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xregHDF5.h
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/*
* MIT License
*
* Copyright (c) 2020-2021 Robert Grupp
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*/
#ifndef XREGHDF5_H_
#define XREGHDF5_H_
#include <array>
#include <fmt/format.h>
#include <H5Cpp.h>
#include "xregCommon.h"
#include "xregAssert.h"
#include "xregExceptionUtils.h"
#include "xregITKBasicImageUtils.h"
namespace xreg
{
template <class T>
H5::DataType LookupH5DataType();
// This is the same as unsigned int
//template <>
//inline H5::DataType LookupH5DataType<hbool_t>()
//{
// return H5::PredType::NATIVE_HBOOL;
//}
template <>
inline H5::DataType LookupH5DataType<char>()
{
return H5::PredType::NATIVE_CHAR;
}
template <>
inline H5::DataType LookupH5DataType<short>()
{
return H5::PredType::NATIVE_SHORT;
}
template <>
inline H5::DataType LookupH5DataType<int>()
{
return H5::PredType::NATIVE_INT;
}
template <>
inline H5::DataType LookupH5DataType<long>()
{
return H5::PredType::NATIVE_LONG;
}
template <>
inline H5::DataType LookupH5DataType<unsigned char>()
{
return H5::PredType::NATIVE_UCHAR;
}
template <>
inline H5::DataType LookupH5DataType<unsigned short>()
{
return H5::PredType::NATIVE_USHORT;
}
template <>
inline H5::DataType LookupH5DataType<unsigned int>()
{
return H5::PredType::NATIVE_UINT;
}
template <>
inline H5::DataType LookupH5DataType<unsigned long>()
{
return H5::PredType::NATIVE_ULONG;
}
template <>
inline H5::DataType LookupH5DataType<float>()
{
return H5::PredType::NATIVE_FLOAT;
}
template <>
inline H5::DataType LookupH5DataType<double>()
{
return H5::PredType::NATIVE_DOUBLE;
}
template <>
inline H5::DataType LookupH5DataType<std::string>()
{
H5::StrType str_type(H5::PredType::C_S1);
str_type.setSize(H5T_VARIABLE);
return str_type;
}
#ifdef _WIN32
template <>
inline H5::DataType LookupH5DataType<unsigned long long>()
{
return H5::PredType::NATIVE_ULLONG;
}
#endif
void SetScalarAttr(const std::string& key, const long val, H5::Group* h5);
long GetScalarLongAttr(const std::string& key, const H5::Group& h5);
H5::DataType GetH5StringDataType();
H5::DataType GetH5StringDataType(const std::string& s);
bool SetStringAttr(const std::string& key, const std::string& val, H5::Group* h5);
std::string GetStringAttr(const std::string& key, const H5::Group& h5);
H5::DataSet WriteStringH5(const std::string& field_name,
const std::string& field_val,
H5::Group* h5,
const bool compress = false);
H5::DataSet WriteSingleScalarH5(const std::string& field_name,
const unsigned char& field_val,
H5::Group* h5);
H5::DataSet WriteSingleScalarH5(const std::string& field_name,
const char& field_val,
H5::Group* h5);
H5::DataSet WriteSingleScalarH5(const std::string& field_name,
const unsigned short& field_val,
H5::Group* h5);
H5::DataSet WriteSingleScalarH5(const std::string& field_name,
const short& field_val,
H5::Group* h5);
H5::DataSet WriteSingleScalarH5(const std::string& field_name,
const unsigned int& field_val,
H5::Group* h5);
H5::DataSet WriteSingleScalarH5(const std::string& field_name,
const int& field_val,
H5::Group* h5);
H5::DataSet WriteSingleScalarH5(const std::string& field_name,
const unsigned long& field_val,
H5::Group* h5);
H5::DataSet WriteSingleScalarH5(const std::string& field_name,
const long& field_val,
H5::Group* h5);
H5::DataSet WriteSingleScalarH5(const std::string& field_name,
const float& field_val,
H5::Group* h5);
H5::DataSet WriteSingleScalarH5(const std::string& field_name,
const double& field_val,
H5::Group* h5);
H5::DataSet WriteSingleScalarH5(const std::string& field_name,
const bool& field_val,
H5::Group* h5);
#ifdef _WIN32
H5::DataSet WriteSingleScalarH5(const std::string& field_name,
const size_type& field_val,
H5::Group* h5);
#endif
H5::DataSet CreateVectorH5UChar(const std::string& field_name,
const unsigned long len,
H5::Group* h5,
const bool compress = true);
H5::DataSet CreateVectorH5Char(const std::string& field_name,
const unsigned long len,
H5::Group* h5,
const bool compress = true);
H5::DataSet CreateVectorH5UShort(const std::string& field_name,
const unsigned long len,
H5::Group* h5,
const bool compress = true);
H5::DataSet CreateVectorH5Short(const std::string& field_name,
const unsigned long len,
H5::Group* h5,
const bool compress = true);
H5::DataSet CreateVectorH5UInt(const std::string& field_name,
const unsigned long len,
H5::Group* h5,
const bool compress = true);
H5::DataSet CreateVectorH5Int(const std::string& field_name,
const unsigned long len,
H5::Group* h5,
const bool compress = true);
H5::DataSet CreateVectorH5ULong(const std::string& field_name,
const unsigned long len,
H5::Group* h5,
const bool compress = true);
H5::DataSet CreateVectorH5Long(const std::string& field_name,
const unsigned long len,
H5::Group* h5,
const bool compress = true);
H5::DataSet CreateVectorH5Float(const std::string& field_name,
const unsigned long len,
H5::Group* h5,
const bool compress = true);
H5::DataSet CreateVectorH5Double(const std::string& field_name,
const unsigned long len,
H5::Group* h5,
const bool compress = true);
H5::DataSet CreateVectorH5Bool(const std::string& field_name,
const unsigned long len,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteVectorH5(const std::string& field_name,
const std::vector<unsigned char>& v,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteVectorH5(const std::string& field_name,
const std::vector<char>& v,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteVectorH5(const std::string& field_name,
const std::vector<unsigned short>& v,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteVectorH5(const std::string& field_name,
const std::vector<short>& v,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteVectorH5(const std::string& field_name,
const std::vector<unsigned int>& v,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteVectorH5(const std::string& field_name,
const std::vector<int>& v,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteVectorH5(const std::string& field_name,
const std::vector<unsigned long>& v,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteVectorH5(const std::string& field_name,
const std::vector<long>& v,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteVectorH5(const std::string& field_name,
const std::vector<float>& v,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteVectorH5(const std::string& field_name,
const std::vector<double>& v,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteVectorH5(const std::string& field_name,
const std::vector<bool>& v,
H5::Group* h5,
const bool compress = true);
#ifdef _WIN32
H5::DataSet WriteVectorH5(const std::string& field_name,
const std::vector<size_type>& v,
H5::Group* h5,
const bool compress = true);
#endif
void WriteVectorElemH5(const unsigned char& x, const unsigned long i, H5::DataSet* h5);
void WriteVectorElemH5(const char& x, const unsigned long i, H5::DataSet* h5);
void WriteVectorElemH5(const unsigned short& x, const unsigned long i, H5::DataSet* h5);
void WriteVectorElemH5(const short& x, const unsigned long i, H5::DataSet* h5);
void WriteVectorElemH5(const unsigned int& x, const unsigned long i, H5::DataSet* h5);
void WriteVectorElemH5(const int& x, const unsigned long i, H5::DataSet* h5);
void WriteVectorElemH5(const unsigned long& x, const unsigned long i, H5::DataSet* h5);
void WriteVectorElemH5(const long& x, const unsigned long i, H5::DataSet* h5);
void WriteVectorElemH5(const float& x, const unsigned long i, H5::DataSet* h5);
void WriteVectorElemH5(const double& x, const unsigned long i, H5::DataSet* h5);
void WriteVectorElemH5(const bool& x, const unsigned long i, H5::DataSet* h5);
H5::DataSet CreateMatrixH5Float(const std::string& field_name,
const unsigned long num_rows,
const unsigned long num_cols,
H5::Group* h5,
const bool compress = true);
H5::DataSet CreateMatrixH5Double(const std::string& field_name,
const unsigned long num_rows,
const unsigned long num_cols,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteMatrixH5(const std::string& field_name,
const Pt2& mat,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteMatrixH5(const std::string& field_name,
const Pt3& mat,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteMatrixH5(const std::string& field_name,
const Pt4& mat,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteMatrixH5(const std::string& field_name,
const Pt5& mat,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteMatrixH5(const std::string& field_name,
const Pt6& mat,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteMatrixH5(const std::string& field_name,
const PtN& mat,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteMatrixH5(const std::string& field_name,
const Mat2x2& mat,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteMatrixH5(const std::string& field_name,
const Mat3x3& mat,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteMatrixH5(const std::string& field_name,
const Mat4x4& mat,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteMatrixH5(const std::string& field_name,
const Mat3x4& mat,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteMatrixH5(const std::string& field_name,
const MatMxN& mat,
H5::Group* h5,
const bool compress = true);
void WriteMatrixRowH5(const float* row_buf, const unsigned long row_idx, H5::DataSet* h5);
void WriteMatrixRowH5(const double* row_buf, const unsigned long row_idx, H5::DataSet* h5);
H5::DataSet WriteAffineTransform4x4(const std::string& field_name,
const FrameTransform& xform,
H5::Group* h5,
const bool compress = true);
void WriteImageH5(const itk::Image<unsigned char,2>* img,
H5::Group* h5,
const bool compress = true);
void WriteImageH5(const itk::Image<unsigned short,2>* img,
H5::Group* h5,
const bool compress = true);
void WriteImageH5(const itk::Image<short,2>* img,
H5::Group* h5,
const bool compress = true);
void WriteImageH5(const itk::Image<float,2>* img,
H5::Group* h5,
const bool compress = true);
void WriteImageH5(const itk::Image<double,2>* img,
H5::Group* h5,
const bool compress = true);
void WriteImageH5(const itk::Image<unsigned char,3>* img,
H5::Group* h5,
const bool compress = true);
void WriteImageH5(const itk::Image<unsigned short,3>* img,
H5::Group* h5,
const bool compress = true);
void WriteImageH5(const itk::Image<short,3>* img,
H5::Group* h5,
const bool compress = true);
void WriteImageH5(const itk::Image<float,3>* img,
H5::Group* h5,
const bool compress = true);
void WriteImageH5(const itk::Image<double,3>* img,
H5::Group* h5,
const bool compress = true);
void WriteSegImageH5(const itk::Image<unsigned char,2>* img,
H5::Group* h5,
const std::unordered_map<unsigned char,std::string>& seg_labels_def = std::unordered_map<unsigned char,std::string>(),
const bool compress = true);
void WriteSegImageH5(const itk::Image<unsigned short,2>* img,
H5::Group* h5,
const std::unordered_map<unsigned short,std::string>& seg_labels_def = std::unordered_map<unsigned short,std::string>(),
const bool compress = true);
void WriteSegImageH5(const itk::Image<unsigned char,3>* img,
H5::Group* h5,
const std::unordered_map<unsigned char,std::string>& seg_labels_def = std::unordered_map<unsigned char,std::string>(),
const bool compress = true);
void WriteSegImageH5(const itk::Image<unsigned short,3>* img,
H5::Group* h5,
const std::unordered_map<unsigned short,std::string>& seg_labels_def = std::unordered_map<unsigned short,std::string>(),
const bool compress = true);
void WriteLandmarksMapH5(const LandMap2& m, H5::Group* h5);
void WriteLandmarksMapH5(const LandMap3& m, H5::Group* h5);
void WriteLandmarksMapH5(const LandMap4& m, H5::Group* h5);
H5::DataSet WriteListOfPointsAsMatrixH5(const std::string& field_name,
const Pt2List& pts,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteListOfPointsAsMatrixH5(const std::string& field_name,
const Pt3List& pts,
H5::Group* h5,
const bool compress = true);
H5::DataSet WriteListOfArraysToMatrixH5(const std::string& field_name,
const std::vector<std::array<size_type,3>>& arrays,
H5::Group* h5,
const bool compress = true);
std::string ReadStringH5(const std::string& field_name,
const H5::Group& h5);
unsigned char ReadSingleScalarH5UChar(const std::string& field_name,
const H5::Group& h5);
char ReadSingleScalarH5Char(const std::string& field_name,
const H5::Group& h5);
unsigned short ReadSingleScalarH5UShort(const std::string& field_name,
const H5::Group& h5);
short ReadSingleScalarH5Short(const std::string& field_name,
const H5::Group& h5);
unsigned int ReadSingleScalarH5UInt(const std::string& field_name,
const H5::Group& h5);
int ReadSingleScalarH5Int(const std::string& field_name,
const H5::Group& h5);
unsigned long ReadSingleScalarH5ULong(const std::string& field_name,
const H5::Group& h5);
long ReadSingleScalarH5Long(const std::string& field_name,
const H5::Group& h5);
float ReadSingleScalarH5Float(const std::string& field_name,
const H5::Group& h5);
double ReadSingleScalarH5Double(const std::string& field_name,
const H5::Group& h5);
bool ReadSingleScalarH5Bool(const std::string& field_name,
const H5::Group& h5);
CoordScalar ReadSingleScalarH5CoordScalar(const std::string& field_name,
const H5::Group& h5);
std::vector<unsigned char>
ReadVectorH5UChar(const std::string& field_name, const H5::Group& h5);
std::vector<char>
ReadVectorH5Char(const std::string& field_name, const H5::Group& h5);
std::vector<unsigned short>
ReadVectorH5UShort(const std::string& field_name, const H5::Group& h5);
std::vector<short>
ReadVectorH5Short(const std::string& field_name, const H5::Group& h5);
std::vector<unsigned int>
ReadVectorH5UInt(const std::string& field_name, const H5::Group& h5);
std::vector<int>
ReadVectorH5Int(const std::string& field_name, const H5::Group& h5);
std::vector<unsigned long>
ReadVectorH5ULong(const std::string& field_name, const H5::Group& h5);
std::vector<long>
ReadVectorH5Long(const std::string& field_name, const H5::Group& h5);
std::vector<float>
ReadVectorH5Float(const std::string& field_name, const H5::Group& h5);
std::vector<double>
ReadVectorH5Double(const std::string& field_name, const H5::Group& h5);
std::vector<bool>
ReadVectorH5Bool(const std::string& field_name, const H5::Group& h5);
std::vector<CoordScalar>
ReadVectorH5CoordScalar(const std::string& field_name, const H5::Group& h5);
std::vector<size_type>
ReadVectorH5SizeType(const std::string& field_name, const H5::Group& h5);
MatMxN ReadMatrixH5CoordScalar(const std::string& field_name, const H5::Group& h5);
MatMxN ReadMatrixH5Float(const std::string& field_name, const H5::Group& h5);
MatMxN_d ReadMatrixH5Double(const std::string& field_name, const H5::Group& h5);
FrameTransform
ReadAffineTransform4x4H5(const std::string& field_name,
const H5::Group& h5);
itk::Image<unsigned char,2>::Pointer
ReadITKImageH5UChar2D(const H5::Group& h5);
itk::Image<char,2>::Pointer
ReadITKImageH5Char2D(const H5::Group& h5);
itk::Image<unsigned short,2>::Pointer
ReadITKImageH5UShort2D(const H5::Group& h5);
itk::Image<short,2>::Pointer
ReadITKImageH5Short2D(const H5::Group& h5);
itk::Image<float,2>::Pointer
ReadITKImageH5Float2D(const H5::Group& h5);
itk::Image<double,2>::Pointer
ReadITKImageH5Double2D(const H5::Group& h5);
itk::Image<unsigned char,3>::Pointer
ReadITKImageH5UChar3D(const H5::Group& h5);
itk::Image<char,3>::Pointer
ReadITKImageH5Char3D(const H5::Group& h5);
itk::Image<unsigned short,3>::Pointer
ReadITKImageH5UShort3D(const H5::Group& h5);
itk::Image<short,3>::Pointer
ReadITKImageH5Short3D(const H5::Group& h5);
itk::Image<float,3>::Pointer
ReadITKImageH5Float3D(const H5::Group& h5);
itk::Image<double,3>::Pointer
ReadITKImageH5Double3D(const H5::Group& h5);
LandMap2 ReadLandmarksMapH5Pt2(const H5::Group& h5);
LandMap3 ReadLandmarksMapH5Pt3(const H5::Group& h5);
LandMap4 ReadLandmarksMapH5Pt4(const H5::Group& h5);
Pt2List ReadLandsAsPtCloudH5Pt2(const H5::Group& h5);
Pt3List ReadLandsAsPtCloudH5Pt3(const H5::Group& h5);
Pt4List ReadLandsAsPtCloudH5Pt4(const H5::Group& h5);
Pt2List
ReadListOfPointsFromMatrixH5Pt2(const std::string& field_name, const H5::Group& h5);
Pt3List
ReadListOfPointsFromMatrixH5Pt3(const std::string& field_name, const H5::Group& h5);
Pt4List
ReadListOfPointsFromMatrixH5Pt4(const std::string& field_name, const H5::Group& h5);
PtNList
ReadListOfPointsFromMatrixH5PtN(const std::string& field_name, const H5::Group& h5);
std::vector<std::array<size_type,3>>
ReadListOfArraysFromMatrixH5Sizes3(const std::string& field_name, const H5::Group& h5);
/// \brief Return a list of item names in a file/group
std::vector<std::string> GetH5ObjNames(const H5::Group& h5);
/// \brief Check to see if an object exists in a group
bool ObjectInGroupH5(const std::string& obj_name, const H5::Group& h5);
/// \brief Open a group if it already exists or create one
H5::Group OpenOrCreateGroupH5(const std::string& group_name, H5::Group* h5);
/// \brief Get lists of names groups and datasets which are direct children of this group/file.
///
/// The first tuple element is the list of group names, the second is the list of dataset names.
std::tuple<std::vector<std::string>,std::vector<std::string>>
GetH5GroupAndDatasetNames(const H5::Group& h5);
/// \brief Instance of this object will disable printing of HDF5 exceptions
/// while in scope.
class HideH5ExceptionPrints
{
public:
HideH5ExceptionPrints();
~HideH5ExceptionPrints();
HideH5ExceptionPrints(const HideH5ExceptionPrints&) = delete;
HideH5ExceptionPrints& operator=(const HideH5ExceptionPrints&) = delete;
private:
H5E_auto2_t auto_print_fn;
void* auto_print_data = nullptr;
};
} // xreg
#endif