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alalekalalek
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Merge pull request #547 from cbalint13:hdf
2 parents 280af82 + 133f9c8 commit 5c67347

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2 files changed

+66
-25
lines changed

2 files changed

+66
-25
lines changed

‎modules/hdf/CMakeLists.txt

Lines changed: 21 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,24 @@
11
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR})
22

3-
find_package(HDF5)
3+
if(WIN32)
4+
# windows cmake internal lookups are broken for now
5+
# will lookup for headers and shared libs given HDF_DIR env
6+
find_path(HDF5_INCLUDE_DIRS hdf5.h HINTS "$ENV{HDF5_DIR}\\..\\include")
7+
find_library(HDF5_C_LIBRARY NAMES hdf5 HINTS "$ENV{HDF5_DIR}\\..\\lib")
8+
if(HDF5_INCLUDE_DIRS AND HDF5_C_LIBRARY)
9+
set(HDF5_FOUND "YES")
10+
set(HDF5_LIBRARIES ${HDF5_C_LIBRARY})
11+
mark_as_advanced(HDF5_LIBRARIES)
12+
mark_as_advanced(HDF5_C_LIBRARY)
13+
mark_as_advanced(HDF5_INCLUDE_DIRS)
14+
add_definitions(-DH5_BUILT_AS_DYNAMIC_LIB -D_HDF5USEDLL_)
15+
else()
16+
set(HDF5_FOUND "NO")
17+
endif()
18+
else()
19+
find_package(HDF5)
20+
endif()
21+
422
if(HDF5_FOUND)
523
set(HAVE_HDF5 1)
624
message(STATUS "HDF5: YES")
@@ -9,13 +27,13 @@ else()
927
message(STATUS "HDF5: NO")
1028
endif()
1129

12-
if(${HDF5_FOUND})
30+
if(HDF5_FOUND)
1331
include_directories(${HDF5_INCLUDE_DIRS})
1432
endif()
1533

1634
set(the_description "Hierarchical Data Format I/O")
1735
ocv_define_module(hdf opencv_core WRAP python)
1836

19-
if(${HDF5_FOUND})
37+
if(HDF5_FOUND)
2038
target_link_libraries(opencv_hdf ${HDF5_LIBRARIES})
2139
endif()

‎modules/hdf/src/hdf5.cpp

Lines changed: 45 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -329,7 +329,7 @@ vector<int> HDF5Impl::dsgetsize( String dslabel, int dims_flag ) const
329329
int n_dims = H5Sget_simple_extent_ndims( fspace );
330330

331331
// dims storage
332-
hsize_t dims[n_dims];
332+
hsize_t *dims = new hsize_t[n_dims];
333333

334334
// output storage
335335
vector<int> SizeVect(0);
@@ -367,6 +367,8 @@ vector<int> HDF5Impl::dsgetsize( String dslabel, int dims_flag ) const
367367
H5Dclose( dsdata );
368368
H5Sclose( fspace );
369369

370+
delete dims;
371+
370372
return SizeVect;
371373
}
372374

@@ -386,7 +388,7 @@ int HDF5Impl::dsgettype( String dslabel ) const
386388
// fetch channs
387389
hsize_t ardims[1];
388390
H5Tget_array_dims( dstype, ardims );
389-
channs = ardims[0];
391+
channs = (int)ardims[0];
390392
// fetch depth
391393
hid_t tsuper = H5Tget_super( dstype );
392394
h5type = H5Tget_native_type( tsuper, H5T_DIR_ASCEND );
@@ -481,9 +483,9 @@ void HDF5Impl::dscreate( const int n_dims, const int* sizes, const int type,
481483

482484
int channs = CV_MAT_CN( type );
483485

484-
hsize_t chunks[n_dims];
485-
hsize_t dsdims[n_dims];
486-
hsize_t maxdim[n_dims];
486+
hsize_t *chunks = new hsize_t[n_dims];
487+
hsize_t *dsdims = new hsize_t[n_dims];
488+
hsize_t *maxdim = new hsize_t[n_dims];
487489

488490
// dimension space
489491
for ( int d = 0; d < n_dims; d++ )
@@ -529,7 +531,7 @@ void HDF5Impl::dscreate( const int n_dims, const int* sizes, const int type,
529531
// expand channs
530532
if ( channs > 1 )
531533
{
532-
hsize_t adims[1] = { channs };
534+
hsize_t adims[1] = { (hsize_t)channs };
533535
dstype = H5Tarray_create( dstype, 1, adims );
534536
}
535537

@@ -540,6 +542,10 @@ void HDF5Impl::dscreate( const int n_dims, const int* sizes, const int type,
540542
if ( channs > 1 )
541543
H5Tclose( dstype );
542544

545+
delete chunks;
546+
delete dsdims;
547+
delete maxdim;
548+
543549
H5Pclose( dsdcpl );
544550
H5Sclose( dspace );
545551
}
@@ -554,7 +560,7 @@ void HDF5Impl::dsread( OutputArray Array, String dslabel ) const
554560
void HDF5Impl::dsread( OutputArray Array, String dslabel,
555561
const int* dims_offset ) const
556562
{
557-
dsread( Array, dslabel, dims_offset );
563+
dsread( Array, dslabel, dims_offset, NULL );
558564
}
559565

560566
// overload
@@ -585,7 +591,7 @@ void HDF5Impl::dsread( OutputArray Array, String dslabel,
585591
// fetch channs
586592
hsize_t ardims[1];
587593
H5Tget_array_dims( dstype, ardims );
588-
channs = ardims[0];
594+
channs = (int) ardims[0];
589595
// fetch depth
590596
hid_t tsuper = H5Tget_super( dstype );
591597
h5type = H5Tget_native_type( tsuper, H5T_DIR_ASCEND );
@@ -602,7 +608,7 @@ void HDF5Impl::dsread( OutputArray Array, String dslabel,
602608
int n_dims = H5Sget_simple_extent_ndims( fspace );
603609

604610
// fetch dims
605-
hsize_t dsdims[n_dims];
611+
hsize_t *dsdims = new hsize_t[n_dims];
606612
H5Sget_simple_extent_dims( fspace, dsdims, NULL );
607613

608614
// set amount by custom offset
@@ -620,8 +626,8 @@ void HDF5Impl::dsread( OutputArray Array, String dslabel,
620626
}
621627

622628
// get memory write window
623-
int mxdims[n_dims];
624-
hsize_t foffset[n_dims];
629+
int *mxdims = new int[n_dims];
630+
hsize_t *foffset = new hsize_t[n_dims];
625631
for ( int d = 0; d < n_dims; d++ )
626632
{
627633
foffset[d] = 0;
@@ -653,6 +659,10 @@ void HDF5Impl::dsread( OutputArray Array, String dslabel,
653659
Mat matrix = Array.getMat();
654660
H5Dread( dsdata, dstype, dspace, fspace, H5P_DEFAULT, matrix.data );
655661

662+
delete dsdims;
663+
delete mxdims;
664+
delete foffset;
665+
656666
H5Tclose( dstype );
657667
H5Sclose( dspace );
658668
H5Sclose( fspace );
@@ -692,9 +702,9 @@ void HDF5Impl::dswrite( InputArray Array, String dslabel,
692702
int n_dims = matrix.dims;
693703
int channs = matrix.channels();
694704

695-
int dsizes[n_dims];
696-
hsize_t dsdims[n_dims];
697-
hsize_t offset[n_dims];
705+
int *dsizes = new int[n_dims];
706+
hsize_t *dsdims = new hsize_t[n_dims];
707+
hsize_t *offset = new hsize_t[n_dims];
698708
// replicate Mat dimensions
699709
for ( int d = 0; d < n_dims; d++ )
700710
{
@@ -738,7 +748,7 @@ void HDF5Impl::dswrite( InputArray Array, String dslabel,
738748
// expand channs
739749
if ( matrix.channels() > 1 )
740750
{
741-
hsize_t adims[1] = { channs };
751+
hsize_t adims[1] = { (hsize_t)channs };
742752
dstype = H5Tarray_create( dstype, 1, adims );
743753
}
744754

@@ -749,6 +759,10 @@ void HDF5Impl::dswrite( InputArray Array, String dslabel,
749759
if ( matrix.channels() > 1 )
750760
H5Tclose( dstype );
751761

762+
delete dsizes;
763+
delete dsdims;
764+
delete offset;
765+
752766
H5Sclose( dspace );
753767
H5Sclose( fspace );
754768
H5Dclose( dsdata );
@@ -793,8 +807,8 @@ void HDF5Impl::dsinsert( InputArray Array, String dslabel,
793807
int n_dims = matrix.dims;
794808
int channs = matrix.channels();
795809

796-
hsize_t dsdims[n_dims];
797-
hsize_t offset[n_dims];
810+
hsize_t *dsdims = new hsize_t[n_dims];
811+
hsize_t *offset = new hsize_t[n_dims];
798812
// replicate Mat dimensions
799813
for ( int d = 0; d < n_dims; d++ )
800814
{
@@ -828,14 +842,14 @@ void HDF5Impl::dsinsert( InputArray Array, String dslabel,
828842
// get actual file space and dims
829843
hid_t fspace = H5Dget_space( dsdata );
830844
int f_dims = H5Sget_simple_extent_ndims( fspace );
831-
hsize_t fsdims[f_dims];
845+
hsize_t *fsdims = new hsize_t[f_dims];
832846
H5Sget_simple_extent_dims( fspace, fsdims, NULL );
833847
H5Sclose( fspace );
834848

835849
CV_Assert( f_dims == n_dims );
836850

837851
// compute new extents
838-
hsize_t nwdims[n_dims];
852+
hsize_t *nwdims = new hsize_t[n_dims];
839853
for ( int d = 0; d < n_dims; d++ )
840854
{
841855
// init
@@ -869,7 +883,7 @@ void HDF5Impl::dsinsert( InputArray Array, String dslabel,
869883
// expand channs
870884
if ( matrix.channels() > 1 )
871885
{
872-
hsize_t adims[1] = { channs };
886+
hsize_t adims[1] = { (hsize_t)channs };
873887
dstype = H5Tarray_create( dstype, 1, adims );
874888
}
875889

@@ -880,6 +894,11 @@ void HDF5Impl::dsinsert( InputArray Array, String dslabel,
880894
if ( matrix.channels() > 1 )
881895
H5Tclose( dstype );
882896

897+
delete dsdims;
898+
delete offset;
899+
delete fsdims;
900+
delete nwdims;
901+
883902
H5Sclose( dspace );
884903
H5Sclose( fspace );
885904
H5Dclose( dsdata );
@@ -976,16 +995,18 @@ void HDF5Impl::kpwrite( const vector<KeyPoint> keypoints, String kplabel,
976995
{
977996
CV_Assert( keypoints.size() > 0 );
978997

998+
int dskdims[1];
979999
hsize_t dsddims[1];
9801000
hsize_t doffset[1];
9811001

9821002
// replicate vector dimension
9831003
doffset[0] = 0;
9841004
dsddims[0] = keypoints.size();
1005+
dskdims[0] = (int)keypoints.size();
9851006

9861007
// pre-create dataset if needed
9871008
if ( hlexists( kplabel ) == false )
988-
kpcreate( dsddims[0], kplabel );
1009+
kpcreate( dskdims[0], kplabel );
9891010

9901011
// set custom amount of data
9911012
if ( counts != H5_NONE )
@@ -1058,7 +1079,7 @@ void HDF5Impl::kpinsert( const vector<KeyPoint> keypoints, String kplabel,
10581079
// get actual file space and dims
10591080
hid_t fspace = H5Dget_space( dsdata );
10601081
int f_dims = H5Sget_simple_extent_ndims( fspace );
1061-
hsize_t fsdims[f_dims];
1082+
hsize_t *fsdims = new hsize_t[f_dims];
10621083
H5Sget_simple_extent_dims( fspace, fsdims, NULL );
10631084
H5Sclose( fspace );
10641085

@@ -1101,6 +1122,8 @@ void HDF5Impl::kpinsert( const vector<KeyPoint> keypoints, String kplabel,
11011122
// write into dataset
11021123
H5Dwrite( dsdata, mmtype, dspace, fspace, H5P_DEFAULT, &keypoints[0] );
11031124

1125+
delete fsdims;
1126+
11041127
H5Tclose( mmtype );
11051128
H5Sclose( dspace );
11061129
H5Sclose( fspace );

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