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changeset 20474:bfe66db8addb

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don't include hdf5.h or use HDF5 typedefs in public header files (bug #43180) * oct-hdf5-types.h: Rename from oct-hdf5-id.h. * oct-hdf5-types.cc: Rename from oct-hdf5-id.cc. * libinterp/corefcn/module.mk: Update. * oct-hdf5-types.h (octave_hdf5_err): New typedef. * oct-hdf5-types.h, oct-hdf5-types.cc (check_hdf5_types): Rename from check_hdf5_id_type. Also check size of herr_t. * load-save.cc: Include oct-hdf5.h. * ls-hdf5.cc: Include oct-hdf5.h instead of oct-hdf5-id.h. Define hdf5_fstreambase functions that require HDF5 types here instead of in ls-hdf5.h. * ls-hdf5.h, ls-hdf5.cc: Use octave types in public interfaces. * ls-hdf5.h, ov-base.h: Include oct-hdf5-types.h instead of oct-hdf5.h. * oct-hdf5.h: Include oct-hdf5-types.h. Define H5T_NATIVE_IDX here. * ls-hdf5.h: Not here.
author John W. Eaton <jwe@octave.org>
date Mon, 15 Jun 2015 17:42:44 -0400
parents 5c088348fddb
children 01895a6acdde
files libinterp/corefcn/load-save.cc libinterp/corefcn/ls-hdf5.cc libinterp/corefcn/ls-hdf5.h libinterp/corefcn/module.mk libinterp/corefcn/oct-hdf5-id.cc libinterp/corefcn/oct-hdf5-id.h libinterp/corefcn/oct-hdf5-types.cc libinterp/corefcn/oct-hdf5-types.h libinterp/corefcn/oct-hdf5.h libinterp/octave-value/ov-base.h
diffstat 8 files changed, 115 insertions(+), 96 deletions(-) [+]
line wrap: on
line diff
--- a/libinterp/corefcn/load-save.cc
+++ b/libinterp/corefcn/load-save.cc
@@ -59,6 +59,7 @@
 #include "gripes.h"
 #include "load-path.h"
 #include "load-save.h"
+#include "oct-hdf5.h"
 #include "oct-obj.h"
 #include "oct-map.h"
 #include "ov-cell.h"
--- a/libinterp/corefcn/ls-hdf5.cc
+++ b/libinterp/corefcn/ls-hdf5.cc
@@ -55,7 +55,7 @@
 #include "error.h"
 #include "gripes.h"
 #include "load-save.h"
-#include "oct-hdf5-id.h"
+#include "oct-hdf5.h"
 #include "oct-obj.h"
 #include "oct-map.h"
 #include "ov-cell.h"
@@ -72,6 +72,57 @@
 #include "ls-utils.h"
 #include "ls-hdf5.h"
 
+hdf5_fstreambase::hdf5_fstreambase (const char *name, int mode, int /* prot */)
+  : file_id (-1), current_item (-1)
+{
+  if (mode & std::ios::in)
+    file_id = H5Fopen (name, H5F_ACC_RDONLY, H5P_DEFAULT);
+  else if (mode & std::ios::out)
+    {
+      if (mode & std::ios::app && H5Fis_hdf5 (name) > 0)
+        file_id = H5Fopen (name, H5F_ACC_RDWR, H5P_DEFAULT);
+      else
+        file_id = H5Fcreate (name, H5F_ACC_TRUNC, H5P_DEFAULT,
+                             H5P_DEFAULT);
+    }
+  if (file_id < 0)
+    std::ios::setstate (std::ios::badbit);
+
+  current_item = 0;
+}
+
+void
+hdf5_fstreambase::close (void)
+{
+  if (file_id >= 0)
+    {
+      if (H5Fclose (file_id) < 0)
+        std::ios::setstate (std::ios::badbit);
+      file_id = -1;
+    }
+}
+
+void
+hdf5_fstreambase::open (const char *name, int mode, int)
+{
+  clear ();
+
+  if (mode & std::ios::in)
+    file_id = H5Fopen (name, H5F_ACC_RDONLY, H5P_DEFAULT);
+  else if (mode & std::ios::out)
+    {
+      if (mode & std::ios::app && H5Fis_hdf5 (name) > 0)
+        file_id = H5Fopen (name, H5F_ACC_RDWR, H5P_DEFAULT);
+      else
+        file_id = H5Fcreate (name, H5F_ACC_TRUNC, H5P_DEFAULT,
+                             H5P_DEFAULT);
+    }
+  if (file_id < 0)
+    std::ios::setstate (std::ios::badbit);
+
+  current_item = 0;
+}
+
 static std::string
 make_valid_identifier (const std::string& nm)
 {
@@ -104,7 +155,7 @@
 // which is all we need it for
 
 bool
-hdf5_types_compatible (hid_t t1, hid_t t2)
+hdf5_types_compatible (octave_hdf5_id t1, octave_hdf5_id t2)
 {
   int n;
   if ((n = H5Tget_nmembers (t1)) != H5Tget_nmembers (t2))
@@ -129,7 +180,7 @@
 // otherwise.
 
 bool
-hdf5_check_attr (hid_t loc_id, const char *attr_name)
+hdf5_check_attr (octave_hdf5_id loc_id, const char *attr_name)
 {
   bool retval = false;
 
@@ -170,7 +221,7 @@
 }
 
 bool
-hdf5_get_scalar_attr (hid_t loc_id, hid_t type_id,
+hdf5_get_scalar_attr (octave_hdf5_id loc_id, octave_hdf5_id type_id,
                       const char *attr_name, void *buf)
 {
   bool retval = false;
@@ -224,8 +275,8 @@
 // H5T_NATIVE_DOUBLE to save as 'double'). Note that any necessary
 // conversions are handled automatically by HDF5.
 
-hid_t
-hdf5_make_complex_type (hid_t num_type)
+octave_hdf5_id
+hdf5_make_complex_type (octave_hdf5_id num_type)
 {
   hid_t type_id = H5Tcreate (H5T_COMPOUND, sizeof (double) * 2);
 
@@ -245,8 +296,8 @@
 // -1 on error, and 0 to tell H5Giterate to continue on to the next item
 // (e.g. if NAME was a data type we don't recognize).
 
-herr_t
-hdf5_read_next_data (hid_t group_id, const char *name, void *dv)
+octave_hdf5_err
+hdf5_read_next_data (octave_hdf5_id group_id, const char *name, void *dv)
 {
   hdf5_callback_data *d = static_cast<hdf5_callback_data *> (dv);
   hid_t type_id = -1;
@@ -588,7 +639,7 @@
                 bool& global, octave_value& tc, std::string& doc,
                 const string_vector& argv, int argv_idx, int argc)
 {
-  check_hdf5_id_type ();
+  check_hdf5_types ();
 
   std::string retval;
 
@@ -663,8 +714,8 @@
 
 // Add an attribute named attr_name to loc_id (a simple scalar
 // attribute with value 1).  Return value is >= 0 on success.
-herr_t
-hdf5_add_attr (hid_t loc_id, const char *attr_name)
+octave_hdf5_err
+hdf5_add_attr (octave_hdf5_id loc_id, const char *attr_name)
 {
   herr_t retval = 0;
 
@@ -698,8 +749,8 @@
   return retval;
 }
 
-herr_t
-hdf5_add_scalar_attr (hid_t loc_id, hid_t type_id,
+octave_hdf5_err
+hdf5_add_scalar_attr (octave_hdf5_id loc_id, octave_hdf5_id type_id,
                       const char *attr_name, void *buf)
 {
   herr_t retval = 0;
@@ -737,7 +788,7 @@
 //    = 0  Not an empty matrix; did nothing
 //    < 0  Error condition
 int
-save_hdf5_empty (hid_t loc_id, const char *name, const dim_vector d)
+save_hdf5_empty (octave_hdf5_id loc_id, const char *name, const dim_vector d)
 {
   hsize_t sz = d.length ();
   OCTAVE_LOCAL_BUFFER (octave_idx_type, dims, sz);
@@ -787,7 +838,7 @@
 //    = 0  Not an empty matrix; did nothing
 //    < 0  Error condition
 int
-load_hdf5_empty (hid_t loc_id, const char *name, dim_vector &d)
+load_hdf5_empty (octave_hdf5_id loc_id, const char *name, dim_vector &d)
 {
   if (! hdf5_check_attr (loc_id, "OCTAVE_EMPTY_MATRIX"))
     return 0;
@@ -826,7 +877,7 @@
 
 // return the HDF5 type id corresponding to the Octave save_type
 
-hid_t
+octave_hdf5_id
 save_type_to_hdf5 (save_type st)
 {
   switch (st)
@@ -865,7 +916,7 @@
 // (stored as HDF5 groups).
 
 bool
-add_hdf5_data (hid_t loc_id, const octave_value& tc,
+add_hdf5_data (octave_hdf5_id loc_id, const octave_value& tc,
                const std::string& name, const std::string& doc,
                bool mark_as_global, bool save_as_floats)
 {
@@ -955,7 +1006,7 @@
                 const std::string& name, const std::string& doc,
                 bool mark_as_global, bool save_as_floats)
 {
-  check_hdf5_id_type ();
+  check_hdf5_types ();
 
   hdf5_ofstream& hs = dynamic_cast<hdf5_ofstream&> (os);
 
--- a/libinterp/corefcn/ls-hdf5.h
+++ b/libinterp/corefcn/ls-hdf5.h
@@ -25,7 +25,7 @@
 
 #if defined (HAVE_HDF5)
 
-#include "oct-hdf5.h"
+#include "oct-hdf5-types.h"
 
 // first, we need to define our own dummy stream subclass, since
 // HDF5 needs to do its own file i/o
@@ -38,7 +38,7 @@
 public:
 
   // HDF5 uses an "id" to refer to an open file
-  hid_t file_id;
+  octave_hdf5_id file_id;
 
   // keep track of current item index in the file
   int current_item;
@@ -47,54 +47,11 @@
 
   ~hdf5_fstreambase () { close (); }
 
-  hdf5_fstreambase (const char *name, int mode, int /* prot */ = 0)
-    : file_id (-1), current_item (-1)
-  {
-    if (mode & std::ios::in)
-      file_id = H5Fopen (name, H5F_ACC_RDONLY, H5P_DEFAULT);
-    else if (mode & std::ios::out)
-      {
-        if (mode & std::ios::app && H5Fis_hdf5 (name) > 0)
-          file_id = H5Fopen (name, H5F_ACC_RDWR, H5P_DEFAULT);
-        else
-          file_id = H5Fcreate (name, H5F_ACC_TRUNC, H5P_DEFAULT,
-                               H5P_DEFAULT);
-      }
-    if (file_id < 0)
-      std::ios::setstate (std::ios::badbit);
-
-    current_item = 0;
-  }
+  hdf5_fstreambase (const char *name, int mode, int /* prot */ = 0);
 
-  void close ()
-  {
-    if (file_id >= 0)
-      {
-        if (H5Fclose (file_id) < 0)
-          std::ios::setstate (std::ios::badbit);
-        file_id = -1;
-      }
-  }
-
-  void open (const char *name, int mode, int)
-  {
-    clear ();
+  void close (void);
 
-    if (mode & std::ios::in)
-      file_id = H5Fopen (name, H5F_ACC_RDONLY, H5P_DEFAULT);
-    else if (mode & std::ios::out)
-      {
-        if (mode & std::ios::app && H5Fis_hdf5 (name) > 0)
-          file_id = H5Fopen (name, H5F_ACC_RDWR, H5P_DEFAULT);
-        else
-          file_id = H5Fcreate (name, H5F_ACC_TRUNC, H5P_DEFAULT,
-                               H5P_DEFAULT);
-      }
-    if (file_id < 0)
-      std::ios::setstate (std::ios::badbit);
-
-    current_item = 0;
-  }
+  void open (const char *name, int mode, int);
 };
 
 // input and output streams, subclassing istream and ostream
@@ -154,29 +111,29 @@
 };
 
 #if HAVE_HDF5_INT2FLOAT_CONVERSIONS
-extern OCTINTERP_API hid_t
+extern OCTINTERP_API octave_hdf5_id
 save_type_to_hdf5 (save_type st)
 #endif
 
-extern OCTINTERP_API hid_t
-hdf5_make_complex_type (hid_t num_type);
+extern OCTINTERP_API octave_hdf5_id
+hdf5_make_complex_type (octave_hdf5_id num_type);
 
 extern OCTINTERP_API bool
-hdf5_types_compatible (hid_t t1, hid_t t2);
+hdf5_types_compatible (octave_hdf5_id t1, octave_hdf5_id t2);
 
-extern OCTINTERP_API herr_t
-hdf5_read_next_data (hid_t group_id, const char *name, void *dv);
+extern OCTINTERP_API octave_hdf5_err
+hdf5_read_next_data (octave_hdf5_id group_id, const char *name, void *dv);
 
 extern OCTINTERP_API bool
-add_hdf5_data (hid_t loc_id, const octave_value& tc,
+add_hdf5_data (octave_hdf5_id loc_id, const octave_value& tc,
                const std::string& name, const std::string& doc,
                bool mark_as_global, bool save_as_floats);
 
 extern OCTINTERP_API int
-save_hdf5_empty (hid_t loc_id, const char *name, const dim_vector d);
+save_hdf5_empty (octave_hdf5_id loc_id, const char *name, const dim_vector d);
 
 extern OCTINTERP_API int
-load_hdf5_empty (hid_t loc_id, const char *name, dim_vector &d);
+load_hdf5_empty (octave_hdf5_id loc_id, const char *name, dim_vector &d);
 
 extern OCTINTERP_API std::string
 read_hdf5_data (std::istream& is,  const std::string& filename, bool& global,
@@ -189,26 +146,20 @@
                 bool mark_as_global, bool save_as_floats);
 
 extern OCTINTERP_API bool
-hdf5_check_attr (hid_t loc_id, const char *attr_name);
+hdf5_check_attr (octave_hdf5_id loc_id, const char *attr_name);
 
 extern OCTINTERP_API bool
-hdf5_get_scalar_attr (hid_t loc_id, hid_t type_id, const char *attr_name,
-                      void *buf);
+hdf5_get_scalar_attr (octave_hdf5_id loc_id, octave_hdf5_id type_id,
+                      const char *attr_name, void *buf);
 
-extern OCTINTERP_API herr_t
-hdf5_add_attr (hid_t loc_id, const char *attr_name);
+extern OCTINTERP_API octave_hdf5_err
+hdf5_add_attr (octave_hdf5_id loc_id, const char *attr_name);
 
 
-extern OCTINTERP_API herr_t
-hdf5_add_scalar_attr (hid_t loc_id, hid_t type_id,
+extern OCTINTERP_API octave_hdf5_err
+hdf5_add_scalar_attr (octave_hdf5_id loc_id, octave_hdf5_id type_id,
                       const char *attr_name, void *buf);
 
-#ifdef USE_64_BIT_IDX_T
-#define H5T_NATIVE_IDX H5T_NATIVE_INT64
-#else
-#define H5T_NATIVE_IDX H5T_NATIVE_INT
-#endif
-
 #endif
 
 #endif
--- a/libinterp/corefcn/module.mk
+++ b/libinterp/corefcn/module.mk
@@ -82,7 +82,7 @@
   corefcn/oct-fstrm.h \
   corefcn/oct-handle.h \
   corefcn/oct-hdf5.h \
-  corefcn/oct-hdf5-id.h \
+  corefcn/oct-hdf5-types.h \
   corefcn/oct-hist.h \
   corefcn/oct-iostrm.h \
   corefcn/oct-lvalue.h \
@@ -216,7 +216,7 @@
   corefcn/mgorth.cc \
   corefcn/nproc.cc \
   corefcn/oct-fstrm.cc \
-  corefcn/oct-hdf5-id.cc \
+  corefcn/oct-hdf5-types.cc \
   corefcn/oct-hist.cc \
   corefcn/oct-iostrm.cc \
   corefcn/oct-lvalue.cc \
rename from libinterp/corefcn/oct-hdf5-id.cc
rename to libinterp/corefcn/oct-hdf5-types.cc
--- a/libinterp/corefcn/oct-hdf5-id.cc
+++ b/libinterp/corefcn/oct-hdf5-types.cc
@@ -26,10 +26,10 @@
 
 #include "error.h"
 #include "oct-hdf5.h"
-#include "oct-hdf5-id.h"
+#include "oct-hdf5-types.h"
 
 bool
-check_hdf5_id_type (bool warn)
+check_hdf5_types (bool warn)
 {
   static bool checked = false;
   static bool ok = false;
@@ -43,6 +43,13 @@
         warning_with_id
           ("Octave:internal",
            "the size of octave_hdf5_id is smaller than the size of HDF5 hid_t");
+
+      ok = sizeof (octave_hdf5_err) >= sizeof (herr_t);
+
+      if (warn && ! ok)
+        warning_with_id
+          ("Octave:internal",
+           "the size of octave_hdf5_err is smaller than the size of HDF5 herr_t");
 #else
       warning_with_id
         ("Octave:internal",
rename from libinterp/corefcn/oct-hdf5-id.h
rename to libinterp/corefcn/oct-hdf5-types.h
--- a/libinterp/corefcn/oct-hdf5-id.h
+++ b/libinterp/corefcn/oct-hdf5-types.h
@@ -20,11 +20,12 @@
 
 */
 
-#if !defined (octave_oct_hdf5_id_h)
-#define octave_oct_hdf5_id_h 1
+#if !defined (octave_oct_hdf5_types_h)
+#define octave_oct_hdf5_types_h 1
 
 typedef int octave_hdf5_id;
+typedef int octave_hdf5_err;
 
-extern bool check_hdf5_id_type (bool warn = true);
+extern bool check_hdf5_types (bool warn = true);
 
 #endif
--- a/libinterp/corefcn/oct-hdf5.h
+++ b/libinterp/corefcn/oct-hdf5.h
@@ -27,8 +27,16 @@
 
 #include <hdf5.h>
 
+#include "oct-hdf5-types.h"
+
 #define HDF5_SAVE_TYPE H5T_NATIVE_UINT8
 
+#ifdef USE_64_BIT_IDX_T
+#define H5T_NATIVE_IDX H5T_NATIVE_INT64
+#else
+#define H5T_NATIVE_IDX H5T_NATIVE_INT
+#endif
+
 #endif
 
 #endif
--- a/libinterp/octave-value/ov-base.h
+++ b/libinterp/octave-value/ov-base.h
@@ -36,7 +36,7 @@
 #include "str-vec.h"
 
 #include "error.h"
-#include "oct-hdf5-id.h"
+#include "oct-hdf5-types.h"
 
 class Cell;
 class mxArray;