comparison layer/Colour3DPlotLayer.cpp @ 997:296ccd36f626 tony-2.0-integration

Merge through to branch for Tony 2.0

     m_binScale(LinearBinScale),
     m_normalizeColumns(false),
     m_normalizeVisibleArea(false),
     m_normalizeHybrid(false),
     m_invertVertical(false),
+    m_rectified(false),
     m_opaque(false),
     m_smooth(false),
     m_peakResolution(256),
     m_miny(0),
     m_maxy(0)

     list.push_back("Normalize Columns");
     list.push_back("Normalize Visible Area");
     list.push_back("Gain");
     list.push_back("Bin Scale");
     list.push_back("Invert Vertical Scale");
+    list.push_back("Show Rectified");
     list.push_back("Opaque");
     list.push_back("Smooth");
     return list;
 }
 

     if (name == "Colour") return tr("Colour");
     if (name == "Colour Scale") return tr("Scale");
     if (name == "Normalize Columns") return tr("Normalize Columns");
     if (name == "Normalize Visible Area") return tr("Normalize Visible Area");
     if (name == "Invert Vertical Scale") return tr("Invert Vertical Scale");
+    if (name == "Show Rectified") return tr("Half-Wave Rectify");
     if (name == "Gain") return tr("Gain");
     if (name == "Opaque") return tr("Always Opaque");
     if (name == "Smooth") return tr("Smooth");
     if (name == "Bin Scale") return tr("Bin Scale");
     return "";

 Colour3DPlotLayer::getPropertyIconName(const PropertyName &name) const
 {
     if (name == "Normalize Columns") return "normalise-columns";
     if (name == "Normalize Visible Area") return "normalise";
     if (name == "Invert Vertical Scale") return "invert-vertical";
+    if (name == "Show Rectified") return "derivative";
     if (name == "Opaque") return "opaque";
     if (name == "Smooth") return "smooth";
     return "";
 }
 

 {
     if (name == "Gain") return RangeProperty;
     if (name == "Normalize Columns") return ToggleProperty;
     if (name == "Normalize Visible Area") return ToggleProperty;
     if (name == "Invert Vertical Scale") return ToggleProperty;
+    if (name == "Show Rectified") return ToggleProperty;
     if (name == "Opaque") return ToggleProperty;
     if (name == "Smooth") return ToggleProperty;
     return ValueProperty;
 }
 

 Colour3DPlotLayer::getPropertyGroupName(const PropertyName &name) const
 {
     if (name == "Normalize Columns" ||
         name == "Normalize Visible Area" ||
 	name == "Colour Scale" ||
+        name == "Show Rectified" ||
         name == "Gain") return tr("Scale");
     if (name == "Bin Scale" ||
         name == "Invert Vertical Scale") return tr("Bins");
     if (name == "Opaque" ||
         name == "Smooth" ||

 
     } else if (name == "Invert Vertical Scale") {
 	
         *deflt = 0;
 	val = (m_invertVertical ? 1 : 0);
+
+    } else if (name == "Show Rectified") {
+
+        if (min) *min = 0;
+        if (max) *max = 0;
+        if (deflt) *deflt = 0;
+        val = (m_rectified ? 1.0 : 0.0);
 
     } else if (name == "Bin Scale") {
 
 	*min = 0;
 	*max = 1;

 	setNormalizeColumns(value ? true : false);
     } else if (name == "Normalize Visible Area") {
 	setNormalizeVisibleArea(value ? true : false);
     } else if (name == "Invert Vertical Scale") {
 	setInvertVertical(value ? true : false);
+    } else if (name == "Show Rectified") {
+        setShowRectified(value > 0.5);
     } else if (name == "Opaque") {
 	setOpaque(value ? true : false);
     } else if (name == "Smooth") {
 	setSmooth(value ? true : false);
     } else if (name == "Bin Scale") {

     cacheInvalid();
     emit layerParametersChanged();
 }
 
 void
+Colour3DPlotLayer::setShowRectified(bool show)
+{
+    if (m_rectified == show) return;
+    m_rectified = show;
+    cacheInvalid();
+    emit layerParametersChanged();
+}
+
+void
 Colour3DPlotLayer::setOpaque(bool n)
 {
     if (m_opaque == n) return;
     m_opaque = n;
     emit layerParametersChanged();

 {
     return m_smooth;
 }
 
 void
-Colour3DPlotLayer::setLayerDormant(const View *v, bool dormant)
+Colour3DPlotLayer::setLayerDormant(const LayerGeometryProvider *v, bool dormant)
 {
     if (dormant) {
 
 #ifdef DEBUG_COLOUR_3D_PLOT_LAYER_PAINT
         cerr << "Colour3DPlotLayer::setLayerDormant(" << dormant << ")"

         Layer::setLayerDormant(v, false);
     }
 }
 
 bool
-Colour3DPlotLayer::isLayerScrollable(const View *v) const
+Colour3DPlotLayer::isLayerScrollable(const LayerGeometryProvider *v) const
 {
     if (m_normalizeVisibleArea) {
         return false;
     }
     if (shouldPaintDenseIn(v)) {

     emit layerParametersChanged();
     return true;
 }
 
 bool
-Colour3DPlotLayer::getYScaleValue(const View *, int,
+Colour3DPlotLayer::getYScaleValue(const LayerGeometryProvider *, int,
                                   double &, QString &) const
 {
     return false;//!!!
 }
 

     return new LinearRangeMapper(0, m_model->getHeight(),
                                  0, m_model->getHeight(), "");
 }
 
 double
-Colour3DPlotLayer::getYForBin(View *v, double bin) const
+Colour3DPlotLayer::getYForBin(LayerGeometryProvider *v, double bin) const
 {
     double y = bin;
     if (!m_model) return y;
     double mn = 0, mx = m_model->getHeight();
     getDisplayExtents(mn, mx);
-    double h = v->height();
+    double h = v->getPaintHeight();
     if (m_binScale == LinearBinScale) {
         y = h - (((bin - mn) * h) / (mx - mn));
     } else {
         double logmin = mn + 1, logmax = mx + 1;
         LogRange::mapRange(logmin, logmax);

     }
     return y;
 }
 
 int
-Colour3DPlotLayer::getIYForBin(View *v, int bin) const
+Colour3DPlotLayer::getIYForBin(LayerGeometryProvider *v, int bin) const
 {
     return int(round(getYForBin(v, bin)));
 }
 
 double
-Colour3DPlotLayer::getBinForY(View *v, double y) const
+Colour3DPlotLayer::getBinForY(LayerGeometryProvider *v, double y) const
 {
     double bin = y;
     if (!m_model) return bin;
     double mn = 0, mx = m_model->getHeight();
     getDisplayExtents(mn, mx);
-    double h = v->height();
+    double h = v->getPaintHeight();
     if (m_binScale == LinearBinScale) {
         bin = mn + ((h - y) * (mx - mn)) / h;
     } else {
         double logmin = mn + 1, logmax = mx + 1;
         LogRange::mapRange(logmin, logmax);

     }
     return bin;
 }
 
 int
-Colour3DPlotLayer::getIBinForY(View *v, int y) const
+Colour3DPlotLayer::getIBinForY(LayerGeometryProvider *v, int y) const
 {
     return int(floor(getBinForY(v, y)));
 }
 
 QString
-Colour3DPlotLayer::getFeatureDescription(View *v, QPoint &pos) const
+Colour3DPlotLayer::getFeatureDescription(LayerGeometryProvider *v, QPoint &pos) const
 {
     if (!m_model) return "";
 
     int x = pos.x();
     int y = pos.y();

         symax = sh;
     }
     if (symin < 0) symin = 0;
     if (symax > sh) symax = sh;
 
- //    double binHeight = double(v->height()) / (symax - symin);
-//    int sy = int((v->height() - y) / binHeight) + symin;
+ //    double binHeight = double(v->getPaintHeight()) / (symax - symin);
+//    int sy = int((v->getPaintHeight() - y) / binHeight) + symin;
 
     int sy = getIBinForY(v, y);
 
     if (sy < 0 || sy >= m_model->getHeight()) {
         return "";

 
     return text;
 }
 
 int
-Colour3DPlotLayer::getColourScaleWidth(QPainter &) const
-{
-    int cw = 20;
+Colour3DPlotLayer::getColourScaleWidth(QPainter &p) const
+{
+    // Font is rotated
+    int cw = p.fontMetrics().height();
     return cw;
 }
 
 int
-Colour3DPlotLayer::getVerticalScaleWidth(View *, bool, QPainter &paint) const
+Colour3DPlotLayer::getVerticalScaleWidth(LayerGeometryProvider *, bool, QPainter &paint) const
 {
     if (!m_model) return 0;
 
     QString sampleText = QString("[%1]").arg(m_model->getHeight());
     int tw = paint.fontMetrics().width(sampleText);

 
     return tw + 13 + getColourScaleWidth(paint);
 }
 
 void
-Colour3DPlotLayer::paintVerticalScale(View *v, bool, QPainter &paint, QRect rect) const
+Colour3DPlotLayer::paintVerticalScale(LayerGeometryProvider *v, bool, QPainter &paint, QRect rect) const
 {
     if (!m_model) return;
 
     int h = rect.height(), w = rect.width();
 

         QString maxstr = QString("%1").arg(max);
         
         paint.save();
 
         QFont font = paint.font();
-        font.setPixelSize(10);
+        font.setPixelSize(int(font.pixelSize() * 0.65));
         paint.setFont(font);
 
         int msw = paint.fontMetrics().width(maxstr);
 
         QMatrix m;

 
     paint.save();
 
     int py = h;
 
+    int defaultFontHeight = paint.fontMetrics().height();
+    
     for (int i = symin; i <= symax; ++i) {
 
         int y0;
 
         y0 = getIYForBin(v, i);
         int h = py - y0;
 
         if (i > symin) {
             if (paint.fontMetrics().height() >= h) {
-                if (h >= 8) {
+                if (h >= defaultFontHeight * 0.8) {
                     QFont tf = paint.font();
-                    tf.setPixelSize(h-2);
+                    tf.setPixelSize(int(h * 0.8));
                     paint.setFont(tf);
                 } else {
                     continue;
                 }
             }

 DenseThreeDimensionalModel::Column
 Colour3DPlotLayer::getColumn(int col) const
 {
     Profiler profiler("Colour3DPlotLayer::getColumn");
 
+    DenseThreeDimensionalModel::Column prev;
+    if (m_rectified && (col > m_model->getStartFrame())) {
+        prev = m_model->getColumn(col - 1);
+    }
+    
     DenseThreeDimensionalModel::Column values = m_model->getColumn(col);
+
+    if (m_rectified && !prev.empty()) {
+        for (int y = 0; y < values.size(); ++y) {
+            if (values[y] < prev[y]) values[y] = 0;
+            else values[y] -= prev[y];
+        }
+    }
+    
     while (values.size() < m_model->getHeight()) values.push_back(0.f);
     if (!m_normalizeColumns && !m_normalizeHybrid) return values;
 
     double colMax = 0.f, colMin = 0.f;
     double min = 0.f, max = 0.f;

 
     delete[] peaks;
 }
 
 bool
-Colour3DPlotLayer::shouldPaintDenseIn(const View *v) const
+Colour3DPlotLayer::shouldPaintDenseIn(const LayerGeometryProvider *v) const
 {
     if (!m_model || !v || !(v->getViewManager())) {
         return false;
     }
     double srRatio =
         v->getViewManager()->getMainModelSampleRate() / m_model->getSampleRate();
     if (m_opaque || 
         m_smooth ||
-        m_model->getHeight() >= v->height() ||
+        m_model->getHeight() >= v->getPaintHeight() ||
         ((m_model->getResolution() * srRatio) / v->getZoomLevel()) < 2) {
         return true;
     }
     return false;
 }
 
 void
-Colour3DPlotLayer::paint(View *v, QPainter &paint, QRect rect) const
+Colour3DPlotLayer::paint(LayerGeometryProvider *v, QPainter &paint, QRect rect) const
 {
 /*
     if (m_model) {
         SVDEBUG << "Colour3DPlotLayer::paint: model says shouldUseLogValueScale = " << m_model->shouldUseLogValueScale() << endl;
     }

 #endif
 
     int completion = 0;
     if (!m_model || !m_model->isOK() || !m_model->isReady(&completion)) {
 	if (completion > 0) {
-	    paint.fillRect(0, 10, v->width() * completion / 100,
+	    paint.fillRect(0, 10, v->getPaintWidth() * completion / 100,
 			   10, QColor(120, 120, 120));
 	}
 	return;
     }
 
-    if (m_normalizeVisibleArea && !m_normalizeColumns) rect = v->rect();
+    if (m_normalizeVisibleArea && !m_normalizeColumns) rect = v->getPaintRect();
 
     sv_frame_t modelStart = m_model->getStartFrame();
     sv_frame_t modelEnd = m_model->getEndFrame();
     int modelResolution = m_model->getResolution();
 

     //  "small".  This is "large"; see paintDense below for "small".
 
     int x0 = rect.left();
     int x1 = rect.right() + 1;
 
-    int h = v->height();
+    int h = v->getPaintHeight();
 
     double srRatio =
         v->getViewManager()->getMainModelSampleRate() / m_model->getSampleRate();
 
     int sx0 = int((double(v->getFrameForX(x0)) / srRatio - double(modelStart))

 	}
     }
 }
 
 void
-Colour3DPlotLayer::paintDense(View *v, QPainter &paint, QRect rect) const
+Colour3DPlotLayer::paintDense(LayerGeometryProvider *v, QPainter &paint, QRect rect) const
 {
     Profiler profiler("Colour3DPlotLayer::paintDense", true);
     if (!m_cache) return;
 
     double modelStart = double(m_model->getStartFrame());

 
     int x0 = rect.left();
     int x1 = rect.right() + 1;
 
     const int w = x1 - x0; // const so it can be used as array size below
-    int h = v->height(); // we always paint full height
+    int h = v->getPaintHeight(); // we always paint full height
     int sh = m_model->getHeight();
 
     int symin = m_miny;
     int symax = m_maxy;
     if (symax <= symin) {

 
     paint.drawImage(x0, 0, img);
 }
 
 bool
-Colour3DPlotLayer::snapToFeatureFrame(View *v, sv_frame_t &frame,
+Colour3DPlotLayer::snapToFeatureFrame(LayerGeometryProvider *v, sv_frame_t &frame,
 				      int &resolution,
 				      SnapType snap) const
 {
     if (!m_model) {
 	return Layer::snapToFeatureFrame(v, frame, resolution, snap);