Improvements to UI and performance.

8 files changed, 69 insertions, 68 deletions

diff --git a/interactionhandler.cpp b/interactionhandler.cpp
index 217f4a5..50d0653 100644
--- a/interactionhandler.cpp
+++ b/interactionhandler.cpp
@@ -6,26 +6,23 @@ InteractionHandler::InteractionHandler(const arma::mat &X,
                                        const arma::vec &labels,
                                        const arma::uvec &sampleIndices)
     : m_X(X)
+    , m_Y(X.n_rows, 3)
     , m_labels(labels)
     , m_sampleIndices(sampleIndices)
     , m_technique(TECHNIQUE_LAMP)
 {
+    m_Y.col(2) = m_labels;
 }
 
 void InteractionHandler::setSubsample(const arma::mat &Ys)
 {
-    arma::mat embedding(m_X.n_rows, Ys.n_cols);
     switch (m_technique) {
     case TECHNIQUE_PLMP:
     case TECHNIQUE_LSP:
     case TECHNIQUE_LAMP:
-        embedding = mp::lamp(m_X, m_sampleIndices, Ys);
+        mp::lamp(m_X, m_sampleIndices, Ys, m_Y);
         break;
     }
 
-    arma::mat Y(embedding.n_rows, embedding.n_cols + 1);
-    Y.cols(0, embedding.n_cols - 1) = embedding;
-    Y.col(Y.n_cols - 1) = m_labels;
-
-    emit subsampleChanged(Y);
+    emit subsampleChanged(m_Y);
 }
diff --git a/interactionhandler.h b/interactionhandler.h
index 3dbeb8a..5468dab 100644
--- a/interactionhandler.h
+++ b/interactionhandler.h
@@ -24,7 +24,7 @@ public slots:
     void setSubsample(const arma::mat &Ys);
 
 private:
-    arma::mat m_X;
+    arma::mat m_X, m_Y;
     arma::vec m_labels;
     arma::uvec m_sampleIndices;
     InteractiveTechnique m_technique;
diff --git a/lamp.cpp b/lamp.cpp
index a9d7a8b..90be140 100644
--- a/lamp.cpp
+++ b/lamp.cpp
@@ -4,12 +4,19 @@
 
 arma::mat mp::lamp(const arma::mat &X, const arma::uvec &sampleIndices, const arma::mat &Ys)
 {
-    arma::mat Xs = X.rows(sampleIndices);
-    arma::uword sampleSize = sampleIndices.n_elem;
     arma::mat projection(X.n_rows, 2);
+    lamp(X, sampleIndices, Ys, projection);
+    return projection;
+}
 
+void mp::lamp(const arma::mat &X, const arma::uvec &sampleIndices, const arma::mat &Ys, arma::mat &Y)
+{
+    const arma::mat &Xs = X.rows(sampleIndices);
+    arma::uword sampleSize = sampleIndices.n_elem;
+
+    #pragma omp parallel for shared(X, Xs, sampleIndices, Ys, Y)
     for (arma::uword i = 0; i < X.n_rows; i++) {
-        arma::rowvec point = X.row(i);
+        const arma::rowvec &point = X.row(i);
 
         // calculate alphas
         arma::rowvec alphas(sampleSize);
@@ -19,7 +26,6 @@ arma::mat mp::lamp(const arma::mat &X, const arma::uvec &sampleIndices, const ar
         }
 
         double alphas_sum = arma::accu(alphas);
-        arma::rowvec alphas_sqrt = arma::sqrt(alphas);
 
         // calculate \tilde{X} and \tilde{Y}
         arma::rowvec Xtil = arma::sum(alphas * Xs, 0) / alphas_sum;
@@ -32,19 +38,19 @@ arma::mat mp::lamp(const arma::mat &X, const arma::uvec &sampleIndices, const ar
         Yhat.each_row() -= Ytil;
 
         // calculate A and B
-        arma::mat At = Xhat.t();
-        At.each_row() %= alphas_sqrt;
-        arma::mat B = Yhat;
-        B.each_col() %= alphas_sqrt.t();
-
-        arma::mat U, V;
-        arma::vec s;
+        alphas = arma::sqrt(alphas);
+        arma::mat &At = Xhat;
+        inplace_trans(At);
+        At.each_row() %= alphas;
+        arma::mat &B = Yhat;
+        B.each_col() %= alphas.t();
+
+        arma::mat U(Ys.n_rows, Ys.n_cols), V(Ys.n_cols, Ys.n_cols);
+        arma::vec s(Ys.n_cols);
         arma::svd(U, s, V, At * B);
         arma::mat M = U.cols(0, 1) * V.t();
 
         // the projection of point i
-        projection.row(i) = (point - Xtil) * M + Ytil;
+        Y(i, arma::span(0, 1)) = (point - Xtil) * M + Ytil;
     }
-
-    return projection;
 }
diff --git a/main_view.qml b/main_view.qml
index 5d86c36..5afe270 100644
--- a/main_view.qml
+++ b/main_view.qml
@@ -11,15 +11,11 @@ ApplicationWindow {
 
     menuBar: MenuBar {
         Menu {
-            title: "Application"
-            MenuItem { action: quitAction }
-        }
-
-        Menu {
             title: "File"
             MenuItem { action: openAction }
             MenuItem { action: savePlotAction }
             MenuItem { action: saveDataAction }
+            MenuItem { action: quitAction }
         }
     }
 
diff --git a/mp.h b/mp.h
index 6508d9d..996da87 100644
--- a/mp.h
+++ b/mp.h
@@ -6,6 +6,7 @@ static const double EPSILON = 1e-3;
 double euclidean(const arma::rowvec &x1, const arma::rowvec &x2);
 arma::mat dist(const arma::mat &X, double (*distCalc)(const arma::rowvec &, const arma::rowvec &) = euclidean);
 arma::mat lamp(const arma::mat &X, const arma::uvec &sampleIndices, const arma::mat &Ys);
+void lamp(const arma::mat &X, const arma::uvec &sampleIndices, const arma::mat &Ys, arma::mat &Y);
 arma::mat forceScheme(const arma::mat &D, arma::mat &Y, size_t maxIter = 20, double tol = 1e-3, double fraction = 8);
 
 } // namespace mp
diff --git a/pm.pro b/pm.pro
index 9608b89..af9a10d 100644
--- a/pm.pro
+++ b/pm.pro
@@ -1,7 +1,7 @@
 QT += qml quick widgets
 
-QMAKE_CXXFLAGS += -std=c++11
-QMAKE_LIBS += -larmadillo
+QMAKE_CXXFLAGS += -std=c++11 -fopenmp
+QMAKE_LIBS += -larmadillo -fopenmp
 HEADERS += colorscale.h \
     scatterplot.h \
     interactionhandler.h \
diff --git a/scatterplot.cpp b/scatterplot.cpp
index b0c8034..8fb0b56 100644
--- a/scatterplot.cpp
+++ b/scatterplot.cpp
@@ -1,12 +1,6 @@
 #include "scatterplot.h"
 
 #include <cmath>
-#include <QSGGeometry>
-#include <QSGGeometryNode>
-#include <QSGOpacityNode>
-#include <QSGMaterial>
-#include <QSGFlatColorMaterial>
-#include <QSGSimpleRectNode>
 
 static const qreal GLYPH_OPACITY = 0.3;
 static const qreal GLYPH_OPACITY_SELECTED = 1.0;
@@ -25,8 +19,8 @@ Scatterplot::Scatterplot(QQuickItem *parent)
         QColor("#9467bd"),
         QColor("#8c564b"),
         QColor("#e377c2"),
-        QColor("#7f7f7f"),
         QColor("#17becf"),
+        QColor("#7f7f7f"),
     }
 {
     setClip(true);
@@ -49,10 +43,7 @@ void Scatterplot::setData(const arma::mat &data)
     m_ymax = data.col(1).max();
 
     m_colorScale.setExtents(m_data.col(2).min(), m_data.col(2).max());
-
     m_selectedGlyphs.clear();
-    for (arma::uword i = 0; i < m_data.n_rows; i++)
-        m_selectedGlyphs.append(false);
 
     update();
 }
@@ -151,21 +142,23 @@ QSGNode *Scatterplot::updatePaintNode(QSGNode *oldNode, UpdatePaintNodeData *)
         yt = m_dragCurrentPos.y() - m_dragOriginPos.y();
     }
 
-    QSGNode *glyphOpacityNode = root->firstChild()->firstChild();
+    QSGNode *node = root->firstChild()->firstChild();
     for (arma::uword i = 0; i < m_data.n_rows; i++) {
         arma::rowvec row = m_data.row(i);
-        moveTranslationF = m_selectedGlyphs[i] ? 1.0 : 0.0;
+        bool isSelected = m_selectedGlyphs.contains(i);
+
+        QSGOpacityNode *glyphOpacityNode = static_cast<QSGOpacityNode *>(node);
+        glyphOpacityNode->setOpacity(isSelected ? GLYPH_OPACITY_SELECTED : GLYPH_OPACITY);
+
+        QSGGeometryNode *glyphNode = static_cast<QSGGeometryNode *>(node->firstChild());
+        QSGGeometry *geometry = glyphNode->geometry();
+        moveTranslationF = isSelected ? 1.0 : 0.0;
         x = fromDataXToScreenX(row[0]) + xt * moveTranslationF;
         y = fromDataYToScreenY(row[1]) + yt * moveTranslationF;
-
-        QSGNode *glyphNode = glyphOpacityNode->firstChild();
-        QSGGeometry *geometry = static_cast<QSGGeometryNode *>(glyphNode)->geometry();
         updateCircleGeometry(geometry, GLYPH_SIZE, x, y);
         glyphNode->markDirty(QSGNode::DirtyGeometry);
 
-        static_cast<QSGOpacityNode *>(glyphOpacityNode)->setOpacity(m_selectedGlyphs[i] ? GLYPH_OPACITY_SELECTED : GLYPH_OPACITY);
-
-        glyphOpacityNode = glyphOpacityNode->nextSibling();
+        node = node->nextSibling();
     }
 
     // Draw selection
@@ -203,21 +196,28 @@ void Scatterplot::mousePressEvent(QMouseEvent *event)
         break;
     case INTERACTION_SELECTING:
     case INTERACTION_MOVING:
-        return; // should not be reached
+        event->ignore();
+        return;
     }
 }
 
 void Scatterplot::mouseMoveEvent(QMouseEvent *event)
 {
     switch (m_currentState) {
-    case INTERACTION_NONE:
-    case INTERACTION_SELECTED:
-        return;
     case INTERACTION_SELECTING:
+        m_dragCurrentPos = event->localPos();
+        update();
+        break;
     case INTERACTION_MOVING:
         m_dragCurrentPos = event->localPos();
+        updateData();
         update();
+        m_dragOriginPos = m_dragCurrentPos;
         break;
+    case INTERACTION_NONE:
+    case INTERACTION_SELECTED:
+        event->ignore();
+        return;
     }
 }
 
@@ -235,7 +235,6 @@ void Scatterplot::mouseReleaseEvent(QMouseEvent *event)
 
     case INTERACTION_MOVING:
         m_currentState = INTERACTION_SELECTED;
-        updateData();
         update();
         break;
     case INTERACTION_NONE:
@@ -246,6 +245,9 @@ void Scatterplot::mouseReleaseEvent(QMouseEvent *event)
 
 bool Scatterplot::selectGlyphs(bool mergeSelection)
 {
+    if (!mergeSelection)
+        m_selectedGlyphs.clear();
+
     qreal x, y;
 
     QRectF selectionRect(m_dragOriginPos, m_dragCurrentPos);
@@ -255,9 +257,11 @@ bool Scatterplot::selectGlyphs(bool mergeSelection)
         x = fromDataXToScreenX(row[0]);
         y = fromDataYToScreenY(row[1]);
 
-        bool contains = selectionRect.contains(x, y);
-        anySelected = anySelected || contains;
-        m_selectedGlyphs[i] = (mergeSelection && m_selectedGlyphs[i]) || contains;
+        if (selectionRect.contains(x, y)) {
+            m_selectedGlyphs.insert(i);
+            if (!anySelected)
+                anySelected = true;
+        }
     }
 
     return anySelected;
@@ -270,14 +274,11 @@ void Scatterplot::updateData()
 
     xt /= (width()  - PADDING);
     yt /= (height() - PADDING);
-    for (arma::uword i = 0; i < m_data.n_rows; i++) {
-        if (!m_selectedGlyphs[i])
-            continue;
-
-        arma::rowvec row = m_data.row(i);
+    for (auto it = m_selectedGlyphs.cbegin(); it != m_selectedGlyphs.cend(); it++) {
+        arma::rowvec row = m_data.row(*it);
         row[0] = ((row[0] - m_xmin) / (m_xmax - m_xmin) + xt) * (m_xmax - m_xmin) + m_xmin;
         row[1] = ((row[1] - m_ymin) / (m_ymax - m_ymin) + yt) * (m_ymax - m_ymin) + m_ymin;
-        m_data.row(i) = row;
+        m_data.row(*it) = row;
     }
 
     // does not send last column (labels)
diff --git a/scatterplot.h b/scatterplot.h
index 2b5aed8..a155daf 100644
--- a/scatterplot.h
+++ b/scatterplot.h
@@ -2,8 +2,7 @@
 #define SCATTERPLOT_H
 
 #include <armadillo>
-#include <QQuickItem>
-#include <QSGNode>
+#include <QtQuick>
 
 #include "colorscale.h"
 
@@ -34,6 +33,11 @@ private:
     float fromDataXToScreenX(float x);
     float fromDataYToScreenY(float y);
 
+    arma::mat m_data;
+    float m_xmin, m_xmax, m_ymin, m_ymax;
+
+    ColorScale m_colorScale;
+
     enum InteractionState {
         INTERACTION_NONE,
         INTERACTION_SELECTING,
@@ -41,12 +45,8 @@ private:
         INTERACTION_MOVING
     } m_currentState;
     QPointF m_dragOriginPos, m_dragCurrentPos;
-    QList<bool> m_selectedGlyphs;
 
-    arma::mat m_data;
-    float m_xmin, m_xmax, m_ymin, m_ymax;
-
-    ColorScale m_colorScale;
+    QSet<int> m_selectedGlyphs;
 };
 
 #endif // SCATTERPLOT_H