Mercurial > hg > orthanc-python
annotate Sources/Plugin.cpp @ 91:55c41aa7053b
On Orthanc stopping, wait for all the queued events to have been processed
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 19 Aug 2021 14:18:23 +0200 |
| parents | 068551520123 |
| children | 627b8a19fb9f |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 2 * Python plugin for Orthanc | |
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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 #include "StorageArea.h" |
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32 |
| 0 | 33 #include "RestCallbacks.h" |
| 34 #include "PythonModule.h" | |
| 35 | |
| 36 #include "Autogenerated/sdk.h" | |
| 37 | |
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38 #include "../Resources/Orthanc/Plugins/OrthancPluginCppWrapper.h" |
| 0 | 39 |
| 40 #include <boost/algorithm/string/predicate.hpp> | |
| 41 #include <boost/filesystem.hpp> | |
| 42 | |
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43 // The "dl_iterate_phdr()" function (to walk through shared libraries) |
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44 // is not available on Microsoft Windows and Apple OS X |
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45 #if defined(_WIN32) |
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46 # define HAS_DL_ITERATE 0 |
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47 #elif defined(__APPLE__) && defined(__MACH__) |
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48 # define HAS_DL_ITERATE 0 |
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49 #else |
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50 # define HAS_DL_ITERATE 1 |
| 0 | 51 #endif |
| 52 | |
| 53 | |
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54 #include "PythonString.h" |
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55 |
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56 PyObject* LookupDictionary(PyObject* module, PyObject* args) |
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57 { |
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58 const char* name = NULL; |
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59 |
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60 if (!PyArg_ParseTuple(args, "s", &name)) |
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61 { |
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62 PyErr_SetString(PyExc_TypeError, "Please provide a string containing the name of the DICOM tag of interest"); |
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63 return NULL; |
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64 } |
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65 else |
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66 { |
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67 OrthancPluginDictionaryEntry entry; |
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68 |
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69 OrthancPluginErrorCode code = OrthancPluginLookupDictionary(OrthancPlugins::GetGlobalContext(), &entry, name); |
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70 if (code == OrthancPluginErrorCode_Success) |
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71 { |
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72 /** |
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73 * "PyGILState_Ensure()" can be invoked several times from the |
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74 * same thread, so no problem in creating a PythonLock even if |
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75 * the GIL is already locked. |
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76 **/ |
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77 PythonLock lock; |
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78 |
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79 PythonObject kw(lock, PyDict_New()); |
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80 PyDict_SetItemString(kw.GetPyObject(), "Group", PyLong_FromUnsignedLong(entry.group)); |
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81 PyDict_SetItemString(kw.GetPyObject(), "Element", PyLong_FromUnsignedLong(entry.element)); |
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82 PyDict_SetItemString(kw.GetPyObject(), "ValueRepresentation", PyLong_FromUnsignedLong(entry.vr)); |
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83 PyDict_SetItemString(kw.GetPyObject(), "MinMultiplicity", PyLong_FromUnsignedLong(entry.minMultiplicity)); |
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84 PyDict_SetItemString(kw.GetPyObject(), "MaxMultiplicity", PyLong_FromUnsignedLong(entry.maxMultiplicity)); |
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85 |
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86 return kw.Release(); |
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87 } |
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88 else |
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89 { |
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90 std::string message = "Unknown DICOM tag: " + std::string(name); |
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91 PyErr_SetString(PyExc_TypeError, message.c_str()); |
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92 return NULL; |
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93 } |
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94 } |
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95 } |
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96 |
| 0 | 97 |
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98 PyObject* CreateDicom(PyObject* module, PyObject* args) |
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99 { |
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100 // The GIL is locked at this point (no need to create "PythonLock") |
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101 const char* json = NULL; |
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102 PyObject* pixelData = NULL; |
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103 long int flags = 0; |
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104 |
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105 if (!PyArg_ParseTuple(args, "sOl", &json, &pixelData, &flags)) |
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106 { |
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107 PyErr_SetString(PyExc_TypeError, "Please provide a JSON string, an orthanc.Image object, and a set of orthanc.CreateDicomFlags"); |
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108 return NULL; |
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109 } |
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110 else |
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111 { |
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112 OrthancPluginImage* image = NULL; |
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113 |
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114 if (pixelData == Py_None) |
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115 { |
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116 // No pixel data |
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117 } |
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118 else if (Py_TYPE(pixelData) == GetOrthancPluginImageType()) |
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119 { |
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120 image = reinterpret_cast<sdk_OrthancPluginImage_Object*>(pixelData)->object_; |
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121 } |
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122 else |
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123 { |
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124 PyErr_SetString(PyExc_TypeError, "Second parameter is not a valid orthanc.Image object"); |
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125 return NULL; |
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126 } |
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127 |
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128 OrthancPlugins::MemoryBuffer buffer; |
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129 OrthancPluginErrorCode code = OrthancPluginCreateDicom(OrthancPlugins::GetGlobalContext(), *buffer, json, image, |
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130 static_cast<OrthancPluginCreateDicomFlags>(flags)); |
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131 |
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132 if (code == OrthancPluginErrorCode_Success) |
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133 { |
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134 return PyBytes_FromStringAndSize(buffer.GetData(), buffer.GetSize()); |
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135 } |
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136 else |
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137 { |
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138 PyErr_SetString(PyExc_ValueError, "Cannot create the DICOM instance"); |
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139 return NULL; |
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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 |
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145 PyObject* GetInstanceData(sdk_OrthancPluginDicomInstance_Object* self, PyObject *args) |
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146 { |
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147 // The GIL is locked at this point (no need to create "PythonLock") |
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148 |
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149 if (self->object_ == NULL) |
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150 { |
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151 PyErr_SetString(PyExc_ValueError, "Invalid object"); |
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152 return NULL; |
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153 } |
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154 else |
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155 { |
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156 OrthancPluginDicomInstance* instance = reinterpret_cast<sdk_OrthancPluginDicomInstance_Object*>(self)->object_; |
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157 |
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158 const void* data = OrthancPluginGetInstanceData(OrthancPlugins::GetGlobalContext(), instance); |
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159 size_t size = OrthancPluginGetInstanceSize(OrthancPlugins::GetGlobalContext(), instance); |
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160 |
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161 if (data == NULL && |
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162 size != 0) |
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163 { |
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164 PyErr_SetString(PyExc_ValueError, "Accessing an invalid orthanc.DicomInstance object"); |
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165 return NULL; |
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166 } |
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167 else |
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168 { |
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169 return PyBytes_FromStringAndSize(reinterpret_cast<const char*>(data), size); |
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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 /** |
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176 * Contrarily to "OrthancPluginGetImageBuffer()" that provides a |
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177 * read-write pointer, the method "orthanc.Image.GetImageBuffer()" |
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178 * returns a copy of the image buffer. Use "CreateImageFromBuffer()" |
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179 * to create an image from a Python buffer. |
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180 **/ |
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181 PyObject* GetImageBuffer(sdk_OrthancPluginImage_Object* self, PyObject *args) |
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182 { |
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183 // The GIL is locked at this point (no need to create "PythonLock") |
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184 |
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185 if (self->object_ == NULL) |
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186 { |
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187 PyErr_SetString(PyExc_ValueError, "Invalid object"); |
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188 return NULL; |
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189 } |
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190 else |
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191 { |
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192 OrthancPluginImage* image = reinterpret_cast<sdk_OrthancPluginImage_Object*>(self)->object_; |
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193 |
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194 const void* buffer = OrthancPluginGetImageBuffer(OrthancPlugins::GetGlobalContext(), image); |
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195 size_t size = (OrthancPluginGetImagePitch(OrthancPlugins::GetGlobalContext(), image) * |
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196 OrthancPluginGetImageHeight(OrthancPlugins::GetGlobalContext(), image)); |
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197 |
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198 if (buffer == NULL && |
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199 size != 0) |
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200 { |
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201 PyErr_SetString(PyExc_ValueError, "Accessing an invalid orthanc.Image object"); |
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202 return NULL; |
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203 } |
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204 else |
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205 { |
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206 return PyBytes_FromStringAndSize(reinterpret_cast<const char*>(buffer), size); |
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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 /** |
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213 * This function is the Python alternative for function |
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214 * "OrthancPluginCreateImageAccessor()". Indeed, it is not possible to |
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215 * share a memory buffer between Orthanc and Python, so we have to |
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216 * create a copy of the image. |
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217 **/ |
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218 PyObject* CreateImageFromBuffer(PyObject* module, PyObject* args) |
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219 { |
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220 // The GIL is locked at this point (no need to create "PythonLock") |
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221 |
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222 unsigned long format, width, height, sourcePitch; |
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223 Py_buffer buffer; |
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224 |
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225 if (!PyArg_ParseTuple(args, "kkkks*", &format, &width, &height, &sourcePitch, &buffer)) |
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226 { |
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227 PyErr_SetString(PyExc_TypeError, "5 arguments are needed: image.PixelFormat, width, height, pitch and memory buffer"); |
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228 return NULL; |
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229 } |
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230 else if (static_cast<Py_ssize_t>(sourcePitch * height) != buffer.len) |
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231 { |
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232 PyBuffer_Release(&buffer); |
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233 |
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234 PyErr_SetString(PyExc_TypeError, "The size of the memory buffer must match the product of height by pitch"); |
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235 return NULL; |
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236 } |
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237 else |
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238 { |
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239 OrthancPluginImage* image = OrthancPluginCreateImage( |
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240 OrthancPlugins::GetGlobalContext(), static_cast<OrthancPluginPixelFormat>(format), width, height); |
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241 |
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242 if (image == NULL) |
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243 { |
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244 PyBuffer_Release(&buffer); |
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245 |
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246 PyErr_SetString(PyExc_ValueError, "Cannot create the image"); |
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247 return NULL; |
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248 } |
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249 else |
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250 { |
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251 // Copy the image line by line |
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252 unsigned long targetPitch = OrthancPluginGetImagePitch(OrthancPlugins::GetGlobalContext(), image); |
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253 |
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254 const uint8_t* sourcePixels = reinterpret_cast<const uint8_t*>(buffer.buf); |
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255 uint8_t* targetPixels = reinterpret_cast<uint8_t*>(OrthancPluginGetImageBuffer(OrthancPlugins::GetGlobalContext(), image)); |
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256 |
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257 unsigned long rowSize = std::min(sourcePitch, targetPitch); |
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258 |
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259 for (unsigned int y = 0; y < height; y++) |
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260 { |
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261 memcpy(targetPixels, sourcePixels, rowSize); |
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262 targetPixels += targetPitch; |
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263 sourcePixels += sourcePitch; |
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264 } |
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265 |
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266 PyBuffer_Release(&buffer); |
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267 |
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268 { |
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269 PyObject *argList = Py_BuildValue("Lb", image, false /* not borrowed */); |
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270 PyObject *python = PyObject_CallObject((PyObject *) GetOrthancPluginImageType(), argList); |
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271 Py_DECREF(argList); |
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272 return python; |
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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 |
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278 |
|
63
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279 |
| 0 | 280 static bool pythonEnabled_ = false; |
| 281 static std::string userScriptName_; | |
| 282 static std::vector<PyMethodDef> globalFunctions_; | |
| 283 | |
| 284 | |
| 285 static void InstallClasses(PyObject* module) | |
| 286 { | |
| 287 RegisterOrthancSdk(module); | |
| 288 } | |
| 289 | |
| 290 | |
| 291 static void SetupGlobalFunctions() | |
| 292 { | |
| 293 if (!globalFunctions_.empty()) | |
| 294 { | |
| 295 ORTHANC_PLUGINS_THROW_EXCEPTION(BadSequenceOfCalls); | |
| 296 } | |
| 297 | |
| 298 /** | |
| 299 * Add all the manual global functions | |
| 300 **/ | |
| 301 | |
| 302 std::list<PyMethodDef> functions; | |
| 303 | |
| 304 { | |
| 305 PyMethodDef f = { "RegisterRestCallback", RegisterRestCallback, METH_VARARGS, "" }; | |
| 306 functions.push_back(f); | |
| 307 } | |
| 308 | |
| 309 { | |
| 310 PyMethodDef f = { "RegisterOnChangeCallback", RegisterOnChangeCallback, METH_VARARGS, "" }; | |
| 311 functions.push_back(f); | |
| 312 } | |
| 313 | |
| 314 { | |
| 315 PyMethodDef f = { "RegisterOnStoredInstanceCallback", RegisterOnStoredInstanceCallback, | |
| 316 METH_VARARGS, "" }; | |
| 317 functions.push_back(f); | |
| 318 } | |
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319 |
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320 |
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321 /** |
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322 * New in release 3.0 |
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323 **/ |
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324 |
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325 { |
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326 PyMethodDef f = { "RegisterIncomingHttpRequestFilter", RegisterIncomingHttpRequestFilter, METH_VARARGS, "" }; |
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327 functions.push_back(f); |
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328 } |
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329 |
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330 |
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331 /** |
|
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332 * New in release 3.2 |
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333 **/ |
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334 |
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335 { |
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336 PyMethodDef f = { "LookupDictionary", LookupDictionary, METH_VARARGS, "" }; |
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337 functions.push_back(f); |
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338 } |
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339 |
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340 { |
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341 PyMethodDef f = { "CreateDicom", CreateDicom, METH_VARARGS, "" }; |
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342 functions.push_back(f); |
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343 } |
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344 |
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345 { |
|
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346 PyMethodDef f = { "CreateImageFromBuffer", CreateImageFromBuffer, METH_VARARGS, "" }; |
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347 functions.push_back(f); |
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348 } |
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349 |
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350 { |
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351 PyMethodDef f = { "RegisterFindCallback", RegisterFindCallback, METH_VARARGS, "" }; |
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352 functions.push_back(f); |
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353 } |
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354 |
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355 { |
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356 PyMethodDef f = { "RegisterMoveCallback", RegisterMoveCallback, METH_VARARGS, "" }; |
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357 functions.push_back(f); |
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358 } |
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359 |
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360 { |
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361 PyMethodDef f = { "RegisterWorklistCallback", RegisterWorklistCallback, METH_VARARGS, "" }; |
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362 functions.push_back(f); |
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363 } |
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364 |
| 0 | 365 |
| 366 /** | |
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367 * New in release 3.3 |
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368 **/ |
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369 |
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370 { |
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371 PyMethodDef f = { "RegisterStorageArea", RegisterStorageArea, METH_VARARGS, "" }; |
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372 functions.push_back(f); |
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373 } |
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374 |
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375 |
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376 /** |
| 0 | 377 * Append all the global functions that were automatically generated |
| 378 **/ | |
| 379 | |
| 380 const PyMethodDef* sdk = GetOrthancSdkFunctions(); | |
| 381 | |
| 382 for (size_t i = 0; sdk[i].ml_name != NULL; i++) | |
| 383 { | |
| 384 functions.push_back(sdk[i]); | |
| 385 } | |
| 386 | |
| 387 /** | |
| 388 * Flatten the list of functions into the vector | |
| 389 **/ | |
| 390 | |
| 391 globalFunctions_.resize(functions.size()); | |
| 392 std::copy(functions.begin(), functions.end(), globalFunctions_.begin()); | |
| 393 | |
| 394 PyMethodDef sentinel = { NULL }; | |
| 395 globalFunctions_.push_back(sentinel); | |
| 396 } | |
| 397 | |
| 398 | |
| 399 static PyMethodDef* GetGlobalFunctions() | |
| 400 { | |
| 401 if (globalFunctions_.empty()) | |
| 402 { | |
| 403 // "SetupGlobalFunctions()" should have been called | |
| 404 ORTHANC_PLUGINS_THROW_EXCEPTION(BadSequenceOfCalls); | |
| 405 } | |
| 406 else | |
| 407 { | |
| 408 return &globalFunctions_[0]; | |
| 409 } | |
| 410 } | |
| 411 | |
| 412 | |
| 413 | |
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414 #if HAS_DL_ITERATE == 1 |
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416 #include <dlfcn.h> |
| 0 | 417 #include <link.h> // For dl_phdr_info |
| 418 | |
| 419 static int ForceImportCallback(struct dl_phdr_info *info, size_t size, void *data) | |
| 420 { | |
| 421 /** | |
| 422 * The following line solves the error: "ImportError: | |
| 423 * /usr/lib/python2.7/dist-packages/PIL/_imaging.x86_64-linux-gnu.so: | |
| 424 * undefined symbol: PyExc_SystemError" | |
| 425 * https://stackoverflow.com/a/48517485/881731 | |
| 426 * | |
| 427 * dlopen("/usr/lib/x86_64-linux-gnu/libpython2.7.so", RTLD_NOW | RTLD_LAZY | RTLD_GLOBAL); | |
| 428 * | |
| 429 * Another fix consists in using LD_PRELOAD as follows: | |
| 430 * LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libpython2.7.so ~/Subversion/orthanc/i/Orthanc tutu.json | |
| 431 **/ | |
| 432 | |
| 433 std::string module(info->dlpi_name); | |
| 434 | |
| 435 if (module.find("python") != std::string::npos) | |
| 436 { | |
| 437 OrthancPlugins::LogWarning("Force global loading of Python shared library: " + module); | |
| 438 dlopen(module.c_str(), RTLD_NOW | RTLD_LAZY | RTLD_GLOBAL); | |
| 439 } | |
| 440 | |
| 441 return 0; | |
| 442 } | |
| 443 | |
| 444 #endif | |
| 445 | |
| 446 | |
| 447 extern "C" | |
| 448 { | |
| 449 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* c) | |
| 450 { | |
| 451 OrthancPlugins::SetGlobalContext(c); | |
| 452 OrthancPlugins::LogWarning("Python plugin is initializing"); | |
| 453 | |
| 454 | |
| 455 /* Check the version of the Orthanc core */ | |
| 456 if (OrthancPluginCheckVersion(c) == 0) | |
| 457 { | |
| 458 char info[1024]; | |
| 459 sprintf(info, "Your version of Orthanc (%s) must be above %d.%d.%d to run this plugin", | |
| 460 c->orthancVersion, | |
| 461 ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER, | |
| 462 ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER, | |
| 463 ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER); | |
| 464 OrthancPluginLogError(c, info); | |
| 465 return -1; | |
| 466 } | |
| 11 | 467 |
| 468 OrthancPluginSetDescription(c, "Run Python scripts as Orthanc plugins"); | |
| 469 | |
| 0 | 470 try |
| 471 { | |
| 472 /** | |
| 473 * Detection of the user script | |
| 474 **/ | |
| 475 | |
| 476 OrthancPlugins::OrthancConfiguration config; | |
| 477 | |
| 478 static const char* const OPTION = "PythonScript"; | |
| 479 | |
| 480 std::string script; | |
| 481 if (!config.LookupStringValue(script, OPTION)) | |
| 482 { | |
| 483 pythonEnabled_ = false; | |
| 484 | |
| 485 OrthancPlugins::LogWarning("The option \"" + std::string(OPTION) + "\" is not provided: " + | |
| 486 "Python scripting is disabled"); | |
| 487 } | |
| 488 else | |
| 489 { | |
| 490 pythonEnabled_ = true; | |
| 491 | |
| 492 /** | |
| 493 * Installation of the user script | |
| 494 **/ | |
| 495 | |
| 496 const boost::filesystem::path path(script); | |
| 497 if (!boost::iequals(path.extension().string(), ".py")) | |
| 498 { | |
| 499 OrthancPlugins::LogError("Python script must have the \".py\" file extension: " + | |
| 500 path.string()); | |
| 501 return -1; | |
| 502 } | |
| 503 | |
| 504 if (!boost::filesystem::is_regular_file(path)) | |
| 505 { | |
| 506 OrthancPlugins::LogError("Inexistent directory for the Python script: " + | |
| 507 path.string()); | |
| 508 return -1; | |
| 509 } | |
| 510 | |
| 511 boost::filesystem::path userScriptDirectory = boost::filesystem::absolute(path).parent_path(); | |
| 512 | |
| 513 { | |
| 514 boost::filesystem::path module = path.filename().replace_extension(""); | |
| 515 userScriptName_ = module.string(); | |
| 516 } | |
| 517 | |
| 518 OrthancPlugins::LogWarning("Using Python script \"" + userScriptName_ + | |
| 519 ".py\" from directory: " + userScriptDirectory.string()); | |
| 520 | |
| 521 | |
| 522 /** | |
| 523 * Initialization of Python | |
| 524 **/ | |
| 525 | |
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526 #if HAS_DL_ITERATE == 1 |
| 0 | 527 dl_iterate_phdr(ForceImportCallback, NULL); |
| 528 #endif | |
| 529 | |
| 530 SetupGlobalFunctions(); | |
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531 PythonLock::GlobalInitialize("orthanc", "OrthancException", |
| 0 | 532 GetGlobalFunctions, InstallClasses, |
| 533 config.GetBooleanValue("PythonVerbose", false)); | |
| 534 PythonLock::AddSysPath(userScriptDirectory.string()); | |
| 535 | |
| 536 | |
| 537 /** | |
| 538 * Force loading the declarations in the user script | |
| 539 **/ | |
| 540 | |
| 541 PythonLock lock; | |
| 542 | |
| 543 { | |
| 544 PythonModule module(lock, userScriptName_); | |
| 545 } | |
| 546 | |
| 547 std::string traceback; | |
| 548 if (lock.HasErrorOccurred(traceback)) | |
| 549 { | |
| 550 OrthancPlugins::LogError("Error during the installation of the Python script, " | |
| 551 "traceback:\n" + traceback); | |
| 552 return -1; | |
| 553 } | |
| 554 } | |
| 555 } | |
| 556 catch (ORTHANC_PLUGINS_EXCEPTION_CLASS& e) | |
| 557 { | |
| 558 OrthancPlugins::LogError("Exception while starting the Python plugin: " + | |
| 559 std::string(e.What(c))); | |
| 560 return -1; | |
| 561 } | |
| 562 | |
| 563 return 0; | |
| 564 } | |
| 565 | |
| 566 | |
| 567 ORTHANC_PLUGINS_API void OrthancPluginFinalize() | |
| 568 { | |
| 569 OrthancPlugins::LogWarning("Python plugin is finalizing"); | |
| 570 | |
| 571 if (pythonEnabled_) | |
| 572 { | |
| 573 FinalizeOnChangeCallback(); | |
| 574 FinalizeRestCallbacks(); | |
| 575 FinalizeOnStoredInstanceCallback(); | |
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576 FinalizeIncomingHttpRequestFilter(); |
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577 FinalizeDicomScpCallbacks(); |
| 0 | 578 |
| 579 PythonLock::GlobalFinalize(); | |
| 580 } | |
| 581 } | |
| 582 | |
| 583 | |
| 584 ORTHANC_PLUGINS_API const char* OrthancPluginGetName() | |
| 585 { | |
| 586 return "python"; | |
| 587 } | |
| 588 | |
| 589 | |
| 590 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion() | |
| 591 { | |
| 592 return PLUGIN_VERSION; | |
| 593 } | |
| 594 } |