Mercurial > hg > orthanc-python
annotate Sources/Plugin.cpp @ 108:2389ec6ec803
preparing for release
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 23 Feb 2022 18:40:20 +0100 |
parents | eb6ac5a801d1 |
children | 65ec5597ec70 35c0b2fc751c |
rev | line source |
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0 | 1 /** |
2 * Python plugin for Orthanc | |
101 | 3 * Copyright (C) 2020-2022 Osimis S.A., Belgium |
4 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium | |
0 | 5 * |
6 * This program is free software: you can redistribute it and/or | |
7 * modify it under the terms of the GNU Affero General Public License | |
8 * as published by the Free Software Foundation, either version 3 of | |
9 * the License, or (at your option) any later version. | |
10 * | |
11 * This program is distributed in the hope that it will be useful, but | |
12 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
14 * Affero General Public License for more details. | |
15 * | |
16 * You should have received a copy of the GNU Affero General Public License | |
17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
18 **/ | |
19 | |
20 | |
21 // http://edcjones.tripod.com/refcount.html | |
22 // https://docs.python.org/3/extending/extending.html | |
23 | |
24 // https://www.codevate.com/blog/7-concurrency-with-embedded-python-in-a-multi-threaded-c-application | |
25 // https://fr.slideshare.net/YiLungTsai/embed-python | |
26 | |
27 | |
63
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28 #include "DicomScpCallbacks.h" |
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29 #include "IncomingHttpRequestFilter.h" |
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30 #include "OnChangeCallback.h" |
0 | 31 #include "OnStoredInstanceCallback.h" |
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32 #include "IncomingInstanceFilter.h" |
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33 #include "ReceivedInstanceCallback.h" |
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34 #include "StorageArea.h" |
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35 |
0 | 36 #include "RestCallbacks.h" |
37 #include "PythonModule.h" | |
38 | |
39 #include "Autogenerated/sdk.h" | |
40 | |
36
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41 #include "../Resources/Orthanc/Plugins/OrthancPluginCppWrapper.h" |
0 | 42 |
43 #include <boost/algorithm/string/predicate.hpp> | |
44 #include <boost/filesystem.hpp> | |
45 | |
47
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46 // The "dl_iterate_phdr()" function (to walk through shared libraries) |
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47 // is not available on Microsoft Windows and Apple OS X |
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48 #if defined(_WIN32) |
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49 # define HAS_DL_ITERATE 0 |
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50 #elif defined(__APPLE__) && defined(__MACH__) |
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51 # define HAS_DL_ITERATE 0 |
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52 #else |
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53 # define HAS_DL_ITERATE 1 |
0 | 54 #endif |
55 | |
56 | |
66
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57 #include "PythonString.h" |
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58 |
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59 PyObject* LookupDictionary(PyObject* module, PyObject* args) |
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60 { |
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61 const char* name = NULL; |
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62 |
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63 if (!PyArg_ParseTuple(args, "s", &name)) |
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64 { |
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65 PyErr_SetString(PyExc_TypeError, "Please provide a string containing the name of the DICOM tag of interest"); |
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66 return NULL; |
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67 } |
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68 else |
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69 { |
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70 OrthancPluginDictionaryEntry entry; |
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71 |
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72 OrthancPluginErrorCode code = OrthancPluginLookupDictionary(OrthancPlugins::GetGlobalContext(), &entry, name); |
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73 if (code == OrthancPluginErrorCode_Success) |
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74 { |
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75 /** |
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76 * "PyGILState_Ensure()" can be invoked several times from the |
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77 * same thread, so no problem in creating a PythonLock even if |
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78 * the GIL is already locked. |
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79 **/ |
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80 PythonLock lock; |
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81 |
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82 PythonObject kw(lock, PyDict_New()); |
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83 PyDict_SetItemString(kw.GetPyObject(), "Group", PyLong_FromUnsignedLong(entry.group)); |
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84 PyDict_SetItemString(kw.GetPyObject(), "Element", PyLong_FromUnsignedLong(entry.element)); |
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85 PyDict_SetItemString(kw.GetPyObject(), "ValueRepresentation", PyLong_FromUnsignedLong(entry.vr)); |
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86 PyDict_SetItemString(kw.GetPyObject(), "MinMultiplicity", PyLong_FromUnsignedLong(entry.minMultiplicity)); |
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87 PyDict_SetItemString(kw.GetPyObject(), "MaxMultiplicity", PyLong_FromUnsignedLong(entry.maxMultiplicity)); |
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88 |
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89 return kw.Release(); |
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90 } |
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91 else |
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92 { |
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93 std::string message = "Unknown DICOM tag: " + std::string(name); |
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94 PyErr_SetString(PyExc_TypeError, message.c_str()); |
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95 return NULL; |
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96 } |
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97 } |
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98 } |
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99 |
0 | 100 |
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101 PyObject* CreateDicom(PyObject* module, PyObject* args) |
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102 { |
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103 // The GIL is locked at this point (no need to create "PythonLock") |
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104 const char* json = NULL; |
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105 PyObject* pixelData = NULL; |
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106 long int flags = 0; |
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107 |
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108 if (!PyArg_ParseTuple(args, "sOl", &json, &pixelData, &flags)) |
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109 { |
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110 PyErr_SetString(PyExc_TypeError, "Please provide a JSON string, an orthanc.Image object, and a set of orthanc.CreateDicomFlags"); |
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111 return NULL; |
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112 } |
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113 else |
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114 { |
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115 OrthancPluginImage* image = NULL; |
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116 |
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117 if (pixelData == Py_None) |
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118 { |
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119 // No pixel data |
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120 } |
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121 else if (Py_TYPE(pixelData) == GetOrthancPluginImageType()) |
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122 { |
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123 image = reinterpret_cast<sdk_OrthancPluginImage_Object*>(pixelData)->object_; |
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124 } |
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125 else |
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126 { |
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127 PyErr_SetString(PyExc_TypeError, "Second parameter is not a valid orthanc.Image object"); |
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128 return NULL; |
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129 } |
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130 |
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131 OrthancPlugins::MemoryBuffer buffer; |
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132 OrthancPluginErrorCode code = OrthancPluginCreateDicom(OrthancPlugins::GetGlobalContext(), *buffer, json, image, |
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133 static_cast<OrthancPluginCreateDicomFlags>(flags)); |
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134 |
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135 if (code == OrthancPluginErrorCode_Success) |
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136 { |
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137 return PyBytes_FromStringAndSize(buffer.GetData(), buffer.GetSize()); |
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138 } |
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139 else |
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140 { |
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141 PyErr_SetString(PyExc_ValueError, "Cannot create the DICOM instance"); |
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142 return NULL; |
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143 } |
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144 } |
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145 } |
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146 |
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147 |
65
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148 PyObject* GetInstanceData(sdk_OrthancPluginDicomInstance_Object* self, PyObject *args) |
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149 { |
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150 // The GIL is locked at this point (no need to create "PythonLock") |
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151 |
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152 if (self->object_ == NULL) |
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153 { |
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154 PyErr_SetString(PyExc_ValueError, "Invalid object"); |
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155 return NULL; |
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156 } |
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157 else |
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158 { |
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159 OrthancPluginDicomInstance* instance = reinterpret_cast<sdk_OrthancPluginDicomInstance_Object*>(self)->object_; |
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160 |
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161 const void* data = OrthancPluginGetInstanceData(OrthancPlugins::GetGlobalContext(), instance); |
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162 size_t size = OrthancPluginGetInstanceSize(OrthancPlugins::GetGlobalContext(), instance); |
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163 |
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164 if (data == NULL && |
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165 size != 0) |
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166 { |
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167 PyErr_SetString(PyExc_ValueError, "Accessing an invalid orthanc.DicomInstance object"); |
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168 return NULL; |
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169 } |
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170 else |
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171 { |
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172 return PyBytes_FromStringAndSize(reinterpret_cast<const char*>(data), size); |
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173 } |
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174 } |
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175 } |
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176 |
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177 |
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178 /** |
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179 * Contrarily to "OrthancPluginGetImageBuffer()" that provides a |
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180 * read-write pointer, the method "orthanc.Image.GetImageBuffer()" |
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181 * returns a copy of the image buffer. Use "CreateImageFromBuffer()" |
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182 * to create an image from a Python buffer. |
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183 **/ |
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184 PyObject* GetImageBuffer(sdk_OrthancPluginImage_Object* self, PyObject *args) |
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185 { |
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186 // The GIL is locked at this point (no need to create "PythonLock") |
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187 |
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188 if (self->object_ == NULL) |
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189 { |
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190 PyErr_SetString(PyExc_ValueError, "Invalid object"); |
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191 return NULL; |
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192 } |
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193 else |
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194 { |
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195 OrthancPluginImage* image = reinterpret_cast<sdk_OrthancPluginImage_Object*>(self)->object_; |
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196 |
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197 const void* buffer = OrthancPluginGetImageBuffer(OrthancPlugins::GetGlobalContext(), image); |
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198 size_t size = (OrthancPluginGetImagePitch(OrthancPlugins::GetGlobalContext(), image) * |
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199 OrthancPluginGetImageHeight(OrthancPlugins::GetGlobalContext(), image)); |
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200 |
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201 if (buffer == NULL && |
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202 size != 0) |
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203 { |
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204 PyErr_SetString(PyExc_ValueError, "Accessing an invalid orthanc.Image object"); |
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205 return NULL; |
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206 } |
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207 else |
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208 { |
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209 return PyBytes_FromStringAndSize(reinterpret_cast<const char*>(buffer), size); |
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210 } |
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211 } |
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212 } |
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213 |
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214 |
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215 /** |
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216 * This function is the Python alternative for function |
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217 * "OrthancPluginCreateImageAccessor()". Indeed, it is not possible to |
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218 * share a memory buffer between Orthanc and Python, so we have to |
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219 * create a copy of the image. |
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220 **/ |
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221 PyObject* CreateImageFromBuffer(PyObject* module, PyObject* args) |
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222 { |
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223 // The GIL is locked at this point (no need to create "PythonLock") |
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224 |
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225 unsigned long format, width, height, sourcePitch; |
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226 Py_buffer buffer; |
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227 |
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228 if (!PyArg_ParseTuple(args, "kkkks*", &format, &width, &height, &sourcePitch, &buffer)) |
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229 { |
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230 PyErr_SetString(PyExc_TypeError, "5 arguments are needed: image.PixelFormat, width, height, pitch and memory buffer"); |
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231 return NULL; |
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232 } |
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233 else if (static_cast<Py_ssize_t>(sourcePitch * height) != buffer.len) |
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234 { |
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235 PyBuffer_Release(&buffer); |
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236 |
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237 PyErr_SetString(PyExc_TypeError, "The size of the memory buffer must match the product of height by pitch"); |
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238 return NULL; |
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239 } |
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240 else |
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241 { |
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242 OrthancPluginImage* image = OrthancPluginCreateImage( |
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243 OrthancPlugins::GetGlobalContext(), static_cast<OrthancPluginPixelFormat>(format), width, height); |
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244 |
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245 if (image == NULL) |
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246 { |
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247 PyBuffer_Release(&buffer); |
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248 |
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249 PyErr_SetString(PyExc_ValueError, "Cannot create the image"); |
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250 return NULL; |
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251 } |
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252 else |
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253 { |
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254 // Copy the image line by line |
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255 unsigned long targetPitch = OrthancPluginGetImagePitch(OrthancPlugins::GetGlobalContext(), image); |
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256 |
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257 const uint8_t* sourcePixels = reinterpret_cast<const uint8_t*>(buffer.buf); |
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258 uint8_t* targetPixels = reinterpret_cast<uint8_t*>(OrthancPluginGetImageBuffer(OrthancPlugins::GetGlobalContext(), image)); |
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259 |
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260 unsigned long rowSize = std::min(sourcePitch, targetPitch); |
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261 |
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262 for (unsigned int y = 0; y < height; y++) |
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263 { |
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264 memcpy(targetPixels, sourcePixels, rowSize); |
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265 targetPixels += targetPitch; |
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266 sourcePixels += sourcePitch; |
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267 } |
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268 |
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269 PyBuffer_Release(&buffer); |
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270 |
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271 { |
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272 PyObject *argList = Py_BuildValue("Lb", image, false /* not borrowed */); |
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273 PyObject *python = PyObject_CallObject((PyObject *) GetOrthancPluginImageType(), argList); |
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274 Py_DECREF(argList); |
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275 return python; |
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276 } |
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277 } |
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278 } |
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279 } |
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280 |
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281 |
63
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282 |
0 | 283 static bool pythonEnabled_ = false; |
284 static std::string userScriptName_; | |
285 static std::vector<PyMethodDef> globalFunctions_; | |
286 | |
287 | |
288 static void InstallClasses(PyObject* module) | |
289 { | |
290 RegisterOrthancSdk(module); | |
291 } | |
292 | |
293 | |
294 static void SetupGlobalFunctions() | |
295 { | |
296 if (!globalFunctions_.empty()) | |
297 { | |
298 ORTHANC_PLUGINS_THROW_EXCEPTION(BadSequenceOfCalls); | |
299 } | |
300 | |
301 /** | |
302 * Add all the manual global functions | |
303 **/ | |
304 | |
305 std::list<PyMethodDef> functions; | |
306 | |
307 { | |
308 PyMethodDef f = { "RegisterRestCallback", RegisterRestCallback, METH_VARARGS, "" }; | |
309 functions.push_back(f); | |
310 } | |
311 | |
312 { | |
313 PyMethodDef f = { "RegisterOnChangeCallback", RegisterOnChangeCallback, METH_VARARGS, "" }; | |
314 functions.push_back(f); | |
315 } | |
316 | |
317 { | |
318 PyMethodDef f = { "RegisterOnStoredInstanceCallback", RegisterOnStoredInstanceCallback, | |
319 METH_VARARGS, "" }; | |
320 functions.push_back(f); | |
321 } | |
50
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322 |
63
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323 |
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324 /** |
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325 * New in release 3.0 |
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326 **/ |
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327 |
50
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328 { |
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329 PyMethodDef f = { "RegisterIncomingHttpRequestFilter", RegisterIncomingHttpRequestFilter, METH_VARARGS, "" }; |
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330 functions.push_back(f); |
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331 } |
63
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332 |
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333 |
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334 /** |
64
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335 * New in release 3.2 |
63
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336 **/ |
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337 |
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338 { |
66
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339 PyMethodDef f = { "LookupDictionary", LookupDictionary, METH_VARARGS, "" }; |
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340 functions.push_back(f); |
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341 } |
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342 |
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343 { |
63
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344 PyMethodDef f = { "CreateDicom", CreateDicom, METH_VARARGS, "" }; |
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345 functions.push_back(f); |
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346 } |
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347 |
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348 { |
65
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349 PyMethodDef f = { "CreateImageFromBuffer", CreateImageFromBuffer, METH_VARARGS, "" }; |
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350 functions.push_back(f); |
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351 } |
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352 |
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353 { |
63
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354 PyMethodDef f = { "RegisterFindCallback", RegisterFindCallback, METH_VARARGS, "" }; |
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355 functions.push_back(f); |
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356 } |
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357 |
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358 { |
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359 PyMethodDef f = { "RegisterMoveCallback", RegisterMoveCallback, METH_VARARGS, "" }; |
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360 functions.push_back(f); |
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361 } |
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362 |
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363 { |
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364 PyMethodDef f = { "RegisterWorklistCallback", RegisterWorklistCallback, METH_VARARGS, "" }; |
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365 functions.push_back(f); |
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366 } |
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367 |
0 | 368 |
369 /** | |
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370 * New in release 3.3 |
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371 **/ |
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372 |
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373 { |
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374 PyMethodDef f = { "RegisterStorageArea", RegisterStorageArea, METH_VARARGS, "" }; |
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375 functions.push_back(f); |
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376 } |
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377 |
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378 |
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379 /** |
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380 * New in release 3.5 |
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381 **/ |
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382 |
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383 { |
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384 PyMethodDef f = { "RegisterIncomingCStoreInstanceFilter", RegisterIncomingCStoreInstanceFilter, METH_VARARGS, "" }; |
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385 functions.push_back(f); |
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386 } |
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387 |
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388 { |
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389 PyMethodDef f = { "RegisterReceivedInstanceCallback", RegisterReceivedInstanceCallback, METH_VARARGS, "" }; |
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390 functions.push_back(f); |
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391 } |
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392 |
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393 /** |
0 | 394 * Append all the global functions that were automatically generated |
395 **/ | |
396 | |
397 const PyMethodDef* sdk = GetOrthancSdkFunctions(); | |
398 | |
399 for (size_t i = 0; sdk[i].ml_name != NULL; i++) | |
400 { | |
401 functions.push_back(sdk[i]); | |
402 } | |
403 | |
404 /** | |
405 * Flatten the list of functions into the vector | |
406 **/ | |
407 | |
408 globalFunctions_.resize(functions.size()); | |
409 std::copy(functions.begin(), functions.end(), globalFunctions_.begin()); | |
410 | |
411 PyMethodDef sentinel = { NULL }; | |
412 globalFunctions_.push_back(sentinel); | |
413 } | |
414 | |
415 | |
416 static PyMethodDef* GetGlobalFunctions() | |
417 { | |
418 if (globalFunctions_.empty()) | |
419 { | |
420 // "SetupGlobalFunctions()" should have been called | |
421 ORTHANC_PLUGINS_THROW_EXCEPTION(BadSequenceOfCalls); | |
422 } | |
423 else | |
424 { | |
425 return &globalFunctions_[0]; | |
426 } | |
427 } | |
428 | |
429 | |
430 | |
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431 #if HAS_DL_ITERATE == 1 |
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433 #include <dlfcn.h> |
0 | 434 #include <link.h> // For dl_phdr_info |
435 | |
436 static int ForceImportCallback(struct dl_phdr_info *info, size_t size, void *data) | |
437 { | |
438 /** | |
439 * The following line solves the error: "ImportError: | |
440 * /usr/lib/python2.7/dist-packages/PIL/_imaging.x86_64-linux-gnu.so: | |
441 * undefined symbol: PyExc_SystemError" | |
442 * https://stackoverflow.com/a/48517485/881731 | |
443 * | |
444 * dlopen("/usr/lib/x86_64-linux-gnu/libpython2.7.so", RTLD_NOW | RTLD_LAZY | RTLD_GLOBAL); | |
445 * | |
446 * Another fix consists in using LD_PRELOAD as follows: | |
447 * LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libpython2.7.so ~/Subversion/orthanc/i/Orthanc tutu.json | |
448 **/ | |
449 | |
450 std::string module(info->dlpi_name); | |
451 | |
452 if (module.find("python") != std::string::npos) | |
453 { | |
454 OrthancPlugins::LogWarning("Force global loading of Python shared library: " + module); | |
455 dlopen(module.c_str(), RTLD_NOW | RTLD_LAZY | RTLD_GLOBAL); | |
456 } | |
457 | |
458 return 0; | |
459 } | |
460 | |
461 #endif | |
462 | |
463 | |
464 extern "C" | |
465 { | |
466 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* c) | |
467 { | |
468 OrthancPlugins::SetGlobalContext(c); | |
469 OrthancPlugins::LogWarning("Python plugin is initializing"); | |
470 | |
471 | |
472 /* Check the version of the Orthanc core */ | |
473 if (OrthancPluginCheckVersion(c) == 0) | |
474 { | |
475 char info[1024]; | |
476 sprintf(info, "Your version of Orthanc (%s) must be above %d.%d.%d to run this plugin", | |
477 c->orthancVersion, | |
478 ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER, | |
479 ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER, | |
480 ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER); | |
481 OrthancPluginLogError(c, info); | |
482 return -1; | |
483 } | |
11 | 484 |
485 OrthancPluginSetDescription(c, "Run Python scripts as Orthanc plugins"); | |
486 | |
0 | 487 try |
488 { | |
489 /** | |
490 * Detection of the user script | |
491 **/ | |
492 | |
493 OrthancPlugins::OrthancConfiguration config; | |
494 | |
495 static const char* const OPTION = "PythonScript"; | |
496 | |
497 std::string script; | |
498 if (!config.LookupStringValue(script, OPTION)) | |
499 { | |
500 pythonEnabled_ = false; | |
501 | |
502 OrthancPlugins::LogWarning("The option \"" + std::string(OPTION) + "\" is not provided: " + | |
503 "Python scripting is disabled"); | |
504 } | |
505 else | |
506 { | |
507 pythonEnabled_ = true; | |
508 | |
509 /** | |
510 * Installation of the user script | |
511 **/ | |
512 | |
513 const boost::filesystem::path path(script); | |
514 if (!boost::iequals(path.extension().string(), ".py")) | |
515 { | |
516 OrthancPlugins::LogError("Python script must have the \".py\" file extension: " + | |
517 path.string()); | |
518 return -1; | |
519 } | |
520 | |
521 if (!boost::filesystem::is_regular_file(path)) | |
522 { | |
523 OrthancPlugins::LogError("Inexistent directory for the Python script: " + | |
524 path.string()); | |
525 return -1; | |
526 } | |
527 | |
528 boost::filesystem::path userScriptDirectory = boost::filesystem::absolute(path).parent_path(); | |
529 | |
530 { | |
531 boost::filesystem::path module = path.filename().replace_extension(""); | |
532 userScriptName_ = module.string(); | |
533 } | |
534 | |
535 OrthancPlugins::LogWarning("Using Python script \"" + userScriptName_ + | |
536 ".py\" from directory: " + userScriptDirectory.string()); | |
537 | |
538 | |
539 /** | |
540 * Initialization of Python | |
541 **/ | |
542 | |
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543 #if HAS_DL_ITERATE == 1 |
0 | 544 dl_iterate_phdr(ForceImportCallback, NULL); |
545 #endif | |
546 | |
547 SetupGlobalFunctions(); | |
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548 PythonLock::GlobalInitialize("orthanc", "OrthancException", |
0 | 549 GetGlobalFunctions, InstallClasses, |
550 config.GetBooleanValue("PythonVerbose", false)); | |
551 PythonLock::AddSysPath(userScriptDirectory.string()); | |
552 | |
553 | |
554 /** | |
555 * Force loading the declarations in the user script | |
556 **/ | |
557 | |
558 PythonLock lock; | |
559 | |
560 { | |
561 PythonModule module(lock, userScriptName_); | |
562 } | |
563 | |
564 std::string traceback; | |
565 if (lock.HasErrorOccurred(traceback)) | |
566 { | |
567 OrthancPlugins::LogError("Error during the installation of the Python script, " | |
568 "traceback:\n" + traceback); | |
569 return -1; | |
570 } | |
571 } | |
572 } | |
573 catch (ORTHANC_PLUGINS_EXCEPTION_CLASS& e) | |
574 { | |
575 OrthancPlugins::LogError("Exception while starting the Python plugin: " + | |
576 std::string(e.What(c))); | |
577 return -1; | |
578 } | |
579 | |
580 return 0; | |
581 } | |
582 | |
583 | |
584 ORTHANC_PLUGINS_API void OrthancPluginFinalize() | |
585 { | |
586 OrthancPlugins::LogWarning("Python plugin is finalizing"); | |
587 | |
588 if (pythonEnabled_) | |
589 { | |
590 FinalizeOnChangeCallback(); | |
591 FinalizeRestCallbacks(); | |
592 FinalizeOnStoredInstanceCallback(); | |
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593 FinalizeIncomingHttpRequestFilter(); |
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594 FinalizeDicomScpCallbacks(); |
0 | 595 |
596 PythonLock::GlobalFinalize(); | |
597 } | |
598 } | |
599 | |
600 | |
601 ORTHANC_PLUGINS_API const char* OrthancPluginGetName() | |
602 { | |
603 return "python"; | |
604 } | |
605 | |
606 | |
607 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion() | |
608 { | |
609 return PLUGIN_VERSION; | |
610 } | |
611 } |