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hdf5/tools/h5repack/h5repack_parse.c
Allen Byrne b947f7e911 [svn-r30321] HDFFV-9974: Correct parsing of UD filter parameters. 
Verified by user, who reported issue.
2016-08-25 13:57:27 -05:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "h5repack.h"
#include "h5tools.h"
#include "h5tools_utils.h"
/*-------------------------------------------------------------------------
* Function: parse_filter
*
* Purpose: read filter information
*
* Return: a list of names, the number of names and its compression type
*
* <name of filter> can be:
* GZIP, to apply the HDF5 GZIP filter (GZIP compression)
* SZIP, to apply the HDF5 SZIP filter (SZIP compression)
* SHUF, to apply the HDF5 shuffle filter
* FLET, to apply the HDF5 checksum filter
* NBIT, to apply the HDF5 NBIT filter (NBIT compression)
* SOFF, to apply the HDF5 scale+offset filter (compression)
* UD, to apply a User Defined filter k,m,n1[,…,nm]
* NONE, to remove the filter
*
* Examples:
* "GZIP=6"
* "A,B:NONE"
*-------------------------------------------------------------------------
*/
obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt,
pack_opt_t *options, int *is_glb) {
size_t i, m, u;
char c;
size_t len = HDstrlen(str);
int k, l, p, q, end_obj = -1, no_param = 0;
unsigned j, n;
char sobj[MAX_NC_NAME];
char scomp[10];
char stype[6];
char smask[3];
obj_list_t* obj_list = NULL;
unsigned pixels_per_block;
/* initialize compression info */
HDmemset(filt, 0, sizeof(filter_info_t));
*is_glb = 0;
/* check for the end of object list and number of objects */
for (i = 0, n = 0; i < len; i++) {
c = str[i];
if (c == ':')
end_obj = (int) i;
if (c == ',')
n++;
}
/* Check for missing : */
if (end_obj == -1) {
/* apply to all objects */
options->all_filter = 1;
*is_glb = 1;
}
n++;
obj_list = (obj_list_t *) HDmalloc(n * sizeof(obj_list_t));
if (obj_list == NULL) {
error_msg("could not allocate object list\n");
return NULL;
}
*n_objs = n;
/* get object list */
if (end_obj > 0)
for (j = 0, k = 0, n = 0; j < (unsigned) end_obj; j++, k++) {
c = str[j];
sobj[k] = c;
if (c == ',' || j == (unsigned) (end_obj - 1)) {
if (c == ',')
sobj[k] = '\0';
else
sobj[k + 1] = '\0';
HDstrcpy(obj_list[n].obj, sobj);
HDmemset(sobj, 0, sizeof(sobj));
n++;
k = -1;
}
}
/* nothing after : */
if (end_obj + 1 == (int) len) {
if (obj_list)
HDfree(obj_list);
error_msg("input Error: Invalid compression type in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
/* get filter additional parameters */
m = 0;
for (i = (size_t)(end_obj + 1), k = 0, j = 0; i < len; i++, k++) {
c = str[i];
scomp[k] = c;
if (c == '=' || i == len - 1) {
if (c == '=') { /*one more parameter */
scomp[k] = '\0'; /*cut space */
/*-------------------------------------------------------------------------
* H5Z_FILTER_SZIP
* szip has the format SZIP=<pixels per block,coding>
* pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN'
* example SZIP=8,NN
*-------------------------------------------------------------------------
*/
if (HDstrcmp(scomp, "SZIP") == 0) {
l = -1; /* mask index check */
for (m = 0, u = i + 1; u < len; u++, m++) {
if (str[u] == ',') {
stype[m] = '\0'; /* end digit of szip */
l = 0; /* start EC or NN search */
u++; /* skip ',' */
}
c = str[u];
if (!HDisdigit(c) && l == -1) {
if (obj_list)
HDfree(obj_list);
error_msg("compression parameter not digit in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
if (l == -1)
stype[m] = c;
else {
smask[l] = c;
l++;
if (l == 2) {
smask[l] = '\0';
i = len - 1; /* end */
(*n_objs)--; /* we counted an extra ',' */
if (HDstrcmp(smask,"NN") == 0)
filt->cd_values[j++] = H5_SZIP_NN_OPTION_MASK;
else if (HDstrcmp(smask,"EC") == 0)
filt->cd_values[j++] = H5_SZIP_EC_OPTION_MASK;
else {
error_msg("szip mask must be 'NN' or 'EC' \n");
HDexit(EXIT_FAILURE);
}
}
}
} /* u */
} /*if */
/*-------------------------------------------------------------------------
* H5Z_FILTER_SCALEOFFSET
* scaleoffset has the format SOFF=<scale_factor,scale_type>
* scale_type can be
* integer datatype, H5Z_SO_INT (IN)
* float datatype using D-scaling method, H5Z_SO_FLOAT_DSCALE (DS)
* float datatype using E-scaling method, H5Z_SO_FLOAT_ESCALE (ES) , not yet implemented
* for integer datatypes, scale_factor denotes Minimum Bits
* for float datatypes, scale_factor denotes decimal scale factor
* examples
* SOFF=31,IN
* SOFF=3,DF
*-------------------------------------------------------------------------
*/
else if (HDstrcmp(scomp, "SOFF") == 0) {
l = -1; /* mask index check */
for (m = 0, u = i + 1; u < len; u++, m++) {
if (str[u] == ',') {
stype[m] = '\0'; /* end digit */
l = 0; /* start 'IN' , 'DS', or 'ES' search */
u++; /* skip ',' */
}
c = str[u];
if (!HDisdigit(c) && l == -1) {
if (obj_list)
HDfree(obj_list);
error_msg("compression parameter is not a digit in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
if (l == -1)
stype[m] = c;
else {
smask[l] = c;
l++;
if (l == 2) {
smask[l] = '\0';
i = len - 1; /* end */
(*n_objs)--; /* we counted an extra ',' */
if (HDstrcmp(smask,"IN") == 0)
filt->cd_values[j++] = H5Z_SO_INT;
else if (HDstrcmp(smask, "DS") == H5Z_SO_FLOAT_DSCALE)
filt->cd_values[j++] = H5Z_SO_FLOAT_DSCALE;
else {
error_msg("scale type must be 'IN' or 'DS' \n");
HDexit(EXIT_FAILURE);
}
}
}
} /* u */
} /*if */
/*-------------------------------------------------------------------------
* User Defined
* has the format UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>
* BZIP2 example
* UD=307,1,9
*-------------------------------------------------------------------------
*/
else if (HDstrcmp(scomp, "UD") == 0) {
l = -1; /* filter number index check */
p = -1; /* CD_VAL count check */
for (m = 0, q = 0, u = i + 1; u < len; u++, m++, q++) {
if (str[u] == ',') {
stype[q] = '\0'; /* end digit */
if (l == -1) {
filt->filtn = HDatoi(stype);
l = 0;
}
else if (p == -1) {
filt->cd_nelmts = HDstrtoull(stype, NULL, 0);
p = 0;
}
else
filt->cd_values[j++] = (unsigned)HDstrtoul(stype, NULL, 0);
q = 0;
u++; /* skip ',' */
}
c = str[u];
if (!HDisdigit(c) && l == -1) {
if (obj_list)
HDfree(obj_list);
error_msg("filter number parameter is not a digit in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
stype[q] = c;
} /* for u */
stype[q] = '\0';
} /*if */
/*-------------------------------------------------------------------------
* all other filters
*-------------------------------------------------------------------------
*/
else {
/* here we could have 1 or 2 digits */
for (m = 0, u = i + 1; u < len; u++, m++) {
c = str[u];
if (!HDisdigit(c)) {
if (obj_list)
HDfree(obj_list);
error_msg("compression parameter is not a digit in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
stype[m] = c;
} /* u */
stype[m] = '\0';
} /*if */
filt->cd_values[j++] = (unsigned) HDstrtoul(stype, NULL, 0);
if(filt->cd_nelmts == 0)
j = 0;
i += m; /* jump */
}
else if (i == len - 1) { /*no more parameters */
scomp[k + 1] = '\0';
no_param = 1;
}
/*-------------------------------------------------------------------------
* translate from string to filter symbol
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* H5Z_FILTER_NONE
*-------------------------------------------------------------------------
*/
if (HDstrcmp(scomp, "NONE") == 0) {
filt->filtn = H5Z_FILTER_NONE;
filt->cd_nelmts = 0;
}
/*-------------------------------------------------------------------------
* H5Z_FILTER_DEFLATE
*-------------------------------------------------------------------------
*/
else if (HDstrcmp(scomp, "GZIP") == 0) {
filt->filtn = H5Z_FILTER_DEFLATE;
filt->cd_nelmts = 1;
if (no_param) { /*no more parameters, GZIP must have parameter */
if (obj_list)
HDfree(obj_list);
error_msg("missing compression parameter in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
}
/*-------------------------------------------------------------------------
* H5Z_FILTER_SZIP
*-------------------------------------------------------------------------
*/
else if (HDstrcmp(scomp, "SZIP") == 0) {
filt->filtn = H5Z_FILTER_SZIP;
filt->cd_nelmts = 2;
if (no_param) { /*no more parameters, SZIP must have parameter */
if (obj_list)
HDfree(obj_list);
error_msg("missing compression parameter in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
}
/*-------------------------------------------------------------------------
* H5Z_FILTER_SHUFFLE
*-------------------------------------------------------------------------
*/
else if (HDstrcmp(scomp, "SHUF") == 0) {
filt->filtn = H5Z_FILTER_SHUFFLE;
filt->cd_nelmts = 0;
if (m > 0) { /*shuffle does not have parameter */
if (obj_list)
HDfree(obj_list);
error_msg("extra parameter in SHUF <%s>\n", str);
HDexit(EXIT_FAILURE);
}
}
/*-------------------------------------------------------------------------
* H5Z_FILTER_FLETCHER32
*-------------------------------------------------------------------------
*/
else if (HDstrcmp(scomp, "FLET") == 0) {
filt->filtn = H5Z_FILTER_FLETCHER32;
filt->cd_nelmts = 0;
if (m > 0) { /*shuffle does not have parameter */
if (obj_list)
HDfree(obj_list);
error_msg("extra parameter in FLET <%s>\n", str);
HDexit(EXIT_FAILURE);
}
}
/*-------------------------------------------------------------------------
* H5Z_FILTER_NBIT
*-------------------------------------------------------------------------
*/
else if (HDstrcmp(scomp, "NBIT") == 0) {
filt->filtn = H5Z_FILTER_NBIT;
filt->cd_nelmts = 0;
if (m > 0) { /*nbit does not have parameter */
if (obj_list)
HDfree(obj_list);
error_msg("extra parameter in NBIT <%s>\n", str);
HDexit(EXIT_FAILURE);
}
}
/*-------------------------------------------------------------------------
* H5Z_FILTER_SCALEOFFSET
*-------------------------------------------------------------------------
*/
else if (HDstrcmp(scomp, "SOFF") == 0) {
filt->filtn = H5Z_FILTER_SCALEOFFSET;
filt->cd_nelmts = 2;
if (no_param) { /*no more parameters, SOFF must have parameter */
if (obj_list)
HDfree(obj_list);
error_msg("missing compression parameter in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
}
/*-------------------------------------------------------------------------
* User Defined Filter
*-------------------------------------------------------------------------
*/
else if (HDstrcmp(scomp, "UD") == 0) {
/* parameters does not match count */
if (filt->cd_nelmts != j) {
if (obj_list)
HDfree(obj_list);
error_msg("incorrect number of compression parameters in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
}
else {
if (obj_list)
HDfree(obj_list);
error_msg("invalid filter type in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
}
} /*i*/
/*-------------------------------------------------------------------------
* check valid parameters
*-------------------------------------------------------------------------
*/
switch (filt->filtn) {
/*-------------------------------------------------------------------------
* H5Z_FILTER_DEFLATE
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_DEFLATE:
if (filt->cd_values[0] > 9) {
if (obj_list)
HDfree(obj_list);
error_msg("invalid compression parameter in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_SZIP
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SZIP:
pixels_per_block = filt->cd_values[0];
if ((pixels_per_block % 2) == 1) {
if (obj_list)
HDfree(obj_list);
error_msg("pixels_per_block is not even in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
if (pixels_per_block > H5_SZIP_MAX_PIXELS_PER_BLOCK) {
if (obj_list)
HDfree(obj_list);
error_msg("pixels_per_block is too large in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
if ((HDstrcmp(smask,"NN") != 0) && (HDstrcmp(smask,"EC") != 0)) {
if (obj_list)
HDfree(obj_list);
error_msg("szip mask must be 'NN' or 'EC' \n");
HDexit(EXIT_FAILURE);
}
break;
default:
break;
};
return obj_list;
}
/*-------------------------------------------------------------------------
* Function: parse_layout
*
* Purpose: read layout info
*
* Return: a list of names, the number of names and its chunking info for
* chunked. NULL, on error
* the layout type can be:
* CHUNK, to apply chunking layout
* CONTI, to apply contiguous layout
* COMPA, to apply compact layout
*
* Example:
* "AA,B,CDE:CHUNK=10X10"
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December 30, 2003
*
*-------------------------------------------------------------------------
*/
obj_list_t* parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about layout needed */
pack_opt_t *options) {
obj_list_t* obj_list = NULL;
unsigned i, j, n;
char c;
size_t len = HDstrlen(str);
int k, end_obj = -1, c_index;
char sobj[MAX_NC_NAME];
char sdim[10];
char slayout[10];
HDmemset(sdim, '\0', sizeof(sdim));
HDmemset(sobj, '\0', sizeof(sobj));
HDmemset(slayout, '\0', sizeof(slayout));
/* check for the end of object list and number of objects */
for (i = 0, n = 0; i < len; i++) {
c = str[i];
if (c == ':')
end_obj = (int) i;
if (c == ',')
n++;
}
if (end_obj == -1) { /* missing : chunk all */
options->all_layout = 1;
}
n++;
obj_list = (obj_list_t*) HDmalloc(n * sizeof(obj_list_t));
if (obj_list == NULL) {
error_msg("could not allocate object list\n");
return NULL;
}
*n_objs = n;
/* get object list */
if (end_obj > 0)
for (j = 0, k = 0, n = 0; j < (unsigned) end_obj; j++, k++) {
c = str[j];
sobj[k] = c;
if (c == ',' || j == (unsigned) (end_obj - 1)) {
if (c == ',')
sobj[k] = '\0';
else
sobj[k + 1] = '\0';
HDstrcpy(obj_list[n].obj, sobj);
HDmemset(sobj, 0, sizeof(sobj));
n++;
k = -1;
}
}
/* nothing after : */
if (end_obj + 1 == (int) len) {
if (obj_list)
HDfree(obj_list);
error_msg("in parse layout, no characters after : in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
/* get layout info */
for (j = (unsigned) (end_obj + 1), n = 0; n <= 5; j++, n++) {
if (n == 5) {
slayout[n] = '\0'; /*cut string */
if (HDstrcmp(slayout, "COMPA") == 0)
pack->layout = H5D_COMPACT;
else if (HDstrcmp(slayout, "CONTI") == 0)
pack->layout = H5D_CONTIGUOUS;
else if (HDstrcmp(slayout, "CHUNK") == 0)
pack->layout = H5D_CHUNKED;
else {
error_msg("in parse layout, not a valid layout in <%s>\n", str);
HDexit(EXIT_FAILURE);
}
}
else {
c = str[j];
slayout[n] = c;
}
} /* j */
if (pack->layout == H5D_CHUNKED) {
/*-------------------------------------------------------------------------
* get chunk info
*-------------------------------------------------------------------------
*/
k = 0;
if (j > len) {
if (obj_list)
HDfree(obj_list);
error_msg("in parse layout, <%s> Chunk dimensions missing\n", str);
HDexit(EXIT_FAILURE);
}
for (i = j, c_index = 0; i < len; i++) {
c = str[i];
sdim[k] = c;
k++; /*increment sdim index */
if (!HDisdigit(c) && c != 'x' && c != 'N' && c != 'O' && c != 'N' && c != 'E') {
if (obj_list)
HDfree(obj_list);
error_msg("in parse layout, <%s> Not a valid character in <%s>\n", sdim, str);
HDexit(EXIT_FAILURE);
}
if (c == 'x' || i == len - 1) {
if (c == 'x') {
sdim[k - 1] = '\0';
k = 0;
pack->chunk.chunk_lengths[c_index] = HDstrtoull(sdim, NULL, 0);
if (pack->chunk.chunk_lengths[c_index] == 0) {
if (obj_list)
HDfree(obj_list);
error_msg("in parse layout, <%s> conversion to number in <%s>\n", sdim, str);
HDexit(EXIT_FAILURE);
}
c_index++;
}
else if (i == len - 1) { /*no more parameters */
sdim[k] = '\0';
k = 0;
if (HDstrcmp(sdim,"NONE") == 0) {
pack->chunk.rank = -2;
}
else {
pack->chunk.chunk_lengths[c_index] = HDstrtoull(sdim, NULL, 0);
if (pack->chunk.chunk_lengths[c_index] == 0) {
if (obj_list)
HDfree(obj_list);
error_msg("in parse layout, <%s> conversion to number in <%s>\n", sdim, str);
HDexit(EXIT_FAILURE);
}
pack->chunk.rank = c_index + 1;
}
} /*if */
} /*if c=='x' || i==len-1 */
} /*i*/
} /*H5D_CHUNKED*/
return obj_list;
}
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