Mercurial > hg > orthanc-book

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correct extensions of Nexus
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 22 May 2024 17:08:31 +0200
parents 55c44a245b09
children 4df0d8c542f2
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1 .. _stl-plugin:
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4 STL plugin for Orthanc
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5 ======================
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6
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7 .. contents::
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8
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9
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10 Overview
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11 --------
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13 This **official** plugin by the `ICTEAM institute of UCLouvain
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14 <https://orthanc.uclouvain.be/>`__ extends Orthanc with support for
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15 `Encapsulated 3D Manufacturing Model IODs
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16 <https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.85.html>`_.
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17 As of release 1.0 of the plugin, this support is limited to `STL files
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18 <https://en.wikipedia.org/wiki/STL_(file_format)>`__.
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19
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20 The plugin allows to attach STL files to existing DICOM studies and to
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21 generate a STL mesh from structure sets (i.e., DICOM RT-STRUCT) or
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22 from `NIfTI binary volumes
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23 <https://en.wikipedia.org/wiki/Neuroimaging_Informatics_Technology_Initiative>`__.
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24 A high-level description of these features is `available as a paper
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25 <https://doi.org/10.1145/3632047.3632051>`__.
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26
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27 Importantly, any creation of a STL file requires the version of
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28 Orthanc to be above or equal to 1.12.1.
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29
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30 **For researchers**: `Please cite this paper
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31 <https://doi.org/10.1145/3632047.3632051>`__.
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34 Compilation
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35 -----------
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36
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37 .. highlight:: bash
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38
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39 Official releases can be `downloaded from the Orthanc homepage
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40 <https://orthanc.uclouvain.be/downloads/sources/orthanc-stl/index.html>`__. As
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41 an alternative, the `repository containing the source code
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42 <https://orthanc.uclouvain.be/hg/orthanc-stl/>`__ can be accessed
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43 using Mercurial.
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44
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45 The procedure to compile this plugin is similar of that for the
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46 :ref:`core of Orthanc <binaries>`. The following commands should work
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47 on most GNU/Linux distributions, provided Docker is installed::
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48
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49 $ mkdir Build
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50 $ cd Build
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51 $ ../Resources/CreateJavaScriptLibraries.sh
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52 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
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53 $ make
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54
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55 The compilation will produce a shared library ``libOrthancSTL.so``
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56 that contains the STL plugin for Orthanc.
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57
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58 Pre-compiled Linux Standard Base (LSB) binaries `are available for
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59 download <https://orthanc.uclouvain.be/downloads/linux-standard-base/orthanc-stl/index.html>`__.
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60
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61 Pre-compiled binaries for `Microsoft Windows <https://orthanc.uclouvain.be/downloads/windows-32/orthanc-stl/index.html>`__
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62 and `macOS <https://orthanc.uclouvain.be/downloads/macos/orthanc-stl/index.html>`__ are available as well.
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63
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64 Furthermore, the :ref:`Docker images <docker>`
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65 ``jodogne/orthanc-plugins`` and ``orthancteam/orthanc`` also contain the
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66 plugin. Debian and Ubuntu packages can be found in the
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67 :ref:`standalone repository <binaries>`
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68 ``https://debian.orthanc-labs.com/``.
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69
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70
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71 .. _stl_orthanc_explorer:
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72
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73 Usage using Orthanc Explorer
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74 ----------------------------
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75
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76 The plugin extends the default :ref:`Orthanc Explorer
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77 <orthanc-explorer>` Web interface with some new features.
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78
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79
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80 .. _stl_attach:
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81
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82 Attach STL file
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83 ^^^^^^^^^^^^^^^
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84
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85 An existing STL file can be attached to an existing DICOM study by
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86 clicking on the "*Attach STL model*" yellow button:
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87
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88 .. image:: stl/attach.png
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89 :align: center
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90 :width: 480
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91
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92 After selecting the STL file, entering a series description, and
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93 clicking on the "*Import*" button, Orthanc creates a new DICOM
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94 instance that embeds the STL file. Orthanc Explorer then automatically
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95 opens the parent DICOM series containing the newly created DICOM STL
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96 instance. A button entitled "*STL viewer*" can then be used to render
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97 the STL:
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98
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99 .. image:: stl/viewers.png
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100 :align: center
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101 :width: 480
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102
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103 Note how the STL plugin provides two viewers:
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104
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105 * One `very basic custom viewer
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106 <https://orthanc.uclouvain.be/hg/orthanc-stl/file/OrthancSTL-1.0/WebApplications/three.js>`__
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107 with a small footprint that is directly built using the well-known
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108 `Three.js library <https://en.wikipedia.org/wiki/Three.js>`__.
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109
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110 * One slightly more advanced Web viewer that corresponds to `Online 3D
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111 Viewer <https://github.com/kovacsv/Online3DViewer>`__ running in
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112 `engine mode
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113 <https://kovacsv.github.io/Online3DViewer/Page_Usage.html>`__.
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114
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115 Here is a screenshot of a rendering using the Online3DViewer embedded
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116 viewer:
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117
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118 .. image:: stl/o3dv.png
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119 :align: center
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120 :width: 480
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121
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122
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123 .. _stl_rt_struct:
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124
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125 Create STL from RT-STRUCT
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126 ^^^^^^^^^^^^^^^^^^^^^^^^^
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127
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128 The plugin can also be used to create a STL model from DICOM structure
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129 sets (RT-STRUCT) that are routinely used in the context of
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130 radiotherapy and nuclear medicine. To this end, open a DICOM RT-STRUCT
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131 series using Orthanc Explorer:
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132
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133 .. image:: stl/rt-struct.png
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134 :align: center
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135 :width: 480
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136
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137 As can be seen in this screenshot, an interface opens to choose the
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138 structure set of interest, as well as the resolution of the
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139 intermediate 3D bitmap that will be used to create the STL mesh. After
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140 clicking on the "*Generate*" button, just like if :ref:`attaching an
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141 existing STL file <stl_attach>`, Orthanc Explorer will open the newly
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142 created DICOM series and will propose to open a STL viewer.
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143
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144 Internally, the 3D model is generated using the well-known `marching
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145 cubes algorithm <https://en.wikipedia.org/wiki/Marching_cubes>`__, as
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146 implemented by the `VTK library <https://en.wikipedia.org/wiki/VTK>`__
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147 by Kitware. Additional technical details can be found in the
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148 `reference paper <https://doi.org/10.1145/3632047.3632051>`__.
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149
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150
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151 Create STL from binary NIfTI
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152 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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153
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154 .. highlight:: json
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155
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156 Besides converting :ref:`RT-STRUCT to STL <stl_rt_struct>`, it is also
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157 possible to convert a `NIfTI
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158 <https://en.wikipedia.org/wiki/Neuroimaging_Informatics_Technology_Initiative>`__
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159 3D binary bitmap into a STL mesh. As this use case is very specific,
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160 it must be explicitly enabled in the :ref:`configuration file of
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161 Orthanc <configuration>` as follows::
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162
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163 {
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164 "Plugins" : [ "libOrthancSTL.so" ],
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165 "STL" : {
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166 "EnableNIfTI" : true
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167 }
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168 }
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169
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170 If the ``EnableNIfTI`` option is present, a new button entitled
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171 "*Attach NIfTI 3D model*" appears if opening an existing DICOM study:
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172
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173 .. image:: stl/nifti.png
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174 :align: center
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175 :width: 480
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176
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177 This dialog box can be used to upload a NIfTI volume, and to generate
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178 a 3D mesh with a specific resolution through the marching cubes
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179 algorithm.
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180
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181
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182 REST API
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183 --------
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184
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185 Besides :ref:`extending the Orthanc Explorer user interface
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186 <stl_orthanc_explorer>`, the STL plugin adds dedicated routes to the
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187 REST API of Orthanc.
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188
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189
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190 DICOM-ization of STL files
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191 ^^^^^^^^^^^^^^^^^^^^^^^^^^
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192
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193 The creation of a DICOM instance that embeds an existing STL file can
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194 be done using the ``/tools/create-dicom`` `route
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195 <https://orthanc.uclouvain.be/api/#tag/System/paths/~1tools~1create-dicom/post>`__
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196 in the built-in REST API of Orthanc (starting with version
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197 1.12.1). This route can be used similarly to the :ref:`DICOM-ization
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198 of PDF files <pdf>`, with the `data URI scheme
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199 <https://en.wikipedia.org/wiki/Data_URI_scheme>`__ using ``model/stl``
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200 instead of ``application/pdf``. Here is a working example in Python 3:
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201
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202 .. literalinclude:: stl/dicomize.py
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203 :language: python
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204
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205 Note that if the ``Parent`` field is not provided, a new DICOM study
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206 will be created.
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207
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208
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209 Extraction of STL from DICOM
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210 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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211
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212 .. highlight:: txt
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213
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214 The route ``/instances/{id}/stl`` can be used to extract a STL from a
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215 DICOM instance embedding a STL file, where ``id`` is the :ref:`Orthanc
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216 identifier <orthanc-ids>` of the DICOM instance. For instance::
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217
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218 $ curl http://localhost:8042/instances/a88c4c3f-8f2bd6fd-02080bed-92ab6817-2cb3c26e/stl > /tmp/liver.stl
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219 $ meshlab /tmp/liver.stl
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220
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221 Evidently, an error is generated for DICOM instances that do not embed
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222 a STL file. Note that ``meshlab`` is a well-known desktop application
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223 to display STL file.
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224
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225
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226 Listing structures of a DICOM RT-STRUCT
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227 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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228
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229 .. highlight:: txt
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230
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231 The STL plugin provides the list of the names of the structures that
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232 are part of a DICOM RT-STRUCT instance with :ref:`Orthanc identifier
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233 <orthanc-ids>` ``id`` at route ``/stl/rt-struct/{id}``. For instance::
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234
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235 $ curl http://localhost:8042/stl/rt-struct/f0dc2345-8f627774-f66083ae-a14d781e-1187b513
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236 [
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237 "Esophagus",
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238 "Heart",
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239 "Lung_L",
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240 "Lung_R",
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241 "SpinalCord"
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242 ]
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243
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244
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245 Generating a STL mesh from RT-STRUCT
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246 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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247
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248 A DICOM RT-STRUCT instance can be converted into a DICOM STL instance
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249 using the ``/stl/encode-rtstruct`` route provided by the STL plugin.
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250 Here is a sample Python script:
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251
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252 .. literalinclude:: stl/rt-struct.py
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253 :language: python
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254
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255 Note that contrarily to :ref:`the default user interface
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256 <stl_rt_struct>`, this route can be used to encode multiple structure
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257 sets as a single STL model.
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258
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259
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260 Generating a STL mesh from NIfTI
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261 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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262
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263 Here is a sample Python 3 script to convert a NIfTI file as a DICOM
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264 STL instance:
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265
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266 .. literalinclude:: stl/nifti.py
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267 :language: python
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268
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269
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270 Support for Nexus
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271 -----------------
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272
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273 Starting with release 1.1, the STL plugin provides support for the
1071
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274 DICOM-ization of 3D models encoded using the `Nexus file format (.NXS
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275 and .NXZ extensions) <https://vcg.isti.cnr.it/nexus/>`__. Nexus
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276 provides a way to publish large, **textured 3D models** over Internet,
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277 with **adaptive rendering** depending on the available network
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278 bandwidth. Nexus is notably popular for the preservation of **cultural
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279 heritage**.
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280
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281
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282 The plugin ships the static HTML/CSS/JavaScript assets of the official
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283 Nexus Web viewer, so that it can easily be opened right from Orthanc
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284 Explorer, as depicted in the following screenshot:
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285
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286 .. image:: stl/nexus.png
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287 :align: center
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288 :width: 800
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289
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290
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291 Internals
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292 ^^^^^^^^^
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293
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294 Because Nexus is not endorsed by the DICOM specification, the plugin
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295 encapsulates the Nexus file using the `Raw Data IOD
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296 <https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.37.3.html>`__.
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297 The Nexus file is encoded as the ``(0x4205,0x1001)`` private DICOM
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298 tag.
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299
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300
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301 Configuration
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302 ^^^^^^^^^^^^^
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303
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304 .. highlight:: json
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305
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306 As it is non-standard, support for Nexus must be explicitly enabled in
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307 the configuration file of Orthanc as follows::
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308
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309 {
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310 "Plugins" : [ "libOrthancSTL.so" ],
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311 "STL" : {
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312 "EnableNexus" : true
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313 }
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314 }
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315
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316
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317 REST API
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318 ^^^^^^^^
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319
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320 The STL plugin extends the REST API with two routes that are dedicated
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321 to the handling of Nexus files:
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322
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323 1. ``/stl/create-nexus`` can be used to DICOM-ize a Nexus file. This
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324 route is a wrapper around the ``/tools/create-dicom``
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325 :ref:`standard route of Orthanc <image-dicomization>`. The Nexus
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326 file must be provided as a `Base64 string
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327 <https://en.wikipedia.org/wiki/Base64>`__ in the ``Content`` field
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328 of the request. Here is a sample Python script::
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329
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330 .. literalinclude:: stl/nexus.py
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331 :language: python
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332
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333 2. ``/instances/{id}/nexus`` provides access to a DICOM-ized Nexus
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334 file by decapsulating it from the DICOM instance whose
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335 :ref:`Orthanc identifier <orthanc-identifiers>` is
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336 ``id``. Importantly, this route supports `HTTP range requests
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337 <https://developer.mozilla.org/en-US/docs/Web/HTTP/Range_requests>`__
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338 for adaptive streaming of Nexus models over Internet.