diff --git a/Modules/Python/PythonPath.h.in b/Modules/Python/PythonPath.h.in
index 2f06a8943c..1c01e76078 100644
--- a/Modules/Python/PythonPath.h.in
+++ b/Modules/Python/PythonPath.h.in
@@ -1,7 +1,7 @@
-#define PYTHONPATH_ITK_LIBRARY_DIRS "@ITK_LIBRARY_DIRS@"
-#define PYTHONPATH_WRAP_ITK_DIR "@ITK_DIR@/Wrapping/WrapITK/Python"
-
-#define PYTHONPATH_VTK_LIBRARY_DIRS "@VTK_LIBRARY_DIRS@"
-#define PYTHONPATH_VTK_PYTHON_WRAPPING_DIR "@VTK_DIR@/Wrapping/Python"
-
-#define PYTHONPATH_OPEN_CV_LIBRARY_DIRS "@OpenCV_DIR@/lib"
+#define PYTHONPATH_COMMAND "import sys\n"\
+"sys.path.append('@ITK_LIBRARY_DIRS@')\n"\
+"sys.path.append('@ITK_DIR@/Wrapping/WrapITK/Python')\n"\
+"sys.path.append('@ITK_LIBRARY_DIRS@')\n"\
+"sys.path.append('@VTK_LIBRARY_DIRS@')\n"\
+"sys.path.append('@VTK_DIR@/Wrapping/Python')\n"\
+"sys.path.append('@OpenCV_DIR@/lib')"
diff --git a/Modules/Python/QmitkCtkPythonShell.cpp b/Modules/Python/QmitkCtkPythonShell.cpp
index 58b62e522e..cabe523711 100644
--- a/Modules/Python/QmitkCtkPythonShell.cpp
+++ b/Modules/Python/QmitkCtkPythonShell.cpp
@@ -1,80 +1,81 @@
/*===================================================================
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 "QmitkCtkPythonShell.h"
#include <ctkAbstractPythonManager.h>
#include <QDragEnterEvent>
#include <QDropEvent>
#include <QMimeData>
#include <QUrl>
#include "mitkPythonService.h"
#include <mitkModuleContext.h>
#include <usServiceReference.h>
#include <mitkGetModuleContext.h>
struct QmitkCtkPythonShellData
{
mitk::PythonService* m_PythonService;
};
QmitkCtkPythonShell::QmitkCtkPythonShell(QWidget* parent)
: ctkPythonConsole(parent), d( new QmitkCtkPythonShellData )
{
mitk::ModuleContext* context = mitk::GetModuleContext();
mitk::ServiceReference serviceRef = context->GetServiceReference<mitk::IPythonService>();
d->m_PythonService = dynamic_cast<mitk::PythonService*> ( context->GetService<mitk::IPythonService>(serviceRef) );
assert( d->m_PythonService );
this->initialize( d->m_PythonService->GetPythonManager() );
}
QmitkCtkPythonShell::~QmitkCtkPythonShell()
{
delete d;
}
void QmitkCtkPythonShell::dragEnterEvent(QDragEnterEvent *event)
{
event->accept();
}
void QmitkCtkPythonShell::dropEvent(QDropEvent *event)
{
QList<QUrl> urls = event->mimeData()->urls();
for(int i = 0; i < urls.size(); i++)
{
d->m_PythonService->Execute( urls[i].toString(), mitk::IPythonService::SINGLE_LINE_COMMAND );
}
}
bool QmitkCtkPythonShell::canInsertFromMimeData( const QMimeData *source ) const
{
return true;
}
void QmitkCtkPythonShell::executeCommand(const QString& command)
{
+ MITK_DEBUG("QmitkCtkPythonShell") << "executing command " << command.toStdString();
ctkPythonConsole::executeCommand(command);
d->m_PythonService->NotifyObserver(command);
}
void QmitkCtkPythonShell::Paste(const QString &command)
{
if( this->isVisible() )
{
this->executeCommand( command );
}
}
diff --git a/Modules/Python/QmitkPythonVariableStackTableModel.cpp b/Modules/Python/QmitkPythonVariableStackTableModel.cpp
index 68e25862ee..fec5626ce7 100755
--- a/Modules/Python/QmitkPythonVariableStackTableModel.cpp
+++ b/Modules/Python/QmitkPythonVariableStackTableModel.cpp
@@ -1,218 +1,219 @@
/*===================================================================
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 "QmitkPythonVariableStackTableModel.h"
#include <QMimeData>
#include <mitkModuleContext.h>
#include <usServiceReference.h>
#include <mitkDataNode.h>
#include <mitkGetModuleContext.h>
#include <QStringList>
#include <QMessageBox>
const QString QmitkPythonVariableStackTableModel::MITK_IMAGE_VAR_NAME = "mitkImage";
const QString QmitkPythonVariableStackTableModel::MITK_SURFACE_VAR_NAME = "mitkSurface";
QmitkPythonVariableStackTableModel::QmitkPythonVariableStackTableModel(QObject *parent)
:QAbstractTableModel(parent)
{
mitk::ModuleContext* context = mitk::GetModuleContext();
mitk::ServiceReference serviceRef = context->GetServiceReference<mitk::IPythonService>();
m_PythonService = context->GetService<mitk::IPythonService>(serviceRef);
m_PythonService->AddPythonCommandObserver( this );
}
QmitkPythonVariableStackTableModel::~QmitkPythonVariableStackTableModel()
{
m_PythonService->RemovePythonCommandObserver( this );
}
bool QmitkPythonVariableStackTableModel::dropMimeData ( const QMimeData * data, Qt::DropAction action, int row, int column, const QModelIndex & parent )
{
// Early exit, returning true, but not actually doing anything (ignoring data).
if (action == Qt::IgnoreAction)
return true;
// Note, we are returning true if we handled it, and false otherwise
bool returnValue = false;
if(data->hasFormat("application/x-mitk-datanodes"))
{
MITK_DEBUG("QmitkPythonVariableStackTableModel") << "dropped MITK DataNode";
returnValue = true;
QString arg = QString(data->data("application/x-mitk-datanodes").data());
QStringList listOfDataNodeAddressPointers = arg.split(",");
QStringList::iterator slIter;
int i = 0;
int j = 0;
for (slIter = listOfDataNodeAddressPointers.begin();
slIter != listOfDataNodeAddressPointers.end();
slIter++)
{
long val = (*slIter).toLong();
mitk::DataNode* node = static_cast<mitk::DataNode *>((void*)val);
mitk::Image* mitkImage = dynamic_cast<mitk::Image*>(node->GetData());
+ MITK_DEBUG("QmitkPythonVariableStackTableModel") << "mitkImage is not null " << (mitkImage != 0? "true": "false");
if( mitkImage )
{
QString varName = MITK_IMAGE_VAR_NAME;
if( i > 0 )
varName = QString("%1%2").arg(MITK_IMAGE_VAR_NAME).arg(i);
- MITK_DEBUG("varName") << "varName" << varName;
+ MITK_DEBUG("varName") << "varName" << varName.toStdString();
bool exportAsCvImage = m_PythonService->IsOpenCvPythonWrappingAvailable();
if( mitkImage->GetDimension() == 2 && exportAsCvImage )
{
int ret = QMessageBox::question(NULL, "Export option",
"2D image detected. Export as OpenCV image to Python instead of an ITK image?",
QMessageBox::Yes | QMessageBox::No, QMessageBox::No);
exportAsCvImage = ret == QMessageBox::Yes;
if(exportAsCvImage)
{
m_PythonService->CopyToPythonAsCvImage( mitkImage, MITK_IMAGE_VAR_NAME );
++i;
}
}
if( !exportAsCvImage )
{
if( m_PythonService->IsItkPythonWrappingAvailable() )
{
m_PythonService->CopyToPythonAsItkImage( mitkImage, MITK_IMAGE_VAR_NAME );
++i;
}
else
{
MITK_ERROR << "ITK Python wrapping not available. Skipping export for image " << node->GetName();
}
}
}
else
{
mitk::Surface* surface = dynamic_cast<mitk::Surface*>(node->GetData());
if( surface )
{
QString varName = MITK_SURFACE_VAR_NAME;
if( j > 0 )
varName = QString("%1%2").arg(MITK_SURFACE_VAR_NAME).arg(j);
MITK_DEBUG("varName") << "varName" << varName;
if( m_PythonService->IsVtkPythonWrappingAvailable() )
{
m_PythonService->CopyToPythonAsVtkPolyData( surface, MITK_SURFACE_VAR_NAME );
++j;
}
else
{
MITK_ERROR << "VTK Python wrapping not available. Skipping export for surface " << node->GetName();
}
}
}
}
}
return returnValue;
}
QVariant QmitkPythonVariableStackTableModel::headerData(int section, Qt::Orientation orientation,
int role) const
{
QVariant headerData;
// show only horizontal header
if ( role == Qt::DisplayRole )
{
if( orientation == Qt::Horizontal )
{
// first column: "Attribute"
if(section == 0)
headerData = "Attribute";
else if(section == 1)
headerData = "Value";
else if(section == 2)
headerData = "Type";
}
}
return headerData;
}
Qt::ItemFlags QmitkPythonVariableStackTableModel::flags(const QModelIndex &index) const
{
Qt::ItemFlags flags = QAbstractItemModel::flags(index);
if(index.isValid())
return Qt::ItemIsDragEnabled | Qt::ItemIsDropEnabled | flags;
else
return Qt::ItemIsDropEnabled | flags;
}
int QmitkPythonVariableStackTableModel::rowCount(const QModelIndex &) const
{
return m_VariableStack.size();
}
int QmitkPythonVariableStackTableModel::columnCount(const QModelIndex &) const
{
return 3;
}
QVariant QmitkPythonVariableStackTableModel::data(const QModelIndex &index, int role) const
{
if (index.isValid() && !m_VariableStack.empty())
{
if(role == Qt::DisplayRole)
{
mitk::PythonVariable item = m_VariableStack.at(index.row());
if(index.column() == 0)
return item.m_Name;
if(index.column() == 1)
return item.m_Value;
if(index.column() == 2)
return item.m_Type;
}
}
return QVariant();
}
QStringList QmitkPythonVariableStackTableModel::mimeTypes() const
{
return QAbstractTableModel::mimeTypes();
QStringList types;
types << "application/x-mitk-datanodes";
types << "application/x-qabstractitemmodeldatalist";
return types;
}
Qt::DropActions QmitkPythonVariableStackTableModel::supportedDropActions() const
{
return Qt::CopyAction | Qt::MoveAction;
}
void QmitkPythonVariableStackTableModel::CommandExecuted(const QString &pythonCommand)
{
MITK_DEBUG("QmitkPythonVariableStackTableModel") << "command was executed " << pythonCommand.toStdString();
m_VariableStack = m_PythonService->GetVariableStack();
QAbstractTableModel::reset();
}
QList<mitk::PythonVariable> QmitkPythonVariableStackTableModel::GetVariableStack() const
{
return m_VariableStack;
}
diff --git a/Modules/Python/QmitkPythonVariableStackTableView.cpp b/Modules/Python/QmitkPythonVariableStackTableView.cpp
index 53273e136a..f3bf206bb1 100755
--- a/Modules/Python/QmitkPythonVariableStackTableView.cpp
+++ b/Modules/Python/QmitkPythonVariableStackTableView.cpp
@@ -1,75 +1,84 @@
/*===================================================================
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 "QmitkPythonVariableStackTableView.h"
#include <usModuleContext.h>
#include <usServiceReference.h>
#include <mitkGetModuleContext.h>
#include <mitkRenderingManager.h>
QmitkPythonVariableStackTableView::QmitkPythonVariableStackTableView(QWidget *parent)
:QTableView(parent)
{
m_TableModel = new QmitkPythonVariableStackTableModel(parent);
m_TableModel->CommandExecuted("");
this->setSelectionBehavior( QAbstractItemView::SelectRows );
this->setAlternatingRowColors(true);
this->setDropIndicatorShown(true);
this->setAcceptDrops(true);
this->setModel( m_TableModel );
mitk::ModuleContext* context = mitk::GetModuleContext();
mitk::ServiceReference serviceRef = context->GetServiceReference<mitk::IPythonService>();
m_PythonService = context->GetService<mitk::IPythonService>(serviceRef);
connect( this, SIGNAL(doubleClicked ( const QModelIndex& )), this, SLOT( OnVariableStackDoubleClicked(const QModelIndex&) ) );
}
QmitkPythonVariableStackTableView::~QmitkPythonVariableStackTableView()
{
}
void QmitkPythonVariableStackTableView::SetDataStorage(mitk::DataStorage *_DataStorage)
{
m_DataStorage = _DataStorage;
}
void QmitkPythonVariableStackTableView::OnVariableStackDoubleClicked(const QModelIndex &index)
{
if( m_DataStorage.IsNull() || m_PythonService == 0 )
{
MITK_ERROR << "QmitkPythonVariableStackTableView not configured correctly. Quit";
return;
}
+ int row = index.row();
QList<mitk::PythonVariable> variableStack = m_TableModel->GetVariableStack();
- QString varName = variableStack.at(index.row()).m_Name;
+ {
+ MITK_DEBUG("QmitkPythonVariableStackTableView") << "row " << row;
+ MITK_DEBUG("QmitkPythonVariableStackTableView") << "variableStack.size(): " << variableStack.size();
+ }
+
+ QString varName = variableStack.at(row).m_Name;
- MITK_DEBUG("QmitkPythonVariableStackTableView") << varName;
+ {
+ MITK_DEBUG("QmitkPythonVariableStackTableView") << varName.toStdString();
+ }
mitk::Image::Pointer mitkImage = m_PythonService->CopyItkImageFromPython(varName);
if( mitkImage.IsNotNull() )
{
std::string nodeName = varName.toStdString();
mitk::DataNode::Pointer node = mitk::DataNode::New();
+ node->SetName ( nodeName );
m_DataStorage->Add(node);
node->SetData( mitkImage );
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
}
diff --git a/Modules/Python/mitkPythonActivator.cpp b/Modules/Python/mitkPythonActivator.cpp
index 7de905e7c4..62963304e8 100644
--- a/Modules/Python/mitkPythonActivator.cpp
+++ b/Modules/Python/mitkPythonActivator.cpp
@@ -1,101 +1,61 @@
/*===================================================================
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.
===================================================================*/
#ifndef mitkPythonActivator_h
#define mitkPythonActivator_h
// Microservices
#include <usModuleActivator.h>
#include "mitkModuleContext.h"
#include "mitkPythonService.h"
#include <usServiceRegistration.h>
-#include "PythonPath.h"
namespace mitk
{
///
/// installs the PythonService
/// runs all initial commands (setting env paths etc)
///
class PythonActivator : public mitk::ModuleActivator
{
public:
void Load(mitk::ModuleContext* context)
{
- // Registering PythonService as MicroService
- m_PythonService = itk::SmartPointer<mitk::PythonService>(new PythonService());
+ // Registering PythonService as MicroService
+ m_PythonService = itk::SmartPointer<mitk::PythonService>(new PythonService());
- ServiceProperties _PythonServiceProps;
- _PythonServiceProps["Name"] = std::string("PythonService");
+ ServiceProperties _PythonServiceProps;
+ _PythonServiceProps["Name"] = std::string("PythonService");
- context->RegisterService<mitk::IPythonService>(m_PythonService, _PythonServiceProps);
-
- MITK_DEBUG("PythonActivator") << "registering python paths";
-
- QString _PYTHONPATH_ITK_LIBRARY_DIRS(PYTHONPATH_ITK_LIBRARY_DIRS);
- MITK_DEBUG("PythonActivator") << "_PYTHONPATH_ITK_LIBRARY_DIRS" << _PYTHONPATH_ITK_LIBRARY_DIRS.toStdString();
-
- QString _PYTHONPATH_WRAP_ITK_DIR(PYTHONPATH_WRAP_ITK_DIR);
- MITK_DEBUG("PythonActivator") << "_PYTHONPATH_WRAP_ITK_DIR" << _PYTHONPATH_WRAP_ITK_DIR.toStdString();
-
- QString _PYTHONPATH_VTK_LIBRARY_DIRS(PYTHONPATH_VTK_LIBRARY_DIRS);
- MITK_DEBUG("PythonActivator") << "_PYTHONPATH_VTK_LIBRARY_DIRS" << _PYTHONPATH_VTK_LIBRARY_DIRS.toStdString();
-
- QString _PYTHONPATH_VTK_PYTHON_WRAPPING_DIR(PYTHONPATH_VTK_PYTHON_WRAPPING_DIR);
- MITK_DEBUG("PythonActivator") << "_PYTHONPATH_VTK_PYTHON_WRAPPING_DIR" << _PYTHONPATH_VTK_PYTHON_WRAPPING_DIR.toStdString();
-
- QString _PYTHONPATH_OPEN_CV_LIBRARY_DIRS(PYTHONPATH_OPEN_CV_LIBRARY_DIRS);
- MITK_DEBUG("PythonActivator") << "_PYTHONPATH_OPEN_CV_LIBRARY_DIRS" << _PYTHONPATH_OPEN_CV_LIBRARY_DIRS.toStdString();
-
- QString basecommand = "sys.path.append('%1');";
- QString pythonCommand;
-
- pythonCommand = basecommand.arg(_PYTHONPATH_ITK_LIBRARY_DIRS);
- MITK_DEBUG("PythonActivator") << "issuing command " << pythonCommand.toStdString();
- m_PythonService->Execute(pythonCommand, mitk::IPythonService::SINGLE_LINE_COMMAND );
-
- pythonCommand = basecommand.arg(_PYTHONPATH_WRAP_ITK_DIR);
- MITK_DEBUG("PythonActivator") << "issuing command " << pythonCommand.toStdString();
- m_PythonService->Execute(pythonCommand, mitk::IPythonService::SINGLE_LINE_COMMAND );
-
- pythonCommand = basecommand.arg(_PYTHONPATH_VTK_LIBRARY_DIRS);
- MITK_DEBUG("PythonActivator") << "issuing command " << pythonCommand.toStdString();
- m_PythonService->Execute(pythonCommand, mitk::IPythonService::SINGLE_LINE_COMMAND );
-
- pythonCommand = basecommand.arg(_PYTHONPATH_VTK_PYTHON_WRAPPING_DIR);
- MITK_DEBUG("PythonActivator") << "issuing command " << pythonCommand.toStdString();
- m_PythonService->Execute(pythonCommand, mitk::IPythonService::SINGLE_LINE_COMMAND );
-
- pythonCommand = basecommand.arg(_PYTHONPATH_OPEN_CV_LIBRARY_DIRS);
- MITK_DEBUG("PythonActivator") << "issuing command " << pythonCommand.toStdString();
- m_PythonService->Execute(pythonCommand, mitk::IPythonService::SINGLE_LINE_COMMAND );
+ context->RegisterService<mitk::IPythonService>(m_PythonService, _PythonServiceProps);
}
- void Unload(mitk::ModuleContext* )
+ void Unload(mitk::ModuleContext* context)
{
+ m_PythonService = 0;
}
~PythonActivator()
{
}
private:
itk::SmartPointer<mitk::PythonService> m_PythonService;
};
}
US_EXPORT_MODULE_ACTIVATOR(mitkPython, mitk::PythonActivator)
#endif
diff --git a/Modules/Python/mitkPythonService.cpp b/Modules/Python/mitkPythonService.cpp
index b45a36a4f7..ae86c6c6d6 100644
--- a/Modules/Python/mitkPythonService.cpp
+++ b/Modules/Python/mitkPythonService.cpp
@@ -1,379 +1,422 @@
/*===================================================================
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();
+
+ QVariant 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.";
+ }
+
+ }
+ //QVariant result = m_PythonManager.executeString( "5+5", ctkAbstractPythonManager::EvalInput );
+ //MITK_DEBUG("mitk::PythonService") << "result of '5+5': " << result.toString().toStdString();
}
mitk::PythonService::~PythonService()
{
}
QVariant mitk::PythonService::Execute(const QString &pythonCommand, int commandType)
{
{
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);
return result;
}
QList<mitk::PythonVariable> mitk::PythonService::GetVariableStack() const
{
QList<mitk::PythonVariable> list;
PyObject* dict = PyImport_GetModuleDict();
PyObject* object = PyDict_GetItemString(dict, "__main__");
PyObject* dirMain = PyObject_Dir(object);
PyObject* tempObject;
if(dirMain)
{
QString 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.toLocal8Bit().data());
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.append(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 QString &command)
{
MITK_DEBUG("mitk::PythonService") << "number of observer " << m_Observer.size();
foreach(mitk::PythonCommandObserver* observer, m_Observer)
{
observer->CommandExecuted(command);
}
}
QString mitk::PythonService::GetTempImageName(const QString& ext) const
{
QString tmpFolder = QDir::tempPath();
QString fileName = tmpFolder + QDir::separator() + m_TmpImageName + ext;
return fileName;
}
bool mitk::PythonService::CopyToPythonAsItkImage(mitk::Image *image, const QString &varName)
{
// save image
QString fileName = this->GetTempImageName( QString::fromStdString(mitk::IOUtil::DEFAULTIMAGEEXTENSION) );
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("import itk\n") );
- command.append( QString("imageType = itk.Image[%1, %2]\n") .arg( type ).arg( dim ) );
+ 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, 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 QString &varName)
{
mitk::Image::Pointer mitkImage;
QString command;
QString fileName = GetTempImageName( QString::fromStdString( mitk::IOUtil::DEFAULTIMAGEEXTENSION ) );
MITK_DEBUG("PythonService") << "Saving temporary file with python itk code " << fileName.toStdString();
- command.append( QString("import itk\n") );
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, 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 QString& varName )
{
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( QString::fromStdString(".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("import cv\n") );
+
command.append( QString("%1 = cv.LoadImage(\"%2\")\n") .arg( varName ).arg( fileName ) );
MITK_DEBUG("PythonService") << "Issuing python command " << command.toStdString();
this->Execute(command, 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 QString& varName )
{
mitk::Image::Pointer mitkImage;
QString command;
QString fileName = GetTempImageName( QString::fromStdString( ".bmp" ) );
MITK_DEBUG("PythonService") << "run python command to save image with opencv to " << fileName.toStdString();
- command.append( QString("import cv\n") );
+
command.append( QString( "cv.SaveImage(\"%1\", %2)\n").arg( fileName ).arg( varName ) );
MITK_DEBUG("PythonService") << "Issuing python command " << command.toStdString();
this->Execute(command, 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 QString& varName )
{
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, 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 QString& varName )
{
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("import vtk\n") );
+
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, 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 true; //TODO
+ return m_ItkWrappingAvailable; //TODO
}
bool mitk::PythonService::IsOpenCvPythonWrappingAvailable()
{
- return true; //TODO
+ return m_OpenCVWrappingAvailable; //TODO
}
bool mitk::PythonService::IsVtkPythonWrappingAvailable()
{
- return true; //TODO
+ return m_VtkWrappingAvailable; //TODO
}
diff --git a/Modules/Python/mitkPythonService.h b/Modules/Python/mitkPythonService.h
index 687e31c163..8428504ee6 100644
--- a/Modules/Python/mitkPythonService.h
+++ b/Modules/Python/mitkPythonService.h
@@ -1,92 +1,94 @@
/*===================================================================
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.
===================================================================*/
#ifndef mitkPythonService_h
#define mitkPythonService_h
#include "mitkIPythonService.h"
#include <itkLightObject.h>
#include <ctkAbstractPythonManager.h>
#include "mitkSurface.h"
namespace mitk
{
///
/// implementation of the IPythonService using ctkabstractpythonmanager
/// \see IPythonService
class PythonService: public itk::LightObject, public mitk::IPythonService
{
public:
///
/// instantiate python manager here
PythonService();
///
/// empty implementation...
~PythonService();
///
/// \see IPythonService::Execute()
QVariant Execute( const QString& pythonCommand, int commandType = SINGLE_LINE_COMMAND );
///
/// \see IPythonService::GetVariableStack()
QList<PythonVariable> GetVariableStack() const;
///
/// \see IPythonService::AddPythonCommandObserver()
void AddPythonCommandObserver( PythonCommandObserver* observer );
///
/// \see IPythonService::RemovePythonCommandObserver()
void RemovePythonCommandObserver( PythonCommandObserver* observer );
///
/// \see IPythonService::NotifyObserver()
void NotifyObserver( const QString& command );
///
/// \see IPythonService::IsItkPythonWrappingAvailable()
bool IsItkPythonWrappingAvailable();
///
/// \see IPythonService::CopyToPythonAsItkImage()
bool CopyToPythonAsItkImage( mitk::Image* image, const QString& varName );
///
/// \see IPythonService::CopyItkImageFromPython()
mitk::Image::Pointer CopyItkImageFromPython( const QString& varName );
///
/// \see IPythonService::IsOpenCvPythonWrappingAvailable()
bool IsOpenCvPythonWrappingAvailable();
///
/// \see IPythonService::CopyToPythonAsCvImage()
bool CopyToPythonAsCvImage( mitk::Image* image, const QString& varName );
///
/// \see IPythonService::CopyCvImageFromPython()
mitk::Image::Pointer CopyCvImageFromPython( const QString& varName );
///
/// \see IPythonService::IsVtkPythonWrappingAvailable()
bool IsVtkPythonWrappingAvailable();
///
/// \see IPythonService::CopyToPythonAsVtkPolyData()
bool CopyToPythonAsVtkPolyData( mitk::Surface* surface, const QString& varName );
///
/// \see IPythonService::CopyVtkPolyDataFromPython()
mitk::Surface::Pointer CopyVtkPolyDataFromPython( const QString& varName );
///
/// \return the ctk abstract python manager instance
ctkAbstractPythonManager* GetPythonManager();
protected:
QString GetTempImageName(const QString &ext) const;
private:
QList<PythonCommandObserver*> m_Observer;
ctkAbstractPythonManager m_PythonManager;
static const QString m_TmpImageName;
-
+ bool m_ItkWrappingAvailable;
+ bool m_OpenCVWrappingAvailable;
+ bool m_VtkWrappingAvailable;
};
}
#endif
diff --git a/Modules/Python/resources/PythonSnippets.xml b/Modules/Python/resources/PythonSnippets.xml
index 7b9ceb16e7..61fc3cf768 100644
--- a/Modules/Python/resources/PythonSnippets.xml
+++ b/Modules/Python/resources/PythonSnippets.xml
@@ -1,4 +1,4 @@
<?xml version="1.0" encoding="UTF-8"?>
<PythonSnippets>
- <PythonSnippet key="medianfilter" value="filter = itk.MedianImageFilter[ IMAGE, IMAGE ].New() filter.SetRadius( 1 ) filter.SetInput( IMAGE ) filter.Update() IMAGE = filter.GetOutput()"/>
+ <PythonSnippet key="medianfilter" value="filter = itk.MedianImageFilter[ mitkImage, mitkImage ].New() filter.SetRadius( 1 ) filter.SetInput( mitkImage ) filter.Update() mitkImage_new = filter.GetOutput()"/>
</PythonSnippets>