orthanc: OrthancCppClient/Series.cpp comparison

comparison OrthancCppClient/Series.cpp @ 986:de18e90d5507

fix GetVoxelSizeZ

author	Sebastien Jodogne <s.jodogne@gmail.com>
date	Tue, 01 Jul 2014 16:51:18 +0200
parents	a811bdf8b8eb
children	6e7e5ed91c2d

comparison

equal deleted inserted replaced

-:ef02bd1c2f0e
+:de18e90d5507
 SliceLocator(Instance& someSlice)
 {
 /**
 * Compute the slice normal from Image Orientation Patient.
 * http://nipy.sourceforge.net/nibabel/dicom/dicom_orientation.html#dicom-z-from-slice
+* http://dicomiseasy.blogspot.be/2013/06/getting-oriented-using-image-plane.html
 * http://www.itk.org/pipermail/insight-users/2003-September/004762.html
 **/
 std::vector<float> cosines;
-someSlice.SplitVectorOfFloats(cosines, "ImageOrientationPatient");
+someSlice.SplitVectorOfFloats(cosines, "ImageOrientationPatient");  // 0020-0037
 if (cosines.size() != 6)
 {
 throw OrthancClientException(Orthanc::ErrorCode_BadFileFormat);
 }
 * Compute the distance of some slice along the slice normal.
 **/
 float ComputeSliceLocation(Instance& instance) const
 {
 std::vector<float> ipp;
-instance.SplitVectorOfFloats(ipp, "ImagePositionPatient");
+instance.SplitVectorOfFloats(ipp, "ImagePositionPatient");  // 0020-0032
 if (ipp.size() != 3)
 {
 throw OrthancClientException(Orthanc::ErrorCode_BadFileFormat);
 }
 {
 uint8_t* p = reinterpret_cast<uint8_t*>(target_) + y * lineStride_;
 if (instance_.GetPixelFormat() == format_)
 {
-memcpy(p, instance_.GetBuffer(y), 2 * instance_.GetWidth());
+memcpy(p, instance_.GetBuffer(y), GetBytesPerPixel(instance_.GetPixelFormat()) * instance_.GetWidth());
 }
 else if (instance_.GetPixelFormat() == PixelFormat_Grayscale8 &&
 format_ == PixelFormat_RGB24)
 {
 const uint8_t* s = reinterpret_cast<const uint8_t*>(instance_.GetBuffer(y));
 {
 try
 {
 if (GetInstanceCount() == 0)
 {
+// Empty image, use some default value (should never happen)
+voxelSizeX_ = 1;
+voxelSizeY_ = 1;
+voxelSizeZ_ = 1;
+sliceThickness_ = 1;
 return true;
 }
-Instance& i1 = GetInstance(0);
+// Choose a reference slice
+Instance& reference = GetInstance(0);
+// Check that all the child instances share the same 3D parameters
 for (unsigned int i = 0; i < GetInstanceCount(); i++)
 {
 Instance& i2 = GetInstance(i);
-if (std::string(i1.GetTagAsString("Columns")) != std::string(i2.GetTagAsString("Columns")) ||
+if (std::string(reference.GetTagAsString("Columns")) != std::string(i2.GetTagAsString("Columns")) ||
-std::string(i1.GetTagAsString("Rows")) != std::string(i2.GetTagAsString("Rows")) ||
+std::string(reference.GetTagAsString("Rows")) != std::string(i2.GetTagAsString("Rows")) ||
-std::string(i1.GetTagAsString("ImageOrientationPatient")) != std::string(i2.GetTagAsString("ImageOrientationPatient")) ||
+std::string(reference.GetTagAsString("ImageOrientationPatient")) != std::string(i2.GetTagAsString("ImageOrientationPatient")) ||
-std::string(i1.GetTagAsString("SliceThickness")) != std::string(i2.GetTagAsString("SliceThickness")) ||
+std::string(reference.GetTagAsString("SliceThickness")) != std::string(i2.GetTagAsString("SliceThickness")) ||
-std::string(i1.GetTagAsString("PixelSpacing")) != std::string(i2.GetTagAsString("PixelSpacing")))
+std::string(reference.GetTagAsString("PixelSpacing")) != std::string(i2.GetTagAsString("PixelSpacing")))
 {
 return false;
 }
 }
-SliceLocator locator(GetInstance(0));
+// Extract X/Y voxel size and slice thickness
+std::string s = GetInstance(0).GetTagAsString("PixelSpacing");  // 0028-0030
+size_t pos = s.find('\\');
+assert(pos != std::string::npos);
+std::string sy = s.substr(0, pos);
+std::string sx = s.substr(pos + 1);
+try
+{
+voxelSizeX_ = boost::lexical_cast<float>(sx);
+voxelSizeY_ = boost::lexical_cast<float>(sy);
+}
+catch (boost::bad_lexical_cast)
+{
+throw OrthancClientException(Orthanc::ErrorCode_BadFileFormat);
+}
+sliceThickness_ = GetInstance(0).GetTagAsFloat("SliceThickness");  // 0018-0050
+// Compute the location of each slice to extract the voxel size along Z
+voxelSizeZ_ = std::numeric_limits<float>::infinity();
+SliceLocator locator(reference);
+float referenceSliceLocation = locator.ComputeSliceLocation(reference);
 std::set<float> l;
 for (unsigned int i = 0; i < GetInstanceCount(); i++)
 {
-l.insert(locator.ComputeSliceLocation(GetInstance(i)));
+float location = locator.ComputeSliceLocation(GetInstance(i));
-}
+float distanceToReferenceSlice = fabs(location - referenceSliceLocation);
+l.insert(location);
+if (distanceToReferenceSlice > std::numeric_limits<float>::epsilon() &&
+distanceToReferenceSlice < voxelSizeZ_)
+{
+voxelSizeZ_ = distanceToReferenceSlice;
+}
+}
+// Make sure that 2 slices do not share the same Z location
 return l.size() == GetInstanceCount();
 }
 catch (OrthancClientException)
 {
 return false;
 {
 ReadSeries();
 status_ = Status3DImage_NotTested;
 url_ = std::string(connection_.GetOrthancUrl()) + "/series/" + id_;
-isVoxelSizeRead_ = false;
 voxelSizeX_ = 0;
 voxelSizeY_ = 0;
 voxelSizeZ_ = 0;
+sliceThickness_ = 0;
 instances_.SetThreadCount(connection.GetThreadCount());
 }
 if (GetInstanceCount() == 0)
 return 0;
 else
 return GetInstance(0).GetTagAsInt("Rows");
 }
-void Series::LoadVoxelSize()
-{
-if (isVoxelSizeRead_)
-{
-return;
-}
-Check3DImage();
-if (GetInstanceCount() == 0)
-{
-// Empty image, use some default value
-voxelSizeX_ = 1;
-voxelSizeY_ = 1;
-voxelSizeZ_ = 1;
-}
-else
-{
-try
-{
-std::string s = GetInstance(0).GetTagAsString("PixelSpacing");
-size_t pos = s.find('\\');
-assert(pos != std::string::npos);
-std::string sy = s.substr(0, pos);
-std::string sx = s.substr(pos + 1);
-voxelSizeX_ = boost::lexical_cast<float>(sx);
-voxelSizeY_ = boost::lexical_cast<float>(sy);
-voxelSizeZ_ = GetInstance(0).GetTagAsFloat("SliceThickness");
-}
-catch (boost::bad_lexical_cast)
-{
-throw OrthancClientException(Orthanc::ErrorCode_NotImplemented);
-}
-}
-isVoxelSizeRead_ = true;
-}
 const char* Series::GetMainDicomTag(const char* tag, const char* defaultValue) const
 {
 if (series_["MainDicomTags"].isMember(tag))
 {
 }
 }
 float Series::GetVoxelSizeX()
 {
-LoadVoxelSize();
+Check3DImage();   // Is3DImageInternal() will compute the voxel sizes
 return voxelSizeX_;
 }
 float Series::GetVoxelSizeY()
 {
-LoadVoxelSize();
+Check3DImage();   // Is3DImageInternal() will compute the voxel sizes
 return voxelSizeY_;
 }
 float Series::GetVoxelSizeZ()
 {
-LoadVoxelSize();
+Check3DImage();   // Is3DImageInternal() will compute the voxel sizes
 return voxelSizeZ_;
+}
+float Series::GetSliceThickness()
+{
+Check3DImage();   // Is3DImageInternal() will compute the voxel sizes
+return sliceThickness_;
 }
 void Series::Load3DImage(void* target,
 Orthanc::PixelFormat format,
 int64_t lineStride,

Mercurial > hg > orthanc

comparison OrthancCppClient/Series.cpp @ 986:de18e90d5507