diff --git a/Modules/PythonService/mitkPythonService.cpp b/Modules/PythonService/mitkPythonService.cpp index f153c44b4c..01d7a044af 100644 --- a/Modules/PythonService/mitkPythonService.cpp +++ b/Modules/PythonService/mitkPythonService.cpp @@ -1,633 +1,633 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkPythonService.h" #include #ifdef _DEBUG #undef _DEBUG #include #define _DEBUG #else #include #endif #include "PythonPath.h" #include #include #include #include #include #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION #include #include #ifndef WIN32 #include #endif #include "swigpyrun.h" #include typedef itksys::SystemTools ist; mitk::PythonService::PythonService() : m_ItkWrappingAvailable(true), m_ErrorOccured(false) { // for Linux, libpython needs to be opened before initializing the Python Interpreter to enable imports #ifndef WIN32 std::vector pythonIncludeVector; // get libpython file to open (taken from "Python3_INCLUDE_DIR" variable from CMake to dynamically do it for different python versions) boost::split(pythonIncludeVector, PYTHON_INCLUDE, boost::is_any_of( "/" ) ); std::string libPython = "lib"+pythonIncludeVector[pythonIncludeVector.size()-1]+".so"; dlopen(libPython.c_str(), RTLD_LAZY | RTLD_GLOBAL); #endif // Initialize Python interpreter and ensure global interpreter lock in order to execute python code safely if (!Py_IsInitialized()) { Py_Initialize(); } PyGILState_Ensure(); std::string programPath = mitk::IOUtil::GetProgramPath(); std::replace(programPath.begin(), programPath.end(), '\\', '/'); programPath.append("/"); MITK_INFO << programPath; std::string pythonCommand; // execute a string which imports packages that are needed and sets paths to directories pythonCommand.append("import SimpleITK as sitk\n"); pythonCommand.append("import SimpleITK._SimpleITK as _SimpleITK\n"); pythonCommand.append("import numpy\n"); pythonCommand.append("import site, sys\n"); pythonCommand.append("import os\n"); pythonCommand.append("sys.path.append('')\n"); pythonCommand.append("sys.path.append('" + programPath + "')\n"); pythonCommand.append("sys.path.append('" + std::string(BIN_DIR) + "')\n"); pythonCommand.append("sys.path.append('" +std::string(EXTERNAL_DIST_PACKAGES) + "')\n"); pythonCommand.append("\nsite.addsitedir('"+std::string(EXTERNAL_SITE_PACKAGES)+"')\n"); // in python 3.8 onwards, the path system variable is not longer used to find dlls // that's why the dlls that are needed for swig wrapping need to be searched manually std::string searchForDll = "if sys.version_info[1] > 7:\n" " os.add_dll_directory('"+std::string(EP_DLL_DIR)+"')\n"; pythonCommand.append(searchForDll); if (PyRun_SimpleString(pythonCommand.c_str()) == -1) { MITK_ERROR << "Something went wrong in setting the path in Python"; } PyObject *main = PyImport_AddModule("__main__"); m_GlobalDictionary = PyModule_GetDict(main); m_LocalDictionary = m_GlobalDictionary; m_ThreadState = PyEval_SaveThread(); } mitk::PythonService::~PythonService() { } void mitk::PythonService::AddRelativeSearchDirs(std::vector< std::string > dirs) { for (const auto& dir : dirs) { try { std::string path = std::string(MITK_ROOT) + dir; // sys.path.append enables to call scripts which are located in the given path std::string pythonCommand = "import sys\nsys.path.append('" + path + "')\n"; this->Execute(pythonCommand.c_str()); } catch (const mitk::Exception&) { mitkThrow() << "An error occured setting the relative project path"; } } } void mitk::PythonService::AddAbsoluteSearchDirs(std::vector< std::string > dirs) { - for (const auto dir : dirs) + for (const auto& dir : dirs) { try { // sys.path.append enables to call scripts which are located in the given path std::string pythonCommand = "import sys\nsys.path.append('" + dir + "')\n"; this->Execute(pythonCommand.c_str()); } catch (const mitk::Exception&) { mitkThrow() << "An error occured setting the absolute project path"; } } } std::string mitk::PythonService::Execute(const std::string &stdpythonCommand, int commandType) { if (!Py_IsInitialized()) { Py_Initialize(); } std::string result = ""; PyGILState_Ensure(); try { // command type is start symbol for python interpreter switch (commandType) { case IPythonService::SINGLE_LINE_COMMAND: commandType = Py_single_input; break; case IPythonService::MULTI_LINE_COMMAND: commandType = Py_file_input; break; case IPythonService::EVAL_COMMAND: commandType = Py_eval_input; break; default: commandType = Py_file_input; } // executes python code given as string // if result is NULL, an error occured PyObject* executionResult = PyRun_String(stdpythonCommand.c_str(), commandType, m_GlobalDictionary, m_LocalDictionary); // notifies registered observers that command has been executed this->NotifyObserver(stdpythonCommand); // if no error occured, the result is represented as string which is returned if (executionResult) { PyObject *objectsRepresentation = PyObject_Repr(executionResult); const char *resultChar = PyUnicode_AsUTF8(objectsRepresentation); result = std::string(resultChar); m_ThreadState = PyEval_SaveThread(); m_ErrorOccured = false; } else { m_ErrorOccured = true; mitkThrow() << "An error occured while running the Python code"; } } catch (const mitk::Exception& ) { PyErr_Print(); m_ThreadState = PyEval_SaveThread(); throw; } return result; } void mitk::PythonService::ExecuteScript(const std::string &pythonScript) { // read given file as string std::ifstream t(pythonScript.c_str()); std::string str((std::istreambuf_iterator(t)), std::istreambuf_iterator()); t.close(); // pass the file as string to the Execute() function try { this->Execute(str.c_str(), MULTI_LINE_COMMAND); } catch (const mitk::Exception&) { throw; } } std::vector mitk::PythonService::GetVariableStack() { // variables are returned as a list of type mitk::PythonVariable std::vector list; PyGILState_Ensure(); try { // vaiables are taken from the main module // get dictionary where these variables are stored PyObject *dict = PyImport_GetModuleDict(); PyObject *object = PyDict_GetItemString(dict, "__main__"); if (!object) { mitkThrow() << "An error occured getting the Dictionary"; } PyObject *dirMain = PyObject_Dir(object); PyObject *tempObject = nullptr; if (dirMain) { std::string name, attrValue, attrType; //iterate over python list of variables to get desired representation and store in returned variable list for (int i = 0; i < PyList_Size(dirMain); i++) { // get variable at current index tempObject = PyList_GetItem(dirMain, i); if (!tempObject) { mitkThrow() << "An error occured getting an item from the dictionary"; } // get variable name as string PyObject *objectsRepresentation = PyObject_Repr(tempObject); const char *objectChar = PyUnicode_AsUTF8(objectsRepresentation); std::string name = std::string(objectChar); name = name.substr(1, name.size() - 2); // get variable type as string tempObject = PyObject_GetAttrString(object, name.c_str()); if (!tempObject) { mitkThrow() << "Could not get the attribute to determine type"; } attrType = tempObject->ob_type->tp_name; // get variable value as string PyObject *valueStringRepresentation = PyObject_Repr(tempObject); const char *valueChar = PyUnicode_AsUTF8(valueStringRepresentation); std::string attrValue = std::string(valueChar); // build variable type to store mitk::PythonVariable var; var.m_Name = name; var.m_Value = attrValue; var.m_Type = attrType; list.push_back(var); } } m_ThreadState = PyEval_SaveThread(); } catch (const mitk::Exception&) { m_ThreadState = PyEval_SaveThread(); throw; } return list; } std::string mitk::PythonService::GetVariable(const std::string& name) { // get all variables from python context std::vector allVars; try { allVars = this->GetVariableStack(); } catch (const mitk::Exception&) { mitkThrow() << "Error getting the variable stack"; } // search for variable with given name for (const auto& var: allVars) { if (var.m_Name == name) { return var.m_Value; } } return ""; } bool mitk::PythonService::DoesVariableExist(const std::string& name) { bool varExists = false; // get all variables from python context std::vector allVars; try { allVars = this->GetVariableStack(); } catch (const mitk::Exception&) { mitkThrow() << "Error getting the variable stack"; } // check if variable with given name exists in context for (const auto& var: allVars) { if (var.m_Name == name) { varExists = true; break; } } return varExists; } void mitk::PythonService::AddPythonCommandObserver(mitk::PythonCommandObserver *observer) { //only add observer if it isn't already in list of observers if (!(std::find(m_Observer.begin(), m_Observer.end(), observer) != m_Observer.end())) { m_Observer.push_back(observer); } } void mitk::PythonService::RemovePythonCommandObserver(mitk::PythonCommandObserver *observer) { // iterate over all registered observers and remove the passed observer for (std::vector::iterator iter = m_Observer.begin(); iter != m_Observer.end(); ++iter) { if (*iter == observer) { m_Observer.erase(iter); break; } } } void mitk::PythonService::NotifyObserver(const std::string &command) { // call CommandExecuted() from observer interface in order to inform observers that command has been executed for (const auto& observer: this->m_Observer) { observer->CommandExecuted(command); } } int mitk::PythonService::GetNumberOfObserver() { return m_Observer.size(); } bool mitk::PythonService::IsSimpleItkPythonWrappingAvailable() { return m_ItkWrappingAvailable; } bool mitk::PythonService::CopyToPythonAsSimpleItkImage(mitk::Image::Pointer image, const std::string &stdvarName) { // this string is a python command which consists of two functions // setup() is called in order to create an image variable on python side. At this point this is a MITK image // convert_to_sitk() converts the MITK image from the previous step into a SimpleITK image. Spacing and Origin need to be set manually // as these informations get lost when converting the image to an numpy array and back (only contains pixel information) std::string transferToPython = "import pyMITK\n" "import SimpleITK as sitk\n" "mitk_image = None\n" "geometry = None\n" +stdvarName+" = None\n" "\n" "def setup(image_from_cxx):\n" " print ('setup called with', image_from_cxx)\n" " global mitk_image\n" " mitk_image = image_from_cxx\n" "\n" "def convert_to_sitk(spacing, origin):\n" " np = pyMITK.GetArrayViewFromImage(mitk_image)\n" " global "+stdvarName+"\n" " "+stdvarName+" = sitk.GetImageFromArray(np)\n" " npSpacingArray = numpy.array(spacing , dtype=float)\n" " "+stdvarName+".SetSpacing(npSpacingArray)\n" " npOriginArray = numpy.array(origin , dtype=float)\n" " " +stdvarName +".SetOrigin(npOriginArray)\n"; // execute code to make the implemented functions available in the Python context (function is not executed, only definition loaded in Python) this->Execute(transferToPython); mitk::Image::Pointer *img = ℑ PyGILState_Ensure();//PyGILState_STATE gState = PyGILState_Ensure(); //necessary for transfer array from C++ to Python - import_array(); + _import_array(); PyObject *main = PyImport_ImportModule("__main__"); if (main == NULL) { mitkThrow() << "Something went wrong getting the main module"; } // create new pyobject from given image using SWIG swig_type_info *pTypeInfo = nullptr; pTypeInfo = SWIG_TypeQuery("_p_itk__SmartPointerT_mitk__Image_t"); int owned = 0; PyObject *pInstance = SWIG_NewPointerObj(reinterpret_cast(img), pTypeInfo, owned); if (pInstance == NULL) { mitkThrow() << "Something went wrong creating the Python instance of the image"; } // get image spacing and convert it to Python array int numberOfImageDimension = image->GetDimension(); auto spacing = image->GetGeometry()->GetSpacing(); auto *spacingptr = &spacing; npy_intp dims[] = {numberOfImageDimension}; PyObject *spacingArray = PyArray_SimpleNewFromData(1, dims, NPY_DOUBLE, (void *)spacingptr); // get image origin and convert it to Python array auto origin = image->GetGeometry()->GetOrigin(); auto *originptr = &origin; PyObject *originArray = PyArray_SimpleNewFromData(1, dims, NPY_DOUBLE, (void *)originptr); // transfer image to python context by calling setup() function which was defined in Python string above PyObject *setup = PyObject_GetAttrString(main, "setup"); PyObject *result = PyObject_CallFunctionObjArgs(setup, pInstance, NULL); if (result == NULL) { mitkThrow() << "Something went wrong setting the MITK image in Python"; } // convert MITK image in Python context to SimpleITK image and tranfer correct origin and spacing calling convert_to_sitk() from above PyObject *convert = PyObject_GetAttrString(main, "convert_to_sitk"); result = PyObject_CallFunctionObjArgs(convert,spacingArray, originArray, NULL); if (result == NULL) { mitkThrow() << "Something went wrong converting the MITK image to a SimpleITK image"; } m_ThreadState = PyEval_SaveThread(); return true; } mitk::Image::Pointer mitk::PythonService::CopySimpleItkImageFromPython(const std::string &stdvarName) { mitk::Image::Pointer mitkImage; // Python code to convert SimpleITK image to MITK image std::string convertToMITKImage = "import SimpleITK as sitk\n" "import pyMITK\n" "numpy_array = sitk.GetArrayViewFromImage("+stdvarName+")\n" "mitk_image = pyMITK.GetImageFromArray(numpy_array)\n" "spacing = "+stdvarName+".GetSpacing()\n" "origin = "+stdvarName +".GetOrigin()\n"; // after executing this, the desired mitk image is available in the Python context with the variable name mitk_image this->Execute(convertToMITKImage); - PyGILState_Ensure();//PyGILState_STATE gState = PyGILState_Ensure(); + PyGILState_Ensure(); // get dictionary with variables from main context PyObject *main = PyImport_AddModule("__main__"); PyObject *globals = PyModule_GetDict(main); // get mitk_image from Python context PyObject *pyImage = PyDict_GetItemString(globals, "mitk_image"); if (pyImage==NULL) { mitkThrow() << "Could not get image from Python"; } // res is status variable to check if result when getting the image from Python context is OK int res = 0; void *voidImage; swig_type_info *pTypeInfo = nullptr; pTypeInfo = SWIG_TypeQuery("_p_itk__SmartPointerT_mitk__Image_t"); // get image from Python context as C++ void pointer res = SWIG_ConvertPtr(pyImage, &voidImage, pTypeInfo, 0); if (!SWIG_IsOK(res)) { mitkThrow() << "Could not cast image to C++ type"; } // cast C++ void pointer to mitk::Image::Pointer mitkImage = *(reinterpret_cast(voidImage)); // as spacing and origin again got lost when transferring between SimpleITK and MITK (see CopyToPythonAsSimpleItkImage()) we need to set them manually // get spacing from Python context PyObject *spacing = PyDict_GetItemString(globals, "spacing"); mitk::Vector3D spacingMITK; // convert Python Array to C++ vector for (int i = 0; i < PyTuple_GET_SIZE(spacing); i++) { PyObject *spacingPy = PyTuple_GetItem(spacing, i); double elem = PyFloat_AsDouble(spacingPy); spacingMITK[i] = elem; } // get origin from Python context PyObject *origin = PyDict_GetItemString(globals, "origin"); mitk::Point3D originMITK; // convert Python Array to Point3D for (int i = 0; i < PyTuple_GET_SIZE(origin); i++) { PyObject *originPy = PyTuple_GetItem(origin, i); double elem = PyFloat_AsDouble(originPy); originMITK[i] = elem; } m_ThreadState = PyEval_SaveThread(); // set origin and spacing correctly mitkImage->GetGeometry()->SetSpacing(spacingMITK); mitkImage->GetGeometry()->SetOrigin(originMITK); return mitkImage; } bool mitk::PythonService::CopyMITKImageToPython(mitk::Image::Pointer &image, const std::string &stdvarName) { // this string is a python command which consists one functions // setup() is called in order to create an image variable on python side. This is the MITK image which is passed std::string transferToPython = "import pyMITK\n" + stdvarName +" = None\n" "\n" "def setup(image_from_cxx):\n" " print ('setup called with', image_from_cxx)\n" " global "+stdvarName+"\n" " "+stdvarName+" = image_from_cxx\n"; // execute code to make the implemented functions available in the Python context (function is not executed, only // definition loaded in Python) this->Execute(transferToPython); mitk::Image::Pointer *img = ℑ // load main context to have access to defined function from above - PyGILState_Ensure();//PyGILState_STATE gState = PyGILState_Ensure(); + PyGILState_Ensure(); PyObject *main = PyImport_ImportModule("__main__"); if (main == NULL) { mitkThrow() << "Something went wrong getting the main module"; } // create new pyobject from given image using SWIG swig_type_info *pTypeInfo = nullptr; pTypeInfo = SWIG_TypeQuery("_p_itk__SmartPointerT_mitk__Image_t"); int owned = 0; PyObject *pInstance = SWIG_NewPointerObj(reinterpret_cast(img), pTypeInfo, owned); if (pInstance == NULL) { mitkThrow() << "Something went wrong creating the Python instance of the image"; } // call setup() function in Python with created PyObject of image PyObject *setup = PyObject_GetAttrString(main, "setup"); PyObject *result = PyObject_CallFunctionObjArgs(setup, pInstance, NULL); if (result == NULL) { mitkThrow() << "Something went wrong setting the MITK image in Python"; } m_ThreadState = PyEval_SaveThread(); return true; } mitk::Image::Pointer GetImageFromPyObject(PyObject *pyImage) { // helper function to get a MITK image from a PyObject mitk::Image::Pointer mitkImage; // res is status variable to check if result when getting the image from Python context is OK int res = 0; void *voidImage; swig_type_info *pTypeInfo = nullptr; pTypeInfo = SWIG_TypeQuery("_p_itk__SmartPointerT_mitk__Image_t"); // get image from Python context as C++ void pointer res = SWIG_ConvertPtr(pyImage, &voidImage, pTypeInfo, 0); if (!SWIG_IsOK(res)) { mitkThrow() << "Could not cast image to C++ type"; } // cast C++ void pointer to mitk::Image::Pointer mitkImage = *(reinterpret_cast(voidImage)); return mitkImage; } mitk::Image::Pointer mitk::PythonService::CopyMITKImageFromPython(const std::string &stdvarName) { mitk::Image::Pointer mitkImage; PyGILState_Ensure(); // get image from Python context as PyObject PyObject *main = PyImport_AddModule("__main__"); PyObject *globals = PyModule_GetDict(main); PyObject *pyImage = PyDict_GetItemString(globals, stdvarName.c_str()); if (pyImage==NULL) { mitkThrow() << "Could not get image from Python"; } // convert PyObject to mitk::Image mitkImage = GetImageFromPyObject(pyImage); m_ThreadState = PyEval_SaveThread(); return mitkImage; } std::vector mitk::PythonService::CopyListOfMITKImagesFromPython(const std::string &listVarName) { std::vector mitkImages; - PyGILState_Ensure();//PyGILState_STATE gState = PyGILState_Ensure(); + PyGILState_Ensure(); // get the list of the variable name as python list PyObject *main = PyImport_AddModule("__main__"); PyObject *globals = PyModule_GetDict(main); PyObject *pyImageList = PyDict_GetItemString(globals, listVarName.c_str()); if (pyImageList == NULL) { mitkThrow() << "Could not get image list from Python"; } // iterate over python list of images and convert them to C++ mitk::Image for (int i = 0; i < PyList_GET_SIZE(pyImageList);i++) { PyObject *pyImage = PyList_GetItem(pyImageList, i); mitk::Image::Pointer img = GetImageFromPyObject(pyImage); mitkImages.push_back(img); } m_ThreadState = PyEval_SaveThread(); return mitkImages; } bool mitk::PythonService::PythonErrorOccured() const { return m_ErrorOccured; }