Merge pull request #547 from cbalint13:hdf

modules/hdf/CMakeLists.txt

 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR})
 
-find_package(HDF5)
+if(WIN32)
+  # windows cmake internal lookups are broken for now
+  # will lookup for headers and shared libs given HDF_DIR env
+  find_path(HDF5_INCLUDE_DIRS hdf5.h HINTS "$ENV{HDF5_DIR}\\..\\include")
+  find_library(HDF5_C_LIBRARY NAMES hdf5 HINTS "$ENV{HDF5_DIR}\\..\\lib")
+  if(HDF5_INCLUDE_DIRS AND HDF5_C_LIBRARY)
+    set(HDF5_FOUND "YES")
+    set(HDF5_LIBRARIES ${HDF5_C_LIBRARY})
+    mark_as_advanced(HDF5_LIBRARIES)
+    mark_as_advanced(HDF5_C_LIBRARY)
+    mark_as_advanced(HDF5_INCLUDE_DIRS)
+    add_definitions(-DH5_BUILT_AS_DYNAMIC_LIB -D_HDF5USEDLL_)
+  else()
+     set(HDF5_FOUND "NO")
+  endif()
+else()
+  find_package(HDF5)
+endif()
+
 if(HDF5_FOUND)
     set(HAVE_HDF5 1)
     message(STATUS "HDF5:   YES")
@@ -9,13 +27,13 @@ else()
     message(STATUS "HDF5:   NO")
 endif()
 
-if(${HDF5_FOUND})
+if(HDF5_FOUND)
   include_directories(${HDF5_INCLUDE_DIRS})
 endif()
 
 set(the_description "Hierarchical Data Format I/O")
 ocv_define_module(hdf opencv_core WRAP python)
 
-if(${HDF5_FOUND})
+if(HDF5_FOUND)
   target_link_libraries(opencv_hdf ${HDF5_LIBRARIES})
 endif()

modules/hdf/src/hdf5.cpp

@@ -329,7 +329,7 @@ vector<int> HDF5Impl::dsgetsize( String dslabel, int dims_flag ) const
     int n_dims = H5Sget_simple_extent_ndims( fspace );
 
     // dims storage
-    hsize_t dims[n_dims];
+    hsize_t *dims = new hsize_t[n_dims];
 
     // output storage
     vector<int> SizeVect(0);
@@ -367,6 +367,8 @@ vector<int> HDF5Impl::dsgetsize( String dslabel, int dims_flag ) const
     H5Dclose( dsdata );
     H5Sclose( fspace );
 
+    delete dims;
+
     return SizeVect;
 }
 
@@ -386,7 +388,7 @@ int HDF5Impl::dsgettype( String dslabel ) const
       // fetch channs
       hsize_t ardims[1];
       H5Tget_array_dims( dstype, ardims );
-      channs = ardims[0];
+      channs = (int)ardims[0];
       // fetch depth
       hid_t tsuper = H5Tget_super( dstype );
       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,
 
     int channs = CV_MAT_CN( type );
 
-    hsize_t chunks[n_dims];
-    hsize_t dsdims[n_dims];
-    hsize_t maxdim[n_dims];
+    hsize_t *chunks = new hsize_t[n_dims];
+    hsize_t *dsdims = new hsize_t[n_dims];
+    hsize_t *maxdim = new hsize_t[n_dims];
 
     // dimension space
     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,
     // expand channs
     if ( channs > 1 )
     {
-      hsize_t adims[1] = { channs };
+      hsize_t adims[1] = { (hsize_t)channs };
       dstype = H5Tarray_create( dstype, 1, adims );
     }
 
@@ -540,6 +542,10 @@ void HDF5Impl::dscreate( const int n_dims, const int* sizes, const int type,
     if ( channs > 1 )
       H5Tclose( dstype );
 
+    delete chunks;
+    delete dsdims;
+    delete maxdim;
+
     H5Pclose( dsdcpl );
     H5Sclose( dspace );
 }
@@ -554,7 +560,7 @@ void HDF5Impl::dsread( OutputArray Array, String dslabel ) const
 void HDF5Impl::dsread( OutputArray Array, String dslabel,
              const int* dims_offset ) const
 {
-    dsread( Array, dslabel, dims_offset );
+    dsread( Array, dslabel, dims_offset, NULL );
 }
 
 // overload
@@ -585,7 +591,7 @@ void HDF5Impl::dsread( OutputArray Array, String dslabel,
       // fetch channs
       hsize_t ardims[1];
       H5Tget_array_dims( dstype, ardims );
-      channs = ardims[0];
+      channs = (int) ardims[0];
       // fetch depth
       hid_t tsuper = H5Tget_super( dstype );
       h5type = H5Tget_native_type( tsuper, H5T_DIR_ASCEND );
@@ -602,7 +608,7 @@ void HDF5Impl::dsread( OutputArray Array, String dslabel,
     int n_dims = H5Sget_simple_extent_ndims( fspace );
 
     // fetch dims
-    hsize_t dsdims[n_dims];
+    hsize_t *dsdims = new hsize_t[n_dims];
     H5Sget_simple_extent_dims( fspace, dsdims, NULL );
 
     // set amount by custom offset
@@ -620,8 +626,8 @@ void HDF5Impl::dsread( OutputArray Array, String dslabel,
     }
 
     // get memory write window
-    int mxdims[n_dims];
-    hsize_t foffset[n_dims];
+    int *mxdims = new int[n_dims];
+    hsize_t *foffset = new hsize_t[n_dims];
     for ( int d = 0; d < n_dims; d++ )
     {
       foffset[d] = 0;
@@ -653,6 +659,10 @@ void HDF5Impl::dsread( OutputArray Array, String dslabel,
     Mat matrix = Array.getMat();
     H5Dread( dsdata, dstype, dspace, fspace, H5P_DEFAULT, matrix.data );
 
+    delete dsdims;
+    delete mxdims;
+    delete foffset;
+
     H5Tclose( dstype );
     H5Sclose( dspace );
     H5Sclose( fspace );
@@ -692,9 +702,9 @@ void HDF5Impl::dswrite( InputArray Array, String dslabel,
     int n_dims = matrix.dims;
     int channs = matrix.channels();
 
-    int dsizes[n_dims];
-    hsize_t dsdims[n_dims];
-    hsize_t offset[n_dims];
+    int *dsizes = new int[n_dims];
+    hsize_t *dsdims = new hsize_t[n_dims];
+    hsize_t *offset = new hsize_t[n_dims];
     // replicate Mat dimensions
     for ( int d = 0; d < n_dims; d++ )
     {
@@ -738,7 +748,7 @@ void HDF5Impl::dswrite( InputArray Array, String dslabel,
     // expand channs
     if ( matrix.channels() > 1 )
     {
-      hsize_t adims[1] = { channs };
+      hsize_t adims[1] = { (hsize_t)channs };
       dstype = H5Tarray_create( dstype, 1, adims );
     }
 
@@ -749,6 +759,10 @@ void HDF5Impl::dswrite( InputArray Array, String dslabel,
     if ( matrix.channels() > 1 )
       H5Tclose( dstype );
 
+    delete dsizes;
+    delete dsdims;
+    delete offset;
+
     H5Sclose( dspace );
     H5Sclose( fspace );
     H5Dclose( dsdata );
@@ -793,8 +807,8 @@ void HDF5Impl::dsinsert( InputArray Array, String dslabel,
     int n_dims = matrix.dims;
     int channs = matrix.channels();
 
-    hsize_t dsdims[n_dims];
-    hsize_t offset[n_dims];
+    hsize_t *dsdims = new hsize_t[n_dims];
+    hsize_t *offset = new hsize_t[n_dims];
     // replicate Mat dimensions
     for ( int d = 0; d < n_dims; d++ )
     {
@@ -828,14 +842,14 @@ void HDF5Impl::dsinsert( InputArray Array, String dslabel,
     // get actual file space and dims
     hid_t fspace = H5Dget_space( dsdata );
     int f_dims = H5Sget_simple_extent_ndims( fspace );
-    hsize_t fsdims[f_dims];
+    hsize_t *fsdims = new hsize_t[f_dims];
     H5Sget_simple_extent_dims( fspace, fsdims, NULL );
     H5Sclose( fspace );
 
     CV_Assert( f_dims == n_dims );
 
     // compute new extents
-    hsize_t nwdims[n_dims];
+    hsize_t *nwdims = new hsize_t[n_dims];
     for ( int d = 0; d < n_dims; d++ )
     {
       // init
@@ -869,7 +883,7 @@ void HDF5Impl::dsinsert( InputArray Array, String dslabel,
     // expand channs
     if ( matrix.channels() > 1 )
     {
-      hsize_t adims[1] = { channs };
+      hsize_t adims[1] = { (hsize_t)channs };
       dstype = H5Tarray_create( dstype, 1, adims );
     }
 
@@ -880,6 +894,11 @@ void HDF5Impl::dsinsert( InputArray Array, String dslabel,
     if ( matrix.channels() > 1 )
       H5Tclose( dstype );
 
+    delete dsdims;
+    delete offset;
+    delete fsdims;
+    delete nwdims;
+
     H5Sclose( dspace );
     H5Sclose( fspace );
     H5Dclose( dsdata );
@@ -976,16 +995,18 @@ void HDF5Impl::kpwrite( const vector<KeyPoint> keypoints, String kplabel,
 {
     CV_Assert( keypoints.size() > 0 );
 
+    int dskdims[1];
     hsize_t dsddims[1];
     hsize_t doffset[1];
 
     // replicate vector dimension
     doffset[0] = 0;
     dsddims[0] = keypoints.size();
+    dskdims[0] = (int)keypoints.size();
 
     // pre-create dataset if needed
     if ( hlexists( kplabel ) == false )
-      kpcreate( dsddims[0], kplabel );
+      kpcreate( dskdims[0], kplabel );
 
     // set custom amount of data
     if ( counts != H5_NONE )
@@ -1058,7 +1079,7 @@ void HDF5Impl::kpinsert( const vector<KeyPoint> keypoints, String kplabel,
     // get actual file space and dims
     hid_t fspace = H5Dget_space( dsdata );
     int f_dims = H5Sget_simple_extent_ndims( fspace );
-    hsize_t fsdims[f_dims];
+    hsize_t *fsdims = new hsize_t[f_dims];
     H5Sget_simple_extent_dims( fspace, fsdims, NULL );
     H5Sclose( fspace );
 
@@ -1101,6 +1122,8 @@ void HDF5Impl::kpinsert( const vector<KeyPoint> keypoints, String kplabel,
     // write into dataset
     H5Dwrite( dsdata, mmtype, dspace, fspace, H5P_DEFAULT, &keypoints[0] );
 
+    delete fsdims;
+
     H5Tclose( mmtype );
     H5Sclose( dspace );
     H5Sclose( fspace );