ADD_EXECUTABLE(clitkTransformLandmarks clitkTransformLandmarks.cxx ${clitkTransformLandmarks_GGO_C})
TARGET_LINK_LIBRARIES(clitkTransformLandmarks clitkCommon ITKIO)
+ WRAP_GGO(clitkLineProfile_GGO_C clitkLineProfile.ggo)
+ ADD_EXECUTABLE(clitkLineProfile clitkLineProfile.cxx clitkLineProfileGenericFilter.cxx ${clitkLineProfile_GGO_C})
+ TARGET_LINK_LIBRARIES(clitkLineProfile clitkCommon ITKIO)
+
ENDIF(CLITK_BUILD_TOOLS)
+
--- /dev/null
+#include "clitkLineProfile_ggo.h"
+#include "clitkLineProfileGenericFilter.h"
+
+
+bool verbose = false;
+
+template <unsigned int Dimension>
+void run(const args_info_clitkLineProfile& argsInfo);
+
+int main(int argc, char** argv)
+{
+ GGO(clitkLineProfile, args_info);
+
+ clitk::LineProfileGenericFilter::Pointer filter = clitk::LineProfileGenericFilter::New();
+ filter->SetArgsInfo(args_info);
+ filter->Update();
+
+ return EXIT_SUCCESS;
+}
+
+
--- /dev/null
+#File clitkLineProfile.ggo
+package "clitkLineProfile"
+version "1.0"
+purpose "Get the HU profile along the given line. Output to stdout."
+
+option "config" - "Config file" string no
+option "verbose" v "Verbose" flag off
+
+option "input" i "Input image" string yes
+option "p0" - "First point of the line" int no multiple default="0"
+option "p1" - "Second point of the line" int no multiple default="0"
+#option "output" o "Output file containing formated line points and values" string yes
--- /dev/null
+#include "clitkLineProfileGenericFilter.h"
+
+namespace clitk
+{
+ //-----------------------------------------------------------
+ // Constructor
+ //-----------------------------------------------------------
+ LineProfileGenericFilter::LineProfileGenericFilter()
+ : ImageToImageGenericFilter<Self>("Resample")
+ {
+ m_Verbose=false;
+
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ //InitializeImageType<4>();
+ }
+ //--------------------------------------------------------------------
+ //--------------------------------------------------------------------
+ template<unsigned int Dim>
+ void LineProfileGenericFilter::InitializeImageType()
+ {
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+ //ADD_IMAGE_TYPE(Dim, short);
+ }
+ //--------------------------------------------------------------------
+
+}
\ No newline at end of file
--- /dev/null
+/*=========================================================================
+ 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 clitkLineProfileGenericFilter_h
+#define clitkLineProfileGenericFilter_h
+
+/* =================================================
+ * @file clitkLineProfileGenericFilter.h
+ * @author
+ * @date
+ *
+ * @brief
+ *
+ ===================================================*/
+
+#include "clitkImageToImageGenericFilter.h"
+#include "clitkLineProfile_ggo.h"
+
+
+namespace clitk
+{
+
+ class ITK_EXPORT LineProfileGenericFilter:
+ public ImageToImageGenericFilter<LineProfileGenericFilter>
+ {
+ public:
+ //----------------------------------------
+ // Constructor & Destructor
+ //----------------------------------------
+ LineProfileGenericFilter();
+ ~LineProfileGenericFilter() {};
+
+
+ //----------------------------------------
+ // ITK
+ //----------------------------------------
+ typedef LineProfileGenericFilter Self;
+ typedef itk::LightObject Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ // Method for creation through the object factory
+ itkNewMacro(Self);
+
+ // Run-time type information (and related methods)
+ itkTypeMacro( SetSpacingGenericFilter, LightObject );
+
+ //----------------------------------------
+ // Typedefs
+ //----------------------------------------
+ typedef args_info_clitkLineProfile ArgsInfoType;
+
+ //----------------------------------------
+ // Set & Get
+ //----------------------------------------
+ void SetArgsInfo(const ArgsInfoType & a)
+ {
+ m_ArgsInfo=a;
+ m_Verbose=m_ArgsInfo.verbose_flag;
+ SetIOVerbose(m_Verbose);
+ SetInputFilename(m_ArgsInfo.input_arg);
+ }
+
+ //----------------------------------------
+ // Templated members
+ //----------------------------------------
+ template<class InputImageType> void UpdateWithInputImageType();
+
+ protected:
+
+ //----------------------------------------
+ // Templated members
+ //----------------------------------------
+ //template <unsigned int Dimension> void UpdateWithDim(std::string PixelType, unsigned int Components);
+ template<unsigned int Dim> void InitializeImageType();
+
+ //----------------------------------------
+ // Data members
+ //----------------------------------------
+ args_info_clitkLineProfile m_ArgsInfo;
+ bool m_Verbose;
+
+ };
+}
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkLineProfileGenericFilter.txx"
+#endif
+
+#endif // clitkLineProfileGenericFilter_h
\ No newline at end of file
--- /dev/null
+/*=========================================================================
+ 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 clitkLineProfileGenericFilter_cxx
+#define clitkLineProfileGenericFilter_cxx
+
+/* =================================================
+ * @file clitkLineProfileGenericFilter.cxx
+ * @author
+ * @date
+ *
+ * @brief
+ *
+ ===================================================*/
+
+#include "itkBresenhamLine.h"
+
+namespace clitk
+{
+
+//-----------------------------------------------------------
+ // Update
+ //-----------------------------------------------------------
+ template<class InputImageType>
+ void LineProfileGenericFilter::UpdateWithInputImageType()
+ {
+ typedef InputImageType ImageType;
+
+ if (m_Verbose)
+ std::cout << "LineProfileGenericFilter::UpdateWithInputImageType" << std::endl;
+
+ // type checks
+ if (m_ArgsInfo.p0_given != ImageType::ImageDimension ||
+ m_ArgsInfo.p1_given != ImageType::ImageDimension)
+ throw std::logic_error("Dimension of input points and image do not match.");
+
+ typename ImageType::Pointer image = this->template GetInput<InputImageType>(0);
+ typename ImageType::RegionType region = image->GetLargestPossibleRegion();
+
+ typedef typename ImageType::PointType PointType;
+ PointType p0, p1;
+ for (unsigned int i = 0; i < ImageType::ImageDimension; i++) {
+ p0[i] = m_ArgsInfo.p0_arg[i];
+ p1[i] = m_ArgsInfo.p1_arg[i];
+ }
+
+ // compute params of line between p0 and p1
+ // length (magnitude) must be an integer value, so it's
+ // the max distance along one the axes plus one to account
+ // for the last point.
+ typedef itk::BresenhamLine<ImageType::ImageDimension> LineType;
+ typename LineType::LType direction = p1 - p0;
+ typename LineType::LType::RealValueType mag = 0;
+ for (unsigned int i = 0; i < ImageType::ImageDimension; i++) {
+ if (direction[i] > mag)
+ mag = direction[i];
+ }
+ mag++;
+
+ if (m_Verbose)
+ std::cout << "Building line with direction = " << direction << " and length = " << mag << "..." << std::endl;
+
+ // build the line itself
+ LineType line;
+ typename LineType::OffsetArray offsets;
+ offsets = line.BuildLine(direction, mag);
+
+ if (m_Verbose)
+ std::cout << "Line has " << offsets.size() << " points" << std::endl;
+
+ // fill the output vectors
+ typedef typename ImageType::PixelType PixelType;
+ typedef typename ImageType::OffsetType OffsetType;
+ typedef typename ImageType::IndexType IndexType;
+ typedef std::vector<IndexType> IndexArrayType;
+ typedef std::vector<PixelType> ValueArrayType;
+
+ IndexType index0, index1;
+ for (unsigned int i = 0; i < ImageType::ImageDimension; i++) {
+ index0[i] = m_ArgsInfo.p0_arg[i];
+ index1[i] = m_ArgsInfo.p1_arg[i];
+ }
+
+ if (m_Verbose)
+ std::cout << "Getting profile along line..." << std::endl;
+
+ IndexType index;
+ IndexArrayType line_indices;
+ ValueArrayType line_values;
+ for (size_t i = 0; i < offsets.size(); i++)
+ {
+ index = index0 + offsets[i];
+ if (m_Verbose) {
+ std::cout << "index " << i << " = " << index << std::endl;
+ }
+
+ if (region.IsInside(index)) {
+ if (m_Verbose)
+ std::cout << "value " << i << " = " << image->GetPixel(index) << std::endl;
+
+ line_indices.push_back(index);
+ line_values.push_back(image->GetPixel(index));
+ }
+ else if (m_Verbose)
+ std::cout << "index outside image" << std::endl;
+ }
+
+ if (m_Verbose) {
+ std::cout << "I bring to you The Computed Points!" << std::endl;
+ }
+
+ for (size_t i = 0; i < line_indices.size(); i++) {
+ std::cout << line_indices[i] << " " << line_values[i] << std::endl;
+ }
+ }
+
+
+} //end clitk
+
+#endif //#define clitkLineProfileGenericFilter_cxx
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff