Add histogram tool

[clitk.git] / tools / clitkHistogramImageGenericFilter.cxx

diff --git a/tools/clitkHistogramImageGenericFilter.cxx b/tools/clitkHistogramImageGenericFilter.cxx
new file mode 100644 (file)
index 0000000..49e3fa0
--- /dev/null
+++ b/tools/clitkHistogramImageGenericFilter.cxx
@@ -0,0 +1,165 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to:
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef clitkHistogramImageGenericFilter_cxx
+#define clitkHistogramImageGenericFilter_cxx
+
+/* =================================================
+ * @file   clitkHistogramImageGenericFilter.cxx
+ * @author Thomas Baudier <thomas.baudier@creatis.insa-lyon.fr>
+ * @date   22 dec 2015
+ *
+ * @brief
+ *
+ ===================================================*/
+
+#include "clitkHistogramImageGenericFilter.h"
+
+// itk include
+#include <itkImageToHistogramFilter.h>
+#include <itkStatisticsImageFilter.h>
+
+#include <clitkCommon.h>
+
+
+
+namespace clitk
+{
+
+//--------------------------------------------------------------------
+HistogramImageGenericFilter::HistogramImageGenericFilter():
+  ImageToImageGenericFilter<Self>("HistogramImage")
+{
+  InitializeImageType<2>();
+  InitializeImageType<3>();
+  InitializeImageType<4>();
+  mBinSize = 100;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<unsigned int Dim>
+void HistogramImageGenericFilter::InitializeImageType()
+{
+  ADD_DEFAULT_IMAGE_TYPES(Dim);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+vtkFloatArray* HistogramImageGenericFilter::GetArrayX()
+{
+  return(mArrayX);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+vtkFloatArray* HistogramImageGenericFilter::GetArrayY()
+{
+  return(mArrayY);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void HistogramImageGenericFilter::SetArgsInfo(const args_info_type & a)
+{
+  mArgsInfo=a;
+  if (mArgsInfo.verbose_given)
+    SetIOVerbose(mArgsInfo.verbose_flag);
+  if (mArgsInfo.imagetypes_given && mArgsInfo.imagetypes_flag)
+    this->PrintAvailableImageTypes();
+
+  if (mArgsInfo.input_given) {
+    SetInputFilename(mArgsInfo.input_arg);
+  }
+  if (mArgsInfo.output_given) {
+    SetOutputFilename(mArgsInfo.output_arg);
+  }
+  if (mArgsInfo.size_given) {
+    SetSizeBin(mArgsInfo.size_arg);
+  }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void HistogramImageGenericFilter::SetSizeBin(const double size)
+{
+  mBinSize = size;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class InputImageType>
+void
+HistogramImageGenericFilter::UpdateWithInputImageType()
+{
+
+  // Reading input
+  typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+  typedef typename InputImageType::PixelType PixelType;
+  typedef typename InputImageType::IndexType IndexType;
+  typedef typename itk::Statistics::ImageToHistogramFilter<InputImageType> HistogramFilterType;
+  typedef typename itk::StatisticsImageFilter<InputImageType> StatisticsImageFilterType;
+
+  //compute range
+  typename StatisticsImageFilterType::Pointer statisticsImageFilter = StatisticsImageFilterType::New ();
+  statisticsImageFilter->SetInput(input);
+  statisticsImageFilter->Update();
+  double range = statisticsImageFilter->GetMaximum() - statisticsImageFilter->GetMinimum();
+  //compute bin number
+  typedef typename HistogramFilterType::HistogramSizeType SizeType;
+  SizeType binNumber(1);
+  mBinSize = std::log(range);
+  binNumber[0] = (int)(range/mBinSize);
+  if (binNumber[0] == 0)
+    binNumber[0] = 1;
+
+  //compute histogram
+  typename HistogramFilterType::Pointer histogramFilter = HistogramFilterType::New();
+  histogramFilter->SetHistogramSize(binNumber);
+  histogramFilter->SetAutoMinimumMaximum(true);
+  typename HistogramFilterType::HistogramMeasurementVectorType lowerBound(1);
+  typename HistogramFilterType::HistogramMeasurementVectorType upperBound(1);
+  lowerBound[0] = statisticsImageFilter->GetMinimum();
+  upperBound[0] = statisticsImageFilter->GetMaximum();
+  histogramFilter->SetHistogramBinMinimum(lowerBound);
+  histogramFilter->SetHistogramBinMaximum(upperBound);
+  histogramFilter->SetInput(input);
+  histogramFilter->Update();
+
+  mArrayX = vtkSmartPointer<vtkFloatArray>::New();
+  mArrayY = vtkSmartPointer<vtkFloatArray>::New();
+
+  for(unsigned int i = 0; i < histogramFilter->GetOutput()->GetSize()[0]; ++i)
+  {
+    mArrayY->InsertNextTuple1(histogramFilter->GetOutput()->GetFrequency(i));
+    mArrayX->InsertNextTuple1(statisticsImageFilter->GetMinimum() + (i+0.5)*mBinSize);
+  }
+}
+//--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif  //#define clitkHistogramImageGenericFilter_cxx