-#ifndef clitkBinarizeImageGenericFilter_txx
-#define clitkBinarizeImageGenericFilter_txx
-
-/* =================================================
- * @file clitkBinarizeImageGenericFilter.txx
- * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
- * @date 29 june 2009
- *
- * @brief
- *
- ===================================================*/
+/*=========================================================================
+ 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://oncora1.lyon.fnclcc.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 CLITKBINARIZEIMAGEGENERICFILTER_TXX
+#define CLITKBINARIZEIMAGEGENERICFILTER_TXX
+
+// itk include
+#include "itkBinaryThresholdImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+#include <clitkCommon.h>
+// #include <tiff.h>
namespace clitk
{
template<class args_info_type>
template<unsigned int Dim>
void BinarizeImageGenericFilter<args_info_type>::InitializeImageType() {
- ADD_IMAGE_TYPE(Dim, char);
- ADD_IMAGE_TYPE(Dim, short);
- ADD_IMAGE_TYPE(Dim, int);
- ADD_IMAGE_TYPE(Dim, float);
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
}
//--------------------------------------------------------------------
void BinarizeImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a) {
mArgsInfo=a;
SetIOVerbose(mArgsInfo.verbose_flag);
-
if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
if (mArgsInfo.input_given) {
// Reading input
typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
-
+
// Main filter
typedef typename InputImageType::PixelType PixelType;
- typedef itk::Image<int, InputImageType::ImageDimension> OutputImageType;
+ typedef itk::Image<char, InputImageType::ImageDimension> OutputImageType;
// Filter
typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
thresholdFilter->SetInput(input);
- if(mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
- if(mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
-
- DD(mArgsInfo.lower_given);
- DD(mArgsInfo.upper_given);
- DD(mArgsInfo.lower_arg);
- DD(mArgsInfo.upper_arg);
-
- DD(mArgsInfo.inside_arg);
- DD(mArgsInfo.outside_arg);
- DD(mArgsInfo.inside_given);
- DD(mArgsInfo.outside_given);
-
- thresholdFilter->SetInsideValue(mArgsInfo.inside_arg);
- thresholdFilter->SetOutsideValue(mArgsInfo.outside_arg);
-
- thresholdFilter->Update();
-
- // Write/Save results
- typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
- this->template SetNextOutput<OutputImageType>(outputImage);
+ thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
+
+ if (mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
+ if (mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
+
+ // DD(mArgsInfo.lower_given);
+ // DD(mArgsInfo.upper_given);
+ // DD(mArgsInfo.lower_arg);
+ // DD(mArgsInfo.upper_arg);
+ // DD(mArgsInfo.fg_arg);
+ // DD(mArgsInfo.bg_arg);
+ // DD(mArgsInfo.fg_given);
+ // DD(mArgsInfo.bg_given);
+ // DD(mArgsInfo.mode_arg);
+
+// <<<<<<< clitkBinarizeImageGenericFilter.txx
+// DD(mArgsInfo.useFG_flag);
+// DD(mArgsInfo.useBG_flag);
+
+// thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
+
+// // Keep BG value to 0 if maskFilterType is used after
+// if (mArgsInfo.useBG_flag && mArgsInfo.useFG_flag) {
+// thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
+// }
+// else {
+// DD("0");
+// thresholdFilter->SetOutsideValue(0);
+// }
+
+// // thresholdFilter->Update();
+
+// // If no BG or no FG : new image, copy input with MaskImageFilter
+// // If setFG -> FG BG have been changed
+// if (mArgsInfo.useBG_flag && mArgsInfo.useFG_flag) {
+// =======
+ /* Three modes :
+ - FG -> only use FG value for pixel in the Foreground (or Inside), keep input values for outside
+ - BG -> only use BG value for pixel in the Background (or Outside), keep input values for inside
+ - both -> use FG and BG (real binary image)
+ */
+ if (mArgsInfo.mode_arg == std::string("both")) {
+ thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
+ thresholdFilter->Update();
+ //>>>>>>> 1.5
+ typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
+ this->template SetNextOutput<OutputImageType>(outputImage);
+ }
+ else {
+ typename InputImageType::Pointer outputImage;
+ thresholdFilter->SetOutsideValue(0);
+ if (mArgsInfo.mode_arg == std::string("BG")) {
+ typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
+ typename maskFilterType::Pointer maskFilter = maskFilterType::New();
+ maskFilter->SetInput1(input);
+ maskFilter->SetInput2(thresholdFilter->GetOutput());
+ maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
+ maskFilter->Update();
+ outputImage = maskFilter->GetOutput();
+ }
+ else {
+ typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
+ typename maskFilterType::Pointer maskFilter = maskFilterType::New();
+ maskFilter->SetInput1(input);
+ maskFilter->SetInput2(thresholdFilter->GetOutput());
+ maskFilter->SetOutsideValue(mArgsInfo.fg_arg);
+ maskFilter->Update();
+ outputImage = maskFilter->GetOutput();
+ }
+ // Write/Save results
+ this->template SetNextOutput<InputImageType>(outputImage);
+ }
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff