WIP: hdf5 documentation
All checks were successful
ci/woodpecker/push/woodpecker Pipeline was successful
All checks were successful
ci/woodpecker/push/woodpecker Pipeline was successful
This commit is contained in:
parent
eb3055ddca
commit
be3f5521e8
8 changed files with 317 additions and 33 deletions
|
@ -2,10 +2,9 @@
|
|||
/**
|
||||
|
||||
@file include/ranges/ranges.h
|
||||
@brief ...
|
||||
@brief Ranges main header
|
||||
|
||||
|
||||
Copyright (c) 2022 Christian Zimmermann. All rights reserved.
|
||||
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
|
||||
Mail: chizeta@f3l.de
|
||||
|
||||
**/
|
||||
|
|
|
@ -1,3 +1,13 @@
|
|||
// -*- C++ -*-
|
||||
/**
|
||||
|
||||
@file opt/hdf5/include/cnorxz_hdf5.cc.h
|
||||
@brief CNORXZ HDF5 template sources header
|
||||
|
||||
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
|
||||
Mail: chizeta@f3l.de
|
||||
|
||||
**/
|
||||
|
||||
#include "h5_content_base.cc.h"
|
||||
#include "h5_type_id.cc.h"
|
||||
|
|
|
@ -1,3 +1,13 @@
|
|||
// -*- C++ -*-
|
||||
/**
|
||||
|
||||
@file opt/hdf5/include/cnorxz_hdf5.h
|
||||
@brief CNORXZ HDF5 main header
|
||||
|
||||
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
|
||||
Mail: chizeta@f3l.de
|
||||
|
||||
**/
|
||||
|
||||
#include "h5_content_base.h"
|
||||
#include "h5_file.h"
|
||||
|
|
|
@ -1,3 +1,13 @@
|
|||
// -*- C++ -*-
|
||||
/**
|
||||
|
||||
@file opt/hdf5/include/h5_content_base.h
|
||||
@brief Abstract content base class declaration
|
||||
|
||||
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
|
||||
Mail: chizeta@f3l.de
|
||||
|
||||
**/
|
||||
|
||||
#ifndef __cxz_h5_content_base_h__
|
||||
#define __cxz_h5_content_base_h__
|
||||
|
@ -11,50 +21,123 @@ namespace CNORXZ
|
|||
namespace hdf5
|
||||
{
|
||||
// TODO: IO save error handling !!!
|
||||
|
||||
|
||||
/** *****
|
||||
Enum indicating the content type.
|
||||
Used by ContainerBase derivates to indicate the derived type.
|
||||
*/
|
||||
enum class ContentType {
|
||||
ATTR = 1,
|
||||
FILE = 2,
|
||||
GROUP = 3,
|
||||
DSET = 4,
|
||||
TABLE = 5,
|
||||
VALUE = 6,
|
||||
NONE = 0,
|
||||
FILE = 1,
|
||||
GROUP = 2,
|
||||
DSET = 3,
|
||||
TABLE = 4,
|
||||
};
|
||||
|
||||
|
||||
/** ****
|
||||
Abstract base class for handling hdf5 objects.
|
||||
*/
|
||||
class ContentBase
|
||||
{
|
||||
public:
|
||||
DEFAULT_MEMBERS(ContentBase);
|
||||
DEFAULT_MEMBERS(ContentBase); /**< Default constructors and assignments. */
|
||||
|
||||
/** Construct the class.
|
||||
@param _name Content name.
|
||||
@param _parent Parent content object. Leave null for the root object.
|
||||
*/
|
||||
ContentBase(const String& _name, const ContentBase* _parent = nullptr);
|
||||
|
||||
/** Virtual default destructor. */
|
||||
virtual ~ContentBase() = default;
|
||||
|
||||
/** Get the content type.
|
||||
@return Content type.
|
||||
*/
|
||||
virtual ContentType type() const = 0;
|
||||
|
||||
/** Check if in read-only mode
|
||||
@return True if read-only else false.
|
||||
*/
|
||||
virtual bool ro() const = 0;
|
||||
|
||||
/** Open object.
|
||||
@return Reference to this object.
|
||||
*/
|
||||
virtual ContentBase& open() = 0;
|
||||
|
||||
/** Close object.
|
||||
@return Reference to this object.
|
||||
*/
|
||||
virtual ContentBase& close() = 0;
|
||||
|
||||
/** Get object path.
|
||||
@return Absolute hdf5 file internal path of this object.
|
||||
*/
|
||||
virtual String path() const = 0;
|
||||
|
||||
/** Get the file name.
|
||||
@return Name of the hdf5 file this object is stored in.
|
||||
*/
|
||||
virtual String filename() const = 0;
|
||||
|
||||
/** Get object name.
|
||||
@return The name of this object.
|
||||
*/
|
||||
const String& name() const;
|
||||
const ContentBase* parent() const;
|
||||
RangePtr range() const;
|
||||
hid_t id() const;
|
||||
inline bool isOpen() const { return mId != 0; }
|
||||
|
||||
/** Get parent object.
|
||||
@return Pointer to the parent of this object.
|
||||
*/
|
||||
const ContentBase* parent() const;
|
||||
|
||||
/** Get object id.
|
||||
@return hdf5 id of the h5 object maintained by this object.
|
||||
*/
|
||||
hid_t id() const;
|
||||
|
||||
/** Check if object is open, i.e. if there is a valid hdf5 id.
|
||||
@return True if object is open else false.
|
||||
*/
|
||||
bool isOpen() const;
|
||||
|
||||
/** Add attribute to this object.
|
||||
@tparam T Attribute value type.
|
||||
@param name Attribute name.
|
||||
@param value Attribute value.
|
||||
*/
|
||||
template <typename T>
|
||||
ContentBase& addAttribute(const String& name, const T& value);
|
||||
|
||||
/** Get an attribute of this object.
|
||||
@param name Attribute name.
|
||||
@return The attribute value as DType.
|
||||
*/
|
||||
DType getAttribute(const String& name) const;
|
||||
|
||||
/** Check if attribute of given name exists in this object.
|
||||
@param name Attribute name.
|
||||
@return True if attribute exists else false.
|
||||
*/
|
||||
bool attributeExists(const String& name) const;
|
||||
|
||||
/** Get all attributes of this object.
|
||||
@return Std map of key-value pairs.
|
||||
*/
|
||||
std::map<String,DType> getAttributes() const;
|
||||
|
||||
/** Get all attributes of this object and all its parent objects, recursively.
|
||||
@return Std map of key-value pairs.
|
||||
*/
|
||||
std::map<String,DType> getRecursiveAttributes() const; // + all parent's attributes
|
||||
|
||||
protected:
|
||||
String mName;
|
||||
const ContentBase* mParent = nullptr;
|
||||
RangePtr mRange;
|
||||
hid_t mId = 0;
|
||||
String mName; /**< Name of this object. */
|
||||
const ContentBase* mParent = nullptr; /**< Pointer to this object's parent. */
|
||||
hid_t mId = 0; /**< hdf5 identifier of the hdf5 object handled by this object. */
|
||||
};
|
||||
|
||||
/** Shortcut for a shared pointer to an abstract content object. */
|
||||
typedef Sptr<ContentBase> ContentPtr;
|
||||
|
||||
}
|
||||
|
|
|
@ -1,3 +1,13 @@
|
|||
// -*- C++ -*-
|
||||
/**
|
||||
|
||||
@file opt/hdf5/include/h5_file.h
|
||||
@brief Group declaration.
|
||||
|
||||
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
|
||||
Mail: chizeta@f3l.de
|
||||
|
||||
**/
|
||||
|
||||
#ifndef __cxz_h5_file_h__
|
||||
#define __cxz_h5_file_h__
|
||||
|
@ -10,14 +20,25 @@ namespace CNORXZ
|
|||
{
|
||||
namespace hdf5
|
||||
{
|
||||
// maybe introduce abstraction layer between as base for File and Group
|
||||
/** ****
|
||||
Class to handle hdf5 file objects.
|
||||
Objects of this type usually serve as root object
|
||||
so they don't have any parent.
|
||||
*/
|
||||
class File : public Group
|
||||
{
|
||||
public:
|
||||
typedef URange<String> RangeT;
|
||||
|
||||
DEFAULT_MEMBERS(File);
|
||||
DEFAULT_MEMBERS(File); /**< Default constructors and assignments. */
|
||||
|
||||
/** Construct the class.
|
||||
@param _name Path to the hdf5 file to be handled.
|
||||
@param _ro Open in read-only mode if true, otherwise have write access.
|
||||
*/
|
||||
File(const String& fname, bool _ro = true);
|
||||
|
||||
/** Destructor. Release all involved hdf5 ids. */
|
||||
~File();
|
||||
|
||||
virtual ContentType type() const override final;
|
||||
|
|
|
@ -1,3 +1,13 @@
|
|||
// -*- C++ -*-
|
||||
/**
|
||||
|
||||
@file opt/hdf5/include/h5_group.h
|
||||
@brief Group declaration.
|
||||
|
||||
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
|
||||
Mail: chizeta@f3l.de
|
||||
|
||||
**/
|
||||
|
||||
#ifndef __cxz_h5_group_h__
|
||||
#define __cxz_h5_group_h__
|
||||
|
@ -9,11 +19,21 @@ namespace CNORXZ
|
|||
{
|
||||
namespace hdf5
|
||||
{
|
||||
/** ****
|
||||
Class to handle hdf5 groups.
|
||||
*/
|
||||
class Group : public ContentBase
|
||||
{
|
||||
public:
|
||||
DEFAULT_MEMBERS(Group);
|
||||
DEFAULT_MEMBERS(Group); /**< Default constructors and assignments. */
|
||||
|
||||
/** Construct the class.
|
||||
@param _name Group name.
|
||||
@param _parent Parent content object.
|
||||
*/
|
||||
Group(const String& gname, const ContentBase* _parent);
|
||||
|
||||
/** Destructor. Release all involved hdf5 ids. */
|
||||
~Group();
|
||||
|
||||
virtual ContentType type() const override;
|
||||
|
@ -23,43 +43,114 @@ namespace CNORXZ
|
|||
virtual String path() const override;
|
||||
virtual String filename() const override;
|
||||
|
||||
virtual Int exists() const;
|
||||
/** 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
|
||||
|
||||
/** Get object contained by this group.
|
||||
@param name Object name.
|
||||
@return Pointer to the object.
|
||||
*/
|
||||
const ContentPtr& get(const String& name) const;
|
||||
|
||||
/** Get object contained by this group as group.
|
||||
Checks if the object is a group.
|
||||
@param name Group name.
|
||||
@return Pointer to the group.
|
||||
*/
|
||||
Sptr<Group> getGroup(const String& name) const;
|
||||
|
||||
/** Get object contained by this group as table.
|
||||
Checks if the object is a table.
|
||||
@param name Table name.
|
||||
@return Pointer to the table.
|
||||
*/
|
||||
Sptr<Table> getTable(const String& name) const;
|
||||
|
||||
/** Get object contained by this group as dataset.
|
||||
Checks if the object is a table.
|
||||
@param name Dataset name.
|
||||
@return Pointer to the dataset.
|
||||
*/
|
||||
Sptr<Dataset> getDataset(const String& name) const;
|
||||
|
||||
/** Get object contained by this group as table for given value type.
|
||||
Checks if the object is a table.
|
||||
@tparam Ts Table entry types.
|
||||
@param name Table name.
|
||||
@param proto Empty prototype (template argument resolution).
|
||||
@return Pointer to the table.
|
||||
*/
|
||||
template <typename... Ts>
|
||||
Sptr<STable<Ts...>> getTable(const String& name, Tuple<Ts...> proto);
|
||||
|
||||
/** Get object contained by this group as dataset for given value type.
|
||||
Checks if the object is a dataset.
|
||||
@tparam T Dataset value type.
|
||||
@param name Dataset name.
|
||||
@param proto Empty prototype (template argument resolution).
|
||||
@return Pointer to the dataset.
|
||||
*/
|
||||
template <typename T>
|
||||
Sptr<SDataset<T>> getDataset(const String& name, T proto);
|
||||
|
||||
/** Get objects contained by this group.
|
||||
@returns MArray of object pointers.
|
||||
*/
|
||||
const MArray<ContentPtr>& get() const;
|
||||
|
||||
/** Add a new group to this group.
|
||||
@param name Name of the created group.
|
||||
*/
|
||||
Group& addGroup(const String& name);
|
||||
|
||||
/** Add a new table to this group.
|
||||
@tparam Ts Table element types.
|
||||
@param name Name of the created table.
|
||||
@param data Table data.
|
||||
@param fnames Table field names.
|
||||
*/
|
||||
template <typename... Ts>
|
||||
Group& addTable(const String& name, const ArrayBase<Tuple<Ts...>>& data,
|
||||
const Arr<String,sizeof...(Ts)>& fnames);
|
||||
|
||||
/** Add a new dataset to this group.
|
||||
@tparam T Value type.
|
||||
@param name Name of the created dataset.
|
||||
@param data Dataset data.
|
||||
*/
|
||||
template <typename T>
|
||||
Group& addDataset(const String& name, const ArrayBase<T>& data);
|
||||
|
||||
/** Iterate over all group elements (const).
|
||||
@param F function object to be executed on each group element.
|
||||
*/
|
||||
template <class F>
|
||||
decltype(auto) iter(F&& f) const;
|
||||
|
||||
/** Iterate recursively over all group elements (const).
|
||||
@param F function object to be executed on each group element.
|
||||
*/
|
||||
template <class F>
|
||||
decltype(auto) iterRecursive(F&& f) const;
|
||||
|
||||
/** Iterate over all group elements.
|
||||
@param F function object to be executed on each group element.
|
||||
*/
|
||||
template <class F>
|
||||
decltype(auto) iter(F&& f);
|
||||
|
||||
/** Iterate recursively over all group elements.
|
||||
@param F function object to be executed on each group element.
|
||||
*/
|
||||
template <class F>
|
||||
decltype(auto) iterRecursive(F&& f);
|
||||
|
||||
protected:
|
||||
|
||||
MArray<ContentPtr> mCont; /**< Group elements. */
|
||||
|
||||
template <typename C, class F>
|
||||
static void recursion(const C& c, F&& f)
|
||||
{
|
||||
|
@ -72,8 +163,6 @@ namespace CNORXZ
|
|||
}
|
||||
}
|
||||
|
||||
MArray<ContentPtr> mCont;
|
||||
|
||||
void mkCont();
|
||||
AIndex<ContentPtr> getIndexTo(const String& name) const;
|
||||
BIndex<ContentPtr> getIndexTo(const String& name);
|
||||
|
|
|
@ -1,3 +1,13 @@
|
|||
// -*- C++ -*-
|
||||
/**
|
||||
|
||||
@file opt/hdf5/include/h5_table.h
|
||||
@brief Table declaration.
|
||||
|
||||
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
|
||||
Mail: chizeta@f3l.de
|
||||
|
||||
**/
|
||||
|
||||
#ifndef __cxz_h5_table_h__
|
||||
#define __cxz_h5_table_h__
|
||||
|
@ -9,13 +19,23 @@ namespace CNORXZ
|
|||
{
|
||||
namespace hdf5
|
||||
{
|
||||
/** ****
|
||||
Class to handle hdf5 tables.
|
||||
*/
|
||||
class Table : public ContentBase
|
||||
{
|
||||
public:
|
||||
typedef std::pair<SizeT,String> FieldID;
|
||||
|
||||
DEFAULT_MEMBERS(Table);
|
||||
DEFAULT_MEMBERS(Table); /**< Default constructors and assignments. */
|
||||
|
||||
/** Construct the class.
|
||||
@param _name Table name.
|
||||
@param _parent Parent content object.
|
||||
*/
|
||||
Table(const String& name, const ContentBase* _parent);
|
||||
|
||||
/** Destructor. Release all involved hdf5 ids. */
|
||||
~Table();
|
||||
|
||||
virtual ContentType type() const override final;
|
||||
|
@ -25,17 +45,57 @@ namespace CNORXZ
|
|||
virtual String path() const override final;
|
||||
virtual String filename() const override final;
|
||||
|
||||
/** Ininitialize table field names.
|
||||
@param fnames Table field names.
|
||||
*/
|
||||
Table& initFieldNames(const Vector<String>& fnames);
|
||||
|
||||
/** Initialize the table.
|
||||
@param n Number of records (rows).
|
||||
@param data Table data.
|
||||
@param dsize Record type size.
|
||||
@param chunk_size Chunk size.
|
||||
*/
|
||||
Table& initTable(SizeT n, const void* data, SizeT dsize, SizeT chunk_size);
|
||||
|
||||
/** Append records to the table.
|
||||
@param n Number of records to append.
|
||||
@param data Records data.
|
||||
*/
|
||||
Table& appendRecords(SizeT n, const void* data);
|
||||
|
||||
/** Read records.
|
||||
@param pos Number of first record to read.
|
||||
@param n Number of records to read.
|
||||
@param data Target pointer.
|
||||
*/
|
||||
Table& readRecords(SizeT pos, SizeT n, char* data);
|
||||
|
||||
/** Read record.
|
||||
@param pos Number of the record to be read.
|
||||
@return DType array with containing the record data.
|
||||
*/
|
||||
MArray<DType> readRecord(SizeT pos) const;
|
||||
|
||||
/** Read table.
|
||||
@return DType array containing the table data.
|
||||
*/
|
||||
MArray<DType> read() const;
|
||||
|
||||
/** Iterate over table records.
|
||||
@param F function object to be executed on each table record.
|
||||
*/
|
||||
template <class F>
|
||||
decltype(auto) iterRecords(F&& f) const;
|
||||
|
||||
|
||||
/** Get fields range.
|
||||
@return Pointer to the range.
|
||||
*/
|
||||
const RangePtr& fields() const;
|
||||
|
||||
/** Get records range.
|
||||
@return Pointer to the range.
|
||||
*/
|
||||
const RangePtr& records() const;
|
||||
|
||||
protected:
|
||||
|
|
|
@ -1,3 +1,15 @@
|
|||
// -*- C++ -*-
|
||||
/**
|
||||
|
||||
@file opt/hdf5/lib/h5_content_base.cc
|
||||
@brief Content base member function implementation.
|
||||
|
||||
Implementation of all non-virtual member functions of ContentBase.
|
||||
|
||||
Copyright (c) 2024 Christian Zimmermann. All rights reserved.
|
||||
Mail: chizeta@f3l.de
|
||||
|
||||
**/
|
||||
|
||||
#include "h5_content_base.h"
|
||||
|
||||
|
@ -19,16 +31,16 @@ namespace CNORXZ
|
|||
return mParent;
|
||||
}
|
||||
|
||||
RangePtr ContentBase::range() const
|
||||
{
|
||||
return mRange;
|
||||
}
|
||||
|
||||
hid_t ContentBase::id() const
|
||||
{
|
||||
return mId;
|
||||
}
|
||||
|
||||
bool isOpen() const
|
||||
{
|
||||
return mId != 0;
|
||||
}
|
||||
|
||||
DType ContentBase::getAttribute(const String& name) const
|
||||
{
|
||||
CXZ_ASSERT(attributeExists(name), "no attribute with name '" << name
|
||||
|
|
Loading…
Reference in a new issue