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this commits includes several changes which should have been done in

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multiple steps:
- the functions for inquiring datasets and attributes do not return
  an HDF5 type any more but an enum of type h5_types_t. This change
  was required for the Python module.
- bugfix in reading attributes: See https://git.psi.ch/H5hut/src/issues/4
- several consts and macros have been moved from the public C-API to
  the core API
- more consitent file naming
- several 'private' function have been moved to their 'private' header
  files as 'static inline'.
- minor formatting changes
This commit is contained in:
gsell
2016-06-17 10:44:25 +02:00
parent bbbaa6a21b
commit bdcc8f2089
89 changed files with 1105 additions and 1050 deletions
Download Patch File Download Diff File Expand all files Collapse all files
src/include/H5Block_attribs.h
+5 -6
View File
@@ -12,7 +12,6 @@
#include <string.h>
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5b_attribs.h"
@@ -192,7 +191,7 @@ H5Block3dSetFieldOrigin (
f,
field_name,
H5BLOCK_FIELD_ORIGIN_NAME,
(hid_t)H5_FLOAT64_T,
(hid_t)H5_FLOAT64,
origin,
3));
}
@@ -220,7 +219,7 @@ H5Block3dGetFieldOrigin (
f,
field_name,
H5BLOCK_FIELD_ORIGIN_NAME,
H5_FLOAT64_T,
H5_FLOAT64,
origin));
*x_origin = origin[0];
@@ -254,7 +253,7 @@ H5Block3dSetFieldSpacing (
f,
field_name,
H5BLOCK_FIELD_SPACING_NAME,
(hid_t)H5_FLOAT64_T,
(hid_t)H5_FLOAT64,
spacing,
3));
}
@@ -282,7 +281,7 @@ H5Block3dGetFieldSpacing (
f,
field_name,
H5BLOCK_FIELD_SPACING_NAME,
H5_FLOAT64_T,
H5_FLOAT64,
spacing));
*x_spacing = spacing[0];
*y_spacing = spacing[1];
@@ -751,7 +750,7 @@ H5BlockReadFieldAttribString (
f,
field_name,
attrib_name,
H5_STRING_T,
H5_STRING,
(void*)buffer));
}
src/include/H5Block_io.h
-1
View File
@@ -10,7 +10,6 @@
#ifndef __H5BLOCK_IO_H
#define __H5BLOCK_IO_H
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5b_io.h"
src/include/H5Block_model.h
-1
View File
@@ -10,7 +10,6 @@
#ifndef __H5BLOCK_MODEL
#define __H5BLOCK_MODEL
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5b_model.h"
src/include/H5Fed_adjacency.h
-1
View File
@@ -11,7 +11,6 @@
#define __H5FED_ADJACENCY_H
#include "h5core/h5_types.h"
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5t_adjacencies.h"
src/include/H5Fed_model.h
-1
View File
@@ -11,7 +11,6 @@
#define __H5FED_MODEL_H
#include "h5core/h5_types.h"
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5t_model.h"
src/include/H5Fed_retrieve.h
-1
View File
@@ -11,7 +11,6 @@
#define __H5FED_RETRIEVE_H
#include "h5core/h5_types.h"
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5_syscall.h"
#include "h5core/h5t_map.h"
src/include/H5Fed_store.h
-1
View File
@@ -11,7 +11,6 @@
#define __H5FED_STORE_H
#include "h5core/h5_types.h"
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5t_store.h"
src/include/H5Fed_tags.h
-1
View File
@@ -11,7 +11,6 @@
#define __H5FED_TAGS_H
#include "h5core/h5_types.h"
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5t_tags.h"
src/include/H5Part_io.h
-1
View File
@@ -10,7 +10,6 @@
#ifndef H5PART_IO
#define H5PART_IO
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5u_io.h"
src/include/H5Part_model.h
+2 -3
View File
@@ -10,7 +10,6 @@
#ifndef H5PART_MODEL
#define H5PART_MODEL
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5u_model.h"
@@ -71,7 +70,7 @@ H5PartGetDatasetName (
(h5_file_p)f,
(long long)idx,
name, (unsigned long long)len);
H5_API_RETURN (h5u_get_dataset_info(f, idx, name, len, NULL, NULL));
H5_API_RETURN (h5u_get_dataset_info_by_idx(f, idx, name, len, NULL, NULL));
}
/**
@@ -109,7 +108,7 @@ H5PartGetDatasetInfo (
(long long)idx,
name, (long long unsigned)len_name,
type, nelems);
H5_API_RETURN (h5u_get_dataset_info (
H5_API_RETURN (h5u_get_dataset_info_by_idx (
f, idx, name, len_name, type, nelems));
}
/**
src/include/H5_attachments.h
-1
View File
@@ -10,7 +10,6 @@
#ifndef __H5_ATTACHMENTS_H
#define __H5_ATTACHMENTS_H
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5_model.h"
#include "h5core/h5_attachments.h"
src/include/H5_debug.h
-1
View File
@@ -10,7 +10,6 @@
#ifndef __H5_DEBUG_H
#define __H5_DEBUG_H
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
/**
src/include/H5_error.f90 → src/include/H5_err.f90
View File
src/include/H5_error.h → src/include/H5_err.h
-1
View File
@@ -10,7 +10,6 @@
#ifndef __H5_ERROR_H
#define __H5_ERROR_H
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
/**
src/include/H5_file.h
-1
View File
@@ -10,7 +10,6 @@
#ifndef __H5_FILE_H
#define __H5_FILE_H
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5_file.h"
src/include/H5_file_attribs.h
+5 -6
View File
@@ -12,7 +12,6 @@
#include <string.h>
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5_file_attribs.h"
@@ -369,7 +368,7 @@ H5ReadFileAttribString (
H5_API_RETURN (h5_read_file_attrib (
f,
attrib_name,
H5_STRING_T,
H5T_C_S1,
(void*)buffer));
}
@@ -385,7 +384,7 @@ H5ReadFileAttribFloat64 (
H5_API_RETURN (h5_read_file_attrib (
f,
attrib_name,
H5_FLOAT64_T,
H5_FLOAT64,
(void*)buffer));
}
@@ -401,7 +400,7 @@ H5ReadFileAttribFloat32 (
H5_API_RETURN (h5_read_file_attrib (
f,
attrib_name,
H5_FLOAT32_T,
H5_FLOAT32,
(void*)buffer));
}
@@ -417,7 +416,7 @@ H5ReadFileAttribInt64 (
H5_API_RETURN (h5_read_file_attrib (
f,
attrib_name,
H5_INT64_T,
H5_INT64,
(void*)buffer));
}
@@ -433,7 +432,7 @@ H5ReadFileAttribInt32 (
H5_API_RETURN (h5_read_file_attrib (
f,
attrib_name,
H5_INT32_T,
H5_INT32,
(void*)buffer));
}
///< @}
src/include/H5_model.h
-1
View File
@@ -10,7 +10,6 @@
#ifndef __H5_MODEL_H
#define __H5_MODEL_H
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5_model.h"
src/include/H5_step_attribs.h
+5 -6
View File
@@ -12,7 +12,6 @@
#include <string.h>
#include "h5core/h5_init.h"
#include "h5core/h5_debug.h"
#include "h5core/h5_step_attribs.h"
@@ -366,7 +365,7 @@ H5ReadStepAttribString (
H5_API_RETURN (h5_read_step_attrib (
f,
attrib_name,
H5_STRING_T,
H5_STRING,
(void*)buffer));
}
@@ -382,7 +381,7 @@ H5ReadStepAttribFloat64 (
H5_API_RETURN (h5_read_step_attrib (
f,
attrib_name,
H5_FLOAT64_T,
H5_FLOAT64,
(void*)buffer));
}
@@ -398,7 +397,7 @@ H5ReadStepAttribFloat32 (
H5_API_RETURN (h5_read_step_attrib (
f,
attrib_name,
H5_FLOAT32_T,
H5_FLOAT32,
(void*)buffer));
}
@@ -414,7 +413,7 @@ H5ReadStepAttribInt64 (
h5_err_t h5err = h5_read_step_attrib (
f,
attrib_name,
H5_INT64_T,
H5_INT64,
(void*)buffer);
H5_API_RETURN (h5err);
}
@@ -431,7 +430,7 @@ H5ReadStepAttribInt32 (
H5_API_RETURN (h5_read_step_attrib (
f,
attrib_name,
H5_INT32_T,
H5_INT32,
(void*)buffer));
}
///< @}
src/include/H5hut.f90
+1 -1
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@@ -15,7 +15,7 @@ MODULE H5hut
include 'H5_step_attribs.f90'
include 'H5_log.f90'
include 'H5_debug.f90'
include 'H5_error.f90'
include 'H5_err.f90'
include 'H5Part_model.f90'
include 'H5Part_io.f90'
src/include/H5hut.h
+1 -1
View File
@@ -21,7 +21,7 @@
#include "H5_step_attribs.h"
#include "H5_log.h"
#include "H5_debug.h"
#include "H5_error.h"
#include "H5_err.h"
#include "H5Part_io.h"
#include "H5Part_model.h"
src/include/h5core/Makefile.am
+1 -2
View File
@@ -3,11 +3,10 @@ otherincludedir = $(includedir)/h5core
include_HEADERS = \
h5_attachments.h \
h5_debug.h \
h5_errorhandling.h \
h5_err.h \
h5_file.h \
h5_file_attribs.h \
h5_step_attribs.h \
h5_init.h \
h5_model.h \
h5_syscall.h \
h5_types.h \
src/include/h5core/h5_debug.h
+7 -10
View File
@@ -13,12 +13,10 @@
#include <stdio.h>
#include <stddef.h>
#include "h5core/h5_types.h"
#include "h5core/h5_errorhandling.h"
extern const char* H5_VER_STRING;
#ifdef __cplusplus
extern "C" {
#endif
#include "h5core/h5_types.h"
#include "h5core/h5_err.h"
#define H5_VERBOSE_NONE (0)
#define H5_VERBOSE_ERROR (1)
@@ -79,6 +77,10 @@ struct call_stack {
extern h5_int32_t h5_debug_level;
extern struct call_stack h5_call_stack;
#ifdef __cplusplus
extern "C" {
#endif
static inline void
h5_call_stack_init (
const char* fname,
@@ -305,7 +307,6 @@ h5_debug (
ret_value = expr; \
goto done; \
done: \
h5_call_stack_reset (); \
return ret_value;
#define __FUNC_RETURN(expr, mask) \
@@ -347,9 +348,6 @@ done: \
//////////////////////////////////////////////////////////////////////////////
#define H5_API_ENTER(type, fmt, ...) \
if (!h5_initialized) { \
h5_initialize(); \
} \
__API_ENTER(type, H5_DEBUG_API, fmt, __VA_ARGS__)
#define H5_API_LEAVE(expr) __API_LEAVE(expr)
#define H5_API_RETURN(expr) __API_RETURN(expr, H5_DEBUG_API);
@@ -368,7 +366,6 @@ h5_err_t
h5_get_debuglevel (
void);
#ifdef __cplusplus
}
#endif
src/include/h5core/h5_errorhandling.h → src/include/h5core/h5_err.h
+2 -2
View File
@@ -7,8 +7,8 @@
License: see file COPYING in top level of source distribution.
*/
#ifndef __H5CORE_H5_ERRORHANDLING_H
#define __H5CORE_H5_ERRORHANDLING_H
#ifndef __H5CORE_H5_ERROR_H
#define __H5CORE_H5_ERROR_H
#include <stdarg.h>
#include <stdio.h>
src/include/h5core/h5_file.h
+20
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@@ -18,6 +18,26 @@
#include "h5core/h5_types.h"
/*
file modes:
H5_O_RDONLY:
read data from existing file
H5_O_WRONLY:
create new file, if file not exists; write new or overwrite
existing data
H5_O_APPENDONLY:
allows to append new data to an existing file
H5_O_RDWR:
create new file, if file not exists; read and (over-)write data
*/
#define H5_O_RDWR 0x00000001
#define H5_O_RDONLY 0x00000002
#define H5_O_WRONLY 0x00000004
#define H5_O_APPENDONLY 0x00000008
#ifdef __cplusplus
extern "C" {
src/include/h5core/h5_init.h
-40
View File
@@ -1,40 +0,0 @@
/*
Copyright (c) 2006-2016, The Regents of the University of California,
through Lawrence Berkeley National Laboratory (subject to receipt of any
required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
Institut (Switzerland). All rights reserved.
License: see file COPYING in top level of source distribution.
*/
#ifndef __H5CORE_H5_H
#define __H5CORE_H5_H
#include "h5core/h5_types.h"
// dummy MPI calls for serial code
#if !defined (PARALLEL_IO)
typedef int MPI_Comm;
#define MPI_Init(argc, argv)
#define MPI_Comm_size(comm, nprocs) {(void)comm; *nprocs = 1; }
#define MPI_Comm_rank(comm, myproc) {(void)comm; *myproc = 0; }
#define MPI_Finalize()
#define MPI_COMM_WORLD (0)
#define MPI_COMM_SELF (1)
#endif
#ifdef __cplusplus
extern "C" {
#endif
extern int h5_initialized;
h5_err_t
h5_initialize (void);
#ifdef __cplusplus
}
#endif
#endif
src/include/h5core/h5_types.h
+25 -46
View File
@@ -10,49 +10,35 @@
#ifndef __H5CORE_H5_TYPES_H
#define __H5CORE_H5_TYPES_H
//#include <hdf5.h>
#include <stdarg.h>
#include <stdint.h>
#ifdef __cplusplus
extern "C" {
#endif
/*
file modes:
H5_O_RDONLY: read data from existing file
H5_O_WRONLY: create new file, if file not exists; write new or overwrite existing data
H5_O_APPENDONLY: allows to append new data to an existing file
H5_O_RDWR: create new file, if file not exists; read and (over-)write data
*/
#define H5_O_RDWR 0x00000001
#define H5_O_RDONLY 0x00000002
#define H5_O_WRONLY 0x00000004
#define H5_O_APPENDONLY 0x00000008
#define H5_VFD_MPIO_POSIX 0x00000010
#define H5_VFD_MPIO_INDEPENDENT 0x00000020
#define H5_VFD_MPIO_COLLECTIVE 0x00000040
#define H5_VFD_CORE 0x00000080
#define H5_FLUSH_FILE 0x00001000
#define H5_FLUSH_STEP 0x00002000
#define H5_FLUSH_DATASET 0x00004000
#define H5_FS_LUSTRE 0x00010000
#define H5_ID_T H5T_NATIVE_INT64
#define H5_FLOAT64_T H5T_NATIVE_DOUBLE
#define H5_FLOAT32_T H5T_NATIVE_FLOAT
#define H5_INT64_T H5T_NATIVE_INT64
#define H5_INT32_T H5T_NATIVE_INT32
#define H5_INT16_T H5T_NATIVE_INT16
#define H5_UINT16_T H5T_NATIVE_UINT16
#define H5_STRING_T H5T_NATIVE_CHAR
#define H5_COMPOUND_T H5T_COMPOUND
extern const char* H5_VER_STRING;
#define H5_STRING H5T_C_S1
#define H5_INT16 H5T_NATIVE_INT16
#define H5_UINT16 H5T_NATIVE_UINT16
#define H5_INT32 H5T_NATIVE_INT32
#define H5_UINT32 H5T_NATIVE_UINT32
#define H5_INT64 H5T_NATIVE_INT64
#define H5_UINT64 H5T_NATIVE_UINT64
#define H5_FLOAT32 H5T_NATIVE_FLOAT
#define H5_FLOAT64 H5T_NATIVE_DOUBLE
#define H5_ID H5T_NATIVE_INT64
#define H5_COMPOUND H5T_COMPOUND
typedef enum {
H5_STRING_T,
H5_INT16_T,
H5_UINT16_T,
H5_INT32_T,
H5_UINT32_T,
H5_INT64_T,
H5_UINT64_T,
H5_FLOAT32_T,
H5_FLOAT64_T,
H5_ID_T,
H5_COMPOUND_T
} h5_types_t;
#ifdef WIN32
typedef __int64 int64_t;
#endif /* WIN32 */
@@ -155,14 +141,7 @@ typedef struct {
struct h5_idxmap;
typedef struct h5_idxmap h5_idxmap_t;
#define H5_TRIANGLE_MESH (H5_OID_TRIANGLE)
#define H5_TETRAHEDRAL_MESH (H5_OID_TETRAHEDRON)
#define H5_PROP_DEFAULT (0)
#define H5_PROP_FILE (1)
#ifdef __cplusplus
}
#endif
#endif
src/include/h5core/h5u_model.h
+1 -1
View File
@@ -21,7 +21,7 @@ h5u_get_num_datasets (
const h5_file_t);
h5_err_t
h5u_get_dataset_info (
h5u_get_dataset_info_by_idx (
const h5_file_t,
const h5_id_t, char* const, const h5_size_t, h5_int64_t* const,
h5_size_t* const);