mitkTumorInvasionClassification.h

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/*===================================================================

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 TumorInvasionAnalysis_H
#define TumorInvasionAnalysis_H

// MITK
#include "mitkCommon.h"
#include <MitkTumorInvasionAnalysisExports.h>
// DATA
#include <mitkDataCollection.h>
// FORESTS
#include <mitkVigraRandomForestClassifier.h>

namespace mitk
{
  class MITKTUMORINVASIONANALYSIS_EXPORT TumorInvasionClassification
  {
  public:
    TumorInvasionClassification();
    ~TumorInvasionClassification() {}
    void SelectTrainingSamples(DataCollection *collection, unsigned int mode = 0);

    void PrepareResponseSamples(DataCollection *collection);

    void LearnProgressionFeatures(DataCollection *collection,
                                  std::vector<std::string> modalitiesList,
                                  size_t forestSize = 300,
                                  size_t treeDepth = 10);

    void PredictInvasion(DataCollection *collection, std::vector<std::string> modalitiesList);

    void SanitizeResults(DataCollection *collection, std::string resultID = "RESULT");

    void SetTrainMargin(size_t dil2d, size_t dil3d)
    {
      m_TargetDil2D = dil2d;
      m_TargetDil3D = dil3d;
    }

    void SetClassRatio(ScalarType ratio) { m_ClassRatio = ratio; }
    void SetGlobalsStatsFile(std::string fn) { m_GlobalStatsFile = fn; }
    void SamplesWeightingActivated(bool isActive) { m_WeightSamples = isActive; }
    void SetTargetID(std::string targetID = "TARGET") { m_TargetID = targetID; }
    void SetTumorID(std::string tumorID = "GTV") { m_TumorID = tumorID; }
    void SetMaskID(std::string maskID = "BRAINMASK") { m_MaskID = maskID; }
    void SetResultID(std::string resultID = "RESULT") { m_ResultID = resultID; }
    void UseRandomizedTrees(bool useRandom) { m_Randomize = useRandom; }
    void DescriptionToLogFile(DataCollection *collection, std::string outputFile);

    void SaveRandomForest(std::string filename);

    void LoadRandomForest(std::string);

  protected:
  private:
    // DATA
    mitk::VigraRandomForestClassifier m_Forest;
    unsigned int m_TargetDil2D;
    unsigned int m_TargetDil3D;

    ScalarType m_ClassRatio;

    std::string m_GlobalStatsFile;

    std::string m_TargetID;
    std::string m_TumorID;
    std::string m_MaskID;
    std::string m_ResultID;

    bool m_Randomize;
    bool m_WeightSamples;
  };
} // end namespace
#endif