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| -rw-r--r-- | src/H5Zscaleoffset.c | 813 |
1 files changed, 813 insertions, 0 deletions
diff --git a/src/H5Zscaleoffset.c b/src/H5Zscaleoffset.c new file mode 100644 index 0000000..21bb3f5 --- /dev/null +++ b/src/H5Zscaleoffset.c @@ -0,0 +1,813 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by the Board of Trustees of the University of Illinois. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the files COPYING and Copyright.html. COPYING can be found at the root * + * of the source code distribution tree; Copyright.html can be found at the * + * root level of an installed copy of the electronic HDF5 document set and * + * is linked from the top-level documents page. It can also be found at * + * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * + * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* currently this filter only handles integer datatype + * does not consider fill value + */ + +#define H5Z_PACKAGE /*suppress error about including H5Zpkg */ + +#include "H5private.h" /* Generic Functions */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5MMprivate.h" /* Memory management */ +#include "H5Ppublic.h" /* Property lists */ +#include "H5Oprivate.h" /* Object headers */ +#include "H5Tpublic.h" /* Datatype functions */ +#include "H5Zpkg.h" /* Data filters */ + +#ifdef H5_HAVE_FILTER_SCALEOFFSET + +/* Struct of parameters needed for compressing/decompressing one atomic datatype */ +typedef struct { + size_t size; + unsigned order; + unsigned minbits; +} parms_atomic; + +/* Local function prototypes */ +static herr_t H5Z_can_apply_scaleoffset(hid_t dcpl_id, hid_t type_id, hid_t space_id); +static herr_t H5Z_set_local_scaleoffset(hid_t dcpl_id, hid_t type_id, hid_t space_id); +static size_t H5Z_filter_scaleoffset(unsigned flags, size_t cd_nelmts, const unsigned cd_values[], + size_t nbytes, size_t *buf_size, void **buf); +void H5Z_scaleoffset_precompress(void *data, unsigned d_nelmts, unsigned type, unsigned filavail, + unsigned *minbits, unsigned long_long *minval); +void H5Z_scaleoffset_postdecompress(void *data, unsigned d_nelmts, unsigned type, unsigned filavail, + unsigned long_long minval); +void H5Z_scaleoffset_next_byte(size_t *j, int *buf_len); +void H5Z_scaleoffset_decompress_one_byte(void *data, size_t data_offset, int k, int begin_i, + unsigned char *buffer, size_t *j, int *buf_len, parms_atomic p); +void H5Z_scaleoffset_compress_one_byte(void *data, size_t data_offset, int k, int begin_i, + unsigned char *buffer, size_t *j, int *buf_len, parms_atomic p); +void H5Z_scaleoffset_decompress_one_atomic(void *data, size_t data_offset, unsigned char *buffer, + size_t *j, int *buf_len, parms_atomic p); +void H5Z_scaleoffset_compress_one_atomic(void *data, size_t data_offset, unsigned char *buffer, + size_t *j, int *buf_len, parms_atomic p); +void H5Z_scaleoffset_decompress(void *data, unsigned d_nelmts, unsigned char *buffer, + parms_atomic p); +void H5Z_scaleoffset_compress(void *data, unsigned d_nelmts, unsigned char *buffer, + size_t buffer_size, parms_atomic p); + +/* This message derives from H5Z */ +H5Z_class_t H5Z_SCALEOFFSET[1] = {{ + H5Z_CLASS_T_VERS, /* H5Z_class_t version */ + H5Z_FILTER_SCALEOFFSET, /* Filter id number */ + 1, /* Assume encoder present: check before registering */ + 1, /* decoder_present flag (set to true) */ + "scaleoffset", /* Filter name for debugging */ + H5Z_can_apply_scaleoffset, /* The "can apply" callback */ + H5Z_set_local_scaleoffset, /* The "set local" callback */ + H5Z_filter_scaleoffset, /* The actual filter function */ +}}; + +/* Local macros */ +#define H5Z_SCALEOFFSET_USER_NPARMS 1 /* Number of parameters that users can set */ +#define H5Z_SCALEOFFSET_TOTAL_NPARMS 7 /* Total number of parameters for filter */ +#define H5Z_SCALEOFFSET_PARM_MINBITS 0 /* "User" parameter for minimum number of bits */ +#define H5Z_SCALEOFFSET_PARM_NELMTS 1 /* "Local" parameter for number of elements in the chunk */ +#define H5Z_SCALEOFFSET_PARM_CLASS 2 /* "Local" parameter for datatype class */ +#define H5Z_SCALEOFFSET_PARM_SIZE 3 /* "Local" parameter for datatype size */ +#define H5Z_SCALEOFFSET_PARM_TYPE 4 /* "Local" parameter for integer types */ +#define H5Z_SCALEOFFSET_PARM_ORDER 5 /* "Local" parameter for datatype byte order */ +#define H5Z_SCALEOFFSET_PARM_FILAVAIL 6 /* "Local" parameter for dataset fill value existence */ + +#define H5Z_SCALEOFFSET_CLS_INTEGER 0 /* Integer (datatype class) */ +#define H5Z_SCALEOFFSET_CLS_FLOAT 1 /* Floating point (datatype class) */ + +#define H5Z_SCALEOFFSET_ORDER_LE 0 /* Little endian (datatype byte order) */ +#define H5Z_SCALEOFFSET_ORDER_BE 1 /* Big endian (datatype byte order) */ + +#define H5Z_SCALEOFFSET_FILL_UNDEFINED 0 /* Fill value is not defined */ +#define H5Z_SCALEOFFSET_FILL_DEFINED 1 /* Fill value is defined */ + +/* Local variables */ +/* can not use pfill_val now + * pfill_val: pointer to buffer containing fill value of dataset fill value if is defined + */ +static void *pfill_val; + +enum H5Z_scaleoffset_type {t_uchar, t_ushort, t_uint, t_ulong, t_ulong_long, + t_schar, t_short, t_int, t_long, t_long_long}; + + +/*------------------------------------------------------------------------- + * Function: H5Z_can_apply_scaleoffset + * + * Purpose: Check the parameters for scaleoffset compression for + * validity and whether they fit a particular dataset. + * + * Note: + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Xiaowen Wu + * Friday, February 4, 2005 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5Z_can_apply_scaleoffset(hid_t UNUSED dcpl_id, hid_t type_id, hid_t UNUSED space_id) +{ + H5T_class_t dtype_class; /* Datatype's class */ + unsigned dtype_size; /* Datatype's size (in bytes) */ + H5T_order_t dtype_order; /* Datatype's endianness order */ + herr_t ret_value=TRUE; /* Return value */ + + FUNC_ENTER_NOAPI(H5Z_can_apply_scaleoffset, FAIL) + + /* Get datatype's class, for checking the "datatype class" */ + if((dtype_class = H5Tget_class(type_id)) == H5T_NO_CLASS ) + HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype class") + + /* Get datatype's size, for checking the "datatype size" */ + if((dtype_size = H5Tget_size(type_id)) == 0) + HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype size") + + /* Codes below apply to integer or floating point datatype */ + if(dtype_class == H5T_INTEGER || dtype_class == H5T_FLOAT) { + /* Get datatype's endianness order */ + if((dtype_order = H5Tget_order(type_id)) == H5T_ORDER_ERROR) + HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "can't retrieve datatype endianness order") + + /* Range check datatype's endianness order */ + /* (Note: this may not handle non-atomic datatypes well) */ + if(dtype_order != H5T_ORDER_LE && dtype_order != H5T_ORDER_BE) + HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype endianness order") + } else + HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "datatype class not supported by scaleoffset") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5Z_can_apply_scaleoffset() */ + + +/*------------------------------------------------------------------------- + * Function: H5Z_set_local_scaleoffset + * + * Purpose: Set the "local" dataset parameters for scaleoffset + * compression. + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Xiaowen Wu + * Friday, February 4, 2005 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5Z_set_local_scaleoffset(hid_t dcpl_id, hid_t type_id, hid_t space_id) +{ + unsigned flags; /* Filter flags */ + size_t cd_nelmts=H5Z_SCALEOFFSET_USER_NPARMS; /* Number of filter parameters */ + unsigned cd_values[H5Z_SCALEOFFSET_TOTAL_NPARMS]; /* Filter parameters */ + hssize_t npoints; /* Number of points in the dataspace */ + H5T_class_t dtype_class; /* Datatype's class */ + H5T_order_t dtype_order; /* Datatype's endianness order */ + size_t dtype_size; /* Datatype's size (in bytes) */ + H5T_sign_t dtype_sign; /* Datatype's sign */ + enum H5Z_scaleoffset_type type; /* Integer type */ + H5D_fill_value_t status; /* Status of fill value in property list */ + herr_t ret_value=SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(H5Z_set_local_scaleoffset, FAIL) + + /* Get the filter's current parameters */ +#ifdef H5_WANT_H5_V1_6_COMPAT + if(H5Pget_filter_by_id(dcpl_id,H5Z_FILTER_SCALEOFFSET,&flags,&cd_nelmts,cd_values,0,NULL)<0) +#else + if(H5Pget_filter_by_id(dcpl_id,H5Z_FILTER_SCALEOFFSET,&flags,&cd_nelmts,cd_values,0,NULL,NULL)<0) +#endif + HGOTO_ERROR(H5E_PLINE, H5E_CANTGET, FAIL, "can't get scaleoffset parameters") + + /* Get total number of elements in the chunk */ + if ((npoints=H5Sget_simple_extent_npoints(space_id))<0) + HGOTO_ERROR(H5E_PLINE, H5E_CANTGET, FAIL, "unable to get number of points in the dataspace") + + /* Set "local" parameter for this dataset's number of elements */ + H5_ASSIGN_OVERFLOW(cd_values[H5Z_SCALEOFFSET_PARM_NELMTS],npoints,hssize_t,unsigned); + + /* Get datatype's class */ + if((dtype_class=H5Tget_class(type_id))==H5T_NO_CLASS ) + HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype class") + + /* Set "local" parameter for datatype's class */ + switch(dtype_class) { + case H5T_INTEGER: cd_values[H5Z_SCALEOFFSET_PARM_CLASS] = H5Z_SCALEOFFSET_CLS_INTEGER; + break; + case H5T_FLOAT: cd_values[H5Z_SCALEOFFSET_PARM_CLASS] = H5Z_SCALEOFFSET_CLS_FLOAT; + break; + default: + HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "datatype class not supported by scaleoffset") + } /* end switch */ + + /* Get datatype's size */ + if((dtype_size=H5Tget_size(type_id))==0) + HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype size") + + /* Set "local" parameter for datatype size */ + cd_values[H5Z_SCALEOFFSET_PARM_SIZE] = dtype_size; + + /* Get datatype's sign */ + if((dtype_sign=H5Tget_sign(type_id))==H5T_SGN_ERROR) + HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype sign") + + if(dtype_class==H5T_INTEGER) { + if(dtype_sign==H5T_SGN_NONE) { /* unsigned integer */ + if(dtype_size == sizeof(unsigned char)) + type = t_uchar; + else if(dtype_size == sizeof(unsigned short)) + type = t_ushort; + else if(dtype_size == sizeof(unsigned int)) + type = t_uint; + else if(dtype_size == sizeof(unsigned long)) + type = t_ulong; + else if(dtype_size == sizeof(unsigned long_long)) + type = t_ulong_long; + else + HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "integer size not matched") + } + + if(dtype_sign==H5T_SGN_2) { /* signed integer */ + if(dtype_size == sizeof(signed char)) + type = t_schar; + else if(dtype_size == sizeof(short)) + type = t_short; + else if(dtype_size == sizeof(int)) + type = t_int; + else if(dtype_size == sizeof(long)) + type = t_long; + else if(dtype_size == sizeof(long_long)) + type = t_long_long; + else + HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "integer size not matched") + } + + /* Set "local" parameter for integer types */ + cd_values[H5Z_SCALEOFFSET_PARM_TYPE] = type; + } + + /* Get datatype's endianness order */ + if((dtype_order=H5Tget_order(type_id))==H5T_ORDER_ERROR) + HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype endianness order") + + /* Set "local" parameter for datatype endianness */ + switch(dtype_order) { + case H5T_ORDER_LE: /* Little-endian byte order */ + cd_values[H5Z_SCALEOFFSET_PARM_ORDER] = H5Z_SCALEOFFSET_ORDER_LE; + break; + case H5T_ORDER_BE: /* Big-endian byte order */ + cd_values[H5Z_SCALEOFFSET_PARM_ORDER] = H5Z_SCALEOFFSET_ORDER_BE; + break; + default: + HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype endianness order") + } /* end switch */ + + /* Check whether fill value is defined for dataset */ + if(H5Pfill_value_defined(dcpl_id, &status)<0) + HGOTO_ERROR(H5E_PLINE, H5E_CANTGET, FAIL, "unable to determine if fill value is defined") + + /* Set local parameter for availability of fill value */ + if(status == H5D_FILL_VALUE_UNDEFINED) + cd_values[H5Z_SCALEOFFSET_PARM_FILAVAIL] = H5Z_SCALEOFFSET_FILL_UNDEFINED; + else { + cd_values[H5Z_SCALEOFFSET_PARM_FILAVAIL] = H5Z_SCALEOFFSET_FILL_DEFINED; +#if 0 + /* Get dataset fill value */ + if(H5Pget_fill_value(dcpl_id, type_id, pfill_val)<0) + HGOTO_ERROR(H5E_PLINE, H5E_CANTGET, FAIL, "unable to get fill value") +#endif + } + + /* Modify the filter's parameters for this dataset */ + if(H5Pmodify_filter(dcpl_id, H5Z_FILTER_SCALEOFFSET, flags, H5Z_SCALEOFFSET_TOTAL_NPARMS, cd_values)<0) + HGOTO_ERROR(H5E_PLINE, H5E_CANTSET, FAIL, "can't set local scaleoffset parameters") + +done: + FUNC_LEAVE_NOAPI(ret_value) + +} /* end H5Z_set_local_scaleoffset() */ + + +/*------------------------------------------------------------------------- + * Function: H5Z_filter_scaleoffset + * + * Purpose: Implement an I/O filter for storing packed integer/float + * data using scale and offset method. + * + * Return: Success: Size of buffer filtered + * Failure: 0 + * + * Programmer: Xiaowen Wu + * Monday, February 7, 2005 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static size_t +H5Z_filter_scaleoffset (unsigned flags, size_t cd_nelmts, const unsigned cd_values[], + size_t nbytes, size_t *buf_size, void **buf) +{ + size_t ret_value = 0; /* return value */ + size_t size_out = 0; /* size of output buffer */ + unsigned d_nelmts = 0; /* number of data elements in the chunk */ + unsigned minbits = 0; /* minimum number of bits to store values */ + unsigned long_long minval= 0; /* minimum value of input buffer */ + unsigned char *outbuf = NULL; /* pointer to new output buffer */ + parms_atomic p; /* paramters needed for compress/decompress functions */ + unsigned buf_offset; /* buffer offset because of parameters stored in file */ + + FUNC_ENTER_NOAPI(H5Z_filter_scaleoffset, 0) + + /* check arguments */ + if (cd_nelmts!=H5Z_SCALEOFFSET_TOTAL_NPARMS) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, 0, "invalid scaleoffset number of paramters") + + /* copy a filter parameter to d_nelmts */ + d_nelmts = cd_values[H5Z_SCALEOFFSET_PARM_NELMTS]; + + /* check and assign value to minimum number of bits if set by user */ + if(cd_values[H5Z_SCALEOFFSET_PARM_MINBITS]!=0) { + if(cd_values[H5Z_SCALEOFFSET_PARM_MINBITS]>cd_values[H5Z_SCALEOFFSET_PARM_SIZE]*8) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, 0, "invalid scaleoffset minimum number of bits") + minbits = cd_values[H5Z_SCALEOFFSET_PARM_MINBITS]; + } + + /* prepare paramters to pass to compress/decompress functions */ + p.size = cd_values[H5Z_SCALEOFFSET_PARM_SIZE]; + p.order = cd_values[H5Z_SCALEOFFSET_PARM_ORDER]; + + /* input; decompress */ + if (flags & H5Z_FLAG_REVERSE) { + /* get values of minbits and minval from input buffer */ + HDmemcpy(&minbits, *buf, sizeof(unsigned)); + HDmemcpy(&minval, (unsigned char*)(*buf)+sizeof(unsigned), sizeof(unsigned long_long)); + + assert(minbits < p.size * 8); + + /* no need to process the data */ + if(minbits == cd_values[H5Z_SCALEOFFSET_PARM_SIZE] * 8) { + ret_value = *buf_size; + goto done; + } + + size_out = d_nelmts * p.size; + + /* allocate memory space for decompressed buffer */ + if(NULL==(outbuf = H5MM_malloc(size_out))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "memory allocation failed for scaleoffset decompression") + +#if 0 + /* the data buffer all have same value */ + if(minbits == 0) { + } +#endif + + p.minbits = minbits; + + /* decompress the buffer */ + buf_offset = sizeof(unsigned) + sizeof(unsigned long_long); + H5Z_scaleoffset_decompress(outbuf, d_nelmts, (unsigned char*)(*buf)+buf_offset, p); + + /* postprocess after decompress */ + H5Z_scaleoffset_postdecompress(outbuf, d_nelmts, cd_values[H5Z_SCALEOFFSET_PARM_TYPE], + cd_values[H5Z_SCALEOFFSET_PARM_FILAVAIL], minval); + } + /* output; compress */ + else { + /* preprocess before compress */ + H5Z_scaleoffset_precompress(*buf, d_nelmts, cd_values[H5Z_SCALEOFFSET_PARM_TYPE], + cd_values[H5Z_SCALEOFFSET_PARM_FILAVAIL], &minbits, &minval); + + assert(minbits < p.size * 8); + + /* no need to process the data */ + if(minbits == p.size * 8) { + ret_value = *buf_size; + goto done; + } +#if 0 + /* the data buffer all have same value */ + if(minbits == 0) { + *buf_size = 0; + ret_value = 0; + goto done; + } +#endif + p.minbits = minbits; + + /* calculate buffer size after compression, may be 1 bigger + * minbits and minval are stored in the front of the compressed buffer + */ + size_out = nbytes * p.minbits / (p.size * 8) + 1 + + sizeof(unsigned) + sizeof(unsigned long_long); + + /* allocate memory space for compressed buffer */ + if(NULL==(outbuf = H5MM_malloc(size_out))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "memory allocation failed for scaleoffset compression") + + /* first store minbits and minval in output buffer */ + HDmemcpy(outbuf, &minbits, sizeof(unsigned)); + HDmemcpy(outbuf+sizeof(unsigned), &minval, sizeof(unsigned long_long)); + + /* compress the buffer */ + buf_offset = sizeof(unsigned) + sizeof(unsigned long_long); + H5Z_scaleoffset_compress(*buf, d_nelmts, outbuf+buf_offset, size_out-buf_offset, p); +#if 0 + printf("After compress:\n"); + for(i = 0; i < size_out; i++) { + printf("%02x ", ((unsigned char *)(outbuf))[i]); + if((i+1)%4==0) printf("\n"); + } +#endif + } + + /* free the input buffer */ + H5MM_xfree(*buf); + + /* set return values */ + *buf = outbuf; + outbuf = NULL; + *buf_size = size_out; + ret_value = size_out; + +done: + if(outbuf) + H5MM_xfree(outbuf); + FUNC_LEAVE_NOAPI(ret_value) +} + +/* ======== Scaleoffset Algorithm =============================================== + * assume one byte has 8 bit + * assume padding bit is 0 + * assume size of unsigned char is one byte + * assume one data item of certain datatype is stored continously in bytes + * atomic datatype is treated on byte basis + */ + +void H5Z_scaleoffset_precompress(void *data, unsigned d_nelmts, unsigned type, unsigned filavail, + unsigned *minbits, unsigned long_long *minval) +{ + unsigned i; + unsigned long_long span; /* span of values of input buffer data */ + enum H5Z_scaleoffset_type t; /* integer type */ + + t = type; + if(type == t_uchar) { + unsigned char *buf, min, max; + buf = data; min = max = buf[0]; + for(i = 0; i < d_nelmts; i++) { /* find maximum and minimum values */ + if(buf[i] > max) max = buf[i]; + if(buf[i] < min) min = buf[i]; + } + span = max - min + 1; *minval = min; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] -= min; + } + else if(type == t_ushort) { + unsigned short *buf, min, max; + buf = data; min = max = buf[0]; + for(i = 0; i < d_nelmts; i++) { /* find maximum and minimum values */ + if(buf[i] > max) max = buf[i]; + if(buf[i] < min) min = buf[i]; + } + span = max - min + 1; *minval = min; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] -= min; + } + else if(type == t_uint) { + unsigned int *buf, min, max; + buf = data; min = max = buf[0]; + for(i = 0; i < d_nelmts; i++) { /* find maximum and minimum values */ + if(buf[i] > max) max = buf[i]; + if(buf[i] < min) min = buf[i]; + } + span = max - min + 1; *minval = min; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] -= min; + } + else if(type == t_ulong) { + unsigned long *buf, min, max; + buf = data; min = max = buf[0]; + for(i = 0; i < d_nelmts; i++) { /* find maximum and minimum values */ + if(buf[i] > max) max = buf[i]; + if(buf[i] < min) min = buf[i]; + } + span = max - min + 1; *minval = min; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] -= min; + } + else if(type == t_ulong_long) { + unsigned long_long *buf, min, max; + buf = data; min = max = buf[0]; + for(i = 0; i < d_nelmts; i++) { /* find maximum and minimum values */ + if(buf[i] > max) max = buf[i]; + if(buf[i] < min) min = buf[i]; + } + span = max - min + 1; *minval = min; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] -= min; + } + else if(type == t_schar) { + signed char *buf, min, max; + buf = data; min = max = buf[0]; + for(i = 0; i < d_nelmts; i++) { /* find maximum and minimum values */ + if(buf[i] > max) max = buf[i]; + if(buf[i] < min) min = buf[i]; + } + span = max - min + 1; *minval = min; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] -= min; + } + else if(type == t_short) { + short *buf, min, max; + buf = data; min = max = buf[0]; + for(i = 0; i < d_nelmts; i++) { /* find maximum and minimum values */ + if(buf[i] > max) max = buf[i]; + if(buf[i] < min) min = buf[i]; + } + span = max - min + 1; *minval = min; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] -= min; + } + else if(type == t_int) { + int *buf, min, max; + buf = data; min = max = buf[0]; + for(i = 0; i < d_nelmts; i++) { /* find maximum and minimum values */ + if(buf[i] > max) max = buf[i]; + if(buf[i] < min) min = buf[i]; + } + span = max - min + 1; *minval = min; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] -= min; + } else if(type == t_long) { + long *buf, min, max; + buf = data; min = max = buf[0]; + for(i = 0; i < d_nelmts; i++) { /* find maximum and minimum values */ + if(buf[i] > max) max = buf[i]; + if(buf[i] < min) min = buf[i]; + } + span = max - min + 1; *minval = min; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] -= min; + } + else if(type == t_long_long) { + long_long *buf, min, max; + buf = data; min = max = buf[0]; + for(i = 0; i < d_nelmts; i++) { /* find maximum and minimum values */ + if(buf[i] > max) max = buf[i]; + if(buf[i] < min) min = buf[i]; + } + span = max - min + 1; *minval = min; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] -= min; + } +#if 0 + /* if minbits not set by application, calculate minbits */ + if(*minbits == 0) { + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + *minbits = HDceil(log(span)*M_LOG2E); + else + *minbits = HDceil(log(span+1)*M_LOG2E); + } +#endif +} + +void H5Z_scaleoffset_postdecompress(void *data, unsigned d_nelmts, unsigned type, unsigned filavail, + unsigned long_long minval) +{ + unsigned i; + long_long sminval = *(long_long*)&minval; /* for signed integer types */ + enum H5Z_scaleoffset_type t; /* integer type */ + + t = type; + if(type == t_uchar) { + unsigned char *buf = data; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] += minval; + } + else if(type == t_ushort) { + unsigned short *buf = data; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] += minval; + } + else if(type == t_uint) { + unsigned int *buf = data; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] += minval; + } + else if(type == t_ulong) { + unsigned long *buf = data; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] += minval; + } + else if(type == t_ulong_long) { + unsigned long_long *buf = data; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] += minval; + } + else if(type == t_schar) { + signed char *buf = data; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] += sminval; + } + else if(type == t_short) { + short *buf = data; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] += sminval; + } + else if(type == t_int) { + int *buf = data; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] += sminval; + } + else if(type == t_long) { + long *buf = data; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] += sminval; + } + else if(type == t_long_long) { + long_long *buf = data; + if(filavail == H5Z_SCALEOFFSET_FILL_UNDEFINED) + for(i = 0; i < d_nelmts; i++) buf[i] += sminval; + } +} + +void H5Z_scaleoffset_next_byte(size_t *j, int *buf_len) +{ + ++(*j); + *buf_len = 8 * sizeof(unsigned char); +} + +void H5Z_scaleoffset_decompress_one_byte(void *data, size_t data_offset, int k, int begin_i, +unsigned char *buffer, size_t *j, int *buf_len, parms_atomic p) +{ + int dat_len; /* dat_len is the number of bits to be copied in each data byte */ + unsigned char val; /* value to be copied in each data byte */ + + /* initialize value and bits of unsigned char to be copied */ + val = buffer[*j]; + + if(k == begin_i) + dat_len = p.minbits % 8; + else + dat_len = 8; + + if(*buf_len > dat_len) { + ((unsigned char *)data)[data_offset + k] = + ((val >> (*buf_len - dat_len)) & ~(~0 << dat_len)); + *buf_len -= dat_len; + } else { + ((unsigned char *)data)[data_offset + k] = + ((val & ~(~0 << *buf_len)) << (dat_len - *buf_len)); + dat_len -= *buf_len; + H5Z_scaleoffset_next_byte(j, buf_len); + if(dat_len == 0) return; + + val = buffer[*j]; + ((unsigned char *)data)[data_offset + k] |= + ((val >> (*buf_len - dat_len)) & ~(~0 << dat_len)); + *buf_len -= dat_len; + } +} + +void H5Z_scaleoffset_decompress_one_atomic(void *data, size_t data_offset, unsigned char *buffer, + size_t *j, int *buf_len, parms_atomic p) +{ + /* begin_i: the index of byte having first significant bit */ + int k, begin_i, dtype_len; + + assert(p.minbits > 0); + + dtype_len = p.size * 8; + + if(p.order == H5Z_SCALEOFFSET_ORDER_LE) { /* little endian */ + begin_i = p.size - 1 - (dtype_len - p.minbits) / 8; + + for(k = begin_i; k >= 0; k--) + H5Z_scaleoffset_decompress_one_byte(data, data_offset, k, begin_i, + buffer, j, buf_len, p); + } + + if(p.order == H5Z_SCALEOFFSET_ORDER_BE) { /* big endian */ + begin_i = (dtype_len - p.minbits) / 8; + + for(k = begin_i; k <= p.size - 1; k++) + H5Z_scaleoffset_decompress_one_byte(data, data_offset, k, begin_i, + buffer, j, buf_len, p); + } +} + +void H5Z_scaleoffset_decompress(void *data, unsigned d_nelmts, unsigned char *buffer, + parms_atomic p) +{ + /* i: index of data, j: index of buffer, + buf_len: number of bits to be filled in current byte */ + size_t i, j; + int buf_len; + + /* may not have to initialize to zeros */ + for(i = 0; i < d_nelmts*p.size; i++) + ((unsigned char *)data)[i] = 0; + + /* initialization before the loop */ + j = 0; + buf_len = sizeof(unsigned char) * 8; + + /* decompress */ + for(i = 0; i < d_nelmts; i++) + H5Z_scaleoffset_decompress_one_atomic(data, i*p.size, buffer, &j, &buf_len, p); +} + +void H5Z_scaleoffset_compress_one_byte(void *data, size_t data_offset, int k, int begin_i, +unsigned char *buffer, size_t *j, int *buf_len, parms_atomic p) +{ + int dat_len; /* dat_len is the number of bits to be copied in each data byte */ + unsigned char val; /* value to be copied in each data byte */ + + /* initialize value and bits of unsigned char to be copied */ + val = ((unsigned char *)data)[data_offset + k]; + + if(k == begin_i) + dat_len = p.minbits % 8; + else + dat_len = 8; + + if(*buf_len > dat_len) { + buffer[*j] |= (val & ~(~0 << dat_len)) << (*buf_len - dat_len); + *buf_len -= dat_len; + } else { + buffer[*j] |= (val >> (dat_len - *buf_len)) & ~(~0 << *buf_len); + dat_len -= *buf_len; + H5Z_scaleoffset_next_byte(j, buf_len); + if(dat_len == 0) return; + + buffer[*j] = (val & ~(~0 << dat_len)) << (*buf_len - dat_len); + *buf_len -= dat_len; + } +} + +void H5Z_scaleoffset_compress_one_atomic(void *data, size_t data_offset, unsigned char *buffer, + size_t *j, int *buf_len, parms_atomic p) +{ + /* begin_i: the index of byte having first significant bit */ + int k, begin_i, dtype_len; + + assert(p.minbits > 0); + + dtype_len = p.size * 8; + + if(p.order == H5Z_SCALEOFFSET_ORDER_LE) { /* little endian */ + begin_i = p.size - 1 - (dtype_len - p.minbits) / 8; + + for(k = begin_i; k >= 0; k--) + H5Z_scaleoffset_compress_one_byte(data, data_offset, k, begin_i, + buffer, j, buf_len, p); + } + + if(p.order == H5Z_SCALEOFFSET_ORDER_BE) { /* big endian */ + begin_i = (dtype_len - p.minbits) / 8; + + for(k = begin_i; k <= p.size - 1; k++) + H5Z_scaleoffset_compress_one_byte(data, data_offset, k, begin_i, + buffer, j, buf_len, p); + } +} + +void H5Z_scaleoffset_compress(void *data, unsigned d_nelmts, unsigned char *buffer, + size_t buffer_size, parms_atomic p) +{ + /* i: index of data, j: index of buffer, + buf_len: number of bits to be filled in current byte */ + size_t i, j; + int buf_len; + + /* must initialize buffer to be zeros */ + for(j = 0; j < buffer_size; j++) + buffer[j] = 0; + + /* initialization before the loop */ + j = 0; + buf_len = sizeof(unsigned char) * 8; + + /* compress */ + for(i = 0; i < d_nelmts; i++) + H5Z_scaleoffset_compress_one_atomic(data, i*p.size, buffer, &j, &buf_len, p); +} +#endif /* H5_HAVE_FILTER_SCALEOFFSET */ |