ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/tools ${PROJECT_BINARY_DIR}/tools)
ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/segmentation ${PROJECT_BINARY_DIR}/segmentation)
ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/registration ${PROJECT_BINARY_DIR}/registration)
+ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/scripts ${PROJECT_BINARY_DIR}/scripts)
ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/tests ${PROJECT_BINARY_DIR}/tests)
ENDIF(BUILD_TESTING)
-#=========================================================
-# Install scripts when running make install
-SET(SCRIPTS
- ${CLITK_SOURCE_DIR}/scripts/calculate_motion_amplitude.sh
- ${CLITK_SOURCE_DIR}/scripts/midp_common.sh
- ${CLITK_SOURCE_DIR}/scripts/registration.sh
- ${CLITK_SOURCE_DIR}/scripts/create_midP.sh
- ${CLITK_SOURCE_DIR}/scripts/create_midP-2.0.sh
- ${CLITK_SOURCE_DIR}/scripts/create_mhd_4D.sh
- ${CLITK_SOURCE_DIR}/scripts/create_mhd_4D_pattern.sh
- ${CLITK_SOURCE_DIR}/scripts/create_midP_masks.sh
- ${CLITK_SOURCE_DIR}/scripts/create_midP_masks-2.0.sh
- ${CLITK_SOURCE_DIR}/scripts/pts_to_landmarks.sh
- ${CLITK_SOURCE_DIR}/scripts/create_mhd_3D.sh
- ${CLITK_SOURCE_DIR}/scripts/dicom_info.sh
-)
-
-INSTALL (FILES ${SCRIPTS} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
namespace clitk
{
+//--------------------------------------------------------------------
+template < >
+itk::Matrix<double, 3, 3>
+GetForwardAffineMatrix<2>(itk::Array<double> transformParameters)
+{
+ return GetForwardAffineMatrix2D(transformParameters);
+}
+
+//--------------------------------------------------------------------
+template < >
+itk::Matrix<double, 4, 4>
+GetForwardAffineMatrix<3>(itk::Array<double> transformParameters)
+{
+ return GetForwardAffineMatrix3D(transformParameters);
+}
+
//--------------------------------------------------------------------
template < >
itk::Matrix<double, 3, 3>
return GetBackwardAffineMatrix3D(transformParameters);
}
+//--------------------------------------------------------------------
+template <>
+itk::Matrix<double, 2, 2> GetRotationMatrix<2>(itk::Array<double> rotationParameters)
+{
+ return GetRotationMatrix2D(rotationParameters);
+}
+
+//--------------------------------------------------------------------
+template <>
+itk::Matrix<double, 3, 3> GetRotationMatrix<3>(itk::Array<double> rotationParameters)
+{
+ return GetRotationMatrix3D(rotationParameters);
+}
+
}
//============================================================================
itk::Matrix<double, 3, 3> GetForwardAffineMatrix2D(itk::Array<double> transformParameters);
itk::Matrix<double, 4, 4> GetForwardAffineMatrix3D(itk::Array<double> transformParameters);
+ template <unsigned int Dimension > itk::Matrix<double, Dimension+1, Dimension+1> GetForwardAffineMatrix(itk::Array<double> transformParameters);
itk::Matrix<double, 3, 3> GetBackwardAffineMatrix2D(itk::Array<double> transformParameters);
itk::Matrix<double, 4, 4> GetBackwardAffineMatrix3D(itk::Array<double> transformParameters);
template <unsigned int Dimension > itk::Matrix<double, Dimension+1, Dimension+1> GetBackwardAffineMatrix(itk::Array<double> transformParameters);
itk::Matrix<double, 3, 3> GetRotationMatrix3D(itk::Array<double> rotationParameters);
+ itk::Matrix<double, 2, 2> GetRotationMatrix2D(itk::Array<double> rotationParameters);
+ template <unsigned int Dimension> itk::Matrix<double, Dimension, Dimension> GetRotationMatrix(itk::Array<double> rotationParameters);
itk::Point<double, 3> GetRotatedPoint3D(itk::Array<double> rotationParameters, itk::Point<double, 3> input);
itk::Matrix<double, 4, 4> GetCenteredRotationMatrix3D(itk::Array<double> rotationParameters,itk::Point<double,3> centerOfRotation);
// itk::Matrix<double, 4, 4> GetComposedMatrix3D(itk::Matrix<double, 4, 4> firstTransform, itk::Matrix<double, 4, 4> secondTransform);
matrix[2][2]= cos(rotationParameters[0])*cos(rotationParameters[1]);
return matrix;
}
-
-
-
+
+ inline itk::Matrix<double, 2, 2> GetRotationMatrix2D(itk::Array<double> rotationParameters)
+ {
+ itk::Matrix<double, 2, 2> matrix;
+ matrix[0][0] = cos(rotationParameters[0]);
+ matrix[1][0] = sin(rotationParameters[0]);
+ matrix[0][1] = -matrix[1][0];
+ matrix[1][1] = matrix[0][0];
+ return matrix;
+ }
+
//========================================================================================
inline itk::Point<double, 3> GetRotatedPoint3D(itk::Array<double> rotationParameters, itk::Point<double, 3> input)
{
--- /dev/null
+#=========================================================
+# Install scripts when running make install
+SET(SCRIPTS
+ ${CLITK_SOURCE_DIR}/scripts/calculate_motion_amplitude.sh
+ ${CLITK_SOURCE_DIR}/scripts/calculate_contour_stats.sh
+ ${CLITK_SOURCE_DIR}/scripts/midp_common.sh
+ ${CLITK_SOURCE_DIR}/scripts/registration.sh
+ ${CLITK_SOURCE_DIR}/scripts/create_midP.sh
+ ${CLITK_SOURCE_DIR}/scripts/create_midP-2.0.sh
+ ${CLITK_SOURCE_DIR}/scripts/create_mhd_4D.sh
+ ${CLITK_SOURCE_DIR}/scripts/create_mhd_4D_pattern.sh
+ ${CLITK_SOURCE_DIR}/scripts/create_midP_masks.sh
+ ${CLITK_SOURCE_DIR}/scripts/create_midP_masks-2.0.sh
+ ${CLITK_SOURCE_DIR}/scripts/pts_to_landmarks.sh
+ ${CLITK_SOURCE_DIR}/scripts/create_mhd_3D.sh
+ ${CLITK_SOURCE_DIR}/scripts/dicom_info.sh
+)
+
+INSTALL (FILES ${SCRIPTS} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
--- /dev/null
+#! /bin/bash +x
+
+select_contour_gui()
+{
+ local roi_list=$@
+ roi=`zenity --list --title="Available Contours" --column="Please choose a contour:" $roi_list`
+ case $? in
+ 0)
+ if [ -z $roi ]
+ then
+ zenity --warning --text="You must choose one contour."
+ select_contour $roi_list
+ else
+ rtstruct_roi_name=$roi
+ fi;;
+ 1)
+ if zenity --question --text="Do you really wish to quit?"
+ then
+ exit
+ else
+ select_contour $roi_list
+ fi;;
+ -1)
+ zenity --error --text="Unexpected error. Please relaunch the application."
+ exit;;
+ esac
+}
+
+select_contour()
+{
+ local roi_list=$@
+ echo "Available Contours:"
+ for r in $roi_list; do
+ echo $r
+ done
+
+ echo "Please choose a contour number:"
+ read rtstruct_roi_number
+}
+
+select_roi()
+{
+ rtstruct_roi_name_list=( `clitkDicomInfo ${rtstruct_file} | grep "3006|0026" | cut -d '[' -f 4 | sed 's/| V 3006|0026[LO] [ROI Name] \|]//'` )
+ rtstruct_roi_number_list=( `clitkDicomInfo ${rtstruct_file} | grep "3006|0022" | cut -d '[' -f 4 | sed 's/| V 3006|0026[LO] [ROI Number] \|]//'` )
+ rtstruct_roi_list=( )
+ for i in $(seq 0 1 $(( ${#rtstruct_roi_name_list[@]} - 1 ))); do
+ rtstruct_roi_list[$i]=${rtstruct_roi_number_list[$i]}:${rtstruct_roi_name_list[$i]}
+ done
+
+ if [ $gui_mode = 1 ]; then
+ select_contour_gui ${rtstruct_roi_list[@]}
+ rtstruct_roi=`echo ${rtstruct_roi_name} | cut -d ':' -f 1`
+ rtstruct_roi_name=`echo ${rtstruct_roi_name} | cut -d ':' -f 2`
+ else
+ select_contour ${rtstruct_roi_list[@]}
+ rtstruct_roi=$rtstruct_roi_number
+ rtstruct_roi_name=${rtstruct_roi_name_list[$(( $rtstruct_roi_number - 1))]}
+ fi
+}
+
+############# main
+
+if echo $* | grep "\-h"; then
+ echo Usage: calculate_motion_amplitude.sh { RTSTRUCT_FILE REFERENCE_IMAGE | --gui }
+
+ exit 0
+fi
+
+
+rtstruct_roi=0
+
+if echo $* | grep "\-\-gui" > /dev/null 2>&1; then
+ if [ $# != 1 ]; then
+ echo Invalid arguments. Type \'`basename $0` -h\' for help
+ exit -1
+ fi
+
+ gui_mode=1
+ rtstruct_file=`zenity --file-selection --title="Select RT Struct file."`
+ select_roi
+ rtstruct_ref_image=`zenity --file-selection --title="Select Reference Image."`
+else
+ if [ $# != 2 ]; then
+ echo Invalid arguments. Type \'`basename $0` -h\' for help
+ exit -1
+ fi
+
+ gui_mode=0
+ rtstruct_file=$1
+ rtstruct_ref_image=$2
+ select_roi
+fi
+
+
+#echo "Processing \"${rtstruct_roi_list[$roi_struct]}\"..."
+# create ROI mask from rtstruct
+roi_mask=roi_${rtstruct_roi_name}.mhd
+clitkDicomRTStruct2Image -i ${rtstruct_file} -o ${roi_mask} -j ${rtstruct_ref_image} -r ${rtstruct_roi} 2> /tmp/err.txt
+if cat /tmp/err.txt | grep -q "No ROI"; then
+ echo Invalid contour number.
+ exit -3
+fi
+
+# guarantees the same sampling for roi mask and vector image
+roi_mask2=resampled_${roi_mask}
+clitkResampleImage -i ${roi_mask} -o ${roi_mask2} --like ${rtstruct_ref_image}
+
+# calculate stats
+clitkImageStatistics -i ${rtstruct_ref_image} -m ${roi_mask2} --verbose 2> /dev/null | tail -n 8 > /tmp/result.txt
+
+if [ $gui_mode = 1 ]; then
+ cat /tmp/result.txt | zenity --text-info --title "Restuls for \"${rtstruct_roi_name}\""
+else
+ echo "Restuls for \"${rtstruct_roi_name}\""
+ cat /tmp/result.txt
+fi
+
+rm `basename $roi_mask .mhd`.{mhd,raw}
+rm `basename $roi_mask2 .mhd`.{mhd,raw}
+rm /tmp/err.txt
+rm /tmp/result.txt
option "spacing" - "New output spacing if different from input" double no multiple
option "origin" - "New output origin if different from input" double no multiple
option "matrix" m "Affine matrix (homogene) filename" string no
+option "rotate" r "Rotation to apply (radians)" double no multiple
+option "translate" t "Translation to apply (mm)" double no multiple
option "pad" - "Edge padding value" double no default="0.0"
section "Interpolation"
// Matrix
typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
- if (m_ArgsInfo.matrix_given) {
- matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
- if (m_Verbose) std::cout<<"Reading the matrix..."<<std::endl;
- } else {
- matrix.SetIdentity();
+ if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
+ {
+ if (m_ArgsInfo.matrix_given)
+ {
+ std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
+ return;
+ }
+ itk::Array<double> transformParameters(2 * Dimension);
+ int pos = 0;
+ if (Dimension == 2)
+ transformParameters[pos++] = m_ArgsInfo.rotate_arg[0];
+ else
+ for (unsigned int i = 0; i < 3; i++)
+ transformParameters[pos++] = m_ArgsInfo.rotate_arg[i];
+ for (unsigned int i = 0; i < Dimension && i < 3; i++)
+ transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
+ if (Dimension == 4)
+ {
+ matrix.SetIdentity();
+ itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
+ for (unsigned int i = 0; i < 3; ++i)
+ for (unsigned int j = 0; j < 3; ++j)
+ matrix[i][j] = tmp[i][j];
+ for (unsigned int i = 0; i < 3; ++i)
+ matrix[i][4] = tmp[i][3];
+ }
+ else
+ matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
+ }
+ else
+ {
+ if (m_ArgsInfo.matrix_given)
+ {
+ matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
+ if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
+ }
+ else
+ matrix.SetIdentity();
}
- if (m_Verbose) std::cout<<"Using the following matrix:"<<std::endl;
- if (m_Verbose) std::cout<<matrix<<std::endl;
- typename itk::Matrix<double, Dimension, Dimension> rotationMatrix=clitk::GetRotationalPartMatrix(matrix);
- typename itk::Vector<double,Dimension> translationPart= clitk::GetTranslationPartMatrix(matrix);
+ if (m_Verbose)
+ std::cout << "Using the following matrix:" << std::endl
+ << matrix << std::endl;
+ typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
+ typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
// Transform
typedef itk::AffineTransform<double, Dimension> AffineTransformType;
// Matrix
typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
- if (m_ArgsInfo.matrix_given)
- matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
+ if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
+ {
+ if (m_ArgsInfo.matrix_given)
+ {
+ std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
+ return;
+ }
+ itk::Array<double> transformParameters(2 * Dimension);
+ int pos = 0;
+ if (Dimension == 2)
+ transformParameters[pos++] = m_ArgsInfo.rotate_arg[0];
+ else
+ for (unsigned int i = 0; i < 3; i++)
+ transformParameters[pos++] = m_ArgsInfo.rotate_arg[i];
+ for (unsigned int i = 0; i < Dimension && i < 3; i++)
+ transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
+ if (Dimension == 4)
+ {
+ matrix.SetIdentity();
+ itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
+ for (unsigned int i = 0; i < 3; ++i)
+ for (unsigned int j = 0; j < 3; ++j)
+ matrix[i][j] = tmp[i][j];
+ for (unsigned int i = 0; i < 3; ++i)
+ matrix[i][4] = tmp[i][3];
+ }
+ else
+ matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
+ }
else
- matrix.SetIdentity();
- if (m_Verbose) std::cout<<"Using the following matrix:"<<std::endl;
- if (m_Verbose) std::cout<<matrix<<std::endl;
- typename itk::Matrix<double, Dimension, Dimension> rotationMatrix=clitk::GetRotationalPartMatrix(matrix);
- typename itk::Vector<double, Dimension> translationPart= clitk::GetTranslationPartMatrix(matrix);
+ {
+ if (m_ArgsInfo.matrix_given)
+ {
+ matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
+ if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
+ }
+ else
+ matrix.SetIdentity();
+ }
+ if (m_Verbose)
+ std::cout << "Using the following matrix:" << std::endl
+ << matrix << std::endl;
+ typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
+ typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
// Transform
typedef itk::AffineTransform<double, Dimension> AffineTransformType;
//----------------------------------------------------------------------------
void vvSlicer::Render()
{
- if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay && !this->mFusion) {
+ if (this->mFusion) {
+ legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
+ legend->UseOpacityOn();
+ legend->SetVisibility(1);
+ }
+ else if (this->GetWindowLevel()->GetLookupTable()) {// && !this->mOverlay && !this->mFusion) {
legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
+ legend->UseOpacityOff();
legend->SetVisibility(1);
} else legend->SetVisibility(0);
double v[4];
// set color table transparency
+ double alpha_range=(double)mFusionThresOpacity/10;
double range_end = frange[0] + (double)mFusionThresOpacity*(frange[1] - frange[0])/100;
- double curr_value = frange[0];
+ double curr_value = fusRange[0];
int nvalues = fusLUT->GetNumberOfTableValues();
- //for (double i = frange[0]; i <= alpha_range_end; i++) {
for (double i = 0; curr_value < range_end; i++) {
fusLUT->GetTableValue(i, v);
v[3] = 0;
+ //if (curr_value >= -alpha_range && curr_value <= alpha_range) v[3] = pow(fabs(curr_value/alpha_range),2);
+ //else v[3] = 1;
fusLUT->SetTableValue(i, v);
- curr_value += (frange[1] - frange[0])/nvalues;
+ curr_value += (fusRange[1] - fusRange[0])/nvalues;
}
}
for ( unsigned int i = 0; i < mSlicers.size(); i++) {
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff