问题描述
我正在尝试编写一个 HDF5 文件，其结构包含一个 int 和一个 float*
I am trying to write a HDF5 file with a structure which contains an int and a float*
typedef struct s1_t {
int a;
float *b;
} s1_t;
但是，在分配 float* 并将值放入其中后，我仍然无法在 hdf5 文件中输出数据.我相信这是因为 write 函数假定复合数据类型是连续的，而动态分配的数组不会.有没有办法通过仍然使用指针数组来解决这个问题?
However, upon allocating the float* and putting values into it, I still can't output the data in my hdf5 file. I believe this is because the write function assumes that the compound data type is contiguous when a dynamically allocated array will not be. Is there any way around this problem by still using a pointer array?
/*
* This example shows how to create a compound data type with an array member,
* and write an array which has the compound data type to the file.
*/
#include "stdio.h"
#include "stdlib.h"
#include "hdf5.h"
#define FILE "DSwith_array_member.h5"
#define DATASETNAME "ArrayOfStructures"
#define LENGTH 10
#define RANK 1
#define ARRAY_RANK 1
#define ARRAY_DIM 3
int
main(void)
{
/* First structure and dataset*/
typedef struct s1_t {
int a;
//float b[ARRAY_DIM];
float *b;
} s1_t;
s1_t s1[LENGTH];
hid_t s1_tid; /* File datatype identifier */
hid_t array_tid; /* Array datatype handle */
hid_t file, dataset, space; /* Handles */
herr_t status;
hsize_t dim[] = {LENGTH}; /* Dataspace dimensions */
hsize_t array_dim[] = {ARRAY_DIM}; /* Array dimensions */
int i, j;
/*
* Initialize the data
*/
for (i = 0; i< LENGTH; i++) {
s1[i].a = i;
s1[i].b = (float*)calloc(ARRAY_DIM, sizeof(float));
for (j = 0; j < ARRAY_DIM; j++) {
s1[i].b[j] = i+j;
}
}
/*
* Create the data space.
*/
space = H5Screate_simple(RANK, dim, NULL);
/*
* Create the file.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create the array data type.
*/
array_tid = H5Tarray_create(H5T_NATIVE_FLOAT, ARRAY_RANK, array_dim);
/*
* Create the memory data type.
*/
s1_tid = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));
H5Tinsert(s1_tid, "a_name", HOFFSET(s1_t, a), H5T_NATIVE_INT);
H5Tinsert(s1_tid, "b_name", HOFFSET(s1_t, b), array_tid);
/*
* Create the dataset.
*/
dataset = H5Dcreate(file, DATASETNAME, s1_tid, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Wtite data to the dataset;
*/
status = H5Dwrite(dataset, s1_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, s1);
/*
* Release resources
*/
H5Tclose(s1_tid);
H5Tclose(array_tid);
H5Sclose(space);
H5Dclose(dataset);
H5Fclose(file);
return 0;
}
推荐答案
你是对的.将结构更改为
You are right. Changing your structure to
typedef struct s1_t {
int a;
float b[ARRAY_DIM];
} s1_t;
会起作用，但我想你知道这一点.
would work, but I guess you know that.
我可以看到两种解决方案:
I can see two solutions:
- 使用临时缓冲区(如上述结构的数组)进行写入.
b_name使用可变长度数组而不是数组.
- Use a temporary buffer, like an array of the structure above, for writing.
- Using a variable length array instead of an array for
b_name.
b_name
使用可变长度数组的示例
Example using a variable length array for b_name
#include "stdio.h"
#include "stdlib.h"
#include "hdf5.h"
#define FILE "DSwith_array_member.h5"
#define DATASETNAME "ArrayOfStructures"
#define LENGTH 10
#define RANK 1
#define ARRAY_RANK 1
#define ARRAY_DIM 3
typedef struct s1_t {
int a;
float *b;
} s1_t;
typedef struct s1_buffer_t {
int a;
hvl_t b;
} s1_buffer_t;
int main(void)
{
s1_t s1[LENGTH];
hid_t s1_tid; /* File datatype identifier */
hid_t file, dataset, space, vlen_tid; /* Handles */
hsize_t dim[] = {LENGTH}; /* Dataspace dimensions */
int i, j;
s1_buffer_t s1_buffer[LENGTH];
for (i = 0; i< LENGTH; i++) {
s1[i].a = i;
s1[i].b = (float*)calloc(ARRAY_DIM, sizeof(float));
for (j = 0; j < ARRAY_DIM; j++) {
s1[i].b[j] = i+j;
}
}
space = H5Screate_simple(RANK, dim, NULL);
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
vlen_tid = H5Tvlen_create(H5T_NATIVE_FLOAT);
s1_tid = H5Tcreate(H5T_COMPOUND, sizeof(s1_buffer_t));
H5Tinsert(s1_tid, "a_name", HOFFSET(s1_t, a), H5T_NATIVE_INT);
H5Tinsert(s1_tid, "b_name", HOFFSET(s1_t, b), vlen_tid);
dataset = H5Dcreate(file, DATASETNAME, s1_tid, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
for (i = 0; i < LENGTH; ++i)
{
s1_buffer[i].a = s1[i].a;
s1_buffer[i].b.len = ARRAY_DIM;
s1_buffer[i].b.p = s1[i].b;
}
H5Dwrite(dataset, s1_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, s1_buffer);
H5Tclose(s1_tid);
H5Tclose(vlen_tid);
H5Sclose(space);
H5Dclose(dataset);
H5Fclose(file);
return 0;
}
如您所见，您仍然需要一个临时缓冲区，但至少它只需要存储指针(来自 s1 的 b 指针)而不是大小为 ARRAY_DIM 就像上面的解决方案 1 一样.
As you can see, you still need a temporary buffer but at least it only needs to store pointers (the b pointers from s1) and not arrays of size ARRAY_DIM as would be the case with solution 1 above.
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