- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
===========================================================================**/
+
#ifndef CLITKIMAGECONVERTGENERICFILTER_CXX
#define CLITKIMAGECONVERTGENERICFILTER_CXX
#include "clitkImageConvertGenericFilter.h"
+#include "vvImageReader.h"
+#include "vvImageWriter.h"
+#include "itkFlipImageFilter.h"
+#include "itkGDCMImageIO.h"
+#include <itkChangeInformationImageFilter.h>
+
+#include "gdcmReader.h"
+#include "gdcmAttribute.h"
+#include "gdcmPrinter.h"
+#include "gdcmDict.h"
+#include "gdcmStringFilter.h"
//--------------------------------------------------------------------
clitk::ImageConvertGenericFilter::ImageConvertGenericFilter():
clitk::ImageToImageGenericFilter<Self>("ImageConvert")
{
mOutputPixelTypeName = "NotSpecified";
- mWarningOccur = false;
- mWarning = "";
mDisplayWarning = true;
+ mWarning = "";
+ mWarningOccur = false;
+ SetCorrectNegativeSpacingFlag(false);
+
InitializeImageType<2>();
InitializeImageType<3>();
InitializeImageType<4>();
void clitk::ImageConvertGenericFilter::InitializeImageType()
{
ADD_DEFAULT_IMAGE_TYPES(Dim);
+ ADD_VEC_IMAGE_TYPE(Dim, 2, float);
+ ADD_VEC_IMAGE_TYPE(Dim, 3, float);
+ ADD_VEC_IMAGE_TYPE(Dim, 2, double);
+ ADD_VEC_IMAGE_TYPE(Dim, 3, double);
}
//--------------------------------------------------------------------
template<class InputImageType>
void clitk::ImageConvertGenericFilter::UpdateWithInputImageType()
{
-
// Verbose stuff
if (m_IOVerbose) {
if (m_InputFilenames.size() == 1) {
}
}
+ if(mVV) {
+ if (mOutputPixelTypeName != "NotSpecified" || m_WriteCompression) {
+ std::cerr << "--vv is not compatible with --compression and --type options." << std::endl;
+ exit(-1);
+ }
- if ((m_PixelTypeName == mOutputPixelTypeName) || (mOutputPixelTypeName == "NotSpecified")) {
- // typename InputImageType::Pointer input = clitk::readImage<InputImageType>(m_InputFilenames);
+ vvImageReader::Pointer reader = vvImageReader::New();
+ reader->SetInputFilenames(m_InputFilenames);
+ reader->Update(vvImageReader::IMAGE);
+
+ vvImageWriter::Pointer writer = vvImageWriter::New();
+ writer->SetOutputFileName(m_OutputFilenames.front());
+ writer->SetSaveTransform(true);
+ writer->SetInput(reader->GetOutput());
+ writer->Update();
+ return;
+ }
+ else if ((m_PixelTypeName == mOutputPixelTypeName) || (mOutputPixelTypeName == "NotSpecified")) {
+
+ // Get input image
typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
- //clitk::writeImage<InputImageType>(input, mOutputFilename, m_IOVerbose);
+
+ if (mCorrectNegativeSpacingFlag) {
+ // Read dicom
+ gdcm::Reader reader;
+ reader.SetFileName(m_InputFilenames[0].c_str());
+ // if (!reader.CanReadFile(m_InputFilenames[0])) {
+ // std::cout << "Error: " << m_InputFilenames[0] << " is not a dicom file. Abort." << std::endl;
+ // exit(0);
+ // }
+ reader.Read();
+
+ // the dataset is the the set of element we are interested in:
+ gdcm::DataSet & ds = reader.GetFile().GetDataSet();
+
+ // Read the attribute SpacingBetweenSlices, check if negative and replace
+ gdcm::Attribute<0x0018,0x0088> SpacingBetweenSlices;
+ SpacingBetweenSlices.SetFromDataSet(ds);
+ double s = SpacingBetweenSlices.GetValue();
+ if (s >=0) {
+ std::cout << "Error: no negative spacing found SpacingBetweenSlices = " << s << " Abort. " << std::endl;
+ exit(0);
+ }
+ s = -s;
+
+ // Set spacing
+ typename InputImageType::SpacingType spacing = input->GetSpacing();
+ spacing[2] = s;
+ input->SetSpacing(spacing);
+
+ // Flip
+ typedef itk::FlipImageFilter< InputImageType > FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+ typedef typename FilterType::FlipAxesArrayType FlipAxesArrayType;
+ FlipAxesArrayType flipArray;
+ flipArray[0] = false;
+ flipArray[1] = false;
+ flipArray[2] = true;
+ filter->SetFlipAxes(flipArray);
+ filter->SetInput(input);
+ filter->Update();
+
+ // Read the attribute Image Position (Patient)
+ gdcm::Tag DetectorInformationSequenceTag(0x0054,0x0022);
+ const gdcm::DataElement & DIS = ds.GetDataElement(DetectorInformationSequenceTag);
+ if (!DIS.GetByteValue()) {
+ std::cout << "Error: could not find 0x0054,0x0022 tag. Abort." << std::endl;
+ exit(0);
+ }
+ gdcm::SmartPointer<gdcm::SequenceOfItems> sqf = DIS.GetValueAsSQ();
+ gdcm::Item & item = sqf->GetItem(1);
+ gdcm::DataSet & ds_position = item.GetNestedDataSet();
+ gdcm::Attribute<0x0020,0x0032> ImagePositionPatient;
+ ImagePositionPatient.SetFromDataSet(ds_position);
+ double x = ImagePositionPatient.GetValue(0);
+ double y = ImagePositionPatient.GetValue(1);
+ double z = ImagePositionPatient.GetValue(2);
+
+ // Set offset
+ typename InputImageType::PointType origin = input->GetOrigin();
+ origin[0] = x;
+ origin[1] = y;
+ origin[2] = z;
+ input->SetOrigin(origin);
+
+ // Orientation
+ typename InputImageType::DirectionType direction = input->GetDirection();
+ direction[2][2] = -1;
+ input->SetDirection(direction);
+
+ // Empty meta info
+ itk::MetaDataDictionary dict;// = new itk::MetaDataDictionary;
+ input->SetMetaDataDictionary(dict);
+ }
+
+ typedef itk::ChangeInformationImageFilter<InputImageType> CIType;
+ typename CIType::Pointer changeInfo = CIType::New();
+ if(mNoNiiMeta) {
+ changeInfo->SetInput(input);
+ typename CIType::PointType o = input->GetOrigin();
+ o[0] *= -1.;
+ o[1] *= -1.;
+ typename CIType::DirectionType d = input->GetDirection();
+ d[0][0] *= -1.;
+ d[1][1] *= -1.;
+ changeInfo->ChangeDirectionOn();
+ changeInfo->ChangeOriginOn();
+ changeInfo->SetOutputOrigin(o);
+ changeInfo->SetOutputDirection(d);
+ changeInfo->Update();
+ input = changeInfo->GetOutput();
+ }
+
this->SetNextOutput<InputImageType>(input);
+
} else {
-#define TRY_TYPE(TYPE) \
- if (IsSameType<TYPE>(mOutputPixelTypeName)) { UpdateWithOutputType<InputImageType, TYPE>(); return; }
- TRY_TYPE(char);
- // TRY_TYPE(signed char);
- TRY_TYPE(uchar);
- TRY_TYPE(short);
- TRY_TYPE(ushort);
- TRY_TYPE(int); // no uint ...
- TRY_TYPE(float);
- TRY_TYPE(double);
-#undef TRY_TYPE
-
- std::string list = CreateListOfTypes<char, uchar, short, ushort, int, float, double>();
- std::cerr << "Error, I don't know the output type '" << mOutputPixelTypeName
- << "'. " << std::endl << "Known types are " << list << "." << std::endl;
- exit(0);
+ // "trick" to call independent versions of update according to the
+ // pixel type (vector or scalar), using partial specializations
+ if (!UpdateWithSelectiveOutputType<InputImageType, ImageConvertTraits<typename InputImageType::PixelType>::IS_VECTOR>::Run(*this, mOutputPixelTypeName))
+ exit(-1);
}
}
//====================================================================
//====================================================================
-template<class InputImageType, class OutputPixelType>
-void clitk::ImageConvertGenericFilter::UpdateWithOutputType()
-{
- // Read
- typename InputImageType::Pointer input =this->template GetInput<InputImageType>(0);
-
- // Typedef
- typedef typename InputImageType::PixelType PixelType;
- // Warning
+template<class PixelType, class OutputPixelType>
+void clitk::ImageConvertGenericFilter::CheckTypes(
+ std::string inType, std::string outType
+)
+{
std::ostringstream osstream;
if (std::numeric_limits<PixelType>::is_signed) {
if (!std::numeric_limits<OutputPixelType>::is_signed) {
- osstream << "Warning, input type is signed (" << m_PixelTypeName << ") while output type is not ("
- << mOutputPixelTypeName << "), use at your own responsability." << std::endl;
- mWarningOccur = true;
+ osstream << "Warning, input type is signed (";
}
}
if (!std::numeric_limits<PixelType>::is_integer) {
if (std::numeric_limits<OutputPixelType>::is_integer) {
- osstream << "Warning, input type is not integer (" << m_PixelTypeName << ") while output type is ("
- << mOutputPixelTypeName << "), use at your own responsability." << std::endl;
- mWarningOccur = true;
+ osstream << "Warning, input type is not integer (";
}
}
// DD(std::numeric_limits<PixelType>::digits10);
// DD(std::numeric_limits<OutputPixelType>::digits10);
if (!std::numeric_limits<PixelType>::is_integer) {
if (std::numeric_limits<OutputPixelType>::is_integer) {
- osstream << "Warning, input type is not integer (" << m_PixelTypeName << ") while output type is ("
- << mOutputPixelTypeName << "), use at your own responsability." << std::endl;
- mWarningOccur = true;
+ osstream << "Warning, input type is not integer (";
}
}
if (std::numeric_limits<PixelType>::digits10 > std::numeric_limits<OutputPixelType>::digits10) {
- osstream << "Warning, possible loss of precision : input type is (" << m_PixelTypeName << ") while output type is ("
- << mOutputPixelTypeName << "), use at your own responsability." << std::endl;
- mWarningOccur = true;
+ osstream << "Warning, possible loss of precision : input type is (" ;
}
- mWarning = osstream.str();
- if (mDisplayWarning) {
- std::cerr << mWarning;
+ if (!osstream.str().empty())
+ {
+ mWarningOccur = true;
+ osstream << inType << ") while output type is (" << outType << "), use at your own responsability." << std::endl;
+ mWarning = osstream.str();
+ if (mDisplayWarning) {
+ std::cerr << mWarning;
+ }
}
-
- // Cast
- typedef itk::Image<OutputPixelType,InputImageType::ImageDimension> OutputImageType;
- typedef itk::CastImageFilter<InputImageType, OutputImageType> FilterType;
- typename FilterType::Pointer filter = FilterType::New();
- filter->SetInput(input);
- filter->Update();
-
- // Write
- SetNextOutput<OutputImageType>(filter->GetOutput());
- //clitk::writeImage<OutputImageType>(filter->GetOutput(), mOutputFilename, m_IOVerbose);
}
-//====================================================================
#endif /* end #define CLITKIMAGECONVERTGENERICFILTER_CXX */
-
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff