diff --git a/Examples/VolumeRendering/VolumeRenderingExample.cpp b/Examples/VolumeRendering/VolumeRenderingExample.cpp
index efc5dabc4567e2a76bad36f2656d7c6a8ac11e68..f4941787e1c85d58aff8fa43562257164fda97c9 100644
--- a/Examples/VolumeRendering/VolumeRenderingExample.cpp
+++ b/Examples/VolumeRendering/VolumeRenderingExample.cpp
@@ -22,6 +22,7 @@
#include "imstkCamera.h"
#include "imstkImageData.h"
#include "imstkKeyboardSceneControl.h"
+#include "imstkLogger.h"
#include "imstkMeshIO.h"
#include "imstkMouseSceneControl.h"
#include "imstkNew.h"
@@ -44,6 +45,8 @@ using namespace imstk;
int
main()
{
+ Logger::startLogger();
+
// SDK and Scene
imstkNew<Scene> scene("VolumeRendering");
diff --git a/Source/DynamicalModels/ObjectModels/imstkSPHModel.cpp b/Source/DynamicalModels/ObjectModels/imstkSPHModel.cpp
index 1f7199aa59205e81f3ce26b731e13045ee5a893f..e9b3f59b35bd59bf9061227f2c392eee2411a4ed 100644
--- a/Source/DynamicalModels/ObjectModels/imstkSPHModel.cpp
+++ b/Source/DynamicalModels/ObjectModels/imstkSPHModel.cpp
@@ -886,7 +886,7 @@ SPHModel::writeStateToVtk()
VTKMeshIO vtkWriter;
std::string filePath = std::string("sph_output_") + std::to_string(m_totalTime) + std::string(".vtu");
- vtkWriter.write(m_geomUnstructuredGrid, filePath, VTU);
+ vtkWriter.write(m_geomUnstructuredGrid, filePath, MeshFileType::VTU);
m_vtkTimeModulo += m_writeToOutputModulo;
m_vtkPreviousTime = m_totalTime;
diff --git a/Source/MeshIO/imstkMeshIO.cpp b/Source/MeshIO/imstkMeshIO.cpp
index 79663bb56f5d68ef668f49a6fd32b84b1c20e042..adb53e471231d1af1bef5c04b788edb9194ebc2e 100644
--- a/Source/MeshIO/imstkMeshIO.cpp
+++ b/Source/MeshIO/imstkMeshIO.cpp
@@ -29,9 +29,29 @@
#include "imstkVTKMeshIO.h"
#include <sys/stat.h>
+#include <unordered_map>
namespace imstk
{
+static std::unordered_map<std::string, MeshFileType> extToType =
+{
+ { "vtk", MeshFileType::VTK },
+ { "vtp", MeshFileType::VTP },
+ { "vtu", MeshFileType::VTU },
+ { "obj", MeshFileType::OBJ },
+ { "stl", MeshFileType::STL },
+ { "ply", MeshFileType::PLY },
+ { "dae", MeshFileType::DAE },
+ { "fbx", MeshFileType::FBX },
+ { "3ds", MeshFileType::_3DS },
+ { "veg", MeshFileType::VEG },
+ { "msh", MeshFileType::MSH },
+ { "dcm", MeshFileType::DCM },
+ { "nrrd", MeshFileType::NRRD },
+ { "nii", MeshFileType::NII },
+ { "mhd", MeshFileType::MHD }
+};
+
std::shared_ptr<PointSet>
MeshIO::read(const std::string& filePath)
{
@@ -54,6 +74,7 @@ MeshIO::read(const std::string& filePath)
case MeshFileType::NRRD:
case MeshFileType::NII:
case MeshFileType::DCM:
+ case MeshFileType::MHD:
return VTKMeshIO::read(filePath, meshType);
break;
case MeshFileType::OBJ:
@@ -68,7 +89,7 @@ MeshIO::read(const std::string& filePath)
case MeshFileType::MSH:
return MSHMeshIO::read(filePath, meshType);
break;
- case UNKNOWN:
+ case MeshFileType::UNKNOWN:
default:
break;
}
@@ -102,74 +123,20 @@ MeshIO::fileExists(const std::string& file, bool& isDirectory)
const MeshFileType
MeshIO::getFileType(const std::string& filePath)
{
- MeshFileType meshType = MeshFileType::UNKNOWN;
-
std::string extString = filePath.substr(filePath.find_last_of(".") + 1);
CHECK(!extString.empty()) << "MeshIO::getFileType error: invalid file name";
- if (extString == "vtk" || extString == "VTK")
- {
- meshType = MeshFileType::VTK;
- }
- else if (extString == "vtp" || extString == "VTP")
- {
- meshType = MeshFileType::VTP;
- }
- else if (extString == "vtu" || extString == "VTU")
- {
- meshType = MeshFileType::VTU;
- }
- else if (extString == "obj" || extString == "OBJ")
- {
- meshType = MeshFileType::OBJ;
- }
- else if (extString == "stl" || extString == "STL")
- {
- meshType = MeshFileType::STL;
- }
- else if (extString == "ply" || extString == "PLY")
- {
- meshType = MeshFileType::PLY;
- }
- else if (extString == "dae" || extString == "DAE")
- {
- meshType = MeshFileType::DAE;
- }
- else if (extString == "fbx" || extString == "FBX")
- {
- meshType = MeshFileType::FBX;
- }
- else if (extString == "3ds" || extString == "3DS")
- {
- meshType = MeshFileType::_3DS;
- }
- else if (extString == "veg" || extString == "VEG")
- {
- meshType = MeshFileType::VEG;
- }
- else if (extString == "msh" || extString == "MSH")
- {
- meshType = MeshFileType::MSH;
- }
- else if (extString == "dcm" || extString == "DCM")
- {
- meshType = MeshFileType::DCM;
- }
- else if (extString == "nrrd" || extString == "NRRD")
- {
- meshType = MeshFileType::NRRD;
- }
- else if (extString == "nii" || extString == "NII")
- {
- meshType = MeshFileType::NII;
- }
- else
+ // To lowercase
+ std::transform(extString.begin(), extString.end(), extString.begin(),
+ [](unsigned char c) { return std::tolower(static_cast<int>(c)); });
+
+ if (extToType.count(extString) == 0)
{
LOG(FATAL) << "MeshIO::getFileType error: unknown file extension";
}
- return meshType;
+ return extToType[extString];
}
bool
@@ -194,6 +161,7 @@ MeshIO::write(const std::shared_ptr<imstk::PointSet> imstkMesh, const std::strin
case MeshFileType::VTP:
case MeshFileType::STL:
case MeshFileType::PLY:
+ case MeshFileType::MHD:
return VTKMeshIO::write(imstkMesh, filePath, meshType);
break;
case MeshFileType::UNKNOWN:
diff --git a/Source/MeshIO/imstkMeshIO.h b/Source/MeshIO/imstkMeshIO.h
index 889ac9de5bf270d9d8b0af2ad44d795cb46640ee..3577b64d38ceaf7ede07db32258a3073ced48834 100644
--- a/Source/MeshIO/imstkMeshIO.h
+++ b/Source/MeshIO/imstkMeshIO.h
@@ -31,7 +31,7 @@ class PointSet;
///
/// \brief Enumeration the mesh file type
///
-enum MeshFileType
+enum class MeshFileType
{
UNKNOWN,
VTK,
@@ -47,7 +47,8 @@ enum MeshFileType
MSH,
NRRD,
DCM,
- NII
+ NII,
+ MHD
};
///
diff --git a/Source/MeshIO/imstkVTKMeshIO.cpp b/Source/MeshIO/imstkVTKMeshIO.cpp
index 2356f502bd41d4231a2cf92171910f1d93ba84d4..0997d2f99c04cd21fefb2d78363da9e1a16e7306 100644
--- a/Source/MeshIO/imstkVTKMeshIO.cpp
+++ b/Source/MeshIO/imstkVTKMeshIO.cpp
@@ -32,6 +32,8 @@
#include <vtkGenericDataObjectReader.h>
#include <vtkGenericDataObjectWriter.h>
#include <vtkImageData.h>
+#include <vtkMetaImageReader.h>
+#include <vtkMetaImageWriter.h>
#include <vtkNIFTIImageReader.h>
#include <vtkNIFTIImageWriter.h>
#include <vtkNrrdReader.h>
@@ -91,6 +93,10 @@ VTKMeshIO::read(const std::string& filePath, MeshFileType meshType)
{
return VTKMeshIO::readVtkImageDataNIFTI(filePath);
}
+ case MeshFileType::MHD:
+ {
+ return VTKMeshIO::readVtkImageData<vtkMetaImageReader>(filePath);
+ }
default:
{
LOG(FATAL) << "VTKMeshIO::read error: file type not supported";
@@ -110,6 +116,10 @@ VTKMeshIO::write(const std::shared_ptr<PointSet> imstkMesh, const std::string& f
{
return VTKMeshIO::writeVtkImageDataNIFTI(imgMesh, filePath);
}
+ case MeshFileType::MHD:
+ {
+ return VTKMeshIO::writeMetaImageData(imgMesh, filePath);
+ }
default:
LOG(WARNING) << "VTKMeshIO::write error: file type not supported for volumetric mesh.";
return false;
@@ -250,7 +260,14 @@ VTKMeshIO::writeVtkImageData(const std::shared_ptr<ImageData> imstkMesh, const s
int* dim = vtkMesh->GetDimensions();
auto writer = vtkSmartPointer<WriterType>::New();
- writer->SetFileDimensionality(3);
+ if (vtkMesh->GetDimensions()[2] == 1)
+ {
+ writer->SetFileDimensionality(2);
+ }
+ else
+ {
+ writer->SetFileDimensionality(3);
+ }
writer->SetInputData(vtkMesh);
writer->SetFileName(filePath.c_str());
writer->Write();
@@ -385,9 +402,6 @@ VTKMeshIO::writeVtkUnstructuredGrid(std::shared_ptr<HexahedralMesh> hMesh, const
return true;
}
-///
-/// \brief Reads vtk image data
-///
template<typename ReaderType>
std::shared_ptr<ImageData>
VTKMeshIO::readVtkImageData(const std::string& filePath)
@@ -400,9 +414,6 @@ VTKMeshIO::readVtkImageData(const std::string& filePath)
return imageData;
}
-///
-/// \brief Reads nifti/nii format image data
-///
std::shared_ptr<ImageData>
VTKMeshIO::readVtkImageDataNIFTI(const std::string& filePath)
{
@@ -415,9 +426,6 @@ VTKMeshIO::readVtkImageDataNIFTI(const std::string& filePath)
return imageData;
}
-///
-/// \brief Write nifti/nii format image data
-///
bool
VTKMeshIO::writeVtkImageDataNIFTI(std::shared_ptr<ImageData> imageData, const std::string& filePath)
{
@@ -431,9 +439,40 @@ VTKMeshIO::writeVtkImageDataNIFTI(std::shared_ptr<ImageData> imageData, const st
auto writer = vtkSmartPointer<vtkNIFTIImageWriter>::New();
writer->SetFileName(filePath.c_str());
- writer->SetFileDimensionality(3);
+ if (vtkMesh->GetDimensions()[2] == 1)
+ {
+ writer->SetFileDimensionality(2);
+ }
+ else
+ {
+ writer->SetFileDimensionality(3);
+ }
writer->SetInputData(vtkMesh);
writer->Update();
return true;
}
+
+bool
+VTKMeshIO::writeMetaImageData(std::shared_ptr<ImageData> imageData, const std::string& filePath)
+{
+ vtkSmartPointer<vtkImageData> vtkMesh = GeometryUtils::copyToVtkImageData(imageData);
+ if (!vtkMesh)
+ {
+ return false;
+ }
+
+ auto writer = vtkSmartPointer<vtkMetaImageWriter>::New();
+ if (vtkMesh->GetDimensions()[2] == 1)
+ {
+ writer->SetFileDimensionality(2);
+ }
+ else
+ {
+ writer->SetFileDimensionality(3);
+ }
+ writer->SetInputData(vtkMesh);
+ writer->SetFileName(filePath.c_str());
+ writer->SetRAWFileName((filePath + ".raw").c_str());
+ writer->Write();
+}
} // imstk
diff --git a/Source/MeshIO/imstkVTKMeshIO.h b/Source/MeshIO/imstkVTKMeshIO.h
index 92dbafda083db45a22578d26af6d9a24ba05707f..24b470ddcc399c7a8b0bcde3a1026e22e061cbe7 100644
--- a/Source/MeshIO/imstkVTKMeshIO.h
+++ b/Source/MeshIO/imstkVTKMeshIO.h
@@ -133,5 +133,10 @@ protected:
/// \brief Write nifti/nii format image data
///
static bool writeVtkImageDataNIFTI(std::shared_ptr<ImageData> imageData, const std::string& filePath);
+
+ ///
+ /// \brief Write meta/mhd format image data
+ ///
+ static bool writeMetaImageData(std::shared_ptr<ImageData> imageData, const std::string& filePath);
};
} // imstk