public void actionPerformed(ActionEvent e) {
if (DBRecordStat.totalVar > 0.0) {
JFrame JFrameAUC = new JFrame("AUCs for each reader and modality");
RefineryUtilities.centerFrameOnScreen(JFrameAUC);
JFrameAUC.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
Object[] colNames = {
"ReaderID", "AUC " + DBRecordStat.modalityA, "AUC " + DBRecordStat.modalityB
};
Object[][] rowContent = new String[(int) DBRecordStat.Nreader][3];
int i = 0;
for (String desc_temp : InputFile1.readerIDs.keySet()) {
rowContent[i][0] = desc_temp;
rowContent[i][1] = Double.toString(DBRecordStat.AUCs[i][0]);
rowContent[i][2] = Double.toString(DBRecordStat.AUCs[i][1]);
i++;
}
JTable tableAUC = new JTable(rowContent, colNames);
JScrollPane scrollPaneAUC = new JScrollPane(tableAUC);
JFrameAUC.add(scrollPaneAUC, BorderLayout.CENTER);
JFrameAUC.setSize(600, 300);
JFrameAUC.setVisible(true);
} else {
JOptionPane.showMessageDialog(
GUI.MRMCobject.getFrame(),
"Pilot study data has not yet been analyzed.",
"Error",
JOptionPane.ERROR_MESSAGE);
}
}
public void actionPerformed(ActionEvent e) {
// System.out.println("study design button pressed");
if (InputFile1.isLoaded()) {
JComboBox<String> choose1 = new JComboBox<String>();
for (String Modality : InputFile1.getModalityIDs()) {
choose1.addItem(Modality);
}
choose1.setSelectedIndex(0);
Object[] message = {"Which modality would you like view?\n", choose1};
JOptionPane.showMessageDialog(
GUI.MRMCobject.getFrame(),
message,
"Choose Modality",
JOptionPane.INFORMATION_MESSAGE,
null);
designMod1 = (String) choose1.getSelectedItem();
TreeMap<String, String[][]> StudyDesignData =
InputFile1.getStudyDesign((String) choose1.getSelectedItem());
final StudyDesignPlot chart =
new StudyDesignPlot(
"Study Design: Modality " + designMod1,
designMod1,
"Case Index",
"Reader",
StudyDesignData,
InputFile1.filename);
chart.pack();
RefineryUtilities.centerFrameOnScreen(chart);
chart.setVisible(true);
} else {
JOptionPane.showMessageDialog(
GUI.MRMCobject.getFrame(),
"Pilot study data has not yet been input.",
"Error",
JOptionPane.ERROR_MESSAGE);
}
}
public void actionPerformed(ActionEvent e) {
// System.out.println("graph button pressed");
if (InputFile1 != null && InputFile1.isLoaded()) {
final BarGraph cpr =
new BarGraph("Cases per Reader", "Readers", "Cases", InputFile1.casesPerReader());
cpr.pack();
RefineryUtilities.centerFrameOnScreen(cpr);
cpr.setVisible(true);
final BarGraph rpc =
new BarGraph("Readers per Case", "Cases", "Readers", InputFile1.readersPerCase());
rpc.pack();
RefineryUtilities.centerFrameOnScreen(rpc);
RefineryUtilities.positionFrameOnScreen(rpc, 0.6, 0.6);
rpc.setVisible(true);
} else {
JOptionPane.showMessageDialog(
GUI.MRMCobject.getFrame(),
"Pilot study data has not yet been input.",
"Error",
JOptionPane.ERROR_MESSAGE);
}
}
public void actionPerformed(ActionEvent e) {
System.out.println("MRMC Variance analysis button clicked. RawStudyCard.varAnalysisListener");
// Check that .imrmc input file has been read
// If there is no JTextFilename, then reader scores have not been read
String name = JTextFilename.getText();
System.out.println("name=" + name);
if (name.equals(null) || name.equals("")) {
JFrame frame = GUI.MRMCobject.getFrame();
JOptionPane.showMessageDialog(
frame,
"Please browse for .imrmc or.csv input file",
" Error",
JOptionPane.ERROR_MESSAGE);
return;
}
// Check that a modality has been selected
if (DBRecordStat.modalityA == GUInterface.NO_MOD
&& DBRecordStat.modalityB == GUInterface.NO_MOD) {
JFrame frame = GUI.MRMCobject.getFrame();
JOptionPane.showMessageDialog(
frame, "You must select at least one modality", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
// Don't allow both modalities to be the same
if (DBRecordStat.modalityA.compareTo(DBRecordStat.modalityB) == 0) {
JFrame frame = GUI.MRMCobject.getFrame();
JOptionPane.showMessageDialog(
frame, "Modalities must be different", " Error", JOptionPane.ERROR_MESSAGE);
return;
}
// Analyze observerData
DBRecordStat.DBRecordStatFill(InputFile1, DBRecordStat);
// Check if variance estimate is negative
if (DBRecordStat.totalVar > 0) GUI.hasNegative = false;
else GUI.hasNegative = true;
if (GUI.hasNegative && FlagMLE == NO_MLE) {
JFrame frame = GUI.MRMCobject.getFrame();
int result =
JOptionPane.showConfirmDialog(
frame,
"The total variance estimate is negative.\n"
+ "Please report to the program developers. This is not expected.\n"
+ "Do you want to proceed with MLE estimates to avoid negatives?");
if (JOptionPane.CANCEL_OPTION == result) {
System.out.println("cancel");
} else if (JOptionPane.YES_OPTION == result) {
FlagMLE = USE_MLE;
DBRecordStat.flagMLE = FlagMLE;
mleCheckBox.setSelected(true);
DBRecordStat.totalVar = DBRecordStat.totalVarMLE;
DBRecordStat.totalVarSingle = DBRecordStat.totalVarMLESingle;
DBRecordStat.testStat = new StatTest(DBRecordStat);
} else if (JOptionPane.NO_OPTION == result) {
FlagMLE = NO_MLE;
}
}
// Update GUI
DBRecordStat.flagMLE = FlagMLE;
DBRecordSize.flagMLE = FlagMLE;
GUI.StatPanel1.setStatPanel();
GUI.StatPanel1.setTable1();
DBRecordSize.Nreader = DBRecordStat.Nreader;
DBRecordSize.Nnormal = DBRecordStat.Nnormal;
DBRecordSize.Ndisease = DBRecordStat.Ndisease;
GUI.SizePanel1.NreaderJTextField.setText(Long.toString(DBRecordStat.Nreader));
GUI.SizePanel1.NnormalJTextField.setText(Long.toString(DBRecordStat.Nnormal));
GUI.SizePanel1.NdiseaseJTextField.setText(Long.toString(DBRecordStat.Ndisease));
}
public void actionPerformed(ActionEvent e) {
// If input file is loaded, then show ROC curves
// Otherwise as for pilot study to be inpu
if (InputFile1.isLoaded()) {
JPanel panel = new JPanel();
int modalitynum = InputFile1.getModalityIDs().size();
JCheckBox[] jCheckboxArray = new javax.swing.JCheckBox[modalitynum];
for (int i = 0; i < modalitynum; i++) {
String modID = InputFile1.getModalityIDs().get(i);
jCheckboxArray[i] = new JCheckBox("" + modID);
panel.add(jCheckboxArray[i]);
}
Object[] message = {"Which modality would you like view?\n", panel};
JOptionPane.showMessageDialog(
GUI.MRMCobject.getFrame(),
message,
"Choose Modality",
JOptionPane.INFORMATION_MESSAGE,
null);
int checkedmod = 0;
for (int i = 0; i < modalitynum; i++) {
if (jCheckboxArray[i].isSelected()) {
checkedmod++;
}
}
String[] rocMod = new String[checkedmod];
String roctitle = "";
int selectmod = 0;
for (int i = 0; i < modalitynum; i++) {
if (jCheckboxArray[i].isSelected()) {
String modID = InputFile1.getModalityIDs().get(i);
rocMod[selectmod] = modID;
roctitle = roctitle + modID + " ";
selectmod++;
}
}
if (selectmod > 0) {
final ROCCurvePlot roc =
new ROCCurvePlot(
"ROC Curve: Modality " + roctitle,
"FPF (1 - Specificity), legend shows symbols for each modalityID:readerID",
"TPF (Sensitivity)",
InputFile1.generateROCpoints(rocMod),
InputFile1.filename);
roc.addData(InputFile1.generatePooledROC(rocMod), "Pooled Average");
roc.pack();
RefineryUtilities.centerFrameOnScreen(roc);
roc.setVisible(true);
} else {
JOptionPane.showMessageDialog(
GUI.MRMCobject.getFrame(),
"Please choose at list one Modality.",
"Error",
JOptionPane.ERROR_MESSAGE);
}
} else {
JOptionPane.showMessageDialog(
GUI.MRMCobject.getFrame(),
"Pilot study data has not yet been input.",
"Error",
JOptionPane.ERROR_MESSAGE);
}
}
public void actionPerformed(ActionEvent e) {
GUI.resetGUI();
if (GUInterface.selectedInput == GUInterface.DescInputChooseMode) {
JOptionPane.showMessageDialog(
GUI.MRMCobject.getFrame(),
"Please choose one kind of input file.",
"Error",
JOptionPane.ERROR_MESSAGE);
return;
}
JFileChooser fc = new JFileChooser();
FileNameExtensionFilter filter =
new FileNameExtensionFilter("iMRMC Input Files (.imrmc or csv)", "csv", "imrmc");
if (GUI.inputfileDirectory != null) fc.setCurrentDirectory(GUI.inputfileDirectory);
fc.setFileFilter(filter);
int returnVal = fc.showOpenDialog((Component) e.getSource());
if (returnVal == JFileChooser.CANCEL_OPTION || returnVal == JFileChooser.ERROR_OPTION) return;
GUI.inputfileDirectory = fc.getCurrentDirectory(); // save last time visit directory
/*
* Get a pointer to the input file and the filename
*/
File f = fc.getSelectedFile();
if (f == null) return;
InputFile1.filename = f.getPath();
JTextFilename.setText(f.getPath());
// GUI.inputfileDirectory = f.getPath();
/*
* Read the .imrmc input file, check for exceptions
*/
try {
InputFile1.ReadInputFile(GUI);
} catch (IOException except) {
except.printStackTrace();
JOptionPane.showMessageDialog(
GUI.MRMCobject.getFrame(), except.getMessage(), "Error", JOptionPane.ERROR_MESSAGE);
GUI.resetGUI();
JTextFilename.setText("");
return;
}
/*
* Compare the experimental design as determined from fields in the header vs. the data
*/
if (!InputFile1.dataCheckResults.isEmpty()) {
JOptionPane.showMessageDialog(
GUI.MRMCobject.getFrame(),
InputFile1.dataCheckResults,
"Warning: Input Header Values Do Not Match Actual Values",
JOptionPane.WARNING_MESSAGE);
} else {
JOptionPane.showMessageDialog(
GUI.MRMCobject.getFrame(),
"NR = "
+ InputFile1.Nreader
+ " N0 = "
+ InputFile1.Nnormal
+ " N1 = "
+ InputFile1.Ndisease
+ " NM = "
+ InputFile1.Nmodality,
"Study Info",
JOptionPane.INFORMATION_MESSAGE);
}
/*
* Initialze modality pulldown menus
*/
for (String ModalityID : InputFile1.getModalityIDs()) {
chooseA.addItem(ModalityID);
chooseB.addItem(ModalityID);
}
DBRecordStat.modalityA = GUInterface.NO_MOD;
DBRecordStat.modalityB = GUInterface.NO_MOD;
}