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https://github.com/HDFGroup/hdf5.git
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427ff7da28
Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
348 lines
12 KiB
Plaintext
348 lines
12 KiB
Plaintext
Example 1: Create a simple fixed size 3-D dataspace in memory and on disk and
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copy the entire dataset to disk.
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{
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hid_t file; /* File ID */
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hid_t dataset; /* Dataset ID */
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hid_t mem_space, file_space; /* Dataspaces for memory and the file */
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uint8 *buf; /* Buffer for data */
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hsize_t curr_dims[3]={3,4,5}; /* Dimensions of the dataset */
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/* Create file */
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file = H5Fcreate("example1.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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/* Create dataspace for dataset in the file */
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/* Selection for dataspace defaults to entire space */
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file_space=H5Screate(H5S_SIMPLE);
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/* Set the extent & type of the dataset's dataspace */
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H5Sset_extent_simple(file_space,3,curr_dims,curr_dims);
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/* Create the dataspace for the dataset in memory */
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/* Selection for dataspace defaults to entire space */
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mem_space=H5Screate(H5S_SIMPLE);
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/* Set the extent & type of the memory dataspace */
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H5Sset_extent_simple(mem_space,3,curr_dims,curr_dims);
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/* Create the dataset on disk */
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dataset=H5Dcreate(file,"Dataset",H5T_NATIVE_UINT8,file_space,H5P_DEFAULT);
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/* Write the dataset to the file */
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H5Dwrite(dataset,H5T_NATIVE_UINT8,mem_space,file_space,H5P_DEFAULT,buf);
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/* Close dataspaces */
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H5Sclose(mem_space);
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H5Sclose(file_space);
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/* Close dataset & file */
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H5Dclose(dataset);
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H5Fclose(file);
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}
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Example 2: Create a simple fixed size 3-D dataspace in memory and on disk and
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copy a hyperslab to disk. The hyperslab blocks are packed and
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contiguous in memory, but are scattered when written to the dataset
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on disk.
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{
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hid_t file; /* File ID */
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hid_t dataset; /* Dataset ID */
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hid_t mem_space, file_space; /* Dataspaces for memory and the file */
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uint8 *buf; /* Buffer for data */
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hsize_t start[3]={3,4,5}; /* Start of hyperslab */
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hsize_t stride[3]={1,2,2}; /* Stride for hyperslab */
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hsize_t count[3]={3,3,3}; /* Hyperslab block count in each dimension */
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hsize_t block[3]={2,2,2}; /* Hyperslab block size in each dimension */
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hsize_t curr_dims[3]={13,14,15}; /* Dimensions of the dataset */
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/* Create file */
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file = H5Fcreate("example2.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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/* Create dataspace for dataset in the file */
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/* Selection for dataspace defaults to entire space */
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file_space=H5Screate(H5S_SIMPLE);
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/* Set the extent & type of the dataset's dataspace */
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H5Sset_extent_simple(file_space,3,curr_dims,curr_dims);
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/* Set the hyperslab selection for a file dataspace */
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H5Sselect_hyperslab(file_space,H5S_SELECT_SET,start,stride,count,block);
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/* Create the dataspace for the dataset in memory */
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/* Selection for dataspace defaults to entire space */
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mem_space=H5Screate(H5S_SIMPLE);
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/* Set the extent & type of the memory dataspace */
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/* Compute the memory dimensions based on the hyperslab blocks to write */
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for(i=0; i<3; i++)
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curr_dims[i]=count[i]*block[i];
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H5Sset_extent_simple(mem_space,3,curr_dims,curr_dims);
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/* Create the dataset on disk */
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dataset=H5Dcreate(file,"Dataset",H5T_NATIVE_UINT8,file_space,H5P_DEFAULT);
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/* Write the hyperslab to the file */
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H5Dwrite(dataset,H5T_NATIVE_UINT8,mem_space,file_space,H5P_DEFAULT,buf);
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/* Close dataspaces */
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H5Sclose(mem_space);
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H5Sclose(file_space);
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/* Close dataset & file */
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H5Dclose(dataset);
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H5Fclose(file);
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}
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Example 3: Create a simple fixed size 3-D dataspace in memory and on disk and
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copy a specific selection of points (with a particular order) to
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disk. The memory and file dataspaces are different sizes, but the number
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of points selected are the same.
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{
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hid_t file; /* File ID */
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hid_t dataset; /* Dataset ID */
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hid_t mem_space, file_space; /* Dataspaces for memory and the file */
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uint8 *buf; /* Buffer for data */
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hsize_t elements[5][3]; /* Dataspace elements selected */
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hsize_t curr_dims[3]={13,14,15}; /* Dimensions of the dataset */
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/* Create file */
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file = H5Fcreate("example3.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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/* Create dataspace for dataset in the file */
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/* Selection for dataspace defaults to entire space */
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file_space=H5Screate(H5S_SIMPLE);
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/* Set the extent & type of the dataset's dataspace */
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H5Sset_extent_simple(file_space,3,curr_dims,curr_dims);
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/* Set the elements for the selection in the file dataspace */
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elements[0]={0,2,4}; /* Yes, I know this won't compile.. :-) */
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elements[1]={3,4,1};
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elements[2]={9,8,3};
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elements[3]={7,2,0};
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elements[4]={6,5,8};
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H5Sselect_elements(file_space,H5S_SELECT_SET,5,elements);
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/* Create the dataspace for the dataset in memory */
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/* Selection for dataspace defaults to entire space */
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mem_space=H5Screate(H5S_SIMPLE);
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/* Set the extent & type of the memory dataspace */
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curr_dims={23,15,18}; /* This won't compile either :-) */
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H5Sset_extent_simple(mem_space,3,curr_dims,curr_dims);
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/* Set the elements for the selection in the file dataspace */
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elements[0]={9,2,1};
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elements[1]={13,1,12};
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elements[2]={4,1,7};
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elements[3]={0,12,0};
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elements[4]={20,10,17};
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H5Sselect_elements(mem_space,H5S_SELECT_SET,5,elements);
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/* Create the dataset on disk */
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dataset=H5Dcreate(file,"Dataset",H5T_NATIVE_UINT8,file_space,H5P_DEFAULT);
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/* Write the hyperslab to the file */
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H5Dwrite(dataset,H5T_NATIVE_UINT8,mem_space,file_space,H5P_DEFAULT,buf);
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/* Close dataspaces */
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H5Sclose(mem_space);
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H5Sclose(file_space);
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/* Close dataset & file */
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H5Dclose(dataset);
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H5Fclose(file);
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}
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Example 4: Create a simple fixed size 3-D dataspace in memory and on disk and
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build up selection hyperslab selections to copy from memory to disk. The
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selection is the same for both dataspaces, but a different offset is used,
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to illustrate the selection offsets.
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{
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hid_t file; /* File ID */
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hid_t dataset; /* Dataset ID */
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hid_t mem_space, file_space; /* Dataspaces for memory and the file */
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uint8 *buf; /* Buffer for data */
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hsize_t start[3]; /* Start of hyperslab */
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hsize_t stride[3]; /* Stride for hyperslab */
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hsize_t count[3]; /* Hyperslab block count in each dimension */
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hsize_t block[3]; /* Hyperslab block size in each dimension */
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hssize_t offset[3]; /* Selection offset */
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hsize_t curr_dims[3]={13,14,15}; /* Dimensions of the dataset */
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/* Create file */
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file = H5Fcreate("example4.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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/* Create dataspace for dataset in the file */
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/* Selection for dataspace defaults to entire space */
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file_space=H5Screate(H5S_SIMPLE);
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/* Set the extent & type of the dataset's dataspace */
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H5Sset_extent_simple(file_space,3,curr_dims,curr_dims);
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/* Build up the selection with a series of hyperslab selections */
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start={0,2,4}; /* Again, this won't compile.. :-) */
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stride={1,1,1};
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count={6,5,8};
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block={1,1,1};
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/* Set the first selection, union the rest in */
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H5Sselect_hyperslab(file_space,H5S_SELECT_SET,start,stride,count,block);
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/* initialize the second hyperslab */
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start={10,9,1}; /* Again, this won't compile.. :-) */
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stride={1,1,1};
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count={2,3,10};
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block={1,1,1};
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/* Union the second hyperslab into the file dataspace's selection */
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H5Sselect_hyperslab(file_space,H5S_SELECT_UNION,start,stride,count,block);
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/* initialize the third hyperslab */
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start={3,10,5}; /* Again, this won't compile.. :-) */
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stride={1,1,1};
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count={8,2,6};
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block={1,1,1};
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/* Union the final hyperslab into the file dataspace's selection */
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H5Sselect_hyperslab(file_space,H5S_SELECT_UNION,start,stride,count,block);
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/* Create the dataspace for the dataset in memory */
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/* Selection for dataspace defaults to entire space */
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mem_space=H5Screate(H5S_SIMPLE);
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/* Set the extent & type of the memory dataspace */
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curr_dims={23,15,18}; /* This won't compile either :-) */
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H5Sset_extent_simple(mem_space,3,curr_dims,curr_dims);
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/* Copy the selection from the file dataspace */
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H5Sselect_op(mem_space,H5S_SELECT_COPY,file_space);
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/* Adjust the offset of the selection in the memory dataspace */
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offset={1,1,1};
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H5Soffset_simple(mem_space,offset);
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/* Create the dataset on disk */
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dataset=H5Dcreate(file,"Dataset",H5T_NATIVE_UINT8,file_space,H5P_DEFAULT);
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/* Write the hyperslab to the file */
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H5Dwrite(dataset,H5T_NATIVE_UINT8,mem_space,file_space,H5P_DEFAULT,buf);
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/* Close dataspaces */
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H5Sclose(mem_space);
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H5Sclose(file_space);
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/* Close dataset & file */
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H5Dclose(dataset);
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H5Fclose(file);
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}
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Example 5: Same as example 1 (create a simple fixed size 3-D dataspace in memory and on disk and
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copy the entire dataset to disk), except that the selection order is changed
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for the memory dataspace, to change between FORTRAN and C array ordering.
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{
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hid_t file; /* File ID */
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hid_t dataset; /* Dataset ID */
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hid_t mem_space, file_space; /* Dataspaces for memory and the file */
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uint8 *buf; /* Buffer for data */
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hsize_t order[3]; /* Dimension ordering for selection */
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hsize_t curr_dims[3]={3,4,5}; /* Dimensions of the dataset */
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/* Create file */
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file = H5Fcreate("example5.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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/* Create dataspace for dataset in the file */
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/* Selection for dataspace defaults to entire space and C array order */
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file_space=H5Screate(H5S_SIMPLE);
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/* Set the extent & type of the dataset's dataspace */
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H5Sset_extent_simple(file_space,3,curr_dims,curr_dims);
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/* Create the dataspace for the dataset in memory */
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/* Selection for dataspace defaults to entire space and C array order */
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mem_space=H5Screate(H5S_SIMPLE);
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/* Set the extent & type of the memory dataspace */
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H5Sset_extent_simple(mem_space,3,curr_dims,curr_dims);
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/* Change selection ordering to FORTRAN order for memory dataspace */
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order={0,1,2};
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H5Sselect_order(mem_space,order);
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/* Create the dataset on disk */
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dataset=H5Dcreate(file,"Dataset",H5T_NATIVE_UINT8,file_space,H5P_DEFAULT);
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/* Write the dataset to the file */
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H5Dwrite(dataset,H5T_NATIVE_UINT8,mem_space,file_space,H5P_DEFAULT,buf);
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/* Close dataspaces */
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H5Sclose(mem_space);
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H5Sclose(file_space);
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/* Close dataset & file */
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H5Dclose(dataset);
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H5Fclose(file);
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}
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Example 6: Create a stored dataspace on disk and use the H5Ssubspace function
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create a dataspace located within that space.
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{
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hid_t file; /* File ID */
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hid_t space1, space2; /* Dataspace IDs */
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hsize_t start[3]; /* Start of hyperslab */
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hsize_t count[3]; /* Hyperslab block count in each dimension */
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hsize_t curr_dims[3]={13,14,15};/* Dimensions of the dataset */
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/* Create file */
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file = H5Fcreate("example6.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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/* Create dataspace #1 */
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space1=H5Screate(H5S_SIMPLE);
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/* Set the extent & type of dataspace #1 */
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H5Sset_extent_simple(space1,3,curr_dims,curr_dims);
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/* Store dataspace #1 on disk */
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H5Scommit(file,"/Dataspaces/Dataspace #1",space1);
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/* Select a contiguous hyperslab in dataspace #1 to create dataspace #2 with */
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start={0,2,4};
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count={6,5,8};
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/*
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* Use stride and block set to NULL to get contiguous, single element sized
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* hyperslab. The stride and block parameters could also be set to all
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* 1's, but this is simpler and easier.
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*/
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H5Sselect_hyperslab(space1,H5S_SELECT_SET,start,NULL,count,NULL);
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/* Create dataspace #2 as a dataspace located within dataspace #1 */
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space2=H5Ssubspace(space1);
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/* Store dataspace #2 on disk also */
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H5Scommit(file,"/Dataspaces/Dataspace #2",space2);
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/*
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* space1 & space2 can be used to create datasets, etc. Any datasets
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* created with space2 can have their dataspace queried to find the parent
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* dataspace and the location within the parent dataspace
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*/
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/* Close dataspaces */
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H5Sclose(space1);
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H5Sclose(space2);
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/* Close file */
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H5Fclose(file);
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}
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