/*=auto=========================================================================

Portions (c) Copyright 2005 Brigham and Women's Hospital (BWH) All Rights Reserved.

See Doc/copyright/copyright.txt
or http://www.slicer.org/copyright/copyright.txt for details.

Program:   3D Slicer
Module:    $RCSfile: vtkQdecModuleGUI.cxx,v $
Date:      $Date: 2006/03/17 15:10:10 $
Version:   $Revision: 1.2 $

=========================================================================auto=*/

#include "vtkSlicerApplication.h"

#include "QdecSubject.h"

// QDec includes
#include "vtkQdecModuleGUI.h"

// vtkSlicer includes
#include "vtkSlicerApplicationLogic.h"
#include "vtkSlicerNodeSelectorWidget.h"

// KWWidgets includes
#include "vtkKWApplication.h"
#include "vtkKWWidget.h"
#include "vtkKWScaleWithEntry.h"
#include "vtkKWEntryWithLabel.h"
#include "vtkKWMenuButtonWithLabel.h"
#include "vtkKWMenuButton.h"
#include "vtkKWScale.h"
#include "vtkKWMenu.h"
#include "vtkKWEntry.h"
#include "vtkKWFrame.h"
#include "vtkKWFrameWithLabel.h"
#include "vtkKWPushButton.h"
#include "vtkKWLoadSaveButtonWithLabel.h"
#include "vtkKWLoadSaveButton.h"
#include "vtkKWLoadSaveDialog.h"
#include "vtkKWMultiColumnList.h"
#include "vtkKWMultiColumnListWithScrollbars.h"
#include "vtkKWLabel.h"
#include "vtkKWListBox.h"
#include "vtkKWListBoxWithScrollbars.h"
#include "vtkKWListBoxWithScrollbarsWithLabel.h"
#include "vtkKWTopLevel.h"

// for setting the zip/unzip/rm paths
#include "vtkKWMessageDialog.h"
#include "vtkKWApplicationSettingsInterface.h"
#include "vtkKWUserInterfaceManager.h"
#include "vtkKWUserInterfaceManagerDialog.h"

#include "vtkSlicerModelsGUI.h"

// for pick events
#include "vtkSlicerViewerWidget.h"
#include "vtkSlicerViewerInteractorStyle.h"

// for path manipulation
#include "itksys/SystemTools.hxx"

// for scalar overlays
#include "vtkMRMLProceduralColorNode.h"

// STL includes
#include <string>
#include <iostream>
#include <sstream>

// VTK includes
#include "vtkObjectFactory.h"
#include "vtkCommand.h"

//------------------------------------------------------------------------------
vtkQdecModuleGUI* vtkQdecModuleGUI::New()
{
  // First try to create the object from the vtkObjectFactory
  vtkObject* ret = vtkObjectFactory::CreateInstance("vtkQdecModuleGUI");
  if(ret)
    {
      return (vtkQdecModuleGUI*)ret;
    }
  // If the factory was unable to create the object, then create it here.
  return new vtkQdecModuleGUI;
}

//----------------------------------------------------------------------------
vtkQdecModuleGUI::vtkQdecModuleGUI()
{
  this->NAMICLabel = NULL;
  this->SubjectsDirectoryButton = NULL;
  this->LoadTableButton = NULL;
  this->LoadResultsButton = NULL;
  this->DesignEntry = NULL;
  this->DiscreteFactorsListBox = NULL;
  this->ContinuousFactorsListBox = NULL;
  this->ApplyButton = NULL;
  this->MultiColumnList = NULL;
  this->MeasureLabel = NULL;
  this->MeasureMenu = NULL;
  this->HemisphereLabel = NULL;
  this->HemisphereMenu = NULL;
  this->SmoothnessLabel = NULL;
  this->SmoothnessMenu = NULL;
  this->QuestionLabel = NULL;
  this->QuestionMenu = NULL;
  this->Logic = NULL;

  this->Index = 2;

  // for picking
  this->ViewerWidget = NULL;
  this->InteractorStyle = NULL;
}

//----------------------------------------------------------------------------
vtkQdecModuleGUI::~vtkQdecModuleGUI()
{
  if (this->GetLogic() &&
      this->GetLogic()->GetTclScriptLoaded())
    {
    vtkSlicerApplication *app = (vtkSlicerApplication *)this->GetApplication();
    if (app)
      {
      app->Script("vtkFreeSurferReadersExit");
      }
    }
  this->RemoveMRMLNodeObservers ( );
  this->RemoveLogicObservers ( );
  this->SetLogic( vtkObjectPointer(&this->Logic), NULL );
 
  if ( this->NAMICLabel )
    {
    this->NAMICLabel->SetParent ( NULL );
    this->NAMICLabel->Delete();
    this->NAMICLabel = NULL;
    }

  if ( this->SubjectsDirectoryButton )
    {
    this->SubjectsDirectoryButton->SetParent(NULL);
    this->SubjectsDirectoryButton->Delete();
    this->SubjectsDirectoryButton = NULL;
    }
   
  if ( this->LoadTableButton )
    {
    this->LoadTableButton->SetParent(NULL);
    this->LoadTableButton->Delete();
    this->LoadTableButton = NULL;
    }

  if ( this->LoadResultsButton )
    {
    this->LoadResultsButton->SetParent(NULL);
    this->LoadResultsButton->Delete();
    this->LoadResultsButton = NULL;
    }
  
  if ( this->DesignEntry )
    {
    this->DesignEntry->SetParent(NULL);
    this->DesignEntry->Delete();
    this->DesignEntry = NULL;
    }
  
  if ( this->DiscreteFactorsListBox )
    {
    this->DiscreteFactorsListBox->SetParent ( NULL );
    this->DiscreteFactorsListBox->Delete();
    this->DiscreteFactorsListBox = NULL;
    }
 
   if ( this->ContinuousFactorsListBox )
    {
    this->ContinuousFactorsListBox->SetParent ( NULL );
    this->ContinuousFactorsListBox->Delete();
    this->ContinuousFactorsListBox = NULL;
    }

   if ( this->ApplyButton )
    {
    this->ApplyButton->SetParent(NULL);
    this->ApplyButton->Delete();
    this->ApplyButton = NULL;
    }
 
   if (this->MultiColumnList)
     {
     this->MultiColumnList->SetParent(NULL);
     this->MultiColumnList->Delete();
     this->MultiColumnList = NULL;
     }

   if ( this->MeasureLabel )
    {
    this->MeasureLabel->SetParent ( NULL );
    this->MeasureLabel->Delete();
    this->MeasureLabel = NULL;
    }

   if ( this->MeasureMenu )
    {
    this->MeasureMenu->SetParent ( NULL );
    this->MeasureMenu->Delete();
    this->MeasureMenu = NULL;
    }

    if ( this->HemisphereLabel )
    {
    this->HemisphereLabel->SetParent ( NULL );
    this->HemisphereLabel->Delete();
    this->HemisphereLabel = NULL;
    }

   if ( this->HemisphereMenu )
    {
    this->HemisphereMenu->SetParent ( NULL );
    this->HemisphereMenu->Delete();
    this->HemisphereMenu = NULL;
    }

   if ( this->SmoothnessLabel )
    {
    this->SmoothnessLabel->SetParent ( NULL );
    this->SmoothnessLabel->Delete();
    this->SmoothnessLabel = NULL;
    }

   if ( this->SmoothnessMenu )
    {
    this->SmoothnessMenu->SetParent ( NULL );
    this->SmoothnessMenu->Delete();
    this->SmoothnessMenu = NULL;
    }

   if ( this->QuestionLabel )
    {
    this->QuestionLabel->SetParent ( NULL );
    this->QuestionLabel->Delete();
    this->QuestionLabel = NULL;
    }

   if ( this->QuestionMenu )
    {
    this->QuestionMenu->SetParent ( NULL );
    this->QuestionMenu->Delete();
    this->QuestionMenu = NULL;
    }
   
   this->SetViewerWidget(NULL);   
   this->SetInteractorStyle(NULL);
}

//---------------------------------------------------------------------------
void vtkQdecModuleGUI::CreateModuleEventBindings ( )
{
  vtkDebugMacro("CreateModuleEventBindings");
}

//---------------------------------------------------------------------------
void vtkQdecModuleGUI::ReleaseModuleEventBindings ( )
{
  vtkDebugMacro("ReleaseModuleEventBindings");
}


//----------------------------------------------------------------------------
void vtkQdecModuleGUI::Enter()
{
  vtkDebugMacro("Enter...");
  if ( this->Built == false )
    {
    this->BuildGUI();
    this->AddGUIObservers();
    }
  this->CreateModuleEventBindings();
  this->UpdateGUI();
}

//----------------------------------------------------------------------------
void vtkQdecModuleGUI::Exit()
{
  vtkDebugMacro("Exit: removing observers on picking");
  this->ReleaseModuleEventBindings();
}

//---------------------------------------------------------------------------
void vtkQdecModuleGUI::TearDownGUI ( )
{
  this->Exit();
  if ( this->Built )
    {
    this->RemoveGUIObservers();
    }
}

//----------------------------------------------------------------------------
void vtkQdecModuleGUI::PrintSelf(ostream& os, vtkIndent indent)
{
  os << indent << "vtkQdecModuleGUI" << endl;
  os << indent << "vtkQdecModuleLogic: " << (this->GetLogic() != NULL ? "" : "NULL") << endl;
  if (this->GetLogic() != NULL)
    {
    this->GetLogic()->PrintSelf(os, indent.GetNextIndent());
    }
}

//---------------------------------------------------------------------------
void vtkQdecModuleGUI::AddGUIObservers ( ) 
{
  if (this->SubjectsDirectoryButton)
    {
    this->SubjectsDirectoryButton->GetWidget()->GetLoadSaveDialog()->AddObserver (vtkKWTopLevel::WithdrawEvent, (vtkCommand *)this->GUICallbackCommand );
    }
  if (this->LoadTableButton)
    {
    this->LoadTableButton->GetWidget()->GetLoadSaveDialog()->AddObserver (vtkKWTopLevel::WithdrawEvent, (vtkCommand *)this->GUICallbackCommand );
    }
  if (this->LoadResultsButton)
    {
    this->LoadResultsButton->GetWidget()->GetLoadSaveDialog()->AddObserver (vtkKWTopLevel::WithdrawEvent, (vtkCommand *)this->GUICallbackCommand );
    }
  if (this->ApplyButton)
    {
    this->ApplyButton->AddObserver (vtkKWPushButton::InvokedEvent, (vtkCommand *)this->GUICallbackCommand );
    }
  if (this->QuestionMenu)
    {
    this->QuestionMenu->GetMenu()->AddObserver(vtkKWMenu::MenuItemInvokedEvent, (vtkCommand *)this->GUICallbackCommand );
    }
}

//---------------------------------------------------------------------------
void vtkQdecModuleGUI::RemoveGUIObservers ( )
{
  if (this->SubjectsDirectoryButton)
    {
    this->SubjectsDirectoryButton->GetWidget()->GetLoadSaveDialog()->RemoveObservers (vtkKWTopLevel::WithdrawEvent, (vtkCommand *)this->GUICallbackCommand );
    }
  
  if (this->LoadTableButton)
    {
    this->LoadTableButton->GetWidget()->GetLoadSaveDialog()->RemoveObservers (vtkKWTopLevel::WithdrawEvent, (vtkCommand *)this->GUICallbackCommand );
    }

  if (this->LoadResultsButton)
    {
    this->LoadResultsButton->GetWidget()->GetLoadSaveDialog()->RemoveObservers (vtkKWTopLevel::WithdrawEvent, (vtkCommand *)this->GUICallbackCommand );    
    }

  if (this->ApplyButton)
    {
    this->ApplyButton->RemoveObservers ( vtkKWPushButton::InvokedEvent,  (vtkCommand *)this->GUICallbackCommand );
    }
  
  if (this->QuestionMenu)
    {
    this->QuestionMenu->GetMenu()->RemoveObservers(vtkKWMenu::MenuItemInvokedEvent, (vtkCommand *)this->GUICallbackCommand );
    }
}

//---------------------------------------------------------------------------
void vtkQdecModuleGUI::RemoveMRMLNodeObservers ( )
{
   if ( this->GetApplicationGUI() &&  this->GetApplicationGUI()->GetMRMLScene())
    {
    this->GetApplicationGUI()->GetMRMLScene()->RemoveObservers(vtkMRMLScene::SceneCloseEvent, this->MRMLCallbackCommand);
    }
}

//---------------------------------------------------------------------------
void vtkQdecModuleGUI::RemoveLogicObservers ( ) {
    // Fill in
}


//---------------------------------------------------------------------------
void vtkQdecModuleGUI::ProcessGUIEvents ( vtkObject *caller,
                                           unsigned long event,
                                           void *callData ) 
{

  
  
  vtkKWPushButton *b = vtkKWPushButton::SafeDownCast ( caller );

  if (b == this->ApplyButton && event == vtkKWPushButton::InvokedEvent ) 
    {
    //this->DebugOn();
    if (this->GetDebug() && this->GetLogic())
      {
      this->GetLogic()->DebugOn();
      }

    vtkDebugMacro("Apply button pushed");
    
    std::string cont1 = "none";
    std::string cont2 = "none";
    std::string dis1 = "none";
    std::string dis2 = "none";
    int factorNum = 0;
    for (int i = 0; (i < this->ContinuousFactorsListBox->GetWidget()->GetWidget()->GetNumberOfItems()) && 
                    (factorNum < 2); i++)
      {
      if ( this->ContinuousFactorsListBox->GetWidget()->GetWidget()->GetSelectState(i))
        {
        vtkDebugMacro("\t" <<  this->ContinuousFactorsListBox->GetWidget()->GetWidget()->GetItem(i));
        if (factorNum == 0)
          {
          cont1 = this->ContinuousFactorsListBox->GetWidget()->GetWidget()->GetItem(i);
          }
        else if (factorNum == 1)
          {
          cont2 = this->ContinuousFactorsListBox->GetWidget()->GetWidget()->GetItem(i);
          }
        factorNum++;
        }
      }
    
    factorNum = 0;
    for (int i = 0; (i < this->DiscreteFactorsListBox->GetWidget()->GetWidget()->GetNumberOfItems()) &&
           (factorNum < 2); i++)
      {
      if ( this->DiscreteFactorsListBox->GetWidget()->GetWidget()->GetSelectState(i))
        {
        vtkDebugMacro("\t" <<  this->DiscreteFactorsListBox->GetWidget()->GetWidget()->GetItem(i));
        if (factorNum == 0)
          {    
          dis1 = this->DiscreteFactorsListBox->GetWidget()->GetWidget()->GetItem(i);
          }
        else if (factorNum == 1)
          {
          dis2 = this->DiscreteFactorsListBox->GetWidget()->GetWidget()->GetItem(i);
          }
        factorNum++;
        }
      }
    vtkDebugMacro("Selected discrete factors = " << dis1.c_str() << " and " << dis2.c_str());
    vtkDebugMacro("Selected continuous factors = " << cont1.c_str() << " and " << cont2.c_str());
    vtkDebugMacro("Design name = " << this->DesignEntry->GetWidget()->GetValue());
    vtkDebugMacro("Measure = " << this->MeasureMenu->GetValue());
    vtkDebugMacro("Hemisphere = " << this->HemisphereMenu->GetValue());
    vtkDebugMacro("Smoothness = " << this->SmoothnessMenu->GetValue());

    if (!this->GetLogic())
      {
      vtkErrorMacro("No Logic associated with QDEC GUI, can't create the GLM design");
      return;
      }
    // now pass it into the QDEC project to create a design
    int err = this->GetLogic()->CreateGlmDesign(this->DesignEntry->GetWidget()->GetValue(),
                                                dis1.c_str(), dis2.c_str(), cont1.c_str(), cont2.c_str(),
                                                this->MeasureMenu->GetValue(),
                                                this->HemisphereMenu->GetValue(),
                                                atoi(this->SmoothnessMenu->GetValue()));
    if (err != 0)
      {
      std::string errorMessage;
      if (err == -1)
        {
        errorMessage = "GLM Design: Bad first discrete factor";
        }
      if (err == -2)
        {
        errorMessage = "GLM Design: Bad second discrete factor";
        }
      if (err == -3)
        {
        errorMessage = "GLM Design: Bad first continuous factor";
        }
      if (err == -4)
        {
        errorMessage = "GLM Design: Bad second continuous factor";
        }
      if (err == -5)
        {
        errorMessage = "GLM Design: Zero factors!";
        }
      if (err == -6)
        {
        errorMessage = "GLM Design: could not create working directory";
        }
      if (err == -7)
        {
        errorMessage = "GLM Design: working directory not set, cannot save fsgd file";
        }
      if (err == -8)
        {
        errorMessage = "GLM Design: could not generate contrasts";
        }
      if (err == -9)
        {
        errorMessage = "Could not create the fsgd file";
        }
      if (err == -10)
        {
        errorMessage = "Could not generate contrasts";
        }
      if (err == -11)
        {
        errorMessage = "Could not create y.mgh file, the appropriate analysis may not have been performed on these subjects to provide the input mgh files for the creation of y.mgh";
        }
      if (err == -12)
        {
        errorMessage = "No QDEC Project defined on the logic";
        }
      vtkErrorMacro("Error making the GLM design: " <<  errorMessage.c_str());
      return;
      }

    vtkDebugMacro("Success in making the GLM design.");

    err = this->GetLogic()->RunGlmFit();

    if (err == 1)
      {
      vtkWarningMacro("Unable to run GLM Fit, but succeeded at loading some demo data");
      }
    else if (err != 0)
      {
      
      std::string errorMessage;
      if (err == -1)
        {
        errorMessage = "QdecGlmFit::Run: QdecGlmDesign is invalid";
        }
      if (err == -2)
        {
        errorMessage = "QdecGlmFit::Run: glm fit results are invalid";
        }
      if (err == -3)
        {
        errorMessage = "QdecGlmFit::Run: failed to run fit, and demo data isn't valid";
        }
      if (err == -4)
        {
        errorMessage = "QDEC project not defined on Logic";
        }
      vtkErrorMacro("Error running GLM Fit: " << errorMessage.c_str());
      return;
      }
    vtkDebugMacro("Succeeded in running Glm Fit.");
    
    // get the models logic to use to load the models and scalars (can't access it in the Logic class)
    vtkSlicerModelsLogic *modelsLogic = vtkSlicerModelsGUI::SafeDownCast(vtkSlicerApplication::SafeDownCast(this->GetApplication())->GetModuleGUIByName("Models"))->GetLogic();
    if (this->GetLogic()->LoadResults(modelsLogic, this->GetApplication()) != 0)
      {
      vtkErrorMacro("Unable to load results of GLM fit processing");
      }
    else
      {
      // clear out the questions menu
      this->QuestionMenu->GetMenu()->DeleteAllItems();
      // update the questions menu

      unsigned int numQuestions = this->GetLogic()->GetNumberOfQuestions();
      for (unsigned int i = 0; i < numQuestions; i++)
        {
        this->QuestionMenu->GetMenu()->AddRadioButton(this->GetLogic()->GetQuestion(i).c_str());
        }
      // trigger showing one of the questions
      this->QuestionMenu->GetMenu()->InvokeItem(numQuestions - 1);
      this->QuestionMenu->GetMenu()->InvokeEvent(vtkKWMenu::MenuItemInvokedEvent);
      }
    if (this->GetDebug())
      {
      this->GetLogic()->DebugOff();
      }
    this->DebugOff();
    return;
    }

  vtkKWLoadSaveDialog *browse = vtkKWLoadSaveDialog::SafeDownCast(caller);

  if (browse == this->SubjectsDirectoryButton->GetWidget()->GetLoadSaveDialog() && event == vtkKWTopLevel::WithdrawEvent )
    {
    // If a table file has been selected for loading...
    const char *fileName = this->SubjectsDirectoryButton->GetWidget()->GetFileName();
    if (!fileName || strcmp(fileName,"") == 0)
      {
      vtkDebugMacro("Empty filename");
      this->SubjectsDirectoryButton->GetWidget()->SetText ("None");
      this->GetLogic()->SetSubjectsDirectory("None");
      return;
      }
    vtkDebugMacro("Setting the qdec projects subjects dir to " << fileName);
    this->GetLogic()->SetSubjectsDirectory(fileName);
    return;
    }

  if (browse == this->LoadTableButton->GetWidget()->GetLoadSaveDialog()   && event == vtkKWTopLevel::WithdrawEvent )
    {
    // If a table file has been selected for loading...
    const char *fileName = this->LoadTableButton->GetWidget()->GetFileName();
    if (!fileName || strcmp(fileName,"") == 0)
      {
      vtkDebugMacro("Empty filename");
      this->LoadTableButton->GetWidget()->SetText ("None");
      return;
      }
    vtkDebugMacro("Trying to load file " << fileName);
    if (this->GetLogic()->LoadDataTable(fileName) == 0)
      {
      // failure
      vtkErrorMacro("Error loading table file " << fileName);
      this->LoadTableButton->GetWidget()->SetText ("None");
      }
    else
      {
      browse->SaveLastPathToRegistry("OpenPath");
      vtkDebugMacro("vtkQdecModuleGUI:ProcessGUIEvents: was able to load file " << fileName);
      if (this->GetDebug())
        {
        this->GetLogic()->QDECProject->DumpDataTable ( stdout );
        }
      this->UpdateGUI();
      
      }
    return;
    }

  if (browse == this->LoadResultsButton->GetWidget()->GetLoadSaveDialog()  && event == vtkKWTopLevel::WithdrawEvent )
    {
    // If a results file has been selected for loading...
    const char *fileName = this->LoadResultsButton->GetWidget()->GetFileName();
    if (!fileName || strcmp(fileName,"") == 0)
      {
      vtkDebugMacro("Empty filename");
      this->LoadResultsButton->GetWidget()->SetText ("None");
      return;
      }
    if (this->LoadProjectFile(fileName) == 0)
      {
      vtkDebugMacro("Loaded project file from " << fileName << ", widget text = " << this->LoadResultsButton->GetWidget()->GetText());
      browse->SaveLastPathToRegistry("OpenPath");
      }
    else
      {
      // loading failed
      vtkErrorMacro("Loading results file " << fileName << " failed");
      this->LoadResultsButton->GetWidget()->SetText ("None");
      }
    return;
    }
  
  // check for pick events
  if (event == vtkSlicerViewerInteractorStyle::PlotEvent &&
      vtkSlicerViewerInteractorStyle::SafeDownCast(caller) != NULL &&
      callData != NULL)
    {
    vtkDebugMacro("vtkQdecModuleGUI:ProcessGUIEvents: Plot event!\n");
    // do the pick
    int x = ((int *)callData)[0];
    int y = ((int *)callData)[1];
    if (this->GetViewerWidget() &&
        this->GetViewerWidget()->Pick(x,y) != 0)
      {
      // check for a valid vertex point
      vtkIdType pointID = this->GetViewerWidget()->GetPickedPointID();
      if (pointID != -1)
        {
        // get the node name
        const char *nodeName = this->GetViewerWidget()->GetPickedNodeName();
        if (strcmp(nodeName, "") != 0)
          {
          vtkDebugMacro("vtkQdecModuleGUI:ProcessGUIEvents: got picked node " << nodeName << " with point id = " << pointID);
          double *pickedRAS;
          double RAS[3];
          RAS[0] = RAS[1] = RAS[2] = 0.0;
          pickedRAS = this->GetViewerWidget()->GetPickedRAS();
          if (pickedRAS)
            {
            RAS[0] = pickedRAS[0];
            RAS[1] = pickedRAS[1];
            RAS[2] = pickedRAS[2];
            vtkDebugMacro("Got picked RAS = " << RAS[0] << ", " << RAS[1] << ", " << RAS[2]);
            }
          vtkSlicerApplication *app = (vtkSlicerApplication *)this->GetApplication();
          if (app)
            {
            vtkDebugMacro("Calling: vtkFreeSurferReadersPlotPlotData " << pointID << ", " << nodeName << ", and the RAS points");
            std::string plotReturn = app->Script("vtkFreeSurferReadersPlotPlotData %d %s %g %g %g", pointID, nodeName, RAS[0], RAS[1], RAS[2]);
            vtkDebugMacro("Plot call return value = " << plotReturn.c_str());
            // swallow the pick
            if (this->GUICallbackCommand != NULL)
              {
              vtkDebugMacro("vtkQdecModuleGUI:ProcessGUIEvents: swallowing the pick");
              this->GUICallbackCommand->SetAbortFlag(1);
              }
            else
              {
              vtkErrorMacro("Unable to get the gui call back command that calls process widget events, event = " << event << " is not swallowed here");
              }
            }
          else
            {
            vtkDebugMacro("vtkQdecModuleGUI:ProcessGUIEvents: no application to use to call plot data.");
            }
          }
        else
          {
          vtkDebugMacro("vtkQdecModuleGUI:ProcessGUIEvents: invalid node name");
          }
        }
      else
        {
        vtkDebugMacro("vtkQdecModuleGUI:ProcessGUIEvents: invalid picked point");
        }
      }
    else
      {
      vtkDebugMacro("vtkQdecModuleGUI:ProcessGUIEvents: invalid pick");
      }
    return;
    }
  
  // changing the scalar overlay when the contrast question menu is invoked
  vtkKWMenu *m = vtkKWMenu::SafeDownCast ( caller );
  if (m == this->QuestionMenu->GetMenu() && event == vtkKWMenu::MenuItemInvokedEvent)
    {
    vtkDebugMacro("Got question menu update: " << this->QuestionMenu->GetValue());
    if (strcmp(this->QuestionMenu->GetValue(), "None") != 0 &&
        this->GetLogic())
      {
      std::string scalarName = this->GetLogic()->GetQuestionScalarName(this->QuestionMenu->GetValue());
      vtkDebugMacro("Got question scalar name from logic: " << scalarName.c_str());
      // trigger display change on the model
      if (this->GetLogic()->GetModelNode() != NULL)
        {
        vtkDebugMacro("Setting the active scalars on " << this->GetLogic()->GetModelNode()->GetName() << " to " << scalarName.c_str());
        this->GetLogic()->GetModelNode()->SetActiveScalars(scalarName.c_str(), NULL);
        this->GetLogic()->GetModelNode()->GetModelDisplayNode()->SetActiveScalarName(scalarName.c_str());
        // the color node has the same name as the scalar array name to facilitate
        // this pairing, find the ID by querying the mrml scene
        std::string colorID = "none";
        if (this->GetApplication() &&
            this->GetApplicationGUI()->GetMRMLScene())
          {
          vtkCollection *colorNodes =  this->GetApplicationGUI()->GetMRMLScene()->GetNodesByName(scalarName.c_str());
          if (colorNodes)
            {
            int numberOfNodes = colorNodes->GetNumberOfItems();
            if (numberOfNodes > 0)
              {
              // take the first one
              colorID = vtkMRMLProceduralColorNode::SafeDownCast(colorNodes->GetItemAsObject(0))->GetID();
              }
            else
              {
              vtkErrorMacro("vtkQdecModuleGUI Cannot find a color node with the name " << scalarName.c_str());
              }
            colorNodes->RemoveAllItems();
            colorNodes->Delete();
            }
          else
            {
            vtkErrorMacro("vtkQdecModuleGUI cannot find procedural color nodes to check for the one associated with scalar " << scalarName.c_str());
            }         
          } else { vtkErrorMacro("No application or scene, can't find matching color node"); }
        if (strcmp(colorID.c_str(), "none") != 0)
          {
          // use this node id
          if (strcmp(this->GetLogic()->GetModelNode()->GetModelDisplayNode()->GetColorNodeID(), colorID.c_str()) != 0)
            {
            vtkDebugMacro("Setting the model's display node color node id to " << colorID.c_str());
            this->GetLogic()->GetModelNode()->GetModelDisplayNode()->SetAndObserveColorNodeID(colorID.c_str());
            }
          else { vtkDebugMacro("Model's display node color node is already set to " << colorID.c_str()); }
          }
        else
          {
          vtkErrorMacro("Qdec Module gui unable to find matching color node for scalar array " << scalarName.c_str());
          }
        }
      else
        {
        vtkErrorMacro("Qdec Module Logic has no record of a model node, can't switch scalars");
        }
      }
    }
//  this->DebugOff();
  
}

//---------------------------------------------------------------------------
void vtkQdecModuleGUI::UpdateMRML ()
{

}

//---------------------------------------------------------------------------
void vtkQdecModuleGUI::UpdateGUI ()
{
  if (this->GetLogic() && this->GetLogic()->QDECProject)
    {
    // update the subjects dir
    if (strcmp(this->GetLogic()->GetSubjectsDirectory().c_str(), "") != 0)
      {
      this->SubjectsDirectoryButton->GetWidget()->SetText (this->GetLogic()->GetSubjectsDirectory().c_str());
      this->SubjectsDirectoryButton->GetWidget()->GetLoadSaveDialog()->SetInitialFileName(this->GetLogic()->GetSubjectsDirectory().c_str());
      }
    
    // get the discrete and continuous factors
    vector< string > discreteFactors = this->GetLogic()->QDECProject->GetDiscreteFactors();
    this->DiscreteFactorsListBox->GetWidget()->GetWidget()->DeleteAll();
    for (unsigned int i = 0; i < discreteFactors.size(); i++)
      {
      this->DiscreteFactorsListBox->GetWidget()->GetWidget()->Append(discreteFactors[i].c_str());
      }
      
    vector< string > continuousFactors = this->GetLogic()->QDECProject->GetContinousFactors();

    this->ContinuousFactorsListBox->GetWidget()->GetWidget()->DeleteAll();
    for (unsigned int i = 0; i < continuousFactors.size(); i++)
      {
      this->ContinuousFactorsListBox->GetWidget()->GetWidget()->Append(continuousFactors[i].c_str());
      }    
      
    // now populate the table    
    if (this->MultiColumnList)
      {
      if (this->MultiColumnList->GetWidget()->GetNumberOfRows() != 0)
        {
        //clear out the list box
        this->MultiColumnList->GetWidget()->DeleteAllRows();
        }
      // set up the correct number of columns
      if ((1 + discreteFactors.size() + continuousFactors.size()) !=
          (unsigned int)this->MultiColumnList->GetWidget()->GetNumberOfColumns())
        {
        this->MultiColumnList->GetWidget()->DeleteAllColumns();
        this->MultiColumnList->GetWidget()->AddColumn("Subject");
        for (unsigned int i = 0; i < discreteFactors.size(); i++)
          {
          vtkDebugMacro("Adding a column for discrete factor: " << discreteFactors[i].c_str());
          this->MultiColumnList->GetWidget()->AddColumn(discreteFactors[i].c_str());
          }
        for (unsigned int i = 0; i < continuousFactors.size(); i++)
          {
          vtkDebugMacro("Adding a column for cont factor: " << continuousFactors[i].c_str());
          this->MultiColumnList->GetWidget()->AddColumn(continuousFactors[i].c_str());
          }
        }
      else
        {
        // just make sure the column names are correct
        int col = 1;
        for (unsigned int i = 0; i < discreteFactors.size(); i++)
          {
          vtkDebugMacro("Setting a column name at " << col << " for discrete factor: " << discreteFactors[i].c_str());
          this->MultiColumnList->GetWidget()->SetColumnName(col, discreteFactors[i].c_str());
          col++;
          }
        for (unsigned int i = 0; i < continuousFactors.size(); i++)
          {
          vtkDebugMacro("Setting a column name at " << col << " for continuous factor: " << continuousFactors[i].c_str());
          this->MultiColumnList->GetWidget()->SetColumnName(col, continuousFactors[i].c_str());
          col++;
          }
        }
      
      vector< string > subjectIDs = this->GetLogic()->QDECProject->GetDataTable()->GetSubjectIDs();
      vector< QdecSubject* > subjects = this->GetLogic()->QDECProject->GetDataTable()->GetSubjects();
      for (unsigned int row = 0; row < subjectIDs.size(); row++)
        {
        this->MultiColumnList->GetWidget()->AddRow();
        int col = 0;
        vtkDebugMacro("Setting cell at " << row << " " << col << " to " << subjectIDs[row].c_str());
        this->MultiColumnList->GetWidget()->SetCellText(row, col, subjectIDs[row].c_str());
        col++;
        // these are strings
        for (unsigned int i = 0; i < discreteFactors.size(); i++)
          {
          vtkDebugMacro("Setting cell at " << row << " " << col << " to factor " << discreteFactors[i].c_str() << " = " << subjects[row]->GetDiscreteFactor(discreteFactors[i].c_str()).c_str());
          this->MultiColumnList->GetWidget()->SetCellText(row, col, subjects[row]->GetDiscreteFactor(discreteFactors[i].c_str()).c_str());
          col++;
          }
        // these are numbers
        for (unsigned int i = 0; i < continuousFactors.size(); i++)
          {
          vtkDebugMacro("Setting cell at " << row << " " << col << " to factor " << continuousFactors[i].c_str() << " = " << subjects[row]->GetContinuousFactor(continuousFactors[i].c_str()));
          this->MultiColumnList->GetWidget()->SetCellTextAsDouble(row, col, subjects[row]->GetContinuousFactor(continuousFactors[i].c_str()));
          col++;
          }
        }
      }

    if (this->QuestionMenu)
      {
      // update the questions menu
      unsigned int numQuestions = this->GetLogic()->GetNumberOfQuestions();
      if (numQuestions != (unsigned int)(this->QuestionMenu->GetMenu()->GetNumberOfItems()))
        {
        // clear out the questions menu and reset the text
        this->QuestionLabel->SetText("Question: ");
        if (this->QuestionMenu->GetMenu()->GetNumberOfItems() != 0)
          {
          this->QuestionMenu->GetMenu()->DeleteAllItems();          
          }
        for (unsigned int i = 0; i < numQuestions; i++)
          {
          this->QuestionMenu->GetMenu()->AddRadioButton(this->GetLogic()->GetQuestion(i).c_str());
          }
        // reset the label text to show the model name
        if (this->GetLogic()->GetModelNode())
          {
          std::string newQuestion = std::string("Question: \n(") + std::string(this->GetLogic()->GetModelNode()->GetName()) + std::string(")");
          this->QuestionLabel->SetText(newQuestion.c_str());
          }
        }
      else { vtkDebugMacro("UpdateGUI: not updating question menu"); }
      }
     
    } // end of valid QdecProject
  else
    {
    vtkErrorMacro("UpdateGUI: invalid Logic or Qdec Project");
    }
}

//---------------------------------------------------------------------------
void vtkQdecModuleGUI::ProcessMRMLEvents ( vtkObject * vtkNotUsed(caller),
                                            unsigned long event,
                                            void * vtkNotUsed(callData) ) 
{
  // if parameter node has been changed externally, update GUI widgets with new values
  if (event == vtkMRMLScene::SceneCloseEvent)
    {
    vtkDebugMacro("Got a scene close event in QdecModuleGUI");
    this->Script("vtkFreeSurferReadersGDFPlotCBCloseAllWindows");
    // clear out the gui
    if (this->MultiColumnList && this->MultiColumnList->GetWidget())
      {
      this->MultiColumnList->GetWidget()->DeleteAllRows();
      this->MultiColumnList->GetWidget()->DeleteAllColumns();
      }
    if (this->DiscreteFactorsListBox &&
        this->DiscreteFactorsListBox->GetWidget() &&
        this->DiscreteFactorsListBox->GetWidget()->GetWidget())
      {
      this->DiscreteFactorsListBox->GetWidget()->GetWidget()->DeleteAll();
      }
    if (this->ContinuousFactorsListBox &&
        this->ContinuousFactorsListBox->GetWidget() &&
        this->ContinuousFactorsListBox->GetWidget()->GetWidget())
      {
      this->ContinuousFactorsListBox->GetWidget()->GetWidget()->DeleteAll();
      }
    if (this->QuestionLabel)
      {
      this->QuestionLabel->SetText("Question: ");
      }
    if (this->QuestionMenu &&
        this->QuestionMenu->GetMenu())
      {
      this->QuestionMenu->GetMenu()->DeleteAllItems();
      this->QuestionMenu->GetMenu()->AddRadioButton( "None" );
      this->QuestionMenu->SetValue( "None" );
      }
    }
}




//---------------------------------------------------------------------------
void vtkQdecModuleGUI::BuildGUI ( ) 
{
  vtkSlicerApplication *app = (vtkSlicerApplication *)this->GetApplication();

  if (!app || !this->UIPanel)
    {
    return;
    }
  
  this->UIPanel->AddPage ( "QdecModule", "QdecModule", NULL );
  // ---
  // MODULE GUI FRAME 
  // configure a page for a volume loading UI for now.
  // later, switch on the modulesButton in the SlicerControlGUI
  // ---
    
  // HELP FRAME
  const char *help = "The Qdec Module provides support for the QDEC program from MGH: Query, Design, Estimate, Contrast.\nBefore you start: Set up a subjects directory and set your SUBJECTS_DIR environment variable (you'll need to restart Slicer3). In that directory, put the set of subjects you wish to analyse, along with the fsaverage subject. Then make a subdirectory qdec, and in it place your qdec.table.dat file along with any .level files describing the discrete factors (ie gender.levels will have 'male' and 'female' on two separate lines).\nYou can also load precomputed .qdec archives using the 'Load Results Data File' button. This requires unzip and rm, and you can point Slicer to these applications via the Application Settings interface (View->Application Settings).\nOnce the results are loaded, you can plot results at various vertices by setting the setting the 3DViewer mouse mode to 'pick' using the toolbar button.";
  const char *about = "This work was supported by NA-MIC. See <a>http://na-mic.org/Wiki/index.php/Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration</a> for details on the integration project.";
  vtkKWWidget *page = this->UIPanel->GetPageWidget ( "QdecModule" );
  this->BuildHelpAndAboutFrame ( page, help, about );
  
  this->NAMICLabel = vtkKWLabel::New();
  this->NAMICLabel->SetParent ( this->GetLogoFrame() );
  this->NAMICLabel->Create();
  this->NAMICLabel->SetImageToIcon ( this->GetAcknowledgementIcons()->GetNAMICLogo() );    
  app->Script ( "grid %s -row 0 -column 0 -padx 2 -pady 2 -sticky w", this->NAMICLabel->GetWidgetName());

  // ---
  // Subjects Frame
  vtkSlicerModuleCollapsibleFrame *subjectsFrame = vtkSlicerModuleCollapsibleFrame::New ( );
  subjectsFrame->SetParent ( page );
  subjectsFrame->Create ( );
  subjectsFrame->SetLabelText ("Subjects");
  subjectsFrame->ExpandFrame ( );
  app->Script ( "pack %s -side top -anchor nw -fill x -padx 2 -pady 2 -in %s",
                subjectsFrame->GetWidgetName(),
                this->UIPanel->GetPageWidget("QdecModule")->GetWidgetName());

  this->SubjectsDirectoryButton = vtkKWLoadSaveButtonWithLabel::New();
  this->SubjectsDirectoryButton->SetParent ( subjectsFrame->GetFrame() );
  this->SubjectsDirectoryButton->Create ( );
  this->SubjectsDirectoryButton->SetLabelText ("Set SUBJECTS_DIR:");
  this->SubjectsDirectoryButton->GetWidget()->GetLoadSaveDialog()->SetTitle("Select the FreeSurfer Subjects directory");
  this->SubjectsDirectoryButton->GetWidget()->GetLoadSaveDialog()->ChooseDirectoryOn();
  if (getenv("SUBJECTS_DIR") == NULL)
    {
    this->SubjectsDirectoryButton->GetWidget()->SetText ("None");
    this->SubjectsDirectoryButton->GetWidget()->GetLoadSaveDialog()->SetInitialFileName( "." );
    }
  else
    {
    this->SubjectsDirectoryButton->GetWidget()->SetText (getenv("SUBJECTS_DIR"));
    this->SubjectsDirectoryButton->GetWidget()->GetLoadSaveDialog()->SetInitialFileName(getenv("SUBJECTS_DIR"));
    }
  app->Script("pack %s -side top -anchor nw -padx 2 -pady 4", 
              this->SubjectsDirectoryButton->GetWidgetName());
  
  this->LoadTableButton = vtkKWLoadSaveButtonWithLabel::New();
  this->LoadTableButton->SetParent ( subjectsFrame->GetFrame() );
  this->LoadTableButton->Create ( );
  this->LoadTableButton->SetLabelText ("Load Table Data File:");
  // check to see if there's a qdec table data file in the subjects dir
  
  std::string testDatFile = "None";
  if (getenv("SUBJECTS_DIR") != NULL)
    {
    std::vector<std::string> pathcomponents;
    itksys::SystemTools::SplitPath(getenv("SUBJECTS_DIR"), pathcomponents);
    pathcomponents.push_back("qdec");
    pathcomponents.push_back("qdec.table.dat");
    testDatFile = itksys::SystemTools::JoinPath(pathcomponents);

    if (!itksys::SystemTools::LocateFileInDir(testDatFile.c_str(), testDatFile.c_str(), testDatFile))
      {
      testDatFile = "None";
      }
    }
  this->LoadTableButton->GetWidget()->SetText (testDatFile.c_str());

  this->LoadTableButton->GetWidget()->GetLoadSaveDialog()->SetTitle("Open QDEC table data file");
  this->LoadTableButton->GetWidget()->GetLoadSaveDialog()->RetrieveLastPathFromRegistry("OpenPath");
  this->LoadTableButton->GetWidget()->GetLoadSaveDialog()->SetFileTypes("{ {All} {.*} } { {Data} {.dat} }");
  app->Script("pack %s -side top -anchor nw -padx 2 -pady 4", 
              this->LoadTableButton->GetWidgetName());

  // Load precomputed results
  this->LoadResultsButton = vtkKWLoadSaveButtonWithLabel::New();
  this->LoadResultsButton->SetParent ( subjectsFrame->GetFrame() );
  this->LoadResultsButton->Create ( );
  this->LoadResultsButton->SetLabelText ("Load Results Data File:");
  this->LoadResultsButton->GetWidget()->GetLoadSaveDialog()->SetTitle("Open QDEC file");
  this->LoadResultsButton->GetWidget()->GetLoadSaveDialog()->RetrieveLastPathFromRegistry("OpenPath");
  this->LoadResultsButton->GetWidget()->GetLoadSaveDialog()->SetFileTypes("{ {Data} {.qdec} } { {All} {.*} }");
  app->Script("pack %s -side top -anchor nw -padx 2 -pady 4", 
              this->LoadResultsButton->GetWidgetName());

   // add the multicolumn list to show the data table
  this->MultiColumnList = vtkKWMultiColumnListWithScrollbars::New ( );
  this->MultiColumnList->SetParent ( subjectsFrame->GetFrame() );
  this->MultiColumnList->Create ( );
  this->MultiColumnList->SetHeight(4);
  this->MultiColumnList->GetWidget()->SetSelectionTypeToCell();
  this->MultiColumnList->GetWidget()->MovableRowsOff();
  this->MultiColumnList->GetWidget()->MovableColumnsOff();

  this->MultiColumnList->GetWidget()->AddColumn("Subject");
  //not setting up all columns just yet
  app->Script ( "pack %s -fill both -expand true",
                this->MultiColumnList->GetWidgetName());
  this->MultiColumnList->GetWidget()->SetCellUpdatedCommand(this, "UpdateElement");

  // ---
  // Design Frame
  vtkSlicerModuleCollapsibleFrame *designFrame = vtkSlicerModuleCollapsibleFrame::New ( );
  designFrame->SetParent ( page );
  designFrame->Create ( );
  designFrame->SetLabelText ("Design");
  designFrame->ExpandFrame ( );
  app->Script ( "pack %s -side top -anchor nw -fill x -padx 2 -pady 2 -in %s",
                designFrame->GetWidgetName(),
                this->UIPanel->GetPageWidget("QdecModule")->GetWidgetName());

  this->DesignEntry = vtkKWEntryWithLabel::New();
  this->DesignEntry->SetParent( designFrame->GetFrame());
  this->DesignEntry->SetLabelText ("Design Name:");
  this->DesignEntry->Create();
  this->DesignEntry->GetWidget()->SetValue("Untitled");
  app->Script("pack %s -side top -anchor nw -padx 2 -pady 4 -in %s", 
              this->DesignEntry->GetWidgetName(),
              designFrame->GetFrame()->GetWidgetName());
  
  this->DiscreteFactorsListBox = vtkKWListBoxWithScrollbarsWithLabel::New();
  this->DiscreteFactorsListBox->SetParent( designFrame->GetFrame() );
  this->DiscreteFactorsListBox->SetLabelText("Discrete Factors (choose up to two):" );
  this->DiscreteFactorsListBox->Create();
  this->DiscreteFactorsListBox->GetWidget()->GetWidget()->SetSelectionModeToMultiple();
  this->DiscreteFactorsListBox->GetWidget()->GetWidget()->ExportSelectionOff();
  app->Script("pack %s -side top -anchor nw -padx 2 -pady 4 -in %s", 
              this->DiscreteFactorsListBox->GetWidgetName(),
              designFrame->GetFrame()->GetWidgetName());
  
  this->ContinuousFactorsListBox = vtkKWListBoxWithScrollbarsWithLabel::New();
  this->ContinuousFactorsListBox->SetParent( designFrame->GetFrame() );
  this->ContinuousFactorsListBox->SetLabelText("Continuous Factors (choose two):");
  this->ContinuousFactorsListBox->Create();
  this->ContinuousFactorsListBox->GetWidget()->GetWidget()->SetSelectionModeToMultiple();
  this->ContinuousFactorsListBox->GetWidget()->GetWidget()->ExportSelectionOff();
  app->Script("pack %s -side top -anchor nw -padx 2 -pady 4 -in %s", 
              this->ContinuousFactorsListBox->GetWidgetName(),
              designFrame->GetFrame()->GetWidgetName());

  vtkKWFrameWithLabel* measuresFrame = vtkKWFrameWithLabel::New();
  measuresFrame->SetParent( designFrame->GetFrame() );
  measuresFrame->Create();
  measuresFrame->SetLabelText( "Measures" );
  this->Script( "pack %s -fill x", measuresFrame->GetWidgetName() );

  
  int nRow = 0;
  this->MeasureLabel = vtkKWLabel::New();
  this->MeasureLabel->SetParent(measuresFrame->GetFrame() );
  this->MeasureLabel->Create();
  this->MeasureLabel->SetText("Measure: ");
  this->MeasureLabel->SetJustificationToRight();
  app->Script( "grid %s -column 0 -row %d -sticky ne -in %s",
               this->MeasureLabel->GetWidgetName(), nRow,
               measuresFrame->GetFrame()->GetWidgetName());

  this->MeasureMenu = vtkKWMenuButton::New();
  this->MeasureMenu->SetParent(measuresFrame->GetFrame() );
  this->MeasureMenu->Create();
  this->MeasureMenu->GetMenu()->AddRadioButton("thickness");
  this->MeasureMenu->GetMenu()->AddRadioButton("sulc");
  this->MeasureMenu->GetMenu()->AddRadioButton("curv");
  this->MeasureMenu->GetMenu()->AddRadioButton("jacobian");
  this->MeasureMenu->GetMenu()->AddRadioButton("area");
  this->MeasureMenu->SetValue("thickness");
  app->Script( "grid %s -column 1 -row %d -sticky nw -in %s",
               this->MeasureMenu->GetWidgetName(), nRow,
               measuresFrame->GetFrame()->GetWidgetName());
  
  nRow++;
  this->HemisphereLabel = vtkKWLabel::New();
  this->HemisphereLabel->SetParent(measuresFrame->GetFrame() );
  this->HemisphereLabel->Create();
  this->HemisphereLabel->SetText("Hemisphere: ");
  this->HemisphereLabel->SetJustificationToRight();
  app->Script( "grid %s -column 0 -row %d -sticky ne -in %s",
               this->HemisphereLabel->GetWidgetName(), nRow,
               measuresFrame->GetFrame()->GetWidgetName());

  this->HemisphereMenu = vtkKWMenuButton::New();
  this->HemisphereMenu->SetParent(measuresFrame->GetFrame() );
  this->HemisphereMenu->Create();
  this->HemisphereMenu->GetMenu()->AddRadioButton("lh");
  this->HemisphereMenu->GetMenu()->AddRadioButton("rh");
  this->HemisphereMenu->SetValue("lh");
  app->Script( "grid %s -column 1 -row %d -sticky nw -in %s",
               this->HemisphereMenu->GetWidgetName(), nRow,
               measuresFrame->GetFrame()->GetWidgetName());
  nRow++;

  this->SmoothnessLabel = vtkKWLabel::New();
  this->SmoothnessLabel->SetParent(measuresFrame->GetFrame());
  this->SmoothnessLabel->Create();
  this->SmoothnessLabel->SetText("Smoothness (FWHM, mm): ");
  this->SmoothnessLabel->SetJustificationToRight();
  app->Script( "grid %s -column 0 -row %d -sticky ne -in %s",
               this->SmoothnessLabel->GetWidgetName(), nRow,
               measuresFrame->GetFrame()->GetWidgetName());

  this->SmoothnessMenu = vtkKWMenuButton::New();
  this->SmoothnessMenu->SetParent(measuresFrame->GetFrame());
  this->SmoothnessMenu->Create();
  this->SmoothnessMenu->GetMenu()->AddRadioButton( "0" );
  this->SmoothnessMenu->GetMenu()->AddRadioButton( "5" );
  this->SmoothnessMenu->GetMenu()->AddRadioButton( "10" );
  this->SmoothnessMenu->GetMenu()->AddRadioButton( "15" );
  this->SmoothnessMenu->GetMenu()->AddRadioButton( "20" );
  this->SmoothnessMenu->GetMenu()->AddRadioButton( "25" );
  this->SmoothnessMenu->SetValue( "10" );
  this->Script( "grid %s -column 1 -row %d -sticky nw -in %s",
                this->SmoothnessMenu->GetWidgetName(), nRow,
                measuresFrame->GetFrame()->GetWidgetName());

  // weight the grid
  for( int nRowConfigure = 0; nRowConfigure <= nRow; nRowConfigure++ )
    {
    this->Script( "grid rowconfigure %s %d -pad 4",
                  measuresFrame->GetFrame()->GetWidgetName(),
                  nRowConfigure );
    }
  
  this->ApplyButton = vtkKWPushButton::New();
  this->ApplyButton->SetParent( designFrame->GetFrame() );
  this->ApplyButton->Create();
  this->ApplyButton->SetText("Run GLM Fit");
  this->ApplyButton->SetWidth ( 12 );
  app->Script("pack %s -side top -anchor e -padx 20 -pady 10 -in %s", 
              this->ApplyButton->GetWidgetName(),
              designFrame->GetFrame()->GetWidgetName());
  
#ifdef _WIN32
  // On windows, there is no glm fit binary available, so grey out the button
  this->ApplyButton->EnabledOff();
  this->ApplyButton->SetBalloonHelpString("GLM Fit binary is not available on Windows, please load precomputed results in .qdec files using the 'Load Results Data File' browser");
#endif
  // ---
  // Display Frame
  vtkSlicerModuleCollapsibleFrame *displayFrame = vtkSlicerModuleCollapsibleFrame::New ( );
  displayFrame->SetParent ( page );
  displayFrame->Create ( );
  displayFrame->SetLabelText ("Display");
  displayFrame->ExpandFrame ( );
  app->Script ( "pack %s -side top -anchor nw -fill x -padx 2 -pady 2 -in %s",
                displayFrame->GetWidgetName(),
                this->UIPanel->GetPageWidget("QdecModule")->GetWidgetName());

  // provide a set of radio boxes that will be populated from the Logic's
  // calculated overlays
  this->QuestionLabel = vtkKWLabel::New();
  this->QuestionLabel->SetParent(displayFrame->GetFrame());
  this->QuestionLabel->Create();
  this->QuestionLabel->SetText("Question: ");
  this->QuestionLabel->SetJustificationToRight();
  app->Script( "grid %s -column 0 -row 1 -sticky ne -in %s",
               this->QuestionLabel->GetWidgetName(),
               displayFrame->GetFrame()->GetWidgetName());

  this->QuestionMenu = vtkKWMenuButton::New();
  this->QuestionMenu->SetParent(displayFrame->GetFrame());
  this->QuestionMenu->Create();
  this->QuestionMenu->GetMenu()->AddRadioButton( "None" );
  this->QuestionMenu->SetValue( "None" );
  this->Script( "grid %s -column 1 -row 1 -sticky nw -in %s",
                this->QuestionMenu->GetWidgetName(),
                displayFrame->GetFrame()->GetWidgetName());
  
  measuresFrame->Delete();
  designFrame->Delete();
  subjectsFrame->Delete();
  displayFrame->Delete();
  

  // for plotting
  if (this->GetLogic() && !this->GetLogic()->GetTclScriptLoaded())
    {
      const char *tclScript = this->GetLogic()->GetPlotTclScript();
      vtkDebugMacro("Loading: " << tclScript);
      if (app->LoadScript(tclScript) == 0)
        {
        vtkErrorMacro("vtkQdecModuleGUI::BuildGUI: unable to load in tcl script " << tclScript);
        }
      else
        {
        this->GetLogic()->SetTclScriptLoaded(1);
        }
    }

  // watch for a scene closing event so that the gui gets cleared out
  if ( this->GetApplicationGUI() &&  this->GetApplicationGUI()->GetMRMLScene())
    {
    this->GetApplicationGUI()->GetMRMLScene()->AddObserver( vtkMRMLScene::SceneCloseEvent, this->MRMLCallbackCommand );
    }
  this->Built = true;
}

//---------------------------------------------------------------------------
void vtkQdecModuleGUI::UpdateElement(int row, int col, char * str)
{
  if (!this->MultiColumnList)
    {
    vtkErrorMacro("UpdateElement: cannot update element, multi column list is null");
    return;
    }
  vtkDebugMacro("UpdateElement: row = " << row << ", col = " << col << ", str = " << str << "\n");
  
  // make sure that the row and column exists in the table
  if ((row >= 0) && (row < this->MultiColumnList->GetWidget()->GetNumberOfRows()) &&
      (col >= 0) && (col < this->MultiColumnList->GetWidget()->GetNumberOfColumns()))
    {
    vtkDebugMacro("Valid row " << row << ", column " << col <<  ", valid columns are 0-" << this->MultiColumnList->GetWidget()->GetNumberOfColumns() << "\n");
    } 
  else
    {
    vtkErrorMacro ("Invalid row " << row << " or column " << col <<  ", valid columns are 0-" << this->MultiColumnList->GetWidget()->GetNumberOfColumns() << "\n");
    }
}

//----------------------------------------------------------------------------
void vtkQdecModuleGUI::SetViewerWidget ( vtkSlicerViewerWidget *viewerWidget )
{
  this->ViewerWidget = viewerWidget;
}

//----------------------------------------------------------------------------
void vtkQdecModuleGUI::SetInteractorStyle( vtkSlicerViewerInteractorStyle *interactorStyle )
{
  // note: currently the GUICallbackCommand calls ProcessGUIEvents
  // remove observers
  if (this->InteractorStyle != NULL &&
      this->InteractorStyle->HasObserver(vtkSlicerViewerInteractorStyle::PlotEvent, this->GUICallbackCommand) == 1)
    {
    this->InteractorStyle->RemoveObservers(vtkSlicerViewerInteractorStyle::PlotEvent, (vtkCommand *)this->GUICallbackCommand);
    }
  
  this->InteractorStyle = interactorStyle;

  // add observers
  if (this->InteractorStyle)
    {
    vtkDebugMacro("vtkQdecModuleGUI::SetInteractorStyle: Adding observer on interactor style");
    this->InteractorStyle->AddObserver(vtkSlicerViewerInteractorStyle::PlotEvent, (vtkCommand *)this->GUICallbackCommand);
    }
}

//----------------------------------------------------------------------------
// returns 0 on success, -1 on failure
int vtkQdecModuleGUI::LoadProjectFile(const char *fileName)
{
  const char *tempDir = vtkSlicerApplication::SafeDownCast(this->GetApplication())->GetTemporaryDirectory();
  const char *unzip = vtkSlicerApplication::SafeDownCast(this->GetApplication())->GetUnzip();
  const char *rm = vtkSlicerApplication::SafeDownCast(this->GetApplication())->GetRm();

  std::string newTempDir = std::string(tempDir);
  std::string newFileName = std::string(fileName);

  if (this->GetLogic() == NULL ||
      this->GetLogic()->QDECProject == NULL)
    {
    vtkErrorMacro("LoadProjectFile: Logic or it's associated QDECProject isn't defined yet, unable to load " << fileName);
    return -1;
    }
  // check the paths to unzip and rm
  if (strcmp(unzip, "") != 0 &&
      strcmp(unzip, this->GetLogic()->QDECProject->GetUnzipCommand().c_str()) != 0)
    {
    this->GetLogic()->QDECProject->SetUnzipCommand(unzip);
    }
   if (strcmp(rm, "") != 0 &&
       strcmp(rm, this->GetLogic()->QDECProject->GetRmCommand().c_str()) != 0)
    {
    this->GetLogic()->QDECProject->SetRmCommand(rm);
    }
  vtkDebugMacro("Trying to load file " << newFileName.c_str() << ", using temp dir " << newTempDir.c_str());
  int retval = this->GetLogic()->LoadProjectFile(newFileName.c_str(), newTempDir.c_str());
  if (retval != 0)
    {
    // failure
    vtkErrorMacro("Error loading project data file " << newFileName.c_str());
    if (retval == -2)
      {
      // couldn't open the archive, give user a chance to set the zip file
      vtkKWMessageDialog *dialog = vtkKWMessageDialog::New();
      if (this->GetApplicationGUI() &&
          this->GetApplicationGUI()->GetMainSlicerWindow())
        {
        dialog->SetParent (  this->GetApplicationGUI()->GetMainSlicerWindow() );
        }
      dialog->SetStyleToMessage();
      std::string msg = "The qdec archive failed to open. It should be a ZIP file and there should be one directory inside named qdec_project_archive.\nIf all that is true, maybe the system couldn't find the proper command to unzip it. You can force which application is used to unzip the .qdec file by using the following dialog, then try to open it again.";
      dialog->SetText(msg.c_str());
      dialog->Create ( );
      dialog->Invoke();
      dialog->Delete();
      
      if (this->GetApplicationGUI() &&
          this->GetApplicationGUI()->GetMainSlicerWindow() &&
          this->GetApplicationGUI()->GetMainSlicerWindow()->GetApplicationSettingsInterface())
        {
        this->GetApplicationGUI()->GetMainSlicerWindow()->GetApplicationSettingsInterface()->Show();
        if (this->GetApplicationGUI()->GetMainSlicerWindow()->GetApplicationSettingsInterface()->GetUserInterfaceManager() &&
            this->GetApplicationGUI()->GetMainSlicerWindow()->GetApplicationSettingsInterface()->GetUserInterfaceManager() &&
            vtkKWUserInterfaceManagerDialog::SafeDownCast(this->GetApplicationGUI()->GetMainSlicerWindow()->GetApplicationSettingsInterface()->GetUserInterfaceManager()))
          {
          vtkKWUserInterfaceManagerDialog::SafeDownCast(this->GetApplicationGUI()->GetMainSlicerWindow()->GetApplicationSettingsInterface()->GetUserInterfaceManager())->RaiseSection(0, "Slicer Settings");
          }
        else
          {
          vtkErrorMacro("Couldn't get Slicer Settings Panel");
          }
        }
      else
        {
        vtkErrorMacro("Couldn't get application settings interface");
        }
      }
    return retval;      
    }
  vtkDebugMacro("vtkQdecModuleGUI:ProcessGUIEvents: was able to load file " << newFileName.c_str());
  
  // load the results
  vtkDebugMacro("Reading QDEC results that were in the file " << fileName);
  // get the models logic to use to load the models and scalars (can't access
  // it in the Logic class)
  vtkSlicerApplication *app = vtkSlicerApplication::SafeDownCast(this->GetApplication());
  if (app)
    {
    if (vtkSlicerModelsGUI::SafeDownCast(app->GetModuleGUIByName("Models")))
      {
      vtkSlicerModelsLogic *modelsLogic = vtkSlicerModelsGUI::SafeDownCast(app->GetModuleGUIByName("Models"))->GetLogic();
      if (this->GetLogic()->LoadResults(modelsLogic, app) != 0)
        {
        vtkErrorMacro("Unable to load results of precomputed GLM fit processing from file " << fileName);
        return -1;
        }
      else
        {
        // clear out the questions menu, then update the gui
        this->QuestionMenu->GetMenu()->DeleteAllItems();
        this->UpdateGUI();
        // trigger showing one of the questions
        int numQuestions = this->GetLogic()->GetNumberOfQuestions();
        this->QuestionMenu->GetMenu()->InvokeItem(numQuestions - 1);
        this->QuestionMenu->GetMenu()->InvokeEvent(vtkKWMenu::MenuItemInvokedEvent);
        }
      }
    else
      {
      vtkErrorMacro("Unable to get Models module GUI, can't load results as need to add models");
      return -1;
      }
    }
  else
    {
    vtkErrorMacro("Could not get application to get at the models module");
    return -1;
    }
  // set the project file name on the load button
  if (this->LoadResultsButton)
    {
    this->LoadResultsButton->GetWidget()->SetInitialFileName(fileName);
    }
  return 0;
}

//----------------------------------------------------------------------------
void vtkQdecModuleGUI::Init(void)
{
  vtkSlicerApplicationGUI *appGUI = this->GetApplicationGUI();

  if (appGUI == NULL)
    {
    return;
    }
  
  // get the viewer widget
  vtkSlicerViewerWidget *active_viewer = appGUI->GetActiveViewerWidget();
  this->SetViewerWidget(active_viewer);

  // get the interactor style, to set up plotting events
  if (active_viewer != NULL &&
      active_viewer->GetMainViewer() != NULL &&
      active_viewer->GetMainViewer()->GetRenderWindowInteractor() != NULL &&
      active_viewer->GetMainViewer()->GetRenderWindowInteractor()->GetInteractorStyle() != NULL)
    {
    this->SetInteractorStyle(vtkSlicerViewerInteractorStyle::SafeDownCast(active_viewer->GetMainViewer()->GetRenderWindowInteractor()->GetInteractorStyle()));
    }
  else
    {
    vtkErrorMacro("Init: unable to get the interactor style, plotting will not work.");
    }
}
