adding PSPView definition, CBICA#151

Plugins/upenn.cbica.captk.brain.pseudoprogression/src/internal/QcaptkPseudoProgressionView.cpp

@@ -0,0 +1,372 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+#include "QcaptkPseudoProgressionView.h"
+
+// blueberry
+#include <berryConstants.h>
+#include <berryIWorkbenchPage.h>
+
+// mitk
+#include "mitkApplicationCursor.h"
+#include "mitkStatusBar.h"
+//#include "mitkPlanePositionManager.h"
+#include "captkPseudoProgressionPluginActivator.h"
+
+// Qmitk
+//#include "QmitkRenderWindow.h"
+
+// us
+#include <usGetModuleContext.h>
+#include <usModule.h>
+#include <usModuleContext.h>
+#include <usModuleResource.h>
+#include <usModuleResourceStream.h>
+
+// Qt
+#include <QDateTime>
+#include <QFileDialog>
+#include <QInputDialog>
+#include <QMessageBox>
+#include <QFileDialog>
+
+// CaPTk
+//#include "CaPTkSurvival.h"
+
+const std::string QcaptkPseudoProgressionView::VIEW_ID = "upenn.cbica.captk.views.pseudoprogression";
+
+QcaptkPseudoProgressionView::QcaptkPseudoProgressionView()
+  : m_Parent(nullptr)
+{
+  //m_CaPTkSurvival = new captk::CaPTkSurvival(this);
+}
+
+QcaptkPseudoProgressionView::~QcaptkPseudoProgressionView()
+{
+
+}
+
+void QcaptkPseudoProgressionView::CreateQtPartControl(QWidget *parent)
+{
+  // setup the basic GUI of this view
+  m_Parent = parent;
+
+  m_Controls.setupUi(parent);
+
+
+  /**** Connect signals & slots ****/
+
+  connect(m_Controls.m_cbUsageSelector, SIGNAL(currentTextChanged(QString)),
+          this, SLOT(OnUsageComboBoxCurrentTextChanged(QString)));
+
+  connect(m_Controls.m_cbModelSourceSelector, SIGNAL(currentTextChanged(QString)),
+          this, SLOT(OnModelSourceComboBoxCurrentTextChanged(QString)));
+
+  connect(m_Controls.pushButton_CustomModelDirBrowse, SIGNAL(clicked()),
+          this, SLOT(OnCustomModelDirectoryButtonClicked()));
+
+  connect(m_Controls.pushButton_OutputDirBrowse, SIGNAL(clicked()),
+          this, SLOT(OnOutputDirectoryButtonClicked()));
+
+  connect(m_Controls.pushButton_SubjectDirBrowse, SIGNAL(clicked()),
+          this, SLOT(OnSubjectDirectoryButtonClicked()));
+
+  connect(m_Controls.pushButtonRun, SIGNAL(clicked()),
+          this, SLOT(OnRunButtonPressed()));
+
+  //connect(m_CaPTkSurvival, SIGNAL(done()),
+  //        this, SLOT(OnModuleDone()));
+
+  /**** Initialize widgets ****/
+
+  // Initialize the usage type combo box
+  m_Controls.m_cbUsageSelector->addItems(QStringList() << "Use Existing Model" << "Train New Model");
+  // Set combo box to the last user selected value
+  m_Controls.m_cbUsageSelector->setCurrentText(
+    this->GetPreferences()->Get("SurvivalUsageComboBox", "Use Existing Model")
+  );
+
+  // Initialize model source combo box
+  m_Controls.m_cbModelSourceSelector->addItems(
+    QStringList() << "CBICA CaPTk Model" << "Custom"
+  );
+  // Set combo box to the last user selected value
+  m_Controls.m_cbModelSourceSelector->setCurrentText(
+              this->GetPreferences()->Get("SurvivalModelSourceComboBox", "CBICA CaPTk Model")
+  );
+
+  // Set model information
+  m_Controls.label_PaperInformation->setWordWrap(true);
+  QString modelInfo = ("This is a model trained on de novo glioblastoma cases.<br>"
+                       "Please note that this model was created following certain assumptions<br>"
+                       "(described in the paper below)<br>"
+                       "It can be used for research purposes only.<br><br>"
+                       "L.Macyszyn, et al. Imaging Patterns Predict Patient Survival and Molecular<br>"
+                       "Subtype in Glioblastoma via Machine Learning Techniques, Neuro-Oncology.<br>"
+                       "18(3) : 417-425, 2016.<br><br>"
+                       "<a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767233\" style=\"color:red\">[LINK]</a>");
+  m_Controls.label_PaperInformation->setText(modelInfo);
+  m_Controls.label_PaperInformation->setTextFormat(Qt::RichText);
+  m_Controls.label_PaperInformation->setTextInteractionFlags(Qt::TextBrowserInteraction);
+  m_Controls.label_PaperInformation->setOpenExternalLinks(true);
+}
+
+void QcaptkPseudoProgressionView::Activated()
+{
+
+}
+
+void QcaptkPseudoProgressionView::Deactivated()
+{
+  // Not yet implemented
+}
+
+void QcaptkPseudoProgressionView::Visible()
+{
+  // Not yet implemented
+}
+
+void QcaptkPseudoProgressionView::Hidden()
+{
+  // Not yet implemented
+}
+
+int QcaptkPseudoProgressionView::GetSizeFlags(bool width)
+{
+  if (!width)
+  {
+    return berry::Constants::MIN | berry::Constants::MAX | berry::Constants::FILL;
+  }
+  else
+  {
+    return 0;
+  }
+}
+
+int QcaptkPseudoProgressionView::ComputePreferredSize(bool width,
+                                                          int /*availableParallel*/,
+                                                          int /*availablePerpendicular*/,
+                                                          int preferredResult)
+{
+  if (width == false)
+  {
+    return 100;
+  }
+  else
+  {
+    return preferredResult;
+  }
+}
+
+/************************************************************************/
+/* protected slots                                                      */
+/************************************************************************/
+void QcaptkPseudoProgressionView::OnUsageComboBoxCurrentTextChanged(const QString& text)
+{
+  // set preference to remember usage choice
+  this->GetPreferences()->Put("SurvivalUsageComboBox", text);
+  this->GetPreferences()->Flush();
+
+  if (text == "Use Existing Model") {
+      m_Controls.m_cbModelSourceSelector->setVisible(true);
+      m_Controls.label_Source->setVisible(true);
+      if (m_Controls.m_cbModelSourceSelector->currentText() == "Custom") {
+          m_Controls.lineEdit_CustomModelDir->setVisible(true);
+          m_Controls.label_CustomModelDir->setVisible(true);
+          m_Controls.pushButton_CustomModelDirBrowse->setVisible(true);
+      }
+      else if (m_Controls.m_cbModelSourceSelector->currentText() == "CBICA CaPTk Model") {
+          m_Controls.groupBox_PaperInfo->setVisible(true);
+      }
+
+  }
+  else if (text == "Train New Model") {
+      m_Controls.m_cbModelSourceSelector->setVisible(false);
+      m_Controls.label_Source->setVisible(false);
+      m_Controls.lineEdit_CustomModelDir->setVisible(false);
+      m_Controls.label_CustomModelDir->setVisible(false);
+      m_Controls.pushButton_CustomModelDirBrowse->setVisible(false);
+      m_Controls.groupBox_PaperInfo->setVisible(false);
+
+  }
+}
+
+void QcaptkPseudoProgressionView::OnModelSourceComboBoxCurrentTextChanged(const QString& text)
+{
+  // Set preference to remember model source choice
+  this->GetPreferences()->Put("SurvivalSourceComboBox", text);
+  this->GetPreferences()->Flush();
+
+  // Show/Hide views below it
+  if (text == "CBICA CaPTk Model")
+  {
+    m_Controls.lineEdit_CustomModelDir->setVisible(false);
+    m_Controls.label_CustomModelDir->setVisible(false);
+    m_Controls.pushButton_CustomModelDirBrowse->setVisible(false);
+    m_Controls.groupBox_PaperInfo->setVisible(true);
+    m_Controls.label_PaperInformation->setVisible(true);
+  }
+  else if (text == "Custom")
+  {
+    m_Controls.lineEdit_CustomModelDir->setVisible(true);
+    m_Controls.pushButton_CustomModelDirBrowse->setVisible(true);
+    m_Controls.label_CustomModelDir->setVisible(true);
+    m_Controls.groupBox_PaperInfo->setVisible(false);
+    m_Controls.label_PaperInformation->setVisible(false);
+  }
+
+}
+
+
+void QcaptkPseudoProgressionView::OnSubjectDirectoryButtonClicked()
+{
+  auto dirName = QFileDialog::getExistingDirectory(m_Parent,
+    tr("Select subject directory"), this->GetLastFileOpenPath());
+
+  if(dirName.isEmpty() || dirName.isNull()) { return; }
+
+  // Find and save file information
+  QFileInfo file(dirName);
+  if (!file.isDir()) { return; }
+  this->SetLastFileOpenPath(dirName);
+
+
+
+  // Set the path to the QLineEdit
+  m_Controls.lineEdit_SubjectDir->setText(dirName);
+}
+
+void QcaptkPseudoProgressionView::OnCustomModelDirectoryButtonClicked()
+{
+    auto dirName = QFileDialog::getExistingDirectory(m_Parent,
+                                                     tr("Select model directory"),
+                                                     this->GetLastFileOpenPath());
+
+    if(dirName.isEmpty() || dirName.isNull()) { return; }
+
+    // Find and save file information
+    QFileInfo file(dirName);
+    if (!file.isDir()) { return; }
+    this->SetLastFileOpenPath(dirName);
+
+
+    // Set the path to the QLineEdit
+    m_Controls.lineEdit_CustomModelDir->setText(dirName);
+}
+
+void QcaptkPseudoProgressionView::OnOutputDirectoryButtonClicked()
+{
+  auto dirName = QFileDialog::getExistingDirectory(m_Parent, 
+    tr("Select output directory"), this->GetLastFileOpenPath());
+
+  if(dirName.isEmpty() || dirName.isNull()) { return; }
+
+  // Find and save file information
+  QFileInfo file(dirName);
+  if (!file.isDir()) { return; }
+  this->SetLastFileOpenPath(dirName);
+
+  // Set the path to the QLineEdit
+  m_Controls.lineEdit_OutputDir->setText(dirName);
+}
+
+void QcaptkPseudoProgressionView::OnRunButtonPressed()
+{
+  QString modelDirPath = m_Controls.lineEdit_CustomModelDir->text();
+  QString subjectDirPath = m_Controls.lineEdit_SubjectDir->text();
+  QString outputDirPath = m_Controls.lineEdit_OutputDir->text();
+  bool trainNewModel = false; // true if training, false if using an existing model
+  bool useCustomModel = false; // true if using a custom model, false if using CBICA's CaPTk model
+
+  if (m_Controls.m_cbUsageSelector->currentText() == "Train New Model") {
+      trainNewModel = true;
+      useCustomModel = false;
+  }
+  else if (m_Controls.m_cbUsageSelector->currentText() == "Use Existing Model") {
+      trainNewModel = false;
+
+      if  (m_Controls.m_cbModelSourceSelector->currentText() == "CBICA CaPTk Model") {
+          useCustomModel = false;
+      }
+      else if (m_Controls.m_cbModelSourceSelector->currentText() == "Custom") {
+          useCustomModel = true;
+      }
+
+  }
+  m_Controls.pushButtonRun->setDisabled(true);
+  m_Controls.pushButtonRun->setText("Running Survival Prediction...");
+//  m_CaPTkSurvival->Run(
+//   modelDirPath,
+//   subjectDirPath,
+//   outputDirPath,
+//   trainNewModel,
+//   useCustomModel
+//   );
+}
+
+//void QcaptkPseudoProgressionView::OnModuleDone()
+//{
+//    m_Controls.pushButtonRun->setEnabled(true);
+//    m_Controls.pushButtonRun->setText("Run Survival Prediction");
+//}
+
+/************************************************************************/
+/* protected                                                            */
+/************************************************************************/
+void QcaptkPseudoProgressionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer> &)
+{
+
+}
+
+void QcaptkPseudoProgressionView::OnPreferencesChanged(const berry::IBerryPreferences*)
+{
+
+}
+
+void QcaptkPseudoProgressionView::NodeAdded(const mitk::DataNode *)
+{
+
+}
+
+void QcaptkPseudoProgressionView::NodeRemoved(const mitk::DataNode *)
+{
+
+}
+
+void QcaptkPseudoProgressionView::SetFocus()
+{
+}
+
+void QcaptkPseudoProgressionView::UpdateControls()
+{
+  this->RequestRenderWindowUpdate(mitk::RenderingManager::REQUEST_UPDATE_ALL);
+}
+
+void QcaptkPseudoProgressionView::InitializeListeners()
+{
+
+}
+
+QString QcaptkPseudoProgressionView::GetLastFileOpenPath()
+{
+  return this->GetPreferences()->Get("LastFileOpenPath", "");
+}
+
+void QcaptkPseudoProgressionView::SetLastFileOpenPath(const QString &path)
+{
+  this->GetPreferences()->Put("LastFileOpenPath", path);
+  this->GetPreferences()->Flush();
+}