Mercurial > hg > orthanc-python
annotate Sources/Plugin.cpp @ 77:e7ff5efb100d
Custom exception "orthanc.OrthancException" is raised instead of "ValueError"
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 09 Aug 2021 18:16:42 +0200 |
| parents | 6fc445793796 |
| children | 068551520123 |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 2 * Python plugin for Orthanc | |
|
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upgrade to year 2021
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3 * Copyright (C) 2020-2021 Osimis S.A., Belgium |
| 0 | 4 * |
| 5 * This program is free software: you can redistribute it and/or | |
| 6 * modify it under the terms of the GNU Affero General Public License | |
| 7 * as published by the Free Software Foundation, either version 3 of | |
| 8 * the License, or (at your option) any later version. | |
| 9 * | |
| 10 * This program is distributed in the hope that it will be useful, but | |
| 11 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 13 * Affero General Public License for more details. | |
| 14 * | |
| 15 * You should have received a copy of the GNU Affero General Public License | |
| 16 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 17 **/ | |
| 18 | |
| 19 | |
| 20 // http://edcjones.tripod.com/refcount.html | |
| 21 // https://docs.python.org/3/extending/extending.html | |
| 22 | |
| 23 // https://www.codevate.com/blog/7-concurrency-with-embedded-python-in-a-multi-threaded-c-application | |
| 24 // https://fr.slideshare.net/YiLungTsai/embed-python | |
| 25 | |
| 26 | |
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27 #include "DicomScpCallbacks.h" |
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28 #include "IncomingHttpRequestFilter.h" |
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29 #include "OnChangeCallback.h" |
| 0 | 30 #include "OnStoredInstanceCallback.h" |
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31 |
| 0 | 32 #include "RestCallbacks.h" |
| 33 #include "PythonModule.h" | |
| 34 | |
| 35 #include "Autogenerated/sdk.h" | |
| 36 | |
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37 #include "../Resources/Orthanc/Plugins/OrthancPluginCppWrapper.h" |
| 0 | 38 |
| 39 #include <boost/algorithm/string/predicate.hpp> | |
| 40 #include <boost/filesystem.hpp> | |
| 41 | |
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42 // The "dl_iterate_phdr()" function (to walk through shared libraries) |
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43 // is not available on Microsoft Windows and Apple OS X |
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44 #if defined(_WIN32) |
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45 # define HAS_DL_ITERATE 0 |
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46 #elif defined(__APPLE__) && defined(__MACH__) |
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47 # define HAS_DL_ITERATE 0 |
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48 #else |
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49 # define HAS_DL_ITERATE 1 |
| 0 | 50 #endif |
| 51 | |
| 52 | |
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53 #include "PythonString.h" |
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54 |
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55 PyObject* LookupDictionary(PyObject* module, PyObject* args) |
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56 { |
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57 const char* name = NULL; |
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58 |
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59 if (!PyArg_ParseTuple(args, "s", &name)) |
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60 { |
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61 PyErr_SetString(PyExc_TypeError, "Please provide a string containing the name of the DICOM tag of interest"); |
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62 return NULL; |
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63 } |
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64 else |
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65 { |
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66 OrthancPluginDictionaryEntry entry; |
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67 |
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68 OrthancPluginErrorCode code = OrthancPluginLookupDictionary(OrthancPlugins::GetGlobalContext(), &entry, name); |
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69 if (code == OrthancPluginErrorCode_Success) |
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70 { |
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71 /** |
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72 * "PyGILState_Ensure()" can be invoked several times from the |
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73 * same thread, so no problem in creating a PythonLock even if |
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74 * the GIL is already locked. |
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75 **/ |
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76 PythonLock lock; |
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77 |
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78 PythonObject kw(lock, PyDict_New()); |
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79 PyDict_SetItemString(kw.GetPyObject(), "Group", PyLong_FromUnsignedLong(entry.group)); |
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80 PyDict_SetItemString(kw.GetPyObject(), "Element", PyLong_FromUnsignedLong(entry.element)); |
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81 PyDict_SetItemString(kw.GetPyObject(), "ValueRepresentation", PyLong_FromUnsignedLong(entry.vr)); |
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82 PyDict_SetItemString(kw.GetPyObject(), "MinMultiplicity", PyLong_FromUnsignedLong(entry.minMultiplicity)); |
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83 PyDict_SetItemString(kw.GetPyObject(), "MaxMultiplicity", PyLong_FromUnsignedLong(entry.maxMultiplicity)); |
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84 |
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85 return kw.Release(); |
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86 } |
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87 else |
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88 { |
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89 std::string message = "Unknown DICOM tag: " + std::string(name); |
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90 PyErr_SetString(PyExc_TypeError, message.c_str()); |
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91 return NULL; |
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92 } |
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93 } |
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94 } |
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95 |
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97 PyObject* CreateDicom(PyObject* module, PyObject* args) |
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98 { |
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99 // The GIL is locked at this point (no need to create "PythonLock") |
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100 const char* json = NULL; |
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101 PyObject* pixelData = NULL; |
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102 long int flags = 0; |
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103 |
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104 if (!PyArg_ParseTuple(args, "sOl", &json, &pixelData, &flags)) |
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105 { |
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106 PyErr_SetString(PyExc_TypeError, "Please provide a JSON string, an orthanc.Image object, and a set of orthanc.CreateDicomFlags"); |
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107 return NULL; |
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108 } |
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109 else |
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110 { |
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111 OrthancPluginImage* image = NULL; |
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112 |
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113 if (pixelData == Py_None) |
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114 { |
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115 // No pixel data |
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116 } |
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117 else if (Py_TYPE(pixelData) == GetOrthancPluginImageType()) |
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118 { |
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119 image = reinterpret_cast<sdk_OrthancPluginImage_Object*>(pixelData)->object_; |
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120 } |
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121 else |
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122 { |
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123 PyErr_SetString(PyExc_TypeError, "Second parameter is not a valid orthanc.Image object"); |
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124 return NULL; |
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125 } |
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126 |
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127 OrthancPlugins::MemoryBuffer buffer; |
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128 OrthancPluginErrorCode code = OrthancPluginCreateDicom(OrthancPlugins::GetGlobalContext(), *buffer, json, image, |
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129 static_cast<OrthancPluginCreateDicomFlags>(flags)); |
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130 |
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131 if (code == OrthancPluginErrorCode_Success) |
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132 { |
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133 return PyBytes_FromStringAndSize(buffer.GetData(), buffer.GetSize()); |
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134 } |
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135 else |
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136 { |
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137 PyErr_SetString(PyExc_ValueError, "Cannot create the DICOM instance"); |
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138 return NULL; |
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139 } |
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140 } |
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141 } |
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142 |
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143 |
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144 PyObject* GetInstanceData(sdk_OrthancPluginDicomInstance_Object* self, PyObject *args) |
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145 { |
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146 // The GIL is locked at this point (no need to create "PythonLock") |
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147 |
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148 if (self->object_ == NULL) |
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149 { |
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150 PyErr_SetString(PyExc_ValueError, "Invalid object"); |
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151 return NULL; |
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152 } |
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153 else |
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154 { |
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155 OrthancPluginDicomInstance* instance = reinterpret_cast<sdk_OrthancPluginDicomInstance_Object*>(self)->object_; |
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156 |
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157 const void* data = OrthancPluginGetInstanceData(OrthancPlugins::GetGlobalContext(), instance); |
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158 size_t size = OrthancPluginGetInstanceSize(OrthancPlugins::GetGlobalContext(), instance); |
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159 |
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160 if (data == NULL && |
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161 size != 0) |
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162 { |
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163 PyErr_SetString(PyExc_ValueError, "Accessing an invalid orthanc.DicomInstance object"); |
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164 return NULL; |
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165 } |
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166 else |
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167 { |
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168 return PyBytes_FromStringAndSize(reinterpret_cast<const char*>(data), size); |
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169 } |
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170 } |
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171 } |
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172 |
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173 |
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174 /** |
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175 * Contrarily to "OrthancPluginGetImageBuffer()" that provides a |
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176 * read-write pointer, the method "orthanc.Image.GetImageBuffer()" |
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177 * returns a copy of the image buffer. Use "CreateImageFromBuffer()" |
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178 * to create an image from a Python buffer. |
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179 **/ |
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180 PyObject* GetImageBuffer(sdk_OrthancPluginImage_Object* self, PyObject *args) |
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181 { |
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182 // The GIL is locked at this point (no need to create "PythonLock") |
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183 |
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184 if (self->object_ == NULL) |
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185 { |
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186 PyErr_SetString(PyExc_ValueError, "Invalid object"); |
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187 return NULL; |
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188 } |
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189 else |
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190 { |
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191 OrthancPluginImage* image = reinterpret_cast<sdk_OrthancPluginImage_Object*>(self)->object_; |
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192 |
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193 const void* buffer = OrthancPluginGetImageBuffer(OrthancPlugins::GetGlobalContext(), image); |
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194 size_t size = (OrthancPluginGetImagePitch(OrthancPlugins::GetGlobalContext(), image) * |
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195 OrthancPluginGetImageHeight(OrthancPlugins::GetGlobalContext(), image)); |
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196 |
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197 if (buffer == NULL && |
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198 size != 0) |
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199 { |
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200 PyErr_SetString(PyExc_ValueError, "Accessing an invalid orthanc.Image object"); |
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201 return NULL; |
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202 } |
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203 else |
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204 { |
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205 return PyBytes_FromStringAndSize(reinterpret_cast<const char*>(buffer), size); |
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206 } |
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207 } |
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208 } |
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209 |
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210 |
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211 /** |
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212 * This function is the Python alternative for function |
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213 * "OrthancPluginCreateImageAccessor()". Indeed, it is not possible to |
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214 * share a memory buffer between Orthanc and Python, so we have to |
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215 * create a copy of the image. |
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216 **/ |
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217 PyObject* CreateImageFromBuffer(PyObject* module, PyObject* args) |
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218 { |
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219 // The GIL is locked at this point (no need to create "PythonLock") |
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220 |
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221 unsigned long format, width, height, sourcePitch; |
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222 Py_buffer buffer; |
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223 |
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224 if (!PyArg_ParseTuple(args, "kkkks*", &format, &width, &height, &sourcePitch, &buffer)) |
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225 { |
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226 PyErr_SetString(PyExc_TypeError, "5 arguments are needed: image.PixelFormat, width, height, pitch and memory buffer"); |
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227 return NULL; |
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228 } |
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229 else if (static_cast<Py_ssize_t>(sourcePitch * height) != buffer.len) |
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230 { |
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231 PyBuffer_Release(&buffer); |
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232 |
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233 PyErr_SetString(PyExc_TypeError, "The size of the memory buffer must match the product of height by pitch"); |
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234 return NULL; |
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235 } |
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236 else |
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237 { |
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238 OrthancPluginImage* image = OrthancPluginCreateImage( |
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239 OrthancPlugins::GetGlobalContext(), static_cast<OrthancPluginPixelFormat>(format), width, height); |
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240 |
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241 if (image == NULL) |
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242 { |
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243 PyBuffer_Release(&buffer); |
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244 |
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245 PyErr_SetString(PyExc_ValueError, "Cannot create the image"); |
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246 return NULL; |
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247 } |
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248 else |
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249 { |
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250 // Copy the image line by line |
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251 unsigned long targetPitch = OrthancPluginGetImagePitch(OrthancPlugins::GetGlobalContext(), image); |
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252 |
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253 const uint8_t* sourcePixels = reinterpret_cast<const uint8_t*>(buffer.buf); |
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254 uint8_t* targetPixels = reinterpret_cast<uint8_t*>(OrthancPluginGetImageBuffer(OrthancPlugins::GetGlobalContext(), image)); |
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255 |
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256 unsigned long rowSize = std::min(sourcePitch, targetPitch); |
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257 |
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258 for (unsigned int y = 0; y < height; y++) |
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259 { |
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260 memcpy(targetPixels, sourcePixels, rowSize); |
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261 targetPixels += targetPitch; |
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262 sourcePixels += sourcePitch; |
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263 } |
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264 |
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265 PyBuffer_Release(&buffer); |
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266 |
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267 { |
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268 PyObject *argList = Py_BuildValue("Lb", image, false /* not borrowed */); |
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269 PyObject *python = PyObject_CallObject((PyObject *) GetOrthancPluginImageType(), argList); |
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270 Py_DECREF(argList); |
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271 return python; |
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272 } |
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273 } |
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274 } |
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275 } |
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276 |
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277 |
|
63
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278 |
| 0 | 279 static bool pythonEnabled_ = false; |
| 280 static std::string userScriptName_; | |
| 281 static std::vector<PyMethodDef> globalFunctions_; | |
| 282 | |
| 283 | |
| 284 static void InstallClasses(PyObject* module) | |
| 285 { | |
| 286 RegisterOrthancSdk(module); | |
| 287 } | |
| 288 | |
| 289 | |
| 290 static void SetupGlobalFunctions() | |
| 291 { | |
| 292 if (!globalFunctions_.empty()) | |
| 293 { | |
| 294 ORTHANC_PLUGINS_THROW_EXCEPTION(BadSequenceOfCalls); | |
| 295 } | |
| 296 | |
| 297 /** | |
| 298 * Add all the manual global functions | |
| 299 **/ | |
| 300 | |
| 301 std::list<PyMethodDef> functions; | |
| 302 | |
| 303 { | |
| 304 PyMethodDef f = { "RegisterRestCallback", RegisterRestCallback, METH_VARARGS, "" }; | |
| 305 functions.push_back(f); | |
| 306 } | |
| 307 | |
| 308 { | |
| 309 PyMethodDef f = { "RegisterOnChangeCallback", RegisterOnChangeCallback, METH_VARARGS, "" }; | |
| 310 functions.push_back(f); | |
| 311 } | |
| 312 | |
| 313 { | |
| 314 PyMethodDef f = { "RegisterOnStoredInstanceCallback", RegisterOnStoredInstanceCallback, | |
| 315 METH_VARARGS, "" }; | |
| 316 functions.push_back(f); | |
| 317 } | |
|
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318 |
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319 |
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320 /** |
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321 * New in release 3.0 |
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322 **/ |
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323 |
|
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324 { |
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325 PyMethodDef f = { "RegisterIncomingHttpRequestFilter", RegisterIncomingHttpRequestFilter, METH_VARARGS, "" }; |
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326 functions.push_back(f); |
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327 } |
|
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328 |
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329 |
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330 /** |
|
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331 * New in release 3.2 |
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332 **/ |
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333 |
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334 { |
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335 PyMethodDef f = { "LookupDictionary", LookupDictionary, METH_VARARGS, "" }; |
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336 functions.push_back(f); |
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337 } |
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338 |
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339 { |
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340 PyMethodDef f = { "CreateDicom", CreateDicom, METH_VARARGS, "" }; |
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341 functions.push_back(f); |
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342 } |
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343 |
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344 { |
|
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345 PyMethodDef f = { "CreateImageFromBuffer", CreateImageFromBuffer, METH_VARARGS, "" }; |
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346 functions.push_back(f); |
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347 } |
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348 |
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349 { |
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350 PyMethodDef f = { "RegisterFindCallback", RegisterFindCallback, METH_VARARGS, "" }; |
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351 functions.push_back(f); |
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352 } |
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353 |
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354 { |
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355 PyMethodDef f = { "RegisterMoveCallback", RegisterMoveCallback, METH_VARARGS, "" }; |
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356 functions.push_back(f); |
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357 } |
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358 |
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359 { |
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360 PyMethodDef f = { "RegisterWorklistCallback", RegisterWorklistCallback, METH_VARARGS, "" }; |
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361 functions.push_back(f); |
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362 } |
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363 |
| 0 | 364 |
| 365 /** | |
| 366 * Append all the global functions that were automatically generated | |
| 367 **/ | |
| 368 | |
| 369 const PyMethodDef* sdk = GetOrthancSdkFunctions(); | |
| 370 | |
| 371 for (size_t i = 0; sdk[i].ml_name != NULL; i++) | |
| 372 { | |
| 373 functions.push_back(sdk[i]); | |
| 374 } | |
| 375 | |
| 376 /** | |
| 377 * Flatten the list of functions into the vector | |
| 378 **/ | |
| 379 | |
| 380 globalFunctions_.resize(functions.size()); | |
| 381 std::copy(functions.begin(), functions.end(), globalFunctions_.begin()); | |
| 382 | |
| 383 PyMethodDef sentinel = { NULL }; | |
| 384 globalFunctions_.push_back(sentinel); | |
| 385 } | |
| 386 | |
| 387 | |
| 388 static PyMethodDef* GetGlobalFunctions() | |
| 389 { | |
| 390 if (globalFunctions_.empty()) | |
| 391 { | |
| 392 // "SetupGlobalFunctions()" should have been called | |
| 393 ORTHANC_PLUGINS_THROW_EXCEPTION(BadSequenceOfCalls); | |
| 394 } | |
| 395 else | |
| 396 { | |
| 397 return &globalFunctions_[0]; | |
| 398 } | |
| 399 } | |
| 400 | |
| 401 | |
| 402 | |
|
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403 #if HAS_DL_ITERATE == 1 |
| 0 | 404 |
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405 #include <dlfcn.h> |
| 0 | 406 #include <link.h> // For dl_phdr_info |
| 407 | |
| 408 static int ForceImportCallback(struct dl_phdr_info *info, size_t size, void *data) | |
| 409 { | |
| 410 /** | |
| 411 * The following line solves the error: "ImportError: | |
| 412 * /usr/lib/python2.7/dist-packages/PIL/_imaging.x86_64-linux-gnu.so: | |
| 413 * undefined symbol: PyExc_SystemError" | |
| 414 * https://stackoverflow.com/a/48517485/881731 | |
| 415 * | |
| 416 * dlopen("/usr/lib/x86_64-linux-gnu/libpython2.7.so", RTLD_NOW | RTLD_LAZY | RTLD_GLOBAL); | |
| 417 * | |
| 418 * Another fix consists in using LD_PRELOAD as follows: | |
| 419 * LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libpython2.7.so ~/Subversion/orthanc/i/Orthanc tutu.json | |
| 420 **/ | |
| 421 | |
| 422 std::string module(info->dlpi_name); | |
| 423 | |
| 424 if (module.find("python") != std::string::npos) | |
| 425 { | |
| 426 OrthancPlugins::LogWarning("Force global loading of Python shared library: " + module); | |
| 427 dlopen(module.c_str(), RTLD_NOW | RTLD_LAZY | RTLD_GLOBAL); | |
| 428 } | |
| 429 | |
| 430 return 0; | |
| 431 } | |
| 432 | |
| 433 #endif | |
| 434 | |
| 435 | |
| 436 extern "C" | |
| 437 { | |
| 438 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* c) | |
| 439 { | |
| 440 OrthancPlugins::SetGlobalContext(c); | |
| 441 OrthancPlugins::LogWarning("Python plugin is initializing"); | |
| 442 | |
| 443 | |
| 444 /* Check the version of the Orthanc core */ | |
| 445 if (OrthancPluginCheckVersion(c) == 0) | |
| 446 { | |
| 447 char info[1024]; | |
| 448 sprintf(info, "Your version of Orthanc (%s) must be above %d.%d.%d to run this plugin", | |
| 449 c->orthancVersion, | |
| 450 ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER, | |
| 451 ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER, | |
| 452 ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER); | |
| 453 OrthancPluginLogError(c, info); | |
| 454 return -1; | |
| 455 } | |
| 11 | 456 |
| 457 OrthancPluginSetDescription(c, "Run Python scripts as Orthanc plugins"); | |
| 458 | |
| 0 | 459 try |
| 460 { | |
| 461 /** | |
| 462 * Detection of the user script | |
| 463 **/ | |
| 464 | |
| 465 OrthancPlugins::OrthancConfiguration config; | |
| 466 | |
| 467 static const char* const OPTION = "PythonScript"; | |
| 468 | |
| 469 std::string script; | |
| 470 if (!config.LookupStringValue(script, OPTION)) | |
| 471 { | |
| 472 pythonEnabled_ = false; | |
| 473 | |
| 474 OrthancPlugins::LogWarning("The option \"" + std::string(OPTION) + "\" is not provided: " + | |
| 475 "Python scripting is disabled"); | |
| 476 } | |
| 477 else | |
| 478 { | |
| 479 pythonEnabled_ = true; | |
| 480 | |
| 481 /** | |
| 482 * Installation of the user script | |
| 483 **/ | |
| 484 | |
| 485 const boost::filesystem::path path(script); | |
| 486 if (!boost::iequals(path.extension().string(), ".py")) | |
| 487 { | |
| 488 OrthancPlugins::LogError("Python script must have the \".py\" file extension: " + | |
| 489 path.string()); | |
| 490 return -1; | |
| 491 } | |
| 492 | |
| 493 if (!boost::filesystem::is_regular_file(path)) | |
| 494 { | |
| 495 OrthancPlugins::LogError("Inexistent directory for the Python script: " + | |
| 496 path.string()); | |
| 497 return -1; | |
| 498 } | |
| 499 | |
| 500 boost::filesystem::path userScriptDirectory = boost::filesystem::absolute(path).parent_path(); | |
| 501 | |
| 502 { | |
| 503 boost::filesystem::path module = path.filename().replace_extension(""); | |
| 504 userScriptName_ = module.string(); | |
| 505 } | |
| 506 | |
| 507 OrthancPlugins::LogWarning("Using Python script \"" + userScriptName_ + | |
| 508 ".py\" from directory: " + userScriptDirectory.string()); | |
| 509 | |
| 510 | |
| 511 /** | |
| 512 * Initialization of Python | |
| 513 **/ | |
| 514 | |
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515 #if HAS_DL_ITERATE == 1 |
| 0 | 516 dl_iterate_phdr(ForceImportCallback, NULL); |
| 517 #endif | |
| 518 | |
| 519 SetupGlobalFunctions(); | |
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520 PythonLock::GlobalInitialize("orthanc", "OrthancException", |
| 0 | 521 GetGlobalFunctions, InstallClasses, |
| 522 config.GetBooleanValue("PythonVerbose", false)); | |
| 523 PythonLock::AddSysPath(userScriptDirectory.string()); | |
| 524 | |
| 525 | |
| 526 /** | |
| 527 * Force loading the declarations in the user script | |
| 528 **/ | |
| 529 | |
| 530 PythonLock lock; | |
| 531 | |
| 532 { | |
| 533 PythonModule module(lock, userScriptName_); | |
| 534 } | |
| 535 | |
| 536 std::string traceback; | |
| 537 if (lock.HasErrorOccurred(traceback)) | |
| 538 { | |
| 539 OrthancPlugins::LogError("Error during the installation of the Python script, " | |
| 540 "traceback:\n" + traceback); | |
| 541 return -1; | |
| 542 } | |
| 543 } | |
| 544 } | |
| 545 catch (ORTHANC_PLUGINS_EXCEPTION_CLASS& e) | |
| 546 { | |
| 547 OrthancPlugins::LogError("Exception while starting the Python plugin: " + | |
| 548 std::string(e.What(c))); | |
| 549 return -1; | |
| 550 } | |
| 551 | |
| 552 return 0; | |
| 553 } | |
| 554 | |
| 555 | |
| 556 ORTHANC_PLUGINS_API void OrthancPluginFinalize() | |
| 557 { | |
| 558 OrthancPlugins::LogWarning("Python plugin is finalizing"); | |
| 559 | |
| 560 if (pythonEnabled_) | |
| 561 { | |
| 562 FinalizeOnChangeCallback(); | |
| 563 FinalizeRestCallbacks(); | |
| 564 FinalizeOnStoredInstanceCallback(); | |
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565 FinalizeIncomingHttpRequestFilter(); |
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566 FinalizeDicomScpCallbacks(); |
| 0 | 567 |
| 568 PythonLock::GlobalFinalize(); | |
| 569 } | |
| 570 } | |
| 571 | |
| 572 | |
| 573 ORTHANC_PLUGINS_API const char* OrthancPluginGetName() | |
| 574 { | |
| 575 return "python"; | |
| 576 } | |
| 577 | |
| 578 | |
| 579 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion() | |
| 580 { | |
| 581 return PLUGIN_VERSION; | |
| 582 } | |
| 583 } |