ENH: Added option to set scaling factor for image intensity for 3ddos…

…e file reader

SlicerRt#73

DosxyzNrc3dDoseFileReader/Logic/vtkSlicerDosxyzNrc3dDoseFileReaderLogic.cxx

@@ -58,50 +58,41 @@ vtkSlicerDosxyzNrc3dDoseFileReaderLogic::~vtkSlicerDosxyzNrc3dDoseFileReaderLogi
 {
 }
 
-
-
+//----------------------------------------------------------------------------
 bool vtkSlicerDosxyzNrc3dDoseFileReaderLogic::AreEqualWithTolerance(double a, double b)
 {
   return fabs(a - b) < MAX_TOLERANCE_SPACING;
 }
 
-
-
 //----------------------------------------------------------------------------
 void vtkSlicerDosxyzNrc3dDoseFileReaderLogic::PrintSelf(ostream& os, vtkIndent indent)
 {
   this->Superclass::PrintSelf(os, indent);
 }
-//
-
 
 //----------------------------------------------------------------------------
-void vtkSlicerDosxyzNrc3dDoseFileReaderLogic::LoadDosxyzNrc3dDoseFile(char* filename)
+void vtkSlicerDosxyzNrc3dDoseFileReaderLogic::LoadDosxyzNrc3dDoseFile(char* filename, float intensityScalingFactor/*=1.0*/)
 {
-
   ifstream readFileStream(filename); //todo test that this doesn't crash when filename is null
-
-  if (!readFileStream){
-	  vtkErrorMacro("LoadDosxyzNrc3dDoseFile: The specified file could not be opened.");
-	  return;
+  if (!readFileStream)
+  {
+	vtkErrorMacro("LoadDosxyzNrc3dDoseFile: The specified file could not be opened.");
+	return;
   }
 
   int size[3] = { 0, 0, 0 };
   double spacing[3] = { 0, 0, 0 };
   double origin[3] = { 0, 0, 0 };
-  std::string title = "";
 
   // read in block 1 (number of voxels in x, y, z directions)
   readFileStream >> size[0] >> size[1] >> size[2];
   int numTotalVoxels = size[0] * size[1] * size[2];
 
-
   if (size[0] <= 0 || size[1] <= 0 || size[2] <= 0)
   {
 	vtkErrorMacro("LoadDosxyzNrc3dDoseFile: Number of voxels in X, Y, or Z direction must be greater than zero." << "numVoxelsX " << size[0] << ", numVoxelsY " << size[1] << ", numVoxelsZ " << size[2]);
     return;
   }
-
 
   std::vector<double> voxelBoundariesX(size[0] + 1); 
   std::vector<double> voxelBoundariesY(size[1] + 1);
@@ -135,7 +126,6 @@ void vtkSlicerDosxyzNrc3dDoseFileReaderLogic::LoadDosxyzNrc3dDoseFile(char* file
     counter += 1;
   }
 
-
   // read in block 3 (voxel boundaries, cm, in y direction)
   counter = 0;
   while (!readFileStream.eof() && counter < size[1] + 1)
@@ -183,6 +173,8 @@ void vtkSlicerDosxyzNrc3dDoseFileReaderLogic::LoadDosxyzNrc3dDoseFile(char* file
   floatDosxyzNrc3dDoseVolumeData->SetExtent(0, size[0] - 1, 0, size[1] - 1, 0, size[2] - 1);
   floatDosxyzNrc3dDoseVolumeData->AllocateScalars(VTK_FLOAT, 1); 
 
+  //todo: When loading .3ddose file from python, it is intensityScalarFactor set to 0
+
   float* floatPtr = (float*)floatDosxyzNrc3dDoseVolumeData->GetScalarPointer();
   float currentValue = 0.0;
   for (long z = 0; z < size[2]; z++)
@@ -196,13 +188,13 @@ void vtkSlicerDosxyzNrc3dDoseFileReaderLogic::LoadDosxyzNrc3dDoseFile(char* file
           vtkErrorMacro("LoadDosxyzNrc3dDoseFile: The end of file was reached earlier than specified.");
         }
         readFileStream >> currentValue;
+        currentValue = currentValue * intensityScalingFactor;
         (*floatPtr) = currentValue;
         ++floatPtr;
       }
     }
   }
 
-
   // create volume node for dose values
   vtkSmartPointer<vtkMRMLScalarVolumeNode> dosxyzNrc3dDoseVolumeNode = vtkSmartPointer<vtkMRMLScalarVolumeNode>::New();
   dosxyzNrc3dDoseVolumeNode->SetScene(this->GetMRMLScene());
@@ -230,12 +222,9 @@ void vtkSlicerDosxyzNrc3dDoseFileReaderLogic::LoadDosxyzNrc3dDoseFile(char* file
   dosxyzNrc3dDoseVolumeDisplayNode->SetAndObserveColorNodeID("vtkMRMLColorTableNodeGrey");
   dosxyzNrc3dDoseVolumeNode->SetAndObserveDisplayNodeID(dosxyzNrc3dDoseVolumeDisplayNode->GetID());
 
-
   //todo: read in block 6 (error values array; relative errors)
   //todo: read error values in another volume node
   //todo: do I also need voxelCenters?
 
   readFileStream.close();
 }
-
-

DosxyzNrc3dDoseFileReader/Logic/vtkSlicerDosxyzNrc3dDoseFileReaderLogic.h

@@ -48,7 +48,7 @@ class VTK_SLICER_DOSXYZNRC3DDOSEFILEREADER_LOGIC_EXPORT vtkSlicerDosxyzNrc3dDose
 
   /// Load DosxyzNrc3dDose volume from file
   /// \param filename Path and filename of the DosxyzNrc3dDose file
-  void LoadDosxyzNrc3dDoseFile(char* filename);
+  void LoadDosxyzNrc3dDoseFile(char* filename, float intensityScalingFactor=1.0);
 
   /// Determine if two numbers are equal within a small tolerance (0.001)
   static bool AreEqualWithTolerance(double a, double b);

DosxyzNrc3dDoseFileReader/Resources/UI/qSlicerDosxyzNrc3dDoseFileReaderOptionsWidget.ui

@@ -11,16 +11,29 @@
    </rect>
   </property>
   <property name="windowTitle">
-   <string>Volume Options</string>
+   <string>DosxyzNrc3dDoseFileReader Options</string>
   </property>
   <layout class="QHBoxLayout" name="horizontalLayout">
    <property name="margin">
     <number>0</number>
    </property>
    <item>
-    <widget class="QCheckBox" name="UseImageIntensityScaleAndOffsetCheckBox">
+    <widget class="QLabel" name="ScalingFactorLabel">
+     <property name="toolTip">
+      <string>Scaling factor applied on the dose values</string>
+     </property>
+     <property name="text">
+      <string>Scaling factor:</string>
+     </property>
+    </widget>
+   </item>
+   <item>
+    <widget class="QLineEdit" name="ScalingFactorLineEdit">
+     <property name="toolTip">
+      <string/>
+     </property>
      <property name="text">
-      <string>Use Image Intensity Scale and Image Intensity Offset</string>
+      <string>1.0</string>
      </property>
     </widget>
    </item>

DosxyzNrc3dDoseFileReader/qSlicerDosxyzNrc3dDoseFileReaderOptionsWidget.cxx

@@ -20,6 +20,7 @@
 
 /// Qt includes
 #include <QFileInfo>
+#include <QDebug>
 
 // CTK includes
 #include <ctkFlowLayout.h>
@@ -48,11 +49,13 @@ qSlicerDosxyzNrc3dDoseFileReaderOptionsWidget::qSlicerDosxyzNrc3dDoseFileReaderO
 
   ctkFlowLayout::replaceLayout(this);
 
-  connect(d->UseImageIntensityScaleAndOffsetCheckBox, SIGNAL(toggled(bool)),
-          this, SLOT(updateProperties()));
+  connect(d->ScalingFactorLineEdit, SIGNAL(textChanged(QString)), this, SLOT(updateProperties()));
+
+  // Image instensity scaling factor is 1.0 by default
+  float defaultScalingFactorValue = 1.0;
+  QString defaultScalingFactorString = QString::number(defaultScalingFactorValue);
+  d->ScalingFactorLineEdit->setText(defaultScalingFactorString);
 
-  // Image intensity scale and offset turned off by default
-  d->UseImageIntensityScaleAndOffsetCheckBox->setChecked(false);
 }
 
 //-----------------------------------------------------------------------------
@@ -65,5 +68,13 @@ void qSlicerDosxyzNrc3dDoseFileReaderOptionsWidget::updateProperties()
 {
   Q_D(qSlicerDosxyzNrc3dDoseFileReaderOptionsWidget);
 
-  d->Properties["imageIntensityScaleAndOffset"] = d->UseImageIntensityScaleAndOffsetCheckBox->isChecked();
+  bool ok = false;
+  float scalingFactor = d->ScalingFactorLineEdit->text().toFloat(&ok);
+  if (ok == false)
+  {
+	qCritical() << Q_FUNC_INFO << ": Unable to parse scaling factor parameter " << d->ScalingFactorLineEdit->text() << ". Using default value 1.0";
+	scalingFactor = 1.0;
+  }
+
+  d->Properties["scalingFactor"] = scalingFactor;
 }

DosxyzNrc3dDoseFileReader/qSlicerDosxyzNrc3dDoseFileReaderPlugin.cxx

@@ -103,8 +103,8 @@ bool qSlicerDosxyzNrc3dDoseFileReaderPlugin::load(const IOProperties& properties
   QString fileName = properties["fileName"].toString();
   Q_ASSERT(d->Logic);
 
-  bool useImageIntensityScaleAndOffsetFromFile = properties["imageIntensityScaleAndOffset"].toBool();
-  d->Logic->LoadDosxyzNrc3dDoseFile(fileName.toLatin1().data());
+  float intensityScalingFactor = properties["scalingFactor"].toFloat();
+  d->Logic->LoadDosxyzNrc3dDoseFile(fileName.toLatin1().data(), intensityScalingFactor);
 
   this->setLoadedNodes(QStringList());