From e6da712482021a111e03d5793e9f1bf199fd0309 Mon Sep 17 00:00:00 2001
From: Christian Zimmermann <christian.zimmermann@ur.de>
Date: Wed, 18 Jan 2023 00:49:11 +0100
Subject: [PATCH] ranges: extend + array: init + extend + hdf5: adapt

---
 src/include/array/marray.cc.h            | 23 ++++++
 src/include/array/marray.h               |  2 +
 src/include/ranges/crange.h              |  1 +
 src/include/ranges/mrange.cc.h           | 13 ++++
 src/include/ranges/mrange.h              |  1 +
 src/include/ranges/range_base.h          |  1 +
 src/include/ranges/urange.cc.h           |  9 +++
 src/include/ranges/urange.h              |  1 +
 src/include/ranges/xindex.cc.h           | 12 +++
 src/include/ranges/xindex.h              |  3 +
 src/include/ranges/yrange.h              |  1 +
 src/lib/ranges/crange.cc                 |  6 ++
 src/lib/ranges/yrange.cc                 | 11 +++
 src/opt/hdf5/include/h5_content_base.h   |  5 +-
 src/opt/hdf5/include/h5_file.h           | 14 ++--
 src/opt/hdf5/include/h5_group.h          | 29 ++++---
 src/opt/hdf5/lib/h5_file.cc              | 88 +++++----------------
 src/opt/hdf5/lib/h5_group.cc             | 98 +++++++++++++++++-------
 src/opt/hdf5/tests/h5_basic_unit_test.cc | 16 +++-
 19 files changed, 210 insertions(+), 124 deletions(-)

diff --git a/src/include/array/marray.cc.h b/src/include/array/marray.cc.h
index 6925645..3310586 100644
--- a/src/include/array/marray.cc.h
+++ b/src/include/array/marray.cc.h
@@ -25,6 +25,29 @@ namespace CNORXZ
 	ArrayBase<T>(range), mCont(vec)
     {}
 
+    template <typename T>
+    MArray<T>& MArray<T>::init(const RangePtr& range)
+    {
+	AB::mRange = rangeCast<YRange>(range);
+	mCont.resize(AB::mRange->size());
+	return *this;
+    }
+
+    template <typename T>
+    MArray<T>& MArray<T>::extend(const RangePtr& range)
+    {
+	MArray<T> tmp(AB::mRange->extend(range));
+	auto ei = this->end();
+	auto ti = tmp.begin();
+	// this is not very efficient; remove by sub-index operation once available:
+	for(auto ii = this->begin(); ii != ei; ++ii){
+	    ti.at(ii.meta());
+	    *ti = *ii;
+	}
+	*this = std::move(tmp);
+	return *this;
+    }
+
     template <typename T>
     const T* MArray<T>::data() const
     {
diff --git a/src/include/array/marray.h b/src/include/array/marray.h
index 118f80b..c272cd4 100644
--- a/src/include/array/marray.h
+++ b/src/include/array/marray.h
@@ -21,6 +21,8 @@ namespace CNORXZ
 	MArray(const RangePtr& range);
 	MArray(const RangePtr& range, const Vector<T>& vec);
 	MArray(const RangePtr& range, Vector<T>&& vec);
+	MArray& init(const RangePtr& range);
+	MArray& extend(const RangePtr& range);
 
 	virtual const T* data() const override;
 	virtual T* data() override;
diff --git a/src/include/ranges/crange.h b/src/include/ranges/crange.h
index 1085dea..549bca6 100644
--- a/src/include/ranges/crange.h
+++ b/src/include/ranges/crange.h
@@ -88,6 +88,7 @@ namespace CNORXZ
 	virtual String stringMeta(SizeT pos) const override final;
 	virtual const TypeInfo& type() const override final;
 	virtual const TypeInfo& metaType() const override final;
+	virtual RangePtr extend(const RangePtr& r) const override final;
 
 	SizeT get(SizeT pos) const;
 	SizeT getMeta(SizeT metaPos) const;
diff --git a/src/include/ranges/mrange.cc.h b/src/include/ranges/mrange.cc.h
index 6e0a748..32225f3 100644
--- a/src/include/ranges/mrange.cc.h
+++ b/src/include/ranges/mrange.cc.h
@@ -594,6 +594,19 @@ namespace CNORXZ
 	return i.at(metaPos).pos();
     }
 
+    template <class... Ranges>
+    RangePtr MRange<Ranges...>::extend(const RangePtr& r) const
+    {
+	CXZ_ASSERT( r->dim() == this->dim(), "cannot extend range of dimension "
+		    << this->dim() << " by range of dimension " << r->dim());
+	auto rs = iter<0,NR>( [&](auto i) {
+	    typedef typename std::remove_reference<decltype(*std::get<i>(mRs))>::type RType;
+	    return std::dynamic_pointer_cast<RType>( std::get<i>(mRs)->extend(r->sub(i)) ); },
+	    [](const auto&... e) { return std::make_tuple(e...); }
+	    );
+	return MRangeFactory<Ranges...>( rs ).create();
+    }
+    
     /************************
      *   MRange (private)   *
      ************************/
diff --git a/src/include/ranges/mrange.h b/src/include/ranges/mrange.h
index da24aab..dd80c28 100644
--- a/src/include/ranges/mrange.h
+++ b/src/include/ranges/mrange.h
@@ -179,6 +179,7 @@ namespace CNORXZ
 	virtual String stringMeta(SizeT pos) const override final;
 	virtual const TypeInfo& type() const override final;
 	virtual const TypeInfo& metaType() const override final;
+	virtual RangePtr extend(const RangePtr& r) const override final;
 	
 	decltype(auto) space() const;
 	const MetaType get(SizeT pos) const;
diff --git a/src/include/ranges/range_base.h b/src/include/ranges/range_base.h
index 15ca474..cb51dc8 100644
--- a/src/include/ranges/range_base.h
+++ b/src/include/ranges/range_base.h
@@ -53,6 +53,7 @@ namespace CNORXZ
 	virtual const TypeInfo& metaType() const = 0;
         virtual String stringMeta(SizeT pos) const = 0;
 	virtual DIndex index(SizeT pos = 0) const = 0;
+	virtual RangePtr extend(const RangePtr& r) const = 0;
 	
 	bool operator==(const RangeBase& in) const;
 	bool operator!=(const RangeBase& in) const;
diff --git a/src/include/ranges/urange.cc.h b/src/include/ranges/urange.cc.h
index 4964586..f9d51e8 100644
--- a/src/include/ranges/urange.cc.h
+++ b/src/include/ranges/urange.cc.h
@@ -273,6 +273,15 @@ namespace CNORXZ
 	return typeid(MetaType);
     }
 
+    template <typename MetaType>
+    RangePtr URange<MetaType>::extend(const RangePtr& r) const
+    {
+	auto rx = rangeCast<URange<MetaType>>(r);
+	auto space = mSpace;
+	space.insert(space.end(), rx->mSpace.begin(), rx->mSpace.end());
+	return URangeFactory<MetaType>( space ).create();
+    }
+	
     /*******************
      *   Range Casts   *
      *******************/
diff --git a/src/include/ranges/urange.h b/src/include/ranges/urange.h
index b6493e1..39e5471 100644
--- a/src/include/ranges/urange.h
+++ b/src/include/ranges/urange.h
@@ -95,6 +95,7 @@ namespace CNORXZ
 	virtual String stringMeta(SizeT pos) const override final;
 	virtual const TypeInfo& type() const override final;
 	virtual const TypeInfo& metaType() const override final;
+	virtual RangePtr extend(const RangePtr& r) const override final;
 
 	const MetaType& get(SizeT pos) const;
 	SizeT getMeta(const MetaType& metaPos) const;
diff --git a/src/include/ranges/xindex.cc.h b/src/include/ranges/xindex.cc.h
index 6996244..589c3ec 100644
--- a/src/include/ranges/xindex.cc.h
+++ b/src/include/ranges/xindex.cc.h
@@ -216,6 +216,18 @@ namespace CNORXZ
 	return DXpr<SizeT>(mI->ifor(xpr, std::forward<std::function<SizeT(SizeT,SizeT)>>(f)));
     }
 
+    template <class Index, typename Meta>
+    Index& XIndex<Index,Meta>::get()
+    {
+	return mI->THIS();
+    }
+    
+    template <class Index, typename Meta>
+    const Index& XIndex<Index,Meta>::get() const
+    {
+	return mI->THIS();
+    }
+
     template <class Index>
     inline XIndexPtr xindexPtr(const Sptr<Index>& i)
     {
diff --git a/src/include/ranges/xindex.h b/src/include/ranges/xindex.h
index 663e084..02eca13 100644
--- a/src/include/ranges/xindex.h
+++ b/src/include/ranges/xindex.h
@@ -101,6 +101,9 @@ namespace CNORXZ
 	virtual DXpr<SizeT> ifor(const DXpr<SizeT>& xpr,
 				 std::function<SizeT(SizeT,SizeT)>&& f) const override final;
 
+	Index& get();
+	const Index& get() const;
+
     private:
 	IndexPtr<Index,Meta> mI;
 
diff --git a/src/include/ranges/yrange.h b/src/include/ranges/yrange.h
index 371899f..a7fe749 100644
--- a/src/include/ranges/yrange.h
+++ b/src/include/ranges/yrange.h
@@ -123,6 +123,7 @@ namespace CNORXZ
 	virtual String stringMeta(SizeT pos) const override final;
 	virtual const TypeInfo& type() const override final;
 	virtual const TypeInfo& metaType() const override final;
+	virtual RangePtr extend(const RangePtr& r) const override final;
 
     private:
 
diff --git a/src/lib/ranges/crange.cc b/src/lib/ranges/crange.cc
index 9f3dc03..2d4182d 100644
--- a/src/lib/ranges/crange.cc
+++ b/src/lib/ranges/crange.cc
@@ -172,6 +172,12 @@ namespace CNORXZ
 	return typeid(SizeT);
     }
 
+    RangePtr CRange::extend(const RangePtr& r) const
+    {
+	auto rx = rangeCast<CRange>(r);
+	return CRangeFactory( this->size() + rx->size() ).create();
+    }
+    
     /*******************
      *   Range Casts   *
      *******************/
diff --git a/src/lib/ranges/yrange.cc b/src/lib/ranges/yrange.cc
index 5ff3c45..1699712 100644
--- a/src/lib/ranges/yrange.cc
+++ b/src/lib/ranges/yrange.cc
@@ -484,6 +484,17 @@ namespace CNORXZ
 	return typeid(DType);
     }
 
+    RangePtr YRange::extend(const RangePtr& r) const
+    {
+	CXZ_ASSERT(r->dim() == this->dim(), "cannot extend range of dimension "
+		   << this->dim() << " by range of dimension " << r->dim());
+	Vector<RangePtr> rvec(this->dim());
+	for(SizeT i = 0; i != this->dim(); ++i){
+	    rvec[i] = mRVec[i]->extend( r->sub(i) );
+	}
+	return YRangeFactory( rvec ).create();
+    }
+    
     YRange::YRange(const Vector<RangePtr>& rvec) : mRVec(rvec) {}
     
     YRange::YRange(Vector<RangePtr>&& rvec) : mRVec(std::forward<Vector<RangePtr>>(rvec)) {}
diff --git a/src/opt/hdf5/include/h5_content_base.h b/src/opt/hdf5/include/h5_content_base.h
index bf18bce..3685936 100644
--- a/src/opt/hdf5/include/h5_content_base.h
+++ b/src/opt/hdf5/include/h5_content_base.h
@@ -27,11 +27,9 @@ namespace CNORXZ
 
 	    virtual ContentType type() const = 0;
 	    virtual bool ro() const = 0;
-	    virtual ContentBase& load() = 0;
+	    virtual ContentBase& open() = 0;
 	    virtual ContentBase& write() = 0;
 	    virtual ContentBase& close() = 0;
-	    virtual MArray<Sptr<ContentBase>>* get() = 0;
-	    virtual const MArray<Sptr<ContentBase>>* get() const = 0;
 	    virtual String path() const = 0;
 	    virtual String filename() const = 0;
 
@@ -39,6 +37,7 @@ namespace CNORXZ
 	    const ContentBase* parent() const;
 	    RangePtr range() const;
 	    hid_t id() const;
+	    inline bool isOpen() const { return mId != 0; }
 	    
 	protected:
 	    String mName;
diff --git a/src/opt/hdf5/include/h5_file.h b/src/opt/hdf5/include/h5_file.h
index c312f9a..5c0a5f7 100644
--- a/src/opt/hdf5/include/h5_file.h
+++ b/src/opt/hdf5/include/h5_file.h
@@ -3,14 +3,15 @@
 #define __cxz_h5_file_h__
 
 #include "h5_content_base.h"
-#include <hdf5.h>
+#include "h5_group.h"
+//#include <hdf5.h>
 
 namespace CNORXZ
 {
     namespace hdf5
     {
 	// maybe introduce abstraction layer between as base for File and Group
-	class File : public ContentBase
+	class File : public Group
 	{
 	public:
 	    typedef URange<String> RangeT;
@@ -21,21 +22,16 @@ namespace CNORXZ
 
 	    virtual ContentType type() const override final;
 	    virtual bool ro() const override final;
-	    virtual File& load() override final;
+	    virtual File& open() override final;
 	    virtual File& write() override final;
 	    virtual File& close() override final;
-	    virtual MArray<Sptr<ContentBase>>* get() override final;
-	    virtual const MArray<Sptr<ContentBase>>* get() const override final;
 	    virtual String path() const override final;
 	    virtual String filename() const override final;
 
-	    Int exists() const;
-	    File& set(const RangePtr& range);
-	    File& append(const String& cname);
+	    virtual Int exists() const override final;
 	    
 	private:
 	    bool mRo = true;
-	    MArray<ContentPtr> mCont;
 	};
     }
 }
diff --git a/src/opt/hdf5/include/h5_group.h b/src/opt/hdf5/include/h5_group.h
index e46c1cc..da870c5 100644
--- a/src/opt/hdf5/include/h5_group.h
+++ b/src/opt/hdf5/include/h5_group.h
@@ -15,21 +15,26 @@ namespace CNORXZ
 	    Group(const String& gname, const ContentBase* _parent);
 	    ~Group();
 
-	    virtual ContentType type() const override final;
-	    virtual bool ro() const override final;
-	    virtual Group& load() override final;
-	    virtual Group& write() override final;
-	    virtual Group& close() override final;
-	    virtual MArray<Sptr<ContentBase>>* get() override final;
-	    virtual const MArray<Sptr<ContentBase>>* get() const override final;
-	    virtual String path() const override final;
-	    virtual String filename() const override final;
+	    virtual ContentType type() const override;
+	    virtual bool ro() const override;
+	    virtual Group& open() override; // load group if existing, else create new group
+	    virtual Group& write() override;
+	    virtual Group& close() override;
+	    virtual String path() const override;
+	    virtual String filename() const override;
 
-	    bool exists() const;
-	    Group& append(const ContentPtr& c);
+	    virtual Int exists() const;
+
+	    const MArray<ContentPtr>& get() const;
+	    Group& addGroup(const String& name);
+
+	    template <typename T>
+	    Group& addData(const String& name, const ArrayBase<T>& data);
 	    
-	private:
+	protected:
 	    MArray<ContentPtr> mCont;
+
+	    void mkCont();
 	};
 	
     }
diff --git a/src/opt/hdf5/lib/h5_file.cc b/src/opt/hdf5/lib/h5_file.cc
index 48b389a..3f400ee 100644
--- a/src/opt/hdf5/lib/h5_file.cc
+++ b/src/opt/hdf5/lib/h5_file.cc
@@ -7,8 +7,26 @@ namespace CNORXZ
     namespace hdf5
     {
 	File::File(const String& fname, bool _ro) :
-	    ContentBase(fname),
+	    Group(fname, nullptr),
 	    mRo(_ro)
+	{}
+
+	File::~File()
+	{
+	    this->close();
+	}
+
+	ContentType File::type() const
+	{
+	    return ContentType::FILE;
+	}
+	
+	bool File::ro() const
+	{
+	    return mRo;
+	}
+	
+	File& File::open()
 	{
 	    Int ex = this->exists();
 	    const String fn = this->filename();
@@ -27,27 +45,7 @@ namespace CNORXZ
 		}
 	    }
 	    CXZ_ASSERT( mId > 0, "error while opening file '" << fn << "'" );
-	}
-
-	File::~File()
-	{
-	    this->close();
-	}
-
-	ContentType File::type() const
-	{
-	    return ContentType::FILE;
-	}
-	
-	bool File::ro() const
-	{
-	    return mRo;
-	}
-	
-	File& File::load()
-	{
-	    // !!!
-	    
+	    this->mkCont();
 	    return *this;
 	}
 	
@@ -75,16 +73,6 @@ namespace CNORXZ
 	    return *this;
 	}
 	
-	MArray<Sptr<ContentBase>>* File::get()
-	{
-	    return &mCont;
-	}
-	
-	const MArray<Sptr<ContentBase>>* File::get() const
-	{
-	    return &mCont;
-	}
-	    
 	String File::path() const
 	{
 	    return String("/");
@@ -111,41 +99,5 @@ namespace CNORXZ
 	    return ex;
 	}
 	
-	File& File::set(const RangePtr& range)
-	{
-	    if(mCont.range() != nullptr){
-		CXZ_ERROR("IMPLEMENT");
-		// operator+ for RangePtr!!!
-	    }
-	    else {
-		mCont = MArray<ContentPtr>(range);
-	    }
-	    return *this;
-	}
-	
-	File& File::append(const String& cname)
-	{
-	    if(mCont.range() != nullptr){
-		auto oldrange = std::dynamic_pointer_cast<URange<String>>(mCont.range());
-		Vector<String> names(oldrange->size());
-		for(auto i = oldrange->begin(); i != oldrange->end(); ++i){
-		    names[i.lex()] = *i;
-		}
-		names[names.size()-1] = cname;
-		auto range = URangeFactory<String>( names ).create();
-		MArray<ContentPtr> ncont( range );
-		auto j = ncont.begin();
-		for(auto i = mCont.begin(); i != mCont.end(); ++i){
-		    j.at( i.meta() );
-		    ncont[j] = mCont[i];
-		}
-		mCont = ncont;
-	    }
-	    else {
-		auto range = URangeFactory<String>( Vector<String>({cname}) ).create();
-		mCont = MArray<ContentPtr>( range );
-	    }
-	    return *this;
-	}
     }
 }
diff --git a/src/opt/hdf5/lib/h5_group.cc b/src/opt/hdf5/lib/h5_group.cc
index 0709bd0..3a512b8 100644
--- a/src/opt/hdf5/lib/h5_group.cc
+++ b/src/opt/hdf5/lib/h5_group.cc
@@ -7,21 +7,11 @@ namespace CNORXZ
     {
 	Group::Group(const String& gname, const ContentBase* _parent) :
 	    ContentBase(gname, _parent)
-	{
-	    if(this->exists()){
-		mId = H5Gopen( mParent->id(), mName.c_str(), H5P_DEFAULT );
-	    }
-	    else {
-		mId = H5Gcreate( mParent->id(), mName.c_str(),
-				 H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
-	    }
-	}
+	{}
 	
 	Group::~Group()
 	{
-	    if(mId != 0){
-		H5Gclose(mId);
-	    }
+	    this->close();
 	}
 
 	ContentType Group::type() const
@@ -37,9 +27,16 @@ namespace CNORXZ
 	    return false;
 	}
 	
-	Group& Group::load()
+	Group& Group::open()
 	{
-	    // load content!!!
+	    if(this->exists()){
+		mId = H5Gopen( mParent->id(), mName.c_str(), H5P_DEFAULT );
+	    }
+	    else {
+		mId = H5Gcreate( mParent->id(), mName.c_str(),
+				 H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
+	    }
+	    this->mkCont();
 	    return *this;
 	}
 	
@@ -51,19 +48,12 @@ namespace CNORXZ
 
 	Group& Group::close()
 	{
+	    if(mId != 0){
+		H5Gclose(mId);
+	    }
 	    return *this;
 	}
 	
-	MArray<Sptr<ContentBase>>* Group::get()
-	{
-	    return &mCont;
-	}
-	
-	const MArray<Sptr<ContentBase>>* Group::get() const
-	{
-	    return &mCont;
-	}
-	
 	String Group::path() const
 	{
 	    if(mParent){
@@ -80,15 +70,67 @@ namespace CNORXZ
 	    return String();
 	}
 	
-	bool Group::exists() const
+	Int Group::exists() const
 	{
-	    return H5Lexists(mParent->id(), mName.c_str(), H5P_DEFAULT) != 0;
+	    return H5Lexists(mParent->id(), mName.c_str(), H5P_DEFAULT) != 0 ? 1 : 0;
 	}
 
-	Group& Group::append(const ContentPtr& c)
+	const MArray<ContentPtr>& Group::get() const
 	{
+	    return mCont;
+	}
 
-	    return *this;
+	struct InitContData
+	{
+	    const ContentBase* parent;
+	    BIndex<ContentPtr> index;
+	};
+
+	static herr_t addName(hid_t id, const char* name, const H5L_info_t* info, void* x)
+	{
+	    Vector<String>* names = reinterpret_cast<Vector<String>*>(x);
+	    names->push_back(String(name));
+	    return 0;
+	}
+	
+	static herr_t initCont(hid_t id, const char* name, const H5L_info_t* info, void* x)
+	{
+	    const String sname(name);
+	    InitContData* icd = reinterpret_cast<InitContData*>(x);
+	    BIndex<ContentPtr>& index = icd->index;
+	    UIndex<String>& ui = std::dynamic_pointer_cast<XIndex<UIndex<String>,String>>
+		(index.pack()[0])->get();
+	    ui.at(sname);
+	    index();
+	    H5O_info_t oinfo;
+	    H5Oget_info(id, &oinfo, H5O_INFO_BASIC);
+	    switch (oinfo.type) {
+	    case H5O_TYPE_GROUP: {
+		*index = std::make_shared<Group>(sname, icd->parent);
+		break;
+	    }/*
+	    case H5O_TYPE_DATASET: {
+		*index = std::make_shared<DSet>(sname, );
+		break;
+		}*/
+	    default:
+		return 1;
+	    }
+	    return 0;
+	}
+
+	void Group::mkCont()
+	{
+	    Vector<String> names;
+	    H5Literate( mId, H5_INDEX_NAME, H5_ITER_NATIVE, NULL,
+			addName, reinterpret_cast<void*>(&names) );
+	    mCont.init( URangeFactory<String>( names ).create() );
+
+	    InitContData icd;
+	    icd.index = mCont.begin();
+	    icd.parent = this;
+	    H5Literate( mId, H5_INDEX_NAME, H5_ITER_NATIVE, NULL,
+			initCont, reinterpret_cast<void*>(&icd) );
 	}
 
     }
diff --git a/src/opt/hdf5/tests/h5_basic_unit_test.cc b/src/opt/hdf5/tests/h5_basic_unit_test.cc
index 7496ab0..5635d55 100644
--- a/src/opt/hdf5/tests/h5_basic_unit_test.cc
+++ b/src/opt/hdf5/tests/h5_basic_unit_test.cc
@@ -2,7 +2,7 @@
 #include <cstdlib>
 #include <iostream>
 #include <fstream>
-#include <filesystem>
+#include <cstdio>
 
 #include "gtest/gtest.h"
 
@@ -12,7 +12,6 @@ namespace
 {
     using namespace CNORXZ;
     using namespace CNORXZ::hdf5;
-    namespace sfs = std::filesystem;
     
     class NoFile_Test : public ::testing::Test
     {
@@ -38,10 +37,12 @@ namespace
 	Group_Test()
 	{
 	    mFileName = "test_file.h5";
-	    sfs::remove(mFileName);
+	    std::remove(mFileName.c_str());
+	    mGrps = { "gr1", "gr2" };
 	}
 
 	String mFileName;
+	Vector<String> mGrps;
     };
 
     TEST_F(NoFile_Test, NoFile)
@@ -63,12 +64,19 @@ namespace
 	File h5f(mFileName, false);
 	EXPECT_FALSE(h5f.ro());
 	//h5f.append("gr1");
-	auto grange = URangeFactory<String>( Vector<String>( { "gr1", "gr2" } ) ).create();
+	auto grange = URangeFactory<String>( mGrps ).create();
 	h5f.set( grange );
 	for(auto i = grange->begin(); i != grange->end(); ++i){
 	    (*h5f.get())[i] = std::make_shared<Group>( i.meta().str(), &h5f );
 	}
     }
+
+    TEST_F(Group_Test, Read)
+    {
+	File h5f(mFileName, true);
+	EXPECT_TRUE(h5f.ro());
+	
+    }
 }
 
 // check write to new file