hdf5: several fixes + yrange: add setSub member function + dindex: add missing operator*(dindex,index)

src/include/ranges/dindex.cc.h

@@ -5,7 +5,7 @@
    @brief ...
 
 
-   Copyright (c) 2022 Christian Zimmermann. All rights reserved.
+   Copyright (c) 2024 Christian Zimmermann. All rights reserved.
    Mail: chizeta@f3l.de
    
 **/
@@ -40,6 +40,12 @@ namespace CNORXZ
 	}
     }
 
+    template <class I>
+    decltype(auto) operator*(const Sptr<DIndex>& a, const Sptr<I>& b)
+    {
+	return iptrMul(a, b);
+    }
+
     template <class I>
     I indexAs(const DIndex& i)
     {

src/include/ranges/dindex.h

@@ -2,10 +2,9 @@
 /**
    
    @file include/ranges/dindex.h
-   @brief ...
+   @brief DIndex declaration
 
-
+   Copyright (c) 2024 Christian Zimmermann. All rights reserved.
-   Copyright (c) 2022 Christian Zimmermann. All rights reserved.
    Mail: chizeta@f3l.de
    
 **/
@@ -154,6 +153,13 @@ namespace CNORXZ
 	XIndexPtr mI;
     };
 
+    /** Make index pack of a DIndex and another index.
+	@param a pointer to DIndex.
+	@param b pointer to another index.
+     */
+    template <class I>
+    decltype(auto) operator*(const Sptr<DIndex>& a, const Sptr<I>& b);
+
     /** Trait-specialization:
 	DIndex can have sub-indices
      */

src/include/ranges/yrange.h

@@ -186,6 +186,12 @@ namespace CNORXZ
 	 */
 	YIndex& setFormat(const YFormat& bs);
 
+	/** Set position of given sub index and update total index position.
+	    @param ind Sub-index number [0,dim()-1].
+	    @param lex Lexicographic position to be assigned to the index.
+	 */
+	YIndex& setSub(SizeT ind, SizeT lex);
+	
     private:
 	inline Vector<SizeT> mkFormat() const;
 	inline Vector<SizeT> mkLexFormat() const;

src/lib/ranges/yrange.cc

@@ -494,6 +494,19 @@ namespace CNORXZ
 	return *this;
     }
 
+    YIndex& YIndex::setSub(SizeT ind, SizeT lex)
+    {
+	CXZ_ASSERT(ind < dim(), "got index number (" << ind << ") larger than dimension ("
+		   << dim() << ")");
+	auto& idx = mIs[ind];
+	CXZ_ASSERT(lex < idx->lmax().val(), "tried to set sub-index position " << lex
+		   << ", which is out of scope; maximum position in range is " << idx->lmax().val() );
+	(*idx) = lex;
+	(*this)();
+	return *this;
+    }
+
+
     /****************************
      *   non-member functions   *
      ****************************/

src/opt/hdf5/include/h5_dataset.cc.h

@@ -12,6 +12,7 @@ namespace CNORXZ
 	Dataset& Dataset::init(const ArrayBase<T>& data)
 	{
 	    const hid_t tid = getTypeId(*data.data());
+	    VCHECK(tid);
 	    init(data.range(), tid);
 	    if(data.begin().formatIsTrivial()){
 		Vector<hsize_t> dims(mDataRange->dim());
@@ -83,11 +84,11 @@ namespace CNORXZ
 	{
 	    Vector<hsize_t> fpos(beg.dim());
 	    if constexpr(has_static_sub<I>::value){
-		iter<0,index_dim<I>::value> ( [&](auto i) { fpos[i] = beg.pack().get(i).lex(); }, NoF{} );
+		iter<0,index_dim<I>::value> ( [&](auto i) { fpos[i] = beg.THIS().pack().get(i)->lex(); }, NoF{} );
 	    }
 	    else if constexpr(has_sub<I>::value){
 		for(SizeT i = 0; i != beg.dim(); ++i){
-		    fpos[i] = beg.pack().get(i).lex();
+		    fpos[i] = beg.THIS().pack().get(i)->lex();
 		}
 	    }
 	    else {

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

@@ -48,17 +48,17 @@ namespace CNORXZ
 	
 	inline hid_t TypeId<SizeT>::get()
 	{
-	    return H5T_NATIVE_ULONG;
+	    return H5Tcopy( H5T_NATIVE_ULONG );
 	}
 
 	inline hid_t TypeId<Int>::get()
 	{
-	    return H5T_NATIVE_INT;
+	    return H5Tcopy( H5T_NATIVE_INT );
 	}
 
 	inline hid_t TypeId<Double>::get()
 	{
-	    return H5T_NATIVE_DOUBLE;
+	    return H5Tcopy( H5T_NATIVE_DOUBLE );
 	}
 
 	template <typename T, SizeT N>

src/opt/hdf5/lib/h5_dataset.cc

@@ -77,6 +77,7 @@ namespace CNORXZ
 	Dataset& Dataset::init(const RangePtr& dataRange, hid_t type)
 	{
 	    CXZ_ASSERT(not isOpen(), "tried to initialize dataset that is already extisting");
+	    mDataRange = dataRange;
 	    const H5T_class_t tc = H5Tget_class(type);
 	    CXZ_ASSERT(tc != H5T_NO_CLASS, "id does not correspond to a data type"); // (did not found anythng better to check if type id is valid)...
 	    const hid_t dcpl_id = H5Pcreate(H5P_DATASET_CREATE);

src/opt/hdf5/tests/CMakeLists.txt

@@ -1,5 +1,7 @@
 
+add_definitions(-DTEST_NUMBER_FILE="${CMAKE_SOURCE_DIR}/src/tests/numbers.txt")
+include_directories(${CMAKE_SOURCE_DIR}/src/tests)
 add_executable(h5basic h5_basic_unit_test.cc)
-add_dependencies(h5basic cnorxz cnorxzhdf5)
+add_dependencies(h5basic cnorxz cnorxzhdf5 test_lib)
-target_link_libraries(h5basic ${GTEST_BOTH_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${HDF5_LIBS} cnorxz cnorxzhdf5)
+target_link_libraries(h5basic ${GTEST_BOTH_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${HDF5_LIBS} cnorxz cnorxzhdf5 test_lib)
 add_test(NAME h5basic COMMAND h5basic)

src/opt/hdf5/tests/h5_basic_unit_test.cc

@@ -7,11 +7,13 @@
 #include "gtest/gtest.h"
 
 #include "cnorxz_hdf5.h"
+#include "test_numbers.h"
 
 namespace
 {
     using namespace CNORXZ;
     using namespace CNORXZ::hdf5;
+    using Test::Numbers;
 
     static const String testh5file = "test_file.h5";
     
@@ -58,6 +60,16 @@ namespace
 		iter<0,3>( [&](auto jj)
 		{ j = jj; mTabD[i*j] = DType(tget<jj>(v[i.lex()])); }, NoF{} );
 	    }
+
+	    const SizeT ddim = 5;
+	    Vector<RangePtr> dranges(ddim);
+	    dranges[0] = CRangeFactory(7).create();
+	    dranges[1] = CRangeFactory(3).create();
+	    dranges[2] = CRangeFactory(13).create();
+	    dranges[3] = CRangeFactory(5).create();
+	    dranges[4] = CRangeFactory(2).create();
+	    const RangePtr drange = yrange(dranges);
+	    mData = MArray<Double>( drange, Numbers::get(0,drange->size()) );
 	}
 
 	String mFileName;
@@ -65,6 +77,7 @@ namespace
 	Arr<String,3> mFs;
 	MArray<Tuple<Double,Int,SizeT>> mTabA;
 	MArray<DType> mTabD;
+	MArray<Double> mData;
     };
 
     
@@ -118,10 +131,18 @@ namespace
 	File h5f(mFileName, false);
 	h5f.open();
 	h5f.getGroup("gr1")->open().addTable("tab1", mTabA, mFs);
-	h5f.getGroup("gr2")->open().addTable("tab1", mTabA, mFs);
+	//h5f.getGroup("gr2")->open().addTable("tab1", mTabA, mFs);
 	h5f.getGroup("moregroups")->open().getGroup("evenmore")->open().getGroup("need")->open().addTable("tab1", mTabA, mFs);
 	h5f.close();
     }
+
+    TEST_F(Group_Test, CreateDataset)
+    {
+	File h5f(mFileName, false);
+	h5f.open();
+	h5f.getGroup("gr2")->open().addDataset("dat1", mData);
+	h5f.close();
+    }
     
     TEST_F(Group_Test, Read)
     {
@@ -181,6 +202,42 @@ namespace
 	h5f.close();
     }
 
+    TEST_F(Group_Test, ReadDataset)
+    {
+	File h5f(mFileName, true);
+	h5f.open();
+	auto dset = h5f.getGroup("gr2")->open().getDataset("dat1", Double{});
+	auto data = dset->read();
+	EXPECT_EQ(data.range()->dim(), 5u);
+	for(SizeT i = 0; i != 5u; ++i){
+	    EXPECT_EQ( data.range()->sub(i)->size(), mData.range()->sub(i)->size() );
+	}
+	auto i = std::make_shared<CIndex>(data.range());
+	i->ifor( operation( [](Double a, Double b) { EXPECT_EQ(a,b); }, data(i), mData(i) ), NoF{} )();
+	h5f.close();
+    }
+    
+    TEST_F(Group_Test, ReadDatasetPart)
+    {
+	File h5f(mFileName, true);
+	h5f.open();
+	auto dset = h5f.getGroup("gr2")->open().getDataset("dat1", Double{});
+	YIndex beg(dset->dataRange());
+	beg.setSub(0,2);
+	YIndex end = beg - 1;
+	end.setSub(0,2);
+	auto data = dset->read(beg,end);
+	EXPECT_EQ( data.range()->dim(), 5u );
+	EXPECT_EQ( data.range()->sub(0)->size(), 1u );
+	for(SizeT i = 1; i != 5u; ++i){
+	    EXPECT_EQ( data.range()->sub(i)->size(), mData.range()->sub(i)->size() );
+	}
+	auto i = std::make_shared<CIndex>(data.range());
+	auto j = std::make_shared<DIndex>( beg.pack().get(0) );
+	i->ifor( operation( [](Double a, Double b) { EXPECT_EQ(a,b); }, data(i), mData(j*i) ), NoF{} )();
+	h5f.close();
+    }
+    
     TEST_F(Group_Test, Read2)
     {
 	File h5f(mFileName, true);