Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Fetching contributors…

Cannot retrieve contributors at this time

256 lines (202 sloc) 6.983 kb
/*
Copyright (C) 2010 Francesc Alted
http://blosc.pytables.org
License: MIT (see LICENSE.txt)
Filter program that allows the use of the Blosc filter in HDF5.
This is based on the LZF filter interface (http://h5py.alfven.org)
by Andrew Collette.
*/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <errno.h>
#include "hdf5.h"
#include "../blosc/blosc.h"
#include "blosc_filter.h"
#if H5Epush_vers == 2
/* 1.8.x */
#define PUSH_ERR(func, minor, str) H5Epush(H5E_DEFAULT, __FILE__, func, __LINE__, H5E_ERR_CLS, H5E_PLINE, minor, str)
#else
/* 1.6.x */
#define PUSH_ERR(func, minor, str) H5Epush(__FILE__, func, __LINE__, H5E_PLINE, minor, str)
#endif
#if H5Pget_filter_by_id_vers == 2
/* 1.8.x */
#define GET_FILTER(a,b,c,d,e,f,g) H5Pget_filter_by_id(a,b,c,d,e,f,g,NULL)
#else
/* 1.6.x */
#define GET_FILTER H5Pget_filter_by_id
#endif
#if H5Z_class_t_vers == 2
/* 1.8.x where x >= 3 */
#define H5Z_16API 0
#else
/* 1.6.x and 1.8.x with x < 3*/
#define H5Z_16API 1
#endif
size_t blosc_filter(unsigned flags, size_t cd_nelmts,
const unsigned cd_values[], size_t nbytes,
size_t *buf_size, void **buf);
herr_t blosc_set_local(hid_t dcpl, hid_t type, hid_t space);
/* Register the filter, passing on the HDF5 return value */
int register_blosc(char **version, char **date){
int retval;
#if H5Z_16API
H5Z_class_t filter_class = {
(H5Z_filter_t)(FILTER_BLOSC),
"blosc",
NULL,
(H5Z_set_local_func_t)(blosc_set_local),
(H5Z_func_t)(blosc_filter)
};
#else
H5Z_class_t filter_class = {
H5Z_CLASS_T_VERS,
(H5Z_filter_t)(FILTER_BLOSC),
1, 1,
"blosc",
NULL,
(H5Z_set_local_func_t)(blosc_set_local),
(H5Z_func_t)(blosc_filter)
};
#endif
retval = H5Zregister(&filter_class);
if(retval<0){
PUSH_ERR("register_blosc", H5E_CANTREGISTER, "Can't register Blosc filter");
}
*version = strdup(BLOSC_VERSION_STRING);
*date = strdup(BLOSC_VERSION_DATE);
return 1; /* lib is available */
}
/* Filter setup. Records the following inside the DCPL:
1. If version information is not present, set slots 0 and 1 to the filter
revision and Blosc version, respectively.
2. Compute the type size in bytes and store it in slot 2.
3. Compute the chunk size in bytes and store it in slot 3.
*/
herr_t blosc_set_local(hid_t dcpl, hid_t type, hid_t space){
int ndims;
int i;
herr_t r;
unsigned int typesize, basetypesize;
unsigned int bufsize;
hsize_t chunkdims[32];
unsigned int flags;
size_t nelements = 8;
unsigned int values[] = {0,0,0,0,0,0,0,0};
hid_t super_type;
H5T_class_t class;
r = GET_FILTER(dcpl, FILTER_BLOSC, &flags, &nelements, values, 0, NULL);
if(r<0) return -1;
if(nelements < 4) nelements = 4; /* First 4 slots reserved. */
/* Set Blosc info in first two slots */
values[0] = FILTER_BLOSC_VERSION;
values[1] = BLOSC_VERSION_FORMAT;
ndims = H5Pget_chunk(dcpl, 32, chunkdims);
if(ndims<0) return -1;
if(ndims>32){
PUSH_ERR("blosc_set_local", H5E_CALLBACK, "Chunk rank exceeds limit");
return -1;
}
typesize = H5Tget_size(type);
if (typesize==0) return -1;
/* Get the size of the base type, even for ARRAY types */
class = H5Tget_class(type);
if (class == H5T_ARRAY) {
/* Get the array base component */
super_type = H5Tget_super(type);
basetypesize = H5Tget_size(super_type);
/* Release resources */
H5Tclose(super_type);
}
else {
basetypesize = typesize;
}
/* Limit large typesizes (they are pretty inneficient to shuffle
and, in addition, Blosc does not handle typesizes larger than
blocksizes). */
if (basetypesize > BLOSC_MAX_TYPESIZE) basetypesize = 1;
values[2] = basetypesize;
/* Get the size of the chunk */
bufsize = typesize;
for (i=0; i<ndims; i++) {
bufsize *= chunkdims[i];
}
values[3] = bufsize;
#ifdef BLOSC_DEBUG
fprintf(stderr, "Blosc: Computed buffer size %d\n", bufsize);
#endif
r = H5Pmodify_filter(dcpl, FILTER_BLOSC, flags, nelements, values);
if(r<0) return -1;
return 1;
}
/* The filter function */
size_t blosc_filter(unsigned flags, size_t cd_nelmts,
const unsigned cd_values[], size_t nbytes,
size_t *buf_size, void **buf){
void* outbuf = NULL;
int status = 0; /* Return code from Blosc routines */
size_t typesize;
size_t outbuf_size;
int clevel = 5; /* Compression level default */
int doshuffle = 1; /* Shuffle default */
/* Filter params that are always set */
typesize = cd_values[2]; /* The datatype size */
outbuf_size = cd_values[3]; /* Precomputed buffer guess */
/* Optional params */
if (cd_nelmts >= 5) {
clevel = cd_values[4]; /* The compression level */
}
if (cd_nelmts >= 6) {
doshuffle = cd_values[5]; /* Shuffle? */
}
/* We're compressing */
if(!(flags & H5Z_FLAG_REVERSE)){
#ifdef BLOSC_DEBUG
fprintf(stderr, "Blosc: Compress %zd chunk w/buffer %zd\n", nbytes, outbuf_size);
#endif
/* Allocate an output buffer exactly as long as the input data; if
the result is larger, we simply return 0. The filter is flagged
as optional, so HDF5 marks the chunk as uncompressed and
proceeds.
*/
outbuf_size = (*buf_size);
outbuf = malloc(outbuf_size);
if(outbuf == NULL){
PUSH_ERR("blosc_filter", H5E_CALLBACK,
"Can't allocate compression buffer");
goto failed;
}
status = blosc_compress(clevel, doshuffle, typesize, nbytes,
*buf, outbuf, nbytes);
if (status < 0) {
PUSH_ERR("blosc_filter", H5E_CALLBACK, "Blosc compression error");
goto failed;
}
/* We're decompressing */
} else {
#ifdef BLOSC_DEBUG
fprintf(stderr, "Blosc: Decompress %zd chunk w/buffer %zd\n", nbytes, outbuf_size);
#endif
free(outbuf);
outbuf = malloc(outbuf_size);
if(outbuf == NULL){
PUSH_ERR("blosc_filter", H5E_CALLBACK, "Can't allocate decompression buffer");
goto failed;
}
status = blosc_decompress(*buf, outbuf, outbuf_size);
if(status <= 0){ /* decompression failed */
PUSH_ERR("blosc_filter", H5E_CALLBACK, "Blosc decompression error");
goto failed;
} /* if !status */
} /* compressing vs decompressing */
if(status != 0){
free(*buf);
*buf = outbuf;
*buf_size = outbuf_size;
return status; /* Size of compressed/decompressed data */
}
failed:
free(outbuf);
return 0;
} /* End filter function */
Jump to Line
Something went wrong with that request. Please try again.