major refactoring. We no longer will use findChild unless absolutely

necessary. Within dialogs, we call members of ui directly.

CONTRIBUTING.md

@@ -38,7 +38,7 @@ Names
 * Setters are named in PascalCase like other functions, but are named after the variables they set (e.g. `SetName()` for the setter of the `name_` member).
 * Getters are named after the member they return (e.g. the getter for `abscissa_` is named `abscissa()`). Getters that return pointers to members have `_ptr` appended to the end of their names. Where getters that return copies and getters that return references both exist, the getter that returns the reference is named with `_ref` appended.
 * Every function belongs to a namespace, either the namespace of its parent class or a namespace like `Vespucci::Math` or `BinaryImport`.
-* Widgets in Qt forms are named using Qt style inside .ui files, but use our style inside C++ classes (e.g. `nameLineEdit` becomes `name_line_edit_`). The type of the widget should be included in the name.
+* Widgets in Qt forms are named using Qt camelCase style inside .ui files. The type of the widget should be included in the name because they have to be called something. Widgets should be accessed using the ui member of the form class.
 * As mentioned above, an exception exists for a function whose sole purpose is to call the member of one of the class's members.
 
 Types

Test/Test.pro

@@ -92,6 +92,12 @@ macx{
     CONFIG += app_bundle c++11
     QMAKE_MACOSX_DEPLOYMENT_TARGET = 10.7
 
+    QMAKE_CXXFLAGS += --system-header-prefix=/usr \
+                      --system-header-prefix=$$PWD/../armadillo \
+                      --system-header-prefix=$$PWD/../mlpack \
+                      --system-header-prefix=$$PWD/../yaml-cpp \
+                      --system-header-prefix=$$PWD/../quazip
+
     LIBS += -L/usr/lib -lc++
 
     LIBS += -L$$OUT_PWD/../VespucciLibrary/ -lvespucci

Vespucci/GUI/Analysis/bandratiodialog.cpp

@@ -31,20 +31,10 @@ BandRatioDialog::BandRatioDialog(QWidget *parent,
     workspace_ = ws;
     dataset_ = workspace_->GetDataset(dataset_key);
 
-    spectrum_custom_plot_ = findChild<QCustomPlot *>("spectrumPlot");
-    first_min_line_edit_ = findChild<QLineEdit *>("firstMinLineEdit");
-    first_max_line_edit_ = findChild<QLineEdit *>("firstMaxLineEdit");
-    second_min_line_edit_ = findChild<QLineEdit *>("secondMinLineEdit");
-    second_max_line_edit_ = findChild<QLineEdit *>("secondMaxLineEdit");
-    name_line_edit_ = findChild<QLineEdit *>("nameLineEdit");
-    method_combo_box_ = findChild<QComboBox *>("peakComboBox");
-    range_label_ = findChild<QLabel *>("rangeLabel");
-    search_window_spin_box_ = findChild<QSpinBox*>("searchWindowSpinBox");
-
-    first_min_line_ = new QCPItemStraightLine(spectrum_custom_plot_);
-    first_max_line_ = new QCPItemStraightLine(spectrum_custom_plot_);
-    second_min_line_ = new QCPItemStraightLine(spectrum_custom_plot_);
-    second_max_line_ = new QCPItemStraightLine(spectrum_custom_plot_);
+    first_min_line_ = new QCPItemStraightLine(ui->spectrumCustomPlot);
+    first_max_line_ = new QCPItemStraightLine(ui->spectrumCustomPlot);
+    second_min_line_ = new QCPItemStraightLine(ui->spectrumCustomPlot);
+    second_max_line_ = new QCPItemStraightLine(ui->spectrumCustomPlot);
 
     first_min_line_->point1->setCoords(0, 0);
     first_min_line_->point2->setCoords(0, 1);
@@ -65,23 +55,23 @@ BandRatioDialog::BandRatioDialog(QWidget *parent,
 
 
     QString label_text = QString::number(min) + "–" + QString::number(max);
-    range_label_->setText(label_text);
+    ui->rangeLabel->setText(label_text);
 
     uword origin = dataset_->FindOrigin();
 
     QVector<double> plot_data = dataset_->PointSpectrum(origin);
     QVector<double> wavelength = dataset_->WavelengthQVector();
     if (plot_data.isEmpty()){plot_data = dataset_->PointSpectrum(0);}
 
-    first_min_line_edit_->setValidator(validator);
-    first_max_line_edit_->setValidator(validator);
-    second_min_line_edit_->setValidator(validator);
-    second_max_line_edit_->setValidator(validator);
-    spectrum_custom_plot_->addGraph();
-    spectrum_custom_plot_->graph(0)->addData(wavelength, plot_data);
-    spectrum_custom_plot_->rescaleAxes();
-    spectrum_custom_plot_->setInteraction(QCP::iRangeDrag, true);
-    spectrum_custom_plot_->setInteraction(QCP::iRangeZoom, true);
+    ui->firstMinLineEdit->setValidator(validator);
+    ui->firstMaxLineEdit->setValidator(validator);
+    ui->secondMinLineEdit->setValidator(validator);
+    ui->secondMaxLineEdit->setValidator(validator);
+    ui->spectrumCustomPlot->addGraph();
+    ui->spectrumCustomPlot->graph(0)->addData(wavelength, plot_data);
+    ui->spectrumCustomPlot->rescaleAxes();
+    ui->spectrumCustomPlot->setInteraction(QCP::iRangeDrag, true);
+    ui->spectrumCustomPlot->setInteraction(QCP::iRangeZoom, true);
 }
 
 BandRatioDialog::~BandRatioDialog()
@@ -95,16 +85,16 @@ BandRatioDialog::~BandRatioDialog()
 /// instantiates the map data
 void BandRatioDialog::on_buttonBox_accepted()
 {
-    if (first_min_line_edit_->text().isEmpty() || first_max_line_edit_->text().isEmpty() || second_min_line_edit_->text().isEmpty() || second_max_line_edit_->text().isEmpty()){
+    if (ui->firstMinLineEdit->text().isEmpty() || ui->firstMaxLineEdit->text().isEmpty() || ui->secondMinLineEdit->text().isEmpty() || ui->secondMaxLineEdit->text().isEmpty()){
         QMessageBox::warning(this, "Invalid Input!", "You must enter numbers for left and right bounds.");
         return;
     }
 
 
-    double first_entered_min = first_min_line_edit_->text().toDouble();
-    double second_entered_min = second_min_line_edit_->text().toDouble();
-    double first_entered_max = first_max_line_edit_->text().toDouble();
-    double second_entered_max = second_max_line_edit_->text().toDouble();
+    double first_entered_min = ui->firstMinLineEdit->text().toDouble();
+    double second_entered_min = ui->secondMinLineEdit->text().toDouble();
+    double first_entered_max = ui->firstMaxLineEdit->text().toDouble();
+    double second_entered_max = ui->secondMaxLineEdit->text().toDouble();
 
     if (first_entered_min < dataset_->abscissa_ptr()->min() || second_entered_min < dataset_->abscissa_ptr()->min()){
         QMessageBox::warning(this, "Invalid Input!", "You have entered a left bound that is smaller than the smallest number on the spectral abscissa");
@@ -115,13 +105,13 @@ void BandRatioDialog::on_buttonBox_accepted()
         QMessageBox::warning(this, "Invalid Input!", "You have entered a right bound that is larger than the largest number on the spectral abscissa");
         return;
     }
-    uint bound_window = search_window_spin_box_->value();
+    uint bound_window = ui->searchWindowSpinBox->value();
 
 
-    QString name = name_line_edit_->text();
-    QString value_method = method_combo_box_->currentText();
+    QString name = ui->nameLineEdit->text();
+    QString value_method = ui->methodComboBox->currentText();
 
-    if (value_method == "Riemann Sum"){
+    if (value_method == "Empirical"){
         try{
             dataset_->BandRatio(name, first_entered_min, first_entered_max,
                              second_entered_min, second_entered_max,
@@ -138,7 +128,7 @@ void BandRatioDialog::on_buttonBox_accepted()
         }
     }
     else{
-        QMessageBox::warning(this, "Error Occurred", "A non-fatal error occurred: invalid input from method_combo_box_");
+        QMessageBox::warning(this, "Error Occurred", "A non-fatal error occurred: invalid input from ui->methodComboBox");
     }
 
     close();
@@ -163,9 +153,9 @@ void BandRatioDialog::on_firstMinLineEdit_textChanged(const QString &arg1)
         return;
     first_min_line_->point1->setCoords(value, 0);
     first_min_line_->point2->setCoords(value, 1);
-    if (!spectrum_custom_plot_->hasItem(first_min_line_))
-        spectrum_custom_plot_->addItem(first_min_line_);
-    spectrum_custom_plot_->repaint();
+    if (!ui->spectrumCustomPlot->hasItem(first_min_line_))
+        ui->spectrumCustomPlot->addItem(first_min_line_);
+    ui->spectrumCustomPlot->repaint();
 }
 
 void BandRatioDialog::on_firstMaxLineEdit_textChanged(const QString &arg1)
@@ -176,9 +166,9 @@ void BandRatioDialog::on_firstMaxLineEdit_textChanged(const QString &arg1)
         return;
     first_max_line_->point1->setCoords(value, 0);
     first_max_line_->point2->setCoords(value, 1);
-    if (!spectrum_custom_plot_->hasItem(first_max_line_))
-        spectrum_custom_plot_->addItem(first_max_line_);
-    spectrum_custom_plot_->repaint();
+    if (!ui->spectrumCustomPlot->hasItem(first_max_line_))
+        ui->spectrumCustomPlot->addItem(first_max_line_);
+    ui->spectrumCustomPlot->repaint();
 }
 
 void BandRatioDialog::on_secondMinLineEdit_textChanged(const QString &arg1)
@@ -189,8 +179,8 @@ void BandRatioDialog::on_secondMinLineEdit_textChanged(const QString &arg1)
         return;
     second_min_line_->point1->setCoords(value, 0);
     second_min_line_->point2->setCoords(value, 1);
-    if (!spectrum_custom_plot_->hasItem(second_min_line_))
-        spectrum_custom_plot_->addItem(second_min_line_);
+    if (!ui->spectrumCustomPlot->hasItem(second_min_line_))
+        ui->spectrumCustomPlot->addItem(second_min_line_);
 }
 
 void BandRatioDialog::on_secondMaxLineEdit_textChanged(const QString &arg1)
@@ -201,7 +191,7 @@ void BandRatioDialog::on_secondMaxLineEdit_textChanged(const QString &arg1)
         return;
     second_max_line_->point1->setCoords(value, 0);
     second_max_line_->point2->setCoords(value, 1);
-    if (!spectrum_custom_plot_->hasItem(second_max_line_))
-        spectrum_custom_plot_->addItem(second_max_line_);
+    if (!ui->spectrumCustomPlot->hasItem(second_max_line_))
+        ui->spectrumCustomPlot->addItem(second_max_line_);
 }
 

Vespucci/GUI/Analysis/bandratiodialog.h

@@ -54,62 +54,14 @@ private slots:
 
 private:
     Ui::BandRatioDialog *ui;
-
-    ///
-    /// \brief workspace
-    /// Pointer to the workspace (which contains dataset list)
-    QSharedPointer<VespucciWorkspace> workspace_;
-
-    ///
-    /// \brief spectrum_custom_plot_
-    /// Pointer to the plot inside this window that displays a preview of the data
-    QCustomPlot *spectrum_custom_plot_;
-
-    ///
-    /// \brief first_min_line_edit_
-    /// User enteres first minimum here
-    QLineEdit *first_min_line_edit_;
-
-    ///
-    /// \brief first_max_line_edit_
-    /// User enters first maximum here
-    QLineEdit *first_max_line_edit_;
-
-    ///
-    /// \brief second_min_line_edit_
-    /// User enters second minimum here
-    QLineEdit *second_min_line_edit_;
-
-    ///
-    /// \brief second_max_line_edit_
-    /// User enteres second maximum here
-    QLineEdit *second_max_line_edit_;
-
-
-    ///
-    /// \brief integration_method_selector_combo_box_
-    /// User selects the integration method here
-    QComboBox *method_combo_box_;
-
-    ///
-    /// \brief name_line_edit_
-    /// User enters map name here
-    QLineEdit *name_line_edit_;
-
-    QSpinBox *search_window_spin_box_;
     ///
     /// \brief data_index_
     /// Index of the VespucciDataset object in the various lists
     int data_index_;
 
-    ///
-    /// \brief range_label_
-    /// Displays the valid range
-    QLabel *range_label_;
-
     ///
     /// \brief first_min_line_
-    ///
+   ///
     QCPItemStraightLine *first_min_line_;
     ///
     /// \brief first_max_line_
@@ -128,8 +80,8 @@ private slots:
     /// \brief dataset_
     /// Points to the dataset we're working with.
     QSharedPointer<VespucciDataset> dataset_;
+    QSharedPointer<VespucciWorkspace> workspace_;
 
-    QCheckBox *map_check_box_;
 };
 
 #endif // BANDRATIODIALOG_H

Vespucci/GUI/Analysis/bandratiodialog.ui

@@ -74,7 +74,7 @@
      </property>
      <layout class="QVBoxLayout" name="verticalLayout">
       <item>
-       <widget class="QCustomPlot" name="spectrumPlot" native="true">
+       <widget class="QCustomPlot" name="spectrumCustomPlot" native="true">
         <property name="minimumSize">
          <size>
           <width>600</width>
@@ -161,28 +161,14 @@
         </item>
        </layout>
       </item>
-      <item row="3" column="0">
-       <widget class="QLabel" name="label_7">
-        <property name="text">
-         <string>Peak Determination</string>
-        </property>
-       </widget>
-      </item>
-      <item row="3" column="1">
-       <widget class="QComboBox" name="peakComboBox">
+      <item row="4" column="0">
+       <widget class="QLabel" name="label">
         <property name="toolTip">
-         <string/>
+         <string>Search window for inflection points.</string>
+        </property>
+        <property name="text">
+         <string>Search Window Size</string>
         </property>
-        <item>
-         <property name="text">
-          <string>Riemann Sum</string>
-         </property>
-        </item>
-        <item>
-         <property name="text">
-          <string>Gaussian Fit</string>
-         </property>
-        </item>
        </widget>
       </item>
       <item row="4" column="1">
@@ -201,16 +187,22 @@
         </property>
        </widget>
       </item>
-      <item row="4" column="0">
-       <widget class="QLabel" name="label">
-        <property name="toolTip">
-         <string>Search window for inflection points.</string>
-        </property>
+      <item row="3" column="0">
+       <widget class="QLabel" name="label_6">
         <property name="text">
-         <string>Search Window Size</string>
+         <string>Quantification</string>
         </property>
        </widget>
       </item>
+      <item row="3" column="1">
+       <widget class="QComboBox" name="methodComboBox">
+        <item>
+         <property name="text">
+          <string>Empirical</string>
+         </property>
+        </item>
+       </widget>
+      </item>
      </layout>
     </widget>
    </item>

Vespucci/GUI/Analysis/classicalleastsquaresdialog.cpp

@@ -6,13 +6,11 @@ ClassicalLeastSquaresDialog::ClassicalLeastSquaresDialog(QWidget *parent, QShare
     ui(new Ui::ClassicalLeastSquaresDialog)
 {
     ui->setupUi(this);
-    reference_combo_box_ = findChild<QComboBox *>("datasetComboBox");
-    name_line_edit_= findChild<QLineEdit *>("nameLineEdit");
 
     workspace_ = ws;
     dataset_ = workspace_->GetDataset(dataset_key);
     QStringList matrix_keys = dataset_->AuxiliaryMatrixKeys();
-    reference_combo_box_->addItems(matrix_keys);
+    ui->referenceComboBox->addItems(matrix_keys);
 
 }
 
@@ -25,9 +23,9 @@ ClassicalLeastSquaresDialog::~ClassicalLeastSquaresDialog()
 
 void ClassicalLeastSquaresDialog::on_buttonBox_accepted()
 {
-    QString name = name_line_edit_->text();
+    QString name = ui->nameLineEdit->text();
     try{
-        dataset_->ClassicalLeastSquares(name, reference_combo_box_->currentText());
+        dataset_->ClassicalLeastSquares(name, ui->referenceComboBox->currentText());
     }catch(exception e){
         workspace_->main_window()->DisplayExceptionWarning(e);
     }

Vespucci/GUI/Analysis/classicalleastsquaresdialog.h

@@ -21,8 +21,6 @@ private slots:
 
 private:
     Ui::ClassicalLeastSquaresDialog *ui;
-    QComboBox *reference_combo_box_;
-    QLineEdit *name_line_edit_;
     QSharedPointer<VespucciWorkspace> workspace_;
     QSharedPointer<VespucciDataset> dataset_;
 };

Vespucci/GUI/Analysis/kmeansdialog.cpp

@@ -31,13 +31,9 @@ KMeansDialog::KMeansDialog(QWidget *parent, QSharedPointer<VespucciWorkspace> ws
     ui(new Ui::KMeansDialog)
 {
     ui->setupUi(this);
-    name_line_edit_ = findChild<QLineEdit *>("nameLineEdit");
-    cluster_spin_box_ = findChild<QSpinBox *>("clustersSpinBox");
-    prediction_check_box_ = findChild<QCheckBox *>("predictionCheckBox");
-    metric_combo_box_ = findChild<QComboBox *>("metricComboBox");
     workspace_ = ws;
     dataset_ = workspace_->GetDataset(dataset_key);
-    name_line_edit_->setEnabled(false);
+    ui->nameLineEdit->setEnabled(false);
 }
 
 KMeansDialog::~KMeansDialog()
@@ -51,13 +47,13 @@ KMeansDialog::~KMeansDialog()
 void KMeansDialog::on_buttonBox_accepted()
 {
 
-    QString metric_text = metric_combo_box_->currentText();
+    QString metric_text = ui->metricComboBox->currentText();
     int clusters;
-    QString name = name_line_edit_->text();
-    if (prediction_check_box_->isChecked())
+    QString name = ui->nameLineEdit->text();
+    if (ui->predictionCheckBox->isChecked())
         clusters = 0;
     else
-        clusters = cluster_spin_box_->value();
+        clusters = ui->clustersSpinBox->value();
     try{
         dataset_->KMeans(clusters, metric_text, name);
     }catch(exception e){
@@ -79,5 +75,5 @@ void KMeansDialog::on_buttonBox_rejected()
 
 void KMeansDialog::on_predictionCheckBox_clicked(bool checked)
 {
-    cluster_spin_box_->setEnabled(!checked);
+    ui->clustersSpinBox->setEnabled(!checked);
 }