+ {
+ selectedConnection_ = c;
+ selectedType_ = (isInstance ? ResourceType.INSTANCE : ResourceType.SERIES);
+ selectedUuid_ = uuid;
+ }
+
+ public void Unserialize(String s)
+ {
+ if (s.length() == 0)
+ {
+ // Add default Orthanc server
+ AddOrthancServer(new OrthancConnection());
+ }
+ else
+ {
+ String decoded = new String(DatatypeConverter.parseBase64Binary(s));
+ JSONArray config = (JSONArray) JSONValue.parse(decoded);
+ if (config != null)
+ {
+ for (int i = 0; i < config.size(); i++)
+ {
+ AddOrthancServer(OrthancConnection.Unserialize((JSONObject) config.get(i)));
+ }
+ }
+ }
+ }
+
+ public String Serialize()
+ {
+ JSONArray servers = new JSONArray();
+
+ for (int i = 0; i < root_.getChildCount(); i++)
+ {
+ MyTreeNode node = (MyTreeNode) root_.getChildAt(i);
+ servers.add(node.GetConnection().Serialize());
+ }
+
+ String config = servers.toJSONString();
+ return DatatypeConverter.printBase64Binary(config.getBytes());
+ }
+}
diff --git a/debian/README.Debian b/debian/README.Debian
deleted file mode 100644
index b4751bc..0000000
--- a/debian/README.Debian
+++ /dev/null
@@ -1,7 +0,0 @@
-This is a plugin for ImageJ to browse and download the content of an
-Orthanc server.
-
-Homepage: http://www.orthanc-server.com/static.php?page=imagej
-
-The plugin is accessible from the "File" -> "Import" -> "Orthanc" menu
-entry in ImageJ.
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index c88d212..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,12 +0,0 @@
-orthanc-imagej (1.1+dfsg-1) unstable; urgency=medium
-
- * New upstream version.
- * Updated URLs to the project, the code repository and the downloads.
-
- -- Sebastien Jodogne <s.jodogne at gmail.com> Fri, 15 Apr 2016 11:44:54 +0200
-
-orthanc-imagej (1.0.0+dfsg-1) unstable; urgency=low
-
- * Initial release. (Closes: #772561)
-
- -- Sebastien Jodogne <s.jodogne at gmail.com> Mon, 15 Dec 2014 15:55:43 +0100
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index ec63514..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-9
diff --git a/debian/control b/debian/control
deleted file mode 100644
index 4b62b52..0000000
--- a/debian/control
+++ /dev/null
@@ -1,35 +0,0 @@
-Source: orthanc-imagej
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Sebastien Jodogne <s.jodogne at gmail.com>,
- Andreas Tille <tille at debian.org>
-Section: science
-Priority: optional
-Standards-Version: 3.9.7
-Build-Depends: cmake (>= 2.8),
- default-jdk | openjdk-8-jdk,
- debhelper (>= 9),
- imagej,
- libjson-simple-java
-Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/orthanc-imagej/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/orthanc-imagej/trunk/
-Homepage: http://www.orthanc-server.com/static.php?page=imagej
-
-Package: orthanc-imagej
-Architecture: all
-Depends: ${misc:Depends},
- default-jre | openjdk-8-jre,
- imagej,
- libjson-simple-java
-Recommends: orthanc
-Description: ImageJ plugin to import images from Orthanc
- This ImageJ plugin allows ImageJ to browse the content of an Orthanc
- server, then import 2D/3D DICOM images from Orthanc into ImageJ.
- Orthanc is a lightweight, RESTful DICOM server for healthcare and
- medical research.
- .
- This plugin simplifies the indexation of DICOM images if using
- ImageJ (e.g. for quality control of DICOM modalities, or for
- pedagogical use). There is also no need to carry on any complex
- network configuration, since the plugin directly uses the REST
- API of Orthanc. This makes its installation and its use
- quite straightforward.
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index 5a11a28..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,29 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: OrthancImageJ
-Upstream-Contact: Sebastien Jodogne <s.jodogne at gmail.com>
-Source: https://bitbucket.org/sjodogne/orthanc-imagej/
-Files-Excluded: org/*
-
-Files: *
-Copyright: 2012-2016 CHU of Liege (Belgium), and Sebastien Jodogne <s.jodogne at gmail.com>
-License: GPL-3
-
-
-License: GPL-3
- 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 3 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 package; if not, write to the Free Software Foundation, Inc.,
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- .
- On Debian systems, the full text of the GNU General Public License
- version 3 can be found in the file
- `/usr/share/common-licenses/GPL-3'.
diff --git a/debian/dirs b/debian/dirs
deleted file mode 100644
index db0cbfb..0000000
--- a/debian/dirs
+++ /dev/null
@@ -1 +0,0 @@
-usr/share/imagej/plugins
diff --git a/debian/install b/debian/install
deleted file mode 100644
index 6a8750a..0000000
--- a/debian/install
+++ /dev/null
@@ -1 +0,0 @@
-Build/Orthanc_Import.jar usr/share/imagej/plugins/
diff --git a/debian/patches/json-simple b/debian/patches/json-simple
deleted file mode 100644
index 097d359..0000000
--- a/debian/patches/json-simple
+++ /dev/null
@@ -1,38 +0,0 @@
-Description: Patch to link against Debian's libjson-simple-java package
-Author: Sebastien Jodogne <s.jodogne at gmail.com>
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
-Index: OrthancImageJ-1.1/CMakeLists.txt
-===================================================================
---- OrthancImageJ-1.1.orig/CMakeLists.txt
-+++ OrthancImageJ-1.1/CMakeLists.txt
-@@ -6,7 +6,7 @@ find_package(Java REQUIRED)
- include(UseJava)
-
- set(CMAKE_JAVA_COMPILE_FLAGS "-source" "1.6" "-target" "1.6")
--set(CMAKE_JAVA_INCLUDE_PATH /usr/share/java/ij.jar)
-+set(CMAKE_JAVA_INCLUDE_PATH /usr/share/java/ij.jar:/usr/share/java/json-simple.jar)
-
- # The name of an ImageJ plugin must contain an underscore
- # http://imagejdocu.tudor.lu/doku.php?id=howto:plugins:howto_create_an_imagej_plugin_jar_file
-@@ -19,20 +19,6 @@ add_jar(Orthanc_Import
- ${CMAKE_SOURCE_DIR}/com/orthancserver/PreviewPanel.java
- ${CMAKE_SOURCE_DIR}/com/orthancserver/SelectImageDialog.java
- ${CMAKE_SOURCE_DIR}/com/orthancserver/HttpsTrustModifier.java
--
-- # Sources of the "json-simple" toolkit
-- ${CMAKE_SOURCE_DIR}/org/json/simple/ItemList.java
-- ${CMAKE_SOURCE_DIR}/org/json/simple/JSONArray.java
-- ${CMAKE_SOURCE_DIR}/org/json/simple/JSONAware.java
-- ${CMAKE_SOURCE_DIR}/org/json/simple/JSONObject.java
-- ${CMAKE_SOURCE_DIR}/org/json/simple/JSONStreamAware.java
-- ${CMAKE_SOURCE_DIR}/org/json/simple/JSONValue.java
-- ${CMAKE_SOURCE_DIR}/org/json/simple/parser/ContainerFactory.java
-- ${CMAKE_SOURCE_DIR}/org/json/simple/parser/ContentHandler.java
-- ${CMAKE_SOURCE_DIR}/org/json/simple/parser/JSONParser.java
-- ${CMAKE_SOURCE_DIR}/org/json/simple/parser/ParseException.java
-- ${CMAKE_SOURCE_DIR}/org/json/simple/parser/Yylex.java
-- ${CMAKE_SOURCE_DIR}/org/json/simple/parser/Yytoken.java
- )
-
- # Add the "plugins.config" file that is expected by ImageJ in the JAR file
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index 33ce5e2..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1 +0,0 @@
-json-simple
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index 36e6248..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/make -f
-
-JSON_SIMPLE_JAR = /usr/share/java/json-simple.jar
-
-%:
- dh $@ --parallel --builddirectory=Build
-
-override_dh_auto_configure:
- dh_auto_configure -- -DCMAKE_JAVA_INCLUDE_PATH=${JSON_SIMPLE_JAR}
-
-override_dh_auto_install:
- dh_auto_install
- dh_link ${JSON_SIMPLE_JAR} usr/share/imagej/plugins/Orthanc_Import_json-simple.jar
-
-override_dh_installchangelogs:
- dh_installchangelogs -k NEWS
-
-get-orig-source:
- uscan --verbose --force-download --repack --compression xz
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
deleted file mode 100644
index 7cf8c15..0000000
--- a/debian/upstream/metadata
+++ /dev/null
@@ -1,6 +0,0 @@
-Reference:
- Author: S. Jodogne and C. Bernard and M. Devillers and E. Lenaerts and P. Coucke
- Title: "Orthanc -- A Lightweight, RESTful DICOM Server for Healthcare and Medical Research"
- Type: book
- Booktitle: Proc. of the International Symposium on Biomedical Imaging
- Year: 2013
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index 1407b5b..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,3 +0,0 @@
-version=3
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,downloadurlmangle=s/\/browse\.php\?path=//g,repack,compression=xz" \
-http://www.orthanc-server.com/browse.php?path=/imagej downloads/get\.php\?path=/imagej/OrthancImageJ-(\d\S*)\.tar\.gz
diff --git a/plugins.config b/plugins.config
new file mode 100644
index 0000000..cebd549
--- /dev/null
+++ b/plugins.config
@@ -0,0 +1 @@
+File>Import, "Orthanc", com.orthancserver.Orthanc
--
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