diff --git a/Modules/Python/mitkPythonService.cpp b/Modules/Python/mitkPythonService.cpp
index 41881e8f8a..8fe3dc225f 100644
--- a/Modules/Python/mitkPythonService.cpp
+++ b/Modules/Python/mitkPythonService.cpp
@@ -1,431 +1,431 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "mitkPythonService.h"
#include <Python.h>
#include <mitkIOUtil.h>
#include <QFile>
#include <QDir>
#include <PythonQt.h>
#include "PythonPath.h"
const QString mitk::PythonService::m_TmpImageName("temp_mitk_image");
mitk::PythonService::PythonService()
: m_ItkWrappingAvailable( true ), m_OpenCVWrappingAvailable( true ), m_VtkWrappingAvailable( true )
{
if( !m_PythonManager.isPythonInitialized() )
{
MITK_DEBUG("PythonService") << "initialize python";
m_PythonManager.setInitializationFlags(PythonQt::RedirectStdOut);
m_PythonManager.initialize();
//std::string result = m_PythonManager.executeString( "sys.path", ctkAbstractPythonManager::EvalInput );
//MITK_DEBUG("mitk::PythonService") << "result of 'sys.path': " << result.toString().toStdString();
QString pythonCommand(PYTHONPATH_COMMAND);
MITK_DEBUG("PythonService") << "registering python paths" << PYTHONPATH_COMMAND;
m_PythonManager.executeString( pythonCommand, ctkAbstractPythonManager::FileInput );
MITK_DEBUG("mitk::PythonService") << "Trying to import ITK";
m_PythonManager.executeString( "import itk", ctkAbstractPythonManager::SingleInput );
m_ItkWrappingAvailable = !m_PythonManager.pythonErrorOccured();
MITK_DEBUG("mitk::PythonService") << "m_ItkWrappingAvailable: " << (m_ItkWrappingAvailable? "yes": "no");
if( !m_ItkWrappingAvailable )
{
MITK_WARN << "ITK Python wrapping not available. Please check build settings or PYTHON_PATH settings.";
}
MITK_DEBUG("mitk::PythonService") << "Trying to import OpenCv";
m_PythonManager.executeString( "import cv2", ctkAbstractPythonManager::SingleInput );
m_OpenCVWrappingAvailable = !m_PythonManager.pythonErrorOccured();
MITK_DEBUG("mitk::PythonService") << "m_OpenCVWrappingAvailable: " << (m_OpenCVWrappingAvailable? "yes": "no");
if( !m_OpenCVWrappingAvailable )
{
MITK_WARN << "OpenCV Python wrapping not available. Please check build settings or PYTHON_PATH settings.";
}
MITK_DEBUG("mitk::PythonService") << "Trying to import VTK";
m_PythonManager.executeString( "import vtk", ctkAbstractPythonManager::SingleInput );
m_VtkWrappingAvailable = !m_PythonManager.pythonErrorOccured();
MITK_DEBUG("mitk::PythonService") << "m_VtkWrappingAvailable: " << (m_VtkWrappingAvailable? "yes": "no");
if( !m_VtkWrappingAvailable )
{
MITK_WARN << "VTK Python wrapping not available. Please check build settings or PYTHON_PATH settings.";
}
}
//std::string result = m_PythonManager.executeString( "5+5", ctkAbstractPythonManager::EvalInput );
//MITK_DEBUG("mitk::PythonService") << "result of '5+5': " << result.toString().toStdString();
}
mitk::PythonService::~PythonService()
{
}
std::string mitk::PythonService::Execute(const std::string &stdpythonCommand, int commandType)
{
QString pythonCommand = QString::fromStdString(stdpythonCommand);
{
MITK_DEBUG("mitk::PythonService") << "pythonCommand = " << pythonCommand.toStdString();
MITK_DEBUG("mitk::PythonService") << "commandType = " << commandType;
}
QVariant result;
bool commandIssued = true;
if(commandType == IPythonService::SINGLE_LINE_COMMAND )
result = m_PythonManager.executeString(pythonCommand, ctkAbstractPythonManager::SingleInput );
else if(commandType == IPythonService::MULTI_LINE_COMMAND )
result = m_PythonManager.executeString(pythonCommand, ctkAbstractPythonManager::FileInput );
else if(commandType == IPythonService::EVAL_COMMAND )
result = m_PythonManager.executeString(pythonCommand, ctkAbstractPythonManager::EvalInput );
else
commandIssued = false;
if(commandIssued)
this->NotifyObserver(pythonCommand.toStdString());
return result.toString().toStdString();
}
std::vector<mitk::PythonVariable> mitk::PythonService::GetVariableStack() const
{
std::vector<mitk::PythonVariable> list;
PyObject* dict = PyImport_GetModuleDict();
PyObject* object = PyDict_GetItemString(dict, "__main__");
PyObject* dirMain = PyObject_Dir(object);
PyObject* tempObject;
if(dirMain)
{
std::string attr, attrValue, attrType;
for(int i = 0; i<PyList_Size(dirMain); i++)
{
tempObject = PyList_GetItem(dirMain, i);
attr = PyString_AsString(tempObject);
tempObject = PyObject_GetAttrString(object, attr.c_str());
attrType = tempObject->ob_type->tp_name;
if(PyUnicode_Check(tempObject) || PyString_Check(tempObject))
attrValue = PyString_AsString(tempObject);
else
attrValue = "";
mitk::PythonVariable var;
var.m_Name = attr;
var.m_Value = attrValue;
var.m_Type = attrType;
list.push_back(var);
}
}
return list;
}
void mitk::PythonService::AddPythonCommandObserver(mitk::PythonCommandObserver *observer)
{
if(!m_Observer.contains(observer))
m_Observer.append(observer);
}
void mitk::PythonService::RemovePythonCommandObserver(mitk::PythonCommandObserver *observer)
{
m_Observer.removeOne(observer);
}
void mitk::PythonService::NotifyObserver(const std::string &command)
{
MITK_DEBUG("mitk::PythonService") << "number of observer " << m_Observer.size();
for( size_t i=0; i< m_Observer.size(); ++i )
{
m_Observer.at(i)->CommandExecuted(command);
}
}
QString mitk::PythonService::GetTempImageName(const std::string& ext) const
{
QString tmpFolder = QDir::tempPath();
QString fileName = tmpFolder + QDir::separator() + m_TmpImageName + QString::fromStdString(ext);
return fileName;
}
bool mitk::PythonService::CopyToPythonAsItkImage(mitk::Image *image, const std::string &stdvarName)
{
QString varName = QString::fromStdString( stdvarName );
// save image
QString fileName = this->GetTempImageName( mitk::IOUtil::DEFAULTIMAGEEXTENSION );
- MITK_DEBUG("PythonService") << "Saving temporary file " << fileName;
+ MITK_DEBUG("PythonService") << "Saving temporary file " << fileName.toStdString();
if( !mitk::IOUtil::SaveImage(image, fileName.toStdString()) )
{
MITK_ERROR << "Temporary file could not be created.";
}
else
{
// TODO CORRECT TYPE SETUP, MAKE MITK_DEBUG("PythonService") MITK_DEBUG("PythonService")
int dim = image->GetDimension();
mitk::PixelType pixelType = image->GetPixelType();
itk::ImageIOBase::IOPixelType ioPixelType = image->GetPixelType().GetPixelTypeId();
// default pixeltype: unsigned short
QString type = "US";
if( ioPixelType == itk::ImageIOBase::SCALAR )
{
if( pixelType.GetTypeId() == typeid(double) )
type = "D";
else if( pixelType.GetTypeId() == typeid(float) )
type = "F";
if( pixelType.GetTypeId() == typeid(long double) )
type = "LD";
else if( pixelType.GetTypeId() == typeid(short) )
type = "SS";
else if( pixelType.GetTypeId() == typeid(signed char) )
type = "SC";
else if( pixelType.GetTypeId() == typeid(signed int) )
type = "SI";
else if( pixelType.GetTypeId() == typeid(signed long) )
type = "SL";
else if( pixelType.GetTypeId() == typeid(signed short) )
type = "SS";
else if( pixelType.GetTypeId() == typeid(unsigned char) )
type = "UC";
else if( pixelType.GetTypeId() == typeid(unsigned int) )
type = "UI";
else if( pixelType.GetTypeId() == typeid(unsigned long) )
type = "UL";
else if( pixelType.GetTypeId() == typeid(unsigned short) )
type = "US";
}
MITK_DEBUG("PythonService") << "Got mitk image with type " << type.toStdString() << " and dim " << dim;
QString command;
command.append( QString("imageType = itk.Image[itk.%1, %2]\n") .arg( type ).arg( dim ) );
command.append( QString("readerType = itk.ImageFileReader[imageType]\n") );
command.append( QString("reader = readerType.New()\n") );
command.append( QString("reader.SetFileName( \"%1\" )\n") .arg(fileName) );
command.append( QString("reader.Update()\n") );
command.append( QString("%1 = reader.GetOutput()\n").arg( varName ) );
MITK_DEBUG("PythonService") << "Issuing python command " << command.toStdString();
this->Execute( command.toStdString(), IPythonService::MULTI_LINE_COMMAND );
QFile file( fileName );
MITK_DEBUG("PythonService") << "Removing file " << fileName.toStdString();
file.remove();
return true;
}
return false;
}
mitk::Image::Pointer mitk::PythonService::CopyItkImageFromPython(const std::string &stdvarName)
{
QString varName = QString::fromStdString( stdvarName );
mitk::Image::Pointer mitkImage;
QString command;
QString fileName = GetTempImageName( mitk::IOUtil::DEFAULTIMAGEEXTENSION );
MITK_DEBUG("PythonService") << "Saving temporary file with python itk code " << fileName.toStdString();
command.append( QString( "writer = itk.ImageFileWriter[ %1 ].New()\n").arg( varName ) );
command.append( QString( "writer.SetFileName( \"%1\" )\n").arg(fileName) );
command.append( QString( "writer.SetInput( %1 )\n").arg(varName) );
command.append( QString( "writer.Update()\n" ) );
MITK_DEBUG("PythonService") << "Issuing python command " << command.toStdString();
this->Execute(command.toStdString(), IPythonService::MULTI_LINE_COMMAND );
try
{
MITK_DEBUG("PythonService") << "Loading temporary file " << fileName.toStdString() << " as MITK image";
mitkImage = mitk::IOUtil::LoadImage( fileName.toStdString() );
}
catch(std::exception& e)
{
MITK_ERROR << e.what();
}
QFile file(fileName);
if( file.exists() )
{
MITK_DEBUG("PythonService") << "Removing temporary file " << fileName.toStdString();
file.remove();
}
return mitkImage;
}
bool mitk::PythonService::CopyToPythonAsCvImage( mitk::Image* image, const std::string& stdvarName )
{
QString varName = QString::fromStdString( stdvarName );
bool convert = false;
if(image->GetDimension() != 2)
{
MITK_ERROR << "Only 2D images allowed for OpenCV images";
return convert;
}
// try to save mitk image
QString fileName = this->GetTempImageName( ".bmp" );
MITK_DEBUG("PythonService") << "Saving temporary file " << fileName.toStdString();
if( !mitk::IOUtil::SaveImage(image, fileName.toStdString()) )
{
MITK_ERROR << "Temporary file " << fileName.toStdString() << " could not be created.";
return convert;
}
QString command;
command.append( QString("%1 = cv.LoadImage(\"%2\")\n") .arg( varName ).arg( fileName ) );
MITK_DEBUG("PythonService") << "Issuing python command " << command.toStdString();
this->Execute(command.toStdString(), IPythonService::MULTI_LINE_COMMAND );
MITK_DEBUG("PythonService") << "Removing file " << fileName.toStdString();
QFile file(fileName);
file.remove();
convert = true;
return convert;
}
mitk::Image::Pointer mitk::PythonService::CopyCvImageFromPython( const std::string& stdvarName )
{
QString varName = QString::fromStdString( stdvarName );
mitk::Image::Pointer mitkImage;
QString command;
QString fileName = GetTempImageName( ".bmp" );
MITK_DEBUG("PythonService") << "run python command to save image with opencv to " << fileName.toStdString();
command.append( QString( "cv.SaveImage(\"%1\", %2)\n").arg( fileName ).arg( varName ) );
MITK_DEBUG("PythonService") << "Issuing python command " << command.toStdString();
this->Execute(command.toStdString(), IPythonService::MULTI_LINE_COMMAND );
try
{
MITK_DEBUG("PythonService") << "Loading temporary file " << fileName.toStdString() << " as MITK image";
mitkImage = mitk::IOUtil::LoadImage( fileName.toStdString() );
}
catch(std::exception& e)
{
MITK_ERROR << e.what();
}
QFile file(fileName);
if( file.exists() )
{
MITK_DEBUG("PythonService") << "Removing temporary file " << fileName.toStdString();
file.remove();
}
return mitkImage;
}
ctkAbstractPythonManager *mitk::PythonService::GetPythonManager()
{
return &m_PythonManager;
}
mitk::Surface::Pointer mitk::PythonService::CopyVtkPolyDataFromPython( const std::string& stdvarName )
{
QString varName = QString::fromStdString( stdvarName );
mitk::Surface::Pointer newSurface;
QString command;
QString fileName = GetTempImageName( ".stl" );
MITK_DEBUG("PythonService") << "run python command to save polydata with vtk to " << fileName.toStdString();
command = QString (
"vtkStlWriter = vtk.vtkSTLWriter()\n"
"vtkStlWriter.SetInput(%1)\n"
"vtkStlWriter.SetFileName(\"%2\")\n"
"vtkStlWriter.Write()\n").arg(varName).arg(fileName);
MITK_DEBUG("PythonService") << "Issuing python command " << command.toStdString();
this->Execute(command.toStdString(), IPythonService::MULTI_LINE_COMMAND );
try
{
MITK_DEBUG("PythonService") << "Loading temporary file " << fileName.toStdString() << " as MITK Surface";
newSurface = mitk::IOUtil::LoadSurface( fileName.toStdString() );
}
catch(std::exception& e)
{
MITK_ERROR << e.what();
}
QFile file(fileName);
if( file.exists() )
{
MITK_DEBUG("PythonService") << "Removing temporary file " << fileName.toStdString();
file.remove();
}
return newSurface;
}
bool mitk::PythonService::CopyToPythonAsVtkPolyData( mitk::Surface* surface, const std::string& stdvarName )
{
QString varName = QString::fromStdString( stdvarName );
bool convert = false;
// try to save mitk image
QString fileName = this->GetTempImageName( ".stl" );
MITK_DEBUG("PythonService") << "Saving temporary file " << fileName.toStdString();
if( !mitk::IOUtil::SaveSurface( surface, fileName.toStdString() ) )
{
MITK_ERROR << "Temporary file " << fileName.toStdString() << " could not be created.";
return convert;
}
QString command;
command.append( QString("vtkStlReader = vtk.vtkSTLReader()\n") );
command.append( QString("vtkStlReader.SetFileName(\"%1\")\n").arg( fileName ) );
command.append( QString("%1 = vtkStlReader.GetOutput()").arg( fileName ) );
MITK_DEBUG("PythonService") << "Issuing python command " << command.toStdString();
this->Execute(command.toStdString(), IPythonService::MULTI_LINE_COMMAND );
MITK_DEBUG("PythonService") << "Removing file " << fileName.toStdString();
QFile file(fileName);
file.remove();
convert = true;
return convert;
}
bool mitk::PythonService::IsItkPythonWrappingAvailable()
{
return m_ItkWrappingAvailable;
}
bool mitk::PythonService::IsOpenCvPythonWrappingAvailable()
{
return m_OpenCVWrappingAvailable;
}
bool mitk::PythonService::IsVtkPythonWrappingAvailable()
{
return m_VtkWrappingAvailable;
}