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annotate Sphinx/source/plugins/orthanc-explorer-2.rst @ 923:169568647bc6
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author | Alain Mazy <am@osimis.io> |
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date | Mon, 20 Mar 2023 13:32:26 +0100 |
parents | ce1fca061765 |
children | c9d2ae104b1b |
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845 | 1 .. _orthanc-explorer-2: |
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4 Orthanc Explorer 2 plugin | |
5 ========================= | |
6 | |
7 .. contents:: | |
8 | |
9 | |
10 Introduction | |
11 ------------ | |
12 | |
13 This plugin provides a new User Interface (UI) to Orthanc. It aims at being | |
14 more user-friendly, more configurable and more evolutive than the default | |
15 Orthanc UI which was developed mainly for testing/administrative purpose. | |
16 | |
17 .. image:: ../images/OE2-screenshot-study-list.png | |
18 :align: center | |
19 :width: 1000px | |
20 | |
21 | | |
22 | |
23 Note that a major difference between the legacy UI and Orthanc Explorer 2 (OE2) | |
24 is that OE2 works only at the study level, not the patient level. The main page is | |
25 the study list in which, of course, you can apply a filter to display only the studies of a single patient. | |
26 | |
922 | 27 Since version 0.7.0, once connected to `Keycloak <https://www.keycloak.org/>`__ and an external web service, OE2 is able to handle user permissions |
28 and sharing of links to access a single study. This is demonstrated in this TBD sample. | |
845 | 29 |
30 How to get it ? | |
31 --------------- | |
32 | |
33 The source code is available on `GitHub <https://github.com/orthanc-server/orthanc-explorer-2>`__. | |
34 | |
35 Binaries are included in: | |
36 | |
37 - The `osimis/orthanc Docker image <https://hub.docker.com/r/osimis/orthanc>`__ | |
38 - The `Windows Installer <https://orthanc.osimis.io/win-installer/OrthancInstaller-Win64-latest.exe>`__ (only for 64bits platform) | |
39 - The `MacOS packages <https://orthanc.osimis.io/osx/stable/orthancAndPluginsOSX.stable.zip>`__ | |
40 | |
41 Release notes are available `here <https://github.com/orthanc-server/orthanc-explorer-2/blob/master/release-notes.md>`__. | |
42 | |
43 Depending on the configuration, the plugin can replace the default Orthanc UI you are redirected to when accessing orthanc at `http://localhost:8042/ <http://localhost:8042/>`__. | |
44 In any case, the new and old UI can coexist: | |
45 | |
46 - Orthanc Explorer 2 is available at `http://localhost:8042/ui/app/ <http://localhost:8042/ui/app/>`__ | |
47 - Legacy UI remains available at `http://localhost:8042/app/explorer.html <http://localhost:8042/app/explorer.html>`__ | |
48 | |
49 | |
50 Configuration | |
51 ------------- | |
52 | |
53 .. highlight:: json | |
54 | |
55 The plugin must be configured through a configuration file. The minimal configuration to include in your orthanc configuration file is:: | |
56 | |
57 "OrthancExplorer2" : { | |
58 "Enable": true, | |
59 "IsDefaultOrthancUI": true | |
60 } | |
61 | |
62 There are many more options that are documented in the | |
63 `default configuration file <https://github.com/orthanc-server/orthanc-explorer-2/blob/master/Plugin/DefaultConfiguration.json>`__. | |
64 | |
65 Main features you can configure: | |
66 | |
67 - Root URL | |
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faq: Can the Stone Web Viewer display DICOM-SR
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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68 - Whether OE2 becomes the default Orthanc UI |
845 | 69 - Configure the side menu |
70 - Configure the actions available on the resources | |
71 - Configure the columns of the main study list | |
922 | 72 - Configure `Keycloak <https://www.keycloak.org/>`__ integration and :ref:`authorization plugin <authorization>` |
845 | 73 |
74 | |
75 Advanced features | |
76 ----------------- | |
77 | |
915 | 78 |
79 Direct access to a selection of studies | |
80 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
81 | |
845 | 82 You may open the OE2 interface directly on a specific study or patient by specifying DICOM Tags directly in the URL. |
83 e.g:: | |
84 | |
869 | 85 http://localhost:8042/ui/app/#/filtered-studies?PatientID="00000169" |
845 | 86 http://localhost:8042/ui/app/#/filtered-studies?StudyDate=20220512-20220513&ModalitiesInStudy=CR\DX |
869 | 87 http://localhost:8042/ui/app/#/filtered-studies?StudyInstanceUID="1.2.3" |
88 http://localhost:8042/ui/app/#/filtered-studies?StudyInstanceUID="1.2.3"&expand | |
89 http://localhost:8042/ui/app/#/filtered-studies?StudyInstanceUID="1.2.3"&expand=study | |
90 http://localhost:8042/ui/app/#/filtered-studies?StudyInstanceUID="1.2.3"&expand=series | |
91 | |
92 By default, OE2 will add a wildcard ``*`` at the beginning and at the end of the search text. Therefore, searching | |
93 for ``PatientID=1234`` will actually search for ``PatientID=*1234*``. If you do not want to have these extra wildcards | |
94 added, you should use ``"`` at the beginning and/or at the end of the search text. Therefore, searching for | |
95 ``PatientID="1234"`` will return only the studies whose ``PatientID`` is exactly ``1234``. | |
96 These ``"`` can also be used in the User Interface search fields. | |
845 | 97 |
98 | |
915 | 99 DICOM Modifications |
100 ^^^^^^^^^^^^^^^^^^^ | |
101 | |
102 Since version 0.6.0, it is possible to edit some of the DICOM Tags directly in the User Interface. | |
103 :ref:`DICOM Modification <anonymization>` is quite a complex topic that is provided by Orthanc | |
104 Rest API. The Orthanc Explorer 2 User Interface aims at simplifying its use but is also limiting | |
105 it to common use cases mainly related to correcting errors in Patient and Study DICOM Tags. | |
106 | |
107 At study level, it is possible to: | |
108 | |
109 - Modify a Study | |
110 | |
111 - to attach it to another existing patient by providing the ``PatientID`` if e.g. the study was | |
112 acquired for the wrong patient. | |
113 - to edit the patient in all its studies if e.g. the ``PatientName`` was misspelled. | |
114 - correct patient or study tags in this study only if e.g. the ``StudyDescription`` was incorrect. | |
115 | |
116 - Anonymize a Study and possibly provide the anonymized ``PatientID`` or ``PatientName`` to | |
117 e.g. force it to a specific identifier for a clinical study. | |
118 | |
119 .. image:: ../images/OE2-modify-study.png | |
120 :align: center | |
121 :width: 1000px | |
122 | |
123 | | |
124 | |
125 | |
126 At series level, it is possible to: | |
127 | |
128 - Modify a Series | |
129 | |
130 - to move it to another existing study by providing the ``StudyInstanceUID`` if e.g. the operator | |
131 forgot to switch patient in the modality | |
132 - to move it to a new study if e.g. the operator forgot to switch patient in the modality | |
133 - correct series tags in this series only if e.g. the ``SeriesDescription`` was incorrect. | |
134 | |
135 - Anonymize a Series and possibly provide the anonymized ``PatientID`` or ``PatientName`` to | |
136 e.g. force it to a specific identifier for a clinical study. | |
137 | |
138 .. image:: ../images/OE2-modify-series.png | |
139 :align: center | |
140 :width: 1000px | |
141 | |
142 | | |
143 | |
144 Each time you modify a study, the user interface might propose you 3 modification modes related to | |
145 the handling of the :ref:`DICOM identifiers <dicom-identifiers>` . | |
146 | |
147 - You may modify the original study and have Orthanc generates new ``StudyInstanceUID``, ``SeriesInstanceUID`` | |
148 and ``SOPInstanceUID`` DICOM Tags. This means the that orthanc identifiers will change and the source | |
149 study will be deleted. | |
150 - You may keep the original ``StudyInstanceUID``, ``SeriesInstanceUID`` and ``SOPInstanceUID`` DICOM Tags. | |
151 This means the that orthanc identifiers will not change (unless you also change the ``PatientID`` and the | |
916 | 152 study will be modified "in place"). |
915 | 153 - You may keep the original study and create a modified copy. In this case, of course, the new modified copy |
154 will have a different orthanc identifiers. | |
155 | |
156 | |
157 .. image:: ../images/OE2-modify-options.png | |
158 :align: center | |
159 :width: 700px | |
160 | |
161 | | |
162 | |
163 There are many options related to DICOM Modification in the plugin | |
164 `default configuration file <https://github.com/orthanc-server/orthanc-explorer-2/blob/master/Plugin/DefaultConfiguration.json>`__. | |
165 Check the ``Modifications`` section and the ``PatientMainTags``, ``StudyMainTags``, ``SeriesMainTags``, ``EnableAnonymization`` | |
166 and ``EnableModification`` configurations. | |
167 | |
168 | |
922 | 169 Retrieve a study from a distant modality and open the viewer |
170 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
845 | 171 |
922 | 172 If you want to open e.g. the :ref:`Stone Web viewer <stone_webviewer>`:: on a study that is not yet |
173 stored in Orthanc but that you know that it is stored in a remote modality, you may use this endpoint:: | |
174 | |
923 | 175 http://localhost:8042/ui/app/retrieve-and-view.html?StudyInstanceUID=1.2.3....&modality=pacs&viewer=stone-viewer |
845 | 176 |
922 | 177 This will first check if the study is already in Orthanc, if not, it will retrieve it from the modality and, |
178 once the transfer is complete, open the viewer. | |
845 | 179 |
922 | 180 This feature has been introduced in v 0.7.0. |
845 | 181 |
182 | |
183 Bug reports & support | |
184 --------------------- | |
185 | |
186 As usual, you can get support and report issues from the `Orthanc Users group <https://groups.google.com/g/orthanc-users>`__. | |
187 | |
188 You may also directly introduce bugs or feature requests in `GitHub <https://github.com/orthanc-server/orthanc-explorer-2/issues>`__. | |
189 | |
922 | 190 The plugin is currently maintained by the `Orthanc Team <https://orthanc.team/>`__ who, like many of you, enjoys |
191 receiving a salary for his work. Feel free to hire us if you need a specific feature or bug fixed. | |
845 | 192 |
193 Donations to `Open Collective <https://opencollective.com/orthanc>`__ may also be used to maintain/develop this plugin. |