Initial vibrational spectra plot

- Needs spectral broadening
- Needs to be general for other spectra
- ChartDialog needs more methods

Signed-off-by: Geoff Hutchison <[email protected]>

avogadro/qtplugins/spectra/CMakeLists.txt

@@ -12,3 +12,5 @@ avogadro_plugin(Spectra
   "${plugin_srcs}"
   "vibrationdialog.ui"
 )
+
+target_link_libraries(Spectra PRIVATE Avogadro::Vtk)

avogadro/qtplugins/spectra/spectra.cpp

@@ -11,6 +11,9 @@
 #include <avogadro/core/vector.h>
 #include <avogadro/qtgui/molecule.h>
 
+#include <avogadro/vtk/chartdialog.h>
+#include <avogadro/vtk/chartwidget.h>
+
 #include <QAction>
 #include <QDebug>
 #include <QtCore/QTimer>
@@ -27,6 +30,12 @@ Spectra::Spectra(QObject* p)
   action->setText(tr("Vibrational Modes…"));
   connect(action, SIGNAL(triggered()), SLOT(openDialog()));
   m_actions.push_back(action);
+
+  action = new QAction(this);
+  action->setEnabled(false);
+  action->setText(tr("Spectra…"));
+  connect(action, SIGNAL(triggered()), SLOT(showSpectraChart()));
+  m_actions.push_back(action);
 }
 
 Spectra::~Spectra() {}
@@ -50,6 +59,7 @@ void Spectra::setMolecule(QtGui::Molecule* mol)
     isVibrational = true;
 
   m_actions[0]->setEnabled(isVibrational);
+  m_actions[1]->setEnabled(isVibrational);
   m_molecule = mol;
   if (m_dialog)
     m_dialog->setMolecule(mol);
@@ -212,6 +222,55 @@ void Spectra::openDialog()
   m_dialog->show();
 }
 
+void Spectra::showSpectraChart()
+{
+  if (m_molecule == nullptr || m_molecule->vibrationFrequencies().empty())
+    return;
+
+  std::vector<float> xData;
+  std::vector<float> yData;
+  // generate the raw stick spectrum
+  float maxIntensity = 0.0f;
+  for (unsigned int x = 0; x < 4000; ++x) {
+    xData.push_back(static_cast<float>(x));
+    // check if x is near a frequency and add a peak
+    bool found = false;
+    for (auto index = 0; index < m_molecule->vibrationFrequencies().size();
+         ++index) {
+      auto freq = m_molecule->vibrationFrequencies()[index];
+      if (std::abs(static_cast<int>(x) - static_cast<int>(freq)) < 2) {
+        yData.push_back(m_molecule->vibrationIRIntensities()[index]);
+        if (m_molecule->vibrationIRIntensities()[index] > maxIntensity)
+          maxIntensity = m_molecule->vibrationIRIntensities()[index];
+
+        found = true;
+        break;
+      }
+    }
+    if (!found)
+      yData.push_back(0.0f);
+  }
+
+  auto xTitle = tr("Wavenumbers (cm⁻¹)");
+  auto yTitle = tr("Transmission");
+  auto windowName = tr("Vibrational Spectra");
+
+  if (!m_chartDialog) {
+    m_chartDialog.reset(
+      new VTK::ChartDialog(qobject_cast<QWidget*>(this->parent())));
+  }
+
+  m_chartDialog->setWindowTitle(windowName);
+  auto* chart = m_chartDialog->chartWidget();
+  chart->clearPlots();
+  chart->setXAxisTitle(xTitle.toStdString());
+  chart->setYAxisTitle(yTitle.toStdString());
+  chart->addPlot(xData, yData, VTK::color4ub{ 255, 0, 0, 255 });
+  chart->setXAxisLimits(4000.0, 0.0);
+  chart->setYAxisLimits(maxIntensity, 0.0);
+  m_chartDialog->show();
+}
+
 void Spectra::advanceFrame()
 {
   if (++m_currentFrame >= m_totalFrames)

avogadro/qtplugins/spectra/spectra.h

@@ -13,6 +13,11 @@ class QDialog;
 class QTimer;
 
 namespace Avogadro {
+
+namespace VTK {
+  class ChartDialog;
+}
+
 namespace QtPlugins {
 
 class VibrationDialog;
@@ -53,6 +58,7 @@ public slots:
   void startVibrationAnimation();
   void stopVibrationAnimation();
   void openDialog();
+  void showSpectraChart();
 
 private slots:
   void advanceFrame();
@@ -63,6 +69,7 @@ private slots:
   QtGui::Molecule* m_molecule;
 
   VibrationDialog* m_dialog;
+  QScopedPointer<VTK::ChartDialog> m_chartDialog;
 
   QTimer* m_timer;
 

avogadro/vtk/chartwidget.cpp

@@ -15,6 +15,7 @@
 #include <vtkRenderWindow.h>
 #include <vtkStringArray.h>
 #include <vtkTable.h>
+#include <vtkTextProperty.h>
 
 #include <QHBoxLayout>
 
@@ -113,16 +114,26 @@ void ChartWidget::clearPlots()
   m_table->RemoveAllColumns();
 }
 
-void ChartWidget::setXAxisTitle(const char* title)
+void ChartWidget::setXAxisTitle(const std::string title)
 {
   auto* axis = m_chart->GetAxis(vtkAxis::BOTTOM);
   axis->SetTitle(title);
+  axis->SetTitleVisible(true);
+  axis->GetTitleProperties()->SetFontSize(18);
+  axis->GetTitleProperties()->SetBold(true);
+
+  axis->GetLabelProperties()->SetFontSize(14);
 }
 
-void ChartWidget::setYAxisTitle(const char* title)
+void ChartWidget::setYAxisTitle(const std::string title)
 {
   auto* axis = m_chart->GetAxis(vtkAxis::LEFT);
   axis->SetTitle(title);
+  axis->SetTitleVisible(true);
+  axis->GetTitleProperties()->SetFontSize(18);
+  axis->GetTitleProperties()->SetBold(true);
+
+  axis->GetLabelProperties()->SetFontSize(14);
 }
 
 void ChartWidget::setTickLabels(Axis a, const std::vector<float>& tickPositions,
@@ -161,6 +172,27 @@ void ChartWidget::setAxisLimits(Axis a, float min, float max)
   customAxis->SetBehavior(vtkAxis::FIXED);
 }
 
+void ChartWidget::setXAxisLimits(float min, float max)
+{
+  setAxisLimits(Axis::x, min, max);
+}
+
+void ChartWidget::setYAxisLimits(float min, float max)
+{
+  setAxisLimits(Axis::y, min, max);
+}
+
+void ChartWidget::setAxisLogScale(Axis a, bool logScale)
+{
+  auto customAxis = axis(a);
+
+  // We need a valid axis and equal sizes vectors of points/labels.
+  if (!customAxis)
+    return;
+
+  customAxis->SetLogScale(logScale);
+}
+
 vtkAxis* ChartWidget::axis(Axis a)
 {
   if (a == Axis::x)

avogadro/vtk/chartwidget.h

@@ -6,7 +6,9 @@
 #include "avogadrovtkexport.h"
 
 #include <QWidget>
+
 #include <array>
+#include <string>
 
 #include <vtkNew.h>
 
@@ -43,14 +45,18 @@ class AVOGADROVTK_EXPORT ChartWidget : public QWidget
 
   void clearPlots();
 
-  void setXAxisTitle(const char* title);
+  void setXAxisTitle(const std::string title);
 
-  void setYAxisTitle(const char* title);
+  void setYAxisTitle(const std::string title);
 
   void setTickLabels(Axis a, const std::vector<float>& tickPositions,
                      const std::vector<std::string>& tickLabels);
 
   void setAxisLimits(Axis a, float min, float max);
+  void setXAxisLimits(float min, float max);
+  void setYAxisLimits(float min, float max);
+
+  void setAxisLogScale(Axis a, bool logScale);
 
 private:
   void renderViews();