annotate Applications/Samples/README.md @ 1953:0661115af939 deep-learning

first successful application of deep learning
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 16 Aug 2022 15:05:51 +0200
parents 9b69970fbdb5
children 5653b6335642
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1 General
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2 =======
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3 These samples assume that a recent version of Orthanc is checked out in an
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4 `orthanc` folder next to the `orthanc-stone` folder. Let's call the top folder
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5 the `devroot` folder. This name does not matter and is not used anywhere.
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6
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7 Here's the directory layout that we suggest:
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8
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9 ```
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10 devroot/
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11 |
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12 +- orthanc/
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13 |
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14 +- orthanc-stone/
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15 |
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16 ...
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17 ```
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18
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19 Orthanc can be retrieved with:
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20 ```
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21 hg clone https://hg.orthanc-server.com/orthanc
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22 ```
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23
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24 Furthermore, the samples usually assume that an Orthanc is running locally,
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25 without authentication, on port 8042. The samples can easily be tweaked if
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26 your setup is different.
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27
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28 When Dicom resources are to be displayed, their IDs can be supplied in the
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29 various ways suitable for the platform (command-line arguments, URL parameters
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30 or through the GUI)
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31
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33 This repo contains two sample projects:
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35 SingleFrameViewer
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36 -----------------
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38 This sample application displays a single frame of a Dicom instance that can
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39 be loaded from Orthanc, either by using the Orthanc REST API or through the
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40 Dicomweb server functionality of Orthanc.
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41
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42 RtViewer
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43 --------
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44
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45 This sample application displays set of Radiotherapy data:
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46 - a CT scan
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47 - an RT-Dose
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48 - an RT-Struct
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49
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50 The WebAssembly version displays 3 viewports with MPR data
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51 while the SDL sample displays a single viewport.
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54 WebAssembly samples
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55 ===================
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56
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57 Building the WebAssembly samples require the Emscripten SDK
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58 (https://emscripten.org/). This SDK goes far beyond the simple compilation to
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59 the wasm (Web Assembly) bytecode and provides a comprehensive library that
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60 eases porting native C and C++ programs and libraries. The Emscripten SDK also
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61 makes it easy to generate the companion Javascript files requires to use a
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62 wasm module in a web application.
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63
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64 Although Emscripten runs on all major platforms, Stone of Orthanc is developed
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65 and tested with the Linux version of Emscripten.
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66
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67 Emscripten runs perfectly fine under the Windows Subsystem for Linux (that is
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68 the environment used quite often by the Stone of Orthanc team)
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69
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70 **Important note:** The following examples **and the build scripts** will
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71 assume that you have installed the Emscripten SDK in `~/apps/emsdk`.
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72
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73 The following packages should get you going (a Debian-like distribution such
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74 as Debian or Ubuntu is assumed)
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75
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76 ```
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77 sudo apt-get update
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78 sudo apt-get install -y build-essential curl wget git python cmake pkg-config
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79 sudo apt-get install -y mercurial unzip npm ninja-build p7zip-full gettext-base
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80 ```
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81
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82 To build the Wasm samples, just launch the `build-wasm-samples.sh` script from
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83 this folder. Optionaly, you can pass the build type as an argument.
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84 We suggest that you do *not* use the `Debug` configuration unless you really
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85 need it, for the additional checks that are made will lead to a very long
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86 build time and much slower execution (more severe than with a native non-wasm
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87 target)
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88
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89 In order to run the sample, you may serve it with the ServeFolders plugin.
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90 You can i.e: add such a section in your orthanc configuration file:
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91
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92 ```
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93 {
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94 "Plugins" : ["LibServeFolders.so],
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95 "ServeFolders" : {
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96 "/single-frame-viewer" : "..../out/install-stone-wasm-samples-RelWithDebInfo/SingleFrameViewer",
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97 "/rt-viewer": "..../out/install-stone-wasm-samples-RelWithDebInfo/RtViewer"
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98 }
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99 }
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100 ```
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101
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102 You'll then be able to open the single-frame-viewer demo at `http://localhost:8042/single-frame-viewer/index.html`
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103
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104 The rt-viewer demo at
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105 `http://localhost:8044/rt-viewer/index.html?ctseries=a04ecf01-79b2fc33-58239f7e-ad9db983-28e81afa&rtdose=eac822ef-a395f94e-e8121fe0-8411fef8-1f7bffad&rtstruct=54460695-ba3885ee-ddf61ac0-f028e31d-a6e474d9`. Note that you must provide 3 ids in the url:
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106
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107 - the CT series Orthanc ID
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108 - the RT-Dose instance Orthanc ID
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109 - the RT-Struct instance Orthanc ID
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110
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111
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112 RtViewer
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113 -----------------
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114
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115 This sample application displays three MPR views of a CT+RTDOSE+RTSTRUCT dataset, loaded from Orthanc. The Orthanc IDs of the dataset must be supplied as URL parameters like:
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116
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117 ```
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118 http://localhost:9979/stone-rtviewer/index.html?loglevel=info&ctseries=a04ecf01-79b2fc33-58239f7e-ad9db983-28e81afa&rtdose=830a69ff-8e4b5ee3-b7f966c8-bccc20fb-d322dceb&rtstruct=54460695-ba3885ee-ddf61ac0-f028e31d-a6e474d9
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119 ```
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120
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121 (notice the loglevel parameter that can be `warning`, `info` or `trace`, in increasing verbosity order)
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122
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123 This sample uses plain Javascript and requires the
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124 Emscripten toolchain and cmake, in addition to a few standard packages.
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125
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126 To build it, just launch the `build-wasm-RtViewer.sh` script from
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127 this folder. Optionaly, you can pass the build type as an argument.
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128 We suggest that you do *not* use the `Debug` configuration unless you really
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129 need it, for the additional checks that are made will lead to a very long
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130 build time and much slower execution (more severe than with a native non-wasm
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131 target)
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132
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133 In order to run the sample, you may serve it with the ServeFolders plugin.
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134 You can i.e: add such a section in your orthanc configuration file:
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135
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136 ```
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137 {
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138 "Plugins" : ["LibServeFolders.so],
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139 "ServeFolders" : {
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140 "/rt-viewer" : "..../out/install-stone-wasm-RtViewer-RelWithDebInfo"
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141 }
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142 }
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143 ```
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144
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145 You'll then be able to open the demo at `http://localhost:8042/rt-viewer/index.html`
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146
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147
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148 RtViewerPlugin
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149 ---------------
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150 This C++ plugin allows to extend the Orthanc Explorer to add a button labeled "Stone RT Viewer"
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151 in the series page.
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152
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153 It also embeds and serves the RT Viewer files and is thus a standalone way of using this viewer.
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154
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155 Please note that building this plugin requires that the RtViewer be built inside the wasm-binaries
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156 folder of the repo.
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157
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158 This will automatically be the case if you use the `<REPO-ROOT>/OrthancStone/Samples/WebAssembly/docker-build.sh` script.
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159
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160 If you use the `build-wasm-samples.sh` script above, you will have the copy `RtViewer` **folder**
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161 from `<REPO-ROOT>/out/install-stone-wasm-RtViewer-RelWithDebInfo` to `<REPO-ROOT>/wasm-binaries/`.
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162
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163 TL;DR: Build like this (assuming `~/orthanc-stone` is the repo ):
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164
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165 ```
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166 ~/orthanc-stone/OrthancStone/Samples/WebAssembly/docker-build.sh
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167 ~/orthanc-stone/OrthancStone/Samples/RtViewerPlugin/docker-build.sh
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168 ```
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169
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170 Once this is done, the plugin can be found in:
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171
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172 ```
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173 ~/orthanc-stone/wasm-binaries/share/orthanc/plugins/libRtViewerPlugin.so
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174 ```
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175
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176 Add this path to the `"Plugins"` section of your Orthanc configuration, start Orthanc, and you
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177 should now see a "Stone MPR RT Viewer" button in the Orthanc Explorer, at the *series* level.
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178
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179 Open it on a CT series, and the RTSTRUCT and RTDOSE series of the same study will be loaded in
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180 the viewer.
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181
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182 Native samples
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183 =================
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184
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185 ### Windows build
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186
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187 Here's how to build the SdlSimpleViewer example using Visual Studio 2019
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188 (the shell is Powershell, but the legacy shell can also be used with some
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189 tweaks). This example is meant to be launched from the folder above
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190 orthanc-stone.
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191
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192 ```
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193 # create the build folder and navigate to it
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194 $buildDir = "build-stone-sdlviewer-msvc16-x64"
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195
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196 if (-not (Test-Path $buildDir)) {
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197 mkdir -p $buildDir | Out-Null
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198 }
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199
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200 cd $buildDir
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201
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202 # perform the configuration
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203 cmake -G "Visual Studio 16 2019" -A x64 `
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204 -DMSVC_MULTIPLE_PROCESSES=ON `
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205 -DALLOW_DOWNLOADS=ON `
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206 -DSTATIC_BUILD=ON `
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207 -DOPENSSL_NO_CAPIENG=ON `
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208 ../orthanc-stone/OrthancStone/Samples/Sdl
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209
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210 $solutionPath = ls -filter *.sln
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211 Write-Host "Solution file(s) available at: $solutionPath"
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212 ```
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213
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214 The initial configuration step will be quite lengthy, for CMake needs to
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215 setup its internal cache based on your environment and build tools.
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216
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217 Subsequent runs will be several orders of magnitude faster!
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218
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219 One the solution (.sln) file is ready, you can open it using the Visual Studio
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220 IDE and choose Build --> Build solution.
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221
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222 An alternative is to execute `cmake --build .` in the build folder created by
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223 the script.
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224
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225 In order to run the sample, make sure you've an Orthanc server running i.e. on
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226 port 8042 and launch:
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227
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228 ```
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229 ./SdlSimpleViewer --orthanc http://localhost:8042 --instance 7fc84013-abef174e-3354ca83-b9cdb2a4-f1a74368
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230
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231 ./RtViewerSdl --orthanc http://localhost:8042 --ctseries a04ecf01-79b2fc33-58239f7e-ad9db983-28e81afa --rtdose 830a69ff-8e4b5ee3-b7f966c8-bccc20fb-d322dceb --rtstruct 54460695-ba3885ee-ddf61ac0-f028e31d-a6e474d9
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232 ```
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233
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234
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235 RtViewer
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236 ---------------
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237
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238 ### Windows build
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239
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240 Here's how to build the SdlSimpleViewer example using Visual Studio 2019
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241 (the shell is Powershell, but the legacy shell can also be used with some
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242 tweaks). This example is meant to be launched from the folder above
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243 orthanc-stone.
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244
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245 ```
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246 $buildRootDir = "out"
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247 $buildDirName = "build-stone-sdl-RtViewer-msvc16-x64"
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248 $buildDir = Join-Path -Path $buildRootDir -ChildPath $buildDirName
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249
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250 if (-not (Test-Path $buildDir)) {
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251 mkdir -p $buildDir | Out-Null
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252 }
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253
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254 cd $buildDir
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255
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256 cmake -G "Visual Studio 16 2019" -A x64 `
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257 -DMSVC_MULTIPLE_PROCESSES=ON `
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258 -DALLOW_DOWNLOADS=ON `
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259 -DSTATIC_BUILD=ON `
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260 -DOPENSSL_NO_CAPIENG=ON `
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261 ../../orthanc-stone/OrthancStone/Samples/Sdl/RtViewer
1406
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262 ```
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263
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264 Executing `cmake --build .` in the build folder will launch the Microsoft
5d7ee14dc1eb Mouse wheel handler is now OK in SDL and Wasm
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265 builder on the solution.
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266
5d7ee14dc1eb Mouse wheel handler is now OK in SDL and Wasm
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267 Alternatively, you can open and build the solution using Visual Studio 2019.
5d7ee14dc1eb Mouse wheel handler is now OK in SDL and Wasm
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268