mitkTotalSegmentatorTool.h

Go to the documentation of this file.

/*============================================================================
 
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.
 
============================================================================*/
#ifndef mitkTotalSegmentatorTool_h
#define mitkTotalSegmentatorTool_h
 
#include <mitkSegWithPreviewTool.h>
#include <MitkPythonSegmentationExports.h>
 
#include <functional>
#include <map>
#include <string>
#include <vector>
 
namespace us
{
  class ModuleResource;
}
 
namespace mitk
{
  class MITKPYTHONSEGMENTATION_EXPORT TotalSegmentatorTool : public SegWithPreviewTool
  {
  public:
    mitkClassMacro(TotalSegmentatorTool, SegWithPreviewTool);
    itkFactorylessNewMacro(Self);
    itkCloneMacro(Self);
 
    enum class Speed
    {
      Normal,
      Fast,
      Fastest
    };
 
    using CommandRunner = std::function<bool(const std::string& executable, const std::vector<std::string>& args)>;
 
    const char *GetName() const override;
 
    mitk::Label::AlgorithmType GetAlgorithmType() const override;
 
    us::ModuleResource GetIconResource() const override;
    void Activated() override;
 
    itkSetMacro(Task, std::string);
    itkGetConstMacro(Task, std::string);
 
    itkSetMacro(Speed, Speed);
    itkGetConstMacro(Speed, Speed);
 
    itkSetMacro(Device, std::string);
    itkGetConstMacro(Device, std::string);
 
    itkSetMacro(ExecutablePath, std::string);
    itkGetConstMacro(ExecutablePath, std::string);
 
    void SetLabelNameLookup(const std::map<mitk::Label::PixelType, std::string>& lookup);
 
    void SetCommandRunner(CommandRunner runner);
 
    const std::string& GetLastErrorMessage() const;
 
  protected:
    TotalSegmentatorTool();
    ~TotalSegmentatorTool() override;
 
    void DoUpdatePreview(const Image* inputAtTimeStep, const Image* oldSegAtTimeStep, MultiLabelSegmentation* previewImage, TimeStepType timeStep) override;
    void UpdatePrepare() override;
 
  private:
    std::vector<std::string> BuildArguments(const std::string& inputImagePath, const std::string& outputImagePath) const;
 
    void MapLabelsToSegmentation(const MultiLabelSegmentation* source, MultiLabelSegmentation* dest) const;
 
    std::string m_MitkTempDir;
    std::string m_Task = "total";
    Speed m_Speed = Speed::Normal;
    std::string m_Device = "gpu";
    std::string m_ExecutablePath;
    std::map<mitk::Label::PixelType, std::string> m_LabelNameLookup;
    CommandRunner m_CommandRunner;
    std::string m_LastErrorMessage;
  };
} // namespace mitk
#endif