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dev #2

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chizeta merged 32 commits from dev into main 2024-02-02 20:36:53 +01:00
Conversation 0 Commits 32 Files changed 51 +241 -99
17 changed files with 241 additions and 99 deletions
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20
src/include/base/types.h
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@ -6,7 +6,7 @@
This file contains the declaration of all library types
Copyright (c) 2022 Christian Zimmermann. All rights reserved.
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
Mail: chizeta@f3l.de
**/
@ -28,9 +28,9 @@
namespace CNORXZ
{
/**********************
* standard types *
**********************/
/*====================+
| standard types |
=====================*/
typedef std::intptr_t PtrId;
typedef int32_t Int;
@ -80,9 +80,9 @@ namespace CNORXZ
template <SizeT N>
using CSizeT = std::integral_constant<SizeT,N>;
/*********************
* library types *
*********************/
/*===================+
| library types |
+===================*/
/***
Naming Prefixes:
@ -302,9 +302,9 @@ namespace CNORXZ
template <class CXpr>
class Contraction;
/*********************
* derived types *
*********************/
/*===================+
| derived types |
+===================*/
template <typename T>
using Vector = std::vector<T,Allocator<T>>;

10
src/opt/hdf5/include/h5_content_base.cc.h
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@ -1,3 +1,13 @@
// -*- C++ -*-
/**
@file opt/hdf5/include/h5_content_base.cc.h
@brief Implementation of template member functions of ContentBase
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
Mail: chizeta@f3l.de
**/
#ifndef __cxz_h5_content_base_cc_h__
#define __cxz_h5_content_base_cc_h__

5
src/opt/hdf5/include/h5_content_base.h
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@ -81,6 +81,11 @@ namespace CNORXZ
*/
virtual String filename() const = 0;
/** Check if group exists in the parent object.
@return True if object exists, else false.
*/
virtual bool exists() const = 0;
/** Get object name.
@return The name of this object.
*/

10
src/opt/hdf5/include/h5_dataset.cc.h
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@ -1,3 +1,13 @@
// -*- C++ -*-
/**
@file opt/hdf5/include/h5_dataset.cc.h
@brief Implementation of template member functions of Dataset and SDataset.
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
Mail: chizeta@f3l.de
**/
#ifndef __cxz_h5_dataset_cc_h__
#define __cxz_h5_dataset_cc_h__

61
src/opt/hdf5/include/h5_dataset.h
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@ -1,3 +1,13 @@
// -*- C++ -*-
/**
@file opt/hdf5/include/h5_dataset.h
@brief Dataset declaration.
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
Mail: chizeta@f3l.de
**/
#ifndef __cxz_h5_dataset_h__
#define __cxz_h5_dataset_h__
@ -9,11 +19,21 @@ namespace CNORXZ
{
namespace hdf5
{
/** ****
Class to handle hdf5 datasets.
*/
class Dataset : public ContentBase
{
public:
DEFAULT_MEMBERS(Dataset);
DEFAULT_MEMBERS(Dataset); /**< Default constructors and assignments. */
/** Construct the class.
@param _name Dataset name.
@param _parent Parent content object.
*/
Dataset(const String& name, const ContentBase* _parent);
/** Destructor. Release all involved hdf5 ids. */
~Dataset();
virtual ContentType type() const override final;
@ -22,32 +42,59 @@ namespace CNORXZ
virtual Dataset& close() override final;
virtual String path() const override final;
virtual String filename() const override final;
virtual bool exists() const override final;
bool exists() const;
/** Initalize the dataset.
@param dataRange A potentially multi-dimensional range characterizing the dataset.
@param type Data type id.
*/
Dataset& init(const RangePtr& dataRange, hid_t type);
/** Initalize the dataset.
@param data Array containing the dataset.
*/
template <typename T>
Dataset& init(const ArrayBase<T>& data);
/** Get the data range.
@return Pointer to the range.
*/
const RangePtr& dataRange() const;
protected:
RangePtr mDataRange;
hid_t mType;
hid_t mFilespace;
RangePtr mDataRange; /**< The data range. */
hid_t mType; /**< The data type identifier. */
hid_t mFilespace; /**< The hdf5 file space identifier. */
};
/** ****
Class to handle hdf5 datasets, the value type is known at compile time.
@tparam T Dataset value type.
*/
template <typename T>
class SDataset : public Dataset
{
public:
DEFAULT_MEMBERS(SDataset);
DEFAULT_MEMBERS(SDataset); /**< Default constructors and assignments. */
/** Construct the class.
@param _name Dataset name.
@param _parent Parent content object.
*/
SDataset(const String& name, const ContentBase* _parent);
/** Read the dataset.
@return Array containing the dataset values.
*/
MArray<T> read() const;
/** Read a given subset of the dataset.
The subset needs to be hypercubic.
@param beg Index indicating the begin edge of the hypercube.
@param end Index indicating the end edge of the hypercube (inclusive).
@return Array containing the dataset values.
*/
template <class I, typename M>
MArray<T> read(const IndexInterface<I,M>& beg, const IndexInterface<I,M>& end) const;

6
src/opt/hdf5/include/h5_file.h
View file

@ -47,8 +47,12 @@ namespace CNORXZ
virtual File& close() override final;
virtual String path() const override final;
virtual String filename() const override final;
virtual bool exists() const override final;
virtual Int exists() const override final;
/** Check if handled file is in hdf5 format.
@return True if file is in hdf5 format, else false.
*/
bool ishdf5() const;
private:
bool mRo = true;

30
src/opt/hdf5/include/h5_group.cc.h
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@ -1,3 +1,13 @@
// -*- C++ -*-
/**
@file opt/hdf5/include/h5_group.cc.h
@brief Implementation of template member functions of Group.
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
Mail: chizeta@f3l.de
**/
#ifndef __cxz_h5_group_cc_h__
#define __cxz_h5_group_cc_h__
@ -9,6 +19,26 @@ namespace CNORXZ
{
namespace hdf5
{
template <SizeT I, typename... Ts>
constexpr const auto& tget(const Tuple<Ts...>& t)
{
return std::get<sizeof...(Ts)-I-1>(t);
}
template <SizeT I, typename... Ts>
constexpr auto& tget(Tuple<Ts...>& t)
{
return std::get<sizeof...(Ts)-I-1>(t);
}
template <SizeT N, typename... Ts>
SizeT getTupleOffset(const Tuple<Ts...>& t, CSizeT<N> i)
{
const PtrId beg = reinterpret_cast<PtrId>(&t);
const PtrId pos = reinterpret_cast<PtrId>(&tget<i>(t));
return pos - beg;
}
template <typename... Ts>
Sptr<STable<Ts...>> Group::getTable(const String& name, Tuple<Ts...> proto)
{

6
src/opt/hdf5/include/h5_group.h
View file

@ -42,11 +42,7 @@ namespace CNORXZ
virtual Group& close() override;
virtual String path() const override;
virtual String filename() const override;
/** Check if group exists in the parent object.
@return 1 if group exists, 0 if not, -1 if an error occured.
*/
virtual Int exists() const; // TODO: virtual function of base class
virtual bool exists() const override;
/** Get object contained by this group.
@param name Object name.

10
src/opt/hdf5/include/h5_table.cc.h
View file

@ -1,3 +1,13 @@
// -*- C++ -*-
/**
@file opt/hdf5/include/h5_table.cc.h
@brief Implementation of template member functions of Table and STable.
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
Mail: chizeta@f3l.de
**/
#ifndef __cxz_h5_table_cc_h__
#define __cxz_h5_table_cc_h__

1
src/opt/hdf5/include/h5_table.h
View file

@ -44,6 +44,7 @@ namespace CNORXZ
virtual Table& close() override final;
virtual String path() const override final;
virtual String filename() const override final;
virtual bool exists() const override final;
/** Ininitialize table field names.
@param fnames Table field names.

50
src/opt/hdf5/include/h5_type_id.cc.h
View file

@ -1,3 +1,13 @@
// -*- C++ -*-
/**
@file opt/hdf5/include/h5_type_id.h
@brief TypeId template implementation.
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
Mail: chizeta@f3l.de
**/
#ifndef __cxz_h5_type_id_cc_h__
#define __cxz_h5_type_id_cc_h__
@ -8,37 +18,9 @@ namespace CNORXZ
{
namespace hdf5
{
template <typename... Ts>
decltype(auto) reverseTuple(const Tuple<Ts...>& t)
{
return iter<0,sizeof...(Ts)>
( [&](auto i) { return tget<i>(t); },
[](const auto&... e) { return std::make_tuple(e...); } );
}
template <SizeT I, typename... Ts>
constexpr const auto& tget(const Tuple<Ts...>& t)
{
return std::get<sizeof...(Ts)-I-1>(t);
}
template <SizeT I, typename... Ts>
constexpr auto& tget(Tuple<Ts...>& t)
{
return std::get<sizeof...(Ts)-I-1>(t);
}
template <SizeT N, typename... Ts>
SizeT getTupleOffset(const Tuple<Ts...>& t, CSizeT<N> i)
{
const PtrId beg = reinterpret_cast<PtrId>(&t);
const PtrId pos = reinterpret_cast<PtrId>(&tget<i>(t));
return pos - beg;
}
/**************
* TypeId *
**************/
/*============+
| TypeId |
+============*/
template <typename T>
inline hid_t TypeId<T>::get()
@ -68,9 +50,9 @@ namespace CNORXZ
return arrtype;
}
/*****************
* getTypeId *
*****************/
/*===============+
| getTypeId |
+===============*/
template <typename T>
hid_t getTypeId(T x)

78
src/opt/hdf5/include/h5_type_id.h
View file

@ -1,3 +1,13 @@
// -*- C++ -*-
/**
@file opt/hdf5/include/h5_type_id.h
@brief TypeId template declaration.
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
Mail: chizeta@f3l.de
**/
#ifndef __cxz_h5_type_id_h__
#define __cxz_h5_type_id_h__
@ -8,43 +18,57 @@ namespace CNORXZ
{
namespace hdf5
{
template <typename... Ts>
decltype(auto) reverseTuple(const Tuple<Ts...>& t);
template <typename... Ts>
using RTuple = typename std::remove_reference<decltype(reverseTuple(Tuple<Ts...>()))>::type;
template <SizeT I, typename... Ts>
constexpr const auto& tget(const Tuple<Ts...>& t);
template <SizeT I, typename... Ts>
constexpr auto& tget(Tuple<Ts...>& t);
template <SizeT N, typename... Ts>
SizeT getTupleOffset(const Tuple<Ts...>& t, CSizeT<N> i);
/**************
* TypeId *
**************/
/** ****
Get a valid hdf5 id for a given type.
Return 0 if not implemented.
@tparam T The type.
*/
template <typename T>
struct TypeId { static inline hid_t get(); };
struct TypeId
{
/** Get the type id. */
static inline hid_t get();
};
/** Specialization of TypeId for SizeT. */
template <>
struct TypeId<SizeT> { static inline hid_t get(); };
struct TypeId<SizeT>
{
/** Get the type id for SizeT. */
static inline hid_t get();
};
/** Specialization of TypeId for Int. */
template <>
struct TypeId<Int> { static inline hid_t get(); };
struct TypeId<Int>
{
/** Get the type id for Int. */
static inline hid_t get();
};
/** Specialization of TypeId for Double. */
template <>
struct TypeId<Double> { static inline hid_t get(); };
struct TypeId<Double>
{
/** Get the type id for Double. */
static inline hid_t get();
};
/** Specialization of TypeId for an array
@tparam T Element type.
@tparam N Array size.
*/
template <typename T, SizeT N>
struct TypeId<Arr<T,N>> { static inline hid_t get(); };
/*****************
* getTypeId *
*****************/
struct TypeId<Arr<T,N>>
{
/** Get the type id for the given array. */
static inline hid_t get();
};
/** Wrapper function for TypeId::get()
@param Variable of given type.
@return A type id of the input variable's type.
*/
template <typename T>
hid_t getTypeId(T x);
}

12
src/opt/hdf5/include/h5_types.h
View file

@ -1,3 +1,15 @@
// -*- C++ -*-
/**
@file opt/hdf5/include/types.h
@brief Declaration of hdf5 related library types
This file contains the declaration of all hdf5 related library types
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
Mail: chizeta@f3l.de
**/
#ifndef __h5_types_h__
#define __h5_types_h__

22
src/opt/hdf5/lib/h5_file.cc
View file

@ -33,7 +33,7 @@ namespace CNORXZ
}
Int ex = this->exists();
const String fn = this->filename();
CXZ_ASSERT( ex != 2, "tried to open non-h5 file '" << fn << "'" );
CXZ_ASSERT( ishdf5(), "tried to open non-h5 file '" << fn << "'" );
if(mRo){
CXZ_ASSERT( ex == 1, "could not open file as read-only: '"
<< fn << "' does not exist'");
@ -79,21 +79,25 @@ namespace CNORXZ
return name();
}
Int File::exists() const
bool File::exists() const
{
Int ex = 0;
bool ex = false;
std::ifstream fs(this->filename().c_str(), std::ios_base::binary);
if(fs.good()){
ex = 1; // file exists
ex = true; // file exists
}
fs.close();
if(ex != 0){
if(H5Fis_hdf5(this->filename().c_str()) <= 0){
ex = 2; // file not in h5 format
}
}
return ex;
}
bool File::ishdf5() const
{
if(exists()){
if(H5Fis_hdf5(this->filename().c_str()) <= 0){
return false;
}
}
return true; // a non-existing file can be created in hdf5 format
}
}
}

4
src/opt/hdf5/lib/h5_group.cc
View file

@ -69,9 +69,9 @@ namespace CNORXZ
return String();
}
Int Group::exists() const
bool Group::exists() const
{
return H5Lexists(mParent->id(), mName.c_str(), H5P_DEFAULT) != 0 ? 1 : 0;
return H5Lexists(mParent->id(), mName.c_str(), H5P_DEFAULT) != 0;
}
const ContentPtr& Group::get(const String& name) const

9
src/opt/hdf5/lib/h5_table.cc
View file

@ -9,7 +9,7 @@ namespace CNORXZ
Table::Table(const String& name, const ContentBase* _parent) :
ContentBase(name, _parent)
{
if(H5Lexists(mParent->id(), mName.c_str(), H5P_DEFAULT)){
if(exists()){
hsize_t nfields = 0;
hsize_t nrecords = 0;
H5TBget_table_info(mParent->id(), mName.c_str(), &nfields, &nrecords);
@ -90,6 +90,13 @@ namespace CNORXZ
return mParent->filename();
}
bool Table::exists() const
{
htri_t x = H5Lexists(mParent->id(), mName.c_str(), H5P_DEFAULT);
VCHECK(x);
return x;
}
Table& Table::initFieldNames(const Vector<String>& fnames)
{
CXZ_ASSERT(mFields == nullptr, "fields already initialized");

2
src/opt/hdf5/tests/h5_basic_unit_test.cc
View file

@ -58,7 +58,7 @@ namespace
CIndex j(fs);
for(i = 0; i.lex() != rs->size(); ++i){
iter<0,3>( [&](auto jj)
{ j = jj; mTabD[i*j] = DType(tget<jj>(v[i.lex()])); }, NoF{} );
{ j = jj; mTabD[i*j] = DType(std::get<3-jj-1>(v[i.lex()])); }, NoF{} );
}
const SizeT ddim = 5;