annotate Sphinx/source/users/cookbook.rst @ 358:011b01ccf52d

fixing external hyperlinks
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 30 Mar 2020 18:47:35 +0200
parents 8aa416899db4
children 987fbbc2b59e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1 .. highlight:: bash
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
2 .. _cookbook:
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
3
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
4 Quickstart
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
5 ==========
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
6
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
7 .. contents::
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
8 :depth: 2
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
9
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
10
31
93bbfaf0e62c worklist instructions migrated to a specific page, indexing of Osimis Web viewer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 28
diff changeset
11 .. _binaries:
28
dc235678897c webviewer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 26
diff changeset
12
0
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
13 Obtaining binaries
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
14 ------------------
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
15
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
16 To obtain the Orthanc binaries, you have several possibilities:
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
17
358
011b01ccf52d fixing external hyperlinks
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 292
diff changeset
18 * `Download pre-compiled packages <https://www.orthanc-server.com/download.php>`__.
54
bd0fbf1f0143 docker documentation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
19 * :ref:`Use Docker <docker>`.
292
8aa416899db4 added a tuto to connect a modality to Orthanc
Alain Mazy <alain@mazy.be>
parents: 54
diff changeset
20 * :ref:`Compile Orthanc by yourself <compiling>`.
26
7f98cfa8708f docker, upload issue
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
21 * External contributors are also maintaining `Vagrant VM for Orthanc
358
011b01ccf52d fixing external hyperlinks
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 292
diff changeset
22 <https://github.com/jodogne/OrthancContributed/blob/master/Links.md#user-content-vagrant>`__.
0
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
23
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
24
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
25 .. _orthanc-explorer:
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
26
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
27 Opening Orthanc Explorer
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
28 ------------------------
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
29
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
30 The most straightforward way to use Orthanc consists in opening
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
31 **Orthanc Explorer**, the embedded administrative interface of
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
32 Orthanc, with a Web browser. Once Orthanc is running, open the
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
33 following URL: http://localhost:8042/app/explorer.html. Please note
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
34 that:
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
35
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
36 * The port number 8042 depends on your :ref:`configuration
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
37 <configuration>`.
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
38 * Orthanc Explorer does not work with Microsoft Internet
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
39 Explorer. Please use Mozilla Firefox, Google Chrome, Apple Safari,
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
40 or `any WebKit-based Web browser <https://en.wikipedia.org/wiki/WebKit>`__.
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
41
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
42
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
43 Uploading DICOM files
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
44 ---------------------
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
45
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
46 The Orthanc Explorer interface contains a user-friendly page to upload
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
47 DICOM files. You can reach the upload page at
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
48 http://localhost:8042/app/explorer.html#upload. Then, you can drag and
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
49 drop your DICOM files and click on the Upload button.
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
50
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
51 You can `watch this video tutorial
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
52 <https://www.youtube.com/watch?v=4dOcXGMlcFo&hd=1>`__ that shows how
26
7f98cfa8708f docker, upload issue
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
53 to upload files to Orthanc through Orthanc Explorer with Chromium.
7f98cfa8708f docker, upload issue
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
54
7f98cfa8708f docker, upload issue
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
55 **Important:** There is currently a `known issue
7f98cfa8708f docker, upload issue
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
56 <https://bitbucket.org/sjodogne/orthanc/issues/21/dicom-files-missing-after-uploading-with>`__
7f98cfa8708f docker, upload issue
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
57 that prevents Mozilla Firefox to correctly upload all DICOM files.
0
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
58
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
59
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
60 Uploading through the DICOM protocol
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
61 ------------------------------------
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
62
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
63 Once Orthanc is up and running, any imaging modality can send
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
64 instances to Orthanc through the DICOM protocol (with the C-Store
292
8aa416899db4 added a tuto to connect a modality to Orthanc
Alain Mazy <alain@mazy.be>
parents: 54
diff changeset
65 command). Check :ref:`this tutorial <configure-modality>` to
8aa416899db4 added a tuto to connect a modality to Orthanc
Alain Mazy <alain@mazy.be>
parents: 54
diff changeset
66 connect your modality to Orthanc.
0
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
67
292
8aa416899db4 added a tuto to connect a modality to Orthanc
Alain Mazy <alain@mazy.be>
parents: 54
diff changeset
68 You can also use the standard command-line tool ``storescu`` from the
358
011b01ccf52d fixing external hyperlinks
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 292
diff changeset
69 `DCMTK software <https://dicom.offis.de/dcmtk.php.en>`__ to manually
011b01ccf52d fixing external hyperlinks
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 292
diff changeset
70 send DICOM images to Orthanc, for instance::
0
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
71
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
72 $ storescu -aec ORTHANC localhost 4242 *.dcm
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
73
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
74 will send all the files with ".dcm" extension to the instance of
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
75 Orthanc that is running on the ``localhost``, whose application entity
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
76 title (AET) is ``ORTHANC``, and whose DICOM port is
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
77 ``4242``. Obviously, all these parameters depend on your
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
78 :ref:`configuration <configuration>`. Please check the :ref:`FAQ
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
79 <dicom>` if you encounter any problem.
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
80
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
81
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
82 Next steps
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
83 ----------
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
84
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
85 1. Read the general introduction ":ref:`dicom-guide`".
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
86 2. Have a look at your :ref:`configuration file <configuration>`.
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
87 3. Drive Orthanc through its :ref:`REST API <rest>`.
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
88 4. Automate DICOM tasks with :ref:`Lua scripts <lua>`.
901e8961f46e initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
89