PlotCanvas.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#pragma once

// OpenMS_GUI config
#include <OpenMS/VISUAL/OpenMS_GUIConfig.h>

//OpenMS
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/VersionInfo.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/DRange.h>
#include <OpenMS/KERNEL/DimMapper.h>
#include <OpenMS/VISUAL/LayerDataBase.h>
#include <OpenMS/VISUAL/MISC/CommonDefs.h>

//QT
#include <QtWidgets>
#include <QRubberBand>

class QWheelEvent;
class QKeyEvent;
class QMouseEvent;
class QFocusEvent;
class QMenu;

//STL
#include <stack>
#include <vector>

namespace OpenMS
{
  class PlotWidget;
  class LayerDataChrom;
  class LayerDataPeak;
  class LayerDataFeature;
  class LayerDataConsensus;

  using LayerDataBaseUPtr = std::unique_ptr<LayerDataBase>;
  using LayerDataChromUPtr = std::unique_ptr<LayerDataChrom>;
  using LayerDataPeakUPtr = std::unique_ptr<LayerDataPeak>;
  using LayerDataFeatureUPtr = std::unique_ptr<LayerDataFeature>;
  using LayerDataConsensusUPtr = std::unique_ptr<LayerDataConsensus>;

  class LayerStack
  {
    public:
      void addLayer(LayerDataBaseUPtr new_layer);

      const LayerDataBase& getLayer(const Size index) const;

      LayerDataBase& getLayer(const Size index);

      const LayerDataBase& getCurrentLayer() const;

      LayerDataBase& getCurrentLayer();

      void setCurrentLayer(Size index);
      
      Size getCurrentLayerIndex() const;
      
      bool empty() const;

      Size getLayerCount() const;

      void removeLayer(Size layer_index);

      void removeCurrentLayer();
  
  protected:
      std::vector<LayerDataBaseUPtr> layers_;
  private:
      Size current_layer_ = -1;
  };

  class OPENMS_GUI_DLLAPI PlotCanvas :
    public QWidget,
    public DefaultParamHandler
  {
    Q_OBJECT

public:

    typedef LayerDataBase::ExperimentType ExperimentType;
    typedef LayerDataBase::ExperimentSharedPtrType ExperimentSharedPtrType;
    typedef LayerDataBase::ConstExperimentSharedPtrType ConstExperimentSharedPtrType;
    typedef LayerDataBase::ODExperimentSharedPtrType ODExperimentSharedPtrType;
    typedef LayerDataBase::FeatureMapType FeatureMapType;
    typedef LayerDataBase::FeatureMapSharedPtrType FeatureMapSharedPtrType;
    typedef LayerDataBase::ConsensusMapType ConsensusMapType;
    typedef LayerDataBase::ConsensusMapSharedPtrType ConsensusMapSharedPtrType;

    typedef ExperimentType::SpectrumType SpectrumType;
    typedef SpectrumType::ConstIterator SpectrumConstIteratorType;
    typedef SpectrumType::PeakType PeakType;
    using RangeType = RangeAllType;
   
    using AreaXYType = Area<2>::AreaXYType;
    using VisibleArea = Area<2>;

    using GenericArea = Area<2>;

    using PixelArea = Area<2>;

    using UnitRange = RangeAllType;

    using PointOnAxis = DimMapper<2>::Point;

    enum ActionModes
    {
      AM_TRANSLATE,   
      AM_ZOOM,        
      AM_MEASURE      
    };

    enum IntensityModes
    {
      IM_NONE,        
      IM_PERCENTAGE,  
      IM_SNAP,        
      IM_LOG          
    };


    PlotCanvas(const Param& preferences, QWidget* parent = nullptr);

    ~PlotCanvas() override;

    inline void setPlotWidget(PlotWidget* widget)
    {
      spectrum_widget_ = widget;
    }

    inline PlotWidget* getPlotWidget() const
    {
      return spectrum_widget_;
    }

    inline Int getActionMode() const
    {
      return action_mode_;
    }

    inline IntensityModes getIntensityMode() const
    {
      return intensity_mode_;
    }

    inline void setIntensityMode(IntensityModes mod)
    {
      intensity_mode_ = mod;
      intensityModeChange_();
    }

    inline bool gridLinesShown() const
    {
      return show_grid_;
    }

    const LayerDataBase& getLayer(Size index) const
    {
      return layers_.getLayer(index);
    }
    LayerDataBase& getLayer(Size index)
    {
      return layers_.getLayer(index);
    }

    const LayerDataBase& getCurrentLayer() const
    {
      return layers_.getCurrentLayer();
    }
    LayerDataBase& getCurrentLayer()
    {
      return layers_.getCurrentLayer();
    }

    inline Size getCurrentLayerIndex() const
    {
      return layers_.getCurrentLayerIndex();
    }

    bool getLayerFlag(LayerDataBase::Flags f) const
    {
      return getLayerFlag(layers_.getCurrentLayerIndex(), f);
    }

    void setLayerFlag(LayerDataBase::Flags f, bool value)
    {
      setLayerFlag(layers_.getCurrentLayerIndex(), f, value);
    }

    bool getLayerFlag(Size layer, LayerDataBase::Flags f) const
    {
      return layers_.getLayer(layer).flags.test(f);
    }

    void setLayerFlag(Size layer, LayerDataBase::Flags f, bool value)
    {
      //abort if there are no layers
      if (layers_.empty()) return;

      layers_.getLayer(layer).flags.set(f, value);
      update_buffer_ = true;
      update();
    }

    inline void setLabel(LayerDataBase::LabelType label)
    {
      //abort if there are no layers
      if (layers_.empty()) return;
      layers_.getCurrentLayer().label = label;
      update_buffer_ = true;
      update();
    }

    const VisibleArea& getVisibleArea() const
    {
      return visible_area_;
    }

    bool isVisible(const PointOnAxis& p) const
    {
      return visible_area_.getAreaXY().encloses(p);
    }

    PixelArea getPixelRange() const
    {
      int X_pixel_count = buffer_.width();
      int Y_pixel_count = buffer_.height();
      PixelArea area(&unit_mapper_);
      area.setArea(AreaXYType(0, 0, X_pixel_count, Y_pixel_count));
      return area;
    }

    virtual void setFilters(const DataFilters & filters);

    inline Size getLayerCount() const
    {
      return layers_.getLayerCount();
    }

    virtual void activateLayer(Size layer_index) = 0;
    virtual void removeLayer(Size layer_index) = 0;

    void removeLayers()
    {
      for (Size i = getLayerCount(); i > 0; --i)
      {
        removeLayer(i-1);
      }
      visible_area_.clear(); // reset visible area
    }

    bool addLayer(std::unique_ptr<LayerData1DBase> layer);

    bool addPeakLayer(ExperimentSharedPtrType map, ODExperimentSharedPtrType od_map, const String& filename = "", const bool use_noise_cutoff = false);

    bool addChromLayer(ExperimentSharedPtrType map, ODExperimentSharedPtrType od_map, const String& filename = "");


    bool addLayer(FeatureMapSharedPtrType map, const String & filename = "");

    bool addLayer(ConsensusMapSharedPtrType map, const String & filename = "");

    bool addLayer(std::vector<PeptideIdentification> & peptides,
                  const String & filename = "");

    inline float getCurrentMinIntensity() const
    {
      return layers_.getCurrentLayer().getMinIntensity();
    }

    inline float getCurrentMaxIntensity() const
    {
      return layers_.getCurrentLayer().getMaxIntensity();
    }

    inline float getMinIntensity(Size index) const
    {
      return getLayer(index).getMinIntensity();
    }

    inline float getMaxIntensity(Size index) const
    {
      return getLayer(index).getMaxIntensity();
    }

    void setLayerName(Size i, const String & name);

    String getLayerName(Size i);

    inline void setCurrentLayerParameters(const Param& param)
    {
      getCurrentLayer().param = param;
      emit preferencesChange();
    }

    const RangeType& getDataRange() const;

    double getSnapFactor();

    double getPercentageFactor() const;

    virtual void showCurrentLayerPreferences() = 0;

    virtual void showMetaData(bool modifiable = false, Int index = -1);

public slots:

    void changeVisibility(Size i, bool b);

    void changeLayerFilterState(Size i, bool b);

    void showGridLines(bool show);

    void resetZoom(bool repaint = true);

    void setVisibleArea(const VisibleArea& area);

    void setVisibleArea(const RangeAllType& area);

    void setVisibleArea(const AreaXYType& area);

    void setVisibleAreaX(double min, double max);

    void setVisibleAreaY(double min, double max);

    void saveCurrentLayer(bool visible);

    virtual void horizontalScrollBarChange(int value);

    virtual void verticalScrollBarChange(int value);

    void setAdditionalContextMenu(QMenu * menu);

    virtual void updateLayer(Size i) = 0;


    AreaXYType canvasPixelArea() const
    {
      return AreaXYType({0, 0}, {(float)width(), (float)height()});
    }

    const DimMapper<2>& getMapper() const;

    void setMapper(const DimMapper<2>& mapper);

  signals:
    void layerModficationChange(Size layer, bool modified);

    void layerActivated(QWidget * w);

    void layerZoomChanged(QWidget * w);

    void visibleAreaChanged(const VisibleArea& area);

    void sendCursorStatus(const String& x_value, const String& y_value);

    void sendStatusMessage(std::string message, OpenMS::UInt time);

    void recalculateAxes();

    void updateVScrollbar(float, float, float, float);

    void updateHScrollbar(float, float, float, float);

    void changeLegendVisibility();

    void actionModeChange();

    void preferencesChange();

protected slots:

    void updateCursor_();

protected:

    void drawText_(QPainter & painter, QStringList text);

    double getIdentificationMZ_(const Size layer_index,
                                    const PeptideIdentification & peptide) const;

    virtual bool finishAdding_() = 0;

    void popIncompleteLayer_(const QString& error_message = "");


    void resizeEvent(QResizeEvent * e) override;
    void wheelEvent(QWheelEvent * e) override;
    void keyPressEvent(QKeyEvent * e) override;
    void keyReleaseEvent(QKeyEvent * e) override;
    void focusOutEvent(QFocusEvent * e) override;
    void leaveEvent(QEvent * e) override;
    void enterEvent(QEvent * e) override;

    virtual void intensityModeChange_();

    void dimensionsChanged_();

    virtual void changeVisibleArea_(VisibleArea new_area, bool repaint = true, bool add_to_stack = false);

    virtual void recalculateSnapFactor_();


    virtual void zoom_(int x, int y, bool zoom_in);
    void zoomBack_();
    virtual void zoomForward_();
    void zoomAdd_(const VisibleArea& area);
    void zoomClear_();


    virtual void translateLeft_(Qt::KeyboardModifiers m);
    virtual void translateRight_(Qt::KeyboardModifiers m);
    virtual void translateForward_();
    virtual void translateBackward_();

    virtual void updateScrollbars_();

    inline PointXYType widgetToData_(double x, double y)
    {
      const auto& xy = visible_area_.getAreaXY();
      return PointXYType(
                xy.minX() + x / width() * xy.width(),
                xy.minY() + (height() - y) / height() * xy.height()
                );
    }

    inline PointXYType widgetToData_(const QPoint& pos)
    {
      return widgetToData_(pos.x(), pos.y());
    }

    virtual void paintGridLines_(QPainter & painter);

    QImage buffer_;

    DimMapper<2> unit_mapper_;

    ActionModes action_mode_ = AM_TRANSLATE;

    IntensityModes intensity_mode_ = IM_NONE;

    LayerStack layers_;

    VisibleArea visible_area_;

    void recalculateRanges_();

    RangeType overall_data_range_;

    bool show_grid_ = true;

    std::vector<VisibleArea> zoom_stack_;
    std::vector<VisibleArea>::iterator zoom_pos_ = zoom_stack_.end();

    virtual void update_(const char* caller_name);

    void modificationStatus_(Size layer_index, bool modified);

    bool update_buffer_ = false;

    PlotWidget* spectrum_widget_ = nullptr;

    QPoint last_mouse_pos_;

    double percentage_factor_ = 1.0;

    std::vector<double> snap_factors_ = {1.0};

    QRubberBand rubber_band_;

    QMenu* context_add_ = nullptr;

    bool show_timing_ = false;

    PeakIndex selected_peak_;
    PeakIndex measurement_start_;

    void addDataProcessing_(PeakMap & map, DataProcessing::ProcessingAction action) const
    {
      std::set<DataProcessing::ProcessingAction> actions;
      actions.insert(action);

      DataProcessingPtr p = boost::shared_ptr<DataProcessing>(new DataProcessing);
      //actions
      p->setProcessingActions(actions);
      //software
      p->getSoftware().setName("PlotCanvas");
      //version
      p->getSoftware().setVersion(VersionInfo::getVersion());
      //time
      p->setCompletionTime(DateTime::now());

      for (Size i = 0; i < map.size(); ++i)
      {
        map[i].getDataProcessing().push_back(p);
      }
    }

  };
}