hdf5: type declaration in separate file + some reorgs in table code

src/opt/hdf5/include/cnorxz_hdf5.cc.h

@@ -1,4 +1,4 @@
 
-#include "h5_types.cc.h"
+#include "h5_type_id.cc.h"
 #include "h5_group.cc.h"
 #include "h5_table.cc.h"

src/opt/hdf5/include/cnorxz_hdf5.h

@@ -3,6 +3,6 @@
 #include "h5_file.h"
 #include "h5_group.h"
 #include "h5_table.h"
-#include "h5_types.h"
+#include "h5_type_id.h"
 
 #include "cnorxz_hdf5.cc.h"

src/opt/hdf5/include/h5_file.h

@@ -2,9 +2,9 @@
 #ifndef __cxz_h5_file_h__
 #define __cxz_h5_file_h__
 
+#include "h5_types.h"
 #include "h5_content_base.h"
 #include "h5_group.h"
-//#include <hdf5.h>
 
 namespace CNORXZ
 {

src/opt/hdf5/include/h5_group.cc.h

@@ -2,10 +2,31 @@
 #ifndef __cxz_h5_group_cc_h__
 #define __cxz_h5_group_cc_h__
 
+#include "h5_group.h"
+
 namespace CNORXZ
 {
     namespace hdf5
     {
+	template <typename... Ts>
+	Sptr<STable<Ts...>> Group::getTable(const String& name, Tuple<Ts...> proto)
+	{
+	    auto i = this->getIndexTo(name);
+	    auto tab = std::dynamic_pointer_cast<Table>( *i );
+	    if(tab == nullptr){
+		auto stab = std::dynamic_pointer_cast<STable<Ts...>>(*i);
+		CXZ_ASSERT(stab != nullptr, "wrong format for table '" << name << "'");
+		return stab;
+	    }
+	    else {
+		const RangePtr fields = tab->fields();
+		(*i)->close();
+		*i = std::make_shared<STable<Ts...>>(name, this, fields);
+		return *i;
+	    }
+	}
+
+	
 	template <typename T>
 	Group& Group::addData(const String& name, const ArrayBase<T>& data)
 	{

src/opt/hdf5/include/h5_group.h

@@ -2,6 +2,7 @@
 #ifndef __cxz_h5_group_h__
 #define __cxz_h5_group_h__
 
+#include "h5_types.h"
 #include "h5_content_base.h"
 
 namespace CNORXZ
@@ -26,6 +27,11 @@ namespace CNORXZ
 
 	    const ContentPtr& get(const String& name) const;
 	    Sptr<Group> getGroup(const String& name) const;
+	    Sptr<Table> getTable(const String& name) const;
+
+	    template <typename... Ts>
+	    Sptr<STable<Ts...>> getTable(const String& name, Tuple<Ts...> proto);
+	    
 	    const MArray<ContentPtr>& get() const;
 	    Group& addGroup(const String& name);
 
@@ -40,6 +46,8 @@ namespace CNORXZ
 	    MArray<ContentPtr> mCont;
 
 	    void mkCont();
+	    AIndex<ContentPtr> getIndexTo(const String& name) const;
+	    BIndex<ContentPtr> getIndexTo(const String& name);
 	};
     }
 }

src/opt/hdf5/include/h5_table.cc.h

@@ -3,7 +3,7 @@
 #define __cxz_h5_table_cc_h__
 
 #include "h5_table.h"
-#include "h5_types.h"
+#include "h5_type_id.h"
 
 namespace CNORXZ
 {
@@ -60,24 +60,12 @@ namespace CNORXZ
 	template <typename... Ts>
 	STable<Ts...>& STable<Ts...>::appendRecord(const Tuple<Ts...>& t)
 	{
-	    constexpr hsize_t chunk_size = sizeof(t);
-	    constexpr Int compress = 0;
 	    RangePtr appr = CRangeFactory(1).create();
 	    if(mRecords == nullptr){
-		mRecords = appr;
+		initTable(1, &t, sizeof(t), sizeof(t));
-		Vector<const char*> fields(mFields->size());
-		auto fr = std::dynamic_pointer_cast<URange<String>>(mFields);
-		for(auto fi = fr->begin(); fi != fr->end(); ++fi){
-		    fields[fi.lex()] = (*fi).c_str();
-		}
-		H5TBmake_table(mName.c_str(), mParent->id(), mName.c_str(), mFields->size(),
-			       mRecords->size(), sizeof(t), fields.data(), mOffsets.data(),
-			       mTypes.data(), chunk_size, NULL, compress, &t);
 	    }
 	    else {
-		mRecords = mRecords->extend(appr);
+		Table::appendRecord(1, &t, sizeof(t));
-		H5TBappend_records(mParent->id(), mName.c_str(), 1, sizeof(t),
-				   mOffsets.data(), mSizes.data(), &t);
 	    }
 	    return *this;
 	}

src/opt/hdf5/include/h5_table.h

@@ -2,6 +2,7 @@
 #ifndef __cxz_h5_table_h__
 #define __cxz_h5_table_h__
 
+#include "h5_types.h"
 #include "h5_content_base.h"
 
 namespace CNORXZ
@@ -23,8 +24,11 @@ namespace CNORXZ
 	    virtual String filename() const override final;
 
 	    Table& initFieldNames(const Vector<String>& fnames);
-	    Table& appendRecord(SizeT n, const char* data);
+	    Table& initTable(SizeT n, const void* data, SizeT dsize, SizeT chunk_size);
+	    Table& appendRecord(SizeT n, const void* data, SizeT dsize);
 	    Table& readRecord(SizeT pos, SizeT n, char* data);
+	    const RangePtr& fields() const;
+	    const RangePtr& records() const;
 
 	protected:
 	    RangePtr mRecords;

src/opt/hdf5/include/h5_type_id.cc.h

@@ -1,6 +1,6 @@
 
-#ifndef __cxz_h5_types_cc_h__
+#ifndef __cxz_h5_type_id_cc_h__
-#define __cxz_h5_types_cc_h__
+#define __cxz_h5_type_id_cc_h__
 
 #include "base/types.h"
 

src/opt/hdf5/include/h5_type_id.h

@@ -0,0 +1,40 @@
+
+#ifndef __cxz_h5_type_id_h__
+#define __cxz_h5_type_id_h__
+
+namespace CNORXZ
+{
+    namespace hdf5
+    {
+	template <SizeT N, typename... Ts>
+	SizeT getTupleOffset(const Tuple<Ts...>& t, CSizeT<N> i);
+
+	/**************
+	 *   TypeId   *
+	 **************/
+ 
+	template <typename T>
+	struct TypeId { static inline hid_t get(); };
+
+	template <>
+	struct TypeId<SizeT> { static inline hid_t get(); };
+	
+	template <>
+	struct TypeId<Int> { static inline hid_t get(); };
+
+	template <>
+	struct TypeId<Double> { static inline hid_t get(); };
+
+	template <typename T, SizeT N>
+	struct TypeId<Arr<T,N>> { static inline hid_t get(); };
+
+	/*****************
+	 *   getTypeId   *
+	 *****************/
+
+	template <typename T>
+	hid_t getTypeId(T x);
+    }
+}
+
+#endif

src/opt/hdf5/include/h5_types.h

@@ -1,39 +1,27 @@
 
-#ifndef __cxz_h5_types_h__
+#ifndef __h5_types_h__
-#define __cxz_h5_types_h__
+#define __h5_types_h__
 
 namespace CNORXZ
 {
     namespace hdf5
     {
-	template <SizeT N, typename... Ts>
+	// definition -> h5_content_base.h
-	SizeT getTupleOffset(const Tuple<Ts...>& t, CSizeT<N> i);
+	class ContentBase;
 
-	/**************
+	// definition -> h5_group.h
-	 *   TypeId   *
+	class Group;
-	 **************/
- 
-	template <typename T>
-	struct TypeId { static inline hid_t get(); };
 
-	template <>
+	// definition -> h5_file.h
-	struct TypeId<SizeT> { static inline hid_t get(); };
+	class File;
+
+	// definition -> h5_table.h
+	class Table;
+
+	// definition -> h5_table.h
+	template <typename... Ts>
+	class STable;
 	
-	template <>
-	struct TypeId<Int> { static inline hid_t get(); };
-
-	template <>
-	struct TypeId<Double> { static inline hid_t get(); };
-
-	template <typename T, SizeT N>
-	struct TypeId<Arr<T,N>> { static inline hid_t get(); };
-
-	/*****************
-	 *   getTypeId   *
-	 *****************/
-
-	template <typename T>
-	hid_t getTypeId(T x);
     }
 }
 

src/opt/hdf5/lib/h5_group.cc

@@ -73,10 +73,7 @@ namespace CNORXZ
 
 	const ContentPtr& Group::get(const String& name) const
 	{
-	    CXZ_ASSERT(this->isOpen(), "tried to get content of closed group");
+	    auto i = this->getIndexTo(name);
-	    auto dvec = [](const String& n) { return Vector<DType>({DType(n)}); };
-	    auto i = mCont.begin();
-	    i.at(dvec(name));
 	    return *i;
 	}
 
@@ -191,5 +188,23 @@ namespace CNORXZ
 			initCont, reinterpret_cast<void*>(&icd) );
 	}
 
+	AIndex<ContentPtr> Group::getIndexTo(const String& name) const
+	{
+	    CXZ_ASSERT(this->isOpen(), "tried to get content of closed group");
+	    auto dvec = [](const String& n) { return Vector<DType>({DType(n)}); };
+	    auto i = mCont.begin();
+	    i.at(dvec(name));
+	    return i;
+	}
+
+	BIndex<ContentPtr> Group::getIndexTo(const String& name)
+	{
+	    CXZ_ASSERT(this->isOpen(), "tried to get content of closed group");
+	    auto dvec = [](const String& n) { return Vector<DType>({DType(n)}); };
+	    auto i = mCont.begin();
+	    i.at(dvec(name));
+	    return i;
+	}
+	
     }
 }

src/opt/hdf5/lib/h5_table.cc

@@ -90,5 +90,47 @@ namespace CNORXZ
 	    mFields = URangeFactory<String>(fnames).create();
 	    return *this;
 	}
+
+	Table& Table::initTable(SizeT n, const void* data, SizeT dsize, SizeT chunk_size)
+	{
+	    const Int compress = 0;
+	    mRecords = CRangeFactory(n).create();
+	    Vector<const char*> fields(mFields->size());
+	    auto fr = std::dynamic_pointer_cast<URange<String>>(mFields);
+	    for(auto fi = fr->begin(); fi != fr->end(); ++fi){
+		fields[fi.lex()] = (*fi).c_str();
+	    }
+	    const herr_t err = H5TBmake_table
+		(mName.c_str(), mParent->id(), mName.c_str(), mFields->size(), mRecords->size(), dsize,
+		 fields.data(), mOffsets.data(), mTypes.data(), chunk_size, NULL, compress, data);
+	    CXZ_ASSERT(err >= 0, "error while initialzing table: error code = " << err);
+	    return *this;
+	}
+	
+	Table& Table::appendRecord(SizeT n, const void* data, SizeT dsize)
+	{
+	    mRecords = mRecords->extend( CRangeFactory(1).create() );
+	    const herr_t err = H5TBappend_records(mParent->id(), mName.c_str(), n, dsize,
+						  mOffsets.data(), mSizes.data(), data);
+	    CXZ_ASSERT(err >= 0, "error while appending record to table: error code = " << err);
+	    return *this;
+	}
+	
+	Table& Table::readRecord(SizeT pos, SizeT n, char* data)
+	{
+	    CXZ_ERROR("not implemented!!!");
+	    return *this;
+	}
+	
+	const RangePtr& Table::fields() const
+	{
+	    return mFields;
+	}
+	
+	const RangePtr& Table::records() const
+	{
+	    return mRecords;
+	}
+
     }
 }