# HG changeset patch # User John W. Eaton # Date 1434404564 14400 # Node ID bfe66db8addb63e53b460bc95d0cf91428caa5c6 # Parent 5c088348fddbbf433c93c370962a075ccb03e9eb 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. diff -r 5c088348fddb -r bfe66db8addb libinterp/corefcn/load-save.cc --- a/libinterp/corefcn/load-save.cc Mon Jun 15 21:56:34 2015 +0200 +++ b/libinterp/corefcn/load-save.cc Mon Jun 15 17:42:44 2015 -0400 @@ -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" diff -r 5c088348fddb -r bfe66db8addb libinterp/corefcn/ls-hdf5.cc --- a/libinterp/corefcn/ls-hdf5.cc Mon Jun 15 21:56:34 2015 +0200 +++ b/libinterp/corefcn/ls-hdf5.cc Mon Jun 15 17:42:44 2015 -0400 @@ -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 (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 (os); diff -r 5c088348fddb -r bfe66db8addb libinterp/corefcn/ls-hdf5.h --- a/libinterp/corefcn/ls-hdf5.h Mon Jun 15 21:56:34 2015 +0200 +++ b/libinterp/corefcn/ls-hdf5.h Mon Jun 15 17:42:44 2015 -0400 @@ -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 diff -r 5c088348fddb -r bfe66db8addb libinterp/corefcn/module.mk --- a/libinterp/corefcn/module.mk Mon Jun 15 21:56:34 2015 +0200 +++ b/libinterp/corefcn/module.mk Mon Jun 15 17:42:44 2015 -0400 @@ -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 \ diff -r 5c088348fddb -r bfe66db8addb libinterp/corefcn/oct-hdf5-id.cc --- a/libinterp/corefcn/oct-hdf5-id.cc Mon Jun 15 21:56:34 2015 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -/* - -Copyright (C) 2015 John W. Eaton - -This file is part of Octave. - -Octave is free software; you can redistribute it and/or modify it -under the terms of the GNU General Public License as published by the -Free Software Foundation; either version 3 of the License, or (at your -option) any later version. - -Octave is distributed in the hope that it will be useful, but WITHOUT -ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or -FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License -for more details. - -You should have received a copy of the GNU General Public License -along with Octave; see the file COPYING. If not, see -. - -*/ - -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "error.h" -#include "oct-hdf5.h" -#include "oct-hdf5-id.h" - -bool -check_hdf5_id_type (bool warn) -{ - static bool checked = false; - static bool ok = false; - - if (! checked) - { -#if defined (HAVE_HDF5) - ok = sizeof (octave_hdf5_id) >= sizeof (hid_t); - - if (warn && ! ok) - warning_with_id - ("Octave:internal", - "the size of octave_hdf5_id is smaller than the size of HDF5 hid_t"); -#else - warning_with_id - ("Octave:internal", - "check_hdf5_id_type called but Octave was not compiled with support for HDF5"); -#endif - - checked = true; - } - - return ok; -} diff -r 5c088348fddb -r bfe66db8addb libinterp/corefcn/oct-hdf5-id.h --- a/libinterp/corefcn/oct-hdf5-id.h Mon Jun 15 21:56:34 2015 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -/* - -Copyright (C) 2015 John W. Eaton - -This file is part of Octave. - -Octave is free software; you can redistribute it and/or modify it -under the terms of the GNU General Public License as published by the -Free Software Foundation; either version 3 of the License, or (at your -option) any later version. - -Octave is distributed in the hope that it will be useful, but WITHOUT -ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or -FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License -for more details. - -You should have received a copy of the GNU General Public License -along with Octave; see the file COPYING. If not, see -. - -*/ - -#if !defined (octave_oct_hdf5_id_h) -#define octave_oct_hdf5_id_h 1 - -typedef int octave_hdf5_id; - -extern bool check_hdf5_id_type (bool warn = true); - -#endif diff -r 5c088348fddb -r bfe66db8addb libinterp/corefcn/oct-hdf5-types.cc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/libinterp/corefcn/oct-hdf5-types.cc Mon Jun 15 17:42:44 2015 -0400 @@ -0,0 +1,63 @@ +/* + +Copyright (C) 2015 John W. Eaton + +This file is part of Octave. + +Octave is free software; you can redistribute it and/or modify it +under the terms of the GNU General Public License as published by the +Free Software Foundation; either version 3 of the License, or (at your +option) any later version. + +Octave is distributed in the hope that it will be useful, but WITHOUT +ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +for more details. + +You should have received a copy of the GNU General Public License +along with Octave; see the file COPYING. If not, see +. + +*/ + +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "error.h" +#include "oct-hdf5.h" +#include "oct-hdf5-types.h" + +bool +check_hdf5_types (bool warn) +{ + static bool checked = false; + static bool ok = false; + + if (! checked) + { +#if defined (HAVE_HDF5) + ok = sizeof (octave_hdf5_id) >= sizeof (hid_t); + + if (warn && ! ok) + 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", + "check_hdf5_id_type called but Octave was not compiled with support for HDF5"); +#endif + + checked = true; + } + + return ok; +} diff -r 5c088348fddb -r bfe66db8addb libinterp/corefcn/oct-hdf5-types.h --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/libinterp/corefcn/oct-hdf5-types.h Mon Jun 15 17:42:44 2015 -0400 @@ -0,0 +1,31 @@ +/* + +Copyright (C) 2015 John W. Eaton + +This file is part of Octave. + +Octave is free software; you can redistribute it and/or modify it +under the terms of the GNU General Public License as published by the +Free Software Foundation; either version 3 of the License, or (at your +option) any later version. + +Octave is distributed in the hope that it will be useful, but WITHOUT +ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +for more details. + +You should have received a copy of the GNU General Public License +along with Octave; see the file COPYING. If not, see +. + +*/ + +#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_types (bool warn = true); + +#endif diff -r 5c088348fddb -r bfe66db8addb libinterp/corefcn/oct-hdf5.h --- a/libinterp/corefcn/oct-hdf5.h Mon Jun 15 21:56:34 2015 +0200 +++ b/libinterp/corefcn/oct-hdf5.h Mon Jun 15 17:42:44 2015 -0400 @@ -27,8 +27,16 @@ #include +#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 diff -r 5c088348fddb -r bfe66db8addb libinterp/octave-value/ov-base.h --- a/libinterp/octave-value/ov-base.h Mon Jun 15 21:56:34 2015 +0200 +++ b/libinterp/octave-value/ov-base.h Mon Jun 15 17:42:44 2015 -0400 @@ -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;