WIP: hdf5 documentation
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8 changed files with 317 additions and 33 deletions
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@ -2,10 +2,9 @@
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/**
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/**
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@file include/ranges/ranges.h
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@file include/ranges/ranges.h
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@brief ...
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@brief Ranges main header
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Copyright (c) 2024 Christian Zimmermann. All rights reserved.
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Copyright (c) 2022 Christian Zimmermann. All rights reserved.
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Mail: chizeta@f3l.de
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Mail: chizeta@f3l.de
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**/
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**/
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@ -1,3 +1,13 @@
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// -*- C++ -*-
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/**
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@file opt/hdf5/include/cnorxz_hdf5.cc.h
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@brief CNORXZ HDF5 template sources header
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Copyright (c) 2024 Christian Zimmermann. All rights reserved.
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Mail: chizeta@f3l.de
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**/
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#include "h5_content_base.cc.h"
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#include "h5_content_base.cc.h"
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#include "h5_type_id.cc.h"
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#include "h5_type_id.cc.h"
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@ -1,3 +1,13 @@
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// -*- C++ -*-
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/**
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@file opt/hdf5/include/cnorxz_hdf5.h
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@brief CNORXZ HDF5 main header
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Copyright (c) 2024 Christian Zimmermann. All rights reserved.
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Mail: chizeta@f3l.de
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**/
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#include "h5_content_base.h"
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#include "h5_content_base.h"
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#include "h5_file.h"
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#include "h5_file.h"
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@ -1,3 +1,13 @@
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// -*- C++ -*-
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/**
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@file opt/hdf5/include/h5_content_base.h
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@brief Abstract content base class declaration
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Copyright (c) 2024 Christian Zimmermann. All rights reserved.
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Mail: chizeta@f3l.de
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**/
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#ifndef __cxz_h5_content_base_h__
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#ifndef __cxz_h5_content_base_h__
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#define __cxz_h5_content_base_h__
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#define __cxz_h5_content_base_h__
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@ -12,49 +22,122 @@ namespace CNORXZ
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{
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{
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// TODO: IO save error handling !!!
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// TODO: IO save error handling !!!
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/** *****
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Enum indicating the content type.
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Used by ContainerBase derivates to indicate the derived type.
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*/
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enum class ContentType {
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enum class ContentType {
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ATTR = 1,
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NONE = 0,
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FILE = 2,
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FILE = 1,
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GROUP = 3,
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GROUP = 2,
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DSET = 4,
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DSET = 3,
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TABLE = 5,
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TABLE = 4,
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VALUE = 6,
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};
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};
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/** ****
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Abstract base class for handling hdf5 objects.
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*/
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class ContentBase
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class ContentBase
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{
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{
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public:
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public:
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DEFAULT_MEMBERS(ContentBase);
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DEFAULT_MEMBERS(ContentBase); /**< Default constructors and assignments. */
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/** Construct the class.
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@param _name Content name.
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@param _parent Parent content object. Leave null for the root object.
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*/
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ContentBase(const String& _name, const ContentBase* _parent = nullptr);
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ContentBase(const String& _name, const ContentBase* _parent = nullptr);
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/** Virtual default destructor. */
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virtual ~ContentBase() = default;
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virtual ~ContentBase() = default;
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/** Get the content type.
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@return Content type.
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*/
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virtual ContentType type() const = 0;
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virtual ContentType type() const = 0;
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/** Check if in read-only mode
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@return True if read-only else false.
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*/
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virtual bool ro() const = 0;
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virtual bool ro() const = 0;
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/** Open object.
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@return Reference to this object.
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*/
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virtual ContentBase& open() = 0;
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virtual ContentBase& open() = 0;
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/** Close object.
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@return Reference to this object.
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*/
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virtual ContentBase& close() = 0;
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virtual ContentBase& close() = 0;
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/** Get object path.
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@return Absolute hdf5 file internal path of this object.
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*/
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virtual String path() const = 0;
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virtual String path() const = 0;
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/** Get the file name.
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@return Name of the hdf5 file this object is stored in.
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*/
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virtual String filename() const = 0;
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virtual String filename() const = 0;
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/** Get object name.
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@return The name of this object.
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*/
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const String& name() const;
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const String& name() const;
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const ContentBase* parent() const;
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RangePtr range() const;
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hid_t id() const;
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inline bool isOpen() const { return mId != 0; }
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/** Get parent object.
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@return Pointer to the parent of this object.
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*/
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const ContentBase* parent() const;
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/** Get object id.
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@return hdf5 id of the h5 object maintained by this object.
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*/
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hid_t id() const;
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/** Check if object is open, i.e. if there is a valid hdf5 id.
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@return True if object is open else false.
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*/
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bool isOpen() const;
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/** Add attribute to this object.
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@tparam T Attribute value type.
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@param name Attribute name.
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@param value Attribute value.
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*/
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template <typename T>
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template <typename T>
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ContentBase& addAttribute(const String& name, const T& value);
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ContentBase& addAttribute(const String& name, const T& value);
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/** Get an attribute of this object.
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@param name Attribute name.
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@return The attribute value as DType.
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*/
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DType getAttribute(const String& name) const;
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DType getAttribute(const String& name) const;
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/** Check if attribute of given name exists in this object.
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@param name Attribute name.
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@return True if attribute exists else false.
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*/
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bool attributeExists(const String& name) const;
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bool attributeExists(const String& name) const;
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/** Get all attributes of this object.
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@return Std map of key-value pairs.
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*/
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std::map<String,DType> getAttributes() const;
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std::map<String,DType> getAttributes() const;
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/** Get all attributes of this object and all its parent objects, recursively.
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@return Std map of key-value pairs.
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*/
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std::map<String,DType> getRecursiveAttributes() const; // + all parent's attributes
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std::map<String,DType> getRecursiveAttributes() const; // + all parent's attributes
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protected:
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protected:
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String mName;
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String mName; /**< Name of this object. */
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const ContentBase* mParent = nullptr;
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const ContentBase* mParent = nullptr; /**< Pointer to this object's parent. */
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RangePtr mRange;
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hid_t mId = 0; /**< hdf5 identifier of the hdf5 object handled by this object. */
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hid_t mId = 0;
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};
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};
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/** Shortcut for a shared pointer to an abstract content object. */
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typedef Sptr<ContentBase> ContentPtr;
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typedef Sptr<ContentBase> ContentPtr;
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}
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}
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// -*- C++ -*-
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/**
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@file opt/hdf5/include/h5_file.h
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@brief Group declaration.
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Copyright (c) 2024 Christian Zimmermann. All rights reserved.
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Mail: chizeta@f3l.de
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**/
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#ifndef __cxz_h5_file_h__
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#ifndef __cxz_h5_file_h__
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#define __cxz_h5_file_h__
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#define __cxz_h5_file_h__
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{
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{
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namespace hdf5
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namespace hdf5
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{
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{
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// maybe introduce abstraction layer between as base for File and Group
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/** ****
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Class to handle hdf5 file objects.
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Objects of this type usually serve as root object
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so they don't have any parent.
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*/
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class File : public Group
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class File : public Group
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{
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{
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public:
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public:
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typedef URange<String> RangeT;
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typedef URange<String> RangeT;
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DEFAULT_MEMBERS(File);
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DEFAULT_MEMBERS(File); /**< Default constructors and assignments. */
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/** Construct the class.
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@param _name Path to the hdf5 file to be handled.
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@param _ro Open in read-only mode if true, otherwise have write access.
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*/
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File(const String& fname, bool _ro = true);
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File(const String& fname, bool _ro = true);
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/** Destructor. Release all involved hdf5 ids. */
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~File();
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~File();
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virtual ContentType type() const override final;
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virtual ContentType type() const override final;
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// -*- C++ -*-
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/**
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@file opt/hdf5/include/h5_group.h
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@brief Group declaration.
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Copyright (c) 2024 Christian Zimmermann. All rights reserved.
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Mail: chizeta@f3l.de
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**/
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#ifndef __cxz_h5_group_h__
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#ifndef __cxz_h5_group_h__
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#define __cxz_h5_group_h__
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#define __cxz_h5_group_h__
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{
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{
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namespace hdf5
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namespace hdf5
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{
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{
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/** ****
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Class to handle hdf5 groups.
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*/
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class Group : public ContentBase
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class Group : public ContentBase
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{
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{
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public:
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public:
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DEFAULT_MEMBERS(Group);
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DEFAULT_MEMBERS(Group); /**< Default constructors and assignments. */
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/** Construct the class.
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@param _name Group name.
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@param _parent Parent content object.
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*/
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Group(const String& gname, const ContentBase* _parent);
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Group(const String& gname, const ContentBase* _parent);
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/** Destructor. Release all involved hdf5 ids. */
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~Group();
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~Group();
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virtual ContentType type() const override;
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virtual ContentType type() const override;
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virtual String path() const override;
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virtual String path() const override;
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virtual String filename() const override;
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virtual String filename() const override;
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virtual Int exists() const;
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/** Check if group exists in the parent object.
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@return 1 if group exists, 0 if not, -1 if an error occured.
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*/
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virtual Int exists() const; // TODO: virtual function of base class
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/** Get object contained by this group.
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@param name Object name.
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@return Pointer to the object.
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*/
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const ContentPtr& get(const String& name) const;
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const ContentPtr& get(const String& name) const;
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/** Get object contained by this group as group.
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Checks if the object is a group.
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@param name Group name.
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@return Pointer to the group.
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*/
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Sptr<Group> getGroup(const String& name) const;
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Sptr<Group> getGroup(const String& name) const;
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/** Get object contained by this group as table.
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Checks if the object is a table.
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@param name Table name.
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@return Pointer to the table.
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*/
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Sptr<Table> getTable(const String& name) const;
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Sptr<Table> getTable(const String& name) const;
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/** Get object contained by this group as dataset.
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Checks if the object is a table.
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@param name Dataset name.
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@return Pointer to the dataset.
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*/
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Sptr<Dataset> getDataset(const String& name) const;
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Sptr<Dataset> getDataset(const String& name) const;
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/** Get object contained by this group as table for given value type.
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Checks if the object is a table.
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@tparam Ts Table entry types.
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@param name Table name.
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@param proto Empty prototype (template argument resolution).
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@return Pointer to the table.
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*/
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template <typename... Ts>
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template <typename... Ts>
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Sptr<STable<Ts...>> getTable(const String& name, Tuple<Ts...> proto);
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Sptr<STable<Ts...>> getTable(const String& name, Tuple<Ts...> proto);
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/** Get object contained by this group as dataset for given value type.
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Checks if the object is a dataset.
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@tparam T Dataset value type.
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@param name Dataset name.
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@param proto Empty prototype (template argument resolution).
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@return Pointer to the dataset.
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*/
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template <typename T>
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template <typename T>
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Sptr<SDataset<T>> getDataset(const String& name, T proto);
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Sptr<SDataset<T>> getDataset(const String& name, T proto);
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/** Get objects contained by this group.
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@returns MArray of object pointers.
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*/
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const MArray<ContentPtr>& get() const;
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const MArray<ContentPtr>& get() const;
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/** Add a new group to this group.
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@param name Name of the created group.
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*/
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Group& addGroup(const String& name);
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Group& addGroup(const String& name);
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/** Add a new table to this group.
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@tparam Ts Table element types.
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@param name Name of the created table.
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@param data Table data.
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@param fnames Table field names.
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*/
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template <typename... Ts>
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template <typename... Ts>
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Group& addTable(const String& name, const ArrayBase<Tuple<Ts...>>& data,
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Group& addTable(const String& name, const ArrayBase<Tuple<Ts...>>& data,
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||||||
const Arr<String,sizeof...(Ts)>& fnames);
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const Arr<String,sizeof...(Ts)>& fnames);
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/** Add a new dataset to this group.
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@tparam T Value type.
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||||||
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@param name Name of the created dataset.
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@param data Dataset data.
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*/
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template <typename T>
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template <typename T>
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Group& addDataset(const String& name, const ArrayBase<T>& data);
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Group& addDataset(const String& name, const ArrayBase<T>& data);
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/** Iterate over all group elements (const).
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@param F function object to be executed on each group element.
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*/
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template <class F>
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template <class F>
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decltype(auto) iter(F&& f) const;
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decltype(auto) iter(F&& f) const;
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/** Iterate recursively over all group elements (const).
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@param F function object to be executed on each group element.
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||||||
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*/
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||||||
template <class F>
|
template <class F>
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||||||
decltype(auto) iterRecursive(F&& f) const;
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decltype(auto) iterRecursive(F&& f) const;
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||||||
|
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||||||
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/** Iterate over all group elements.
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@param F function object to be executed on each group element.
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*/
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||||||
template <class F>
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template <class F>
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decltype(auto) iter(F&& f);
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decltype(auto) iter(F&& f);
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/** Iterate recursively over all group elements.
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@param F function object to be executed on each group element.
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||||||
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*/
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||||||
template <class F>
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template <class F>
|
||||||
decltype(auto) iterRecursive(F&& f);
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decltype(auto) iterRecursive(F&& f);
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||||||
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protected:
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protected:
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|
||||||
|
MArray<ContentPtr> mCont; /**< Group elements. */
|
||||||
|
|
||||||
template <typename C, class F>
|
template <typename C, class F>
|
||||||
static void recursion(const C& c, F&& f)
|
static void recursion(const C& c, F&& f)
|
||||||
{
|
{
|
||||||
|
@ -72,8 +163,6 @@ namespace CNORXZ
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
MArray<ContentPtr> mCont;
|
|
||||||
|
|
||||||
void mkCont();
|
void mkCont();
|
||||||
AIndex<ContentPtr> getIndexTo(const String& name) const;
|
AIndex<ContentPtr> getIndexTo(const String& name) const;
|
||||||
BIndex<ContentPtr> getIndexTo(const String& name);
|
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__
|
#ifndef __cxz_h5_table_h__
|
||||||
#define __cxz_h5_table_h__
|
#define __cxz_h5_table_h__
|
||||||
|
@ -9,13 +19,23 @@ namespace CNORXZ
|
||||||
{
|
{
|
||||||
namespace hdf5
|
namespace hdf5
|
||||||
{
|
{
|
||||||
|
/** ****
|
||||||
|
Class to handle hdf5 tables.
|
||||||
|
*/
|
||||||
class Table : public ContentBase
|
class Table : public ContentBase
|
||||||
{
|
{
|
||||||
public:
|
public:
|
||||||
typedef std::pair<SizeT,String> FieldID;
|
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);
|
Table(const String& name, const ContentBase* _parent);
|
||||||
|
|
||||||
|
/** Destructor. Release all involved hdf5 ids. */
|
||||||
~Table();
|
~Table();
|
||||||
|
|
||||||
virtual ContentType type() const override final;
|
virtual ContentType type() const override final;
|
||||||
|
@ -25,17 +45,57 @@ namespace CNORXZ
|
||||||
virtual String path() const override final;
|
virtual String path() const override final;
|
||||||
virtual String filename() const override final;
|
virtual String filename() const override final;
|
||||||
|
|
||||||
|
/** Ininitialize table field names.
|
||||||
|
@param fnames Table field names.
|
||||||
|
*/
|
||||||
Table& initFieldNames(const Vector<String>& fnames);
|
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);
|
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);
|
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);
|
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;
|
MArray<DType> readRecord(SizeT pos) const;
|
||||||
|
|
||||||
|
/** Read table.
|
||||||
|
@return DType array containing the table data.
|
||||||
|
*/
|
||||||
MArray<DType> read() const;
|
MArray<DType> read() const;
|
||||||
|
|
||||||
|
/** Iterate over table records.
|
||||||
|
@param F function object to be executed on each table record.
|
||||||
|
*/
|
||||||
template <class F>
|
template <class F>
|
||||||
decltype(auto) iterRecords(F&& f) const;
|
decltype(auto) iterRecords(F&& f) const;
|
||||||
|
|
||||||
|
/** Get fields range.
|
||||||
|
@return Pointer to the range.
|
||||||
|
*/
|
||||||
const RangePtr& fields() const;
|
const RangePtr& fields() const;
|
||||||
|
|
||||||
|
/** Get records range.
|
||||||
|
@return Pointer to the range.
|
||||||
|
*/
|
||||||
const RangePtr& records() const;
|
const RangePtr& records() const;
|
||||||
|
|
||||||
protected:
|
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"
|
#include "h5_content_base.h"
|
||||||
|
|
||||||
|
@ -19,16 +31,16 @@ namespace CNORXZ
|
||||||
return mParent;
|
return mParent;
|
||||||
}
|
}
|
||||||
|
|
||||||
RangePtr ContentBase::range() const
|
|
||||||
{
|
|
||||||
return mRange;
|
|
||||||
}
|
|
||||||
|
|
||||||
hid_t ContentBase::id() const
|
hid_t ContentBase::id() const
|
||||||
{
|
{
|
||||||
return mId;
|
return mId;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
bool isOpen() const
|
||||||
|
{
|
||||||
|
return mId != 0;
|
||||||
|
}
|
||||||
|
|
||||||
DType ContentBase::getAttribute(const String& name) const
|
DType ContentBase::getAttribute(const String& name) const
|
||||||
{
|
{
|
||||||
CXZ_ASSERT(attributeExists(name), "no attribute with name '" << name
|
CXZ_ASSERT(attributeExists(name), "no attribute with name '" << name
|
||||||
|
|
Loading…
Reference in a new issue