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remove HDF5 wrapper functions

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This commit is contained in:
conrad
2022-12-01 18:01:07 +10:00
parent ff77799e8d
commit 44ef7e7e3e
10 changed files with 171 additions and 596 deletions
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CMakeLists.txt
-52
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@@ -52,7 +52,6 @@ set(ARMA_USE_WRAPPER true)
set(ARMA_USE_LAPACK false)
set(ARMA_USE_BLAS false)
set(ARMA_USE_ATLAS false)
set(ARMA_USE_HDF5_CMAKE false)
set(ARMA_USE_ARPACK false)
set(ARMA_USE_EXTERN_RNG false)
set(ARMA_USE_SUPERLU false) # Caveat: only SuperLU version 5.x can be used!
@@ -188,12 +187,6 @@ else()
option(BUILD_SHARED_LIBS "build shared library" ON)
endif()
option(DETECT_HDF5 "Detect HDF5 and include HDF5 support, if found" ON)
# set(DETECT_HDF5 false)
## uncomment the above line to disable the detection of the HDF5 library;
## you can also disable HDF5 detection directly on the command line:
## cmake -D DETECT_HDF5=false .
option(OPENBLAS_PROVIDES_LAPACK "Assume that OpenBLAS provides LAPACK functions" OFF)
## Example use on the command line:
## cmake -D OPENBLAS_PROVIDES_LAPACK=true .
@@ -247,7 +240,6 @@ message(STATUS "CMAKE_COMPILER_IS_GNUCXX = ${CMAKE_COMPILER_IS_GNUCXX}" )
message(STATUS "")
message(STATUS "*** Options:" )
message(STATUS "BUILD_SHARED_LIBS = ${BUILD_SHARED_LIBS}" )
message(STATUS "DETECT_HDF5 = ${DETECT_HDF5}" )
message(STATUS "OPENBLAS_PROVIDES_LAPACK = ${OPENBLAS_PROVIDES_LAPACK}")
message(STATUS "ALLOW_FLEXIBLAS_LINUX = ${ALLOW_FLEXIBLAS_LINUX}" )
message(STATUS "ALLOW_OPENBLAS_MACOS = ${ALLOW_OPENBLAS_MACOS}" )
@@ -453,49 +445,6 @@ endif()
find_package(PkgConfig)
if(DETECT_HDF5)
find_package(HDF5 QUIET COMPONENTS C)
if(NOT HDF5_FOUND)
# On Debian systems, the HDF5 package has been split into multiple packages
# so that it is co-installable. But this may mean that the include files
# are hidden somewhere very odd that the FindHDF5.cmake script will not
# find. Thus, we'll also quickly check pkgconfig to see if there is
# information on what to use there.
if (PKG_CONFIG_FOUND)
pkg_check_modules(HDF5 hdf5)
# But using pkgconfig is a little weird because HDF5_LIBRARIES won't be
# filled with exact library paths, like the other scripts. So instead
# what we get is HDF5_LIBRARY_DIRS which is the equivalent of what we'd
# pass to -L. So we have to add those...
if (HDF5_FOUND)
link_directories("${HDF5_LIBRARY_DIRS}")
endif()
endif()
endif()
message(STATUS "HDF5_FOUND = ${HDF5_FOUND}")
if(HDF5_FOUND)
set(ARMA_USE_HDF5_CMAKE true)
set(CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${HDF5_INCLUDE_DIRS})
set(ARMA_LIBS ${ARMA_LIBS} ${HDF5_LIBRARIES})
# Since we called HDF5 with no arguments, the script will find only the C
# bindings. So HDF5_INCLUDE_DIRS may now contain one or two elements; if it
# contains two, the first is what the user passed as HDF5_INCLUDE_DIR and we
# should use that as ARMA_HDF5_INCLUDE_DIR. Otherwise, the one entry in
# HDF5_INCLUDE_DIRS is the correct include directory. So, in either case we
# can use the first element in the list. Issue a status message, too, just
# for good measure.
list(GET HDF5_INCLUDE_DIRS 0 ARMA_HDF5_INCLUDE_DIR)
message(STATUS "ARMA_HDF5_INCLUDE_DIR = ${ARMA_HDF5_INCLUDE_DIR}")
message(STATUS "")
message(STATUS "*** If use of HDF5 is causing problems,")
message(STATUS "*** rerun cmake with HDF5 detection disabled:")
message(STATUS "*** cmake -D DETECT_HDF5=false .")
message(STATUS "")
endif()
endif()
include(ARMA_FindARPACK)
message(STATUS "ARPACK_FOUND = ${ARPACK_FOUND}")
@@ -539,7 +488,6 @@ message(STATUS "*** ARMA_USE_WRAPPER = ${ARMA_USE_WRAPPER}")
message(STATUS "*** ARMA_USE_LAPACK = ${ARMA_USE_LAPACK}")
message(STATUS "*** ARMA_USE_BLAS = ${ARMA_USE_BLAS}")
message(STATUS "*** ARMA_USE_ATLAS = ${ARMA_USE_ATLAS}")
message(STATUS "*** ARMA_USE_HDF5_CMAKE = ${ARMA_USE_HDF5_CMAKE}")
message(STATUS "*** ARMA_USE_ARPACK = ${ARMA_USE_ARPACK}")
message(STATUS "*** ARMA_USE_EXTERN_RNG = ${ARMA_USE_EXTERN_RNG}")
message(STATUS "*** ARMA_USE_SUPERLU = ${ARMA_USE_SUPERLU}")
include/armadillo
-1
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@@ -152,7 +152,6 @@ namespace arma
#include "armadillo_bits/def_lapack.hpp"
#include "armadillo_bits/def_arpack.hpp"
#include "armadillo_bits/def_superlu.hpp"
#include "armadillo_bits/def_hdf5.hpp"
#include "armadillo_bits/translate_blas.hpp"
#include "armadillo_bits/translate_atlas.hpp"
include/armadillo_bits/config.hpp
-10
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@@ -159,14 +159,6 @@
//// Comment out the above line to disable checking for nonfinite matrices
#endif
// #define ARMA_USE_HDF5_CMAKE
#if defined(ARMA_USE_HDF5_CMAKE) && defined(ARMA_USE_WRAPPER)
#undef ARMA_USE_HDF5
#define ARMA_USE_HDF5
// #define ARMA_HDF5_INCLUDE_DIR /usr/include/
#endif
#if !defined(ARMA_MAT_PREALLOC)
#define ARMA_MAT_PREALLOC 16
#endif
@@ -268,7 +260,6 @@
#if defined(ARMA_DONT_USE_WRAPPER)
#undef ARMA_USE_WRAPPER
#undef ARMA_USE_HDF5_CMAKE
#endif
#if defined(ARMA_DONT_USE_FORTRAN_HIDDEN_ARGS)
@@ -315,7 +306,6 @@
#if defined(ARMA_DONT_USE_HDF5)
#undef ARMA_USE_HDF5
#undef ARMA_USE_HDF5_CMAKE
#endif
#if defined(ARMA_DONT_OPTIMISE_BAND) || defined(ARMA_DONT_OPTIMISE_SOLVE_BAND)
include/armadillo_bits/config.hpp.cmake
-10
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@@ -159,14 +159,6 @@
//// Comment out the above line to disable checking for nonfinite matrices
#endif
#cmakedefine ARMA_USE_HDF5_CMAKE
#if defined(ARMA_USE_HDF5_CMAKE) && defined(ARMA_USE_WRAPPER)
#undef ARMA_USE_HDF5
#define ARMA_USE_HDF5
#define ARMA_HDF5_INCLUDE_DIR ${ARMA_HDF5_INCLUDE_DIR}/
#endif
#if !defined(ARMA_MAT_PREALLOC)
#define ARMA_MAT_PREALLOC 16
#endif
@@ -268,7 +260,6 @@
#if defined(ARMA_DONT_USE_WRAPPER)
#undef ARMA_USE_WRAPPER
#undef ARMA_USE_HDF5_CMAKE
#endif
#if defined(ARMA_DONT_USE_FORTRAN_HIDDEN_ARGS)
@@ -315,7 +306,6 @@
#if defined(ARMA_DONT_USE_HDF5)
#undef ARMA_USE_HDF5
#undef ARMA_USE_HDF5_CMAKE
#endif
#if defined(ARMA_DONT_OPTIMISE_BAND) || defined(ARMA_DONT_OPTIMISE_SOLVE_BAND)
include/armadillo_bits/def_hdf5.hpp
-156
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@@ -1,156 +0,0 @@
// SPDX-License-Identifier: Apache-2.0
//
// Copyright 2008-2016 Conrad Sanderson (http://conradsanderson.id.au)
// Copyright 2008-2016 National ICT Australia (NICTA)
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
// ------------------------------------------------------------------------
#if defined(ARMA_USE_HDF5)
#if !defined(ARMA_USE_HDF5_CMAKE)
// macros needed if the wrapper run-time library is not being used
#define arma_H5Tcopy H5Tcopy
#define arma_H5Tcreate H5Tcreate
#define arma_H5Tinsert H5Tinsert
#define arma_H5Tequal H5Tequal
#define arma_H5Tclose H5Tclose
#define arma_H5Dopen H5Dopen
#define arma_H5Dget_type H5Dget_type
#define arma_H5Dclose H5Dclose
#define arma_H5Dwrite H5Dwrite
#define arma_H5Dget_space H5Dget_space
#define arma_H5Dread H5Dread
#define arma_H5Dcreate H5Dcreate
#define arma_H5Sget_simple_extent_ndims H5Sget_simple_extent_ndims
#define arma_H5Sget_simple_extent_dims H5Sget_simple_extent_dims
#define arma_H5Sclose H5Sclose
#define arma_H5Screate_simple H5Screate_simple
#define arma_H5Ovisit H5Ovisit
#define arma_H5Eset_auto H5Eset_auto
#define arma_H5Eget_auto H5Eget_auto
#define arma_H5Fopen H5Fopen
#define arma_H5Fcreate H5Fcreate
#define arma_H5Fclose H5Fclose
#define arma_H5Fis_hdf5 H5Fis_hdf5
#define arma_H5Gcreate H5Gcreate
#define arma_H5Gopen H5Gopen
#define arma_H5Gclose H5Gclose
#define arma_H5Lexists H5Lexists
#define arma_H5Ldelete H5Ldelete
#define arma_H5T_NATIVE_UCHAR H5T_NATIVE_UCHAR
#define arma_H5T_NATIVE_CHAR H5T_NATIVE_CHAR
#define arma_H5T_NATIVE_SHORT H5T_NATIVE_SHORT
#define arma_H5T_NATIVE_USHORT H5T_NATIVE_USHORT
#define arma_H5T_NATIVE_INT H5T_NATIVE_INT
#define arma_H5T_NATIVE_UINT H5T_NATIVE_UINT
#define arma_H5T_NATIVE_LONG H5T_NATIVE_LONG
#define arma_H5T_NATIVE_ULONG H5T_NATIVE_ULONG
#define arma_H5T_NATIVE_LLONG H5T_NATIVE_LLONG
#define arma_H5T_NATIVE_ULLONG H5T_NATIVE_ULLONG
#define arma_H5T_NATIVE_FLOAT H5T_NATIVE_FLOAT
#define arma_H5T_NATIVE_DOUBLE H5T_NATIVE_DOUBLE
#else
// prototypes for the wrapper functions defined in the wrapper run-time library (src/wrapper.cpp)
extern "C"
{
// Wrapper functions for H5* functions.
hid_t arma_H5Tcopy(hid_t dtype_id);
hid_t arma_H5Tcreate(H5T_class_t cl, size_t size);
herr_t arma_H5Tinsert(hid_t dtype_id, const char* name, size_t offset, hid_t field_id);
htri_t arma_H5Tequal(hid_t dtype_id1, hid_t dtype_id2);
herr_t arma_H5Tclose(hid_t dtype_id);
hid_t arma_H5Dopen(hid_t loc_id, const char* name, hid_t dapl_id);
hid_t arma_H5Dget_type(hid_t dataset_id);
herr_t arma_H5Dclose(hid_t dataset_id);
hid_t arma_H5Dcreate(hid_t loc_id, const char* name, hid_t dtype_id, hid_t space_id, hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id);
herr_t arma_H5Dwrite(hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t xfer_plist_id, const void* buf);
hid_t arma_H5Dget_space(hid_t dataset_id);
herr_t arma_H5Dread(hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t xfer_plist_id, void* buf);
int arma_H5Sget_simple_extent_ndims(hid_t space_id);
int arma_H5Sget_simple_extent_dims(hid_t space_id, hsize_t* dims, hsize_t* maxdims);
herr_t arma_H5Sclose(hid_t space_id);
hid_t arma_H5Screate_simple(int rank, const hsize_t* current_dims, const hsize_t* maximum_dims);
herr_t arma_H5Ovisit(hid_t object_id, H5_index_t index_type, H5_iter_order_t order, H5O_iterate_t op, void* op_data);
herr_t arma_H5Eset_auto(hid_t estack_id, H5E_auto_t func, void* client_data);
herr_t arma_H5Eget_auto(hid_t estack_id, H5E_auto_t* func, void** client_data);
hid_t arma_H5Fopen(const char* name, unsigned flags, hid_t fapl_id);
hid_t arma_H5Fcreate(const char* name, unsigned flags, hid_t fcpl_id, hid_t fapl_id);
herr_t arma_H5Fclose(hid_t file_id);
htri_t arma_H5Fis_hdf5(const char* name);
hid_t arma_H5Gcreate(hid_t loc_id, const char* name, hid_t lcpl_id, hid_t gcpl_id, hid_t gapl_id);
hid_t arma_H5Gopen(hid_t loc_id, const char* name, hid_t gapl_id);
herr_t arma_H5Gclose(hid_t group_id);
htri_t arma_H5Lexists(hid_t loc_id, const char* name, hid_t lapl_id);
herr_t arma_H5Ldelete(hid_t loc_id, const char* name, hid_t lapl_id);
// Wrapper variables that represent the hid_t values for the H5T_NATIVE_*
// types. Note that H5T_NATIVE_UCHAR itself is a macro that resolves to about
// forty other macros, and we definitely don't want to hijack those,
// so this is the best way to go about wrapping these...
extern hid_t arma_H5T_NATIVE_UCHAR;
extern hid_t arma_H5T_NATIVE_CHAR;
extern hid_t arma_H5T_NATIVE_SHORT;
extern hid_t arma_H5T_NATIVE_USHORT;
extern hid_t arma_H5T_NATIVE_INT;
extern hid_t arma_H5T_NATIVE_UINT;
extern hid_t arma_H5T_NATIVE_LONG;
extern hid_t arma_H5T_NATIVE_ULONG;
extern hid_t arma_H5T_NATIVE_LLONG;
extern hid_t arma_H5T_NATIVE_ULLONG;
extern hid_t arma_H5T_NATIVE_FLOAT;
extern hid_t arma_H5T_NATIVE_DOUBLE;
}
// Lastly, we have to hijack H5open() and H5check_version(), which are called
// by some expanded macros of the other H5* functions. This means we can't
// create arma_H5open(), because we can't modify those macros. Instead, we'll
// create arma::H5open() and arma::H5check_version(), and then issue a using
// directive so that arma::H5open() and arma::H5check_version() are always
// called.
//
// There is potential danger in the use of a using directive like this, but in
// this case, I can't think of a better way to solve the problem, and I doubt
// this will cause problems in any situations that aren't truly bizarre. And
// if it does cause problems, the user can #define ARMA_DONT_USE_WRAPPER or
// #undef ARMA_USE_WRAPPER in their Armadillo configuration.
herr_t H5open();
herr_t H5check_version(unsigned majnum, unsigned minnum, unsigned relnum);
using arma::H5open;
using arma::H5check_version;
#endif
#endif
include/armadillo_bits/diskio_meat.hpp
+58 -58
View File
@@ -1204,12 +1204,12 @@ diskio::save_hdf5_binary(const Mat<eT>& x, const hdf5_name& spec, std::string& e
const bool append = bool(spec.opts.flags & hdf5_opts::flag_append);
const bool replace = bool(spec.opts.flags & hdf5_opts::flag_replace);
const bool use_existing_file = ((append || replace) && (arma_H5Fis_hdf5(spec.filename.c_str()) > 0));
const bool use_existing_file = ((append || replace) && (H5Fis_hdf5(spec.filename.c_str()) > 0));
const std::string tmp_name = (use_existing_file) ? std::string() : diskio::gen_tmp_name(spec.filename);
// Set up the file according to HDF5's preferences
hid_t file = (use_existing_file) ? arma_H5Fopen(spec.filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT) : arma_H5Fcreate(tmp_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
hid_t file = (use_existing_file) ? H5Fopen(spec.filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT) : H5Fcreate(tmp_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if(file < 0) { return false; }
@@ -1218,7 +1218,7 @@ diskio::save_hdf5_binary(const Mat<eT>& x, const hdf5_name& spec, std::string& e
dims[1] = x.n_rows;
dims[0] = x.n_cols;
hid_t dataspace = arma_H5Screate_simple(2, dims, NULL); // treat the matrix as a 2d array dataspace
hid_t dataspace = H5Screate_simple(2, dims, NULL); // treat the matrix as a 2d array dataspace
hid_t datatype = hdf5_misc::get_hdf5_type<eT>();
// If this returned something invalid, well, it's time to crash.
@@ -1236,11 +1236,11 @@ diskio::save_hdf5_binary(const Mat<eT>& x, const hdf5_name& spec, std::string& e
// Create another group...
if(loc != 0) // Ignore the first /, if there is a leading /.
{
hid_t gid = arma_H5Gcreate((groups.size() == 0) ? file : groups[groups.size() - 1], full_name.substr(0, loc).c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hid_t gid = H5Gcreate((groups.size() == 0) ? file : groups[groups.size() - 1], full_name.substr(0, loc).c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if((gid < 0) && use_existing_file)
{
gid = arma_H5Gopen((groups.size() == 0) ? file : groups[groups.size() - 1], full_name.substr(0, loc).c_str(), H5P_DEFAULT);
gid = H5Gopen((groups.size() == 0) ? file : groups[groups.size() - 1], full_name.substr(0, loc).c_str(), H5P_DEFAULT);
}
groups.push_back(gid);
@@ -1255,14 +1255,14 @@ diskio::save_hdf5_binary(const Mat<eT>& x, const hdf5_name& spec, std::string& e
if(use_existing_file && replace)
{
arma_H5Ldelete(last_group, dataset_name.c_str(), H5P_DEFAULT);
H5Ldelete(last_group, dataset_name.c_str(), H5P_DEFAULT);
// NOTE: H5Ldelete() in HDF5 v1.8 doesn't reclaim the deleted space; use h5repack to reclaim space: h5repack oldfile.h5 newfile.h5
// NOTE: has this behaviour changed in HDF5 1.10 ?
// NOTE: https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2017-August/010482.html
// NOTE: https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2017-August/010486.html
}
hid_t dataset = arma_H5Dcreate(last_group, dataset_name.c_str(), datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hid_t dataset = H5Dcreate(last_group, dataset_name.c_str(), datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if(dataset < 0)
{
@@ -1272,15 +1272,15 @@ diskio::save_hdf5_binary(const Mat<eT>& x, const hdf5_name& spec, std::string& e
}
else
{
save_okay = (arma_H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, x.mem) >= 0);
save_okay = (H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, x.mem) >= 0);
arma_H5Dclose(dataset);
H5Dclose(dataset);
}
arma_H5Tclose(datatype);
arma_H5Sclose(dataspace);
for(size_t i = 0; i < groups.size(); ++i) { arma_H5Gclose(groups[i]); }
arma_H5Fclose(file);
H5Tclose(datatype);
H5Sclose(dataspace);
for(size_t i = 0; i < groups.size(); ++i) { H5Gclose(groups[i]); }
H5Fclose(file);
if((use_existing_file == false) && (save_okay == true)) { save_okay = diskio::safe_rename(tmp_name, spec.filename); }
@@ -2562,7 +2562,7 @@ diskio::load_hdf5_binary(Mat<eT>& x, const hdf5_name& spec, std::string& err_msg
bool load_okay = false;
hid_t fid = arma_H5Fopen(spec.filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
hid_t fid = H5Fopen(spec.filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
if(fid >= 0)
{
@@ -2589,22 +2589,22 @@ diskio::load_hdf5_binary(Mat<eT>& x, const hdf5_name& spec, std::string& err_msg
if(dataset >= 0)
{
hid_t filespace = arma_H5Dget_space(dataset);
hid_t filespace = H5Dget_space(dataset);
// This must be <= 2 due to our search rules.
const int ndims = arma_H5Sget_simple_extent_ndims(filespace);
const int ndims = H5Sget_simple_extent_ndims(filespace);
hsize_t dims[2];
const herr_t query_status = arma_H5Sget_simple_extent_dims(filespace, dims, NULL);
const herr_t query_status = H5Sget_simple_extent_dims(filespace, dims, NULL);
// arma_check(query_status < 0, "Mat::load(): cannot get size of HDF5 dataset");
if(query_status < 0)
{
err_msg = "cannot get size of HDF5 dataset";
arma_H5Sclose(filespace);
arma_H5Dclose(dataset);
arma_H5Fclose(fid);
H5Sclose(filespace);
H5Dclose(dataset);
H5Fclose(fid);
return false;
}
@@ -2614,14 +2614,14 @@ diskio::load_hdf5_binary(Mat<eT>& x, const hdf5_name& spec, std::string& err_msg
try { x.set_size(dims[1], dims[0]); } catch(...) { err_msg = "not enough memory"; return false; }
// Now we have to see what type is stored to figure out how to load it.
hid_t datatype = arma_H5Dget_type(dataset);
hid_t datatype = H5Dget_type(dataset);
hid_t mat_type = hdf5_misc::get_hdf5_type<eT>();
// If these are the same type, it is simple.
if(arma_H5Tequal(datatype, mat_type) > 0)
if(H5Tequal(datatype, mat_type) > 0)
{
// Load directly; H5S_ALL used so that we load the entire dataset.
hid_t read_status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(x.memptr()));
hid_t read_status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(x.memptr()));
if(read_status >= 0) { load_okay = true; }
}
@@ -2634,14 +2634,14 @@ diskio::load_hdf5_binary(Mat<eT>& x, const hdf5_name& spec, std::string& err_msg
}
// Now clean up.
arma_H5Tclose(datatype);
arma_H5Tclose(mat_type);
arma_H5Sclose(filespace);
H5Tclose(datatype);
H5Tclose(mat_type);
H5Sclose(filespace);
}
arma_H5Dclose(dataset);
H5Dclose(dataset);
arma_H5Fclose(fid);
H5Fclose(fid);
if(load_okay == false)
{
@@ -2680,7 +2680,7 @@ diskio::load_auto_detect(Mat<eT>& x, const std::string& name, std::string& err_m
#if defined(ARMA_USE_HDF5)
// We're currently using the C bindings for the HDF5 library, which don't support C++ streams
if( arma_H5Fis_hdf5(name.c_str()) ) { return load_hdf5_binary(x, name, err_msg); }
if( H5Fis_hdf5(name.c_str()) ) { return load_hdf5_binary(x, name, err_msg); }
#endif
std::fstream f;
@@ -3844,12 +3844,12 @@ diskio::save_hdf5_binary(const Cube<eT>& x, const hdf5_name& spec, std::string&
const bool append = bool(spec.opts.flags & hdf5_opts::flag_append);
const bool replace = bool(spec.opts.flags & hdf5_opts::flag_replace);
const bool use_existing_file = ((append || replace) && (arma_H5Fis_hdf5(spec.filename.c_str()) > 0));
const bool use_existing_file = ((append || replace) && (H5Fis_hdf5(spec.filename.c_str()) > 0));
const std::string tmp_name = (use_existing_file) ? std::string() : diskio::gen_tmp_name(spec.filename);
// Set up the file according to HDF5's preferences
hid_t file = (use_existing_file) ? arma_H5Fopen(spec.filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT) : arma_H5Fcreate(tmp_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
hid_t file = (use_existing_file) ? H5Fopen(spec.filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT) : H5Fcreate(tmp_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if(file < 0) { return false; }
@@ -3859,7 +3859,7 @@ diskio::save_hdf5_binary(const Cube<eT>& x, const hdf5_name& spec, std::string&
dims[1] = x.n_cols;
dims[0] = x.n_slices;
hid_t dataspace = arma_H5Screate_simple(3, dims, NULL); // treat the cube as a 3d array dataspace
hid_t dataspace = H5Screate_simple(3, dims, NULL); // treat the cube as a 3d array dataspace
hid_t datatype = hdf5_misc::get_hdf5_type<eT>();
// If this returned something invalid, well, it's time to crash.
@@ -3877,11 +3877,11 @@ diskio::save_hdf5_binary(const Cube<eT>& x, const hdf5_name& spec, std::string&
// Create another group...
if(loc != 0) // Ignore the first /, if there is a leading /.
{
hid_t gid = arma_H5Gcreate((groups.size() == 0) ? file : groups[groups.size() - 1], full_name.substr(0, loc).c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hid_t gid = H5Gcreate((groups.size() == 0) ? file : groups[groups.size() - 1], full_name.substr(0, loc).c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if((gid < 0) && use_existing_file)
{
gid = arma_H5Gopen((groups.size() == 0) ? file : groups[groups.size() - 1], full_name.substr(0, loc).c_str(), H5P_DEFAULT);
gid = H5Gopen((groups.size() == 0) ? file : groups[groups.size() - 1], full_name.substr(0, loc).c_str(), H5P_DEFAULT);
}
groups.push_back(gid);
@@ -3896,14 +3896,14 @@ diskio::save_hdf5_binary(const Cube<eT>& x, const hdf5_name& spec, std::string&
if(use_existing_file && replace)
{
arma_H5Ldelete(last_group, dataset_name.c_str(), H5P_DEFAULT);
H5Ldelete(last_group, dataset_name.c_str(), H5P_DEFAULT);
// NOTE: H5Ldelete() in HDF5 v1.8 doesn't reclaim the deleted space; use h5repack to reclaim space: h5repack oldfile.h5 newfile.h5
// NOTE: has this behaviour changed in HDF5 1.10 ?
// NOTE: https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2017-August/010482.html
// NOTE: https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2017-August/010486.html
}
hid_t dataset = arma_H5Dcreate(last_group, dataset_name.c_str(), datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hid_t dataset = H5Dcreate(last_group, dataset_name.c_str(), datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if(dataset < 0)
{
@@ -3913,15 +3913,15 @@ diskio::save_hdf5_binary(const Cube<eT>& x, const hdf5_name& spec, std::string&
}
else
{
save_okay = (arma_H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, x.mem) >= 0);
save_okay = (H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, x.mem) >= 0);
arma_H5Dclose(dataset);
H5Dclose(dataset);
}
arma_H5Tclose(datatype);
arma_H5Sclose(dataspace);
for(size_t i = 0; i < groups.size(); ++i) { arma_H5Gclose(groups[i]); }
arma_H5Fclose(file);
H5Tclose(datatype);
H5Sclose(dataspace);
for(size_t i = 0; i < groups.size(); ++i) { H5Gclose(groups[i]); }
H5Fclose(file);
if((use_existing_file == false) && (save_okay == true)) { save_okay = diskio::safe_rename(tmp_name, spec.filename); }
@@ -4278,7 +4278,7 @@ diskio::load_hdf5_binary(Cube<eT>& x, const hdf5_name& spec, std::string& err_ms
bool load_okay = false;
hid_t fid = arma_H5Fopen(spec.filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
hid_t fid = H5Fopen(spec.filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
if(fid >= 0)
{
@@ -4305,22 +4305,22 @@ diskio::load_hdf5_binary(Cube<eT>& x, const hdf5_name& spec, std::string& err_ms
if(dataset >= 0)
{
hid_t filespace = arma_H5Dget_space(dataset);
hid_t filespace = H5Dget_space(dataset);
// This must be <= 3 due to our search rules.
const int ndims = arma_H5Sget_simple_extent_ndims(filespace);
const int ndims = H5Sget_simple_extent_ndims(filespace);
hsize_t dims[3];
const herr_t query_status = arma_H5Sget_simple_extent_dims(filespace, dims, NULL);
const herr_t query_status = H5Sget_simple_extent_dims(filespace, dims, NULL);
// arma_check(query_status < 0, "Cube::load(): cannot get size of HDF5 dataset");
if(query_status < 0)
{
err_msg = "cannot get size of HDF5 dataset";
arma_H5Sclose(filespace);
arma_H5Dclose(dataset);
arma_H5Fclose(fid);
H5Sclose(filespace);
H5Dclose(dataset);
H5Fclose(fid);
return false;
}
@@ -4331,14 +4331,14 @@ diskio::load_hdf5_binary(Cube<eT>& x, const hdf5_name& spec, std::string& err_ms
try { x.set_size(dims[2], dims[1], dims[0]); } catch(...) { err_msg = "not enough memory"; return false; }
// Now we have to see what type is stored to figure out how to load it.
hid_t datatype = arma_H5Dget_type(dataset);
hid_t datatype = H5Dget_type(dataset);
hid_t mat_type = hdf5_misc::get_hdf5_type<eT>();
// If these are the same type, it is simple.
if(arma_H5Tequal(datatype, mat_type) > 0)
if(H5Tequal(datatype, mat_type) > 0)
{
// Load directly; H5S_ALL used so that we load the entire dataset.
hid_t read_status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(x.memptr()));
hid_t read_status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(x.memptr()));
if(read_status >= 0) { load_okay = true; }
}
@@ -4351,14 +4351,14 @@ diskio::load_hdf5_binary(Cube<eT>& x, const hdf5_name& spec, std::string& err_ms
}
// Now clean up.
arma_H5Tclose(datatype);
arma_H5Tclose(mat_type);
arma_H5Sclose(filespace);
H5Tclose(datatype);
H5Tclose(mat_type);
H5Sclose(filespace);
}
arma_H5Dclose(dataset);
H5Dclose(dataset);
arma_H5Fclose(fid);
H5Fclose(fid);
if(load_okay == false)
{
@@ -4397,7 +4397,7 @@ diskio::load_auto_detect(Cube<eT>& x, const std::string& name, std::string& err_
#if defined(ARMA_USE_HDF5)
// We're currently using the C bindings for the HDF5 library, which don't support C++ streams
if( arma_H5Fis_hdf5(name.c_str()) ) { return load_hdf5_binary(x, name, err_msg); }
if( H5Fis_hdf5(name.c_str()) ) { return load_hdf5_binary(x, name, err_msg); }
#endif
std::fstream f;
include/armadillo_bits/hdf5_misc.hpp
+111 -111
View File
@@ -46,7 +46,7 @@ inline
hid_t
get_hdf5_type< unsigned char >()
{
return arma_H5Tcopy(arma_H5T_NATIVE_UCHAR);
return H5Tcopy(H5T_NATIVE_UCHAR);
}
template<>
@@ -54,7 +54,7 @@ inline
hid_t
get_hdf5_type< char >()
{
return arma_H5Tcopy(arma_H5T_NATIVE_CHAR);
return H5Tcopy(H5T_NATIVE_CHAR);
}
template<>
@@ -62,7 +62,7 @@ inline
hid_t
get_hdf5_type< short >()
{
return arma_H5Tcopy(arma_H5T_NATIVE_SHORT);
return H5Tcopy(H5T_NATIVE_SHORT);
}
template<>
@@ -70,7 +70,7 @@ inline
hid_t
get_hdf5_type< unsigned short >()
{
return arma_H5Tcopy(arma_H5T_NATIVE_USHORT);
return H5Tcopy(H5T_NATIVE_USHORT);
}
template<>
@@ -78,7 +78,7 @@ inline
hid_t
get_hdf5_type< int >()
{
return arma_H5Tcopy(arma_H5T_NATIVE_INT);
return H5Tcopy(H5T_NATIVE_INT);
}
template<>
@@ -86,7 +86,7 @@ inline
hid_t
get_hdf5_type< unsigned int >()
{
return arma_H5Tcopy(arma_H5T_NATIVE_UINT);
return H5Tcopy(H5T_NATIVE_UINT);
}
template<>
@@ -94,7 +94,7 @@ inline
hid_t
get_hdf5_type< long >()
{
return arma_H5Tcopy(arma_H5T_NATIVE_LONG);
return H5Tcopy(H5T_NATIVE_LONG);
}
template<>
@@ -102,7 +102,7 @@ inline
hid_t
get_hdf5_type< unsigned long >()
{
return arma_H5Tcopy(arma_H5T_NATIVE_ULONG);
return H5Tcopy(H5T_NATIVE_ULONG);
}
template<>
@@ -110,7 +110,7 @@ inline
hid_t
get_hdf5_type< long long >()
{
return arma_H5Tcopy(arma_H5T_NATIVE_LLONG);
return H5Tcopy(H5T_NATIVE_LLONG);
}
template<>
@@ -118,7 +118,7 @@ inline
hid_t
get_hdf5_type< unsigned long long >()
{
return arma_H5Tcopy(arma_H5T_NATIVE_ULLONG);
return H5Tcopy(H5T_NATIVE_ULLONG);
}
template<>
@@ -126,7 +126,7 @@ inline
hid_t
get_hdf5_type< float >()
{
return arma_H5Tcopy(arma_H5T_NATIVE_FLOAT);
return H5Tcopy(H5T_NATIVE_FLOAT);
}
template<>
@@ -134,7 +134,7 @@ inline
hid_t
get_hdf5_type< double >()
{
return arma_H5Tcopy(arma_H5T_NATIVE_DOUBLE);
return H5Tcopy(H5T_NATIVE_DOUBLE);
}
@@ -154,10 +154,10 @@ inline
hid_t
get_hdf5_type< std::complex<float> >()
{
hid_t type = arma_H5Tcreate(H5T_COMPOUND, sizeof(hdf5_complex_t<float>));
hid_t type = H5Tcreate(H5T_COMPOUND, sizeof(hdf5_complex_t<float>));
arma_H5Tinsert(type, "real", HOFFSET(hdf5_complex_t<float>, real), arma_H5T_NATIVE_FLOAT);
arma_H5Tinsert(type, "imag", HOFFSET(hdf5_complex_t<float>, imag), arma_H5T_NATIVE_FLOAT);
H5Tinsert(type, "real", HOFFSET(hdf5_complex_t<float>, real), H5T_NATIVE_FLOAT);
H5Tinsert(type, "imag", HOFFSET(hdf5_complex_t<float>, imag), H5T_NATIVE_FLOAT);
return type;
}
@@ -169,10 +169,10 @@ inline
hid_t
get_hdf5_type< std::complex<double> >()
{
hid_t type = arma_H5Tcreate(H5T_COMPOUND, sizeof(hdf5_complex_t<double>));
hid_t type = H5Tcreate(H5T_COMPOUND, sizeof(hdf5_complex_t<double>));
arma_H5Tinsert(type, "real", HOFFSET(hdf5_complex_t<double>, real), arma_H5T_NATIVE_DOUBLE);
arma_H5Tinsert(type, "imag", HOFFSET(hdf5_complex_t<double>, imag), arma_H5T_NATIVE_DOUBLE);
H5Tinsert(type, "real", HOFFSET(hdf5_complex_t<double>, real), H5T_NATIVE_DOUBLE);
H5Tinsert(type, "imag", HOFFSET(hdf5_complex_t<double>, imag), H5T_NATIVE_DOUBLE);
return type;
}
@@ -192,76 +192,76 @@ is_supported_arma_hdf5_type(hid_t datatype)
// start with most likely used types: double, complex<double>, float, complex<float>
search_type = get_hdf5_type<double>();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
search_type = get_hdf5_type< std::complex<double> >();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
search_type = get_hdf5_type<float>();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
search_type = get_hdf5_type< std::complex<float> >();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
// remaining supported types: u8, s8, u16, s16, u32, s32, u64, s64, ulng_t, slng_t
search_type = get_hdf5_type<u8>();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
search_type = get_hdf5_type<s8>();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
search_type = get_hdf5_type<u16>();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
search_type = get_hdf5_type<s16>();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
search_type = get_hdf5_type<u32>();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
search_type = get_hdf5_type<s32>();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
search_type = get_hdf5_type<u64>();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
search_type = get_hdf5_type<s64>();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
search_type = get_hdf5_type<ulng_t>();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
search_type = get_hdf5_type<slng_t>();
is_equal = ( arma_H5Tequal(datatype, search_type) > 0 );
arma_H5Tclose(search_type);
is_equal = ( H5Tequal(datatype, search_type) > 0 );
H5Tclose(search_type);
if(is_equal) { return true; }
return false;
@@ -297,13 +297,13 @@ hdf5_search_callback
if(info->type == H5O_TYPE_DATASET)
{
// Check type of dataset to see if we could even load it.
hid_t dataset = arma_H5Dopen(loc_id, name, H5P_DEFAULT);
hid_t datatype = arma_H5Dget_type(dataset);
hid_t dataset = H5Dopen(loc_id, name, H5P_DEFAULT);
hid_t datatype = H5Dget_type(dataset);
const bool is_supported = is_supported_arma_hdf5_type(datatype);
arma_H5Tclose(datatype);
arma_H5Dclose(dataset);
H5Tclose(datatype);
H5Dclose(dataset);
if(is_supported == false)
{
@@ -340,7 +340,7 @@ hdf5_search_callback
if(str == search_info->names[string_pos])
{
// We found it exactly.
hid_t match_candidate = arma_H5Dopen(loc_id, name, H5P_DEFAULT);
hid_t match_candidate = H5Dopen(loc_id, name, H5P_DEFAULT);
if(match_candidate < 0)
{
@@ -348,8 +348,8 @@ hdf5_search_callback
}
// Ensure that the dataset is valid and of the correct dimensionality.
hid_t filespace = arma_H5Dget_space(match_candidate);
int num_dims = arma_H5Sget_simple_extent_ndims(filespace);
hid_t filespace = H5Dget_space(match_candidate);
int num_dims = H5Sget_simple_extent_ndims(filespace);
if(num_dims <= search_info->num_dims)
{
@@ -357,14 +357,14 @@ hdf5_search_callback
// If we already have an existing match we have to close it.
if(search_info->best_match != -1)
{
arma_H5Dclose(search_info->best_match);
H5Dclose(search_info->best_match);
}
search_info->best_match_position = string_pos;
search_info->best_match = match_candidate;
}
arma_H5Sclose(filespace);
H5Sclose(filespace);
// There is no possibility of anything better, so terminate the search.
return 1;
}
@@ -393,7 +393,7 @@ hdf5_search_callback
if(substring == search_info->names[string_pos])
{
// We have found the object; it must be better than our existing match.
hid_t match_candidate = arma_H5Dopen(loc_id, name, H5P_DEFAULT);
hid_t match_candidate = H5Dopen(loc_id, name, H5P_DEFAULT);
// arma_check(match_candidate < 0, "Mat::load(): cannot open an HDF5 dataset");
@@ -404,8 +404,8 @@ hdf5_search_callback
// Ensure that the dataset is valid and of the correct dimensionality.
hid_t filespace = arma_H5Dget_space(match_candidate);
int num_dims = arma_H5Sget_simple_extent_ndims(filespace);
hid_t filespace = H5Dget_space(match_candidate);
int num_dims = H5Sget_simple_extent_ndims(filespace);
if(num_dims <= search_info->num_dims)
{
@@ -413,14 +413,14 @@ hdf5_search_callback
// If we already have an existing match we have to close it.
if(search_info->best_match != -1)
{
arma_H5Dclose(search_info->best_match);
H5Dclose(search_info->best_match);
}
search_info->best_match_position = string_pos;
search_info->best_match = match_candidate;
}
arma_H5Sclose(filespace);
H5Sclose(filespace);
}
}
@@ -428,7 +428,7 @@ hdf5_search_callback
// If they are not the same, but we have not found anything and we don't need an exact match, take this.
if((search_info->exact == false) && (search_info->best_match == -1))
{
hid_t match_candidate = arma_H5Dopen(loc_id, name, H5P_DEFAULT);
hid_t match_candidate = H5Dopen(loc_id, name, H5P_DEFAULT);
// arma_check(match_candidate < 0, "Mat::load(): cannot open an HDF5 dataset");
if(match_candidate < 0)
@@ -436,16 +436,16 @@ hdf5_search_callback
return -1;
}
hid_t filespace = arma_H5Dget_space(match_candidate);
int num_dims = arma_H5Sget_simple_extent_ndims(filespace);
hid_t filespace = H5Dget_space(match_candidate);
int num_dims = H5Sget_simple_extent_ndims(filespace);
if(num_dims <= search_info->num_dims)
{
// Valid dataset -- we'll keep it.
search_info->best_match = arma_H5Dopen(loc_id, name, H5P_DEFAULT);
search_info->best_match = H5Dopen(loc_id, name, H5P_DEFAULT);
}
arma_H5Sclose(filespace);
H5Sclose(filespace);
}
}
}
@@ -475,7 +475,7 @@ search_hdf5_file
hdf5_search_info search_info = { names, num_dims, exact, -1, names.size() };
// We'll use the H5Ovisit to track potential entries.
herr_t status = arma_H5Ovisit(hdf5_file, H5_INDEX_NAME, H5_ITER_NATIVE, hdf5_search_callback, void_ptr(&search_info));
herr_t status = H5Ovisit(hdf5_file, H5_INDEX_NAME, H5_ITER_NATIVE, hdf5_search_callback, void_ptr(&search_info));
// Return the best match; it will be -1 if there was a problem.
return (status < 0) ? -1 : search_info.best_match;
@@ -508,13 +508,13 @@ load_and_convert_hdf5
// u8
search_type = get_hdf5_type<u8>();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
Col<u8> v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert(dest, v.memptr(), n_elem);
return status;
@@ -523,13 +523,13 @@ load_and_convert_hdf5
// s8
search_type = get_hdf5_type<s8>();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
Col<s8> v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert(dest, v.memptr(), n_elem);
return status;
@@ -538,13 +538,13 @@ load_and_convert_hdf5
// u16
search_type = get_hdf5_type<u16>();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
Col<u16> v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert(dest, v.memptr(), n_elem);
return status;
@@ -553,13 +553,13 @@ load_and_convert_hdf5
// s16
search_type = get_hdf5_type<s16>();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
Col<s16> v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert(dest, v.memptr(), n_elem);
return status;
@@ -568,13 +568,13 @@ load_and_convert_hdf5
// u32
search_type = get_hdf5_type<u32>();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
Col<u32> v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert(dest, v.memptr(), n_elem);
return status;
@@ -583,13 +583,13 @@ load_and_convert_hdf5
// s32
search_type = get_hdf5_type<s32>();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
Col<s32> v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert(dest, v.memptr(), n_elem);
return status;
@@ -598,13 +598,13 @@ load_and_convert_hdf5
// u64
search_type = get_hdf5_type<u64>();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
Col<u64> v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert(dest, v.memptr(), n_elem);
return status;
@@ -613,13 +613,13 @@ load_and_convert_hdf5
// s64
search_type = get_hdf5_type<s64>();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
Col<s64> v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert(dest, v.memptr(), n_elem);
return status;
@@ -628,13 +628,13 @@ load_and_convert_hdf5
// ulng_t
search_type = get_hdf5_type<ulng_t>();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
Col<ulng_t> v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert(dest, v.memptr(), n_elem);
return status;
@@ -643,13 +643,13 @@ load_and_convert_hdf5
// slng_t
search_type = get_hdf5_type<slng_t>();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
Col<slng_t> v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert(dest, v.memptr(), n_elem);
return status;
@@ -658,13 +658,13 @@ load_and_convert_hdf5
// float
search_type = get_hdf5_type<float>();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
Col<float> v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert(dest, v.memptr(), n_elem);
return status;
@@ -673,13 +673,13 @@ load_and_convert_hdf5
// double
search_type = get_hdf5_type<double>();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
Col<double> v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert(dest, v.memptr(), n_elem);
return status;
@@ -688,8 +688,8 @@ load_and_convert_hdf5
// complex float
search_type = get_hdf5_type< std::complex<float> >();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
@@ -699,7 +699,7 @@ load_and_convert_hdf5
}
Col< std::complex<float> > v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert_cx(dest, v.memptr(), n_elem);
return status;
@@ -708,8 +708,8 @@ load_and_convert_hdf5
// complex double
search_type = get_hdf5_type< std::complex<double> >();
is_equal = (arma_H5Tequal(datatype, search_type) > 0);
arma_H5Tclose(search_type);
is_equal = (H5Tequal(datatype, search_type) > 0);
H5Tclose(search_type);
if(is_equal)
{
@@ -719,7 +719,7 @@ load_and_convert_hdf5
}
Col< std::complex<double> > v(n_elem, arma_nozeros_indicator());
hid_t status = arma_H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
hid_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(v.memptr()));
arrayops::convert_cx(dest, v.memptr(), n_elem);
return status;
@@ -747,16 +747,16 @@ struct hdf5_suspend_printing_errors
hdf5_suspend_printing_errors()
{
// Save old error handler.
arma_H5Eget_auto(H5E_DEFAULT, &old_client_func, &old_client_data);
H5Eget_auto(H5E_DEFAULT, &old_client_func, &old_client_data);
// Disable annoying HDF5 error messages.
arma_H5Eset_auto(H5E_DEFAULT, NULL, NULL);
H5Eset_auto(H5E_DEFAULT, NULL, NULL);
}
inline
~hdf5_suspend_printing_errors()
{
arma_H5Eset_auto(H5E_DEFAULT, old_client_func, old_client_data);
H5Eset_auto(H5E_DEFAULT, old_client_func, old_client_data);
}
#endif
include/armadillo_bits/include_hdf5.hpp
-3
View File
@@ -27,7 +27,6 @@
#include <hdf5.h>
#else
#undef ARMA_USE_HDF5
#undef ARMA_USE_HDF5_CMAKE
#pragma message ("WARNING: use of HDF5 disabled; hdf5.h header not found")
#endif
#else
@@ -48,7 +47,6 @@
#include ARMA_INCFILE_WRAP(ARMA_HDF5_HEADER)
#else
#undef ARMA_USE_HDF5
#undef ARMA_USE_HDF5_CMAKE
#pragma message ("WARNING: use of HDF5 disabled; hdf5.h header not found")
#endif
#else
@@ -63,7 +61,6 @@
#if defined(H5_USE_16_API) || defined(H5_USE_16_API_DEFAULT)
#pragma message ("WARNING: use of HDF5 disabled; incompatible configuration: H5_USE_16_API or H5_USE_16_API_DEFAULT")
#undef ARMA_USE_HDF5
#undef ARMA_USE_HDF5_CMAKE
#endif
#endif
misc/armadillo.spec
+2 -2
View File
@@ -7,7 +7,7 @@ License: ASL 2.0
URL: http://arma.sourceforge.net/
Source: http://sourceforge.net/projects/arma/files/%{name}-%{version}.tar.xz
BuildRequires: gcc-c++, cmake, lapack-devel, arpack-devel, hdf5-devel
BuildRequires: gcc-c++, cmake, lapack-devel, arpack-devel
%{!?openblas_arches:%global openblas_arches x86_64 %{ix86} armv7hl %{power64} aarch64}
%ifarch %{openblas_arches}
BuildRequires: openblas-devel
@@ -36,7 +36,7 @@ computer vision, signal processing, bioinformatics, statistics, finance, etc.
%package devel
Summary: Development headers and documentation for the Armadillo C++ library
Requires: %{name} = %{version}-%{release}
Requires: lapack-devel, arpack-devel, hdf5-devel, libstdc++-devel
Requires: lapack-devel, arpack-devel, libstdc++-devel
%ifarch %{openblas_arches}
Requires: openblas-devel
%endif
src/wrapper1.cpp
-193
View File
@@ -39,20 +39,6 @@
}
#endif
#if defined(ARMA_USE_HDF5_CMAKE)
#undef H5_USE_110_API
#define H5_USE_110_API
#include <hdf5.h>
#if defined(H5_USE_16_API) || defined(H5_USE_16_API_DEFAULT)
#pragma message ("WARNING: use of HDF5 disabled; incompatible configuration: H5_USE_16_API or H5_USE_16_API_DEFAULT")
#undef ARMA_USE_HDF5_CMAKE
#endif
#endif
namespace arma
{
@@ -61,22 +47,6 @@ namespace arma
#include "armadillo_bits/def_lapack.hpp"
#include "armadillo_bits/def_arpack.hpp"
#include "armadillo_bits/def_superlu.hpp"
// no need to include def_hdf5.hpp -- it only contains #defines for when ARMA_USE_HDF5_CMAKE is not defined.
#if defined(ARMA_USE_HDF5_CMAKE)
// Wrapper functions: arma::H5open() and arma::H5check_version() to hijack calls to H5open() and H5check_version()
herr_t H5open()
{
return ::H5open();
}
herr_t H5check_version(unsigned majnum, unsigned minnum, unsigned relnum)
{
return ::H5check_version(majnum, minnum, relnum);
}
#endif
// at this stage we have prototypes for actual BLAS and LAPACK functions
@@ -1592,169 +1562,6 @@ extern "C"
}
#endif
#if defined(ARMA_USE_HDF5_CMAKE)
hid_t arma_H5Tcopy(hid_t dtype_id)
{
return H5Tcopy(dtype_id);
}
hid_t arma_H5Tcreate(H5T_class_t cl, size_t size)
{
return H5Tcreate(cl, size);
}
herr_t arma_H5Tinsert(hid_t dtype_id, const char* name, size_t offset, hid_t field_id)
{
return H5Tinsert(dtype_id, name, offset, field_id);
}
htri_t arma_H5Tequal(hid_t dtype_id1, hid_t dtype_id2)
{
return H5Tequal(dtype_id1, dtype_id2);
}
herr_t arma_H5Tclose(hid_t dtype_id)
{
return H5Tclose(dtype_id);
}
hid_t arma_H5Dopen(hid_t loc_id, const char* name, hid_t dapl_id)
{
return H5Dopen(loc_id, name, dapl_id);
}
hid_t arma_H5Dget_type(hid_t dataset_id)
{
return H5Dget_type(dataset_id);
}
hid_t arma_H5Dcreate(hid_t loc_id, const char* name, hid_t dtype_id, hid_t space_id, hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id)
{
return H5Dcreate(loc_id, name, dtype_id, space_id, lcpl_id, dcpl_id, dapl_id);
}
herr_t arma_H5Dwrite(hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t xfer_plist_id, const void* buf)
{
return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf);
}
herr_t arma_H5Dclose(hid_t dataset_id)
{
return H5Dclose(dataset_id);
}
hid_t arma_H5Dget_space(hid_t dataset_id)
{
return H5Dget_space(dataset_id);
}
herr_t arma_H5Dread(hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t xfer_plist_id, void* buf)
{
return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf);
}
int arma_H5Sget_simple_extent_ndims(hid_t space_id)
{
return H5Sget_simple_extent_ndims(space_id);
}
int arma_H5Sget_simple_extent_dims(hid_t space_id, hsize_t* dims, hsize_t* maxdims)
{
return H5Sget_simple_extent_dims(space_id, dims, maxdims);
}
herr_t arma_H5Sclose(hid_t space_id)
{
return H5Sclose(space_id);
}
hid_t arma_H5Screate_simple(int rank, const hsize_t* current_dims, const hsize_t* maximum_dims)
{
return H5Screate_simple(rank, current_dims, maximum_dims);
}
herr_t arma_H5Ovisit(hid_t object_id, H5_index_t index_type, H5_iter_order_t order, H5O_iterate_t op, void* op_data)
{
return H5Ovisit(object_id, index_type, order, op, op_data);
}
herr_t arma_H5Eset_auto(hid_t estack_id, H5E_auto_t func, void* client_data)
{
return H5Eset_auto(estack_id, func, client_data);
}
herr_t arma_H5Eget_auto(hid_t estack_id, H5E_auto_t* func, void** client_data)
{
return H5Eget_auto(estack_id, func, client_data);
}
hid_t arma_H5Fopen(const char* name, unsigned flags, hid_t fapl_id)
{
return H5Fopen(name, flags, fapl_id);
}
hid_t arma_H5Fcreate(const char* name, unsigned flags, hid_t fcpl_id, hid_t fapl_id)
{
return H5Fcreate(name, flags, fcpl_id, fapl_id);
}
herr_t arma_H5Fclose(hid_t file_id)
{
return H5Fclose(file_id);
}
htri_t arma_H5Fis_hdf5(const char* name)
{
return H5Fis_hdf5(name);
}
hid_t arma_H5Gcreate(hid_t loc_id, const char* name, hid_t lcpl_id, hid_t gcpl_id, hid_t gapl_id)
{
return H5Gcreate(loc_id, name, lcpl_id, gcpl_id, gapl_id);
}
hid_t arma_H5Gopen(hid_t loc_id, const char* name, hid_t gapl_id)
{
return H5Gopen(loc_id, name, gapl_id);
}
herr_t arma_H5Gclose(hid_t group_id)
{
return H5Gclose(group_id);
}
htri_t arma_H5Lexists(hid_t loc_id, const char* name, hid_t lapl_id)
{
return H5Lexists(loc_id, name, lapl_id);
}
herr_t arma_H5Ldelete(hid_t loc_id, const char* name, hid_t lapl_id)
{
return H5Ldelete(loc_id, name, lapl_id);
}
// H5T_NATIVE_* types. The rhs here expands to some macros.
hid_t arma_H5T_NATIVE_UCHAR = H5T_NATIVE_UCHAR;
hid_t arma_H5T_NATIVE_CHAR = H5T_NATIVE_CHAR;
hid_t arma_H5T_NATIVE_SHORT = H5T_NATIVE_SHORT;
hid_t arma_H5T_NATIVE_USHORT = H5T_NATIVE_USHORT;
hid_t arma_H5T_NATIVE_INT = H5T_NATIVE_INT;
hid_t arma_H5T_NATIVE_UINT = H5T_NATIVE_UINT;
hid_t arma_H5T_NATIVE_LONG = H5T_NATIVE_LONG;
hid_t arma_H5T_NATIVE_ULONG = H5T_NATIVE_ULONG;
hid_t arma_H5T_NATIVE_LLONG = H5T_NATIVE_LLONG;
hid_t arma_H5T_NATIVE_ULLONG = H5T_NATIVE_ULLONG;
hid_t arma_H5T_NATIVE_FLOAT = H5T_NATIVE_FLOAT;
hid_t arma_H5T_NATIVE_DOUBLE = H5T_NATIVE_DOUBLE;
#endif
} // end of extern "C"